Docs Anaconda Com en Latest

Anaconda Documentation
Anaconda Inc.
Jun 09, 2021

Contents
1 Anaconda Individual Edition 1
2 Anaconda Commercial Edition 3
3 Anaconda Team Edition 5
4 Anaconda Enterprise Edition 7
5 Anaconda.org 9
5.1 Anaconda Individual Edition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
5.2 Anaconda Commercial Edition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1417
5.3 Anaconda Enterprise 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1440
5.4 Anaconda.org . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2553
5.5 Archive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2595
Index 2839
i
ii
CHAPTER 1
Anaconda Individual Edition
Anaconda Individual Edition is a free, easy-to-install package manager, environment manager, and Python distribution
with a collection of 1,500+ open source packages with free community support. Anaconda is platform-agnostic, so
you can use it whether you are on Windows, macOS, or Linux.
View Anaconda Individual Edition documentation.
1
2 Chapter 1. Anaconda Individual Edition

CHAPTER 2
Anaconda Commercial Edition
Anaconda Commercial Edition is the world’s most popular open-source package distribution and management expe-
rience, optimized for commercial use and compliance with our Terms of Service.
View Anaconda Commercial Edition documentation.
3
4 Chapter 2. Anaconda Commercial Edition

CHAPTER 3
Anaconda Team Edition
Anaconda Team Edition is our latest generation repository for all things Anaconda. With support for all major op-
erating systems, the repository serves as your central conda, PyPI, and CRAN packaging resource for desktop users,
development clusters, CI/CD systems, and production containers.
View Anaconda Team Edition documentation.
5
6 Chapter 3. Anaconda Team Edition

CHAPTER 4
Anaconda Enterprise Edition
Anaconda Enterprise is an enterprise-ready, secure, and scalable data science platform that empowers teams to govern
data science assets, collaborate, and deploy data science projects.
Enterprise 5 includes these capabilities:
• Easily deploy your projects into interactive data applications, live notebooks, and machine learning models with
APIs.
• Share those applications with colleagues and collaborators.
• Manage your data science assets: notebooks, packages, environments, and projects in an integrated data science
experience.
View Anaconda Enterprise 5 documentation.
7
8 Chapter 4. Anaconda Enterprise Edition

CHAPTER 5
Anaconda.org
Anaconda.org is a package management service that makes it easy to find, access, store, and share public notebooks
and environments, as well as conda and PyPI packages.
View Anaconda.org documentation.
5.1 Anaconda Individual Edition
The Most Trusted Distribution for Data Science

Anaconda® is a package manager, an environment manager, a Python/R data science distribution, and a collection of
over 7,500+ open-source packages. Anaconda is free and easy to install, and it offers free community support.
Get the Anaconda Cheat Sheet and then download Anaconda.
Want to install conda and use conda to install just the packages you need? Get Miniconda.
Anaconda Navigator or conda?

After you install Anaconda or Miniconda, if you prefer a desktop graphical user interface (GUI) then use Navigator.
If you prefer to use Anaconda prompt (or terminal on Linux or macOS), then use that and conda. You can also switch
between them.
You can install, remove, or update any Anaconda package with a few clicks in Navigator, or with a single conda
command in Anaconda Prompt (terminal on Linux or macOS).
9
• To try Navigator, after installing Anaconda, click the Navigator icon on your operating system’s program menu,
or in Anaconda prompt (or terminal on Linux or macOS), run the command anaconda-navigator.
• To try conda, after installing Anaconda or Miniconda, take the 20-minute conda test drive and download a
conda cheat sheet.
Packages available in Anaconda

• Over 250 packages are automatically installed with Anaconda.
• Over 7,500 additional open-source packages (including R) can be individually installed from the Anaconda
repository with the conda install command.
• Thousands of other packages are available from Anaconda.org.
• You can download other packages using the pip install command that is installed with Anaconda. Pip
packages provide many of the features of conda packages and in some cases they can work together. However,
the preference should be to install the conda package if it is available.
• You can also make your own custom packages using the conda build command, and you can share them
with others by uploading them to Anaconda.org, PyPI, or other repositories.
Previous versions
Previous versions of Anaconda are available in the archive. For a list of packages included in each previous version,
see Old package lists.
Anaconda2 includes Python 2.7 and Anaconda3 includes Python 3.7. However, it does not matter which one you
download, because you can create new environments that include any version of Python packaged with conda. See
Managing Python with conda.
5.1.1 Installation
Review the system requirements listed below before installing Anaconda Individual Edition. If you don’t want the
hundreds of packages included with Anaconda, you can install Miniconda, a mini version of Anaconda that includes
just conda, its dependencies, and Python.
Tip: Looking for Python 3.5 or 3.6? See our FAQ.
System requirements
• License: Free use and redistribution under the terms of the ../eula.
• Operating system: Windows 8 or newer, 64-bit macOS 10.13+, or Linux, including Ubuntu, RedHat, CentOS
6+, and others.
10 Chapter 5. Anaconda.org
• If your operating system is older than what is currently supported, you can find older versions of the Anaconda
installers in our archive that might work for you. See Using Anaconda on older operating systems for version
recommendations.
• System architecture: Windows- 64-bit x86, 32-bit x86; MacOS- 64-bit x86; Linux- 64-bit x86, 64-bit aarch64
(AWS Graviton2 / arm64), 64-bit Power8/Power9, s390x (Linux on IBM Z & LinuxONE).
• Minimum 5 GB disk space to download and install.
On Windows, macOS, and Linux, it is best to install Anaconda for the local user, which does not require administrator
permissions and is the most robust type of installation. However, if you need to, you can install Anaconda system
wide, which does require administrator permissions.
Installing on Windows
Note: Using Anaconda in a commercial setting? You may need to purchase a license to stay compliant with our Terms
of Service. This can be accomplished through Anaconda Commercial Edition, Anaconda Team Edition, or Anaconda
Enterprise. If you have already purchased Commercial Edition, please proceed to the Authenticating Commercial
Edition section after completing your installation here.
Haven’t purchased Commercial Edition yet? Visit https://anaconda.cloud/register to get started.
1. Download the Anaconda installer.

2. RECOMMENDED: Verify data integrity with SHA-256. For more information on hashes, see What about
cryptographic hash verification?
3. Double click the installer to launch.
Note: To prevent permission errors, do not launch the installer from the Favorites folder.
Note: If you encounter issues during installation, temporarily disable your anti-virus software during install,
then re-enable it after the installation concludes. If you installed for all users, uninstall Anaconda and re-install
it for your user only and try again.
4. Click Next.
5. Read the licensing terms and click “I Agree”.
6. Select an install for “Just Me” unless you’re installing for all users (which requires Windows Administrator
privileges) and click Next.
7. Select a destination folder to install Anaconda and click the Next button. See FAQ.
Note: Install Anaconda to a directory path that does not contain spaces or unicode characters.
Note: Do not install as Administrator unless admin privileges are required.
5.1. Anaconda Individual Edition 11

8. Choose whether to add Anaconda to your PATH environment variable. We recommend not adding Anaconda to
the PATH environment variable, since this can interfere with other software. Instead, use Anaconda software by
opening Anaconda Navigator or the Anaconda Prompt from the Start Menu.
9. Choose whether to register Anaconda as your default Python. Unless you plan on installing and running multiple
versions of Anaconda or multiple versions of Python, accept the default and leave this box checked.
10. Click the Install button. If you want to watch the packages Anaconda is installing, click Show Details.
11. Click the Next button.
12. Optional: To install PyCharm for Anaconda, click on the link to https://www.anaconda.com/pycharm.
Or to install Anaconda without PyCharm, click the Next button.

13. After a successful installation you will see the “Thanks for installing Anaconda” dialog box:
14. If you wish to read more about Anaconda.org and how to get started with Anaconda, check the boxes “Anaconda
Individual Edition Tutorial” and “Learn more about Anaconda”. Click the Finish button.
15. Verify your installation.
Note: If you are behind a company proxy, you may need to do some additional set up. See how to set up your proxy.
Problems?
See troubleshooting.

What’s next?
Get started programming quickly with Anaconda in the Getting started with Anaconda guide.
Installing on macOS
You can install Anaconda using either the graphical installer (“wizard”) or the command line (“manual”) instructions
below. If you are unsure, choose the graphical install.
macOS graphical install
1. Download the graphical macOS installer for your version of Python.

3. Double-click the downloaded file and click continue to start the installation.
4. Answer the prompts on the Introduction, Read Me, and License screens.
5. Click the Install button to install Anaconda in your ~/opt directory (recommended):
6. OR, click the Change Install Location button to install in another location (not recommended).
On the Destination Select screen, select Install for me only.
Note: If you get the error message “You cannot install Anaconda in this location,” reselect Install for me only.
7. Click the continue button.

8. Optional: To install PyCharm for Anaconda, click on the link to https://www.anaconda.com/pycharm.
Or to install Anaconda without PyCharm, click the Continue button.

9. A successful installation displays the following screen:

Using the command-line install
Use this method if you prefer to use a terminal window.
1. In your browser, download the command-line version of the macOS installer for your system.
2. RECOMMENDED: Verify data integrity with SHA-256. For more information on hash verification, see crypto-
graphic hash validation.
• Open a terminal and run the following:
shasum -a 256 /path/filename
Note: Replace /path/filename with your installation’s path and filename.
3. Install for Python 3.7 or 2.7:

• For Python 3.7 enter the following:
bash ~/Downloads/Anaconda3-2020.02-MacOSX-x86_64.sh
• For Python 2.7, open the Terminal.app or iTerm2 terminal application and then enter the following:
bash ~/Downloads/Anaconda2-2019.10-MacOSX-x86_64.sh
Note: Include the bash command regardless of whether or not you are using the Bash shell.
Note: Replace ~/Downloads with your actual path and Anaconda3-2020.02-MacOSX-x86_64.sh

with actual name of the file you downloaded.
4. The installer prompts “In order to continue the installation process, please review the license agreement.” Click
Enter to view the license terms.
5. Scroll to the bottom of the license terms and enter yes to agree to them.
6. The installer prompts you to Press Enter to confirm the location, Press CTRL-C to cancel the installation or
specify an alternate installation directory. If you confirm the default location, it will display PREFIX=/home/
<user>/anaconda<2 or 3> and continue the installation.
Note: Unlike the graphical install, installing the shell file will place it in ~/anaconda<2 or 3> by default, not
~/opt. This is due to limitations with installing .pkg files on macOS Catalina.
Installation may take a few minutes to complete.
Note: We recommend you accept the default install location. Do not choose the path as /usr for the Ana-
conda/Miniconda installation.
7. The installer prompts “Do you wish the installer to initialize Anaconda3 by running conda init?” We recommend
“yes”.
Note: If you enter “no”, then conda will not modify your shell scripts at all. In order to initialize after the
installation process is done, first run source <path to conda>/bin/activate and then run conda
init.
Note: If you are on macOS Catalina, the new default shell is zsh. You will instead need to run source
<path to conda>/bin/activate followed by conda init zsh.
8. The installer displays “Thank you for installing Anaconda!”

9. Optional: The installer describes the partnership between Anaconda and JetBrains and provides a link to install
PyCharm for Anaconda at https://www.anaconda.com/pycharm.
10. Close and open your terminal window for the Anaconda installation to take effect.
11. To control whether or not each shell session has the base environment activated or not, run conda config
--set auto_activate_base False or True. To run conda from anywhere without having the base
environment activated by default, use conda config --set auto_activate_base False. This
only works if you have run conda init first.
Note: conda init is available in conda versions 4.6.12 and later.
Problems?
What’s next?

Installing on Linux
Prerequisites
To use GUI packages with Linux, you will need to install the following extended dependencies for Qt:
De- apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2

bian libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
Red- yum install libXcomposite libXcursor libXi libXtst libXrandr alsa-lib
Hat mesa-libEGL libXdamage mesa-libGL libXScrnSaver
Arch- pacman -Sy libxau libxi libxss libxtst libxcursor libxcomposite
Linux libxdamage libxfixes libxrandr libxrender mesa-libgl alsa-lib libglvnd
Open- zypper install libXcomposite1 libXi6 libXext6 libXau6 libX11-6
Suse/SLES
libXrandr2 libXrender1 libXss1 libXtst6 libXdamage1 libXcursor1 libxcb1
libasound2 libX11-xcb1 Mesa-libGL1 Mesa-libEGL1
Gen- emerge x11-libs/libXau x11-libs/libxcb x11-libs/libX11 x11-libs/
too libXext x11-libs/libXfixes x11-libs/libXrender x11-libs/libXi x11-libs/
libXcomposite x11-libs/libXrandr x11-libs/libXcursor x11-libs/
libXdamage x11-libs/libXScrnSaver x11-libs/libXtst media-libs/alsa-lib
media-libs/mesa
Installation
For x86 systems.

1. In your browser, download the Anaconda installer for Linux.
sha256sum /path/filename
3. Enter the following to install Anaconda for Python 3.7:
bash ~/Downloads/Anaconda3-2020.02-Linux-x86_64.sh
OR Enter the following to install Anaconda for Python 2.7:
bash ~/Downloads/Anaconda2-2019.10-Linux-x86_64.sh
Note: Include the bash command regardless of whether or not you are using Bash shell.
Note: If you did not download to your Downloads directory, replace ~/Downloads/ with the path to the file
you downloaded.
Enter to view license terms.
5. Scroll to the bottom of the license terms and enter “Yes” to agree.
6. The installer prompts you to click Enter to accept the default install location, CTRL-C to cancel the installa-
tion, or specify an alternate installation directory. If you accept the default install location, the installer displays
“PREFIX=/home/<user>/anaconda<2 or 3>” and continues the installation. It may take a few minutes to com-
plete.
“yes”.
init. See FAQ.
8. The installer finishes and displays “Thank you for installing Anaconda<2 or 3>!”
9. The installer provides a link to install PyCharm for Anaconda at https://www.anaconda.com/pycharm.
10. Close and open your terminal window for the installation to take effect, or you can enter the command source
~/.bashrc.
Note: If you install multiple versions of Anaconda, the system defaults to the most current version as long as
you haven’t altered the default install path.
Problems?
What’s next?

Installing on Linux-aarch64 (arm64)
Installation
1. In your browser, download the Anaconda installer for Linux-aarch64.

3. Enter the following to install Anaconda (in this example, the filename is Anaconda3-2021.
04-Linux-aarch64.sh):
bash ~/Downloads/Anaconda3-2021.04-Linux-aarch64.sh
you downloaded.
6. The installer prompts you to click Enter to accept the default install location, CTRL-C to cancel the installation,
or specify an alternate installation directory. If you accept the default install location, the installer displays
“PREFIX=/home/<user>/anaconda3” and continues the installation. It may take a few minutes to complete.
“yes”.
init. See FAQ.
8. The installer finishes and displays “Thank you for installing Anaconda3!”
~/.bashrc.
Problems?
What’s next?
Installing on AWS Graviton2 (arm64)
Installation
1. In your browser, navigate to the Anaconda Installers section of the Anaconda Individual Edition page, and copy
the link for the Linux-aarch64 installer.
2. On your Graviton2 instance, download the installer using curl or wget. For example:
curl -O https://repo.anaconda.com/archive/Anaconda3-2021.04-Linux-aarch64.sh
wget https://repo.anaconda.com/archive/Anaconda3-2021.04-Linux-aarch64.sh

04-Linux-aarch64.sh):
bash ~/Downloads/Anaconda3-2021.04-Linux-aarch64.sh
you downloaded.
“yes”.
init. See FAQ.
9. The installer finishes and displays “Thank you for installing Anaconda3!”
~/.bashrc.
Problems?
What’s next?
Installing on Linux-s390x (IBM Z)
Installation
1. In your browser, download the Anaconda installer for Linux-s390x.

04-Linux-s390x.sh):
bash ~/Downloads/Anaconda3-2021.04-Linux-s390x.sh
you downloaded.

“yes”.
init. See FAQ.
8. The installer finishes and displays “Thank you for installing Anaconda3 !”
~/.bashrc.
Problems?
What’s next?
Installing on Linux POWER
Prerequisites
To use GUI packages with Linux, you will need to install the following extended dependencies for Qt:
Red- yum install libXcomposite libXcursor libXi libXtst libXrandr alsa-lib

Hat mesa-libEGL libXdamage mesa-libGL libXScrnSaver
Open- zypper install libXcomposite1 libXi6 libXext6 libXau6 libX11-6
Suse/SLES
libXrandr2 libXrender1 libXss1 libXtst6 libXdamage1 libXcursor1
libxcb1 libasound2 libX11-xcb1 Mesa-libGL1 Mesa-libEGL1
Installation
1. In your browser, download the Anaconda installer for POWER8 and POWER9.
3. Enter the following to install Anaconda for Python 3.7:
bash ~/Downloads/Anaconda3-2020.02-Linux-ppc64le.sh
OR enter the following to install Anaconda for Python 2.7:
bash ~/Downloads/Anaconda2-2019.10-Linux-ppc64le.sh
you downloaded.
5. Scroll to the bottom of the license terms and enter “Yes” to agree to them.
6. The installer prompts you to click Enter to accept the default install location, CTRL-C to cancel the installa-
tion, or specify an alternate installation directory. If you accept the default install location, the installer displays
“PREFIX=/home/<user>/anaconda<2 or 3>” and continues the installation. It may take a few minutes to com-
plete.
“yes”.

init.
Note: If you enter “No”, you must manually add the path to Anaconda or conda will not work. See FAQ.
8. The installer finishes and displays “Thank you for installing Anaconda<2 or 3>!”
9. The installer provides a link to install PyCharm for Anaconda at https://www.anaconda.com/pycharm.
~/.bashrc.

13. After your install completes, start using Anaconda with the instructions in Getting started with Anaconda.
Note: Anaconda on Power8 or Power9 only supports little endian mode.
Note: If you install multiple versions of Anaconda, the system defaults to the most current version as long as you
haven’t altered the default install path.
Problems?
What’s next?
Installing in silent mode
Windows
Download the installer:

• Miniconda installer for Windows
• Anaconda installer for Windows
Note: The following instructions are for Miniconda. For Anaconda, substitute Anaconda for Miniconda in all of
the commands.
To run the the Windows installer for Miniconda in silent mode, use the /S argument. The following optional arguments
are supported:
• /InstallationType=[JustMe|AllUsers]—Default is JustMe.
• /AddToPath=[0|1]—Default is 1
• /RegisterPython=[0|1]—Make this the system’s default Python. 0 indicates JustMe, which is the
default. 1 indicates AllUsers.
• /S—Install in silent mode.
• /D=<installation path>—Destination installation path. Must be the last argument. Do not wrap in
quotation marks. Required if you use /S.
All arguments are case-sensitive.
EXAMPLE: The following command installs Miniconda for the current user without registering Python as the system’s
default:
start /wait "" Miniconda3-latest-Windows-x86_64.exe /InstallationType=JustMe /

˓→RegisterPython=0 /S /D=%UserProfile%\Miniconda3
Linux & macOS
Note: The following instructions are for Miniconda. For Anaconda, substitute anaconda for miniconda in all of
the commands. Also, substitute the Anaconda installer for the Miniconda installer in the wget step.
To run the silent installation of Miniconda for macOS or Linux, specify the -b and -p arguments of the bash installer.
The following arguments are supported:
• -b—Batch mode with no PATH modifications to ~/.bashrc. Assumes that you agree to the license agreement.
Does not edit the .bashrc or .bash_profile files.
• -p—Installation prefix/path.
• -f—Force installation even if prefix -p already exists.
EXAMPLE:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/
˓→miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
The installer will not prompt you for anything, including setup of your shell to activate conda. To add this activation
in your current shell session:
eval "$(/Users/jsmith/anaconda/bin/conda shell.YOUR_SHELL_NAME hook)"
With this activated shell, you can then install conda’s shell functions for easier access in the future:
conda init
If you’d prefer that conda’s base environment not be activated on startup, set the auto_activate_base parameter
to false:

conda config --set auto_activate_base false
Installing for multiple users
The default Anaconda installation option is “Just Me”, which gives an independent installation of Anaconda that will
not be shared with other users on the same system. The other option is to install for all users.
All users
If you have administrator access, you can choose to install for “All Users”. This is a good option for a multi-user
system where you want to allow users to import Python libraries and run Python applications.
This option does not give write permissions by default so the users will not be able to install packages in the root
environment. It allows an administrator to protect what is in the root environment. If packages are needed in the root
environment, you can elevate the privileges to administrator from the Command Prompt and run install commands.
Multi-user Anaconda installation on Windows
1. Download the Anaconda installer.

2. Double click the installer to launch.
3. Click Next to continue.
4. Read the licensing terms and click “I Agree”.
5. Select an install for “All Users” (this requires administrator privileges on the computer) and click Next.
6. Click “Yes” to allow the installer to make changes to your computer.
7. Select a destination folder that is accessible to the users, the default is C:\ProgramData\Anaconda.
8. After your install is complete, open Computer Management, navigate to Local Users and Groups. Create a new
group for your Anaconda users. Add users to this new group, Anaconda-Users.
9. Navigate to your Anaconda directory and then go to the Properties. Uncheck the box for Attrributes: Read-only
and save changes. Go to the Security tab and click Edit. From there you can add Anaconda-Users and set
permissions. Your group will need read and write privileges.
Multi-user Anaconda installation on Linux
To set up a multi-user Anaconda or Miniconda installation on Linux operating systems:
Note: sudo access is required.
1. Install Anaconda.
2. After installation is complete, create a new group: sudo group add mygroup
3. Change the group ownership to “mygroup” on the entire directory where Anaconda is installed: sudo chgrp
-R mygroup /opt/anaconda2. Replace /opt/anaconda2 with the actual path to your installed Ana-
conda file.
4. Set read and write permission for the owner, root, and the mygroup only: sudo chmod 770 -R /opt/
anaconda2
5. Add users to a group: sudo adduser username mygroup. Users added to the “mygroup” group now
have the ability to access Anaconda, install packages, and create environments.
This is another option for all-user installation. It installs Anaconda at C:\Anaconda, which is not a protected
directory and can have write permissions set for users. This is a good option if your username has spaces in it because
the Anaconda installer cannot install in paths that contain spaces.
Verifying your installation
You can confirm that Anaconda is installed and working with Anaconda Navigator or conda.
Anaconda Navigator
Anaconda Navigator is a graphical user interface that is automatically installed with Anaconda. Navigator will open
if the installation was successful. If Navigator does not open, review our help resources.
• Windows: Click Start, search or select Anaconda Navigator from the menu.
• macOS: Click Launchpad, select Anaconda Navigator. Or, use Cmd+Space to open Spotlight Search and type
“Navigator” to open the program.

• Linux: See next section.
Conda
If you prefer using a command line interface (CLI), you can use conda to verify the installation using Anaconda
Prompt on Windows or terminal on Linux and macOS.
To open Anaconda Prompt:
• Windows: Click Start, search, or select Anaconda Prompt from the menu.
• macOS: Cmd+Space to open Spotlight Search and type “Navigator” to open the program.
• Linux–CentOS: Open Applications - System Tools - terminal.
• Linux–Ubuntu: Open the Dash by clicking the upper left Ubuntu icon, then type “terminal”.
After opening Anaconda Prompt or the terminal, choose any of the following methods to verify:
• Enter conda list. If Anaconda is installed and working, this will display a list of installed packages and
their versions.
• Enter the command python. This command runs the Python shell. If Anaconda is installed and working, the
version information it displays when it starts up will include “Anaconda”. To exit the Python shell, enter the
command quit().
• Open Anaconda Navigator with the command anaconda-navigator. If Anaconda is installed properly,
Anaconda Navigator will open.
Problems?
If you encounter any errors, see the following resources:

• Navigator troubleshooting
• Troubleshooting guide for general troubleshooting
• Help and support for resources such as free community support and bug reports
Anaconda installer file hashes
All installer files are available at https://repo.anaconda.com/archive/ .

You can verify the data integrity of the Anaconda installer files by running a local program to generate their SHA-256
cryptographic hashes and checking the output to be sure it matches the hashes (or “checksums”) below. We do not
suggest MD5 verification as SHA-256 provides greater security.
If the SHA-256 hash that you generate does not match the one here, the file may not have downloaded completely.
Please download it again and re-check. If repeated downloads produce the same result, please contact us to report the
problem, including the file name, the hash you generated, and the hash on the site.
Python 3 Python 2
64-bit Windows 64-bit Windows, Py3 64-bit Windows, Py2
32-bit Windows 32-bit Windows, Py3 32-bit Windows, Py2
macOS graphical installer macOS, Py3 macOS, Py2
macOS command line installer macOS, Py3 macOS, Py2
64-bit Linux 64-bit Linux, Py3 64-bit Linux, Py2
32-bit Linux 32-bit Linux, Py3 32-bit Linux, Py2
Information for all files on a single page
Hashes for all files
Name Size Time modified SHA256 hash

Anaconda3-2021.05-Linux-aarch64.sh 412.6 MiB 2021-05-13 22:08:46 3a3d5a61df5422f7c8c7816217b926ec7
Anaconda3-2021.05-Linux-ppc64le.sh 285.3 MiB 2021-05-13 22:08:47 097064807a9adae3f91fc4c5852cd90df
Anaconda3-2021.05-Linux-s390x.sh 291.7 MiB 2021-05-13 22:08:48 a7d1a83279f439e7d8a6c53aa725552e1
Anaconda3-2021.05-Linux-x86_64.sh 544.4 MiB 2021-05-13 22:08:47 2751ab3d678ff0277ae80f9e8a74f218c
Anaconda3-2021.05-MacOSX-x86_64.pkg 440.3 MiB 2021-05-13 22:08:47 b61e6ca9c338ed39f41408774143f582f
Anaconda3-2021.05-MacOSX-x86_64.sh 432.7 MiB 2021-05-13 22:08:47 0407bee87eeecad521f1e38eb607b0a85
Anaconda3-2021.05-Windows-x86.exe 408.5 MiB 2021-05-13 22:08:48 b95b6ada0a54fe1df06f6cde84f8fa586
Anaconda3-2021.05-Windows-x86_64.exe 477.2 MiB 2021-05-13 22:08:48 93db42390444019e98b442ab281e10916
Anaconda3-2021.04-Linux-aarch64.sh 407.6 MiB 2021-05-07 08:44:23 4a2d3515e41660b3a0598bdd5513d388c
Anaconda3-2021.04-Linux-ppc64le.sh 285.3 MiB 2021-05-10 12:23:03 6954278e3eb85f98ad29a44b0da574156
Anaconda3-2021.04-Linux-s390x.sh 291.7 MiB 2021-05-07 08:45:26 b0b857aa68964cb1388ce1657cc6f32c6
Anaconda3-2021.04-Linux-x86_64.sh 539.9 MiB 2021-05-10 12:21:09 2d6dcbe4360d023c3cecf6a6be8678d90
Anaconda3-2021.04-MacOSX-x86_64.pkg 436.9 MiB 2021-05-10 12:21:10 d3fb9c189d2f7fdefe672dc454432cb82
Anaconda3-2021.04-MacOSX-x86_64.sh 429.3 MiB 2021-05-10 12:21:08 e945565945eb02fcc0755ca9d419ae36c
Anaconda3-2021.04-Windows-x86.exe 405.0 MiB 2021-05-10 12:21:09 61a4e246098886acc1b3cbb977d58ca6d
Anaconda3-2021.04-Windows-x86_64.exe 473.7 MiB 2021-05-10 12:21:09 65fd8be6ab9aed8106bd1c9a228ecd7fd

Table 1 – continued from previous page

Anaconda3-2020.11-Linux-ppc64le.sh 278.9 MiB 2020-11-18 16:45:36 870535ada0a8ae75eeda8cd2bf7dde853
Anaconda3-2020.11-Linux-x86_64.sh 528.8 MiB 2020-11-18 16:45:36 cf2ff493f11eaad5d09ce2b4feaa5ea90
Anaconda3-2020.11-MacOSX-x86_64.pkg 435.3 MiB 2020-11-18 16:45:35 b230c042237ba3e89193d3144179dedda
Anaconda3-2020.11-MacOSX-x86_64.sh 427.8 MiB 2020-11-18 16:45:35 ec11e325c792a6f49dbdbe5e641991d0a
Anaconda3-2020.11-Windows-x86.exe 403.0 MiB 2020-11-18 16:45:34 362de9bc1e9e368dcbcdee1a175a52398
Anaconda3-2020.11-Windows-x86_64.exe 457.2 MiB 2020-11-18 16:45:34 aa523115daf31c431bb392faf75e70d35
Anaconda3-2020.07-Linux-ppc64le.sh 290.4 MiB 2020-07-23 12:16:47 0df7c3784973ab46a9ef9848aced01311
Anaconda3-2020.07-Linux-x86_64.sh 550.1 MiB 2020-07-23 12:16:50 38ce717758b95b3bd0b1797cc6ccfb76f
Anaconda3-2020.07-MacOSX-x86_64.pkg 462.3 MiB 2020-07-23 12:16:42 e095c487d2837e4c984d0fcd2217be42c
Anaconda3-2020.07-MacOSX-x86_64.sh 454.1 MiB 2020-07-23 12:16:44 3980c2a57fde5de2ccfdf0d7973f95ac1
Anaconda3-2020.07-Windows-x86.exe 397.3 MiB 2020-07-23 12:16:51 19803e5ccc357b57051cf7fa272e6b499
Anaconda3-2020.07-Windows-x86_64.exe 467.5 MiB 2020-07-23 12:16:46 66acb9bdf7d2d5925df8762311a85ad72
Anaconda3-2020.02-Linux-ppc64le.sh 276.0 MiB 2020-03-11 10:32:32 d6d1827a38b988cbbe714d6e0357c9e25
Anaconda3-2020.02-Linux-x86_64.sh 521.6 MiB 2020-03-11 10:32:37 2b9f088b2022edb474915d9f69a803d64
Anaconda3-2020.02-MacOSX-x86_64.pkg 442.2 MiB 2020-03-11 10:32:57 4f7cc14b5b1d7aec3d9a5e781dede065e
Anaconda3-2020.02-MacOSX-x86_64.sh 430.1 MiB 2020-03-11 10:32:34 d237e6c976eb9c58368ca156a51bd913d
Anaconda3-2020.02-Windows-x86.exe 423.2 MiB 2020-03-11 10:32:58 d13381d6145c47755b198662af8a5f412
Anaconda3-2020.02-Windows-x86_64.exe 466.3 MiB 2020-03-11 10:32:35 83c2f53c7174253adcc2de7d1293a7408
Anaconda2-2019.10-Linux-ppc64le.sh 295.3 MiB 2019-10-15 09:26:13 0521743829c1b3c301542a20fa0daecda
Anaconda2-2019.10-Linux-x86_64.sh 477.4 MiB 2019-10-15 09:26:03 8b2e7dea2da7d8cc18e822e8ec1804052
Anaconda2-2019.10-MacOSX-x86_64.pkg 635.7 MiB 2019-10-15 09:27:30 d82b6aa37b41782b7823ff712b0899374
Anaconda2-2019.10-MacOSX-x86_64.sh 408.8 MiB 2019-10-15 09:27:31 463cbd0b90c47d02ec341377110653870
Anaconda2-2019.10-Windows-x86.exe 355.6 MiB 2019-10-15 09:26:15 b4731acd02f96923922d995bb16984d71
Anaconda2-2019.10-Windows-x86_64.exe 412.8 MiB 2019-10-15 09:26:08 3e09c8e95e10f077be1e1d26f26df8d6a
Anaconda3-2019.10-Linux-ppc64le.sh 320.3 MiB 2019-10-15 09:26:11 118c579f625555e1b116f0c3fd3842772
Anaconda3-2019.10-Linux-x86_64.sh 505.7 MiB 2019-10-15 09:26:05 46d762284d252e51cd58a8ca6c8adc9da
Anaconda3-2019.10-MacOSX-x86_64.pkg 653.5 MiB 2019-10-15 09:27:33 8b2192cbd586939d68bac00b0f9cbd2bf
Anaconda3-2019.10-MacOSX-x86_64.sh 424.2 MiB 2019-10-15 09:27:31 4f77299ff4170cda64fdfcc27ac609a37
Anaconda3-2019.10-Windows-x86.exe 409.6 MiB 2019-10-15 09:26:10 05e6738919673a6d57b5895b8b4df0b7e
Anaconda3-2019.10-Windows-x86_64.exe 461.5 MiB 2019-10-15 09:27:17 9e632439ed40620b8518f11469ded7316
Anaconda2-2019.07-Linux-ppc64le.sh 298.2 MiB 2019-07-25 09:36:29 ee7f61dab233cdd0acb376ad55e977b16
Anaconda2-2019.07-Linux-x86_64.sh 476.1 MiB 2019-07-25 09:36:01 189e16e7adf9ba4b7b7d06ecdc10ce4ad
Anaconda2-2019.07-MacOSX-x86_64.pkg 634.1 MiB 2019-07-25 09:37:04 7f8a0defa2905bd5e3ca679d6772c896b
Anaconda2-2019.07-MacOSX-x86_64.sh 407.8 MiB 2019-07-25 09:37:45 3e63919eed116826e683ed7d480d06517
Anaconda2-2019.07-Windows-x86.exe 360.5 MiB 2019-07-25 09:36:49 1bd676a51ccdee57c2c01a2bc87fa8b1b
Anaconda2-2019.07-Windows-x86_64.exe 427.2 MiB 2019-07-25 09:36:11 fb7493a5c40d28ab47e54c57f025186dc
Anaconda3-2019.07-Linux-ppc64le.sh 326.0 MiB 2019-07-25 09:36:56 e788094f7a18bfe14038accb26c8809a8
Anaconda3-2019.07-Linux-x86_64.sh 516.8 MiB 2019-07-25 09:36:20 69581cf739365ec7fb95608eef694ba95
Anaconda3-2019.07-MacOSX-x86_64.pkg 653.1 MiB 2019-07-25 09:38:03 bc1a4cb642b775159125521d1dbcf8bd1
Anaconda3-2019.07-MacOSX-x86_64.sh 435.4 MiB 2019-07-25 09:37:06 dcbddbab37c5b5f3873fe24d2617a4325
Anaconda3-2019.07-Windows-x86.exe 418.4 MiB 2019-07-25 09:37:26 3d26ddf9ddb2287822a14ac1da3359a0d
Anaconda3-2019.07-Windows-x86_64.exe 485.8 MiB 2019-07-25 09:37:53 37e753801a881649ceb608449b66ff9da
Anaconda2-2019.03-Linux-ppc64le.sh 291.3 MiB 2019-04-04 16:00:36 3ab35c11b50ff26965266655d7dc76cf2
Anaconda2-2019.03-Linux-x86_64.sh 629.5 MiB 2019-04-04 16:00:35 cedfee5b5a3f62fcdac0a1d2d12396d0f
Anaconda2-2019.03-MacOSX-x86_64.pkg 624.3 MiB 2019-04-04 16:01:08 4e335d60fc9dcfb31caee809143352e28
Anaconda2-2019.03-MacOSX-x86_64.sh 530.2 MiB 2019-04-04 16:00:34 414917d00deaeefa38719992e6437470f
Anaconda2-2019.03-Windows-x86.exe 492.5 MiB 2019-04-04 16:00:43 76be4b3d1f7a1207b786cbb54b3ed5261
Anaconda2-2019.03-Windows-x86_64.exe 586.9 MiB 2019-04-04 16:00:53 96c21ae0d152755e8f4ac4a593da4063e
Anaconda3-2019.03-Linux-ppc64le.sh 314.5 MiB 2019-04-04 16:00:58 b4ecfca3b6d6c284a3f9370f6a5ccfac1

Anaconda3-2019.03-Linux-x86_64.sh 654.1 MiB 2019-04-04 16:00:31 45c851b7497cc14d5ca060064394569f7
Anaconda3-2019.03-MacOSX-x86_64.pkg 637.4 MiB 2019-04-04 16:00:33 1d89450ec2b8236404bab5a47aaa9c69f
Anaconda3-2019.03-MacOSX-x86_64.sh 541.6 MiB 2019-04-04 16:00:27 b232f0b16181f48667d2ca89c04a4ee4b
Anaconda3-2019.03-Windows-x86.exe 545.7 MiB 2019-04-04 16:00:28 03d94f55c4c5e1187382ff414c78e6624
Anaconda3-2019.03-Windows-x86_64.exe 661.7 MiB 2019-04-04 16:00:30 d2c90169879f40816eac91bec585a1f9f
Anaconda2-2018.12-Linux-ppc64le.sh 289.7 MiB 2018-12-21 13:14:33 4ff037544f9191e24887176b44b04100c
Anaconda2-2018.12-Linux-x86.sh 518.6 MiB 2018-12-21 13:13:15 e086c041695c0e50642aee8f4e7adad31
Anaconda2-2018.12-Linux-x86_64.sh 628.2 MiB 2018-12-21 13:13:10 1821d4b623ed449e0acb6df3ecbabd394
Anaconda2-2018.12-MacOSX-x86_64.pkg 640.7 MiB 2018-12-21 13:14:30 f07fb39c41f9cc7839adababdece209d9
Anaconda2-2018.12-MacOSX-x86_64.sh 547.1 MiB 2018-12-21 13:14:31 5c590b1b3cdc2eedd52edce0caabbce66
Anaconda2-2018.12-Windows-x86.exe 458.6 MiB 2018-12-21 13:16:27 d75d51c8f9a7c345128805a55db3856f6
Anaconda2-2018.12-Windows-x86_64.exe 560.6 MiB 2018-12-21 13:16:17 7571d334eac3b9bd4f3e199fc5f493f06
Anaconda3-2018.12-Linux-ppc64le.sh 313.6 MiB 2018-12-21 13:13:03 f636f747d5b581ea05e5f20edb1c9ae5d
Anaconda3-2018.12-Linux-x86.sh 542.7 MiB 2018-12-21 13:13:14 7895052814921d45ed0585d1fb19f8edd
Anaconda3-2018.12-Linux-x86_64.sh 652.5 MiB 2018-12-21 13:13:06 1019d0857e5865f8a6861eaf15bfe535b
Anaconda3-2018.12-MacOSX-x86_64.pkg 652.7 MiB 2018-12-21 13:14:32 e40e076194df57f3fce8734acd5b2e3f6
Anaconda3-2018.12-MacOSX-x86_64.sh 557.0 MiB 2018-12-21 13:13:13 4ccd3944d994fd47e5701c341725a63e9
Anaconda3-2018.12-Windows-x86.exe 509.7 MiB 2018-12-21 13:13:12 3f2955c1874ca452b985627a10859f690
Anaconda3-2018.12-Windows-x86_64.exe 614.3 MiB 2018-12-21 13:14:34 09d84a789013d5e2bfb0148bdd9f5d69a
Anaconda2-5.3.1-Linux-x86.sh 507.6 MiB 2018-11-19 13:37:35 a38017dfa59141c63ec9882a15bd35e7c
Anaconda2-5.3.1-Linux-x86_64.sh 617.8 MiB 2018-11-19 13:37:31 f0650ad2f9ca4ae3f3162d7204a32950b
Anaconda2-5.3.1-MacOSX-x86_64.pkg 628.4 MiB 2018-11-19 13:37:38 7dc614e281df33f09fa006b245a955b94
Anaconda2-5.3.1-MacOSX-x86_64.sh 539.0 MiB 2018-11-19 13:37:43 df81e9d5d7d4c6595609a8d353eab8010
Anaconda2-5.3.1-Windows-x86.exe 458.1 MiB 2018-11-19 13:38:32 59680be839aa8b58477a24519a7575756
Anaconda2-5.3.1-Windows-x86_64.exe 580.1 MiB 2018-11-19 13:37:47 63b8a687cddcf462f9f61993d07ba8838
Anaconda3-5.3.1-Linux-x86.sh 527.3 MiB 2018-11-19 13:38:49 5dab8b2c95595df7fa55b88643f837213
Anaconda3-5.3.1-Linux-x86_64.sh 637.0 MiB 2018-11-19 13:38:46 d4c4256a8f46173b675dd6a62d12f566e
Anaconda3-5.3.1-MacOSX-x86_64.pkg 634.0 MiB 2018-11-19 13:38:54 ee9fb23d4beb30e5ed9d27d5703b46a02
Anaconda3-5.3.1-MacOSX-x86_64.sh 543.7 MiB 2018-11-19 13:38:57 23c373abce2463d4df495f5a1c7e8b0fa
Anaconda3-5.3.1-Windows-x86.exe 509.5 MiB 2018-11-19 13:39:54 a028d0550bf307c69af7c3210f487e230
Anaconda3-5.3.1-Windows-x86_64.exe 632.5 MiB 2018-11-19 13:38:59 295fed5940369d4ea1e2c6d04d418619d
Anaconda2-5.3.0-Linux-ppc64le.sh 285.7 MiB 2018-09-27 16:00:22 b71cdf75ca10875d49170eb64a02920f4
Anaconda2-5.3.0-Linux-x86.sh 507.5 MiB 2018-09-27 16:00:27 58d4229ad7097e1f3387d7f6582dcf2bb
Anaconda2-5.3.0-Linux-x86_64.sh 617.6 MiB 2018-09-27 16:00:25 50eeaab24bfa2472bc6485fe8f0e612ed
Anaconda2-5.3.0-MacOSX-x86_64.pkg 628.3 MiB 2018-09-27 15:59:12 834c221b413bdcbbce434f0a3008511f5
Anaconda2-5.3.0-MacOSX-x86_64.sh 538.9 MiB 2018-09-27 16:00:31 bea3eb7667d265c8fe678ddde8432ac1f
Anaconda2-5.3.0-Windows-x86.exe 457.2 MiB 2018-09-27 15:59:15 f18bdb9a38e5c444a3cb79c5c6bc927fb
Anaconda2-5.3.0-Windows-x86_64.exe 579.0 MiB 2018-09-27 15:59:14 30bf9131df2314c00a9cd5e5f0b7d6184
Anaconda3-5.3.0-Linux-ppc64le.sh 305.1 MiB 2018-09-27 16:01:33 550dd67626172a42eb0dd02a08bc78a67
Anaconda3-5.3.0-Linux-x86.sh 527.2 MiB 2018-09-27 16:01:37 c15ffac2ae35179a15dc5872e5bb405b4
Anaconda3-5.3.0-Linux-x86_64.sh 636.9 MiB 2018-09-27 16:01:35 cfbf5fe70dd1b797ec677e63c61f8efc9
Anaconda3-5.3.0-MacOSX-x86_64.pkg 633.9 MiB 2018-09-27 15:59:18 013e9968f437f91f7a1dfdfe4c7d6f9d3
Anaconda3-5.3.0-MacOSX-x86_64.sh 543.6 MiB 2018-09-27 16:01:41 bc073b6e6d3b2ef29d01a2caf1de7c206
Anaconda3-5.3.0-Windows-x86.exe 508.7 MiB 2018-09-27 16:00:05 1dceb687efbf5a609a66d19dc2528ef78
Anaconda3-5.3.0-Windows-x86_64.exe 631.4 MiB 2018-09-27 15:59:20 1083d05eeec45707940a6c7afb375a5f3
Anaconda2-5.2.0-Linux-ppc64le.sh 269.6 MiB 2018-05-30 13:04:31 a8fcac3f0884520c35103e76549fcc45d
Anaconda2-5.2.0-Linux-x86.sh 488.7 MiB 2018-05-30 13:05:30 402758c24767e9eb3b77312c388725a05
Anaconda2-5.2.0-Linux-x86_64.sh 603.4 MiB 2018-05-30 13:04:33 cb0d7a08b0e2cec4372033d3269979b4e
Anaconda2-5.2.0-MacOSX-x86_64.pkg 616.8 MiB 2018-05-30 13:05:32 f7695a3571eb8e8ae71fe9f413c36f57c


Anaconda2-5.2.0-MacOSX-x86_64.sh 527.1 MiB 2018-05-30 13:05:34 d7d46e566306da5979cd5632079497fe6
Anaconda2-5.2.0-Windows-x86.exe 443.4 MiB 2018-05-30 13:04:17 2b81916c477e64db917821bb48a97000f
Anaconda2-5.2.0-Windows-x86_64.exe 564.0 MiB 2018-05-30 13:04:16 e5ff95332d08a7b006a5bb723e0a5124c
Anaconda3-5.2.0-Linux-ppc64le.sh 288.3 MiB 2018-05-30 13:05:40 024c811526ffc40ed6fa243a25795fbab
Anaconda3-5.2.0-Linux-x86.sh 507.3 MiB 2018-05-30 13:05:46 f3527d085d06f35b6aeb96be2a9253ff9
Anaconda3-5.2.0-Linux-x86_64.sh 621.6 MiB 2018-05-30 13:05:43 09f53738b0cd3bb96f5b1bac488e5528d
Anaconda3-5.2.0-MacOSX-x86_64.pkg 613.1 MiB 2018-05-30 13:07:00 dae8befc73d32b480faef31fa6fb73332
Anaconda3-5.2.0-MacOSX-x86_64.sh 523.3 MiB 2018-05-30 13:07:03 c8089121dc89ffe8f9a0c01205bab75a1
Anaconda3-5.2.0-Windows-x86.exe 506.3 MiB 2018-05-30 13:04:19 64305a4c0041aaf4a3fd0fee4466d7b7f
Anaconda3-5.2.0-Windows-x86_64.exe 631.3 MiB 2018-05-30 13:04:18 2672f6537e2c8a79ae9540cf3c49b18bb
Anaconda2-5.1.0-Linux-ppc64le.sh 267.3 MiB 2018-02-15 09:08:49 ff9baa4d3710bb24bc3a6a40c0f4ef691
Anaconda2-5.1.0-Linux-x86.sh 431.3 MiB 2018-02-15 09:08:51 5af0c7a09a5f3aaf3666c0b362246d342
Anaconda2-5.1.0-Linux-x86_64.sh 533.0 MiB 2018-02-15 09:08:50 5f26ee92860d1dffdcd20910ff2cf7557
Anaconda2-5.1.0-MacOSX-x86_64.pkg 588.0 MiB 2018-02-15 09:08:52 edbe9ef1ee5cfe62e131d7650e07c031a
Anaconda2-5.1.0-MacOSX-x86_64.sh 505.9 MiB 2018-02-15 09:08:53 b686e01aeadb33526d9c154a0ac6f691d
Anaconda2-5.1.0-Windows-x86.exe 419.8 MiB 2018-02-15 09:08:55 fa78c71d88b01e6367f0c3cbd23da1f82
Anaconda2-5.1.0-Windows-x86_64.exe 522.6 MiB 2018-02-15 09:08:54 3674c8d8c233dbea30842f14dc76cc3fe
Anaconda3-5.1.0-Linux-ppc64le.sh 285.7 MiB 2018-02-15 09:08:56 58d1d093450dabefef9279694c9345afe
Anaconda3-5.1.0-Linux-x86.sh 449.7 MiB 2018-02-15 09:08:58 0e940272517d8f8a6f26316a19e4be2bd
Anaconda3-5.1.0-Linux-x86_64.sh 551.2 MiB 2018-02-15 09:08:57 7e6785caad25e33930bc03fac4994a434
Anaconda3-5.1.0-MacOSX-x86_64.pkg 594.7 MiB 2018-02-15 09:09:06 d6bf6309ccafa84314d85ca7421fddc16
Anaconda3-5.1.0-MacOSX-x86_64.sh 511.3 MiB 2018-02-15 09:10:24 be705b3c3a0ca29ee32ce7658890bb5ed
Anaconda3-5.1.0-Windows-x86.exe 435.5 MiB 2018-02-15 09:10:28 7a05da21fd592991d181ac8467faac513
Anaconda3-5.1.0-Windows-x86_64.exe 537.1 MiB 2018-02-15 09:10:26 7d192e58915d7e7fbfd0c987ddc4db38a
Anaconda2-5.0.1-Linux-x86.sh 413.2 MiB 2017-10-24 12:13:07 88c8d698fff16af15862daca10e94a0a4
Anaconda2-5.0.1-Linux-x86_64.sh 507.7 MiB 2017-10-24 12:13:52 23c676510bc87c95184ecaeb327c0b2c8
Anaconda2-5.0.1-MacOSX-x86_64.pkg 562.8 MiB 2017-10-23 20:01:12 22350fe830e6786a263d7727e537f066b
Anaconda2-5.0.1-MacOSX-x86_64.sh 486.5 MiB 2017-10-23 19:51:04 e3a9a5c84cb89ff079b0781ba773a3433
Anaconda2-5.0.1-Windows-x86.exe 403.4 MiB 2017-10-24 12:08:14 1a50fac8644f2128e318337b218299e53
Anaconda2-5.0.1-Windows-x86_64.exe 499.8 MiB 2017-10-23 21:57:22 c43f94c51623850b0c1a826710fe9c8e5
Anaconda3-5.0.1-Linux-x86.sh 431.0 MiB 2017-10-23 18:07:51 991a4b656fcb0236864fbb27ff03bb7f3
Anaconda3-5.0.1-Linux-x86_64.sh 525.3 MiB 2017-10-23 17:52:55 55e4db1919f49c92d5abbf27a4be5986a
Anaconda3-5.0.1-MacOSX-x86_64.pkg 568.9 MiB 2017-10-23 20:01:19 50c28594c785f5828990c950534684885
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Anaconda3-2.4.0-Windows-x86.exe 316.4 MiB 2015-11-02 16:22:25 a69a9fe00ce337b0cfd7d024b79ba5141
Anaconda3-2.4.0-Windows-x86_64.exe 392.3 MiB 2015-11-02 16:22:24 beaa1b803dd30022c6aca1c6f05182bea
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Anaconda-2.3.0-Linux-x86_64.sh 323.9 MiB 2015-07-01 13:35:08 7c02499e9511c127d225992cfe1cd815e
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Anaconda-2.3.0-Windows-x86.exe 277.4 MiB 2015-07-01 13:35:11 3b60ddfb84533539e767889706bd64298
Anaconda-2.3.0-Windows-x86_64.exe 334.7 MiB 2015-07-01 13:35:10 70b4a84e78c721bd46f3de39c75acb37d
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Anaconda-2.2.0-Linux-x86_64.sh 317.3 MiB 2015-03-25 15:20:08 ca2582cb2188073b0f348ad42207211a2


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Anaconda-2.2.0-Windows-x86.exe 274.2 MiB 2015-03-25 15:28:48 247e8e7e386224a3df736ffe607596546
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Anaconda3-2.1.0-Windows-x86.exe 308.7 MiB 2014-09-25 11:09:01 8ffa252aa2b4f63889888ae85a81626ce
Anaconda3-2.1.0-Windows-x86_64.exe 363.3 MiB 2014-09-25 11:11:03 ea4059469b1820069f62bd6c256def625
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Anaconda-2.0.1-Windows-x86_64.exe 343.7 MiB 2014-06-12 15:03:07 5b27e7de356312da711a19ae6a4438c1c
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Anaconda3-2.0.1-Linux-x86_64.sh 304.8 MiB 2014-06-12 14:59:53 3c3b834793e461f3316ad1d9a9178c678
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Anaconda3-2.0.1-Windows-x86.exe 265.7 MiB 2014-06-12 15:00:27 b08803296d7439413d590fd1f967b2012
Anaconda3-2.0.1-Windows-x86_64.exe 319.8 MiB 2014-06-12 15:00:15 e2b6d3d6a9e378fc0d0dd63342417c02b
Anaconda-2.0.0-Linux-x86.sh 298.4 MiB 2014-05-28 16:50:36 efb9d3987134d484d88a9d915437b1bd5
Anaconda-2.0.0-Linux-x86_64.sh 316.9 MiB 2014-05-28 16:50:30 3aa27ddf4a0ba5046ba52b97da99e20eb
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Anaconda-2.0.0-Windows-x86.exe 278.2 MiB 2014-05-28 16:51:02 d86cc7100b4c04ec25768267b81798f70
Anaconda-2.0.0-Windows-x86_64.exe 334.4 MiB 2014-05-28 16:50:53 60078f8677e62e435e5a53f1084e6f39d
Anaconda3-2.0.0-Linux-x86.sh 277.5 MiB 2014-05-27 16:35:55 439761159d5604e182951650a478dd53c
Anaconda3-2.0.0-Linux-x86_64.sh 294.4 MiB 2014-05-27 16:26:59 57ce4f97e300cf94c5724f72d992e9eec
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Anaconda3-2.0.0-Windows-x86.exe 256.9 MiB 2014-05-27 16:59:13 37986ce4c104ed3c82838de74b3a4de17
Anaconda3-2.0.0-Windows-x86_64.exe 310.9 MiB 2014-05-27 17:01:42 a8046fc82da7463ef53cdeaba97c72433
Anaconda-1.9.2-Linux-x86.sh 411.8 MiB 2014-04-08 17:33:09 1f7c850d0b98c011a717b3b757d82077a
Anaconda-1.9.2-Linux-x86_64.sh 484.0 MiB 2014-04-08 17:32:38 7181d399833a2549a9584255bb477487f
Anaconda-1.9.2-MacOSX-x86_64.pkg 281.0 MiB 2014-04-10 10:05:32 2fff6dca12507f675b04ed1f303d0ee99

Anaconda-1.9.2-MacOSX-x86_64.sh 245.4 MiB 2014-04-08 17:34:03 be4611ca671f80b984fa330d4ecf82244
Anaconda-1.9.2-Windows-x86.exe 311.8 MiB 2014-04-08 17:39:25 fe005aeacd1345b856c73d640856b79ed
Anaconda-1.9.2-Windows-x86_64.exe 367.3 MiB 2014-04-08 17:41:16 ef9cfb69c831210fc9000ee5482d2d98b
Anaconda-1.9.1-Linux-x86.sh 411.8 MiB 2014-02-20 13:34:56 9aa39c05f723fee18c54a9cc172998619
Anaconda-1.9.1-Linux-x86_64.sh 483.9 MiB 2014-02-20 13:35:16 f6455e06a72b8cc11c8a96fb88a85518a
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Anaconda-1.9.1-Windows-x86.exe 311.7 MiB 2014-02-20 15:08:42 46cbe29a30cfcd56018f7f69a35525708
Anaconda-1.9.1-Windows-x86_64.exe 367.3 MiB 2014-02-20 15:10:34 d0c3c2faca03b3820ff8fc39688f500bd
Anaconda-1.9.0-Linux-x86.sh 545.3 MiB 2014-02-10 10:23:30 16471e90b3deb7be1b3d449d8883983d8
Anaconda-1.9.0-Linux-x86_64.sh 618.8 MiB 2014-02-10 10:23:05 855f1265e4c0b40d50f5a3a0fe7bae05b
Anaconda-1.9.0-MacOSX-x86_64.pkg 279.8 MiB 2014-02-10 10:23:46 b74134e7626f10fc4d86209a3ebbb19de
Anaconda-1.9.0-MacOSX-x86_64.sh 244.4 MiB 2014-02-10 10:23:47 722fe4d4406e88c5023e7ee21dc1401bb
Anaconda-1.9.0-Windows-x86.exe 308.6 MiB 2014-02-10 10:24:52 2c8c58cf21e537e930535df5a0e8fd4b6
Anaconda-1.9.0-Windows-x86_64.exe 365.1 MiB 2014-02-10 10:24:18 265c7e849688164f7a7fe9df541be0186
Anaconda-1.8.0-Linux-x86.sh 393.0 MiB 2013-11-04 15:37:29 2c08a5cd6ccaa9dc84063b0ee9b007aa8
Anaconda-1.8.0-Linux-x86_64.sh 465.7 MiB 2013-11-04 15:37:12 69f42966d918f4197040e4dd126d2e3cc
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Anaconda-1.8.0-MacOSX-x86_64.sh 228.8 MiB 2013-11-04 13:10:16 5844ca595b5930399a1213db64ab53e9b
Anaconda-1.8.0-Windows-x86.exe 290.0 MiB 2013-11-04 13:54:14 719bc0987be80b46f9c6b745822777fa1
Anaconda-1.8.0-Windows-x86_64.exe 342.1 MiB 2013-11-04 13:55:59 434c2b325a368958b66d52cee4cc710f5
Anaconda-1.7.0-Linux-x86.sh 381.0 MiB 2013-09-08 17:02:26 af372a27a1887e11061485e2a854c5357
Anaconda-1.7.0-Linux-x86_64.sh 452.6 MiB 2013-09-08 17:01:59 6115cfae55a0746b4ae4128be839c99db
Anaconda-1.7.0-MacOSX-x86_64.pkg 256.7 MiB 2013-09-09 12:15:34 d277f7e162c77043e416d03a754389a0d
Anaconda-1.7.0-MacOSX-x86_64.sh 223.3 MiB 2013-09-09 11:52:45 046b592245bc2c11e733acb9700dc5094
Anaconda-1.7.0-Windows-x86.exe 280.6 MiB 2013-09-08 17:10:23 b434776dfeac98f37328c6e538f5a1a53
Anaconda-1.7.0-Windows-x86_64.exe 330.1 MiB 2013-09-08 17:12:00 59a3667fd33f8de1ed476d7ff07917d72
Anaconda-1.6.2-Windows-x86.exe 244.4 MiB 2013-07-09 13:44:58 0873576bbd979e3b7859808bccc2311ed
Anaconda-1.6.2-Windows-x86_64.exe 289.9 MiB 2013-07-09 13:46:28 641fc25c1d13e49cc030df5f4040170d1
Anaconda-1.6.1-Linux-x86.sh 247.1 MiB 2013-07-02 11:59:07 745b9452fd18720deefb465a6687c0d66
Anaconda-1.6.1-Linux-x86_64.sh 317.6 MiB 2013-07-02 11:57:42 81d1819ba08069343f228b9c819cdba0e
Anaconda-1.6.1-MacOSX-x86_64.pkg 197.3 MiB 2013-07-02 17:30:12 7c79819dd40a14e52439664c3e88e89ec
Anaconda-1.6.1-MacOSX-x86_64.sh 170.0 MiB 2013-07-02 11:59:25 bbc15de34208ce8af5aceedeea1334636
Anaconda-1.6.1-Windows-x86.exe 244.4 MiB 2013-07-02 12:02:59 a823dc7688cec49499bb5922783377c26
Anaconda-1.6.1-Windows-x86_64.exe 289.9 MiB 2013-07-02 12:04:26 8cad320d4d6981644fbd1741bd5589d19
Anaconda-1.6.0-Linux-x86.sh 241.6 MiB 2013-06-21 14:23:39 d6aeedfcb39d648fdfb5bd72c4d0b3063
Anaconda-1.6.0-Linux-x86_64.sh 309.5 MiB 2013-06-21 14:23:51 20f5b70193af4b0b8f10aa0e66aabca55
Anaconda-1.6.0-MacOSX-x86_64.sh 169.0 MiB 2013-06-21 14:26:14 e03317888c36c07451a349577b426f435
Anaconda-1.6.0-Windows-x86.exe 244.9 MiB 2013-06-21 14:36:46 3dc2588557455484b3b38feb14fa95d94
Anaconda-1.6.0-Windows-x86_64.exe 290.4 MiB 2013-06-21 14:38:20 6e95dc3612ed430ded28bb48fa1671b32
Anaconda-1.5.1-MacOSX-x86_64.sh 166.2 MiB 2013-05-09 14:26:20 6d3c86a2fdbaeeec2a6c251d5c9034a32
Anaconda-1.5.0-Linux-x86.sh 238.8 MiB 2013-05-08 09:18:43 ca7e356dc1b8c8ef27dfb74b32c77563d
Anaconda-1.5.0-Linux-x86_64.sh 306.7 MiB 2013-05-08 09:18:36 f4cdc194f076e1b438c8a34e7e5f53e70
Anaconda-1.5.0-MacOSX-x86_64.sh 166.2 MiB 2013-05-08 09:18:44 c69609f0f48f33ca5a12d425a9e4d0fc9
Anaconda-1.5.0-Windows-x86.exe 236.0 MiB 2013-05-08 09:18:44 d3dd92fa00d999a94638513daf2d4aeed
Anaconda-1.5.0-Windows-x86_64.exe 280.4 MiB 2013-05-08 09:20:08 7edbe2e51b71c69e7e7a1ec01d8d83954
Anaconda-1.4.0-Linux-x86.sh 220.5 MiB 2013-03-09 16:46:53 065284c5de369c9b89dcae79e7169ce9b
Anaconda-1.4.0-Linux-x86_64.sh 286.9 MiB 2013-03-09 16:46:38 85ae8a0a6e3a41cf7845be3def36ed405
Anaconda-1.4.0-MacOSX-x86_64.sh 156.4 MiB 2013-03-09 16:46:57 e5d5dae6e93bb7df528abc19f5ed3a69c


Anaconda-1.4.0-Windows-x86.exe 210.1 MiB 2013-03-09 16:55:45 e590e45d36d3f164fcaf58cda6a3cb092
Anaconda-1.4.0-Windows-x86_64.exe 241.4 MiB 2013-03-09 16:57:09 6ff0a3bf82fdf5c6f0568d12ff030237e
Anaconda with Python 2 on 64-bit Windows
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Hashes for Anaconda2-2019.10-Windows-x86_64.exe

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exact time file was last modified, as 1571149568.292862

Unix time stamp
time file was last modified, in human 2019-10-15 09:26:08
readable format
exact file size, in bytes 432851808
file size, in human friendly format 412.8 MiB
md5 b152e6f36032ed414ad88cca9ace331a
sha256 3e09c8e95e10f077be1e1d26f26df8d6a13356449e06d7d47ddc066fbaf43

hash on the site.

Unix time stamp
readable format
md5 4813b22808b4042ed54120fd0e44327a
sha256 fb7493a5c40d28ab47e54c57f025186dc26309183b21c8a0df733837e86b1

hash on the site.

Unix time stamp
readable format
md5 042809940fb2f60d979eac02fc4e6c82
sha256 96c21ae0d152755e8f4ac4a593da4063e0f3796064dbe25dbbad163e926f9

hash on the site.

Unix time stamp
readable format
md5 10ff4176a94fcff86e6253b0cc82c782
sha256 7571d334eac3b9bd4f3e199fc5f493f0601890620c22e6d487246bde90497
Hashes for Anaconda2-5.3.1-Windows-x86_64.exe

hash on the site.


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readable format
md5 ff29ffcd1f767cde91bab71110c00294
sha256 63b8a687cddcf462f9f61993d07ba88389c413265d3035a1b1bdb2c481592

hash on the site.

Unix time stamp
readable format
md5 19fb5f9eedf834b4329dcdeac9824516
sha256 30bf9131df2314c00a9cd5e5f0b7d6184c3aec38e4068eaafc962f6201811

hash on the site.

Unix time stamp
readable format
md5 595e427e4b625b6eab92623a28dc4e21
sha256 e5ff95332d08a7b006a5bb723e0a5124c4c4c9a9e4289afdd05941791a79e

hash on the site.

Unix time stamp
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md5 b16d6d6858fc7decf671ac71e6d7cfdb
sha256 3674c8d8c233dbea30842f14dc76cc3feaf4badf7d9dfe4145aa5b6679fab

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md5 b8d9bc02edd61af3f7ece3d07e726e91
sha256 c43f94c51623850b0c1a826710fe9c8e50b0d73708874c9cf9b6ef03806ba

hash on the site.


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md5 8323b1d5f0b1c3fdb5b85efbb099beb0
sha256 5fb73395cdf003613f5d44844da9870dbdc2a35cede0f928b02c38b5ee2eb

hash on the site.

Unix time stamp
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md5 0f60aa52ef3a5d6170aeb6f7e3651f91
sha256 7a8ec1a36f385ebf28a1a8cf63b8b03ac0f7744e1531f5d359ce6a6d90391

hash on the site.

Unix time stamp
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md5 bfd41f4de09a690f8b3525d3fb79bd2f
sha256 c0e13a756a856d7b7757b10d65bee577d8c9826317050eecec42d2e48d2ea
Hashes for Anaconda2-4.3.0.1-Windows-x86_64.exe

hash on the site.

Unix time stamp
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md5 56b181af1959de40e67fb5ef50612ae2
sha256 2198e28e9e8e3c43ab72a8371e5b2d0a9aa6574391aebbcb94bf768a50a57

hash on the site.

Unix time stamp
readable format
md5 2c02e21e542d61760c3e19bf0b3086fe
sha256 1117839746a8eabf7ed26ff311fc74e44a58e319555e306f241e04b32363a

hash on the site.


Unix time stamp
readable format
md5 0a30d509568724dac0ae193e139b9c37
sha256 6254b150edee53000c94e9abfc9c51a2d2e5ef3453d8e7cc7ef0a848d6d3b

hash on the site.

Unix time stamp
readable format
md5 1db0244dbf02579f452d1b19ce245144
sha256 7be13a69df254b86e47612c726b0b2ba9ffa35c060b4d28edb348004c1f72

hash on the site.

Unix time stamp
readable format
md5 6c1066a240b28dbb33e9293a97cd40f5
sha256 7a62880ff9bb7f747d70f518f024dfd1795a26d4130a20d1ff30043d05ec7

hash on the site.

Unix time stamp
readable format
md5 6b2ad997c42fbf58bb1b54baa5619e4f
sha256 213c7d94bdb6f0931edd31bb14ae33ab557cee52c4ac949300e512397a29e

hash on the site.

Unix time stamp
readable format
md5 57e42190411054333781c1208822659d
sha256 4423b43eb23184b4239abc426a564760d6ddf0187ce451468546b88931de4

hash on the site.


Unix time stamp
readable format
md5 733ce916c4c392367c611efd493410b0
sha256 cfbe5539cb7f2e5807ec3d2fa2e59db3a419caa1ef8f0497516dd0c861f92

hash on the site.

Unix time stamp
readable format
md5 00a09d300d13c9f4754165920396625d
sha256 7a40484e58e91f62d91961c8607de586d3ef14645319c0395683e5f718255
Hashes for Anaconda-2.3.0-Windows-x86_64.exe

hash on the site.

Unix time stamp
readable format
md5 93d3d5d2aae82c175cd9ef4a570c2ab0
sha256 70b4a84e78c721bd46f3de39c75acb37d1980a3afa23cf3cef387569606f7

hash on the site.

Unix time stamp
readable format
md5 27230171e315bcdee370ef97ef622158
sha256 1e01d7e1560668f4c05d1cfafcb59b79da1b352671dc913a5ec8b766dde12

hash on the site.

Unix time stamp
readable format
md5 a80eea69583fcee6d3d0f6a63a900b2e
sha256 d9d7c8ed1c914312848407f08fff3d19350c20d754c8872d36ef45ce7541c

hash on the site.


Unix time stamp
readable format
md5 b498d9bf6b266bc09507d2ef9d4b7b55
sha256 5b27e7de356312da711a19ae6a4438c1c857b9c4e357c4aa3275d014db73c

hash on the site.

Unix time stamp
readable format
md5 9ec65c4cc0d640ff36f89193cb9e7b7d
sha256 60078f8677e62e435e5a53f1084e6f39df7f4874892b77d04fbd819033c44

hash on the site.

Unix time stamp
readable format
md5 a610322f6752413c9b02abf72f960ff9
sha256 ef9cfb69c831210fc9000ee5482d2d98ba609d4fbe9e05746f93f569045ba

hash on the site.

Unix time stamp
readable format
md5 b8a404c9f5bfd2452316db3710d2b8ef
sha256 d0c3c2faca03b3820ff8fc39688f500bd140f207aab7553c50005484ff755

hash on the site.

Unix time stamp
readable format
md5 3c5e322e71428167e4d38725e1d92be0
sha256 265c7e849688164f7a7fe9df541be018675772f2e91be39d116e6d0e07181

hash on the site.


Unix time stamp
readable format
md5 dccc94b5e1b77e56385a318c5c91b6d1
sha256 434c2b325a368958b66d52cee4cc710f5ea40e45657854a9be2b54dd50b9c

hash on the site.

Unix time stamp
readable format
md5 c4e6987a83b00da8d36fc4e559df7d01
sha256 59a3667fd33f8de1ed476d7ff07917d726be51de239deaf7ce13ab277bb41

hash on the site.

Unix time stamp
readable format
md5 80bc3fe5f8d2f83110eee775946ed3b8
sha256 641fc25c1d13e49cc030df5f4040170d123072e54b439e7097531a61cc385

hash on the site.

Unix time stamp
readable format
md5 3e63a96cc45f665bf53fa38b18491f94
sha256 8cad320d4d6981644fbd1741bd5589d198f5e4ca1e1f66a10d57c704ee485

hash on the site.

Unix time stamp
readable format
md5 d215a5aca9515f1875cf131b0c35d78d
sha256 6e95dc3612ed430ded28bb48fa1671b32a185c976eba905796707f9b5b44e

hash on the site.


Unix time stamp
readable format
md5 058a62bb0fbaf53870b92798453e718a
sha256 7edbe2e51b71c69e7e7a1ec01d8d83954ada9e885e08adfffdd624b9e1b10

hash on the site.

Unix time stamp
readable format
md5 7e4ff5278e86cc88852abb5da453ae7a
sha256 6ff0a3bf82fdf5c6f0568d12ff030237ee90825bb0ea60e4cf3833db84753

hash on the site.

Unix time stamp
readable format
md5 d62d396a00c6dd51ebf70cde1b5f4c51
sha256 93db42390444019e98b442ab281e1091671b6dce64daf08928d337ffc83cf

hash on the site.

Unix time stamp
readable format
md5 777ff665ef5b5dc323999824cb286c0e
sha256 65fd8be6ab9aed8106bd1c9a228ecd7fd3e23d0d15b9d72415e3a884a69a8

hash on the site.

Unix time stamp
readable format
md5 0841ffcb927a3c2edbd682520f52e546
sha256 aa523115daf31c431bb392faf75e70d35ada935e36dc7b1dd8902baee240b


hash on the site.

Unix time stamp
readable format
md5 7c718535a7dd89fa46b147626ada9e46
sha256 66acb9bdf7d2d5925df8762311a85ad72f57dfd340447bf00636d35a28454

hash on the site.

Unix time stamp
readable format
md5 6b02c1c91049d29fc65be68f2443079a
sha256 83c2f53c7174253adcc2de7d1293a7408c37b295abbbb8feca32cb8428a26

hash on the site.

Unix time stamp
readable format
md5 fafcdbf5feb6dc3081bf07cbb8af1dbe
sha256 9e632439ed40620b8518f11469ded7316eccb489d0dfc41770f72ca2b2202

hash on the site.

Unix time stamp
readable format
md5 56edfc7280fb8def19922a0296b45633
sha256 37e753801a881649ceb608449b66ff9daa35a393409c6e651e56a60c5043b

hash on the site.

Unix time stamp
readable format
md5 bfb4da8555ef5b1baa064ef3f0c7b582
sha256 d2c90169879f40816eac91bec585a1f9f788016fe0a8215ca066299e4b653


hash on the site.

Unix time stamp
readable format
md5 8d068f924a77e8d015906e81e91b31ab
sha256 09d84a789013d5e2bfb0148bdd9f5d69a6baa2127edabb9a8e50e77c6fc57

hash on the site.

Unix time stamp
readable format
md5 3e4d013223d8a71d0fa4d58fe5b31023
sha256 295fed5940369d4ea1e2c6d04d418619d9942c19d925921cbeb941bbc5bd7

hash on the site.

Unix time stamp
readable format
md5 1807a3c595ed2dab9fc7662f2cdf79fd
sha256 1083d05eeec45707940a6c7afb375a5f330d7a24a9de1e6f8d86b4f4e49be

hash on the site.

Unix time stamp
readable format
md5 62244c0382b8142743622fdc3526eda7
sha256 2672f6537e2c8a79ae9540cf3c49b18bb9ba35caec649191b5fa1e759f15b

hash on the site.

Unix time stamp
readable format
md5 83a8b1edcb21fa0ac481b23f65b604c6
sha256 7d192e58915d7e7fbfd0c987ddc4db38a22d5fc47a22db71ac5873ef9ba8a


hash on the site.

Unix time stamp
readable format
md5 3dde7dbbef158db6dc44fce495671c92
sha256 0b1ec18b7425f8c8518d6dc2fc0bc8ec2f06ba57f15727aee4731a4f98278

hash on the site.

Unix time stamp
readable format
md5 fee3fad608d0006afa5c7bca4de3d02b
sha256 53bd80727099b5767b9f20f99e908f9c19cea7572c14f9538dc1c8ca7ab5e

hash on the site.

Unix time stamp
readable format
md5 aa200a1c059a551e0ba9a5314a9554a5
sha256 ea582602541e748053df550514460426202fb4507edf9af4d7d706bc41044

hash on the site.

Unix time stamp
readable format
md5 16f337426454eac463fd0d41c6d2bbb8
sha256 65ce6d7c09884935fee9eb8d318b30e95f75f6efe8a8ba221df282cf22c39
Hashes for Anaconda3-4.3.0.1-Windows-x86_64.exe

hash on the site.

Unix time stamp
readable format
md5 07ea8c5a2306ac8fabf3902bd6623787
sha256 b5954bf7da9a92d351d905dfdfa0e7bee1cfdf8c74ed0532a29416849a92b


hash on the site.

Unix time stamp
readable format
md5 137043b3f9860519967759fc8ea76514
sha256 324568dbef777a6ac8a25c1e8ae1975ffbd95bb621dc91cb3869606cc5924

hash on the site.

Unix time stamp
readable format
md5 0ca5ef4dcfe84376aad073bbb3f8db00
sha256 84e30c99833e142a27fc9ee2c748b03f16c8b1a3ced765024d5db4e68bfbf

hash on the site.

Unix time stamp
readable format
md5 a3be394f8274c391148efdfbc63e8ca4
sha256 b4889513dc574f9d6f96db089315d69d293f8b17635da4d2e6eee118dc105

hash on the site.

Unix time stamp
readable format
md5 50fe73c084b91e55837f4d090809a35e
sha256 9acde60b591233452dba23ac15800f39f2de9b7a180a89916dfa3b6edb326

hash on the site.

Unix time stamp
readable format
md5 a6b7a787c6c574867cee3f2d12ecfc50
sha256 39bf467cd142c1f8fdb7d673fdea273d87ec011af1dbf4b4804c2b0994c61


hash on the site.

Unix time stamp
readable format
md5 6572ceba288b6f145e9b3d0c02a5281c
sha256 4728044d77da715e48d4c95d7f2e3c2a02c4ea7de9d2c69acc851bf294500

hash on the site.

Unix time stamp
readable format
md5 17c562ff74676f004ba8dd029718c09c
sha256 21d155a4b43805042499b8d008835bcdfd9c3a45fe53d1183de9e0a937170

hash on the site.

Unix time stamp
readable format
md5 bc74a4fb4e8455e8e7c61b7f100e3bac
sha256 beaa1b803dd30022c6aca1c6f05182beaea3cd8a17130f73906851269dfe0

hash on the site.

Unix time stamp
readable format
md5 ad4abc78581f6fa68b7f7fc342003f6c
sha256 bd693b61cf191666ae0473327f3c15bcf32b7d09961a0aa0284c10e7ea724

hash on the site.

Unix time stamp
readable format
md5 cd7dae4fd482c94156b4d60bf21d8771
sha256 28c5a13b27a9dbd57c7c633316c5f4beb0cd32cf19b148debd1a81eac86f3


hash on the site.

Unix time stamp
readable format
md5 5d559802f3c699a885c66ea6064f5440
sha256 ea4059469b1820069f62bd6c256def6259d801d7382be70523e081c5adbed

hash on the site.

Unix time stamp
readable format
md5 139c6d32c484e0886c6cbe530b9fbd4c
sha256 e2b6d3d6a9e378fc0d0dd63342417c02bdf6a9676040e05ff8017396d6449

hash on the site.

Unix time stamp
readable format
md5 35fb9536ccb1aca93ec34714e8e69a5b
sha256 a8046fc82da7463ef53cdeaba97c72433c37b211c50fa87f1bc19bdfe5163
Hashes for Anaconda2-2019.10-Windows-x86.exe

hash on the site.

Unix time stamp
readable format
md5 0057a4b9d432ef0b78badee4f74a54a0
sha256 b4731acd02f96923922d995bb16984d71b4a934b7af6737984dd9eb5d8cc6

hash on the site.


Unix time stamp
readable format
md5 38d96b86f4266a125bf3180c225292d9
sha256 1bd676a51ccdee57c2c01a2bc87fa8b1bd48cf7a6c0b16c44a241374f798f

hash on the site.

Unix time stamp
readable format
md5 4b055a00f4f99352bd29db7a4f691f6e
sha256 76be4b3d1f7a1207b786cbb54b3ed526126ee0d4facf41e662b4136224581

hash on the site.

Unix time stamp
readable format
md5 f123fda0ec8928bb7d55d1ca72c0d784
sha256 d75d51c8f9a7c345128805a55db3856f6999dd6aa11f31c0009c640fe0e8d
Hashes for Anaconda2-5.3.1-Windows-x86.exe

hash on the site.

Unix time stamp
readable format
md5 7286587bcfb6a5a164d70fe02c1968d5
sha256 59680be839aa8b58477a24519a7575756bead26b300eb7aae8c82086781bd

hash on the site.

Unix time stamp
readable format
md5 45a5880d1a56aa8e444b43edcc5e6aa2
sha256 f18bdb9a38e5c444a3cb79c5c6bc927fbcd863683b4197713337216af7300

hash on the site.


Unix time stamp
readable format
md5 4a3729b14c2d3fccd3a050821679c702
sha256 2b81916c477e64db917821bb48a97000fad78cd1041022b343cec3cebf9e9

hash on the site.

Unix time stamp
readable format
md5 a09347a53e04a15ee965300c2b95dfde
sha256 fa78c71d88b01e6367f0c3cbd23da1f82e86e02088b0d281437789bfeba59

hash on the site.

Unix time stamp
readable format
md5 623e8d9ca2270cb9823a897dd0e9bfce
sha256 1a50fac8644f2128e318337b218299e53e92ee20ddaf47911ff2be22255c6

hash on the site.

Unix time stamp
readable format
md5 bd3ed48229db828cef4c6b371a8759d1
sha256 078551cfb0df72779897026724f375671e12a5fd384cabeaede5cc325cac1

hash on the site.

Unix time stamp
readable format
md5 51f14d30b08b82cd5e44bbb6b0d63349
sha256 0decd861f8839fdf2cbe4fa306c127f69e50b54374e56d7960ba5217087bf

hash on the site.


Unix time stamp
readable format
md5 4f5ed9917f8c2d2ae2e027e45a85fe8b
sha256 fc363cea3c321c17b43a0bf2137aa845fef349c534fcf511dc285ebb8ae57
Hashes for Anaconda2-4.3.0.1-Windows-x86.exe

hash on the site.

Unix time stamp
readable format
md5 4bff7044ecf0229a0974ba8429520cad
sha256 863702665aa2b55ede2103a8ca7d26435efef614e9d201909c21ec572878f

hash on the site.

Unix time stamp
readable format
md5 ffd6296dc4b359684c54ce6f3d10e144
sha256 a98767acefdeda02fe8d3ef9dadda1a3439fec110ede9bf5d0e359be76ac1

hash on the site.

Unix time stamp
readable format
md5 f4f12af8811759e56464eef5a484963d
sha256 a97ca79cb771568d051ef7773d25c0dda407c63e7ec91305f35dff790aeda

hash on the site.

Unix time stamp
readable format
md5 b319d6867c67723ba74aef4f9dd35f82
sha256 4708d73952a0a8040bf1594ea42027a30e9bacb4d6760cc5d3e4414b6bfd9

hash on the site.


Unix time stamp
readable format
md5 ec44ea5c92542ca0112a6be79aff79bf
sha256 c4ad4eefdffb6d838424c62c8b524352d8b8e4752382b0a09e9d8b7e9e44b

hash on the site.

Unix time stamp
readable format
md5 9fb16479d7eb3dd63cf4ad6704622c8a
sha256 f8185ad2fe89356ab001e55a463b663bcbc9e7699ab7f7c1775a98d5332db

hash on the site.

Unix time stamp
readable format
md5 506c08af8932332303561e822f285d9b
sha256 a0336729f0400ff12fe18a7d5e20c3f9b45f14cd07fe654029daa1ec611e2

hash on the site.

Unix time stamp
readable format
md5 0e6cdba39322c28240f4dceaf7bf72f8
sha256 65fb15559b0ddb5055c110ecdb84823a6fbc8d3938932fbfa0110bb6d3395

hash on the site.

Unix time stamp
readable format
md5 5a5225bd2f74a5be9ef840ae8e62c82a
sha256 2a05db81a0fe4155bc2dd83a689294d3ac7fa1d1a68a5ec6bdafaac9140d4
Hashes for Anaconda-2.3.0-Windows-x86.exe

hash on the site.


Unix time stamp
readable format
md5 7efff6446dcb06e4c44607539c953689
sha256 3b60ddfb84533539e767889706bd64298a73d07a7bfe944a3c5c7f951e395

hash on the site.

Unix time stamp
readable format
md5 32246b48658d4c3faeef425cec64a131
sha256 247e8e7e386224a3df736ffe607596546f4bdd64b44a945fd831db5603782

hash on the site.

Unix time stamp
readable format
md5 4b4303ff83c94f6af128fe43c202756b
sha256 c39193c9018a9c1e9e8f3c1d2692ac635133e9b68e72d7864c75841086337

hash on the site.

Unix time stamp
readable format
md5 579ed15c9599cc49bc073dbbe8870021
sha256 be5a341bc3f9bf8386c686cfc9ad253f3074670c96f130b345b731370ce89

hash on the site.

Unix time stamp
readable format
md5 c3b147e0d5f6d708e884ee03d8856040
sha256 d86cc7100b4c04ec25768267b81798f70a8563a2bdb6dacfe6ec7e45bfbbb

hash on the site.


Unix time stamp
readable format
md5 7217cfa5c5b45de3e683ff09a10ce35b
sha256 fe005aeacd1345b856c73d640856b79ed94a6694245ea8df8cbf94aa7bac7

hash on the site.

Unix time stamp
readable format
md5 5404da4f89dca1a4f5c9efd5ae6fbc5a
sha256 46cbe29a30cfcd56018f7f69a35525708f2d14211a613e7344f91ad4171a8

hash on the site.

Unix time stamp
readable format
md5 02496bcd853574628adfbe1defe5c40f
sha256 2c8c58cf21e537e930535df5a0e8fd4b6d60d4dbe87f13b5964bf2f5f4d27

hash on the site.

Unix time stamp
readable format
md5 3b3bbc639556499d62342f653443553a
sha256 719bc0987be80b46f9c6b745822777fa1f0cb7386ff746fa8e71763bfd997

hash on the site.

Unix time stamp
readable format
md5 91a6398f63a8cc6fa3db3a1e9195b3bf
sha256 b434776dfeac98f37328c6e538f5a1a53199e0c6ca2ef3a39cb3cd2e64db2

hash on the site.


Unix time stamp
readable format
md5 5d9ca457b14fe9af5f8f5e338f9db9e2
sha256 0873576bbd979e3b7859808bccc2311edaea3d34f4d6ed1f6b44b1ba1cf1a

hash on the site.

Unix time stamp
readable format
md5 3cdf41952ad09f00ab03cca5a289fe50
sha256 a823dc7688cec49499bb5922783377c262cbf456830ff8db7c0d4018a2321

hash on the site.

Unix time stamp
readable format
md5 156a48269ae6b2bfc0bede9c3ff719cc
sha256 3dc2588557455484b3b38feb14fa95d941de732e06678365860cd4961c19f

hash on the site.

Unix time stamp
readable format
md5 871f9f4f2321cede8d25ff83f24e70da
sha256 d3dd92fa00d999a94638513daf2d4aeed15a387b820eb08b1907387a4f2e8

hash on the site.

Unix time stamp
readable format
md5 797f4a28462db075de4d21e7977f32a5
sha256 e590e45d36d3f164fcaf58cda6a3cb09252a502af5942e0909324b394710f


hash on the site.

Unix time stamp
readable format
md5 538586430492ddd24b5cb815034715ab
sha256 b95b6ada0a54fe1df06f6cde84f8fa586501ac86eeb86f760106cf87b8716

hash on the site.

Unix time stamp
readable format
md5 7adeb27de653a970476c374408342954
sha256 61a4e246098886acc1b3cbb977d58ca6dd1aeb7a1cd67f4e4f11b12cf6670

hash on the site.

Unix time stamp
readable format
md5 ca1f6f3e75eb346f5ab2d87bab005878
sha256 362de9bc1e9e368dcbcdee1a175a523983c48dd8c04f83caf8d7ceaf7956b

hash on the site.

Unix time stamp
readable format
md5 aa7dcf4d02baa25d14baf5728e29d067
sha256 19803e5ccc357b57051cf7fa272e6b499dfedf13790778dc24af302f894e3

hash on the site.

Unix time stamp
readable format
md5 64ae8d0e5095b9a878d4522db4ce751e
sha256 d13381d6145c47755b198662af8a5f412836adecdb68627bc297be6738a3b


hash on the site.

Unix time stamp
readable format
md5 0e71632df6a17f625c1103b34f66e8ba
sha256 05e6738919673a6d57b5895b8b4df0b7e3f4d7ed0e30faf9c9f1b7d3399e9

hash on the site.

Unix time stamp
readable format
md5 861c83778458be287f4739ef89413cce
sha256 3d26ddf9ddb2287822a14ac1da3359a0db6ceb302b57edb9fcc69061f3927

hash on the site.

Unix time stamp
readable format
md5 f1f636e5d34d129b6b996ff54f4a05b1
sha256 03d94f55c4c5e1187382ff414c78e66244893170fa7aacd0deb71536b7a92

hash on the site.

Unix time stamp
readable format
md5 dc26da1eea1e5cc78121b1d3f80a6e9c
sha256 3f2955c1874ca452b985627a10859f6906eb21d4f6a4c055b78049cf6822b

hash on the site.

Unix time stamp
readable format
md5 52d9041d33c0134dd3824e6c15b458c4
sha256 a028d0550bf307c69af7c3210f487e23004fcb6384f94523e216cc8021390


hash on the site.

Unix time stamp
readable format
md5 72e4f7bf75eb46c60f496d326631fddd
sha256 1dceb687efbf5a609a66d19dc2528ef78a54439a74c98b239041744174c6a

hash on the site.

Unix time stamp
readable format
md5 285387e7b6ea81edba98c011922e235a
sha256 64305a4c0041aaf4a3fd0fee4466d7b7f238fddd9e44a4c8c10f5fa059e82

hash on the site.

Unix time stamp
readable format
md5 7a2291ab99178a4cdec530861494531f
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Unix time stamp
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Unix time stamp
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Unix time stamp
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Hashes for Anaconda3-4.3.0.1-Windows-x86.exe

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Graphical installers for Anaconda with Python 2 on macOS
Hashes for Anaconda2-2019.10-MacOSX-x86_64.pkg

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Hashes for Anaconda2-5.3.1-MacOSX-x86_64.pkg

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Graphical installers for Anaconda with Python 3 on macOS

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Command line installers for Anaconda with Python 2 on macOS
Hashes for Anaconda2-2019.10-MacOSX-x86_64.sh

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Hashes for Anaconda2-5.3.1-MacOSX-x86_64.sh

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Hashes for Anaconda3-2021.04-Linux-s390x.sh

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Hashes for Anaconda3-5.0.0.1-Linux-x86_64.sh

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Hashes for Anaconda3-4.4.0.1-Linux-ppc64le.sh

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Hashes for Anaconda2-2018.12-Linux-x86.sh

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Hashes for Anaconda3-2018.12-Linux-x86.sh

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Hashes for Anaconda3-5.0.0.1-Linux-x86.sh

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Unix time stamp
readable format
md5 860a11c39e58bb574bad5be9d44e2063
sha256 439761159d5604e182951650a478dd53caff52e9dccf17c20ae66689b7b28
Updating from older versions
You can easily update Anaconda to the latest version.

• Windows: Open the Start Menu and choose Anaconda Prompt.
• macOS or Linux: Open a terminal window.
Enter these commands:
conda update conda

conda install anaconda=VersionNumber
More information
The below content provides more details about what is happening when you update Anaconda.
conda update anaconda=VersionNumber grabs the specific release of the Anaconda metapackage, for ex-
ample conda update anaconda=2019.10. That metapackage represents a pinned state that has undergone
testing as a collection. Read more about metapackages.
There is a special “custom” version of the Anaconda metapackage that has all the package dependencies, but none
of them are constrained. The “custom” version is lower in version ordering than any actual release number. conda
update anaconda=VersionNumber may remove packages if the new metapackage that is replacing your old
one has removed packages. As of conda 4.7, when a package loses its connection to the set of specs that have been
requested in the past, it gets removed.
See all of the available Anaconda versions.
conda update --all will unpin everything. This updates all packages in the current environment to the latest
version. In doing so, it drops all the version constraints from the history and tries to make everything as new as it can.
This has the same behavior with removing packages. If any packages are orphaned by an update, they are removed.
conda update --all may not be able to make everything the latest versions because you may have conflicting
constraints in your environment.

With Anaconda 2019.07’s newer Anaconda metapackage, conda update --all will make the metapackage go
to the custom version in order to update other specs.
conda update --all will only update the selected environment. If you have other environments you’d like to
update, you can update them in the command line:
conda update -n myenv --all
When you use conda update pkgName or conda install pkgName, conda may not be able to update or
install that package without changing something else you specified in the past.
In the case of the Anaconda metapackage, when you say conda update ipython but you have Anaconda
2019.03, conda can and should “downgrade” Anaconda to the “custom” version so that iPython can be updated.
When conda cannot fulfill the request for the latest package available, it usually means that newer packages exist for
your spec but are in conflict. To force the change, you can try conda install pkg=newversion.
Uninstalling Anaconda
To uninstall Anaconda, you can do a simple remove of the program. This will leave a few files behind, which for most
users is just fine. See Option A.
If you also want to remove all traces of the configuration files and directories from Anaconda and its programs, you
can download and use the Anaconda-Clean program first, then do a simple remove. See Option B.
1. Option A. Use simple remove to uninstall Anaconda:
• Windows
– Use Windows Explorer to delete the envs and pkgs folders prior to running the uninstall in the
root of your installation.
– In the Control Panel, choose Add or Remove Programs or Uninstall a program, and then select
Python 3.6 (Anaconda) or your version of Python.
• macOS
– Open the Terminal.app or iTerm2 terminal application, and then remove your entire Anaconda
directory, which has a name such as anaconda2, anaconda3, or ~/opt. Enter rm -rf
~/anaconda3 to remove the directory.
• Linux
– Open a terminal window, and then remove your entire Anaconda directory, which has a name
such as anaconda2 or anaconda3, by entering rm -rf ~/anaconda3.
2. Option B. Full uninstall using Anaconda-Clean and simple remove.
Note: Anaconda-Clean must be run before simple remove.
• Install the Anaconda-Clean package from Anaconda Prompt (terminal on Linux or macOS):
conda install anaconda-clean
• In the same window, run one of these commands:

– Remove all Anaconda-related files and directories with a confirmation prompt before deleting each
one:

anaconda-clean
– Or, remove all Anaconda-related files and directories without being prompted to delete each one:
anaconda-clean --yes
Anaconda-Clean creates a backup of all files and directories that might be removed in a folder named
.anaconda_backup in your home directory. Also note that Anaconda-Clean leaves your data files
in the AnacondaProjects directory untouched.
• After using Anaconda-Clean, follow the instructions above in Option A to uninstall Anaconda.
Removing Anaconda path from .bash_profile
If you use Linux or macOS, you may also wish to check the .bash_profile file in your home directory for a line
such as:
export PATH="/Users/jsmith/anaconda3/bin:$PATH"
Note: Replace /Users/jsmith/anaconda3/ with your actual path.
This line adds the Anaconda path to the PATH environment variable. It may refer to either Anaconda or Miniconda.
After uninstalling Anaconda, you may delete this line and save the file.
Silent mode install

You can use silent mode to automatically accept default settings and have no screen prompts appear during installation.
Using Anaconda on older operating systems

We recommend upgrading your operating system. Most OS that are no longer supported in the latest Anaconda are no
longer getting security updates. Upgrading your OS allows you to get the latest packages, performance improvements,
bug fixes, etc.
To use Anaconda on older operating systems, download from our archive. You will not be able to use conda to update
or install packages beyond the Anaconda version noted in the table below, unless you limit it to versions available at
the time that particular version of Anaconda was released. You can see what was available by checking the package
table archives.

Table 2: Outdated operating system support

Operating system How to install Anaconda
macOS 10.10-10.12; Windows Use the command line or graphical installers for Anaconda versions 2019.10
7 and earlier. Download from our archive.
macOS 10.9 Use the command line or graphical installers for Anaconda versions 5.1 and
earlier.
Note: Qt and other packages released after Anaconda Distribution 5.1 (Febru-
ary 15th, 2018) may not work on macOS 10.9, so it may be necessary to not
update certain packages beyond this point.
macOS 10.7 and 10.8 Use the command line installers for Anaconda versions 4.2 and earlier.
macOS 10.5 and 10.6 Use the command line installers for Anaconda versions 1.8 and earlier.
Note: These installer files end in .sh, not .pkg.
Windows XP Use Anaconda versions 2.2 and earlier.

Centos6 (or equivalent) Use Anaconda versions 2020.11 and earlier.
Centos5 (or equivalent) Use Anaconda versions 4.3 and earlier.
Installing Anaconda on a non-networked machine (air gap)

1. Obtain a local copy of the appropriate Anaconda installer for the non-networked machine. You can copy the
Anaconda installer to the target machine using many different methods including a portable hard drive, USB
drive, or CD.
2. After copying the installer to the non-networked machine, follow the detailed installation instructions for your
operating system.
Note: You can install offline copies of both docs.anaconda.com and enterprise-docs.anaconda.com by installing the
conda package anaconda-docs: conda install anaconda-docs
You can install offline copies of documentation for many of Anaconda’s open-source packages by installing the conda
package anaconda-oss-docs: conda install anaconda-oss-docs
Other ways to get Anaconda or Miniconda

You can find the official Anaconda or Miniconda AMIs on the AWS Marketplace.
You can find the official Anaconda and Miniconda Docker images on Docker Hub.
If you have a CDH cluster, you can install the Anaconda parcel using Cloudera Manager. The Anaconda parcel
provides a static installation of Anaconda, based on Python 2.7, that can be used with Python and PySpark jobs on the
cluster.

Troubleshooting
If you experience errors during the installation process, review our Troubleshooting topics.
5.1.2 User guide
Use the following resources to learn how to use Anaconda Individual Edition, including Anaconda Navigator and
conda.
Just starting out?

If you’re new to Anaconda, follow the directions at Getting started with Anaconda to write your first Python project
using Anaconda. Use the navigation tabs at the bottom of the page to go through the user guide in order.
New to Navigator?
Read the Navigator user guide to learn how to use Anaconda’s graphical user interface. Get an overview of the
interface and take your first steps using Navigator at Getting started with Navigator.
Interested in conda?
Conda is an open source package management system and environment management system included in Anaconda
and Miniconda. Learn how to get started with conda.
Ready to dive deeper?

Explore what you can do with Anaconda. The tasks page shows you how to install conda packages, switch between
environments, use IDEs, and more.
Ready to contribute to Anaconda?

See How to contribute to Anaconda by helping resolve issues, improve documentation, add to feedstocks, and con-
tribute code.

Additional resources
• Anaconda cheatsheet
• Frequently asked questions
Getting started with Anaconda
Anaconda Individual Edition contains conda and Anaconda Navigator, as well as Python and hundreds of scientific
packages. When you installed Anaconda, you installed all these too.
Conda works on your command line interface such as Anaconda Prompt on Windows and terminal on macOS and
Linux.
Navigator is a desktop graphical user interface that allows you to launch applications and easily manage conda pack-
ages, environments, and channels without using command-line commands.
You can try both conda and Navigator to see which is right for you to manage your packages and environments. You
can even switch between them, and the work you do with one can be viewed in the other.
Try this simple programming exercise, with Navigator and the command line, to help you decide which approach is
right for you.
When you’re done, see What’s next?.
Your first Python program: Hello, Anaconda!
Use Anaconda Navigator to launch an application. Then, create and run a simple Python program with Spyder and
Jupyter Notebook.
Open Navigator
Choose the instructions for your operating system.

• Windows.
• macOS.
• Linux.
Windows
From the Start menu, click the Anaconda Navigator desktop app.
macOS
Open Launchpad, then click the Anaconda Navigator icon.
Linux
Open a terminal window and type anaconda-navigator.

Run Python in Spyder IDE (integrated development environment)
Tip: Navigator’s Home screen displays several applications for you to choose from. For more information, see links
at the bottom of this page.
1. On Navigator’s Home tab, in the Applications pane on the right, scroll to the Spyder tile and click the Install
button to install Spyder.
Note: If you already have Spyder installed, you can jump right to the Launch step.
2. Launch Spyder by clicking Spyder’s Launch button.

3. In the new file on the left, delete any placeholder text, then type or copy/paste print("Hello Anaconda").
4. In the top menu, click File - Save As and name your new program hello.py.
5. Run your new program by clicking the triangle Run button.
6. You can see your program’s output in the bottom right Console pane.
Close Spyder
From Spyder’s top menu bar, select Spyder - Quit Spyder (In macOS, select Python - Quit Spyder).

Run Python in a Jupyter Notebook
1. On Navigator’s Home tab, in the Applications pane on the right, scroll to the Jupyter Notebook tile and click the
Install button to install Jupyter Notebook.
Note: If you already have Jupyter Notebook installed, you can jump right to the Launch step.
2. Launch Jupyter Notebook by clicking Jupyter Notebook’s Launch button.

This will launch a new browser window (or a new tab) showing the Notebook Dashboard.
3. On the top of the right hand side, there is a dropdown menu labeled “New”. Create a new Notebook with the
Python version you installed.
4. Rename your Notebook. Either click on the current name and edit it or find rename under File in the top menu
bar. You can name it to whatever you’d like, but for this example we’ll use MyFirstAnacondaNotebook.
5. In the first line of the Notebook, type or copy/paste print("Hello Anaconda").
6. Save your Notebook by either clicking the save and checkpoint icon or select File - Save and Checkpoint in the
top menu.
7. Run your new program by clicking the Run button or selecting Cell - Run All from the top menu.

Close Jupyter Notebook
1. From Jupyter Notebooks top menu bar, select File - Close and Halt.
2. Click the Quit button at the upper right of the Notebook Dashboard and close the window or tab.
Close Navigator
From Navigator’s top menu bar, select Anaconda Navigator - Quit Anaconda-Navigator.
Write a Python program using Anaconda Prompt or terminal
Open Anaconda Prompt
Choose the instructions for your operating system.

• Windows.
• macOS.
• Linux.
Windows
From the Start menu, search for and open “Anaconda Prompt”:
macOS
Open Launchpad, then click the terminal icon.
Linux
Open a terminal window.

Start Python
At Anaconda Prompt (terminal on Linux or macOS), type python and press Enter.
The >>> means you are in Python.
Write a Python program
At the >>>, type print("Hello Anaconda!") and press Enter.

When you press enter, your program runs. The words “Hello Anaconda!” print to the screen. You’re programming in
Python!
Exit Python
On Windows, press CTRL-Z and press Enter. On macOS or Linux type exit() and press Enter.
Optional: Launch Spyder or Jupyter Notebook from the command line
1. At the Anaconda Prompt (terminal on Linux or macOS), type spyder and press Enter. Spyder should start up
just like it did when you launched it from Anaconda Navigator.
2. Close Spyder the same way you did in the previous exercise.
3. At the Anaconda Prompt (terminal on Linux or macOS), type jupyter-notebook and press Enter.
Jupyter Notebook should start up just like it did when you launched it from Anaconda Navigator. Close it the same
way you did in the previous exercise.
What’s next?
Using Navigator
• Getting started with Navigator (10 minutes)

• Navigator user guide
Using conda
• Getting started with conda (20 minutes)

• Conda cheat sheet
• Conda user guide
Using Spyder
• Spyder Project Homepage

• Spyder Documentation

Using Jupyter Notebook
• Jupyter Notebook Beginner’s Guide

• Jupyter Project Homepage
• Jupyter Notebook Documentation
Links to IDE documentation
• Eclipse and PyDev

• IDLE
• Sublime Text
• Ninja IDE
• Python Tools for Visual Studio (PTVS)
• Python for Visual Studio Code
• Spyder
• Wing IDE
• IntelliJ
Anaconda Navigator
Desktop Portal to Data Science
Overview
This page describes the tabs, menus, and buttons in the Anaconda Navigator window.
• Online and offline modes

• Home tab
• Environments tab
• Learning tab
• Community tab
• File menu
• Help menu
• Navigator window buttons

The tabs in the left column represent the main components in Navigator. Click a tab to open it.
Tip: To learn more about terms used in Anaconda, see the Glossary.
Online and offline modes
Normally Navigator is used online so that it can download and install packages.
In online mode, Navigator must be able to reach these sites, so they may need to be whitelisted in your network’s
firewall settings.
• https://repo.anaconda.com
• https://conda.anaconda.org for conda-forge and other channels on anaconda.org
• google-public-dns-a.google.com (8.8.8.8:53) to check internet connectivity with Google Public DNS
Offline mode
If Navigator detects that internet access is not available, it automatically enables offline mode and displays this mes-
sage:

In the Preferences dialog, select “Enable offline mode” to enter offline mode even if internet access is available.
Using Navigator in offline mode is equivalent to using the command line conda commands create, install,
remove, and update with the flag --offline so that conda does not connect to the internet.
Home tab
The Home tab, shown in the image above, displays all of the available applications that you can manage with Naviga-
tor.
The first time you open Navigator, the following popular graphical Python applications are already installed or are
available to install:
• JupyterLab
• Jupyter notebook
• Orange data visualization
• Spyder IDE
• Glueviz multidimensional data visualization
• R Studio IDE
• PyCharm
• VS Code
• Anaconda Prompt (Windows only)
• Anaconda PowerShell (Windows only)
You can also build your own Navigator applications.
In each application box, you can:
• Launch the application–Click its Launch button.
• Install an application–Click its Install button.
• Update, remove, or install a specific version of an application–Click the gear icon in the top right corner of the
application box.
Applications are installed in the active environment, which is displayed in the “Applications on” list. To install an
application in a specific environment, first select the environment in the list, then click the application’s Install button.
You can also create a new environment on the Environments tab, then return to the Home tab to install packages in
the new environment.
Environments tab
The Environments tab allows you to manage installed environments, packages, and channels.

The left column lists your environments. Click an environment to activate it.
With Navigator, like with conda, you can create, export, list, remove, and update environments that have different
versions of Python and/or packages installed. Switching or moving between environments is called activating the
environment. Only one environment is active at any point in time. For more information, see Managing environments.
The right column lists packages in the current environment. The default view is Installed packages. To change which
packages are displayed, click the arrow next to the list, then select Not Installed, Upgradeable, or All packages. For
more information, see Managing packages.
Channels are locations where Navigator or conda looks for packages. Click the Channels button to open the Channels
Manager. For more information, see Managing channels.
Learning tab
On the Learning tab you can learn more about Navigator, the Anaconda platform and open data science. Click the
Documentation, Training, Webinars, or Video buttons, then click any item to open it in a browser window.
Community tab
On the Community tab you can learn more about events, free support forums, and social networking relating to
Navigator. Click the Events, Forum, or Social buttons, then click any item to open it in a browser window.

Tip: To get help with Anaconda and Navigator from the community, join the Anaconda forum.
File menu
The Navigator File menu (Anaconda Navigator on macOS) contains the following options:
About–displays information about Navigator, including a link for bug reports and feature requests. In Linux this
is in the Help menu.
Preferences–allows you to set your Navigator preferences.
In the Preferences window you can:
• Set the Anaconda.org API domain if you are going to use channels and packages from anaconda.org.
• Set the Team Edition API domain if you are going to use channels and packages from TE server.
• Set the Enterprise 4 Repository API domain if you are going to use channels and packages from your Repo 4
server.
• Enable or disable SSL verification.
• Optionally set a certificate to verify SSL connections.
• Toggle the option to provide personally non-identifiable information to help improve the product.
• Enable or disable offline mode.
• Hide the offline mode dialog box.
• Hide the Quit dialog box when exiting the program.
• Hide the Update dialog box when starting the program.
• Hide the Close running applications dialog, which normally displays when exiting the program if there are still
running applications that were launched from Navigator.
• Modify Navigator’s display with Enable High DPI scaling option. This option can be useful if Navigator isn’t
displaying correctly on some high DPI screens.
• Show application startup error messages.

• Set the PyCharm Community Edition path if it was not installed in the default location.
• Set the PyCharm Pro path if it was not installed in the default location.
• Set the Visual Studio Code path if it was not installed in the default location.
Tip: Click the Reset to defaults button to change preferences back to their default values.

Warning: Changing the Navigator and Conda configuration files are the advanced features and changing values
directly could cause issues with working the Navigator application and Conda.
• Make changes to the Navigator configuration file (anaconda-navigator.ini).
Note:
There is a base configuration validation tool included, so if the user misses any required section or option
they will be informed through a popup box. See figure below.
• Make changes to the Conda configuration file (.condarc).
Note: There is a base configuration validation tool included. The .condarc file must be a valid yaml format file. If the
content is not in a valid yaml format, the user will receive an error. See figure below.



• Services (macOS only)–links to your computer’s system preferences menu.

• Hide Anaconda-Navigator (macOS only)–hides the Navigator window.
• Hide Others (macOS only)–hides all windows except the Navigator window.
• Show All (macOS only)–shows all windows including the Navigator window.
• Quit Anaconda-Navigator–exits Navigator.
Help menu
The Help menu contains the following options:

• Search–links to your computer’s Help (Windows and macOS only).
• Online Documentation–links to this documentation, which you can read in any web browser. You can also open
the documentation by clicking the Documentation button at the bottom left of the Navigator window.
• Logs viewer–allows you to review the logs of all actions performed in Navigator in the current session. This
option displays a list of log files, including navigator.log, which contains Navigator application logs, and
condamanager.log, which contains logs written by the conda-manager component.
Note: A new log file is created every time you run Navigator, with a sequential number appended to the file
name. More recent log files have higher numbers.
Navigator window buttons
• Sign in to anaconda.org–displayed at the top right. Click to sign into anaconda.org and enable searching for
packages on it. After you have logged in, the button label changes to “Signed in as [username].”
• Documentation–displayed at the bottom left. Click to open Navigator documentation in a browser.
• Developer Blog–displayed at the bottom left. Click to read what our developers have to say about Navigator
development.
• Social media–displayed at the bottom left. Click to see our Twitter, YouTube, and GitHub pages.
Installation
System requirements
Operating systems: Navigator supports the same operating systems that the Anaconda Distribution supports. These
include:
• Windows 8 or newer, 32-bit or 64-bit.
• macOS 10.13+, 64-bit.
• Ubuntu 14+/Centos6+, 64-bit.
Python: Versions 2.7, 3.6, 3.7, and 3.8.
To use Navigator in online mode, you must be able to reach these sites, so you may need to add them to a whitelist in
your network’s firewall settings.
• https://repo.anaconda.com for repositories and installers

• https://conda.anaconda.org for conda-forge and other channels on anaconda.org

• google-public-dns-a.google.com (8.8.8.8:53) to check internet connectivity with Google Public DNS
Installing Navigator
Navigator is automatically installed when you install Anaconda version 4.0.0 or higher.
If you have Miniconda or an older version of Anaconda installed, you can install Navigator from an Anaconda Prompt
by running the command conda install anaconda-navigator.
To start Navigator, see Getting Started.
Uninstalling Navigator
To uninstall Anaconda Navigator, open the Anaconda Prompt (terminal on macOS or Linux), and enter this command:
conda remove anaconda-navigator
To uninstall all of Anaconda see Uninstalling Anaconda.
Configuring Navigator to work with a local Anaconda Repository
If you’re an Anaconda Enterprise subscriber, you can configure Navigator to search for packages in your local Ana-
conda Repository instead of searching on Anaconda.org.
To configure Navigator to search in a local Anaconda Repository:
1. In the top menu bar’s Anaconda Navigator menu (on macOS it’s File), select Preferences.
2. In the Anaconda API domain field, type the address of your local Anaconda Repository.

3. Click Apply.
4. At the top of the Navigator window, click Sign in.
5. In the main login pop-up, click Sign in on the anaconda.org tab.
6. In the Username and Password fields, type your Anaconda Repository username and password.
7. Click the Login button.
Updating Navigator
Every time Navigator starts, it checks whether a new version is available. If one is available, a dialog box is displayed
that allows you to upgrade to a new Navigator version or keep your current version.
Note: We recommend that you keep Navigator updated to the latest version.
Alternate method
If you prefer, you may update Navigator manually.

Open the Anaconda prompt (terminal on Linux or macOS):
Run this command to deactivate conda:
conda deactivate
Then run this command to update Navigator:


conda update anaconda-navigator
Getting started with Navigator
Anaconda Navigator is a graphical user interface to the conda package and environment manager.
This 10-minute guide to Navigator will have you navigating the powerful conda program in a web-like interface
without having to learn command line commands.
SEE ALSO: Getting started with conda to learn how to use conda. Compare the Getting started guides for each to see
which program you prefer.
Before you start
You should have already installed Anaconda.
Contents
• Starting Navigator on Windows, macOS, or Linux. 1 MINUTE

• Managing Navigator. Verify that Anaconda is installed and check that Navigator is updated to the current
version. 1 MINUTE
• Managing environments. Create environments and move easily between them. 3 MINUTES
• Managing Python. Create an environment that has a different version of Python. 2 MINUTES
• Managing packages. Find packages available for you to install. Install packages. 3 MINUTES
TOTAL TIME: 10 MINUTES
Starting Navigator
Windows
• From the Start menu, click the Anaconda Navigator desktop app.
• Or from the Start menu, search for and open “Anaconda Prompt” and type the command
anaconda-navigator.
MacOS
• Open Launchpad, then click the Anaconda-Navigator icon.
• Or open Launchpad and click the terminal icon. Then in terminal, type anaconda-navigator.
Linux



• Open a terminal window and type anaconda-navigator.
Managing Navigator
Verify that Anaconda is installed and running on your system.

• When Navigator starts up, it verifies that Anaconda is installed.
• If Navigator does not start up, go back to Anaconda installation and make sure you followed all the steps.
Check that Navigator is updated to the current version.
• When you start Navigator, it automatically checks for a new version. If Navigator finds a new version, you will
see a dialog box like this:
Click the “Yes” button to update Navigator to the current version.
Tip: We recommend that you always keep Navigator updated to the latest version.
Managing Environments
Navigator uses conda to create separate environments containing files, packages, and their dependencies that will not
interact with other environments.
Create a new environment named snowflakes and install a package in it:
1. In Navigator, click the Environments tab, then click the Create button. The Create new environment dialog
box appears.
2. In the Environment name field, type a descriptive name for your environment.
3. Click Create. Navigator creates the new environment and activates it.

Now you have two environments, the default environment base (root), and snowflakes.
4. Switch between them (activate and deactivate environments) by clicking the name of the environment you want
to use.
Tip: The active environment is the one with the arrow next to its name.
5. Return to the other environment by clicking its name.
Managing Python
When you create a new environment, Navigator installs the same Python version you used when you downloaded and
installed Anaconda. If you want to use a different version of Python, for example Python 3.5, simply create a new
environment and specify the version of Python that you want in that environment.
Create a new environment named “snakes” that contains Python 3.5:
1. In Navigator, click the Environments tab, then click the Create button.
The Create new environment dialog box appears.
2. In the Environment name field, type the descriptive name “snakes” and select the version of Python you want to
use from the Python Packages box (3.8, 3.7, 3.6, 3.5, or 2.7). Select a different version of Python than is in your
other environments, base or snowflakes.
3. Click the Create button.
4. Activate the version of Python you want to use by clicking the name of that environment.

Managing packages
In this section, you check which packages you have installed, check which are available, and look for a specific
package and install it.
1. To find a package you have already installed, click the name of the environment you want to search. The installed
packages are displayed in the right pane.
2. You can change the selection of packages displayed in the right pane at any time by clicking the drop-down box
above it and selecting Installed, Not Installed, Updatable, Selected, or All.
3. Check to see if a package you have not installed named “beautifulsoup4” is available from the Anaconda
repository (must be connected to the Internet). On the Environments tab, in the Search Packages box, type
beautifulsoup4, and from the Search Subset box select All or Not Installed.
4. To install the package into the current environment, check the checkbox next to the package name, then click
the bottom Apply button.
The newly installed program is displayed in your list of installed programs.
More information
• Full documentation
• Free community support

• Paid support options

• Training
Troubleshooting
• Navigator error on start up

• Issues launching or initializing
• PermissionError on macOS Catalina
• Access denied error
• Navigator buttons are missing
• Navigator ignores the “Ok, and don’t show again” option on the help Anaconda improve pop up
• RStudio fails to install in Navigator 1.6.2 if special characters are in install path
• Trouble logging in to Team Edition from Navigator
Navigator error on start up
This is often the result of a corrupted .condarc file. To resolve, delete the .condarc file and restart Navigator.
1. Find the .condarc file.

In Anaconda Prompt or the terminal, enter the command conda info. The output will tell you the location
of your .condarc file(s). You can also search for “.condarc” on your computer.
The .condarc file is frequently found in:
• macOS: /Users/Username

• Linux: ~/.condarc
• Windows: C:\Users\Username
2. Optional: Save custom configurations.
If you had custom configuration in your .condarc file before it was corrupted, save the information so you
can add that configuration back to the new file.
3. Delete the .condarc file.
4. Restart Navigator.
Issues launching or initializing
If you are having problems launching Anaconda Navigator, follow these steps.
If you cannot launch the Anaconda Navigator desktop app, you can still launch it from the terminal or an Anaconda
Prompt with anaconda-navigator.
If you have permissions issues, there may be a problem with the licenses directory, .continuum. Open a terminal or
Anaconda Prompt and delete the .continuum directory. Run rm -rf ~/.continuum on macOS and Linux and
rd /s .continuum on Windows.
Then relaunch Navigator from the desktop app, terminal, or Anaconda Prompt.
If removing the licenses directory does not resolve the issue, manually update Navigator from a terminal or an Ana-
conda Prompt:
If you have updated Navigator and still have problems, remove Anaconda Navigator, then reinstall from terminal or
Anaconda Prompt:
conda remove anaconda-navigator

conda install anaconda-navigator
If none of the above work, please reset Anaconda Navigator configuration back to default values:
anaconda-navigator --reset
PermissionError on macOS Catalina
MacOS Catalina users may experience permission errors where the system does not prompt you for permission to
folders requiring access.
First, update Navigator.
Once updated, you can have Navigator generate the permissions prompt for the first time by launching Spyder and
running something like this in the console (you can replace Desktop with Downloads/Documents folder depending on
which you need access to):
import os
os.listdir('Desktop')

Access denied error
This is caused by a lock file that sometimes gets stuck and isn’t removed when it should be.
In Anaconda Prompt or a terminal, run:
conda update conda

conda update navigator-updater
anaconda-navigator --reset
The last command is the key to fixing the issue as it removes the lock file causing the problem.
Navigator buttons are missing
If your Navigator buttons are missing, try the following:

• Run “Update Index” from the Environments tab of Navigator.
• Quit and restart Navigator.
• If still broken, confirm that your .condarc file is not corrupt. Specifically confirm that your channel settings
contain “defaults”.
• If it’s still broken, try running conda search python from the command line. This will download a fresh
copy of the repodata, which should resolve the problem.
• If none of the above options work, open an issue detailing the error.
Navigator ignores the “Ok, and don’t show again” option on the help Anaconda improve pop up
After starting Navigator, a pop up appears asking if you’d like to provide anonymized usage information to Anaconda.
If you select “Okay, and don’t show again” and the pop up appears again the next time you start Navigator, it may be
due to a privilege conflict.
Specifically, this can occur when Navigator was installed by a user with Administrator privileges, but you are using
it as a regular user without the Administrator privileges. The pop up continues to appear because you do not have
permission to change the pop up box setting.
To resolve this, switch to using an account with Administrator privileges and select the “Ok, and don’t show again”
option in the pop up box. This will apply to all user accounts.
Alternatively, you can edit the .anaconda/navigator/anaconda-navigator.ini configuration file such that
show_startup = False. If show_startup = True, you will continue to see the pop up box.
RStudio fails to install in Navigator 1.6.2 if special characters are in install path
This is a known issue in Navigator 1.6.2 on Windows 7 64-bit.
Trouble logging in to Team Edition from Navigator
If you are having issues logging in or know you’re logged in but cannot interact with Team Edition, try the following
steps:

1. Set logged_api_url, team_edition_token, and team_edition_token_id in the Navigator config file (anaconda-
navigator.ini) to None.
2. Remove channel_alias from the Conda configuration file (.condarc).
3. Try signing in again.
Tutorials
General tasks:
Creating a Python 3.5 environment from Anaconda2 or Anaconda3
1. In Navigator, click the Environments tab, then click the Create button. The Create new environment dialog box
appears.
3. In the Packages list, select “Python” and in the Python version list select “3.5”.
5. Navigator creates the new environment and activates it, as shown by the highlighted green bar. All actions take
place in the active environment.

Creating an R environment and running RStudio
appears.
3. In the Packages list, select “R”.

4. On the drop-down menu, select r to install R with the packages r-base and r-essentials. For more
information please see Using R language with Anaconda.
7. With the new environment active, click the Home button and then click the Install button on the RStudio appli-
cation.
8. Click Launch to run RStudio from Navigator.
9. You will see RStudio running from Navigator.


Managing environments
• Searching for an environment

• Creating a new environment
• Using an environment
• Cloning an environment
• Importing an environment
• Removing an environment
• Advanced environment management
On the Environments tab, the left column displays your environments.
Searching for an environment
In the Search Environments box, type all or part of the environment name.
Creating a new environment
1. At the bottom of the environments list, click the Create button.

2. In the Create Environment dialog box, type a descriptive name for the new environment.
3. Select Python, R, or both for a mixed environment.
4. If applicable, choose a Python version for the new environment.


When you install an R language environment, the https://anaconda.org/r channel is automatically added and made
active and a new channel automatically appears in .condarc.
Using an environment
1. In the environments list, click the environment name.

2. Click the arrow button next to the name. The activation options dialog appears.
3. Select one of the following options for opening the environment: terminal, Python interpreter, IPython Console,
or Jupyter Notebook.
Note: Some of these options may not be available if they were not installed in the environment.
Cloning an environment
1. Click the name of the environment you want to clone.

2. At the bottom of the environments list, click the Clone button.
3. Type a descriptive name for the new environment.
Importing an environment
Each environment has a YAML-formatted configuration file. If someone has given you an environment file that you
want to use, for example my-environment-file.yml, and you have saved it to your computer, you can import it into
Navigator.
1. At the bottom of the environments list, click the Import button.
2. In the Import dialog box, type a descriptive name for the new environment.
3. Click the file folder icon to browse to the YAML file, or type the file name, including its path.
4. Click the Import button.
Removing an environment
1. In the environments list, click the environment you want to remove.

2. At the bottom of the list, click the Remove button.
Advanced environment management
Navigator provides a convenient graphical interface for managing conda environments, channels, and packages. If
you’re comfortable working with Anaconda prompt (terminal on Linux or macOS), you can access additional, ad-
vanced management features. To learn more, see Managing environments with conda.

Managing packages
• Filtering the packages table

• Finding a package
• Installing a package
• Updating a package
• Installing a different package version
• Removing a package
• Advanced package management
On the Navigator Environments tab, the packages table in the right column lists the packages included in the envi-
ronment selected in the left column.
Note: Packages are managed separately for each environment. Changes you make to packages only apply to the
active environment.
Tip: Click a column heading in the table to sort the table by package name, description, or version.

Tip: The Update Index button updates the packages table with all packages that are available in any of the enabled
channels.
Filtering the packages table
By default, only installed packages are shown in the packages table. To filter the table to show different packages,
click the arrow next to Installed, then select which packages to display: Installed, Not installed, Updatable, Selected,
or All.
Note: Selecting the Updatable filter lists packages that are installed and have updates available.
Finding a package
In the Search Packages box, type the name of the package.
Installing a package
1. Select the Not Installed filter to list all packages that are available in the environment’s channels but are not
installed.
Note: Only packages that are compatible with your current environment are listed.
2. Select the name of the package you want to install.

3. Click the Apply button.
4. Review the Install Packages information.
You can filter your packages to be installed by Name, Unlink, Link, and Channel. Unlink indicates what is being
removed. Link is what is being installed in place of the package that is unlinked. Channel shows from where the
package is being installed.
Packages are in a cache and they rely on other packages using hard links, which essentially point to a package instead
of copying it to the environment. Unlink removes the hard link to that package. If the package you are trying to install

is a dependency of other packages, the Link column will show the hard link to the package version that is being created
in order to install your selected package.
Tip: If after installing a new package it doesn’t appear in the packages table, select the Home tab, then click the
Refresh button to reload the packages table.
Updating a package
1. Select the Updatable filter to list all installed packages that have updates available.
2. Click the checkbox next to the package you want to update, then in the menu that appears select Mark for
Update.
OR
In the Version column, click the blue up arrow that indicates there is a newer version available.
Installing a different package version
1. Click the checkbox next to the package whose version you want to change.
2. In the menu that appears, select Mark for specific version installation.
If other versions are available for this package, they are displayed in a list.
3. Click the package version you want to install.

Removing a package
1. Click the checkbox next to the package you want to remove.

2. In the menu that appears, select Mark for removal.

Advanced package management
Navigator provides a convenient graphical interface for managing conda environments, channels, and packages. But
if you’re comfortable working with Anaconda Prompt (terminal on Linux or macOS), you can access additional,
advanced management features. To learn more, see Managing packages with conda.
Managing channels
• Adding a channel
• Deleting a channel
Channels are locations where Navigator and conda look for packages.
You can search and browse packages and channels on anaconda.org.
Note: Navigator and conda only search for packages in active channels. You can temporarily disable a channel by
making it inactive.
EXAMPLE: Let’s say you want to look for packages on the “Milagro” channel of anaconda.org. All three of these
channel variations will look for packages in the same place on Cloud:
• By URL–https://anaconda.org/milagro.
• By conda URL–https://conda.anaconda.org/milagro.
• By name–milagro.
On the Environment tab, click the Channels button to open the Channels Manager.
Adding a channel
1. Click the Add button.
2. Type or paste the channel name, the URL, or the conda URL.
Note: A URL can also contain an access token parameter and value. A URL will automatically be transformed
to a conda URL.
3. Click the Save button.

Deleting a channel
1. Click the trash can icon next to the channel name.

2. Click the Update Channels button.
Building Anaconda Navigator applications
• Who is this for?

• Before you start
• Using a recipe
• Build architecture
• App entry in meta.yaml
• Build
• Upload to Anaconda.org
• Configure Anaconda Navigator
• Troubleshooting
• Additional Information
This tutorial will build an Anaconda Navigator Application (app) of JupyterLab.

Three modifications to the files in the build recipe are required to declare the package as an app. Then, we’ll build
JupyterLab with these recipe modifications. After we build the package, we will upload it to an Anaconda.org channel.
Finally, after adding the channel in Anaconda Navigator, the app will appear on the Home pane.

Who is this for?
This tutorial is for Windows, macOS, and Linux users who wish to generate an Anaconda Navigator app conda package
from a given recipe. Prior knowledge of conda-build or conda recipes is recommended.
Before you start
Note: Applications to be built for Anaconda Navigator should have a graphical user interface. Not all conda packages
have graphical interfaces.
You should already have installed Miniconda or Anaconda. Install conda-build:

conda install conda-build
It is recommended that you use the latest versions of conda and conda-build. To upgrade both packages run:
conda upgrade conda

conda upgrade conda-build
You will also need an account on Anaconda.org. Your username will be referred to as your Anaconda.org channel.
Using a recipe
First, make a new directory called jupyterlab and then change to the new directory:
mkdir jupyterlab
cd jupyterlab
Create the recipe by opening a text file and name it meta.yaml. Copy the recipe from the feedstock:
{% set version = "1.2.4" %}

{% set sha256 = "6adb88acd05b51512c37df477a18c36240823a591c2a51bf6556198414026d8f" %}
package:
name: jupyterlab
version: {{ version }}
source:
fn: jupyterlab-{{ version }}.tar.gz
url: https://pypi.io/packages/source/j/jupyterlab/jupyterlab-{{ version }}.tar.gz
sha256: {{ sha256 }}
build:
noarch: python
number: 0
script: {{ PYTHON }} -m pip install --install-option="--skip-npm" . -vv
entry_points:
- jupyter-lab = jupyterlab.labapp:main
- jupyter-labextension = jupyterlab.labextensions:main
- jupyter-labhub = jupyterlab.labhubapp:main
- jlpm = jupyterlab.jlpmapp:main
app:
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entry: jupyter lab
icon: icon.png
summary: JupyterLab PRE-ALPHA
type: desk
requirements:
host:
- python >=3.5
- pip
- nodejs >=8
run:
- python >=3.5
- jupyterlab_server >=1.0.0,<2.0.0
- notebook >=4.3.1
- tornado !=6.0.0,!=6.0.1,!=6.0.2
- jinja2 >=2.10
test:
requires:
- nodejs
imports:
- jupyterlab
commands:
- jupyter lab --version
- jlpm --version
- jlpm versions
- jupyter labextension list
- jupyter lab path
- jupyter lab build
- jupyter lab clean
about:
home: https://github.com/jupyterlab/jupyterlab
license: BSD-3-Clause
license_family: BSD
license_file: LICENSE
summary: >
An extensible environment for interactive and reproducible computing, based
on the Jupyter Notebook and Architecture.
doc_url: https://jupyterlab.readthedocs.io
dev_url: https://github.com/jupyterlab/jupyterlab
description: >
JupyterLab is the next-generation user interface for Project Jupyter. It
offers all the familiar building blocks of the classic Jupyter Notebook
(notebook, terminal, text editor, file browser, rich outputs, etc.) in a
flexible and powerful user inteface. Eventually, JupyterLab will replace
the classic Jupyter Notebook.
JupyterLab can be extended using extensions that are npm packages and use
our public APIs. You can search for the GitHub topic or npm keyword
`jupyterlab-extension` to find extensions. To learn more about extensions,
see our user documentation.
JupyterLab is suitable for general usage. For JupyterLab extension
developers, the extension APIs will continue to evolve.
extra:
recipe-maintainers:
- jasongrout
- blink1073
- jochym
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(continued from previous page)

- ian-r-rose
- afshin
- ellisonbg
Build architecture
The recipe, as given, is a noarch recipe. This is not compatible with older versions of Navigator. Under the build
section, remove noarch: python.
App entry in meta.yaml
To declare a conda package as an app, the app parameter must be added to to the meta.yaml file. The app section
will contain three keys: entry, summary, and type. In the case of the JupyterLab recipe, replace the app section in the
meta.yaml with the values below.
In the app section, the entry tag defines how the package is to be launched by Anaconda Navigator. For JupyterLab,
separate entry tags are required for Windows, macOS, and Linux operating systems.
In your text editor, open the meta.yaml file and add the following lines. On Windows and Linux the entry tag is:
app:
entry: jupyterlab . [win]
entry: jupyterlab . [linux]
Launch script
For macOS, a launch script must also be provided. In a text editor, create a new file in the conda-build recipe directory
called jupyterlab_mac.command. The contents of this file are:
DIR=$(dirname $0)
$DIR/jupyter-lab ${HOME}
Build.sh script
To make sure that the file gets installed, create a new file in the same directory as the meta.yaml. Title it build.sh and
add these lines to the build.sh script:
$PYTHON -m pip install . --no-deps --ignore-installed -vv

if [ `uname` == Darwin ]
then
cp $RECIPE_DIR/jupyterlab_mac.command $PREFIX/bin
fi
Remove the script key under the build section in the meta.yaml.

Build.bat
Create a new file called build.bat. Include the following:
%PYTHON% -m pip install . --no-deps --ignore-installed -vv
Entry key
Then in the meta.yaml, add this line to the app section:

The completed app section should look like this:
Note: The app icon defaults to the Anaconda logo.
Build
Now that you have the conda-build recipe ready, you can use the conda-build tool to create the package. You will
have to build and upload the JupyterLab package separately on Windows, macOS, and Linux machines in order for the
package to be available on all platforms. If you’re already in the JupyterLab directory, you can type conda build
. in your terminal. Otherwise type conda-build jupyterlab.
When conda-build is finished, it displays the exact path and filename of the conda package. See the Troubleshooting
section if the conda-build command fails.
Windows example file path: C:\Users\username\miniconda\conda-bld\win-64\jupyterlab-1.
2.4-py38_0.tar.bz2
macOS example file path: /Users/username/anaconda3/conda-bld/osx-64/jupyterlab-1.2.
4-py38_0.tar.bz2
Linux example file path: /home/username/miniconda/conda-bld/linux-64/bjupyterlab-1.2.
4-py38_0.tar.bz2
Note: The path and filename will vary depending on your installation and operating system.
Save the path and filename information for the next step.
Upload to Anaconda.org
Now you can upload the new local packages to Anaconda.org. First, log in to Anaconda.org from your terminal:
anaconda login
You will be asked for your Anaconda.org account name and password. If the login was successful you will see output
like the following:
Note: This step must be done in the root conda environment.
Now that you are logged into your channel, you can upload the JupyterLab conda package as follows:

Windows users: anaconda upload C:\Users\username\miniconda\conda-bld\win-64\jupyterlab-1.

2.4-py38_0.tar.bz2
Linux and macOS users: anaconda upload /Users/username/miniconda/conda-bld/osx-64/
jupyterlab-1.2.4-py38_0.tar.bz2
Note: Change your username, path, and filename to the exact username, path, and filename you saved in Step 2.
These will vary depending on your installation and operating system.
For more information about Anaconda.org, see the Anaconda.org documentation page.
Configure Anaconda Navigator
Now that the JupyterLab package has been uploaded to your Anaconda.org channel, you need to add the channel to
Anaconda Navigator.
1. Launch the Anaconda Navigator app. In Windows and Linux it will be available from the Start Menu. On
macOS, you can find it either on the Desktop or through Spotlight.
2. Open the Environments pane on the far left.
3. To add your channel, first click the Channel button. Second, click the Add button. Third, type in the URL to
your Anaconda.org channel: https://conda.anaconda.org/channel
Note: Replace “channel” with your Anaconda.org username.
4. Press Enter and select Update Channels.
5. Close and restart Anaconda Navigator. The JupyterLab app will be displayed on the Home pane.
Troubleshooting
A. Conda-build fails
If the conda recipe fails to build consult the Troubleshooting guide.

B. App does not appear on the home pane
Check that the conda package has been uploaded to your Anaconda.org channel. Check that your channel has been
added to the Channels list.
You may have to remove your .anaconda/navigator directory and restart Navigator. This directory is in your Home
directory.
C. App does not launch
If after installing the application it does not launch, check that it works correctly on the command line with the
following command: conda run jupyterlab
If JupyterLab starts correctly then you may have to remove your .anaconda/navigator directory and restart Navigator.
This directory is in your Home directory.
Additional Information
For more information about adding Start Menu entries in Windows, see the menuinst documentation.
Using multiple versions of Python with Navigator
With Navigator you can have different versions of Python on your computer and easily switch between them by
keeping them in different environments.
To use a different version of Python than the one you are currently using, set up a new environment:
appears.
3. In the Packages list select “Python” and in the Python version list select the version you want to use.

Searching anaconda.org
To search anaconda.org using Anaconda Navigator:

1. If you haven’t already, sign into anaconda.org by clicking the top right sign-in button. If you don’t yet have an
account, you can create one.
2. In Navigator, click the left Environments tab.
3. In the list at the top left of the packages area, select All to search All packages on anaconda.org.
4. In the Search Packages box, type the name of the package you want to search for on anaconda.org.
All packages with that text string are displayed in the Search Results.
For more information on installing and using the packages you find on Anaconda Cloud, see Package installation for
Anaconda.

Integration with Team Edition
• Login Action
• Add default channels Action
• CLI Login Detection
• Login Mechanism
• Integration
• Logout Action
• Change Team Edition API domain
• Troubleshooting
Anaconda Navigator has everything a user needs to setup the Team Edition API domain and login with credentials. It
is easy to add channels and install/update packages from Anaconda Team Edition with Anaconda Navigator.
Login Action
To integrate with Team Edition, click Sign in in the top right corner of the Navigator application. In the main login
pop-up, click Sign in on the Team Edition tab. If this is the first time you are logging in to Team Edition, you’ll be
asked to set your Team Edition domain.
Enter your domain and click Set Domain.
If your domain is correct, you’ll see the login pop-up. Enter the credentials you use to log in to your Team Edition
instance, and then click Login. If all credentials are correct, you will be signed in.

Add default channels Action
After signing in, you’ll see a pop-up with a list of available channels. You can choose what channels to use and
what channels to add to default_channels by clicking on the checkboxes in the Add to default_channels and Add
to channels columns. After you’ve marked channels, click on Add Channels. This step can be skipped by clicking
Skip.

CLI Login Detection
If you have already logged in using CLI, Navigator will detected that and you’ll be asked to check your channels
configuration. See Add default channels Action for further instruction.
Login Mechanism
A few things happen “under the hood” when you successfully log in:
• Your access token is created for Team Edition. This provides you with the ability to access pri-
vate/authenticated/public channels, create environments, and download packages.
• logged_api_url, team_edition_token, and team_edition_token_id in the Navigator config file (anaconda-

navigator.ini) are updated. This is mostly system data to help Navigator integrate with the Team Edition server.
• The Conda configuration file (.condarc) is modified:

1. channels is set to an empty list so you can set appropriate channels
2. default_channels, if present, will be removed
3. channel_alias is set to the login used to access your Team Edition instance.
• The access token is stored locally, which gives Conda ‘native’ access to remote channels and packages.
Integration
Once signed in, you will be able to add private channels in the “Manage Channels” popup using the
<my_channel_name> format, rather than t/<token>/<my_channel_name>.
Click update index to gain access to all packages located in private/authenticated/public channels in the Team Edition
instance.

Logout Action
A few things happen “under the hood” when you successfully log out:
• The Conda configuration file (.condarc) returns to the state it was in before the login. (Navigator saves a copy
of the .condarc file before a login in attempted.)
• logged_api_url, team_edition_token, and team_edition_token_id are set to None in the Navigator config file
(anaconda-navigator.ini).
• The access token created in the Team Edition instance is removed.
• The access token that was stored locally is removed.
Change Team Edition API domain
To set the Team Edition API domain, go to the navigation bar and click on Preferences. In the text field labeled Team
Edition API domain, enter the valid domain name:
Alternatively, this API domain can be set through the Configure Conda action:
1. Click the button Configure Navigator:
2. In the pop-up, find the option team_edition_api_url in the section [main] and enter your domain name (by
default, the value is set to None):
3. Click Save and Restart. The application will restart and the setting will be set.
Yet another option for users is to change this setting directly where the anaconda-navigator.ini file is located by
default.

Note: The domain must be a full path without a trailing slash. For example: http(s)://ate-mysite.com
Troubleshooting
If you are having issues logging in or know you’re logged in but cannot interact with Team Edition, see Trouble logging
in to Team Edition from Navigator.
Integration with Enterprise Edition
• Login Action
• Logout Action
• Change Enterprise Edition API domain
Anaconda Navigator has everything a user needs to setup the Enterprise Edition API domain and login with credentials.
It is easy to add channels and install/update packages from Anaconda Enterprise Edition with Anaconda Navigator.

Login Action
To integrate with Enterprise Edition, click Sign in in the top right corner of the Navigator application. In the main
login pop-up, click Sign in on the Enterprise Edition tab. If this is the first time you are logging in to Enterprise Edition
you’ll be asked to set your Enterprise Edition domain. Enter your domain and click Set Domain.
If your domain is correct, you’ll see the login pop-up. Enter the credentials you use to log in to your Enterprise Edition
platform, and then click Login. If all credentials are correct, you will be signed in.

Logout Action
A few things happen “under the hood” when you successfully log out:
• The Conda configuration file (.condarc) returns to the state it was in before the login. (Navigator saves a copy
of the .condarc file before a login in attempted.)
• The access token created in the Enterprise Edition instance is removed.
• The access token that was stored locally is removed.
Change Enterprise Edition API domain
To set the Enterprise Edition API domain, go to the navigation bar and click on Preferences. In the text field labeled
Enterprise Edition API domain, enter the valid domain name:
Alternatively, this API domain can be set through the Configure Conda action:
1. Click the button Configure Navigator:

2. In the pop-up, find the option enterprise_edition_api_url in the section [main] and enter your domain name
(by default, the value is set to None):
3. Click Save and Restart. The application will restart and the setting will be set.
Yet another option for users is to change this setting directly where the anaconda-navigator.ini file is located by
default.
Note: The domain must be a full path without a trailing slash. For example: http(s)://enterprise-mysite.com
Integration with Commercial Edition
• Login Action
• CLI Login Detection

• Login Mechanism
• Integration
Anaconda Navigator has everything a user needs to setup the Commercial Edition token. It is easy to add channels
and install/update packages from Anaconda Commercial Edition with Anaconda Navigator.
Login Action
To integrate with Commercial Edition, click Sign in in the top right corner of the Navigator application. In the main
login pop-up, click Sign in on the Commercial Edition tab.
Enter your token to log in to your Commercial Edition instance, and then click Set Token. If your token is valid, you
will be signed in.

CLI Login Detection
If you have already logged in using CLI, Navigator will detect that. Note that this works both ways: if you log out
from Commercial Edition in Navigator, your CLI session will be affected accordingly.
Login Mechanism
Navigator uses conda-token tool “under the hood.” See Authenticate to Commercial Edition for more details.
Integration
Once signed in, you will be able to add private channels in the “Manage Channels” pop-up using the
<my_channel_name> format, rather than repo.anaconda.cloud/t/<token>/<my_channel_name>.
Specific examples:
Displaying BioPython help text
After installing a package, you can confirm that the package was installed correctly by opening a Jupyter Notebook
in that environment, importing the package and displaying its help text. In this example we will use the BioPython
package.
1. Start Navigator.
2. To install the BioPython package, follow the instructions in Managing packages.
3. Click the icon to open a Jupyter Notebook.
4. In the Jupyter Notebook, click the New button and select your installed Python version.

5. Copy and paste the following code into the first cell:
import Bio
help(Bio)
6. To run the code, in the menu bar, click Cell then select Run Cells, or use the keyboard shortcut Ctrl-Enter.
The BioPython help text is displayed.
Using the R programming language in Jupyter Notebook
R is a popular programing language for statistics.

To install and run R in a Jupyter Notebook:
1. Start Navigator.
2. To install the R language and r-essentials packages, select Environments to create an new environment. Click
Create.

Name the environment “r-tutorial”. Next to Packages, select Python 3.7 and R. Select r from the dropdown
menu. Click Create.
3. Open the environment with the R package using the Open with Jupyter Notebook option.
4. To create a new notebook for the R language, in the Jupyter Notebook menu, select New, then select R.

5. We will use dplyr to read and manipulate Fisher’s Iris multivariate data set in this tutorial. Copy and paste the
following code into the first cell:
library(dplyr)
iris
7. The iris data table is displayed.
8. Using ggplot, we can create a scatter plot comparing sepal length and width of three iris species. Click + to open
a second cell, then copy and paste the following code into the second cell:
library(ggplot2)
ggplot(data=iris, aes(x=Sepal.Length, y=Sepal.Width, color=Species)) + geom_
˓→point(size=3)
For more resources on using R with Anaconda, see Using R language with Anaconda.
Installing and running Pandas
Pandas is a common Python tool for data manipulation and analysis. This task explains how to use Navigator to set
up and begin working with Pandas in your choice of terminal, Python, IPython, or Jupyter Notebook. The steps are

similar for installing and opening nearly any package.

1. Start Navigator.
2. Click the Environments tab.
3. Click the Create button. When prompted, enter a descriptive name for the environment, such as “Pandas.”
4. Select a Python version to run in the environment.

5. Click OK.
The new environment appears in the environments list.
6. Click the name of the new environment to activate it.
The environment is highlighted with a green background.
7. In the list above the packages table, select All to filter the table to show all packages in all channels.

8. In the Search Packages box, type Pandas.

Pandas appears as a package available for installation.
9. Select the checkbox in front of the Pandas package name.

10. In the menu that appears, select Mark for specific version installation.
11. In the list that appears, select the Pandas version you want to install.

A progress bar appears below the Packages pane while Pandas and its dependencies are installed.
13. To begin using your new environment, click the Environments tab.
14. Click the arrow button next to the Pandas environment name.
15. In the list that appears, select the tool to use to open Pandas: Terminal, Python, IPython, or Jupyter Notebook.
Learn more about Pandas
• 10 Minutes to Pandas
• Pandas Cookbook

Help and support
Anaconda Navigator is copyright 2016-2017 Anaconda®, Inc. It may be copied and distributed freely only as part of
an Anaconda or Miniconda installation.
For free community support for Anaconda and Navigator, join the Anaconda Mailing List.
For Anaconda installation or technical support options, visit our support offerings page.
Training and consulting
Training and consulting is available for all Anaconda products, including Navigator. For more information, please
contact your account representative or email sales@anaconda.com.
Reporting bugs
Please report bugs on the Anaconda GitHub issue tracker.
Release notes
2.0.3 – May 5, 2021
• Reworked login system:

1) Added a main login pop-up to select a repository to connect.
2) Added support of login to Commercial Edition.
3) Added pop-ups to set domain on login for Team Edition and Enterprise Edition.
4) Reworked login pop-ups for anaconda.org, Team Edition, Enterprise Edition.
5) Added pop-up to set up default_channels for Team Edition.
6) Added scroll bar for better user experience and other improvements.
7) Added detection of Commercial Edition user already logged in via CLI.
8) Added detection of Team Edition user already logged in via CLI.
• Added proper checks for SSL errors and unexpected errors.
• Fixed how environment names that begin with underscores are displayed.
• Fixed missing packages while doing setup for ATE/CE channels in default_channels.
• Fixed issue with redirecting users logged in via TE or AE4 to anaconda.org client page.
• Fixed clobbering .condarc settings.
• Fixed application install via Navigator.
• Fixed issue with missing login info in Navigator if the user is logged through the CLI.
• Numerous other bug fixes and improvements.

1.10.0 – October 19, 2020
• Improved Team Edition integration: you can now log in to your Team Edition account from Anaconda Naviga-
tor.
More details at: Integration with Team Edition
• Navigator will now remember the last environment used instead of loading the default environment each time.
• Added a feature to scale Navigator fonts and items if Operating System scaling factor was changed.
• Improved user login experience by separating anaconda.org / Team Edition / Repo4 Enterprise.
• Extended Navigator settings/preferences by adding the following functionalities:
1) Modify Conda configuration file (.condarc) directly from Navigator.
2) Modify Navigator settings file (anaconda-navigator.ini) directly from Navigator.
3) Setup separate API domain names for anaconda.org / Team Edition / Repo4 Enterprise.
4) Set PyCharm and VSCode file paths.
5) Added scroll bar for better user experience and other improvements.
See: Overview
• Added a banner to the navigation pane to show you the most relevant news and tools.
• Fixed bug with Navigator Updater tool:
The bug was a part of the 1.9.12 release, so user will not be able to update from 1.9.12 to 1.10.0 through this
tool. You will need to use the terminal or install 1.10.0 from our official website.
• Added tiles for PyCharm Pro and PyCharm Community / Datalore / IBM Watson Studio Cloud at Home
tab.
• Fixed bug with missing Visual Studio Code tile on the Home tab.
• Fixed bug where the environment would stuck while installing packages.
• Fixed bug where Navigator would hang while loading applications.
• Numerous other bug fixes and improvements.
1.9.12 – February 10, 2020
• Add PyCharm Tile to homepage when installed.

• Add Anaconda Prompt, Anaconda PowerShell Tiles on homepage (Windows only).
• Display pip installed packages in environments.
• Improved the macOS Catalina experience with Navigator,
around granting permissions to the various applications Navigator launches.
• Numerous bug fixes.
1.9 – October 2, 2018
• Add support for Offline Mode for all environment related actions.
• Add support for custom configuration of main windows links.

• Numerous bug fixes and performance enhancements.
1.8 – February 28, 2018
• Remove “Projects” tab.

• Support environment names with spaces on Windows.
• Improve switching between Anaconda API domains.
• Better integration with Visual Studio Code.
1.7 – February 13, 2018
• Add R and MRO documentation tiles.

• Add custom spinner.
• Better handling of Access Denied errors.
• Better integration with Visual Studio Code.
1.6 – May 19, 2017
• Better logging for application launches

• Package list can be filtered by “to be installed”
• Selecting an environment on the Home or Environments tab now selects it on both
• Numerous bug fixes and performance enhancements
1.5 – March 2, 2017
• New Projects tab for working with Anaconda Projects, still in beta status
• Added Navigator Updater and increased visibility of available updates
• Numerous bug fixes and performance enhancements
1.4 – January 31, 2017
• Navigator is out of beta status.

The word “Beta” no longer appears in the title bar.
• R Studio available from the Navigator Home tab.
R Studio is an open-source integrated development environment (IDE) for the R programming language. R
Studio has been added to the R channel and can now be installed and launched from the Navigator Home tab.
To install and launch R Studio, in the R Studio pane, click the Install button, then click the Launch button.

• Orange app returns to the Home tab.

Orange app was removed from version 1.3 due to compatibility issues that have since been resolved. Orange
app is pre-installed starting from version 1.4, so you can click the Launch button to launch it, with no need to
install it first.
• Option to disable or enable SSL verification.
From the top menu bar, select Preferences, select or clear the Enable SSL verification checkbox, then click the
Apply button.
• Support for Anaconda Fusion licenses.
Navigator now supports packages that require a license, including Anaconda Fusion. Installing Anaconda Fusion
now automatically downloads a Fusion trial license from anaconda.org. This license is generated once per user,
so if a user uninstalls Fusion and reinstalls it, the user receives the original license. Trial licenses require users
to register for a free account on anaconda.org.
• Correct display of “no arch” packages.
When Navigator installs “no arch” packages, they now appear correctly on the Environments tab.
• Friendly warning about updating channels for long-term users.
If users have created .condarc files that try to access binstar.org–the original name of anaconda.org–Navigator
now warns that binstar.org channels are outdated.
1.3 – September 27, 2016
• License Manager dialog.

You can now easily upload licenses for applications that require them.
• Applications per environment.
You can install applications to any environment. To do this, on the Home tab, click the Applications menu, then
select the environment in which you want to install an application. If an environment is not selected, applications
are installed by default in the root environment.
• One-click updates and installs.
You can install a new package or update an installed package in the active environment. See Managing packages.
• Clearer indication of option to delete a search filter.
On the Environments tab, when the packages are filtered by a user-defined search string, hovering over the X
button now turns the cursor into an arrow and the X turns red, to emphasize that clicking the X will clear the
search string.
• Channels now support tokens.
The Channel manager now supports security tokens. See Adding a channel.
• Channel name copy and paste support.
• Navigator in a specific environment.
Installing Navigator in an environment other than root now makes that environment the default upon Navigator
startup, both for the Home tab and the Environments tab.
• Table pre-filtering according to Python version.

To avoid unnecessary conflicts, the table that displays a filtered view of packages–according to the Installed, Not
Installed, Upgradeable and Downgradable filter values–does not display packages that are incompatible with the
installed version of Python.
• Dialog size restore.
Upon restart, the application window’s last size and location are preserved, instead of the window’s being
maximized upon startup.
1.2 – August 1, 2016
• Improved condarc support.

Navigator now reads from and writes to the conda configuration file (.condarc). In previous releases, updates
made within Navigator to the conda configuration were not reflected in the .condarc file, and vice versa.
Starting from version 1.2, when you add channels inside Navigator, the .condarc file is updated, and if
.condarc is updated outside Navigator, Navigator correctly reads the available channels.
• Improved channels support.
You can now manage the channels on anaconda.org that you want Navigator to consider active. Active channels
are included when you search for packages and other assets.
• R environment creation support.
Navigator now allows you to install a standalone R language environment or a mixed Python and R environment.
• Conda environment file import.
Navigator now allows you to import environment.yml files.
• Updates for Enterprise users.
Note: You cannot use an Enterprise version of anaconda.org with Navigator.
– Simplified preferences.
Preference options are simplified so that only one URL is needed to set up the API. Changing this value
affects the URL setting of the anaconda-client configuration.
Note: Changing the URL setting in the CLI affects the value displayed in the preferences.
– Proxy.
When using Navigator behind a proxy, the settings must be manually set inside the conda configuration
file. See the conda proxy documentation.
Glossary
Anaconda
A downloadable, free, open-source, high-performance, optimized Python and R distribution with 250+ packages auto-
matically included. Anaconda provides the option to easily install an additional 7,500+ open-source packages for data
science, including advanced and scientific analytics.

Anaconda includes Anaconda Navigator and conda management utilities. Available for Windows, macOS and Linux.
All versions are supported by the development community.
Anaconda.org
A web-based repository hosting service in the cloud. Packages created locally can be published to your channel on
Anaconda Cloud to be shared with the public. Paid subscriptions to Anaconda.org can designate packages as private, to
be shared only with authorized users. Anaconda Cloud is Anaconda’s repository product made available to the public.
Anaconda repository is also available for purchase by companies that wish to maintain their own on-site version of
Anaconda.org. See Anaconda business subscriptions.
Anaconda Enterprise
Anaconda version that includes enterprise technical support, indemnification for a select number of open source pack-
ages, collaborative notebooks, high performance scalability, Hadoop, interactive visualization, governance and secu-
rity. See Anaconda business subscriptions.
Anaconda Navigator
A desktop graphical user interface (GUI) included in all versions of Anaconda that allows you to easily manage conda
packages, environments, channels and notebooks without the need to use the command line interface (CLI).
Anaconda Repository
A private enterprise server on your network where open source and proprietary packages may be stored and retrieved
for installation on a local computer. Anaconda Repository is different from Anaconda.org or the default conda reposi-
tory. The Anaconda Repository is used to govern access to data science assets including packages and notebooks.
Channels
The locations of the repositories where conda looks for packages, often on Anaconda.org (Anaconda.org). Channels
may also go to a private location on a remote or local repository that you or your organization manage.
Command line interface (CLI)
A program in which commands are entered as text, one line at a time, for a computer to execute. This is done in the
Anaconda Prompt in Windows, and in a terminal in macOS and Linux. Conda is executed in a CLI. Contrast with
Graphical User Interface (GUI).
Conda
A package and environment manager program that is packaged with Anaconda and run in a CLI. Using conda, you
can install and update conda packages and their dependencies, and switch between conda environments on your local
computer. Contrast to Anaconda Navigator.

Conda environment
A folder or directory that contains a specific collection of conda packages and their dependencies, so they can be
maintained and run independently without interfering with each other. Environments in Anaconda Navigator are
conda environments.
EXAMPLE: It can be useful to create one environment for packages that run on Python 2, and another for packages
that run on Python 3.
Changes to one environment do not affect other environments.
EXAMPLE: If you upgrade a program in one environment, this will not upgrade the same program in another envi-
ronment.
Conda package
An archive file that contains everything that a software program needs in order to be installed and run, so you do
not have to manually find and install each dependency separately. This can include system-level libraries, Python
modules, executable programs and other components. Managed with conda or Anaconda Navigator. Packages in
Anaconda Navigator are conda packages.
Conda repository
A cloud-based repository that contains 720+ open source certified packages that are easily installed locally via the
conda install command. Can be viewed directly at https://repo.anaconda.com/pkgs/ and used within Anaconda
Navigator when downloading and installing packages from their Environments tab, or by using conda commands in a
Command Line Interface.
Graphical user interface (GUI)
A program with graphic images, icons and menus in which commands are entered by clicking with a mouse and/or
entering text in edit boxes. Anaconda Navigator is a graphical user interface that overlays the conda utility.
Miniconda
A minimal installer for conda that is run from a command line interface (CLI). Like Anaconda, Miniconda is a
free software package that includes the conda package and environment manager, but Miniconda does not include
Anaconda, Anaconda Navigator, or any packages other than those dependencies needed to install it. After Miniconda
is installed, additional conda packages may be installed directly from the command line interface with the command
conda install. See also Anaconda and conda.
Package manager
A collection of software tools that automates the process of installing, upgdating, configuring, and removing computer
programs on a computer. Also known as a package management system. Anaconda Navigator includes the conda
package manager with a GUI overlay for ease of use.

Packages
Software program files and information about the software, such as its name, the specific version and a description,
bundled into a file that can be installed and managed by a package manager.
R packages
Conda packages that install and run the R computer language. Examples include R Essentials, a bundle of 210 popular
open source software programs written in the R computer language. To learn more, see http://conda.pydata.org/docs/
r-with-conda.html.
Repository
Any storage location from which software or software assets may be retrieved and installed on a local computer. See
also: Anaconda Repository and conda repository.
Review this page to learn what Anaconda Navigator is. When you’re ready to start working in Navigator, check out
the user guide topics:
Overview | Installation | Glossary | Getting started with Navigator | Tutorials | Troubleshooting | Release notes | Help
and support
What is Anaconda Navigator?
Anaconda Navigator is a desktop graphical user interface (GUI) included in Anaconda® distribution that allows you
to launch applications and easily manage conda packages, environments, and channels without using command-line
commands. Navigator can search for packages on Anaconda.org or in a local Anaconda Repository. It is available for
Windows, macOS, and Linux.
To get Navigator, get the Navigator Cheat Sheet and install Anaconda.
The Getting started with Navigator section shows how to start Navigator from the shortcuts or from a terminal window.
Why use Navigator?
In order to run, many scientific packages depend on specific versions of other packages. Data scientists often use
multiple versions of many packages and use multiple environments to separate these different versions.
The command-line program conda is both a package manager and an environment manager. This helps data scientists
ensure that each version of each package has all the dependencies it requires and works correctly.

Navigator is an easy, point-and-click way to work with packages and environments without needing to type conda
commands in a terminal window. You can use it to find the packages you want, install them in an environment, run the
packages, and update them – all inside Navigator.
What applications can I access using Navigator?
The following applications are available by default in Navigator:

• JupyterLab
• Jupyter Notebook
• Spyder
• PyCharm
• VSCode
• Glueviz
• Orange 3 App
• RStudio
• Anaconda Prompt (Windows only)
• Anaconda PowerShell (Windows only)
Advanced conda users can also build their own Navigator applications.
How can I run code with Navigator?
The simplest way is with Spyder. From the Navigator Home tab, click Spyder, and write and execute your code.

You can also use Jupyter Notebooks the same way. Jupyter Notebooks are an increasingly popular system that combine
your code, descriptive text, output, images, and interactive interfaces into a single notebook file that is edited, viewed,
and used in a web browser.
Navigator user guide
• Overview
• Getting started with Navigator
• Tutorials
• Troubleshooting
• Release notes
Note: We do not support macOS<10.12 for Anaconda Navigator.
Tasks
Installing conda packages
For more information about using the conda package manager in Anaconda Prompt (terminal on Linux or macOS),
see the conda documentation.
You can also use the graphical interface Anaconda Navigator to install conda packages with just a few clicks.
Open an Anaconda Prompt (terminal on Linux or macOS) and follow these instructions.
Installing a conda package
Enter the command:
conda install package-name
Installing specific versions of conda packages
Include the desired version number or its prefix after the package name:
conda install package-name=2.3.4
To specify only a major version, run:
conda install package-name=2
These commands install into the environment that is currently active. To install into a named environment, run:
conda install package-name=2.3.4 -n some-environment
If the package is specific to a Python version, conda uses the version installed in the current or named environment.
For details on versions, dependencies and channels, see Conda FAQ and Conda Troubleshooting.

Installing packages on a non-networked (air-gapped) computer
To directly install a conda package from your local computer, run:
conda install /package-path/package-filename.tar.bz2
Conda installs packages into the anaconda/pkgs directory.

To install a .tar file containing many conda packages, run the following command:
conda install /packages-path/packages-filename.tar
If conda cannot find the file, try using an absolute path name instead of a relative path name.
Note: Installing packages directly from the file does not resolve dependencies. If your installed package does not
work, it may have missing dependencies that need to be resolved manually.
Switching between Python 2 and Python 3 environments
You can easily maintain separate environments for Python 2 programs and Python 3 programs on the same computer,
without worrying about the programs interacting with each other. Switching to an environment is called activating it.
1. Create a Python 2 environment named py2, install Python 2.7:
conda create --name py2 python=2.7
2. Create a new environment named py3, install Python 3.5:
conda create --name py3 python=3.5
Now you have two environments with which to work. You can install packages and run programs as desired in
either one.
3. Activate and use the Python 2 environment.
Windows:
activate py2
macOS, Linux:
conda activate py2
4. Deactivate the Python 2 environment. Use your py2 environment to install packages and run programs as
desired. When finished, deactivate the environment.
Windows:
deactivate
macOS, Linux:

conda deactivate
5. Activate and use the Python 3 environment.

Windows:
activate py3
macOS, Linux:
conda activate py3
Use the py3 environment to install and run programs as desired. When finished, deactivate the environment
6. Deactivate the Python 3 environment.
Windows:
deactivate
macOS, Linux:
conda deactivate
Configuring a shared package cache
If you have your own installation of Anaconda or Miniconda on your system, you can improve the speed at which
packages are installed or new environments are created and save disk space by setting up the configuration to use a
shared package cache.
Normal installation sets a package cache relative to the install directory. This can be found with the following command
listed under package cache:
conda info
The normal path to the package cache is:
Windows - C:\Users\username\Anaconda{2,3}\pkgs
macOS - ~/opt/anaconda{2,3}
Linux - /home/username/anaconda{2,3}/pkgs
Each user has their own package cache so when a package is installed, the package is put into their own cache and not
shared with anyone else.
The benefit of a shared package cache is that once a particular version of a package has already been downloaded by
a user it will not be downloaded again and stored in a separate cache. This saves disk usage and speeds up the install
as it does not need to download the package again.
Shared package cache setup
Create a directory on your system where the shared users have read and write access.
Then, for each user who will have access, edit the .condarc file found in their home directory.
Windows - C:\Users\username\.condarc
macOS and Linux - /home/username/.condarc

Edit the .condarc with the following entry, specifying the full path to the shared directory:
pkgs_dirs:
- /path/to/shared_directory
Verify the package cache by running conda info again.
Using R language with Anaconda
With Anaconda, you can easily install the R programming language and over 6,000 commonly used R packages for
data science. You can also create and share your own custom R packages.
Note: When using conda to install R packages, you will need to add r- before the regular package name. For
instance, if you want to install rbokeh, you will need to use conda install r-rbokeh or for rJava, type conda
install r-rjava.
The R Essentials bundle contains approximately 200 of the most popular R packages for data science, including the
IRKernel, dplyr, shiny, ggplot2, tidyr, caret, and nnet. It is used as an example in the following guides.
R is the default interpreter installed into new environments. You can specify the R interpreter with the r-base
package. Unless you change the R interpreter, conda will continue to use the default interpreter in each environment.
To run the commands below on Windows, use Start - Anaconda Prompt. On macOS or Linux, open a terminal.
Updating R packages
• Update all of the packages and their dependencies with one command:
conda update r-caret
• If a new version of a package is available in the R channel, you can use conda update to update specific
packages.
Creating and sharing custom R bundles
Creating and sharing custom R bundles is similar to creating and sharing conda packages.
EXAMPLE: Create a simple custom R bundle metapackage named “Custom-R-Bundle” that contains several popular
programs and their dependencies:
conda metapackage custom-r-bundle 0.1.0 --dependencies r-irkernel jupyter r-ggplot2 r-

˓→dplyr --summary "My custom R bundle"
Share the new metapackage by uploading it to your channel on anaconda.org:
conda install anaconda-client

anaconda login
anaconda upload custom-r-bundle-0.1.0-0.tar.bz2
Anyone can now access your custom R bundle from any computer:
conda install -c <your anaconda.org username> custom-r-bundle

Creating an environment with R
1. Download and install Anaconda.

2. Create a new conda environment with all the r-essentials conda packages built from CRAN:
conda create -n r_env r-essentials r-base
3. Activate the environment:
conda activate r_env
4. List the packages in the environment:
conda list
The list shows that the package r-base is installed and r is listed in the build string of the other R packages in the
environment.
Anaconda Navigator, the Anaconda graphical package manager and application launcher, creates R environments by
default.
Creating a new environment with R
When creating a new environment, you can use R by explicitly including r-base in your list of packages.
With conda 4.6:
conda create -n r-environment r-essentials r-base

conda activate r-environment
Mirroring the R channel
Many Anaconda Enterprise customers maintain a local mirror of the R channel.

When mirroring the R channel for the first time, clean the existing packages by running the command
anaconda-server-sync-conda with the option --clean.
Uninstalling R Essentials
To uninstall the R Essentials package, run: conda remove r-essentials
Note: This removes only R Essentials and disables R language support. Other R language packages are not removed.
Using MRO with Anaconda
If you prefer to use the Microsoft R Open (MRO) platform with Anaconda, as opposed to R, you can switch the default
R interpreter from R to MRO. To get MRO, you need to explicitly include mro-base. Anaconda will maintain an
archive of MRO packages but will not update MRO packages. Support for MRO packages will be on a case-by-case
basis.
If you are using MRO, it is recommended to migrate to R. Follow the migration directions.

Switch the default R interpreter from R to MRO
Run conda info and check your version of conda. If your version of conda is below 4.6, run conda update conda
to update conda to the latest version.
Run:
conda config --system --set pinned_packages _r-mutex=*=anacondar*
The default R interpreter will switch from R to MRO.

To learn more about how to use MRO with Anaconda, see Using MRO language with Anaconda.
Resources
Here are some additional resources on using Anaconda with the R programming language:
• R Language packages available for use with Anaconda–There are hundreds of R language packages now avail-
able and several ways to get them.
• Navigator tutorial–Use the R programming language with Anaconda Navigator. The Anaconda Navigator
graphical interface (GUI) makes it easy for even new users to use and run the R language in a Jupyter Notebook.
• Using R packages with Anaconda and anaconda.orgera CDH–Anaconda Scale provides resource management
tools to easily deploy Anaconda across a cluster. It helps you manage multiple conda environments and pack-
ages, including Python and R language, on bare-metal or cloud-based clusters.
• Webinar: Anaconda for R Users–Download the slides from the webinar to see how Anaconda makes package,
dependency and environment management easy with R language and other Open Data Science languages.
Using MRO language with Anaconda
Microsoft R Open (MRO) is the enhanced distribution of R from Microsoft, a complete and free open source platform
for statistical analysis and data science.
MRO was previously the default R interpreter in Anaconda. As of 2019 releases, Anaconda defaults to internal builds
of R, henceforth the “Anaconda R ecosystem.” Learn more about how to use R with Anaconda.
Anaconda maintains an archive of MRO packages but will not update MRO packages. Support for MRO packages
will be on a case-by-case basis.
If you are using MRO, it is recommended to migrate to R. Follow the migration directions below.
Migrate MRO conda environments to use Anaconda R
If you have an MRO-based conda environment and you want to shift over to Anaconda R to fix library errors or for
updates, using conda will fail:
conda install r-base
Using conda will result in unsatisfiable errors because the MRO packages in your environment will conflict with
Anaconda R counterparts. They’re not compatible and the metadata is designed to prevent this coexistence. You can
create a new environment but that could require more effort depending on how many dependencies you have.
To resolve this, use the MRO-migrator tool. This tool removes all MRO-specific packages then updates the remaining
packages to use Anaconda R instead of MRO. The remove-update cycle takes care of the unsatisfiability.

Warning: There’s minimal error handling in this tool. If your environment is not readily reproducible, back it up
before running this tool.
To use the MRO-migrator tool, run its command line:
mro-migrator ~/miniconda3/envs/your-r-env
The default behavior lists which MRO-only packages will be removed. The tool does not change anything by default.
To perform a migration, pass the --execute flag:
mro-migrator --execute ~/miniconda3/envs/your-r-env
MRO-supported operating systems
64-bit systems only for all operating systems - Windows, macOS, and Linux.
Windows 7.0 SP1, Windows 8.1, Windows 10, Windows Server 2008 R2 SP1, and Windows Server 2012.
Linux - CentOS, Red Hat Enterprise Linux, Debian, and Ubuntu.
When using MRO conda packages, starting the R interactive interpreter shows Microsoft R Open in the startup mes-
sage. Anaconda Navigator, the Anaconda graphical package manager and application launcher, also creates R envi-
ronments by default. You may instead select MRO when creating a new conda environment from within Navigator.
Microsoft R Client
Microsoft R Client is a free, community-supported data science tool for high-performance analytics built on top of
MRO. Additionally, R Client introduces the powerful ScaleR technology and its proprietary functions to benefit from
parallelization and remote computing.
Microsoft R Client is available as a conda package (r-mrclient). Users of Windows or RHEL-7/CentOS7/Ubuntu 14.04
and above also have the option to conda install the MicrosoftML R package for machine learning (r-mrclient-mml)
and the pre-trained models for sentiment analysis and image detection (r-mrclient-mlm).
Creating a new environment with MRO instead of R
When creating a new environment, you can use MRO and not R by explicitly including mro-base in your list of
packages.
With conda 4.6.4:
conda create -n mro-environment r-essentials mro-base

conda activate mro-environment
Switch an environment from R to MRO
We recommend using R as your default interpreter in Anaconda, however the directions below show you how to switch
an environment from R to MRO.

Activate the environment containing R
If you use conda 4.4 or later, run:
conda install mro-base
If you use conda 4.3, run:
conda remove --force r-base _r-mutex

conda install mro-base
The environment’s R interpreter will switch from R to MRO.
mro-basics: The MRO Basics metapackage contains everything in the Microsoft MRO installers. It does not include
r-mrclient, r-mrclient-mml, or r-mrclient-mlm.
r-mrclient: Microsoft R Client is a free, community-supported, data science tool for high performance analytics.
r-mrclient-mml: MicrosoftML provides state-of-the-art fast, scalable machine learning algorithms and transforms for
R. Depends on r-mrclient.
r-mrclient-mlm: MicrosoftML Machine Learning Models are pre-trained machine learning models for sentiment
analysis and image detection. Depends on r-mrclient-mml.
Using PyCharm
PyCharm is an IDE that integrates with IPython Notebook, has an interactive Python console, and supports Anaconda
as well as multiple scientific packages. PyCharm supports creating virtual environments for Python with conda.
• Configuring a conda environment in PyCharm

• Adding a package to a project
• Adding a repository to a project
Configuring a conda environment in PyCharm
1. In the Settings/Preferences dialog (,), select Project: <project name> | Project Interpreter.
2. Alternatively, from the Welcome screen, select Configure.
3. Select Preferences.



4. Select Project Interpreter.
5. In the Project Interpreter page, click the gear icon and select Add.
6. In the left-hand pane of the Add Python Interpreter dialog box, select Conda Environment. The following actions
depend on whether the conda environment existed before.
7. If New environment is selected:

1. Specify the location of the new conda environment in the text field or click the folder icon and find
the location in your file system.

Note: The directory where the new conda environment should be located must be empty.
2. Select the Python version from the drop-down list.

3. Specify the location of the conda executable file in the text field or click the ellipsis and find the
location in the conda installation directory.
4. If needed, select the Make available to all projects check box.
8. If Existing environment is selected:
1. Specify the required interpreter: use the drop-down list or click and find one in your file system (for
example, C:\Users\jetbrains\Anaconda3\python.exe).
2. Select the check box Make available to all projects (if needed).
9. Click OK to complete the task.
Adding a package to a project
The project uses the flask package, which is available on the Anaconda defaults channel.
1. To add flask, select Preferences (,).


2. Select + to display the packages available in the defaults channel.
3. The packages in the defaults channel are displayed. Type “flask” into the search bar and select Install.
4. After flask is installed, it will be displayed in the project environment.
Adding a repository to a project
This project uses the bottle package, which is available on the conda-forge channel.
1. To add the conda-forge channel, select Preferences (,).




2. Select + to display the packages available in the defaults channel.
3. To add a repository, select Manage Repositories, select +, and enter “conda-forge”. Select OK.
The packages from both defaults and conda-forge will be displayed.

4. Type “bottle” into the search bar and select Install Package.
5. After bottle is installed, it will be displayed in the project environment.
Using Anaconda behind a company proxy
When using Anaconda with a company proxy, you may encounter an HTTP and SSL error due to custom security
profiles managed by corporate IT departments.




There are 3 potential ways to resolve this. Start with updating the .condarc file before trying the other methods.
Update the .condarc file
We recommend updating your .condarc file to include the proxy_servers key. This is the preferred method
because this will affect only conda and not the system environment variables.
Read more about the .condarc file and using proxies.
For example:
proxy_servers:
http: http://username:password@corp.com:8080
https: https://username:password@corp.com:8080
You can see if your proxy is set by running conda info --all.
Environment variables
You can also resolve this error by updating the system environment variables. This can affect all CLI software across
the whole system.
Windows
To change environment variables on Windows:

1. In the Start menu, search for “env”.
2. Select “Edit Environment Variables for your account”
3. Select “Environment Variables. . . ”
4. Press “New. . . ”
5. Add two variables http_proxy and https_proxy both with the same value: http://proxy-XX:XXX
MacOS
To change environment variables on macOS:

1. Check the current environment variable settings by running printenv in the terminal.
2. To check a specific environment variable, use echo $variable_name.
3. Temporarily change the environment variables by running export variable_name=variable_value.
You can check if it’s there by running conda info --all.
To change your environment variables on macOS permanently, review this guide.

Linux
To change environment variables on Linux:

1. Run export variable_name=variable_value
2. To output the value of the environment variable from the shell, run echo $variable_name.
Read more about unsetting, listing, and persisting environment variables.
Netrc authentication
A .netrc file is an alternate way to accomplish the same goal of setting the *_PROXY environment variables or config-
uring things only for conda in the .condarc file. The risk in this approach is that changing the environment variables
here will affect the system settings as a whole.
Read more about the .netrc file.
TensorFlow
Anaconda makes it easy to install TensorFlow, enabling your data science, machine learning, and artificial intelligence
workflows.
This page shows how to install TensorFlow with the conda package manager included in Anaconda and Miniconda.
TensorFlow with conda is supported on 64-bit Windows 7 or later, 64-bit Ubuntu Linux 14.04 or later, 64-bit CentOS
Linux 6 or later, and macOS 10.10 or later.
The instructions are the same for all operating systems. No apt install or yum install commands are re-
quired.
Install TensorFlow
1. Download and install Anaconda or the smaller Miniconda.

2. On Windows open the Start menu and open an Anaconda Command Prompt. On macOS or Linux open a
terminal window. Use the default bash shell on macOS or Linux.
3. Choose a name for your TensorFlow environment, such as “tf”.
4. To install the current release of CPU-only TensorFlow, recommended for beginners:
conda create -n tf tensorflow
conda activate tf
Or, to install the current release of GPU TensorFlow on Linux or Windows:

conda create -n tf-gpu tensorflow-gpu
conda activate tf-gpu
TensorFlow is now installed and ready to use.

For using TensorFlow with a GPU, refer to the TensorFlow documentation on the topic, specifically the section on
device placement.

CUDA versions
GPU TensorFlow uses CUDA. On Windows and Linux only CUDA 10.0 is supported for the TensorFlow 2.0 release.
Previous versions of TensorFlow support other version of CUDA.
To install GPU TensorFlow with a non-default CUDA version such as 9.0 run:
conda create -n tf-gpu-cuda8 tensorflow-gpu cudatoolkit=9.0

conda activate tf-gpu-cuda8
Python 2
We recommend Python 3, but it is possible to use TensorFlow with Python 2 on Linux and macOS.
CPU-only TensorFlow on Python 2 on Linux or macOS:
conda create -n tf-2 tensorflow python=2

conda activate tf-2
GPU TensorFlow on Python 2 on Linux:
conda create -n tf-2-gpu tensorflow python=2

conda activate tf-2-gpu
Nightly builds
Advanced users may wish to install the latest nightly build of TensorFlow. These nightly builds are unstable and are
only available as pip packages on PyPI.
To install the nightly build of CPU-only TensorFlow:
conda create -n tf-n python

conda activate tf-n
pip install tf-nightly
Or, to install the nightly build of GPU TensorFlow on Linux or Windows:
conda create -n tf-n-gpu python

conda activate tf-n-gpu
pip install tf-nightly-gpu
Nightly build of CPU-only TensorFlow on Python 2 on Linux or macOS:
conda create -n tf-2-n python=2

conda activate tf-2-n
pip install tf-nightly
Nightly build of GPU TensorFlow on Python 2 on Linux:
conda create -n tf-2-n-gpu python=2

conda activate tf-2-n-gpu
pip install tf-nightly-gpu

Cloudera CDH
Cloudera provides Apache Hadoop-based software, support and services, as well as training to business customers.
Their open-source Apache Hadoop distribution, CDH (Cloudera Distribution Including Apache Hadoop), targets
enterprise-class deployments of that technology.
There are two methods of using Anaconda on an existing cluster with Cloudera CDH, Cloudera’s distribution including
Apache Hadoop:
• Use the Anaconda parcel for Cloudera CDH. The following procedure describes how to install the Anaconda
parcel on a CDH cluster using Cloudera Manager. The Anaconda parcel provides a static installation of Ana-
conda, based on Python 2.7, that can be used with Python and PySpark jobs on the cluster.
• Use Anaconda Scale, which provides additional functionality, including the ability to manage multiple conda
environments and packages, including Python and R, alongside an existing CDH cluster. For more information,
see Using Anaconda with Cloudera CDH.
See the blog post Self-service Open Data Science: Custom Anaconda parcels for Cloudera.
Install the Anaconda parcel
1. In the Cloudera Manager Admin Console, in the top navigation bar, click the Parcels icon.
2. At the top right of the parcels page, click the Edit Settings button.
3. In the Remote Parcel Repository URLs section, click the plus symbol, and then add the following repository
URL for the Anaconda parcel:
https://repo.anaconda.com/pkgs/misc/parcels/
4. At the top of the page, click the Save Changes button.

5. In the top navigation bar, click the Parcels icon to return to the list of available parcels, where you should see
the latest version of the Anaconda parcel that is available.
6. To the right of the Anaconda parcel listing, click the Download button.
7. After the parcel is downloaded, click the Distribute button to distribute the parcel to all of the cluster nodes.
8. After the parcel is distributed, click the Activate button to activate the parcel on all of the cluster nodes.
9. When prompted, confirm the activation.

After the parcel is activated, Anaconda is available on all of the cluster nodes.
You can submit Spark jobs along with the PYSPARK_PYTHON environment variable that refers to the location of
Anaconda. For example, enter the following command all on one line:
PYSPARK_PYTHON=/opt/cloudera/parcels/Anaconda/bin/ python spark-submit pyspark_script.

˓→py
Note: The repository URL shown above installs the most recent version of the Anaconda parcel. To install an
older version of the Anaconda parcel, add https://repo.anaconda.com/pkgs/misc/parcels/archive/ to the Remote Parcel
Repository URLs in Cloudera manager, and then follow the above steps with your desired version of the Anaconda
parcel.
Parcel updates
Anaconda builds new Cloudera parcels at least once a year each spring and also offers custom parcel creation for our
enterprise customers. The Anaconda parcel provided at the repository URL shown above is based on Python 2.7. To
use the Anaconda parcel with other versions of Python or with additional packages, contact sales@anaconda.com for
more information about custom Anaconda parcel builds or other enterprise solutions for using Anaconda with cluster
computing.
Anaconda Workgroup and Anaconda Enterprise subscribers can also use Anaconda Repository to create and distribute
their own custom Anaconda parcels for Cloudera Manager.
For more information about managing Cloudera parcels, see the Cloudera documentation.
Amazon AWS
Amazon Web Services (AWS) is a collection of cloud-computing services that make up a cloud-computing platform
offered by Amazon.com.
To see the currently available official Anaconda or Miniconda AMIs please go to AWS marketplace

Docker
Docker is an open platform for developers and system administrators to build, ship, and run distributed applications,
whether on laptops, data center virtual machines, or the cloud. Anaconda, Inc. provides Anaconda and Miniconda
Docker images.
Read the official Docker documentation and specifically the information related to Docker images.
Begin by browsing the available Anaconda images on our Docker profile.
To obtain a fully working Anaconda image:

1. In a terminal window, run this command to display a list of available images:
docker search continuumio
2. Pull the desired image:
docker pull continuumio/miniconda3
3. Create a container using the image:
docker run -t -i continuumio/miniconda3 /bin/bash
This gives you direct access to the container where the conda tool is already available.
4. Test the container:
conda info
You now have a fully working Anaconda image.
To install and launch the Jupyter Notebook, execute the following command all on one line from the host machine:
docker run -i -t -p 8888:8888 continuumio/miniconda3 /bin/bash \

-c "/opt/conda/bin/conda install jupyter -y --quiet && mkdir \
/opt/notebooks && /opt/conda/bin/jupyter notebook \
--notebook-dir=/opt/notebooks --ip='*' --port=8888 \
--no-browser --allow-root"
Note: Line breaks in the example above are for readability only. Enter the command all on one line.
To access the Jupyter notebook open http://localhost:8888 in your browser, or open http://<DOCKER-MACHINE-
IP>:8888 if you are using a Docker Machine VM.
Note: Replace <DOCKER-MACHINE-IP> with your Docker Machine VM IP address.

Using IDEs
Data science is a team sport, so we have built the Anaconda platform to be language-agnostic as well as extensible.
You can use the following IDEs with Anaconda:
• Eclipse and PyDev
• IDLE
• IntelliJ
• Ninja IDE
• Python Tools for Visual Studio (PTVS)
• Python for Visual Studio Code
• Spyder
• Sublime Text
• Microsoft Visual Studio Code (VS Code)
• Wing IDE
Note: IDEs often require you to specify the path to your Python interpreter. See Finding your Anaconda Python
interpreter path.
Microsoft Excel–Anaconda on Windows comes ready to bring the power of Python into Excel. Use one of the many
packages included in Anaconda or connect to an outside integration tool.
Eclipse and PyDev
Eclipse is an open-source platform that provides an array of convenient and powerful code-editing and debugging
tools. PyDev is a Python IDE that runs on top of Eclipse.
If you do not already have Eclipse and PyDev installed:
• Download Eclipse and read the Eclipse resources.
• You may need to install the latest Java JDK/JRE before installing PyDev in order for PyDev to show up in the
Eclipse Preferences menu after PyDev installation.
• Install PyDev.
After you have Eclipse, PyDev, and Anaconda installed, set Anaconda Python as your default:
1. Open the Eclipse Preferences window:
2. In the PyDev list, select Interpreters, and then select Python Interpreter.

3. Click the Browse for python/pypy exe button:
4. In the Interpreter Name box, type Anaconda Python.

5. Browse to your Anaconda Python interpreter path. The interpreter you choose is related to your environment,
so Eclipse will have access to all of the packages in that environment. To add new packages, you may need to
conda install package-name in your Anaconda Prompt or terminal.
6. Click the OK button:
7. In the next window, select the folders to add to the SYSTEM Python path:
1. Select all the folders:


2. Click the OK button.

The Python Interpreters window now displays Anaconda Python:
3. Click the Apply and Close button.

You are now ready to use Anaconda Python with your Eclipse and PyDev installation.
IDLE
IDLE is a very small and simple cross-platform IDE that is included free with Python and is released under the open-
source Python Software Foundation License.
Anaconda and Miniconda include IDLE.
To use IDLE:
1. Find the IDLE program file:
EXAMPLES for Miniconda with Python 3 and user name “jsmith”:
• On macOS, the full path may be /Users/jsmith/miniconda3/bin/idle3.5
• On Windows, the full path may be C:\Users\jsmith\Miniconda3\Scripts\idle
2. Run IDLE from file explorer or from the command line by entering the full path.

Tip: You can make a shortcut to the IDLE program file on your desktop.
IntelliJ
IntelliJ IDEA Community Edition is the open-source version of IntelliJ IDEA, an IDE (Integrated Development Envi-
ronment) for Java, Groovy, and other programming languages such as Scala or Clojure. It is made by JetBrains, maker
of PyCharm Python IDE.
Before you start
You should have both Miniconda and IntelliJ installed and working.
Set up IntelliJ using Miniconda
Find location of Miniconda Python executable:

which python
The system responds with your path to Python. You need this in the next step.
Within IntelliJ
1. Go to File > Project Structure > Platform Settings > SDKs

2. Click the Add (+) icon
3. Choose Python SDK
4. Enter location of Miniconda Python executable /Users/UserName/miniconda3/bin/python
Note: Substitute your actual path to Miniconda that you found in the previous step.
5. Go to File > Project Settings > Project > Project SDK

6. Select from the drop-down: Python 3.6.0 (~/miniconda3/bin/python. . . )
7. Go to Run > Debug
8. Click the Add (+) icon
9. Select Python and then enter the following:
Name: MyProject
Script: /Users/UserName/MyProject/my_file.py
Use Specified Interpreter: Python 3.6.0 (~/miniconda3/bin/python. . . )
For more information, see the IntelliJ IDEA documentation.

Ninja IDE
Ninja IDE is a cross-platform, free, open-source IDE specially designed for Python application development.
To use Anaconda Python with the Ninja IDE:
1. In the Project menu, select Open Project Properties:
2. On the Project Execution tab, in the Python Custom Interpreter box, enter the Anaconda Python interpreter
path to select Anaconda Python:
3. Verify the setup with a test script:

a. To create the test script, enter this code:
import sys
print(sys.version)
b. Run your test script.

In the command output, your Anaconda Python version is listed:
For more information, see the Ninja-IDE documentation.
Python Tools for Visual Studio (PTVS)
Python Tools for Visual Studio is a free, open source plugin that turns Visual Studio into a Python IDE.
If you have installed Anaconda as your default Python installation and installed PTVS, your Visual Studio installation
is already set to use Anaconda’s Python interpreter in PTVS.
To verify this, create a new Python project and then check whether Anaconda is the Python that it uses.
To create a new Python project:

1. In the File menu, select New, and then select Project. The keyboard shortcut is Ctrl-Shift-N.
2. Select Python Application:

To check which Python the project uses:

1. From the Tools menu, select Python Tools, and then select Python Interactive. The keyboard shortcut is Alt+I:
2. In the Python Interactive window, type import sys and then press Enter.
3. Type sys.version and then press Enter.

If PTVS is using Anaconda, your Anaconda Python version is displayed. In the example below, it is Anaconda 1.5.0
(64-bit):
If PTVS does not automatically discover Anaconda, see the official PTVS documentation, especially the section on
Selecting and Installing Python Interpreters and the PTVS installation instructions.
Python for Visual Studio Code
Visual Studio Code (VSC) is a free cross-platform source code editor. The Python for Visual Studio Code extension
allows VSC to connect to Python distributions installed on your computer.
If you’ve installed Anaconda as your default Python installation and installed Python for Visual Studio Code, your
VSC installation is already set to use Anaconda’s Python interpreter.
1. Create a new Python source code file:
1. In the File menu, select Open to choose a directory to place the code.
2. In the File menu, select New File. Your screen will now look like this:

2. Click Plain Text at the bottom of the window to associate the new file with the Python interpreter.
3. In the menu that displays, type or select Python.

4. In the pane on the right, add source code:
5. To save the file, in the File menu, select Save.

6. To open the Debug pane, click the bug icon. Click the gear icon, and then select Python:
7. At the top-right, click the green run arrow next to Python.

The source code is run using your Anaconda Python interpreter:


Spyder
Spyder, the Scientific Python Development Environment, is a free integrated development environment (IDE) that is
included with Anaconda. It includes editing, interactive testing, debugging, and introspection features.
After you have installed Anaconda, start Spyder on Windows, macOS, or Linux by running the command spyder.
Spyder is also pre-installed in Anaconda Navigator, which is included in Anaconda. On the Navigator Home tab,
click the Spyder icon.
For more information about Spyder, see the Spyder web page or the Spyder documentation.
Sublime Text
Sublime Text is a cross-platform text editor for code, markup, and prose. Download and Install Sublime Text.
To use your Anaconda installation with Sublime Text:

1. Download Package control.
2. Open the Sublime Text command palette by pressing CTRL+Shift+p (Windows, Linux) or CMD+Shift+p (ma-
cOS).
3. All Package Control commands begin with “Package Control:”. Start by typing “Package”.
4. Select “Package Control: Install Package”.
5. Search for conda in the command palette and select the conda plugin. When the plugin is installed, a Package
Control Message will open in the Sublime Text window.

6. Change the current Build System to conda by accessing Tools -> Build System -> Conda in the menu bar.
7. Access the conda Commands with the Command Palette by searching for conda.

Microsoft Visual Studio Code (VS Code)
Anaconda Distribution works with Visual Studio Code (VS Code), Microsoft’s lightweight and fast open-source code
editor.
VS Code is free for both private and commercial use, runs on Windows, macOS, and Linux, and includes support
for linting, debugging, task running, version control and Git integration, IntelliSense code completion, and conda
environments.
VS Code is openly extensible and many extensions are available.
In Anaconda Navigator version 1.7 or higher, use the VS Code tile on the home screen to install or launch VS Code.
When you launch VS Code from Navigator, VS Code is configured to use the Python interpreter in the currently
selected environment.
In addition to VS Code, Anaconda fully supports Spyder, Jupyter Notebook, and other IDEs.

Wing IDE
Wing IDE is an IDE designed specifically for the Python programming language. Wing IDE is offered in a paid Pro
version and in free Personal and 101 versions.
To set up your Wing IDE installation to use Anaconda:

1. Navigate to the Python configuration window:
• In Wing 101, in the Edit menu, select Configure Python.
• In Wing Personal and Wing Pro, in the Project menu, select Project Properties.
The Wing 101 menu looks like this:
2. Next to Python Executable, click the Custom radio button.

3. Click the Browse button and navigate to your Anaconda Python interpreter path.
4. For Python Path, click the Custom radio button.
5. Click the Insert button and browse to your Anaconda Python interpreter path.
6. Click the OK button:
7. If you are prompted to reload your Python shell, do so. After the reload, Anaconda is displayed on the Python
Shell tab:

Wing IDE is now set up to Anaconda’s Python.

For more information, see the Wing IDE documentation.
Finding your Anaconda Python interpreter path
IDEs often require you to specify the path to your Python interpreter.
This path varies according to which operating system version and which Anaconda version you use, so you will need
to search your file system to find the correct path to your Python interpreter.
You can search for the Python interpreter with your operating system’s file manager, such as File Explorer on Windows,
Finder on macOS, or Nautilus on Ubuntu Linux.
You can also use the command line to show the location of the Python interpreter in the active conda environment.
Windows
1. From the Start Menu open the Anaconda Prompt.

2. If you want the location of a Python interpreter for a conda environment other than the root conda environment,
run activate environment-name.
3. Run where python.
macOS and Linux
1. Open a terminal window.

2. If you want the location of a Python interpreter for a conda environment other than the root conda environment,
run conda activate environment-name.
3. Run which python.
Examples
• Windows 10 with Anaconda3 and username “jsmith”– C:\Users\jsmith\Anaconda3\python.exe.

The Python image in a conda environment called “my-env” might be in a location such as
C:\Users\jsmith\Anaconda3\envs\my-env\python.exe
• macOS– ~/anaconda/bin/python or /Users/jsmith/anaconda/bin/python
• Linux– ~/anaconda/bin/python or /home/jsmith/anaconda/bin/python
Instead of anaconda, the folder in your home directory might be named one of the following:
• anaconda2
• anaconda3
If you have installed Miniconda instead of Anaconda, the folder might be named:
• miniconda
• miniconda2
• miniconda3
Excel plug-ins for Anaconda
Anaconda on Windows comes ready to interact with Microsoft Excel–quickly, intuitively, and powerfully. You can use
one of the many included packages in Anaconda or you can connect to an outside integration tool to bring the power
of Python into Excel.
The packages described here are available only on Windows unless otherwise noted. Like most Anaconda packages,
this software is written by third-party open-source development teams around the world. Anaconda collects and curates
these programs, builds them into conda packages, and distributes them through the Anaconda platform so our users
can enjoy the benefits of easy installation, version control, package management, and environment management.

What tool should I use?
For a versatile, all-purpose tool, Anaconda includes xlwings, which incorporates the following features:
• Drives Excel interactively from an IPython Session/Notebook.
• Performs one-line conversion to and from a NumPy array or pandas DataFrame.
• Uses Python as Excel’s computation backend by wrapping Python function calls in VBA macros.
• Easily shares Python-integrated Excel workbooks with collaborators who are also running Anaconda, with no
additional installation needed.
Note: The xlwings package is in active development. Additional features may be added in the future. This package
is available for Windows and macOS platforms.
To export data from a Python object into Excel or import the contents of an Excel spreadsheet to perform calculations
or visualizations in Python, Anaconda includes the following libraries and modules:
• openpyxl–Read/write Excel 2007 xlsx/xlsm files.
• xlrd– Extract data from Excel spreadsheets–.xls and .xlsx, versions 2.0 onwards–on any platform.
• xlsxwriter–Write files in the Excel 2007+ XLSX file format.
• xlwt–Generate spreadsheet files that are compatible with Excel 97/2000/XP/2003, OpenOffice.org Calc, and
Gnumeric.
To determine which one best suits your needs, see the documentation for each library or module.
Python-Excel tools not included in Anaconda
• ExcelPython–A free, open-source library that lets you write UDFs and macros in Python, as well as load Python
modules, call methods, and manipulate objects from VBA without modifying the original Python code.
• XLLoop–Open-source software that implements UDFs that are hosted from a server in a variety of languages,
including Python, Java, C++, and R. Installation requires multiple steps to set up the provided Excel add-in and
configure the UDF server.
• ExPy–Freely available demonstration software that is simple to install. Once installed, Excel users have access
to built-in Excel functions that wrap Python code. Documentation and examples are provided at the site.
• PyXLL–A widely used tool that is free for personal or educational use. It implements UDFs written in Python
as add-in functions for Excel.
Using default repositories
When you use a conda command that involves looking for a package to install or upgrade, by default conda searches
the default repository located at https://repo.anaconda.com/pkgs.
Active default channels
Main channel
https://repo.anaconda.com/pkgs/main

Added Sept 26, 2017 with the release of Anaconda 5.0 and conda 4.3.27, the main channel includes packages built by
Anaconda, Inc. with the new compiler stack. The majority of all new Anaconda, Inc. package builds are hosted here.
This is the top priority channel in conda’s default channel list.
More info
Utilizing the New Compilers in Anaconda Distribution 5
R Language channel
https://repo.anaconda.com/pkgs/r
Mirror: https://anaconda.org/r
Anaconda, Inc.’s R conda packages and Microsoft R Open conda packages. This channel is included in conda’s
“defaults” channel. When creating new environments, R is the default R implementation.
MSYS2 channel
https://repo.anaconda.com/pkgs/msys2
Mirror: https://anaconda.org/msys2
Windows only - included in conda’s default channels. Necessary for Anaconda, Inc.’s R conda packages and some
others in /main and /free. It provides a bash shell, Autotools, revision control systems and the like for building native
Windows applications using MinGW-w64 toolchains.
Archived channels
A channel may be archived for a variety of reasons, most often because its packages caused problems (e.g. insecure
compilers, incompatible with newer software) or we no longer upload new packages to them.
Nevertheless, you may wish to use archived channels for one of the following reasons:
• You need packages from those channels for reproducibility
• You are using an old course that requires specific older versions of packages
• The package you need was never built and made available in the Main channel
Free channel
https://repo.anaconda.com/pkgs/free
As of conda 4.7, the free channel was removed from conda’s default channels.
The free channel contains packages built without the new compiler stack. It includes packages built as far back as
Fall 2012. The majority of these packages are compatible with the packages in main. Learn more about the free
channel.
MRO channel
https://repo.anaconda.com/pkgs/mro
Mirror: https://anaconda.org/mro

As of Dec. 19, 2017, this is an empty channel to maintain compatibility with older versions of Conda. Packages in
this channel have been moved to pkgs/mro-archive. New MRO packages are in the pkgs/r channel.
MRO archive
https://repo.anaconda.com/pkgs/mro-archive/
An archive of the full contents of the pkgs/mro channel, taken on Dec 12, 2017. Outdated versions of Microsoft’s
MRO and MRAN availably for archival/reproducibility purposes only.
Archive channel
https://repo.anaconda.com/pkgs/archive
Sometimes a package that is released onto one of the other channels has an issue that forces Anaconda, Inc. to remove
it from the channel. In these cases, the package is archived to this channel for anyone who still needs it.
Pro channel
https://repo.anaconda.com/pkgs/pro
Now deprecated, though still available in conda’s default channels. Packages in this channel were once sold commer-
cially, but are now open source and available without charge. The last package was updated Feb. 2017. Includes MKL
Optimizations, IOPro, and Accelerate.
More info
• Open sourcing Anaconda Accelerate
Anaconda Extras channel
https://anaconda.org/anaconda-extras
This channel contains packages custom built for customers by Anaconda, Inc.
Anaconda channel on anaconda.org
https://anaconda.org/anaconda
The Anaconda channel on anaconda.org is a mirror of the packages available in https://repo.anaconda.com/pkgs/main.
Working with GPU packages
The Anaconda Distribution includes several packages that use the GPU as an accelerator to increase performance,
sometimes by a factor of five or more. These packages can dramatically improve machine learning and simulation use
cases, especially deep learning. Read more about getting started with GPU computing in Anaconda.
While both AMD and NVIDIA are major vendors of GPUs, NVIDIA is currently the most common GPU vendor for
machine learning and cloud computing. The information on this page applies only to NVIDIA GPUs. As of August
27th, 2018, experimental AMD GPU packages for Anaconda are in progress but not yet officially supported.

GPU compatibility
GPU acceleration requires the author of a project such as TensorFlow to implement GPU-specific code paths for
algorithms that can be executed on the GPU. A GPU-accelerated project will call out to NVIDIA-specific libraries for
standard algorithms or use the NVIDIA GPU compiler to compile custom GPU code. Only the algorithms specifically
modified by the project author for GPU usage will be accelerated, and the rest of the project will still run on the CPU.
For most packages, GPU support is either a compile-time or run-time choice, allowing a variant of the package to be
available for CPU-only usage. When GPU support is a compile-time choice, Anaconda will typically need to build
two versions of the package, to allow the user to choose between the “regular” version of the project that runs on CPU
only and the “GPU-enabled” version of the project that runs on GPU.
Due to the different ways that CUDA support is enabled by project authors, there is no universal way to detect GPU
support in a package. For many GPU-enabled packages, there is a dependency on the cudatoolkit package. Other
packages such as Numba do not have a cudatoolkit dependency, because they can be used without the GPU.
Hardware requirements
NVIDIA released the CUDA API for GPU programming in 2006, and all new NVIDIA GPUs released since that
date have been CUDA-capable regardless of market. Although any NVIDIA GPU released in the last 5 years will
technically work with Anaconda, these are the best choices for machine learning and specifically model training use
cases:
• Tesla P100 or V100
• Titan Xp or V
• GeForce 1080 or 1080 Ti
• Various recent Quadro models
Deployed models do not always require a GPU. When a GPU is required for a deployed model, there are other Tesla
GPU models that are more optimized for inference than training, such as the Tesla M4, M40, P4, and P40.
Cloud and on-premise data center deployments require Tesla cards, whereas the GeForce, Quadro, and Titan options
are suitable for use in workstations.
Most users will have an Intel or AMD 64-bit CPU. We recommend having at least two to four times more CPU memory
than GPU memory, and at least 4 CPU cores to support data preparation before model training. There are a limited
number of Anaconda packages with GPU support for IBM POWER 8/9 systems as well.
Software requirements
The best performance and user experience for CUDA is on Linux systems. Windows is also supported. No Apple
computers have been released with an NVIDIA GPU since 2014, so they generally lack the memory for machine
learning applications and only have support for Numba on the GPU.
Anaconda requires that the user has installed a recent NVIDIA driver that meets the version requirements in the table
below. Anaconda does not require the installation of the CUDA SDK.
Ubuntu and some other Linux distributions ship with a third party open-source driver for NVIDIA GPUs called Nou-
veau. CUDA requires replacing the Nouveau driver with the official closed source NVIDIA driver.
All other CUDA libraries are supplied as conda packages.
GPU-enabled packages are built against a specific version of CUDA. Currently supported versions include CUDA
8, 9.0 and 9.2. The NVIDIA drivers are designed to be backward compatible to older CUDA versions, so a system
with NVIDIA driver version 384.81 can support CUDA 9.0 packages and earlier. As a result, if a user is not using

the latest NVIDIA driver, they may need to manually pick a particular CUDA version by selecting the version of the
cudatoolkit conda package in their environment. To select a cudatoolkit version, add a selector such as
cudatoolkit=8.0 to the version specification.
Required NVIDIA driver versions, excerpted from the NVIDIA CUDA Toolkit Release Notes:
CUDA Version Linux x86_64 Driver Version Windows x86_64 Driver Version
CUDA 8.0 (8.0.61 GA2) >= 375.26 >= 376.51
CUDA 9.0 (9.0.76) >= 384.81 >= 385.54
CUDA 9.2 (9.2.88) >= 396.26 >= 397.44
CUDA 9.2 (9.2.148 Update 1) >= 396.37 >= 398.26
Sometimes specific GPU hardware generations have a minimum CUDA version. As of August 27th, 2018, the only
relevant constraint is that the Tesla V100 and Titan V (using the “Volta” GPU architecture) require CUDA 9 or later.
Available packages
TensorFlow
TensorFlow is a general machine learning library, but most popular for deep learning applications. There are three
supported variants of the tensorflow package in Anaconda, one of which is the NVIDIA GPU version. This is
selected by installing the meta-package tensorflow-gpu:
conda install tensorflow-gpu
Other packages such as Keras depend on the generic tensorflow package name and will use whatever version of
TensorFlow is installed. This makes it easy to switch between variants in an environment.
PyTorch
PyTorch is another machine learning library with a deep learning focus. PyTorch detects GPU availability at run-time,
so the user does not need to install a different package for GPU support.
conda install pytorch
Caffe
Caffe was one of the first popular deep learning libraries.
conda install caffe-gpu
Chainer/CuPy (Linux only)
Chainer is a deep learning library that uses NumPy or CuPy for computations.
conda install chainer
Chainer’s companion project CuPy is a GPU-accelerated clone of the NumPy API that can be used as a drop-in
replacement for NumPy with a few changes to user code. When CuPy is installed, Chainer is GPU-accelerated. CuPy
can also be used on its own for general array computation.

conda install cupy
XGBoost
XGBoost is a machine learning library that implements gradient-boosted decision trees. Training several forms of
trees is GPU-accelerated.
conda install py-xgboost-gpu
MXNet
MXNet is a machine learning library supported by various industry partners, most notably Amazon. Like TensorFlow,
it comes in three variants, with the GPU variant selected by the mxnet-gpu meta-package.
conda install mxnet-gpu
Numba
Numba is a general-purpose JIT compiler for Python functions. It provides a way to implement custom GPU algo-
rithms in purely Python syntax when the cudatoolkit package is present.
conda install numba cudatoolkit
GPU support in Anaconda Enterprise
GPU-enabled conda packages can be used in AE 5 projects when the cluster has resource profiles which include GPUs.
For more details see the GPU support section of the AE 5 FAQ.
Using Jupyter Notebook extensions
You can open Jupyter Notebook by running jupyter notebook, or by opening Anaconda Navigator and clicking
the Jupyter Notebook icon.
• Obtaining the extensions

• Uninstalling the extensions
• RISE
• Notebook anaconda.org
• Notebook conda
• Notebook Conda Kernels

With Anaconda you can download and install 4 extensions for the Jupyter Notebook which make the notebook easier
to use:
• RISE
• Notebook anaconda.org (nb_anacondacloud)
• Notebook Conda (nb_conda)
• Notebook Conda Kernels (nb_conda_kernels)
Installing any of the 4 installs all of them. The _nb_ext_conf package is also installed, which activates the extensions.
Obtaining the extensions
To get the extensions using Anaconda Navigator:

1. Install and manage notebook extensions packages like any other packages. See Navigator user guide.
2. To use the new extensions, on the Navigator Home tab, open Jupyter Notebook.
To install all Jupyter Notebook extensions from the command line, run:
conda install nb_conda
Note: These extensions were already installed in Anaconda versions 4.1 and 4.2. If you have Anaconda v4.1 or v4.2
installed, there is no need to install them separately. To begin using them, open a new or existing notebook.
Uninstalling the extensions
To remove all Jupyter Notebook extensions, run:
conda remove nb_conda
Uninstalling nb_conda or any other 1 of the 4 extensions uninstalls all 4.

To disable Jupyter Notebook extensions individually without uninstalling them, run:
python -m nb_conda_kernels.install --disable --prefix=<ENV_PREFIX>
jupyter-nbextension disable nb_conda --py --sys-prefix

jupyter-serverextension disable nb_conda --py --sys-prefix
jupyter-nbextension disable nb_anacondacloud --py --sys-prefix

jupyter-serverextension disable nb_anacondacloud --py --sys-prefix
jupyter-nbextension disable nbpresent --py --sys-prefix

jupyter-serverextension disable nbpresent --py --sys-prefix
Note: Replace <ENV_PREFIX> with your root environment or another conda environment where the extensions
have been installed.

RISE
You can access the install instructions for the RISE extension from anaconda.org.
In-depth documentation can be found there as well.
Notebook anaconda.org
You must have an anaconda.org account for this extension to work. You can sign up for a free account at anaconda.org.
1. You can upload your notebook to your Cloud account with a simple button push:
You can use the Attach conda environment option described below to embed a copy of your conda environment
as an environment.yaml file in the notebook metadata.
2. Sign in to Cloud:
• If you are not signed in to Cloud, a dialog box appears asking for your Cloud username and password.
• You may instead log in at the command line:
anaconda login
Note: This is recommended if you do not have a secure connection.
3. Open Jupyter Notebook, then open the notebook you wish to upload to Cloud.
4. In the top navigation bar, click the Publish to anaconda.org button:
5. In the dialog box that appears, select your username.

6. Type a description of the notebook for display on Cloud:


7. If you want the identical environment to be included when the notebook is downloaded and opened, select the
Attach conda environment checkbox.
8. Click the Publish button.
9. After publishing, you can view the notebook or play the presentation on Cloud from the top navigation bar by
clicking the Cloud button:
Your notebook on anaconda.org will look similar to this one:
For more information on Cloud, see ../../../anaconda-cloud/index.

Notebook conda
This extension provides conda environment and package access from within Jupyter Notebook.
To manage all environments:
1. While viewing the dashboard file manager, select the Conda tab, which shows your current conda environments:
Note: To add a new conda environment, click the + button above the environments list on the right side.
2. Select an environment by clicking its name.

3. In the package management section that displays, the icons from left to right have the following meanings:
• Search for packages in your current environment.
• Refresh your packages list.
• Update selected packages.
• Remove selected packages.
To manage the current kernel environment, in the Kernel menu, select Conda Packages, which displays a list of conda
packages in the current environment:
For more information on using and managing conda packages, see Managing packages.


Notebook Conda Kernels
This extension allows you to use conda environment-based kernels from the dashboard and the notebook’s Kernel
menu. It makes the notebook aware of your conda environments, and it is required for Notebook anaconda.org and
Notebook Conda.
When creating a new notebook on the Files tab, you can pick any of the Python or R language kernels in any of your
environments:
You can also change to those kernels on a current notebook:

Running Jupyter Notebook on a remote server
Follow the following steps to use Jupyter Notebook launched from remote server.
1. Launch Jupyter Notebook from remote server, selecting a port number for <PORT>:
# Replace <PORT> with your selected port number

jupyter notebook --no-browser --port=<PORT>
For example, if you want to use port number 8080, you would run the following:
jupyter notebook --no-browser --port=8080
Or run the following command to launch with default port:
jupyter notebook --no-browser
Please note the port setting. You will need it in the next step.
2. You can access the notebook from your remote machine over SSH by setting up a SSH tunnel. Run the following
command from your local machine:
# Replace <PORT> with the port number you selected in the above step
# Replace <REMOTE_USER> with the remote server username
# Replace <REMOTE_HOST> with your remote server address
ssh -L 8080:localhost:<PORT> <REMOTE_USER>@<REMOTE_HOST>
The above command opens up a new SSH session in the terminal.

3. Open a browser from your local machine and navigate to http://localhost:8080/, the Jupyter Notebook web
interface. Replace 8080 with your port number used in step 1.
Moving Anaconda from one directory to another
Anaconda environment management requires known paths, and Anaconda must know the exact path where it is in-
stalled at installation time.
If you simply copy the Anaconda files to a new directory, Anaconda will not work.
To move Anaconda from one directory to another:
1. OPTIONAL: Save your environments using the conda managing environments instructions.
2. Uninstall Anaconda.
3. Go to the new directory and install it there following the Anaconda installation instructions.
4. OPTIONAL: Restore your environments using the conda managing environments instructions.

Cheat sheet
Download the Anaconda Cheat Sheet for a quick guide to using Anaconda.
Frequently asked questions
• Getting Anaconda
• Installing Anaconda
• Using conda packages
• General
Getting Anaconda
How do I get Anaconda with Python 3.5 or 3.6?

There are three ways to get Anaconda with Python 3.5 or 3.6:
• We recommend that you download the latest version of Anaconda and then make a Python 3.5 (or 3.6) environ-
ment.
• Or download the latest version of Anaconda and run the following command to install Python 3.5 (or 3.6) in the
root environment: conda install python=3.5 or conda install python=3.6.
• Or download the most recent Anaconda installer that included Python 3.5 (Anaconda 4.2.0) or Python 3.6
(Anaconda 5.2.0). You can download either of these from our archive. Scroll down the page until you find the
version you need for your platform.
How do I get previous versions of Anaconda or older versions of packages?

You can download previous versions of Anaconda from the Anaconda installer archive.
The installation procedures for previous versions are the same as the installation for the current version. For graphical
installs, double click the downloaded installer file and follow the prompts. For command line installs, run “bash
filename.sh” and follow the prompts. The installer filenames and hashes for previous versions will be different.
Older versions of packages can usually be downloaded from the package repository or from https://anaconda.org/
anaconda/PackageName.
Note: Replace PackageName with the name of the desired package.
EXAMPLE: At https://anaconda.org/anaconda/beautifulsoup4, previous versions of beautifulsoup4 are shown on the

Files tab.
You can also search for packages from the command line with conda search PackageName.

I am behind a firewall. How can I download Anaconda?

If your corporate security settings do not allow you to download a Windows .exe executable file, download our zipped
file.
Installing Anaconda
How can I install Anaconda on an air-gapped computer?

After you have the file, it’s the same as any other install. Save a local copy of the appropriate Anaconda installer for
the non-networked computer. You can copy the Anaconda installer using many different methods including a portable
hard drive, USB drive, or CD.
After copying the installer to the air-gapped machine, follow the installation instructions for your operating system.
In what folder should I install Anaconda on Windows?

We recommend installing Anaconda or Miniconda into a directory that contains only 7-bit ASCII characters and no
spaces, such as C:\anaconda. Do not install into paths that contain spaces such as C:\Program Files or that
include Unicode characters outside the 7-bit ASCII character set. This helps ensure correct operation and no errors
when using any open-source tools in either Python 3 or Python 2 conda environments.
Should I add Anaconda to the Windows PATH?

When installing Anaconda, we recommend that you do not add Anaconda to the Windows PATH because this can
interfere with other software. Instead, open Anaconda with the Start Menu and select Anaconda Prompt, or use
Anaconda Navigator (Start Menu - Anaconda Navigator).
Should I add Anaconda to the macOS or Linux PATH?

We do not recommend adding Anaconda to the PATH manually. During installation, you will be asked “Do you wish
the installer to initialize Anaconda3 by running conda init?” We recommend “yes”. If you enter “no”, then conda
will not modify your shell scripts at all. In order to initialize after the installation process is done, first run source
<path to conda>/bin/activate and then run conda init.
Note: Replace <path-to-anaconda> with the actual path of your installed Anaconda file.

What is the default path for installing Anaconda?

If you accept the default option to install Anaconda on the “default path” Anaconda is installed in your user home
directory:
• Windows 10: C:\Users\<your-username>\Anaconda3\
• macOS: /Users/<your-username>/anaconda3 for the shell install, ~/opt for the graphical install.
See installing on macOS.
• Linux: /home/<your-username>/anaconda3
Note: If your username includes spaces, as is common on Windows systems, you should not accept the default path.
See In what folder should I install Anaconda on Windows?
I already have Python installed. Can I install Anaconda?

You do not need to uninstall other Python installations or packages before installing Anaconda. Even if you already
have a system Python, another Python installation from a source such as the macOS Homebrew package manager and
globally installed packages from pip such as pandas and NumPy, you do not need to uninstall, remove, or change any
of them.
Install Anaconda or Miniconda normally. There is no need to set the PYTHONPATH environment variable.
To see if the conda installation of Python is in your PATH variable:
• On macOS and Linux, open the terminal and run echo $PATH.
• On Windows, open an Anaconda Prompt and run echo %PATH%.
To see which Python installation is currently set as the default:
• On macOS and Linux, open the terminal and run which python.
• On Windows, open an Anaconda Prompt and run where python.
To see which packages are installed in your current conda environment and their version numbers, in your terminal
window or an Anaconda Prompt, run conda list.
How can I use Anaconda on older systems?

See Outdated operating system support.
Using conda packages
How can I configure or opt out of the Intel Math Kernel Library (MKL)?
For information on configuring and uninstalling MKL, see the Anaconda MKL documentation.

How can I use TKinter?

Make sure the conda package tk is installed:
conda list tk
If it is not installed, run:
conda install tk
Python programs can use TKinter with import Tkinter on Python 2 or import tkinter on Python 3.
How can I use Cython on macOS?

Cython needs a C compiler, so you need to install Xcode.
How can I use Theano?

Theano requires gcc for acceleration.
To install Theano with acceleration:
• On Windows, run conda install theano.
• On Linux and macOS run conda install gcc theano.
Note: Theano is available from the default Anaconda channels for Windows, macOS, and Linux with the command
conda install theano.
How can I use GPUs with Anaconda?

See Working with GPU packages.
General
How is CPython compiled?

• Python 2.6 and 2.7 were compiled with Visual Studio 2008.
• Python 3.3 and 3.4 were compiled with VS 2010.
• Python 3.5 was compiled with VS 2015.

How do I cite Anaconda in an academic paper?

To cite Anaconda in an academic paper, use the recommended format. Example:
Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. <https://anaconda.
com>.
5.1.3 Reference
The following information is provided for your reference, to help you understand some of the core terminology used
in Anaconda Distribution as well as information about the various packages available.
Consult the release notes to see what changes were made between releases. We also include several support resources,
and workarounds for known issues you may encounter while using the product.
Glossary
Anaconda.org
A cloud package repository hosting service at https://www.anaconda.org. With a free account, you can publish pack-
ages you create to be used publicly.
Anaconda Distribution
Open-source repository of hundreds of popular data science packages, along with the conda package and virtual
environment manager for Windows, macOS, and Linux. Conda makes it quick and easy to install, run, and upgrade
complex data science and machine learning environments like scikit-learn, TensorFlow, and SciPy.
Anaconda Enterprise
A software platform for developing, governing, and automating data science and AI pipelines from laptop to pro-
duction. Enterprise enables collaboration between teams of thousands of data scientists running large-scale model
deployments on high-performance production clusters.
Anaconda metapackage
A collection of packages at specific versions that are associated with Distribution installers. Anaconda metapackage
is used to pull all of the other packages into the installer. It contains several core, low-level libraries, including
compression, encryption, linear algebra, and some GUI libraries.
The Anaconda metapackage is useful for creating environments that have all of the Anaconda Distribution packages
in them and it has strong effects on conda’s solver behavior.
Read more about the Anaconda metapackage. Read more about the distinctions between Anaconda Distribution and
the Anaconda metapackage.

Anaconda Navigator
A desktop Graphical User Interface (GUI) included in Anaconda Distribution that allows you to easily use and manage
IDEs, conda packages, environments, channels, and notebooks without the need to use the Command Line Interface
(CLI).
channel
A location in a repository where conda looks for packages. Channels may point to a Cloud repository or a private
location on a remote or local repository that you or your organization created. The conda channel command
has a default set of channels to search beginning with https://repo.anaconda.com/pkgs/. You may override the default
channels to, for example, maintain a private or internal channel. In conda commands and in the .condarc file, these
default channels are referred to by the channel name defaults.
conda
An open-source package and environment manager bundled with Anaconda Distribution that finds, installs, and up-
dates conda packages and their dependencies. Conda also lets you easily switch between conda environments on your
local computer.
conda-build
A tool used to buid conda packages from recipes.
conda environment
A superset of Python virtual environments, conda environments make it easy to create projects with different versions
of Python and avoid issues related to dependencies and version requirements. A conda environment maintains its
own files, directories, and paths so that you can work with specific versions of libraries and/or Python itself without
affecting other Python projects. For example, you may use one conda environment for only Python 2.7 and Python 2.7
packages, and maintain another conda environment with only Python 3.5 and Python 3.5 packages.
conda package

A binary tarball file containing system-level libraries, Python and R modules, executable programs, or other com-
ponents. Conda tracks dependencies between specific packages and platforms, making it simple to create operating
system-specific environments using different combinations of packages.
conda recipe
Instructions used to tell conda-build how to build a package.
Miniconda
A minimal installer for conda. Like Anaconda Distribution, Miniconda is a free software package that includes the
Anaconda Distribution and conda. Miniconda does not include any packages other than those dependencies needed to
install it. After installing Miniconda, you can install additional conda packages directly from the command line using
conda install.
package
Software files and information about the software, such as its name, the specific version, and a description, that are
bundled into a file that can be installed and managed by a package manager. While packages are generally used for
files, they can also be used for metadata alone. When it is, it is called a metapackage.
repository
Any storage location from which software or software assets may be retrieved and installed on a local computer.
How to contribute to Anaconda
Community engagement makes Anaconda Distribution, conda, and conda-build better. We value our open-source
community and encourage all users to contribute to the Anaconda ecosystem. The best contributions start by helping
and encouraging others, especially newcomers who are struggling with something you’ve overcome. See below for
other ways you can contribute.
• Social
• Mailing lists

• GitHub issues
• Stack Overflow
• Documentation
• Conda-forge feedstocks
• Anaconda Enterprise
Social
The easiest way to contribute is to tell your friends about all of the things you can do with Anaconda. Be sure
to mention that Anaconda provides package and environment management and over 7,500+ open source pack-
ages—completely free.
Check our social media to keep up with what’s happening at Anaconda and add to the conversation.
Twitter | Facebook | LinkedIn | SlideShare
Mailing lists
Join the mailing lists to help other users answer questions, debug issues, and suggest solutions.
• Anaconda mailing list.
• Conda mailing list.
• Documentation mailing list.
GitHub issues
If you want to get involved in contributing code for Anaconda, conda, or conda-build, we recommend collaborating
with others, resolving bug issues, and submitting pulll requests with those resolutions.
• Conda issues.
• Conda-build issues.
• Anaconda issues.

Stack Overflow
Answer questions and suggest resolutions and workarounds on Stack Overflow.
Documentation
Notice an error or gap in our documentation? We welcome pull requests for conda and conda-build documentation
improvements and additions.
• Conda documentation.
• Conda GitHub.
• Conda-build documentation.
• Conda-build GitHub.
If a documentation change is needed in Distribution, open a ticket on anaconda-issues.
Example documentation contribution
Follow the directions below to submit a documentation PR using the GitHub interface.
1. Start in the conda or conda-build documentation.
2. Select “Edit on GitHuB” on the page needing the edit.
3. Edit the file in GitHub.

4. Commit your changes.
5. PR review process
• PR is submitted.
• Anaconda community members and/or staff review the PR, providing comments and revisions.
• New contributors sign the CLA.
• PR is merged.

Conda-forge feedstocks
Contribute to conda-forge feedstocks where you can improve, update, and/or add new conda-build recipes to conda-
forge. See our tutorials on how to build conda-build recipes.
The recipes here are often used as the base of recipes used to build packages for defaults/repo.anaconda.com. Helping
conda-forge increases the number and quality of packages available to install with conda, as well as helping Anaconda
do the same for packages shipped in defaults.
Tip: A good way to find feedstocks to work on is to look at the staged recipes issues with the “Package request”
label.
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Release notes

Anaconda 2021.05 (May 13, 2021)
User-facing changes
• Anaconda Navigator has been updated to 2.0.3

• Conda has been updated to 4.10.1
• Added support for the 64-bit AWS Graviton2 (ARM64) platform
• Added support for the 64-bit Linux on IBM Z & LinuxONE (s390x) platform
• Meta-packages are available for Python 3.7, 3.8 and 3.9. The installer uses Python 3.8.
• EULA has been updated to include a more complete cryptography list
• On macOS, all available shells are now initialized for conda as part of the default macOS .pkg installation.
Changes for all x86 platforms
Updated:
• anaconda-project 0.8.4 -> 0.9.1
• astroid 2.4.2 -> 2.5
• astropy 4.0.2 -> 4.2.1
• autopep8 1.5.4 -> 1.5.6
• babel 2.8.1 -> 2.9.0
• bleach 3.2.1 -> 3.3.0
• blosc 1.20.1 -> 1.21.0
• bokeh 2.2.3 -> 2.3.2
• ca-certificates 2020.10.14 -> 2021.4.13
• certifi 2020.6.20 -> 2020.12.5
• cffi 1.14.3 -> 1.14.5
• chardet 3.0.4 -> 4.0.0
• cython 0.29.21 -> 0.29.23
• dask 2.30.0 -> 2021.4.0
• dask-core 2.30.0 -> 2021.4.0
• decorator 4.4.2 -> 5.0.6
• defusedxml 0.6.0 -> 0.7.1
• flake8 3.8.4 -> 3.9.0
• fsspec 0.8.3 -> 0.9.0
• gevent 20.9.0 -> 21.1.2
• greenlet 0.4.17 -> 1.0.0
• hdf5 1.10.4 -> 1.10.6
• importlib-metadata 2.0.0 -> 3.10.0

• importlib_metadata 2.0.0 -> 3.10.0

• ipython 7.19.0 -> 7.22.0
• ipywidgets 7.5.1 -> 7.6.3
• isort 5.6.4 -> 5.8.0
• jedi 0.17.1 -> 0.17.2
• jinja2 2.11.2 -> 2.11.3
• joblib 0.17.0 -> 1.0.1
• jupyter_client 6.1.7 -> 6.1.12
• jupyter_console 6.2.0 -> 6.4.0
• jupyter_core 4.6.3 -> 4.7.1
• jupyterlab 2.2.6 -> 3.0.14
• jupyterlab_server 1.2.0 -> 2.4.0
• keyring 21.4.0 -> 22.3.0
• kiwisolver 1.3.0 -> 1.3.1
• lazy-object-proxy 1.4.3 -> 1.6.0
• libtiff 4.1.0 -> 4.2.0
• llvmlite 0.34.0 -> 0.36.0
• locket 0.2.0 -> 0.2.1
• lxml 4.6.1 -> 4.6.3
• lz4-c 1.9.2 -> 1.9.3
• mkl_fft 1.2.0 -> 1.3.0
• mkl_random 1.1.1 -> 1.2.1
• mock 4.0.2 -> 4.0.3
• more-itertools 8.6.0 -> 8.7.0
• mpmath 1.1.0 -> 1.2.1
• msgpack-python 1.0.0 -> 1.0.2
• nbclient 0.5.1 -> 0.5.3
• nbformat 5.0.8 -> 5.1.3
• nest-asyncio 1.4.2 -> 1.5.1
• nltk 3.5 -> 3.6.1
• notebook 6.1.4 -> 6.3.0
• numba 0.51.2 -> 0.53.1
• numexpr 2.7.1 -> 2.7.3
• numpy 1.19.2 -> 1.20.1
• numpy-base 1.19.2 -> 1.20.1
• openpyxl 3.0.5 -> 3.0.7

• openssl 1.1.1h -> 1.1.1k

• packaging 20.4 -> 20.9
• pandas 1.1.3 -> 1.2.4
• partd 1.1.0 -> 1.2.0
• path 15.0.0 -> 15.1.2
• pillow 8.0.1 -> 8.2.0
• pip 20.2.4 -> 21.0.1
• pkginfo 1.6.1 -> 1.7.0
• prometheus_client 0.8.0 -> 0.10.1
• prompt-toolkit 3.0.8 -> 3.0.17
• prompt_toolkit 3.0.8 -> 3.0.17
• psutil 5.7.2 -> 5.8.0
• py 1.9.0 -> 1.10.0
• pydocstyle 5.1.1 -> 6.0.0
• pygments 2.7.2 -> 2.8.1
• pylint 2.6.0 -> 2.7.4
• pyopenssl 19.1.0 -> 20.0.1
• pytest 6.1.1 -> 6.2.3
• python 3.8.5 -> 3.9.4
• python-language-server 0.35.1 -> 0.36.2
• pytz 2020.1 -> 2021.1
• pyyaml 5.3.1 -> 5.4.1
• pyzmq 19.0.2 -> 20.0.0
• qtawesome 1.0.1 -> 1.0.2
• qtconsole 4.7.7 -> 5.0.3
• regex 2020.10.15 -> 2021.4.4
• requests 2.24.0 -> 2.25.1
• rtree 0.9.4 -> 0.9.7
• ruamel_yaml 0.15.87 -> 0.15.100
• scipy 1.5.2 -> 1.6.2
• seaborn 0.11.0 -> 0.11.1
• setuptools 50.3.1 -> 52.0.0
• singledispatch 3.4.0.3 -> 3.6.1
• snowballstemmer 2.0.0 -> 2.1.0
• sortedcollections 1.2.1 -> 2.1.0
• sortedcontainers 2.2.2 -> 2.3.0

• soupsieve 2.0.1 -> 2.2.1

• sphinx 3.2.1 -> 4.0.1
• spyder 4.1.5 -> 4.2.5
• spyder-kernels 1.9.4 -> 1.10.2
• sqlite 3.33.0 -> 3.35.4
• statsmodels 0.12.0 -> 0.12.2
• sympy 1.6.2 -> 1.8
• terminado 0.9.1 -> 0.9.4
• toml 0.10.1 -> 0.10.2
• tornado 6.0.4 -> 6.1
• tqdm 4.50.2 -> 4.59.0
• typed-ast 1.4.1 -> 1.4.2
• ujson 4.0.1 -> 4.0.2
• urllib3 1.25.11 -> 1.26.4
• watchdog 0.10.3 -> 1.0.2
• wheel 0.35.1 -> 0.36.2
• wrapt 1.11.2 -> 1.12.1
• xlrd 1.2.0 -> 2.0.1
• xlsxwriter 1.3.7 -> 1.3.8
• yapf 0.30.0 -> 0.31.0
• zipp 3.4.0 -> 3.4.1
Added:
• anyio 2.2.0
• appdirs 1.4.4
• black 19.10b0
• jupyter-packaging 0.7.12
• jupyter_server 1.4.1
• jupyterlab_widgets 1.0.0
• mypy_extensions 0.4.3
• nbclassic 0.2.6
• pathspec 0.7.0
• pyerfa 1.7.3
• pyls-black 0.4.6
• pyls-spyder 0.3.2
• sniffio 1.2.0
• textdistance 4.2.1

• three-merge 0.1.1
• tzdata 2020f
Removed:
• pathtools
More changes specific to linux-64
Updated:
• bitarray 1.6.1 -> 2.1.0
• cairo 1.14.12 -> 1.16.0
• cryptography 3.1.1 -> 3.4.7
• distributed 2.30.1 -> 2021.4.1
• docutils 0.16 -> 0.17.1
• expat 2.2.10 -> 2.3.0
• fontconfig 2.13.0 -> 2.13.1
• glib 2.66.1 -> 2.68.1
• gmp 6.1.2 -> 6.2.1
• harfbuzz 2.4.0 -> 2.8.0
• intel-openmp 2020.2 -> 2021.2.0
• jeepney 0.5.0 -> 0.6.0
• lcms2 2.11 -> 2.12
• libedit 3.1.20191231 -> 3.1.20210216
• matplotlib 3.3.2 -> 3.3.4
• matplotlib-base 3.3.2 -> 3.3.4
• mkl 2020.2 -> 2021.2.0
• pandoc 2.11 -> 2.12
• ptyprocess 0.6.0 -> 0.7.0
• readline 8.0 -> 8.1
• scikit-image 0.17.2 -> 0.18.1
• scikit-learn 0.23.2 -> 0.24.1
• secretstorage 3.1.2 -> 3.3.1
• sqlalchemy 1.3.20 -> 1.4.15
• tifffile 2020.10.1 -> 2021.4.8
• wurlitzer 2.0.1 -> 2.1.0
• zeromq 4.3.3 -> 4.3.4
• zope.interface 5.1.2 -> 5.3.0
Added:

• brotli 1.0.9
• brunsli 0.1
• c-ares 1.17.1
• charls 2.2.0
• giflib 5.1.4
• imagecodecs 2021.3.31
• jxrlib 1.1
• lerc 2.2.1
• libaec 1.0.4
• libdeflate 1.7
• libev 4.33
• libuv 1.40.0
• libwebp 1.0.1
• libwebp-base 1.2.0
• libzopfli 1.0.3
• openjpeg 2.3.0
• snappy 1.1.8
• zfp 0.5.5
More changes specific to linux-s390x
Added:
• _libgcc_mutex 0.1
• _openmp_mutex 4.5
• alabaster 0.7.12
• anaconda-client 1.7.2
• anaconda-project 0.9.1
• argon2-cffi 20.1.0
• asn1crypto 1.4.0
• astroid 2.4.2
• astropy 4.2.1
• async_generator 1.10
• attrs 20.3.0
• babel 2.9.0
• backcall 0.2.0
• backports 1.0
• backports.shutil_get_terminal_size 1.0.0

• beautifulsoup4 4.9.3
• bitarray 1.6.1
• bkcharts 0.2
• blas 1.0
• bleach 3.3.0
• blosc 1.21.0
• bokeh 2.3.1
• bottleneck 1.3.2
• brotli 1.0.9
• brotlipy 0.7.0
• bzip2 1.0.8
• c-ares 1.17.1
• ca-certificates 2021.4.13
• cairo 1.16.0
• certifi 2020.12.5
• cffi 1.14.5
• chardet 4.0.0
• click 7.1.2
• cloudpickle 1.6.0
• clyent 1.2.2
• colorama 0.4.4
• contextlib2 0.6.0.post1
• cryptography 3.4.7
• curl 7.71.1
• cycler 0.10.0
• cython 0.29.23
• cytoolz 0.11.0
• dask 2021.4.0
• dask-core 2021.4.0
• dbus 1.13.18
• decorator 5.0.6
• defusedxml 0.7.1
• distributed 2021.4.0
• docutils 0.17
• entrypoints 0.3
• et_xmlfile 1.0.1

• expat 2.3.0
• fastcache 1.1.0
• filelock 3.0.12
• flask 1.1.2
• fontconfig 2.13.1
• freetype 2.10.4
• fribidi 1.0.10
• fsspec 0.9.0
• get_terminal_size 1.0.0
• gevent 21.1.2
• giflib 5.2.1
• glib 2.68.1
• glob2 0.7
• gmp 6.2.1
• gmpy2 2.0.8
• graphite2 1.3.14
• greenlet 1.0.0
• h5py 2.10.0
• harfbuzz 2.8.0
• hdf5 1.10.6
• heapdict 1.0.1
• html5lib 1.1
• icu 68.1
• idna 2.10
• imageio 2.9.0
• imagesize 1.2.0
• importlib-metadata 3.10.0
• importlib_metadata 3.10.0
• iniconfig 1.1.1
• ipykernel 5.3.4
• ipython 7.22.0
• ipython_genutils 0.2.0
• ipywidgets 7.6.3
• isort 5.8.0
• itsdangerous 1.1.0

• jbig 2.1
• jdcal 1.4.1
• jedi 0.17.2
• jinja2 2.11.3
• joblib 1.0.1
• jpeg 9b0
• json5 0.9.5
• jsonschema 3.2.0
• jupyter 1.0.0
• jupyter_client 6.1.12
• jupyter_console 6.4.0
• jupyter_core 4.7.1
• jupyterlab 2.3.1
• jupyterlab_pygments 0.1.2
• jupyterlab_server 1.2.0
• jxrlib 1.1
• kiwisolver 1.3.1
• krb5 1.18.2
• lazy-object-proxy 1.4.3
• lcms2 2.12
• ld_impl_linux-s390x 2.33.1
• libaec 1.0.4
• libarchive 3.4.2
• libcurl 7.71.1
• libdeflate 1.7
• libedit 3.1.20210216
• libev 4.33
• libffi 3.3
• libgcc-ng 9.3.0
• libgfortran-ng 7.5.0
• libgfortran4 7.5.0
• libgomp 9.3.0
• liblief 0.10.1
• libopenblas 0.3.13
• libpng 1.6.37
• libsodium 1.0.18

• libssh2 1.9.0
• libstdcxx-ng 9.3.0
• libtiff 4.2.0
• libtool 2.4.6
• libuuid 1.0.3
• libuv 1.40.0
• libwebp 1.2.0
• libxcb 1.14
• libxml2 2.9.10
• libxslt 1.1.34
• libzopfli 1.0.3
• locket 0.2.1
• lxml 4.6.3
• lz4-c 1.9.3
• lzo 2.10
• markupsafe 1.1.1
• matplotlib 3.3.4
• matplotlib-base 3.3.4
• mccabe 0.6.1
• mistune 0.8.4
• mock 4.0.3
• more-itertools 8.7.0
• mpc 1.1.0
• mpfr 4.0.2
• mpmath 1.2.1
• msgpack-python 1.0.2
• multipledispatch 0.6.0
• nbclient 0.5.3
• nbconvert 6.0.7
• nbformat 5.1.3
• ncurses 6.2
• nest-asyncio 1.5.1
• networkx 2.5
• nltk 3.6.1
• nomkl 3.0
• nose 1.3.7

• notebook 6.3.0
• numexpr 2.7.3
• numpy 1.20.1
• numpy-base 1.20.1
• numpydoc 1.1.0
• olefile 0.46
• openblas 0.3.13
• openblas-devel 0.3.13
• openjpeg 2.3.0
• openpyxl 3.0.7
• openssl 1.1.1k
• packaging 20.9
• pandas 1.2.4
• pandoc 1.16.0
• pandocfilters 1.4.3
• pango 1.45.3
• parso 0.7.0
• partd 1.2.0
• patchelf 0.12
• path 15.1.2
• path.py 12.5.0
• pathlib2 2.3.5
• patsy 0.5.1
• pcre 8.44
• pep8 1.7.1
• pexpect 4.8.0
• pickleshare 0.7.5
• pillow 8.2.0
• pip 21.0.1
• pixman 0.40.0
• pkginfo 1.7.0
• pluggy 0.13.1
• ply 3.11
• prometheus_client 0.10.1
• prompt-toolkit 3.0.17
• prompt_toolkit 3.0.17

• psutil 5.8.0
• ptyprocess 0.7.0
• py 1.10.0
• py-lief 0.10.1
• pycodestyle 2.7.0
• pycosat 0.6.3
• pycparser 2.20
• pycrypto 2.6.1
• pycurl 7.43.0.6
• pyerfa 1.7.1.1
• pyflakes 2.3.1
• pygments 2.8.1
• pylint 2.7.4
• pyodbc 4.0.30
• pyopenssl 20.0.1
• pyparsing 2.4.7
• pyrsistent 0.17.3
• pysocks 1.7.1
• pytables 3.6.1
• pytest 6.2.3
• python 3.9.4
• python-dateutil 2.8.1
• python-libarchive-c 2.9
• pytz 2021.1
• pywavelets 1.1.1
• pyyaml 5.4.1
• pyzmq 20.0.0
• readline 8.1
• regex 2021.4.4
• requests 2.25.1
• rope 0.18.0
• ruamel_yaml 0.15.80
• scikit-image 0.18.1
• scikit-learn 0.24.1
• scipy 1.6.2
• seaborn 0.11.1

• send2trash 1.5.0
• setuptools 51.1.2
• simplegeneric 0.8.1
• singledispatch 3.6.1
• sip 4.19.25
• six 1.15.0
• snappy 1.1.8
• snowballstemmer 2.1.0
• sortedcollections 2.1.0
• sortedcontainers 2.3.0
• soupsieve 2.2.1
• sphinx 4.0.1
• sphinxcontrib 1.0
• sphinxcontrib-applehelp 1.0.2
• sphinxcontrib-devhelp 1.0.2
• sphinxcontrib-htmlhelp 1.0.3
• sphinxcontrib-jsmath 1.0.1
• sphinxcontrib-qthelp 1.0.3
• sphinxcontrib-serializinghtml 1.1.4
• sphinxcontrib-websupport 1.2.4
• sqlalchemy 1.3.17
• sqlite 3.35.4
• statsmodels 0.12.2
• sympy 1.8
• tblib 1.7.0
• terminado 0.9.4
• testpath 0.4.4
• threadpoolctl 2.1.0
• tifffile 2021.3.31
• tk 8.6.10
• toml 0.10.2
• toolz 0.11.1
• tornado 6.1
• tqdm 4.59.0
• traitlets 5.0.5
• typed-ast 1.4.2

• typing_extensions 3.7.4.3
• unicodecsv 0.14.1
• unixodbc 2.3.9
• urllib3 1.26.4
• wcwidth 0.2.5
• webencodings 0.5.1
• werkzeug 1.0.1
• wheel 0.36.2
• widgetsnbextension 3.5.1
• wrapt 1.11.2
• xlrd 2.0.1
• xlsxwriter 1.3.8
• xlwt 1.3.0
• xz 5.2.5
• yaml 0.1.7
• zeromq 4.3.4
• zict 2.0.0
• zipp 3.4.1
• zlib 1.2.11
• zope 1.0
• zope.event 4.5.0
• zope.interface 5.2.0
• zstd 1.4.9
More changes specific to linux-aarch64
Added:
• _openmp_mutex 5.1
• alabaster 0.7.12
• astroid 2.5
• astropy 4.2.1

• attrs 20.3.0
• babel 2.9.0
• backcall 0.2.0
• backports 1.0
• bitarray 1.7.0
• bkcharts 0.2
• blas 1.0
• bleach 3.3.0
• blosc 1.21.0
• bokeh 2.3.1
• boto 2.49.0
• brotli 1.0.9
• brotlipy 0.7.0
• brunsli 0.1
• bzip2 1.0.8
• c-ares 1.17.1
• cached-property 1.5.2
• cairo 1.16.0
• certifi 2020.12.5
• cffi 1.14.5
• chardet 4.0.0
• charls 2.2.0
• click 7.1.2
• clyent 1.2.2
• colorama 0.4.4
• contextlib2 0.6.0.post1
• curl 7.71.1
• cycler 0.10.0
• cython 0.29.23
• cytoolz 0.11.0

• dask 2021.4.0
• dbus 1.13.18
• decorator 5.0.6
• docutils 0.17
• entrypoints 0.3
• expat 2.3.0
• fastcache 1.1.0
• filelock 3.0.12
• flask 1.1.2
• freetype 2.10.4
• fribidi 1.0.10
• fsspec 0.9.0
• gevent 21.1.2
• giflib 5.2.1
• glib 2.68.1
• glob2 0.7
• gmp 6.2.1
• gmpy2 2.0.8
• greenlet 1.0.0
• gst-plugins-base 1.14.1
• gstreamer 1.14.1
• h5py 3.1.0
• harfbuzz 2.8.0
• hdf5 1.12.0
• heapdict 1.0.1
• html5lib 1.1
• icu 68.1
• idna 2.10

• imageio 2.9.0
• imagesize 1.2.0
• importlib_metadata 2.0.0
• iniconfig 1.1.1
• ipykernel 5.3.4
• ipython 7.22.0
• isort 5.8.0
• itsdangerous 1.1.0
• jbig 2.1
• jdcal 1.4.1
• jedi 0.17.2
• jinja2 2.11.3
• joblib 1.0.1
• jpeg 9d
• json5 0.9.5
• jupyter 1.0.0
• jxrlib 1.1
• krb5 1.19.1
• lcms2 2.11
• ld_impl_linux-aarch64 2.36.1
• lerc 2.2.1
• libaec 1.0.4
• libcurl 7.71.1

• libdeflate 1.7
• libedit 3.1.20210216
• libev 4.33
• libffi 3.3
• libgcc-ng 10.2.0
• libgfortran5 10.2.0
• libgomp 10.2.0
• liblief 0.10.1
• libllvm10 10.0.1
• libpng 1.6.37
• libssh2 1.9.0
• libtiff 4.1.0
• libtool 2.4.6
• libuuid 1.0.3
• libuv 1.40.0
• libwebp 1.2.0
• libxcb 1.14
• libxml2 2.9.10
• libxslt 1.1.34
• libzopfli 1.0.3
• llvmlite 0.36.0
• locket 0.2.1
• lxml 4.6.3
• lz4-c 1.9.3
• lzo 2.10
• markupsafe 1.1.1
• matplotlib 3.3.4
• mccabe 0.6.1
• mistune 0.8.4
• mock 4.0.3

• mpc 1.1.0
• mpfr 4.0.2
• mpmath 1.2.1
• nbclient 0.5.3
• nbconvert 6.0.7
• nbformat 5.1.3
• ncurses 6.2
• networkx 2.5
• nltk 3.6.1
• nomkl 3.0
• nose 1.3.7
• notebook 6.3.0
• numba 0.53.1
• numexpr 2.7.3
• numpy 1.20.1
• numpydoc 1.1.0
• olefile 0.46
• openblas 0.3.13
• openjpeg 2.3.0
• openpyxl 3.0.7
• openssl 1.1.1k
• packaging 20.9
• pandas 1.2.4
• pandoc 2.12
• pango 1.45.3
• parso 0.7.0
• partd 1.2.0
• patchelf 0.11
• path 15.1.2
• path.py 12.5.0

• pathlib2 2.3.5
• patsy 0.5.1
• pcre 8.44
• pep8 1.7.1
• pexpect 4.8.0
• pickleshare 0.7.5
• pillow 8.2.0
• pip 21.0.1
• pixman 0.40.0
• pkginfo 1.7.0
• pluggy 0.13.1
• ply 3.11
• psutil 5.8.0
• py 1.10.0
• py-lief 0.10.1
• pycosat 0.6.3
• pycparser 2.20
• pycrypto 2.6.1
• pycurl 7.43.0.6
• pyerfa 1.7.2
• pyflakes 2.3.1
• pygments 2.8.1
• pylint 2.7.4
• pyodbc 4.0.30
• pyopenssl 20.0.1
• pyparsing 2.4.7
• pysocks 1.7.1
• pytables 3.6.1
• pytest 6.2.3
• python 3.9.4

• python-dateutil 2.8.1
• pytz 2021.1
• pyyaml 5.4.1
• pyzmq 20.0.0
• readline 8.1
• regex 2021.4.4
• requests 2.25.1
• rope 0.18.0
• scikit-image 0.18.1
• scikit-learn 0.24.1
• scipy 1.6.2
• seaborn 0.11.1
• setuptools 52.0.0
• singledispatch 3.6.1
• sip 4.19.25
• six 1.15.0
• snappy 1.1.8
• soupsieve 2.2.1
• sphinx 4.0.1
• sqlalchemy 1.3.23

• sqlite 3.35.4
• statsmodels 0.12.2
• sympy 1.8
• tbb 2020.2
• tblib 1.7.0
• terminado 0.9.4
• testpath 0.4.4
• tk 8.6.10
• toml 0.10.2
• toolz 0.11.1
• tornado 6.1
• tqdm 4.59.0
• traitlets 5.0.5
• typed-ast 1.4.2
• unixodbc 2.3.9
• urllib3 1.26.4
• wcwidth 0.2.5
• werkzeug 1.0.1
• wheel 0.36.2
• wrapt 1.12.1
• xlrd 2.0.1
• xlwt 1.3.0
• xz 5.2.5
• yaml 0.1.7
• zeromq 4.3.4
• zfp 0.5.5
• zict 2.0.0
• zipp 3.4.1
• zlib 1.2.11

• zope 1.0
• zope.event 4.5.0
• zstd 1.4.9
More changes specific to linux-ppc64le
Updated:
• bitarray 1.6.1 -> 1.9.2
• cairo 1.14.12 -> 1.16.0
• distributed 2.30.1 -> 2021.4.0
• docutils 0.16 -> 0.17
• expat 2.2.10 -> 2.3.0
• fontconfig 2.13.0 -> 2.13.1
• glib 2.66.1 -> 2.68.1
• gmp 6.1.2 -> 6.2.1
• jupyter_core 4.6.1 -> 4.7.1
• lcms2 2.11 -> 2.12
• libedit 3.1.20191231 -> 3.1.20210216
• matplotlib 3.3.2 -> 3.3.4
• ptyprocess 0.6.0 -> 0.7.0
• pycodestyle 2.6.0 -> 2.7.0
• pyflakes 2.2.0 -> 2.3.1
• readline 8.0 -> 8.1
• scikit-image 0.17.2 -> 0.18.1
• scikit-learn 0.23.2 -> 0.24.1
• sqlalchemy 1.3.20 -> 1.4.7
• tifffile 2020.10.1 -> 2021.4.8
• zeromq 4.3.3 -> 4.3.4
Added:
• brotli 1.0.9
• brunsli 0.1
• c-ares 1.17.1
• charls 2.2.0

• giflib 5.1.4
• jxrlib 1.1
• lerc 2.2.1
• libaec 1.0.4
• libdeflate 1.7
• libev 4.33
• libuv 1.40.0
• libwebp 1.0.1
• libzopfli 1.0.3
• openjpeg 2.3.0
• snappy 1.1.8
• zfp 0.5.5
More changes specific to win-32
Updated:
• bitarray 1.6.1 -> 1.9.2
• comtypes 1.1.7 -> 1.1.9
• cryptography 3.1 -> 3.4.7
• distributed 2.30.1 -> 2021.4.0
• docutils 0.16 -> 0.17
• intel-openmp 2020.2 -> 2021.2.0
• libspatialindex 1.8.5 -> 1.9.3
• matplotlib 3.3.1 -> 3.3.4
• mkl 2020.2 -> 2021.2.0
• pywin32 227 -> 228
• sqlalchemy 1.3.20 -> 1.4.7
• vc 14.1 -> 14.2
• vs2015_runtime 14.16.27012 -> 14.27.29016
• xlwings 0.20.8 -> 0.23.0
• zeromq 4.3.2 -> 4.3.3
Added:

• tbb 2020.0
Updated:
• bitarray 1.6.1 -> 1.9.2
• comtypes 1.1.7 -> 1.1.9
• distributed 2.30.1 -> 2021.4.0
• docutils 0.16 -> 0.17
• intel-openmp 2020.2 -> 2021.2.0
• matplotlib 3.3.2 -> 3.3.4
• mkl 2020.2 -> 2021.2.0
• pandoc 2.11 -> 2.12
• pywin32 227 -> 228
• scikit-image 0.17.2 -> 0.18.1
• scikit-learn 0.23.2 -> 0.24.1
• sqlalchemy 1.3.20 -> 1.4.7
• tifffile 2020.10.1 -> 2021.4.8
• vc 14.1 -> 14.2
• vs2015_runtime 14.16.27012 -> 14.27.29016
• xlwings 0.20.8 -> 0.23.0
• zeromq 4.3.2 -> 4.3.3
Added:
• brotli 1.0.9
• charls 2.2.0
• giflib 5.2.1
• lcms2 2.12
• lerc 2.2.1
• libaec 1.0.4
• libdeflate 1.7
• libzopfli 1.0.3
• openjpeg 2.3.0

• snappy 1.1.8
• tbb 2020.3
• zfp 0.5.5
More changes specific to osx-64
Updated:
• appnope 0.1.0 -> 0.1.2
• appscript 1.1.1 -> 1.1.2
• bitarray 1.6.1 -> 1.9.2
• distributed 2.30.1 -> 2021.4.0
• docutils 0.16 -> 0.17
• expat 2.2.10 -> 2.3.0
• gettext 0.19.8.1 -> 0.21.0
• glib 2.66.1 -> 2.68.1
• gmp 6.1.2 -> 6.2.1
• intel-openmp 2019.4 -> 2021.2.0
• lcms2 2.11 -> 2.12
• libedit 3.1.20191231 -> 3.1.20210216
• matplotlib 3.3.2 -> 3.3.4
• mkl 2019.4 -> 2021.2.0
• pandoc 2.11 -> 2.12
• ptyprocess 0.6.0 -> 0.7.0
• python.app 2 -> 3
• readline 8.0 -> 8.1
• scikit-image 0.17.2 -> 0.18.1
• scikit-learn 0.23.2 -> 0.24.1
• sip 4.19.8 -> 4.19.13
• sqlalchemy 1.3.20 -> 1.4.7
• tifffile 2020.10.1 -> 2021.4.8
• wurlitzer 2.0.1 -> 2.1.0
• xlwings 0.20.8 -> 0.23.0
• zeromq 4.3.3 -> 4.3.4
Added:

• brotli 1.0.9
• brunsli 0.1
• c-ares 1.17.1
• charls 2.2.0
• giflib 5.1.4
• jxrlib 1.1
• lerc 2.2.1
• libaec 1.0.4
• libdeflate 1.7
• libev 4.33
• libuv 1.40.0
• libwebp 1.0.1
• libzopfli 1.0.3
• openjpeg 2.3.0
• snappy 1.1.8
• tbb 2020.3
• zfp 0.5.5
Anaconda 2020.11 (Nov 19, 2020)
User-facing changes
• Anaconda Navigator has been updated to 1.10.0.

• The Python 3.6 meta-package was dropped; meta-packages are now available for Python 3.7 and 3.8 only. The
installer uses Python 3.8.
• Update PyCharm text and links in the GUI installers.
• Clarify EULA for repo.anaconda.com terms-of-service.
Updated:
• asn1crypto 1.3.0 -> 1.4.0
• astropy 4.0.1.post1 -> 4.0.2
• attrs 19.3.0 -> 20.3.0
• autopep8 1.5.3 -> 1.5.4
• babel 2.8.0 -> 2.8.1

• beautifulsoup4 4.9.1 -> 4.9.3

• bitarray 1.4.0 -> 1.6.1
• bleach 3.1.5 -> 3.2.1
• blosc 1.19.0 -> 1.20.1
• bokeh 2.1.1 -> 2.2.3
• ca-certificates 2020.6.24 -> 2020.10.14
• cffi 1.14.0 -> 1.14.3
• cloudpickle 1.5.0 -> 1.6.0
• colorama 0.4.3 -> 0.4.4
• cytoolz 0.10.1 -> 0.11.0
• dask 2.20.0 -> 2.30.0
• dask-core 2.20.0 -> 2.30.0
• distributed 2.20.0 -> 2.30.1
• flake8 3.8.3 -> 3.8.4
• freetype 2.10.2 -> 2.10.4
• fsspec 0.7.4 -> 0.8.3
• gevent 20.6.2 -> 20.9.0
• greenlet 0.4.16 -> 0.4.17
• intervaltree 3.0.2 -> 3.1.0
• ipykernel 5.3.2 -> 5.3.4
• ipython 7.16.1 -> 7.19.0
• isort 4.3.21 -> 5.6.4
• joblib 0.16.0 -> 0.17.0
• jupyterlab 2.1.5 -> 2.2.6
• keyring 21.2.1 -> 21.4.0
• kiwisolver 1.2.0 -> 1.3.0
• llvmlite 0.33.0 -> 0.34.0
• lxml 4.5.2 -> 4.6.1
• mkl_fft 1.1.0 -> 1.2.0
• nbconvert 5.6.1 -> 6.0.7
• nbformat 5.0.7 -> 5.0.8
• networkx 2.4 -> 2.5
• notebook 6.0.3 -> 6.1.4

• numba 0.50.1 -> 0.51.2

• numpy 1.18.5 -> 1.19.2
• numpy-base 1.18.5 -> 1.19.2
• openpyxl 3.0.4 -> 3.0.5
• openssl 1.1.1g -> 1.1.1h
• pandas 1.0.5 -> 1.1.3
• pandocfilters 1.4.2 -> 1.4.3
• path 13.1.0 -> 15.0.0
• path.py 12.4.0 -> 12.5.0
• pillow 7.2.0 -> 8.0.1
• pip 20.1.1 -> 20.2.4
• pkginfo 1.5.0.1 -> 1.6.1
• prompt-toolkit 3.0.5 -> 3.0.8
• psutil 5.7.0 -> 5.7.2
• pycurl 7.43.0.5 -> 7.43.0.6
• pydocstyle 5.0.2 -> 5.1.1
• pygments 2.6.1 -> 2.7.2
• pylint 2.5.3 -> 2.6.0
• pyrsistent 0.16.0 -> 0.17.3
• pytest 5.4.3 -> 6.1.1
• python 3.8.3 -> 3.8.5
• python-jsonrpc-server 0.3.4 -> 0.4.0
• pyzmq 19.0.1 -> 19.0.2
• qtawesome 0.7.2 -> 1.0.1
• qtconsole 4.7.5 -> 4.7.7
• regex 2020.6.8 -> 2020.10.15
• rope 0.17.0 -> 0.18.0
• scikit-learn 0.23.1 -> 0.23.2
• scipy 1.5.0 -> 1.5.2
• seaborn 0.10.1 -> 0.11.0
• setuptools 49.2.0 -> 50.3.1
• sphinx 3.1.2 -> 3.2.1
• sphinxcontrib-websupport 1.2.3 -> 1.2.4
• spyder 4.1.4 -> 4.1.5


• sqlalchemy 1.3.18 -> 1.3.20
• sqlite 3.32.3 -> 3.33.0
• statsmodels 0.11.1 -> 0.12.0
• sympy 1.6.1 -> 1.6.2
• tblib 1.6.0 -> 1.7.0
• terminado 0.8.3 -> 0.9.1
• toolz 0.10.0 -> 0.11.1
• tqdm 4.47.0 -> 4.50.2
• traitlets 4.3.3 -> 5.0.5
• typing_extensions 3.7.4.2 -> 3.7.4.3
• ujson 1.35 -> 4.0.1
• urllib3 1.25.9 -> 1.25.11
• wheel 0.34.2 -> 0.35.1
• xlsxwriter 1.2.9 -> 1.3.7
• zipp 3.1.0 -> 3.4.0
• zope.event 4.4 -> 4.5.0
Added:
• iniconfig 1.1.1
• nbclient 0.5.1
Removed:
• libllvm9
• snappy
Updated:
• dbus 1.13.16 -> 1.13.18
• expat 2.2.9 -> 2.2.10
• fribidi 1.0.9 -> 1.0.10
• glib 2.65.0 -> 2.66.1


• intel-openmp 2020.1 -> 2020.2
• jeepney 0.4.3 -> 0.5.0
• matplotlib 3.2.2 -> 3.3.2
• mkl 2020.1 -> 2020.2
• pandoc 2.10 -> 2.11
• patchelf 0.11 -> 0.12
• pyxdg 0.26 -> 0.27
• ripgrep 11.0.2 -> 12.1.1
• scikit-image 0.16.2 -> 0.17.2
• tbb 2020.0 -> 2020.3
• unixodbc 2.3.7 -> 2.3.9
• zeromq 4.3.2 -> 4.3.3
Added:
• libllvm10 10.0.1
Updated:
• expat 2.2.9 -> 2.2.10
• glib 2.65.0 -> 2.66.1
• jedi 0.17.1 -> 0.17.2
• matplotlib 3.2.2 -> 3.3.2
• pandoc 2.2.1 -> 2.11
• patchelf 0.11 -> 0.12
• scikit-image 0.16.2 -> 0.17.2
• unixodbc 2.3.7 -> 2.3.9
• zeromq 4.3.2 -> 4.3.3
Added:

Updated:
• bcrypt 3.1.7 -> 3.2.0
• cryptography 2.9.2 -> 3.1
• intel-openmp 2020.1 -> 2020.2
• matplotlib 3.2.2 -> 3.3.1
• mkl 2020.1 -> 2020.2
• pandoc 2.9.2.1 -> 2.11
• paramiko 2.7.1 -> 2.7.2
• xlwings 0.19.5 -> 0.20.8
Removed:
• gmpy2
• mpc
• mpfr
• mpir
• tbb
Updated:
• bcrypt 3.1.7 -> 3.2.0
• intel-openmp 2020.1 -> 2020.2
• matplotlib 3.2.2 -> 3.3.2
• mkl 2020.1 -> 2020.2
• pandoc 2.10 -> 2.11
• paramiko 2.7.1 -> 2.7.2

• scikit-image 0.16.2 -> 0.17.2

• xlwings 0.19.5 -> 0.20.8
Added:
Removed:
• gmpy2
• mpc
• mpfr
• mpir
• tbb
Updated:
• dbus 1.13.16 -> 1.13.18
• expat 2.2.9 -> 2.2.10
• glib 2.65.0 -> 2.66.1
• matplotlib 3.2.2 -> 3.3.2
• pandoc 2.10 -> 2.11
• ripgrep 11.0.2 -> 12.1.1
• scikit-image 0.16.2 -> 0.17.2
• unixodbc 2.3.7 -> 2.3.9
• xlwings 0.19.5 -> 0.20.8
• zeromq 4.3.2 -> 4.3.3
Added:
• libllvm10 10.0.1
Removed:
• tbb

Anaconda 2020.07 (July 23, 2020)
User-facing changes
• The installer and base environment now use Python 3.8. Meta-packages for Python 3.6, 3.7, and 3.8 are also
available.
• Fixed an issue where the win-32 installer would install win-64 executables in the base environment.
• Fixed an issue where the Windows installer would hang on systems with >64 cores.
• Update PyCharm text and links in the GUI installers.
• Update EULA to reflect terms-of-service change for repo.anaconda.com
Backend improvements (non-visible changes)
• Fixed signing of PyCharm bundle for macOS 10.15
Updated:
• astroid 2.3.3 -> 2.4.2
• astropy 4.0 -> 4.0.1.post1
• atomicwrites 1.3.0 -> 1.4.0
• autopep8 1.4.4 -> 1.5.3
• backcall 0.1.0 -> 0.2.0
• bitarray 1.2.1 -> 1.4.0
• bleach 3.1.0 -> 3.1.5
• blosc 1.16.3 -> 1.19.0
• bokeh 1.4.0 -> 2.1.1
• ca-certificates 2020.1.1 -> 2020.6.24
• certifi 2019.11.28 -> 2020.6.20
• click 7.0 -> 7.1.2
• cloudpickle 1.3.0 -> 1.5.0
• cryptography 2.8 -> 2.9.2
• curl 7.68.0 -> 7.71.1
• cython 0.29.15 -> 0.29.21
• dask 2.11.0 -> 2.20.0
• dask-core 2.11.0 -> 2.20.0
• decorator 4.4.1 -> 4.4.2
• diff-match-patch 20181111 -> 20200713

• distributed 2.11.0 -> 2.20.0

• flake8 3.7.9 -> 3.8.3
• flask 1.1.1 -> 1.1.2
• freetype 2.9.1 -> 2.10.2
• fsspec 0.6.2 -> 0.7.4
• gevent 1.4.0 -> 20.6.2
• greenlet 0.4.15 -> 0.4.16
• html5lib 1.0.1 -> 1.1
• idna 2.8 -> 2.10
• imageio 2.6.1 -> 2.9.0
• ipykernel 5.1.4 -> 5.3.2
• ipython 7.12.0 -> 7.16.1
• jedi 0.14.1 -> 0.17.1
• jinja2 2.11.1 -> 2.11.2
• joblib 0.14.1 -> 0.16.0
• json5 0.9.1 -> 0.9.5
• jupyter_core 4.6.1 -> 4.6.3
• jupyterlab 1.2.6 -> 2.1.5
• keyring 21.1.0 -> 21.2.1
• kiwisolver 1.1.0 -> 1.2.0
• krb5 1.17.1 -> 1.18.2
• libarchive 3.3.3 -> 3.4.2
• libcurl 7.68.0 -> 7.71.1
• liblief 0.9.0 -> 0.10.1
• libsodium 1.0.16 -> 1.0.18
• libxml2 2.9.9 -> 2.9.10
• libxslt 1.1.33 -> 1.1.34
• llvmlite 0.31.0 -> 0.33.0
• lxml 4.5.0 -> 4.5.2
• lz4-c 1.8.1.2 -> 1.9.2
• matplotlib 3.1.3 -> 3.2.2
• mkl_fft 1.0.15 -> 1.1.0
• mkl_random 1.1.0 -> 1.1.1

• mock 4.0.1 -> 4.0.2

• nbformat 5.0.4 -> 5.0.7
• nltk 3.4.5 -> 3.5
• numba 0.48.0 -> 0.50.1
• numpy 1.18.1 -> 1.18.5
• numpy-base 1.18.1 -> 1.18.5
• numpydoc 0.9.2 -> 1.1.0
• openpyxl 3.0.3 -> 3.0.4
• openssl 1.1.1d -> 1.1.1g
• packaging 20.1 -> 20.4
• pandas 1.0.1 -> 1.0.5
• parso 0.5.2 -> 0.7.0
• pillow 7.0.0 -> 7.2.0
• pip 20.0.2 -> 20.1.1
• psutil 5.6.7 -> 5.7.0
• py 1.8.1 -> 1.9.0
• py-lief 0.9.0 -> 0.10.1
• pycodestyle 2.5.0 -> 2.6.0
• pycparser 2.19 -> 2.20
• pydocstyle 4.0.1 -> 5.0.2
• pyflakes 2.1.1 -> 2.2.0
• pygments 2.5.2 -> 2.6.1
• pylint 2.4.4 -> 2.5.3
• pyparsing 2.4.6 -> 2.4.7
• pyrsistent 0.15.7 -> 0.16.0
• pytest 5.3.5 -> 5.4.3
• python 3.8.1 -> 3.8.3
• python-libarchive-c 2.8 -> 2.9
• pytz 2019.3 -> 2020.1
• pyyaml 5.3 -> 5.3.1
• pyzmq 18.1.1 -> 19.0.1

• qdarkstyle 2.8 -> 2.8.1

• qtawesome 0.6.1 -> 0.7.2
• qtconsole 4.6.0 -> 4.7.5
• requests 2.22.0 -> 2.24.0
• rope 0.16.0 -> 0.17.0
• rtree 0.9.3 -> 0.9.4
• scikit-learn 0.22.1 -> 0.23.1
• scipy 1.4.1 -> 1.5.0
• seaborn 0.10.0 -> 0.10.1
• six 1.14.0 -> 1.15.0
• snappy 1.1.7 -> 1.1.8
• soupsieve 1.9.5 -> 2.0.1
• sphinx 2.4.0 -> 3.1.2
• sphinxcontrib-applehelp 1.0.1 -> 1.0.2
• sphinxcontrib-devhelp 1.0.1 -> 1.0.2
• sphinxcontrib-htmlhelp 1.0.2 -> 1.0.3
• sphinxcontrib-qthelp 1.0.2 -> 1.0.3
• sphinxcontrib-serializinghtml 1.1.3 -> 1.1.4
• spyder 4.0.1 -> 4.1.4
• sqlalchemy 1.3.13 -> 1.3.18
• sqlite 3.31.1 -> 3.32.3
• statsmodels 0.11.0 -> 0.11.1
• sympy 1.5.1 -> 1.6.1
• tk 8.6.8 -> 8.6.10
• tornado 6.0.3 -> 6.0.4
• tqdm 4.42.1 -> 4.47.0
• urllib3 1.25.8 -> 1.25.9
• watchdog 0.10.2 -> 0.10.3
• wcwidth 0.1.8 -> 0.2.5
• werkzeug 1.0.0 -> 1.0.1
• xlsxwriter 1.2.7 -> 1.2.9
• xz 5.2.4 -> 5.2.5

• yaml 0.1.7 -> 0.2.5

• yapf 0.28.0 -> 0.30.0
• zeromq 4.3.1 -> 4.3.2
• zict 1.0.0 -> 2.0.0
• zipp 2.2.0 -> 3.1.0
• zstd 1.3.7 -> 1.4.5
Added:
• brotlipy 0.7.0
• contextvars 2.4
• immutables 0.14
• libllvm9 9.0.1
• regex 2020.6.8
• toml 0.10.1
• zope 1.0
• zope.event 4.4
Removed:
• hypothesis
• pytest-arraydiff
• pytest-astropy
• pytest-astropy-header
• pytest-doctestplus
• pytest-openfiles
• pytest-remotedata
Updated:
• dbus 1.13.12 -> 1.13.16
• expat 2.2.6 -> 2.2.9
• fribidi 1.0.5 -> 1.0.9
• glib 2.63.1 -> 2.65.0
• graphite2 1.3.13 -> 1.3.14
• harfbuzz 1.8.8 -> 2.4.0


• intel-openmp 2020.0 -> 2020.1
• jeepney 0.4.2 -> 0.4.3
• libedit 3.1.20181209 -> 3.1.20191231
• libffi 3.2.1 -> 3.3
• libssh2 1.8.2 -> 1.9.0
• libxcb 1.13 -> 1.14
• mkl 2020.0 -> 2020.1
• mpfr 4.0.1 -> 4.0.2
• pandoc 2.2.3.2 -> 2.10
• pango 1.42.4 -> 1.45.3
• patchelf 0.10 -> 0.11
• pcre 8.43 -> 8.44
• pixman 0.38.0 -> 0.40.0
• readline 7.0 -> 8.0
• setuptools 45.2.0 -> 49.2.0
• wurlitzer 2.0.0 -> 2.0.1
Added:
• lcms2 2.11
Updated:
• expat 2.2.6 -> 2.2.9
• glib 2.63.1 -> 2.65.0
• jedi 0.16.0 -> 0.17.1
• libedit 3.1.20181209 -> 3.1.20191231
• libffi 3.2.1 -> 3.3
• libopenblas 0.3.6 -> 0.3.10
• libssh2 1.8.2 -> 1.9.0
• libxcb 1.13 -> 1.14
• mpfr 4.0.1 -> 4.0.2
• openblas 0.3.6 -> 0.3.10
• openblas-devel 0.3.6 -> 0.3.10
• pandoc 2.0.0.1 -> 2.2.1

• parso 0.6.1 -> 0.7.0

• patchelf 0.10 -> 0.11
• pcre 8.43 -> 8.44
• pixman 0.34.0 -> 0.40.0
• readline 7.0 -> 8.0
• setuptools 45.2.0 -> 49.2.0
• zeromq 4.2.5 -> 4.3.2
Added:
• lcms2 2.11
• liblief 0.10.1
• py-lief 0.10.1
Updated:
• intel-openmp 2020.0 -> 2020.1
• mkl 2020.0 -> 2020.1
• pandoc 2.2.3.2 -> 2.9.2.1
• pynacl 1.3.0 -> 1.4.0
• setuptools 46.0.0 -> 49.2.0
• xlwings 0.17.1 -> 0.19.5
Added:
• gmpy2 2.0.8
• mpc 1.1.0
• mpfr 4.0.2
• mpir 3.0.0
Updated:
• intel-openmp 2020.0 -> 2020.1
• libssh2 1.8.2 -> 1.9.0
• mkl 2020.0 -> 2020.1

• pandoc 2.2.3.2 -> 2.10

• pynacl 1.3.0 -> 1.4.0
• setuptools 45.2.0 -> 49.2.0
• xlwings 0.17.1 -> 0.19.5
Added:
• gmpy2 2.0.8
• mpc 1.1.0
• mpfr 4.0.2
• mpir 3.0.0
Updated:
• appscript 1.1.0 -> 1.1.1
• dbus 1.13.12 -> 1.13.16
• expat 2.2.6 -> 2.2.9
• glib 2.63.1 -> 2.65.0
• libcxx 4.0.1 -> 10.0.0
• libedit 3.1.20181209 -> 3.1.20191231
• libffi 3.2.1 -> 3.3
• libiconv 1.15 -> 1.16
• llvm-openmp 4.0.1 -> 10.0.0
• mpfr 4.0.1 -> 4.0.2
• pandoc 2.2.3.2 -> 2.10
• pcre 8.43 -> 8.44
• readline 7.0 -> 8.0
• setuptools 46.0.0 -> 49.2.0
• wurlitzer 2.0.0 -> 2.0.1
• xlwings 0.17.1 -> 0.19.5
Added:
• lcms2 2.11
Removed:
• libcxxabi

Anaconda 2020.02 (March 11, 2020)
User-facing changes
• Name changed to Anaconda Individual Edition.

• The previous 2019.10 release was the last for Python 2.7, and Python 2 will not be supported going forward.
• Python 3.6, 3.7 and 3.8 meta-packages available, installer is Python 3.7.
• Last official release to support Windows 7.
• Updated links to in GUI installer.
• Anaconda Navigator updated to 1.9.12.
• Deadlock fixes on single core computers.

• Improved menu removal on Windows.
Updated:
• asn1crypto 1.0.1 -> 1.3.0
• astroid 2.3.1 -> 2.3.3
• astropy 3.2.2 -> 4.0
• attrs 19.2.0 -> 19.3.0
• babel 2.7.0 -> 2.8.0
• bitarray 1.0.1 -> 1.2.1
• bokeh 1.3.4 -> 1.4.0
• bottleneck 1.2.1 -> 1.3.2
• ca-certificates 2019.8.28 -> 2020.1.1
• certifi 2019.9.11 -> 2019.11.28
• cffi 1.12.3 -> 1.14.0
• cloudpickle 1.2.2 -> 1.3.0
• colorama 0.4.1 -> 0.4.3
• contextlib2 0.6.0 -> 0.6.0.post1
• cryptography 2.7 -> 2.8
• curl 7.65.3 -> 7.68.0
• cython 0.29.13 -> 0.29.15

• cytoolz 0.10.0 -> 0.10.1

• dask 2.5.2 -> 2.11.0
• dask-core 2.5.2 -> 2.11.0
• decorator 4.4.0 -> 4.4.1
• distributed 2.5.2 -> 2.11.0
• docutils 0.15.2 -> 0.16
• fsspec 0.5.2 -> 0.6.2
• h5py 2.9.0 -> 2.10.0
• imageio 2.6.0 -> 2.6.1
• imagesize 1.1.0 -> 1.2.0
• importlib_metadata 0.23 -> 1.5.0
• ipykernel 5.1.2 -> 5.1.4
• ipython 7.8.0 -> 7.12.0
• jinja2 2.10.3 -> 2.11.1
• joblib 0.13.2 -> 0.14.1
• json5 0.8.5 -> 0.9.1
• jsonschema 3.0.2 -> 3.2.0
• jupyter_core 4.5.0 -> 4.6.1
• jupyterlab 1.1.4 -> 1.2.6
• keyring 18.0.0 -> 21.1.0
• krb5 1.16.1 -> 1.17.1
• libcurl 7.65.3 -> 7.68.0
• libtiff 4.0.10 -> 4.1.0
• llvmlite 0.29.0 -> 0.31.0
• lxml 4.4.1 -> 4.5.0
• matplotlib 3.1.1 -> 3.1.3
• mkl_fft 1.0.14 -> 1.0.15
• mock 3.0.5 -> 4.0.1
• nbconvert 5.6.0 -> 5.6.1
• nbformat 4.4.0 -> 5.0.4
• networkx 2.3 -> 2.4
• notebook 6.0.1 -> 6.0.3

• numexpr 2.7.0 -> 2.7.1

• numpydoc 0.9.1 -> 0.9.2
• openpyxl 3.0.0 -> 3.0.3
• packaging 19.2 -> 20.1
• pandas 0.25.1 -> 1.0.1
• parso 0.5.1 -> 0.5.2
• partd 1.0.0 -> 1.1.0
• path.py 12.0.1 -> 12.4.0
• pillow 6.2.0 -> 7.0.0
• pip 19.2.3 -> 20.0.2
• pluggy 0.13.0 -> 0.13.1
• psutil 5.6.3 -> 5.6.7
• py 1.8.0 -> 1.8.1
• pycurl 7.43.0.3 -> 7.43.0.5
• pygments 2.4.2 -> 2.5.2
• pylint 2.4.2 -> 2.4.4
• pyodbc 4.0.27 -> 4.0.30
• pyopenssl 19.0.0 -> 19.1.0
• pyparsing 2.4.2 -> 2.4.6
• pyrsistent 0.15.4 -> 0.15.7
• pytables 3.5.2 -> 3.6.1
• pytest 5.2.1 -> 5.3.5
• pytest-astropy 0.5.0 -> 0.8.0
• pytest-doctestplus 0.4.0 -> 0.5.0
• python 3.7.4 -> 3.7.6
• python-dateutil 2.8.0 -> 2.8.1
• pywavelets 1.0.3 -> 1.1.1
• pyyaml 5.1.2 -> 5.3
• pyzmq 18.1.0 -> 18.1.1
• qtawesome 0.6.0 -> 0.6.1
• qtconsole 4.5.5 -> 4.6.0
• rope 0.14.0 -> 0.16.0
• ruamel_yaml 0.15.46 -> 0.15.87
• scikit-image 0.15.0 -> 0.16.2
• scipy 1.3.1 -> 1.4.1

• seaborn 0.9.0 -> 0.10.0

• six 1.12.0 -> 1.14.0
• soupsieve 1.9.3 -> 1.9.5
• sphinx 2.2.0 -> 2.4.0
• spyder 3.3.6 -> 4.0.1
• sqlalchemy 1.3.9 -> 1.3.13
• sqlite 3.30.0 -> 3.31.1
• statsmodels 0.10.1 -> 0.11.0
• sympy 1.4 -> 1.5.1
• tblib 1.4.0 -> 1.6.0
• terminado 0.8.2 -> 0.8.3
• testpath 0.4.2 -> 0.4.4
• tqdm 4.36.1 -> 4.42.1
• typed-ast 1.4.0 -> 1.4.1
• urllib3 1.24.2 -> 1.25.8
• wcwidth 0.1.7 -> 0.1.8
• werkzeug 0.16.0 -> 1.0.0
• wheel 0.33.6 -> 0.34.2
• xlsxwriter 1.2.1 -> 1.2.7
• zipp 0.6.0 -> 2.2.0
Added:
• argh 0.26.2
• autopep8 1.4.4
• diff-match-patch 20181111
• flake8 3.7.9
• future 0.18.2
• hypothesis 5.5.4
• intervaltree 3.0.2
• path 13.1.0
• pathtools 0.1.2
• pydocstyle 4.0.1
• pytest-astropy-header 0.1.2
• python-jsonrpc-server 0.3.4

• python-language-server 0.31.7
• qdarkstyle 2.8
• rtree 0.9.3
• ujson 1.35
• watchdog 0.10.2
• yapf 0.28.0
Removed:
• backports.os
Updated:
• dbus 1.13.6 -> 1.13.12
• glib 2.56.2 -> 2.63.1
• intel-openmp 2019.4 -> 2020.0
• jeepney 0.4.1 -> 0.4.2
• mkl 2019.4 -> 2020.0
• ncurses 6.1 -> 6.2
• numba 0.45.1 -> 0.48.0
• numpy 1.17.2 -> 1.18.1
• numpy-base 1.17.2 -> 1.18.1
• patchelf 0.9 -> 0.10
• pexpect 4.7.0 -> 4.8.0
• ripgrep 0.10.0 -> 11.0.2
• scikit-learn 0.21.3 -> 0.22.1
• setuptools 41.4.0 -> 45.2.0
• tbb 2019.4 -> 2020.0
• wurlitzer 1.0.3 -> 2.0.0
Added:
• ld_impl_linux-64 2.33.1
• libspatialindex 1.9.3
• pyxdg 0.26

Updated:
• glib 2.56.2 -> 2.63.1
• h5py 2.8.0 -> 2.10.0
• hdf5 1.10.2 -> 1.10.4
• jedi 0.15.1 -> 0.16.0
• ncurses 6.1 -> 6.2
• numpy 1.17.2 -> 1.18.1
• numpy-base 1.17.2 -> 1.18.1
• parso 0.5.1 -> 0.6.1
• patchelf 0.9 -> 0.10
• pexpect 4.7.0 -> 4.8.0
• pytables 3.4.4 -> 3.6.1
• scikit-learn 0.21.3 -> 0.22.1
• scipy 1.3.0 -> 1.4.1
• setuptools 41.4.0 -> 45.2.0
Added:
• ld_impl_linux-ppc64le 2.33.1
• mock 4.0.1
Removed:
• atomicwrites
Updated:
• intel-openmp 2019.4 -> 2020.0
• mkl 2019.4 -> 2020.0
• numba 0.45.0 -> 0.48.0
• numpy 1.16.5 -> 1.18.1
• numpy-base 1.16.5 -> 1.18.1
• pywin32 223 -> 227
• pywinpty 0.5.5 -> 0.5.7
• setuptools 41.4.0 -> 45.2.0
• tbb 2019.4 -> 2020.0
• xlwings 0.15.10 -> 0.17.1
Added:

• bcrypt 3.1.7
• paramiko 2.7.1
• pexpect 4.8.0
• pynacl 1.3.0
• pywin32-ctypes 0.2.0
Updated:
• intel-openmp 2019.4 -> 2020.0
• mkl 2019.4 -> 2020.0
• numba 0.45.1 -> 0.48.0
• numpy 1.16.5 -> 1.18.1
• numpy-base 1.16.5 -> 1.18.1
• pywin32 223 -> 227
• pywinpty 0.5.5 -> 0.5.7
• scikit-learn 0.21.3 -> 0.22.1
• setuptools 41.4.0 -> 45.2.0
• tbb 2019.4 -> 2020.0
• xlwings 0.15.10 -> 0.17.1
Added:
• bcrypt 3.1.7
• paramiko 2.7.1
• pexpect 4.8.0
• pynacl 1.3.0
• pywin32-ctypes 0.2.0
Updated:
• dbus 1.13.6 -> 1.13.12
• glib 2.56.2 -> 2.63.1
• libssh2 1.8.2 -> 1.9.0
• ncurses 6.1 -> 6.2
• numba 0.45.1 -> 0.48.0

• numpy 1.17.2 -> 1.18.1

• numpy-base 1.17.2 -> 1.18.1
• pexpect 4.7.0 -> 4.8.0
• ripgrep 0.10.0 -> 11.0.2
• scikit-learn 0.21.3 -> 0.22.1
• setuptools 41.4.0 -> 46.0.0
• tbb 2019.8 -> 2020.0
• wurlitzer 1.0.3 -> 2.0.0
• xlwings 0.15.10 -> 0.17.1
Added:
• applaunchservices 0.2.1
Anaconda 2019.10 (October 15, 2019)
User-facing changes
• Updated packages.
• For macOS Catalina, we have notarized the package installers and changed the default install directory to
/opt/anaconda{2,3}.
• Added a new Cython-based Python wrapper to clear up library loading problems with libarchive.
• Extraction scripts work better with older operating systems.
Updated:
• asn1crypto 0.24.0 -> 1.0.1
• astroid 2.2.5 -> 2.3.1
• astropy 3.2.1 -> 3.2.2
• attrs 19.1.0 -> 19.2.0
• bitarray 0.9.3 -> 1.0.1
• ca-certificates 2019.5.15 -> 2019.8.28
• certifi 2019.6.16 -> 2019.9.11
• cloudpickle 1.2.1 -> 1.2.2
• configparser 3.7.4 -> 4.0.2

• contextlib2 0.5.5 -> 0.6.0

• curl 7.65.2 -> 7.65.3
• cython 0.29.12 -> 0.29.13
• dask 2.1.0 -> 2.5.2
• dask-core 2.1.0 -> 2.5.2
• distributed 2.1.0 -> 2.5.2
• docutils 0.14 -> 0.15.2
• heapdict 1.0.0 -> 1.0.1
• imageio 2.5.0 -> 2.6.0
• importlib_metadata 0.17 -> 0.23
• ipykernel 5.1.1 -> 5.1.2
• ipython 7.6.1 -> 7.8.0
• ipywidgets 7.5.0 -> 7.5.1
• jedi 0.13.3 -> 0.15.1
• jinja2 2.10.1 -> 2.10.3
• json5 0.8.4 -> 0.8.5
• jsonschema 3.0.1 -> 3.0.2
• jupyterlab 1.0.2 -> 1.1.4
• libcurl 7.65.2 -> 7.65.3
• lxml 4.3.4 -> 4.4.1
• matplotlib 3.1.0 -> 3.1.1
• mkl-service 2.0.2 -> 2.3.0
• mkl_fft 1.0.12 -> 1.0.14
• mkl_random 1.0.2 -> 1.1.0
• nbconvert 5.5.0 -> 5.6.0
• nltk 3.4.4 -> 3.4.5
• notebook 6.0.0 -> 6.0.1
• numexpr 2.6.9 -> 2.7.0
• openpyxl 2.6.2 -> 3.0.0
• packaging 19.0 -> 19.2
• pandas 0.24.2 -> 0.25.1
• parso 0.5.0 -> 0.5.1

• pathlib2 2.3.4 -> 2.3.5

• pillow 6.1.0 -> 6.2.0
• pip 19.1.1 -> 19.2.3
• pluggy 0.12.0 -> 0.13.0
• pylint 2.3.1 -> 2.4.2
• pyodbc 4.0.26 -> 4.0.27
• pyparsing 2.4.0 -> 2.4.2
• pyrsistent 0.14.11 -> 0.15.4
• pysocks 1.7.0 -> 1.7.1
• pytest 5.0.1 -> 5.2.1
• pytest-openfiles 0.3.2 -> 0.4.0
• pytest-remotedata 0.3.1 -> 0.3.2
• python 3.7.3 -> 3.7.4
• pytz 2019.1 -> 2019.3
• pyyaml 5.1.1 -> 5.1.2
• pyzmq 18.0.0 -> 18.1.0
• qtawesome 0.5.7 -> 0.6.0
• qtpy 1.8.0 -> 1.9.0
• setuptools 41.0.1 -> 41.4.0
• soupsieve 1.8 -> 1.9.3
• sphinx 2.1.2 -> 2.2.0
• sqlalchemy 1.3.5 -> 1.3.9
• sqlite 3.29.0 -> 3.30.0
• statsmodels 0.10.0 -> 0.10.1
• tqdm 4.32.1 -> 4.36.1
• traitlets 4.3.2 -> 4.3.3
• typed-ast 1.3.4 -> 1.4.0
• typing 3.7.4 -> 3.7.4.1
• werkzeug 0.15.4 -> 0.16.0
• wheel 0.33.4 -> 0.33.6
• widgetsnbextension 3.5.0 -> 3.5.1
• xlsxwriter 1.1.8 -> 1.2.1

• zipp 0.5.1 -> 0.6.0

Added:
• fsspec 0.5.2
Updated:
• bokeh 1.2.0 -> 1.3.4
• jeepney 0.4 -> 0.4.1
• numba 0.45.0 -> 0.45.1
• numpy 1.16.4 -> 1.17.2
• numpy-base 1.16.4 -> 1.17.2
• qtconsole 4.5.1 -> 4.5.5
• scikit-learn 0.21.2 -> 0.21.3
• scipy 1.3.0 -> 1.3.1
• wurlitzer 1.0.2 -> 1.0.3
Added:
• ripgrep 0.10.0
• tbb 2019.4
Updated:
• bokeh 1.2.0 -> 1.3.4
• libopenblas 0.2.20 -> 0.3.6
• numexpr 2.6.7 -> 2.7.0
• numpy 1.14.5 -> 1.17.2
• numpy-base 1.14.5 -> 1.17.2
• openblas 0.2.20 -> 0.3.6
• openblas-devel 0.2.20 -> 0.3.6
• scikit-learn 0.19.1 -> 0.21.3
• scipy 1.1.0 -> 1.3.0
Added:
• joblib 0.13.2
• nomkl 3.0

Updated:
• bokeh 1.3.0 -> 1.3.4
• numpy 1.16.4 -> 1.16.5
• numpy-base 1.16.4 -> 1.16.5
• qtconsole 4.5.2 -> 4.5.5
• scipy 1.3.0 -> 1.3.1
• vs2015_runtime 14.15.26706 -> 14.16.27012
• xlwings 0.15.8 -> 0.15.10
Added:
• tbb 2019.4
Updated:
• bokeh 1.3.0 -> 1.3.4
• numba 0.45.0 -> 0.45.1
• numpy 1.16.4 -> 1.16.5
• numpy-base 1.16.4 -> 1.16.5
• qtconsole 4.5.2 -> 4.5.5
• scikit-learn 0.21.2 -> 0.21.3
• scipy 1.2.1 -> 1.3.1
• vs2015_runtime 14.15.26706 -> 14.16.27012
• xlwings 0.15.8 -> 0.15.10
Added:
• tbb 2019.4
Updated:
• bokeh 1.2.0 -> 1.3.4
• numba 0.45.0 -> 0.45.1
• numpy 1.16.4 -> 1.17.2
• numpy-base 1.16.4 -> 1.17.2
• qtconsole 4.5.1 -> 4.5.5
• scikit-learn 0.21.2 -> 0.21.3
• scipy 1.3.0 -> 1.3.1

• wurlitzer 1.0.2 -> 1.0.3

• xlwings 0.15.8 -> 0.15.10
Added:
• ripgrep 0.10.0
• tbb 2019.8
Anaconda 2019.07 (July 24, 2019)
User-facing changes
• Conda install times have decreased by more than half for large packages.
• Conda 4.7.10 improves environment management and error messages.
• Conda constructor now supports building installers with the new .conda file format as well as noarch packages.
• Documentation has been updated for our integration with PyCharm, including more tutorials and improved
navigation for easier use.
• Updated packages, including R packages and ML/AI packages.
• Conda is moving to a quarterly release cycle.

• Conda build 3.18 works with the new .conda file format.
Updated:
• astropy 3.1.2 -> 3.2.1
• babel 2.6.0 -> 2.7.0
• bitarray 0.8.3 -> 0.9.3
• blosc 1.15.0 -> 1.16.3
• bzip2 1.0.6 -> 1.0.8
• ca-certificates 2019.1.23 -> 2019.5.15
• certifi 2019.3.9 -> 2019.6.16
• cffi 1.12.2 -> 1.12.3
• cloudpickle 0.8.0 -> 1.2.1
• cryptography 2.6.1 -> 2.7
• curl 7.64.0 -> 7.65.2
• cython 0.29.6 -> 0.29.12

• cytoolz 0.9.0.1 -> 0.10.0

• dask 1.1.4 -> 2.1.0
• dask-core 1.1.4 -> 2.1.0
• defusedxml 0.5.0 -> 0.6.0
• distributed 1.26.0 -> 2.1.0
• fastcache 1.0.2 -> 1.1.0
• filelock 3.0.10 -> 3.0.12
• flask 1.0.2 -> 1.1.1
• futures 3.2.0 -> 3.3.0
• glob2 0.6 -> 0.7
• intel-openmp 2019.3 -> 2019.4
• ipykernel 5.1.0 -> 5.1.1
• ipython 7.4.0 -> 7.6.1
• ipywidgets 7.4.2 -> 7.5.0
• isort 4.3.16 -> 4.3.21
• jdcal 1.4 -> 1.4.1
• jinja2 2.10 -> 2.10.1
• jupyter_core 4.4.0 -> 4.5.0
• jupyterlab 0.35.4 -> 1.0.2
• kiwisolver 1.0.1 -> 1.1.0
• libcurl 7.64.0 -> 7.65.2
• libpng 1.6.36 -> 1.6.37
• libssh2 1.8.0 -> 1.8.2
• llvmlite 0.28.0 -> 0.29.0
• lxml 4.3.2 -> 4.3.4
• matplotlib 3.0.3 -> 3.1.0
• mkl 2019.3 -> 2019.4
• mkl-service 1.1.2 -> 2.0.2
• mkl_fft 1.0.10 -> 1.0.12
• nbconvert 5.4.1 -> 5.5.0
• networkx 2.2 -> 2.3

• nltk 3.4 -> 3.4.4

• notebook 5.7.8 -> 6.0.0
• numba 0.43.1 -> 0.45.0
• numpy 1.16.2 -> 1.16.4
• numpy-base 1.16.2 -> 1.16.4
• numpydoc 0.8.0 -> 0.9.1
• openpyxl 2.6.1 -> 2.6.2
• openssl 1.1.1b0 -> 1.1.1rc0
• parso 0.3.4 -> 0.5.0
• partd 0.3.10 -> 1.0.0
• path.py 11.5.0 -> 12.0.1
• pathlib2 2.3.3 -> 2.3.4
• pillow 5.4.1 -> 6.1.0
• pip 19.0.3 -> 19.1.1
• pluggy 0.9.0 -> 0.12.0
• psutil 5.6.1 -> 5.6.3
• pycurl 7.43.0.2 -> 7.43.0.3
• pygments 2.3.1 -> 2.4.2
• pyparsing 2.3.1 -> 2.4.0
• pysocks 1.6.8 -> 1.7.0
• pytables 3.5.1 -> 3.5.2
• pytest 4.3.1 -> 5.0.1
• pytz 2018.9 -> 2019.1
• pywavelets 1.0.2 -> 1.0.3
• pyyaml 5.1 -> 5.1.1
• qtpy 1.7.0 -> 1.8.0
• requests 2.21.0 -> 2.22.0
• rope 0.12.0 -> 0.14.0
• scikit-image 0.14.2 -> 0.15.0
• setuptools 40.8.0 -> 41.0.1
• sphinx 1.8.5 -> 2.1.2
• spyder 3.3.3 -> 3.3.6

• sqlalchemy 1.3.1 -> 1.3.5

• sqlite 3.27.2 -> 3.29.0
• statsmodels 0.9.0 -> 0.10.0
• subprocess32 3.5.3 -> 3.5.4
• sympy 1.3 -> 1.4
• tblib 1.3.2 -> 1.4.0
• terminado 0.8.1 -> 0.8.2
• toolz 0.9.0 -> 0.10.0
• tornado 6.0.2 -> 6.0.3
• tqdm 4.31.1 -> 4.32.1
• typed-ast 1.3.1 -> 1.3.4
• typing 3.6.6 -> 3.7.4
• urllib3 1.24.1 -> 1.24.2
• werkzeug 0.14.1 -> 0.15.4
• wheel 0.33.1 -> 0.33.4
• wrapt 1.11.1 -> 1.11.2
• xlsxwriter 1.1.5 -> 1.1.8
• zict 0.1.4 -> 1.0.0
• zipp 0.3.3 -> 0.5.1
Added:
• joblib 0.13.2
• json5 0.8.4
• mock 3.0.5
Updated:
• bokeh 1.0.4 -> 1.2.0
• libgcc-ng 8.2.0 -> 9.1.0
• libstdcxx-ng 8.2.0 -> 9.1.0

• pexpect 4.6.0 -> 4.7.0

• pycairo 1.18.0 -> 1.18.1
• qtconsole 4.4.3 -> 4.5.1
• scikit-learn 0.20.3 -> 0.21.2
• scipy 1.2.1 -> 1.3.0
Added:
Updated:
• bokeh 1.0.4 -> 1.2.0
• pexpect 4.6.0 -> 4.7.0
• pillow 5.3.0 -> 6.1.0
• pycairo 1.18.0 -> 1.18.1
• scikit-image 0.14.1 -> 0.15.0
Added:
Updated:
• bokeh 1.0.4 -> 1.3.0
• qtconsole 4.4.3 -> 4.5.2
• scikit-learn 0.20.3 -> 0.21.1
• scipy 1.2.1 -> 1.3.0
• xlwings 0.15.4 -> 0.15.8
Added:
• liblief 0.9.0
• py-lief 0.9.0
Updated:
• bokeh 1.0.4 -> 1.3.0
• qtconsole 4.4.3 -> 4.5.2
• scikit-learn 0.20.3 -> 0.21.2
• xlwings 0.15.4 -> 0.15.8

Updated:
• bokeh 1.0.4 -> 1.2.0
• pexpect 4.6.0 -> 4.7.0
• qtconsole 4.4.3 -> 4.5.1
• scikit-learn 0.20.3 -> 0.21.2
• scipy 1.2.1 -> 1.3.0
• xlwings 0.15.4 -> 0.15.8
Added:
• llvm-openmp 4.0.1
Anaconda 2019.03 (April 4, 2019)
User-facing changes
• Full conda integration with Windows Powershell.

• The Windows Python package includes an optional feature that, when enabled, will improve DLL handling of
library conflicts.
• This is the first release which includes conda 4.6.
• A link is added to the installer so you have the option to easily install PyCharm for Anaconda.
• Anaconda uninstalls faster on Windows.
Updated:
• astroid 2.1.0 -> 2.2.5
• astropy 3.1 -> 3.1.2
• atomicwrites 1.2.1 -> 1.3.0
• attrs 18.2.0 -> 19.1.0
• bleach 3.0.2 -> 3.1.0
• blosc 1.14.4 -> 1.15.0
• bokeh 1.0.2 -> 1.0.4
• ca-certificates 2018.3.7 -> 2019.1.23
• certifi 2018.11.29 -> 2019.3.9

• cffi 1.11.5 -> 1.12.2

• cloudpickle 0.6.1 -> 0.8.0
• curl 7.63.0 -> 7.64.0
• cython 0.29.2 -> 0.29.6
• dask 1.0.0 -> 1.1.4
• dask-core 1.0.0 -> 1.1.4
• decorator 4.3.0 -> 4.4.0
• distributed 1.25.1 -> 1.26.0
• entrypoints 0.2.3 -> 0.3
• gevent 1.3.7 -> 1.4.0
• h5py 2.8.0 -> 2.9.0
• hdf5 1.10.2 -> 1.10.4
• imageio 2.4.1 -> 2.5.0
• intel-openmp 2019.1 -> 2019.3
• ipython 7.2.0 -> 7.4.0
• isort 4.3.4 -> 4.3.16
• jedi 0.13.2 -> 0.13.3
• jsonschema 2.6.0 -> 3.0.1
• jupyterlab 0.35.3 -> 0.35.4
• keyring 17.0.0 -> 18.0.0
• libcurl 7.63.0 -> 7.64.0
• libpng 1.6.35 -> 1.6.36
• libtiff 4.0.9 -> 4.0.10
• libxml2 2.9.8 -> 2.9.9
• libxslt 1.1.32 -> 1.1.33
• llvmlite 0.26.0 -> 0.28.0
• lxml 4.2.5 -> 4.3.2
• markupsafe 1.1.0 -> 1.1.1
• matplotlib 3.0.2 -> 3.0.3
• mkl 2019.1 -> 2019.3
• mkl_fft 1.0.6 -> 1.0.10

• nbconvert 5.4.0 -> 5.4.1

• notebook 5.7.4 -> 5.7.8
• numba 0.41.0 -> 0.43.1
• numexpr 2.6.8 -> 2.6.9
• numpy 1.15.4 -> 1.16.2
• numpy-base 1.15.4 -> 1.16.2
• openpyxl 2.5.12 -> 2.6.1
• openssl 1.1.1a0 -> 1.1.1b0
• packaging 18.0 -> 19.0
• pandas 0.23.4 -> 0.24.2
• pandoc 1.19.2.1 -> 2.2.3.2
• parso 0.3.1 -> 0.3.4
• partd 0.3.9 -> 0.3.10
• pillow 5.3.0 -> 5.4.1
• pip 18.1 -> 19.0.3
• pkginfo 1.4.2 -> 1.5.0.1
• pluggy 0.8.0 -> 0.9.0
• psutil 5.4.8 -> 5.6.1
• py 1.7.0 -> 1.8.0
• pycodestyle 2.4.0 -> 2.5.0
• pyflakes 2.0.0 -> 2.1.1
• pylint 2.2.2 -> 2.3.1
• pyodbc 4.0.25 -> 4.0.26
• pyopenssl 18.0.0 -> 19.0.0
• pyparsing 2.3.0 -> 2.3.1
• pytables 3.4.4 -> 3.5.1
• pytest 4.0.2 -> 4.3.1
• python 3.7.1 -> 3.7.3
• pytz 2018.7 -> 2018.9
• pywavelets 1.0.1 -> 1.0.2
• pyyaml 3.13 -> 5.1

• pyzmq 17.1.2 -> 18.0.0

• qtawesome 0.5.3 -> 0.5.7
• qtpy 1.5.2 -> 1.7.0
• rope 0.11.0 -> 0.12.0
• scandir 1.9.0 -> 1.10.0
• scikit-image 0.14.1 -> 0.14.2
• scikit-learn 0.20.1 -> 0.20.3
• scipy 1.1.0 -> 1.2.1
• setuptools 40.6.3 -> 40.8.0
• sphinx 1.8.2 -> 1.8.5
• spyder 3.3.2 -> 3.3.3
• sqlalchemy 1.2.15 -> 1.3.1
• sqlite 3.26.0 -> 3.27.2
• ssl_match_hostname 3.5.0.1 -> 3.7.0.1
• tornado 5.1.1 -> 6.0.2
• tqdm 4.28.1 -> 4.31.1
• typed-ast 1.1.0 -> 1.3.1
• wheel 0.32.3 -> 0.33.1
• wrapt 1.10.11 -> 1.11.1
• xlsxwriter 1.1.2 -> 1.1.5
• zeromq 4.2.5 -> 4.3.1
• zict 0.1.3 -> 0.1.4
Added:
• soupsieve 1.8
• zipp 0.3.3
Removed:
• blaze
• conda
• conda-build
• conda-env
• datashape
• flask-cors
• odo

Updated:
• dbus 1.13.2 -> 1.13.6
• graphite2 1.3.12 -> 1.3.13
• libedit 3.1.20170329 -> 3.1.20181209
• pcre 8.42 -> 8.43
• pixman 0.34.0 -> 0.38.0
Updated:
• libedit 3.1.20170329 -> 3.1.20181209
• nbconvert 5.3.1 -> 5.4.1
• pcre 8.42 -> 8.43
Added:
Updated:
• menuinst 1.4.14 -> 1.4.16
• win_inet_pton 1.0.1 -> 1.1.0
• xlwings 0.15.1 -> 0.15.4
Added:
• powershell_shortcut 0.0.1
• pyreadline 2.1
Updated:
• menuinst 1.4.14 -> 1.4.16
• win_inet_pton 1.0.1 -> 1.1.0
• xlwings 0.15.1 -> 0.15.4
Added:
• liblief 0.9.0
• powershell_shortcut 0.0.1
• py-lief 0.9.0

• pyreadline 2.1
Updated:
• appscript 1.0.1 -> 1.1.0
• dbus 1.13.2 -> 1.13.6
• libedit 3.1.20170329 -> 3.1.20181209
• pcre 8.42 -> 8.43
• xlwings 0.15.1 -> 0.15.4
Anaconda 2018.12 (December 21, 2018)
User-facing changes
• Anaconda version numbers now follow a year.month format.

• OpenSSL 1.1.1 is installed on all platforms and versions except for the Python 2.7 on win-32 and win-64.
• This is the last Anaconda release for the linux-32 platform.
• Improvements have been made to conda which will decrease the time it takes to solve and install packages.
Updated:
• alabaster 0.7.11 -> 0.7.12
• astroid 2.0.4 -> 2.1.0
• astropy 3.0.4 -> 3.1
• bleach 2.1.4 -> 3.0.2
• bokeh 0.13.0 -> 1.0.2
• certifi 2018.8.24 -> 2018.11.29
• click 6.7 -> 7.0
• cloudpickle 0.5.5 -> 0.6.1
• colorama 0.3.9 -> 0.4.1
• curl 7.61.0 -> 7.63.0
• cython 0.28.5 -> 0.29.2
• dask 0.19.1 -> 1.0.0

• dask-core 0.19.1 -> 1.0.0

• distributed 1.23.1 -> 1.25.1
• filelock 3.0.8 -> 3.0.10
• flask-cors 3.0.6 -> 3.0.7
• gevent 1.3.6 -> 1.3.7
• idna 2.7 -> 2.8
• intel-openmp 2019.0 -> 2019.1
• ipython 6.5.0 -> 7.2.0
• ipywidgets 7.4.1 -> 7.4.2
• itsdangerous 0.24 -> 1.1.0
• jedi 0.12.1 -> 0.13.2
• jupyterlab 0.34.9 -> 0.35.3
• keyring 13.2.1 -> 17.0.0
• libcurl 7.61.0 -> 7.63.0
• libpng 1.6.34 -> 1.6.35
• llvmlite 0.24.0 -> 0.26.0
• markupsafe 1.0 -> 1.1.0
• matplotlib 2.2.3 -> 3.0.2
• mistune 0.8.3 -> 0.8.4
• mkl 2019.0 -> 2019.1
• mkl_fft 1.0.4 -> 1.0.6
• mkl_random 1.0.1 -> 1.0.2
• mpmath 1.0.0 -> 1.1.0
• networkx 2.1 -> 2.2
• nltk 3.3.0 -> 3.4
• notebook 5.6.0 -> 5.7.4
• numba 0.39.0 -> 0.41.0
• numpy 1.15.1 -> 1.15.4
• numpy-base 1.15.1 -> 1.15.4
• openpyxl 2.5.6 -> 2.5.12
• openssl 1.0.2p -> 1.1.1a0
• packaging 17.1 -> 18.0
• partd 0.3.8 -> 0.3.9
• path.py 11.1.0 -> 11.5.0

• pathlib2 2.3.2 -> 2.3.3

• patsy 0.5.0 -> 0.5.1
• pickleshare 0.7.4 -> 0.7.5
• pillow 5.2.0 -> 5.3.0
• pip 10.0.1 -> 18.1
• pluggy 0.7.1 -> 0.8.0
• psutil 5.4.7 -> 5.4.8
• py 1.6.0 -> 1.7.0
• pycparser 2.18 -> 2.19
• pygments 2.2.0 -> 2.3.1
• pylint 2.1.1 -> 2.2.2
• pyodbc 4.0.24 -> 4.0.25
• pyparsing 2.2.0 -> 2.3.0
• pytest 3.8.0 -> 4.0.2
• pytest-arraydiff 0.2 -> 0.3
• python 3.7.0 -> 3.7.1
• pytz 2018.5 -> 2018.7
• pywavelets 1.0.0 -> 1.0.1
• qt 5.9.6 -> 5.9.7
• qtawesome 0.4.4 -> 0.5.3
• qtconsole 4.4.1 -> 4.4.3
• qtpy 1.5.0 -> 1.5.2
• requests 2.19.1 -> 2.21.0
• scikit-image 0.14.0 -> 0.14.1
• scikit-learn 0.19.2 -> 0.20.1
• setuptools 40.2.0 -> 40.6.3
• six 1.11.0 -> 1.12.0
• sphinx 1.7.9 -> 1.8.2

• spyder 3.3.1 -> 3.3.2

• sqlalchemy 1.2.11 -> 1.2.15
• sqlite 3.24.0 -> 3.26.0
• subprocess32 3.5.2 -> 3.5.3
• sympy 1.2 -> 1.3
• testpath 0.3.1 -> 0.4.2
• tornado 5.1 -> 5.1.1
• tqdm 4.26.0 -> 4.28.1
• urllib3 1.23 -> 1.24.1
• wheel 0.31.1 -> 0.32.3
• xlrd 1.1.0 -> 1.2.0
• xlsxwriter 1.1.0 -> 1.1.2
Added:
• backports.os 0.1.1
• conda 4.5.12
• conda-build 3.17.6
• conda-env 2.6.0
• future 0.17.1
• importlib_metadata 0.6
• krb5 1.16.1
• lz4-c 1.8.1.2
• zstd 1.3.7
Removed:
• appdirs
• automat
• constantly
• hyperlink
• incremental
• pyasn1
• pyasn1-modules
• service_identity

• twisted
• zope
• zope.interface
Updated:
• ipykernel 4.9.0 -> 5.1.0
• jeepney 0.3.1 -> 0.4
• pycairo 1.17.1 -> 1.18.0
Added:
• liblief 0.9.0
• py-lief 0.9.0
• wurlitzer 1.0.2
Updated:
• ipykernel 4.9.0 -> 5.1.0
• jeepney 0.3.1 -> 0.4
• pycairo 1.17.1 -> 1.18.0
Added:
• liblief 0.9.0
• py-lief 0.9.0
• wurlitzer 1.0.2
Updated:
• conda 4.5.11 -> 4.5.12
• conda-build 3.15.1 -> 3.16.3
• ipykernel 4.9.0 -> 5.1.0
• libpng 1.6.32 -> 1.6.35
• pycairo 1.17.1 -> 1.18.0
• tqdm 4.25.0 -> 4.28.1
Added:
• libssh2 1.8.0

Updated:
• backports.shutil_which 3.5.1 -> 3.5.2
• icc_rt 2017.0.4 -> 2019.0.0
• ipykernel 4.10.0 -> 5.1.0
• pywinpty 0.5.4 -> 0.5.5
• xlwings 0.11.8 -> 0.15.1
Added:
• xz 5.2.4
Updated:
• backports.shutil_which 3.5.1 -> 3.5.2
• icc_rt 2017.0.4 -> 2019.0.0
• ipykernel 4.10.0 -> 5.1.0
• pywinpty 0.5.4 -> 0.5.5
• xlwings 0.11.8 -> 0.15.1
Added:
• xz 5.2.4
Anaconda 5.3.1 (Nov 19, 2018)
User-facing changes
• The Anaconda Installers are shipped with a fix for VSCode Installation. xref: https://github.com/ContinuumIO/
anaconda-issues/issues/10286
Anaconda 5.3.0 (Sept 28, 2018)
User-facing changes
• The Anaconda3 installers ship with python 3.7 instead of python 3.6
• Windows installers disallow the character , in installation path to prevent usability issues.
• Instructions in the macOS pkg installer for choice of initializing installation has been improved.

• Installers mimic the funcionality of “conda init” (a highly anticipated feature in conda 4.6) instead of just adding
$PREFIX/bin to PATH in bash profile.
• The repodata_record.json file for each package in the package cache directory is populated correctly, which will
assist in offline installation of packages in new environments.
Updated:
• alabaster 0.7.10 -> 0.7.11
• anaconda-client 1.6.14 -> 1.7.2
• astroid 1.6.3 -> 2.0.4
• astropy 3.0.2 -> 3.0.4
• attrs 18.1.0 -> 18.2.0
• babel 2.5.3 -> 2.6.0
• bitarray 0.8.1 -> 0.8.3
• bleach 2.1.3 -> 2.1.4
• blosc 1.14.3 -> 1.14.4
• bokeh 0.12.16 -> 0.13.0
• boto 2.48.0 -> 2.49.0
• certifi 2018.4.16 -> 2018.8.24
• cloudpickle 0.5.3 -> 0.5.5
• curl 7.60.0 -> 7.61.0
• cython 0.28.2 -> 0.28.5
• dask 0.17.5 -> 0.19.1
• dask-core 0.17.5 -> 0.19.1
• distributed 1.21.8 -> 1.23.1
• filelock 3.0.4 -> 3.0.8
• flask-cors 3.0.4 -> 3.0.6
• freetype 2.8 -> 2.9.1
• gevent 1.3.0 -> 1.3.6
• greenlet 0.4.13 -> 0.4.15
• h5py 2.7.1 -> 2.8.0
• idna 2.6 -> 2.7
• imageio 2.3.0 -> 2.4.1

• imagesize 1.0.0 -> 1.1.0

• intel-openmp 2018.0.0 -> 2019.0
• ipython 6.4.0 -> 6.5.0
• ipywidgets 7.2.1 -> 7.4.1
• jedi 0.12.0 -> 0.12.1
• jupyterlab 0.32.1 -> 0.34.9
• jupyterlab_launcher 0.10.5 -> 0.13.1
• libcurl 7.60.0 -> 7.61.0
• llvmlite 0.23.1 -> 0.24.0
• lxml 4.2.1 -> 4.2.5
• matplotlib 2.2.2 -> 2.2.3
• mkl 2018.0.2 -> 2019.0
• mkl_fft 1.0.1 -> 1.0.4
• multipledispatch 0.5.0 -> 0.6.0
• nbconvert 5.3.1 -> 5.4.0
• notebook 5.5.0 -> 5.6.0
• numba 0.38.0 -> 0.39.0
• numexpr 2.6.5 -> 2.6.8
• numpy 1.14.3 -> 1.15.1
• numpy-base 1.14.3 -> 1.15.1
• olefile 0.45.1 -> 0.46
• openpyxl 2.5.3 -> 2.5.6
• openssl 1.0.2o -> 1.0.2p
• pandas 0.23.0 -> 0.23.4
• parso 0.2.0 -> 0.3.1
• path.py 11.0.1 -> 11.1.0
• pillow 5.1.0 -> 5.2.0
• pluggy 0.6.0 -> 0.7.1
• psutil 5.4.5 -> 5.4.7
• py 1.5.3 -> 1.6.0
• pycurl 7.43.0.1 -> 7.43.0.2
• pyflakes 1.6.0 -> 2.0.0
• pylint 1.8.4 -> 2.1.1
• pyodbc 4.0.23 -> 4.0.24
• pytables 3.4.3 -> 3.4.4

• pytest 3.5.1 -> 3.8.0

• python 3.6.5 -> 3.7.0
• pytz 2018.4 -> 2018.5
• pywavelets 0.5.2 -> 1.0.0
• pyyaml 3.12 -> 3.13
• pyzmq 17.0.0 -> 17.1.2
• qt 5.9.5 -> 5.9.6
• qtconsole 4.3.1 -> 4.4.1
• qtpy 1.4.1 -> 1.5.0
• requests 2.18.4 -> 2.19.1
• rope 0.10.7 -> 0.11.0
• ruamel_yaml 0.15.35 -> 0.15.46
• scandir 1.7 -> 1.9.0
• scikit-image 0.13.1 -> 0.14.0
• scikit-learn 0.19.1 -> 0.19.2
• seaborn 0.8.1 -> 0.9.0
• setuptools 39.1.0 -> 40.2.0
• sphinx 1.7.4 -> 1.7.9
• spyder 3.2.8 -> 3.3.1
• sqlalchemy 1.2.7 -> 1.2.11
• sqlite 3.23.1 -> 3.24.0
• subprocess32 3.5.0 -> 3.5.2
• sympy 1.1.1 -> 1.2
• tk 8.6.7 -> 8.6.8
• tornado 5.0.2 -> 5.1
• typing 3.6.4 -> 3.6.6
• urllib3 1.22 -> 1.23
• xlsxwriter 1.0.4 -> 1.1.0
Added:
• appdirs 1.4.3

• atomicwrites 1.2.1
• automat 0.7.0
• constantly 15.1.0
• hyperlink 18.0.0
• incremental 17.5.0
• keyring 13.2.1
• linecache2 1.0.0
• pyasn1 0.4.4
• pyasn1-modules 0.2.2
• service_identity 17.0.0
• spyder-kernels 0.2.6
• tqdm 4.26.0
• traceback2 1.4.0
• twisted 18.7.0
• typed-ast 1.1.0
• unittest2 1.1.0
• zope 1.0
Updated:
• expat 2.2.5 -> 2.2.6
• fontconfig 2.12.6 -> 2.13.0
• glib 2.56.1 -> 2.56.2
• graphite2 1.3.11 -> 1.3.12
• harfbuzz 1.7.6 -> 1.8.8
• ipykernel 4.8.2 -> 4.9.0
• libgcc-ng 7.2.0 -> 8.2.0
• libgfortran-ng 7.2.0 -> 7.3.0
• libstdcxx-ng 7.2.0 -> 8.2.0
• mpc 1.0.3 -> 1.1.0
• mpfr 3.1.5 -> 4.0.1
• pango 1.41.0 -> 1.42.4
• pexpect 4.5.0 -> 4.6.0

• ptyprocess 0.5.2 -> 0.6.0

• pycairo 1.15.4 -> 1.17.1
• unixodbc 2.3.6 -> 2.3.7
Added:
• fribidi 1.0.5
• jeepney 0.3.1
• libuuid 1.0.3
• secretstorage 3.1.0
Updated:
• expat 2.2.5 -> 2.2.6
• fontconfig 2.12.6 -> 2.13.0
• glib 2.56.1 -> 2.56.2
• graphite2 1.3.11 -> 1.3.12
• harfbuzz 1.7.6 -> 1.8.8
• ipykernel 4.8.2 -> 4.9.0
• libgcc-ng 7.2.0 -> 8.2.0
• libstdcxx-ng 7.2.0 -> 8.2.0
• mpc 1.0.3 -> 1.1.0
• mpfr 3.1.5 -> 4.0.1
• pango 1.41.0 -> 1.42.4
• pexpect 4.5.0 -> 4.6.0
• ptyprocess 0.5.2 -> 0.6.0
• pycairo 1.15.4 -> 1.17.1
• sip 4.19.8 -> 4.19.12
• unixodbc 2.3.6 -> 2.3.7
Added:
• fribidi 1.0.5
• jeepney 0.3.1
• libuuid 1.0.3
• secretstorage 3.1.0

Updated:
• asn1crypto 0.23.0 -> 0.24.0
• astroid 1.6.2 -> 2.0.4
• babel 2.5.0 -> 2.6.0
• backports.functools_lru_cache 1.4 -> 1.5
• bokeh 0.12.15 -> 0.13.0
• conda 4.5.4 -> 4.5.11
• conda-build 3.10.5 -> 3.15.1
• curl 7.55.1 -> 7.61.0
• cython 0.28.1 -> 0.28.5
• decorator 4.1.2 -> 4.3.0
• expat 2.2.5 -> 2.2.6
• filelock 2.0.13 -> 3.0.8
• flask 0.12.2 -> 1.0.2
• fontconfig 2.12.6 -> 2.13.0
• glib 2.56.1 -> 2.56.2
• greenlet 0.4.12 -> 0.4.15
• imageio 2.2.0 -> 2.4.1
• imagesize 0.7.1 -> 1.1.0
• ipykernel 4.8.0 -> 4.9.0
• ipywidgets 7.2.0 -> 7.4.1
• isort 4.2.15 -> 4.3.4
• jedi 0.11.0 -> 0.12.1
• libgcc-ng 7.2.0 -> 8.2.0
• libstdcxx-ng 7.2.0 -> 8.2.0
• numexpr 2.6.5 -> 2.6.7
• numpy 1.13.3 -> 1.14.5
• parso 0.1.1 -> 0.3.1
• patsy 0.4.1 -> 0.5.0
• pep8 1.7.0 -> 1.7.1
• pexpect 4.3.0 -> 4.6.0
• pillow 5.0.0 -> 5.2.0
• pkginfo 1.4.1 -> 1.4.2
• ply 3.10 -> 3.11

• psutil 5.4.1 -> 5.4.7

• ptyprocess 0.5.2 -> 0.6.0
• pycairo 1.13.3 -> 1.17.1
• pycurl 7.43.0 -> 7.43.0.2
• pysocks 1.6.7 -> 1.6.8
• pytz 2017.3 -> 2018.5
• scandir 1.6 -> 1.9.0
• send2trash 1.4.2 -> 1.5.0
• toolz 0.8.2 -> 0.9.0
• typing 3.6.2 -> 3.6.6
• unixodbc 2.3.6 -> 2.3.7
• werkzeug 0.12.2 -> 0.14.1
• zeromq 4.2.3 -> 4.2.5
Added:
• blas 1.0
• gmpy2 2.0.8
• libcurl 7.61.0
• libuuid 1.0.3
• mpc 1.1.0
• mpfr 4.0.1
• tqdm 4.25.0
• twisted 18.4.0
Removed:
• conda-verify
• libssh2
Updated:
• comtypes 1.1.4 -> 1.1.7
• ipykernel 4.8.2 -> 4.10.0
• pywinpty 0.5.1 -> 0.5.4
• vc 14 -> 14.1
• vs2015_runtime 14.0.25123 -> 14.15.26706

Updated:
• comtypes 1.1.4 -> 1.1.7
• ipykernel 4.8.2 -> 4.10.0
• pywinpty 0.5.1 -> 0.5.4
• vc 14 -> 14.1
• vs2015_runtime 14.0.25123 -> 14.15.26706
Anaconda 5.2.0 (May 30, 2018)
User-facing changes
• Windows installers disallow the characters ! % ^ = in installation path to prevent later usability issues
• Improved Windows multi-user installations by providing more dynamic shortcut working directory behavior
• Default channels point to repo.anaconda.com instead of repo.anaconda.com
• Security fixes for more than 20 packages based on a deep-dive of CVE vulnerabilities
• Windows installer uses a trimmed down value for PATH env var, to avoid DLL hell with existing software
• History file in the conda-meta directory is populated correctly to improve behavior of --prune
• Developer certificate for macOS pkg installers has been updated to Anaconda, Inc.
Updated:
• astroid 1.6.1 -> 1.6.3
• astropy 2.0.3 -> 3.0.2
• attrs 17.4.0 -> 18.1.0
• backports.functools_lru_cache 1.4 -> 1.5
• bleach 2.1.2 -> 2.1.3
• bokeh 0.12.13 -> 0.12.16
• ca-certificates 2017.8.26 -> 2018.3.7
• certifi 2018.1.18 -> 2018.4.16
• cffi 1.11.4 -> 1.11.5
• cloudpickle 0.5.2 -> 0.5.3

• curl 7.58.0 -> 7.60.0

• cython 0.27.3 -> 0.28.2
• cytoolz 0.9.0 -> 0.9.0.1
• dask 0.16.1 -> 0.17.5
• dask-core 0.16.1 -> 0.17.5
• decorator 4.2.1 -> 4.3.0
• distributed 1.20.2 -> 1.21.8
• filelock 2.0.13 -> 3.0.4
• flask 0.12.2 -> 1.0.2
• flask-cors 3.0.3 -> 3.0.4
• gevent 1.2.2 -> 1.3.0
• greenlet 0.4.12 -> 0.4.13
• hdf5 1.10.1 -> 1.10.2
• imageio 2.2.0 -> 2.3.0
• imagesize 0.7.1 -> 1.0.0
• ipaddress 1.0.19 -> 1.0.22
• ipykernel 4.8.0 -> 4.8.2
• ipython 6.2.1 -> 6.4.0
• ipywidgets 7.1.1 -> 7.2.1
• isort 4.2.15 -> 4.3.4
• jdcal 1.3 -> 1.4
• jedi 0.11.1 -> 0.12.0
• jupyterlab 0.31.5 -> 0.32.1
• libcurl 7.58.0 -> 7.60.0
• libxml2 2.9.7 -> 2.9.8
• llvmlite 0.21.0 -> 0.23.1
• lxml 4.1.1 -> 4.2.1
• matplotlib 2.1.2 -> 2.2.2
• mkl 2018.0.1 -> 2018.0.2
• multipledispatch 0.4.9 -> 0.5.0
• nltk 3.2.5 -> 3.3.0
• notebook 5.4.0 -> 5.5.0
• numba 0.36.2 -> 0.38.0

• numexpr 2.6.4 -> 2.6.5

• numpy 1.14.0 -> 1.14.3
• numpydoc 0.7.0 -> 0.8.0
• openpyxl 2.4.10 -> 2.5.3
• openssl 1.0.2n -> 1.0.2o
• packaging 16.8 -> 17.1
• pandas 0.22.0 -> 0.23.0
• parso 0.1.1 -> 0.2.0
• path.py 10.5 -> 11.0.1
• pathlib2 2.3.0 -> 2.3.2
• pillow 5.0.0 -> 5.1.0
• pip 9.0.1 -> 10.0.1
• pkginfo 1.4.1 -> 1.4.2
• ply 3.10 -> 3.11
• psutil 5.4.3 -> 5.4.5
• py 1.5.2 -> 1.5.3
• pycodestyle 2.3.1 -> 2.4.0
• pylint 1.8.2 -> 1.8.4
• pyodbc 4.0.22 -> 4.0.23
• pyopenssl 17.5.0 -> 18.0.0
• pyqt 5.6.0 -> 5.9.2
• pysocks 1.6.7 -> 1.6.8
• pytables 3.4.2 -> 3.4.3
• pytest 3.3.2 -> 3.5.1
• python 3.6.4 -> 3.6.5
• pytz 2017.3 -> 2018.4
• pyzmq 16.0.3 -> 17.0.0
• qt 5.6.2 -> 5.9.5
• qtpy 1.3.1 -> 1.4.1
• scandir 1.6 -> 1.7
• scipy 1.0.0 -> 1.1.0
• send2trash 1.4.2 -> 1.5.0
• setuptools 38.4.0 -> 39.1.0
• sip 4.18.1 -> 4.19.8


• sphinx 1.6.6 -> 1.7.4
• spyder 3.2.6 -> 3.2.8
• sqlalchemy 1.2.1 -> 1.2.7
• sqlite 3.22.0 -> 3.23.1
• statsmodels 0.8.0 -> 0.9.0
• subprocess32 3.2.7 -> 3.5.0
• tornado 4.5.3 -> 5.0.2
• typing 3.6.2 -> 3.6.4
• wheel 0.30.0 -> 0.31.1
• xlsxwriter 1.0.2 -> 1.0.4
Added:
• backcall 0.1.0
• blas 1.0
• blosc 1.14.3
• mkl_fft 1.0.1
• mkl_random 1.0.1
• pytest-arraydiff 0.2
• pytest-astropy 0.3.0
• pytest-doctestplus 0.1.3
• pytest-openfiles 0.3.0
• pytest-remotedata 0.2.1
• snappy 1.1.7
Updated:
• dbus 1.12.2 -> 1.13.2
• fontconfig 2.12.4 -> 2.12.6
• glib 2.53.6 -> 2.56.1
• graphite2 1.3.10 -> 1.3.11
• gst-plugins-base 1.12.4 -> 1.14.0
• gstreamer 1.12.4 -> 1.14.0

• harfbuzz 1.7.4 -> 1.7.6

• libedit 3.1 -> 3.1.20170329
• libsodium 1.0.15 -> 1.0.16
• libxcb 1.12 -> 1.13
• ncurses 6.0 -> 6.1
• pcre 8.41 -> 8.42
• pexpect 4.3.1 -> 4.5.0
• unixodbc 2.3.4 -> 2.3.6
• xz 5.2.3 -> 5.2.4
• zeromq 4.2.2 -> 4.2.5
Updated:
• dbus 1.12.2 -> 1.13.2
• fontconfig 2.12.4 -> 2.12.6
• glib 2.53.6 -> 2.56.1
• graphite2 1.3.10 -> 1.3.11
• gstreamer 1.12.4 -> 1.14.0
• harfbuzz 1.7.4 -> 1.7.6
• libedit 3.1 -> 3.1.20170329
• libsodium 1.0.15 -> 1.0.16
• libxcb 1.12 -> 1.13
• ncurses 6.0 -> 6.1
• pcre 8.41 -> 8.42
• pexpect 4.3.1 -> 4.5.0
• unixodbc 2.3.4 -> 2.3.6
• xz 5.2.3 -> 5.2.4
• zeromq 4.2.2 -> 4.2.5
Updated:
• astroid 1.6.1 -> 1.6.2
• bokeh 0.12.13 -> 0.12.15

• cairo 1.14.10 -> 1.14.12

• cffi 1.11.2 -> 1.11.5
• conda 4.4.9 -> 4.5.4
• conda-build 3.4.1 -> 3.10.5
• cython 0.27.3 -> 0.28.1
• cytoolz 0.8.2 -> 0.9.0.1
• dask 0.16.0 -> 0.17.5
• dask-core 0.16.0 -> 0.17.5
• fontconfig 2.12.4 -> 2.12.6
• glib 2.53.6 -> 2.56.1
• ipaddress 1.0.18 -> 1.0.22
• ipywidgets 7.1.1 -> 7.2.0
• libsodium 1.0.15 -> 1.0.16
• libxcb 1.12 -> 1.13
• libxml2 2.9.4 -> 2.9.8
• libxslt 1.1.29 -> 1.1.32
• mistune 0.8.1 -> 0.8.3
• ncurses 6.0 -> 6.1
• pcre 8.41 -> 8.42
• pytest 3.2.5 -> 3.5.1
• setuptools 36.5.0 -> 39.1.0
• sphinx 1.6.3 -> 1.7.4
• sqlite 3.21.0 -> 3.23.1
• tornado 4.5.2 -> 5.0.2
• unixodbc 2.3.4 -> 2.3.6
• xz 5.2.3 -> 5.2.4
• zeromq 4.2.2 -> 4.2.3
Added:
• attrs 18.1.0
• pluggy 0.6.0
Removed:
• gmpy2
• mpc
• mpfr

Updated:
• menuinst 1.4.11 -> 1.4.14
• pywin32 222 -> 223
• pywinpty 0.5 -> 0.5.1
• xlwings 0.11.5 -> 0.11.8
Added:
• m2w64-gcc-libgfortran 5.3.0
• m2w64-gcc-libs 5.3.0
• m2w64-gcc-libs-core 5.3.0
• m2w64-gmp 6.1.0
• m2w64-libwinpthread-git 5.0.0.4634.697f757
• msys2-conda-epoch 20160418
• zeromq 4.2.5
Updated:
• menuinst 1.4.11 -> 1.4.14
• pywin32 222 -> 223
• pywinpty 0.5 -> 0.5.1
• xlwings 0.11.5 -> 0.11.8
Added:
• m2w64-gcc-libgfortran 5.3.0
• m2w64-gcc-libs 5.3.0
• m2w64-gcc-libs-core 5.3.0
• m2w64-gmp 6.1.0
• m2w64-libwinpthread-git 5.0.0.4634.697f757
• msys2-conda-epoch 20160418
• zeromq 4.2.5

Anaconda 5.1.0 (Feb 15, 2018)
User-facing changes
• Microsoft Visual Studio Code added as an install option

• Anaconda Navigator has install and launch options for VS Code
• The installer support link has been replaced with the Getting Started page
• Power packages are built with same recipes as rest of distribution

• Fixed some incomplete Windows installations due to interactions with antivirus software
• Fixed spaces in paths problems on Windows
• Anaconda Navigator was removed from the anaconda metapackage (but not the Anaconda installer)
• Installers present warnings when executed on the wrong platform
Updated:
• anaconda-navigator 1.6.9 -> 1.7.0
• asn1crypto 0.22.0 -> 0.24.0
• astroid 1.5.3 -> 1.6.1
• astropy 2.0.2 -> 2.0.3
• babel 2.5.0 -> 2.5.3
• bleach 2.0.0 -> 2.1.2
• bokeh 0.12.10 -> 0.12.13
• certifi 2017.7.27.1 -> 2018.1.18
• cffi 1.10.0 -> 1.11.4
• cloudpickle 0.4.0 -> 0.5.2
• conda 4.3.27 -> 4.4.10
• conda-build 3.0.27 -> 3.4.1
• curl 7.55.1 -> 7.58.0
• cython 0.26.1 -> 0.27.3
• cytoolz 0.8.2 -> 0.9.0
• dask 0.15.3 -> 0.16.1

• dask-core 0.15.3 -> 0.16.1

• decorator 4.1.2 -> 4.2.1
• distributed 1.19.1 -> 1.20.2
• filelock 2.0.12 -> 2.0.13
• futures 3.1.1 -> 3.2.0
• glob2 0.5 -> 0.6
• h5py 2.7.0 -> 2.7.1
• html5lib 0.999999999 -> 1.0.1
• ipaddress 1.0.18 -> 1.0.19
• ipykernel 4.6.1 -> 4.8.0
• ipython 6.1.0 -> 6.2.1
• ipywidgets 7.0.0 -> 7.1.1
• jedi 0.10.2 -> 0.11.1
• jinja2 2.9.6 -> 2.10
• jupyter_core 4.3.0 -> 4.4.0
• libpng 1.6.32 -> 1.6.34
• libtiff 4.0.8 -> 4.0.9
• libxml2 2.9.4 -> 2.9.7
• libxslt 1.1.29 -> 1.1.32
• llvmlite 0.20.0 -> 0.21.0
• lxml 4.1.0 -> 4.1.1
• matplotlib 2.1.0 -> 2.1.2
• mistune 0.7.4 -> 0.8.3
• mkl 2018.0.0 -> 2018.0.1
• mpmath 0.19 -> 1.0.0
• networkx 2.0 -> 2.1
• nltk 3.2.4 -> 3.2.5
• notebook 5.0.0 -> 5.4.0
• numba 0.35.0 -> 0.36.2
• numexpr 2.6.2 -> 2.6.4
• numpy 1.13.3 -> 1.14.0
• olefile 0.44 -> 0.45.1
• openpyxl 2.4.8 -> 2.4.10

• openssl 1.0.2l -> 1.0.2n

• pandas 0.20.3 -> 0.22.0
• path.py 10.3.1 -> 10.5
• patsy 0.4.1 -> 0.5.0
• pep8 1.7.0 -> 1.7.1
• pillow 4.2.1 -> 5.0.0
• psutil 5.4.0 -> 5.4.3
• py 1.4.34 -> 1.5.2
• pycosat 0.6.2 -> 0.6.3
• pycurl 7.43.0 -> 7.43.0.1
• pylint 1.7.4 -> 1.8.2
• pyodbc 4.0.17 -> 4.0.22
• pyopenssl 17.2.0 -> 17.5.0
• pytest 3.2.1 -> 3.3.2
• python 3.6.3 -> 3.6.4
• pytz 2017.2 -> 2017.3
• pyzmq 16.0.2 -> 16.0.3
• rope 0.10.5 -> 0.10.7
• ruamel_yaml 0.11.14 -> 0.15.35
• scikit-image 0.13.0 -> 0.13.1
• scipy 0.19.1 -> 1.0.0
• seaborn 0.8.0 -> 0.8.1
• setuptools 36.5.0 -> 38.4.0
• sphinx 1.6.3 -> 1.6.6
• spyder 3.2.4 -> 3.2.6
• sqlalchemy 1.1.13 -> 1.2.1
• sqlite 3.20.1 -> 3.22.0
• toolz 0.8.2 -> 0.9.0
• tornado 4.5.2 -> 4.5.3
• werkzeug 0.12.2 -> 0.14.1
• wheel 0.29.0 -> 0.30.0
Added:
• attrs 17.4.0
• libcurl 7.58.0

• parso 0.1.1
• pluggy 0.6.0
Updated:
• comtypes 1.1.2 -> 1.1.4
• jupyterlab 0.27.0 -> 0.31.4
• menuinst 1.4.10 -> 1.4.11
• pywin32 221 -> 222
• xlwings 0.11.4 -> 0.11.5
Added:
• backports.shutil_which 3.5.1
• pywinpty 0.5
• terminado 0.8.1
• winpty 0.4.3
Removed:
• cachecontrol
• distlib
• lockfile
• progress
Updated:
• comtypes 1.1.2 -> 1.1.4
• jupyterlab 0.27.0 -> 0.31.5
• menuinst 1.4.10 -> 1.4.11
• pywin32 221 -> 222
• xlwings 0.11.4 -> 0.11.5
Added:
• backports.shutil_which 3.5.1
• pywinpty 0.5
• terminado 0.8.1
• winpty 0.4.3
Removed:

• cachecontrol
• distlib
• lockfile
• progress
Updated:
• dbus 1.10.22 -> 1.12.2
• expat 2.2.4 -> 2.2.5
• jupyterlab 0.27.0 -> 0.31.5
• libsodium 1.0.13 -> 1.0.15
• pexpect 4.2.1 -> 4.3.1
• terminado 0.6 -> 0.8.1
• xlwings 0.11.4 -> 0.11.5
Updated:
• cairo 1.14.10 -> 1.14.12
• dbus 1.10.22 -> 1.12.2
• expat 2.2.4 -> 2.2.5
• gstreamer 1.12.2 -> 1.12.4
• harfbuzz 1.5.0 -> 1.7.4
• jupyterlab 0.27.0 -> 0.31.5
• libsodium 1.0.13 -> 1.0.15
• pango 1.40.11 -> 1.41.0
• pexpect 4.2.1 -> 4.3.1
• pycairo 1.13.3 -> 1.15.4
• terminado 0.6 -> 0.8.1
Updated:
• cairo 1.14.10 -> 1.14.12
• dbus 1.10.22 -> 1.12.2
• expat 2.2.4 -> 2.2.5


• gstreamer 1.12.2 -> 1.12.4
• harfbuzz 1.5.0 -> 1.7.4
• jupyterlab 0.27.0 -> 0.31.5
• libsodium 1.0.13 -> 1.0.15
• pango 1.40.11 -> 1.41.0
• pexpect 4.2.1 -> 4.3.1
• pycairo 1.13.3 -> 1.15.4
• terminado 0.6 -> 0.8.1
Changes for linux-ppc64le
Updated:
• asn1crypto 0.22.0 -> 0.23.0
• astroid 1.5.3 -> 1.6.1
• astropy 2.0.1 -> 2.0.3
• bleach 1.5.0 -> 2.1.2
• bokeh 0.12.7 -> 0.12.13
• cairo 1.14.8 -> 1.14.10
• certifi 2016.2.28 -> 2018.1.18
• cffi 1.10.0 -> 1.11.2
• cloudpickle 0.4.0 -> 0.5.2
• curl 7.52.1 -> 7.55.1
• cython 0.26 -> 0.27.3
• dask 0.15.2 -> 0.16.0
• distributed 1.18.1 -> 1.20.2
• expat 2.1.0 -> 2.2.5
• filelock 2.0.7 -> 2.0.13
• fontconfig 2.12.1 -> 2.12.4
• freetype 2.5.5 -> 2.8
• futures 3.1.1 -> 3.2.0
• glob2 0.5 -> 0.6
• h5py 2.7.0 -> 2.7.1
• hdf5 1.8.17 -> 1.10.1

• html5lib 0.9999999 -> 1.0.1

• ipykernel 4.6.1 -> 4.8.0
• ipython 5.3.0 -> 5.4.1
• ipython 6.1.0 -> 6.2.1
• ipywidgets 6.0.0 -> 7.1.1
• jedi 0.10.2 -> 0.11.0
• jinja2 2.9.6 -> 2.10
• jupyter_core 4.3.0 -> 4.4.0
• libpng 1.6.30 -> 1.6.32
• libsodium 1.0.10 -> 1.0.15
• libtiff 4.0.6 -> 4.0.9
• lxml 3.7.3 -> 4.1.1
• matplotlib 2.0.2 -> 2.1.2
• mistune 0.7.4 -> 0.8.1
• mpmath 0.19 -> 1.0.0
• nbconvert 5.2.1 -> 5.3.1
• networkx 1.11 -> 2.1
• nltk 3.2.4 -> 3.2.5
• notebook 5.0.0 -> 5.4.0
• numexpr 2.6.2 -> 2.6.4
• numpy 1.13.1 -> 1.13.3
• olefile 0.44 -> 0.45.1
• openblas 0.2.19 -> 0.2.20
• openpyxl 2.4.8 -> 2.4.10
• openssl 1.0.2l -> 1.0.2n
• pandas 0.20.3 -> 0.22.0
• path.py 10.3.1 -> 10.5
• pcre 8.39 -> 8.41
• pexpect 4.2.1 -> 4.3.0
• pillow 4.2.1 -> 5.0.0
• psutil 5.2.2 -> 5.4.1
• py 1.4.34 -> 1.5.2
• pycairo 1.10.0 -> 1.13.3
• pycosat 0.6.2 -> 0.6.3
• pylint 1.7.2 -> 1.8.2

• pyodbc 4.0.16 -> 4.0.22

• pyopenssl 17.0.0 -> 17.5.0
• pytest 3.2.1 -> 3.2.5
• python 2.7.13 -> 2.7.14
• python 3.6.2 -> 3.6.4
• pytz 2017.2 -> 2017.3
• pyzmq 16.0.2 -> 16.0.3
• requests 2.14.2 -> 2.18.4
• ruamel_yaml 0.11.14 -> 0.15.35
• scandir 1.5 -> 1.6
• scikit-image 0.13.0 -> 0.13.1
• scikit-learn 0.19.0 -> 0.19.1
• scipy 0.19.1 -> 1.0.0
• seaborn 0.8 -> 0.8.1
• setuptools 36.4.0 -> 36.5.0
• six 1.10.0 -> 1.11.0
• sqlalchemy 1.1.13 -> 1.2.1
• sqlite 3.13.0 -> 3.21.0
• terminado 0.6 -> 0.8.1
• tk 8.5.18 -> 8.6.7
• wheel 0.29.0 -> 0.30.0
• xlsxwriter 0.9.8 -> 1.0.2
• yaml 0.1.6 -> 0.1.7
• zeromq 4.1.5 -> 4.2.2
• zict 0.1.2 -> 0.1.3
Added:
• backports.functools_lru_cache 1.4
• bzip2 1.0.6
• conda 4.4.9
• conda-env 2.6.0
• conda-verify 3.0.0

• glib 2.53.6
• gmp 6.1.2
• gmpy2 2.0.8
• icu 58.2
• imageio 2.2.0
• libedit 3.1.20170329
• libgcc-ng 7.2.0
• libssh2 1.8.0
• libxcb 1.12
• lzo 2.10
• mccabe 0.6.1
• mpc 1.0.3
• mpfr 3.1.5
• ncurses 6.0
• pandoc 2.0.0.1
• parso 0.1.1
• pysocks 1.6.7
• readline 7.0
• typing 3.6.2
• urllib3 1.22
Removed:
• functools_lru_cache
• libgfortran
• libiconv
Anaconda 5.0.1 (Oct 25, 2017)
The changes detailed here are based on an upgrade from Anaconda 5.0.0.
• R has been updated to version 3.4.2. All R packages (including RStudio) have been rebuilt to be compatible
with the new Anaconda 5.0 compilers.
• Updated many packages, including Python, Numpy, Spyder, Navigator, and Bokeh.

• The MKL library load path has been modified to address issue for Julia users.
• Fixed an OpenSSL issue with WSL on Windows.
• Fixed Anaconda Installer Configuration (AIC) feature for Unix installers.
• Re-enabled spaces in installation paths on Windows (temporarily disabled in 5.0.0).
Updated:
• bokeh 0.12.7 -> 0.12.10
• conda 4.3.27 -> 4.3.30
• conda-build 3.0.22 -> 3.0.27
• dask 0.15.2 -> 0.15.3
• dask-core 0.15.2 -> 0.15.3
• distributed 1.18.3 -> 1.19.1
• lxml 3.8.0 -> 4.1.0
• matplotlib 2.0.2 -> 2.1.0
• networkx 1.11 -> 2.0
• numpy 1.13.1 -> 1.13.3
• psutil 5.2.2 -> 5.4.0
• pyflakes 1.5.0 -> 1.6.0
• pylint 1.7.2 -> 1.7.4
• python 2.7.13 -> 2.7.14
• python 3.6.2 -> 3.6.3
• scandir 1.5 -> 1.6
• scikit-learn 0.19.0 -> 0.19.1
• six 1.10.0 -> 1.11.0
• spyder 3.2.3 -> 3.2.4
• xlsxwriter 0.9.8 -> 1.0.2
• zict 0.1.2 -> 0.1.3
Updated:
• menuinst 1.4.8 -> 1.4.10
Added:
• lzo 2.10

Updated:
• menuinst 1.4.8 -> 1.4.10
Added:
• lzo 2.10
More changes specific to macOS-64
Added:
• bzip2 1.0.6
• lzo 2.10
Added:
• bzip2 1.0.6
Added:
• bzip2 1.0.6
Anaconda 5.0.0.1 (Oct 2, 2017)
• Fixes Python & C compiler fallback path for all cases on x86/x86_64 Linux. Without this fix, people were
required to use our new compilers, which is not something we want to enforce at this time. This was affecting
travis-ci builds and pip installs of packages that require compilation for extensions.
What’s new in Anaconda 5.0?
Anaconda 5.0 was released on Sept 26, 2017.

• Over 100 packages updated and added. MKL is updated to 2018.0.0. JupyterLab alpha preview 0.27.0 is
included.
• All new compilers on macOS and Linux, giving substantial security and performance improvements.
• Where possible, all build recipes use conda-forge as a base, using https://github.com/AnacondaRecipes .
• A new channel, pkgs/main, has been added to defaults. The new channel is given top priority within
defaults and holds packages built with the new compiler stack.
• Continuum Analytics has been renamed to Anaconda, Inc. See this blog post for more.
• Spaces are no longer allowed in the installation path on Windows.
• Transitioned to more flexible dependency pinning of numpy packages, giving wider ranges of compatibility.

Updated:
• astroid 1.4.9 -> 1.5.3
• astropy 1.3.2 -> 2.0.2
• babel 2.4.0 -> 2.5.0
• blaze 0.10.1 -> 0.11.3
• bleach 1.5.0 -> 2.0.0
• bokeh 0.12.5 -> 0.12.7
• boto 2.46.1 -> 2.48.0
• chardet 3.0.3 -> 3.0.4
• cloudpickle 0.2.2 -> 0.4.0
• conda 4.3.21 -> 4.3.27
• curl 7.52.1 -> 7.55.1
• cython 0.25.2 -> 0.26.1
• dask 0.14.3 -> 0.15.2
• decorator 4.0.11 -> 4.1.2
• distributed 1.16.3 -> 1.18.3
• docutils 0.13.1 -> 0.14
• entrypoints 0.2.2 -> 0.2.3
• flask-cors 3.0.2 -> 3.0.3
• freetype 2.5.5 -> 2.8
• gevent 1.2.1 -> 1.2.2
• html5lib 0.999 -> 0.999999999
• idna 2.5 -> 2.6
• ipywidgets 6.0.0 -> 7.0.0
• isort 4.2.5 -> 4.2.15
• libpng 1.6.27 -> 1.6.32
• libtiff 4.0.6 -> 4.0.8
• llvmlite 0.18.0 -> 0.20.0

• lxml 3.7.3 -> 3.8.0

• markupsafe 0.23 -> 1.0
• mkl 2017.0.1 -> 2018.0.0
• nbconvert 5.1.1 -> 5.3.1
• nbformat 4.3.0 -> 4.4.0
• nltk 3.2.3 -> 3.2.4
• numba 0.33.0 -> 0.35.0
• numpy 1.12.1 -> 1.13.1
• numpydoc 0.6.0 -> 0.7.0
• odo 0.5.0 -> 0.5.1
• openpyxl 2.4.7 -> 2.4.8
• pandas 0.20.1 -> 0.20.3
• pathlib2 2.2.1 -> 2.3.0
• pillow 4.1.1 -> 4.2.1
• prompt_toolkit 1.0.14 -> 1.0.15
• py 1.4.33 -> 1.4.34
• pycparser 2.17 -> 2.18
• pylint 1.6.4 -> 1.7.2
• pyodbc 4.0.16 -> 4.0.17
• pyopenssl 17.0.0 -> 17.2.0
• pyparsing 2.1.4 -> 2.2.0
• pytest 3.0.7 -> 3.2.1
• qtconsole 4.3.0 -> 4.3.1
• qtpy 1.2.1 -> 1.3.1
• requests 2.14.2 -> 2.18.4
• rope 0.9.4 -> 0.10.5
• scikit-learn 0.18.1 -> 0.19.0
• scipy 0.19.0 -> 0.19.1
• seaborn 0.7.1 -> 0.8.0
• setuptools 27.2.0 -> 36.5.0
• sip 4.18 -> 4.18.1
• sphinx 1.5.6 -> 1.6.3
• spyder 3.1.4 -> 3.2.3
• sqlalchemy 1.1.9 -> 1.1.13

• sympy 1.0 -> 1.1.1

• testpath 0.3 -> 0.3.1
• tk 8.5.18 -> 8.6.7
• tornado 4.5.1 -> 4.5.2
• wrapt 1.10.10 -> 1.10.11
• xlrd 1.0.0 -> 1.1.0
• xlsxwriter 0.9.6 -> 0.9.8
• zlib 1.2.8 -> 1.2.11
Added:
• bkcharts 0.2
• certifi 2017.7.27.1
• filelock 2.0.12
• glob2 0.5
• imageio 2.2.0
• intel-openmp 2018.0.0
• jupyterlab_launcher 0.4.0
• libssh2 1.8.0
• mccabe 0.6.1
• pkginfo 1.4.1
• pysocks 1.6.7
• typing 3.6.2
• urllib3 1.22
Removed:
• _license

Updated:
• hdf5 1.8.15.1 -> 1.10.1
• icu 57.1 -> 58.2
• ipython 5.3.0 -> 5.4.1
• ipython 5.3.0 -> 6.1.0
• menuinst 1.4.7 -> 1.4.8
• pytables 3.2.2 -> 3.4.2
• python 3.5.3 -> 3.5.4
• python 3.6.1 -> 3.6.2
• pywin32 220 -> 221
• vs2008_runtime 9.00.30729.5054 -> 9.00.30729.1
• xlwings 0.10.4 -> 0.11.4
• xlwt 1.2.0 -> 1.3.0
Added:
• cachecontrol 0.12.3
• distlib 0.2.5
• icc_rt 2017.0.4
• libiconv 1.15
• libxml2 2.9.4
• libxslt 1.1.29
• lockfile 0.12.2
• pandoc 1.19.2.1
• progress 1.3
• sqlite 3.20.1
• vc 14
• vc 9
• win_inet_pton 1.0.1
• wincertstore 0.2
• yaml 0.1.7

Updated:
• hdf5 1.8.15.1 -> 1.10.1
• icu 57.1 -> 58.2
• ipython 5.3.0 -> 5.4.1
• ipython 5.3.0 -> 6.1.0
• menuinst 1.4.7 -> 1.4.8
• pytables 3.2.2 -> 3.4.2
• python 3.5.3 -> 3.5.4
• python 3.6.1 -> 3.6.2
• pywin32 220 -> 221
• vs2008_runtime 9.00.30729.5054 -> 9.00.30729.1
• xlwings 0.10.4 -> 0.11.4
• xlwt 1.2.0 -> 1.3.0
Added:
• cachecontrol 0.12.3
• distlib 0.2.5
• icc_rt 2017.0.4
• libiconv 1.15
• libxml2 2.9.4
• libxslt 1.1.29
• lockfile 0.12.2
• pandoc 1.19.2.1
• progress 1.3
• sqlite 3.20.1
• vc 14
• vc 9
• win_inet_pton 1.0.1
• wincertstore 0.2
• yaml 0.1.7

More changes specific to macOS-64
Updated:
• hdf5 1.8.17 -> 1.10.1
• icu 54.1 -> 58.2
• ipython 5.3.0 -> 5.4.1
• ipython 5.3.0 -> 6.1.0
• libiconv 1.14 -> 1.15
• ptyprocess 0.5.1 -> 0.5.2
• pytables 3.3.0 -> 3.4.2
• python 3.5.3 -> 3.5.4
• python 3.6.1 -> 3.6.2
• python.app 1.2 -> 2
• readline 6.2 -> 7.0
• sqlite 3.13.0 -> 3.20.1
• xlwings 0.10.4 -> 0.11.4
• xz 5.2.2 -> 5.2.3
• yaml 0.1.6 -> 0.1.7
Added:
• dbus 1.10.22
• expat 2.2.4
• gettext 0.19.8.1
• glib 2.53.6
• gmp 6.1.2
• gmpy2 2.0.8
• libcxx 4.0.1
• libcxxabi 4.0.1
• libedit 3.1
• libffi 3.2.1
• libgfortran 3.0.1
• mpc 1.0.3
• mpfr 3.1.5
• ncurses 6.0
• pandoc 1.19.2.1

• pcre 8.41
• zeromq 4.2.2
Updated:
• cairo 1.14.8 -> 1.14.10
• dbus 1.10.10 -> 1.10.22
• expat 2.1.0 -> 2.2.4
• fontconfig 2.12.1 -> 2.12.4
• glib 2.50.2 -> 2.53.6
• gstreamer 1.8.0 -> 1.12.2
• harfbuzz 0.9.39 -> 1.5.0
• hdf5 1.8.17 -> 1.10.1
• icu 54.1 -> 58.2
• ipython 5.3.0 -> 5.4.1
• ipython 5.3.0 -> 6.1.0
• libsodium 1.0.10 -> 1.0.13
• libtool 2.4.2 -> 2.4.6
• pango 1.40.3 -> 1.40.11
• pcre 8.39 -> 8.41
• ptyprocess 0.5.1 -> 0.5.2
• pycairo 1.10.0 -> 1.13.3
• pytables 3.3.0 -> 3.4.2
• python 3.5.3 -> 3.5.4
• python 3.6.1 -> 3.6.2
• readline 6.2 -> 7.0
• sqlite 3.13.0 -> 3.20.1
• xlwt 1.2.0 -> 1.3.0
• xz 5.2.2 -> 5.2.3
• yaml 0.1.6 -> 0.1.7
• zeromq 4.1.5 -> 4.2.2
Added:
• gmp 6.1.2

• gmpy2 2.0.8
• libedit 3.1
• libgcc-ng 7.2.0
• lzo 2.10
• mpc 1.0.3
• mpfr 3.1.5
• ncurses 6.0
• pandoc 1.19.2.1
• patchelf 0.9
Removed:
• libgcc
• libgfortran
• libiconv
Updated:
• cairo 1.14.8 -> 1.14.10
• dbus 1.10.10 -> 1.10.22
• expat 2.1.0 -> 2.2.4
• fontconfig 2.12.1 -> 2.12.4
• glib 2.50.2 -> 2.53.6
• gstreamer 1.8.0 -> 1.12.2
• harfbuzz 0.9.39 -> 1.5.0
• hdf5 1.8.17 -> 1.10.1
• icu 54.1 -> 58.2
• ipython 5.3.0 -> 5.4.1
• ipython 5.3.0 -> 6.1.0
• libsodium 1.0.10 -> 1.0.13
• libtool 2.4.2 -> 2.4.6
• pango 1.40.3 -> 1.40.11
• pcre 8.39 -> 8.41
• ptyprocess 0.5.1 -> 0.5.2

• pycairo 1.10.0 -> 1.13.3

• pytables 3.3.0 -> 3.4.2
• python 3.5.3 -> 3.5.4
• python 3.6.1 -> 3.6.2
• readline 6.2 -> 7.0
• sqlite 3.13.0 -> 3.20.1
• xlwt 1.2.0 -> 1.3.0
• xz 5.2.2 -> 5.2.3
• yaml 0.1.6 -> 0.1.7
• zeromq 4.1.5 -> 4.2.2
Added:
• gmp 6.1.2
• gmpy2 2.0.8
• libedit 3.1
• libgcc-ng 7.2.0
• lzo 2.10
• mpc 1.0.3
• mpfr 3.1.5
• ncurses 6.0
• pandoc 1.15.0.6
• patchelf 0.9
Removed:
• libgcc
• libgfortran
• libiconv
Changes for linux-ppc64le
Updated:
• astroid 1.4.9 -> 1.5.3
• astropy 1.3.2 -> 2.0.1
• babel 2.4.0 -> 2.5.0

• bokeh 0.12.5 -> 0.12.7

• boto 2.46.1 -> 2.48.0
• chardet 3.0.3 -> 3.0.4
• cloudpickle 0.2.2 -> 0.4.0
• cython 0.25.2 -> 0.26
• dask 0.14.3 -> 0.15.2
• decorator 4.0.11 -> 4.1.2
• distributed 1.16.3 -> 1.18.1
• docutils 0.13.1 -> 0.14
• entrypoints 0.2.2 -> 0.2.3
• flask-cors 3.0.2 -> 3.0.3
• gevent 1.2.1 -> 1.2.2
• html5lib 0.999 -> 0.9999999
• idna 2.5 -> 2.6
• ipython 5.3.0 -> 6.1.0
• isort 4.2.5 -> 4.2.15
• libpng 1.6.27 -> 1.6.30
• markupsafe 0.23 -> 1.0
• nbconvert 5.1.1 -> 5.2.1
• nbformat 4.3.0 -> 4.4.0
• nltk 3.2.3 -> 3.2.4
• numpy 1.12.1 -> 1.13.1
• numpydoc 0.6.0 -> 0.7.0
• odo 0.5.0 -> 0.5.1
• openpyxl 2.4.7 -> 2.4.8
• pandas 0.20.1 -> 0.20.3
• pathlib2 2.2.1 -> 2.3.0
• pillow 4.1.1 -> 4.2.1
• prompt_toolkit 1.0.14 -> 1.0.15
• ptyprocess 0.5.1 -> 0.5.2
• py 1.4.33 -> 1.4.34
• pycparser 2.17 -> 2.18

• pyflakes 1.5.0 -> 1.6.0

• pylint 1.6.4 -> 1.7.2
• pyparsing 2.1.4 -> 2.2.0
• pytables 3.2.2 -> 3.4.2
• pytest 3.0.7 -> 3.2.1
• python 3.5.3 -> 3.5.4
• python 3.6.1 -> 3.6.2
• scikit-learn 0.18.1 -> 0.19.0
• scipy 0.19.0 -> 0.19.1
• seaborn 0.7.1 -> 0.8
• setuptools 27.2.0 -> 36.4.0
• sphinx 1.5.6 -> 1.6.3
• sqlalchemy 1.1.9 -> 1.1.13
• sympy 1.0 -> 1.1.1
• testpath 0.3 -> 0.3.1
• tornado 4.5.1 -> 4.5.2
• wrapt 1.10.10 -> 1.10.11
• xlrd 1.0.0 -> 1.1.0
• xlsxwriter 0.9.6 -> 0.9.8
• xlwt 1.2.0 -> 1.3.0
• xz 5.2.2 -> 5.2.3
• zlib 1.2.8 -> 1.2.11
Added:
• bkcharts 0.2
• certifi 2016.2.28
• filelock 2.0.7
• functools_lru_cache 1.4
• glob2 0.5
• jedi 0.10.2
• patchelf 0.9
• pkginfo 1.4.1

• typing 3.6.2
What’s new in Anaconda 4.4?
Anaconda 4.4 was released on May 31, 2017 and includes the following:
• Support added for the “ppc64le” machine type, for the POWER8 LE architecture used by IBM Power Systems
and OpenPOWER servers.
• On Windows, the PATH environment variable is no longer changed by default, as this can cause trouble with
other software. Instead, use Anaconda Navigator or the Anaconda Prompt in the Start Menu under “Anaconda”
to use Anaconda software. If a user does choose to change the PATH variable, Anaconda is no longer appended
to the PATH in system mode, and is now always added to the front of PATH in either system mode or user mode.
• Python 3.5 is updated from 3.5.2 to 3.5.3 and Python 3.6 from 3.6.0 to 3.6.1. Anaconda 4.4 supports Python
2.7, 3.5, and 3.6. Anaconda 4.3 was the last release to support Python 3.4.
• Minimum supported version of CentOS is now CentOS 6. Anaconda 4.3 was the last release to support CentOS
5.
• Applied pycrypto patch for CVE-2013-7439.
• Improved cp_acp support for install paths with non-ASCII characters on Windows.
• conda is updated from 4.3.14 to 4.3.21.
• Navigator is updated from 1.5.0 to 1.6.2.
• Project is updated from 0.4.1 to 0.6.0.
• Added distributed and pyodbc to the installers.
• Updated EULA.
• Conda packages with “mkl” in the package name now contain a file license.txt with a copy of the Intel Simplified
Software License that applies to the Intel Math Kernel Library (MKL).
• Over 90 packages are updated or added.
2017-05-31 4.4.0:
Highlights:
• add support for the ppc64le (POWER8 LE used by IBM Power Systems and OpenPOWER servers) ma-
chine types
Other changes:
• On Windows, the PATH environment variable is no longer changed by default, as this can cause trouble
with other software. The recommended approach is to instead use Anaconda Navigator or the Anaconda
Prompt (located in the Start Menu under “Anaconda”) when you wish to use Anaconda software. Also,
Anaconda will always be added to the front of PATH, for either system or user mode. (Previously it was
appended to the system path.)
• improve cp_acp support for install path on Windows
• updated 80 packages in the installer (and their dependencies)
• added distributed and pyodbc to the installers

• apply pycrypto patch for CVE-2013-7439

• end support for CentOS 5. CentOS 6 is now the minimum supported version.
Updates:
• alabaster from 0.7.9 to 0.7.10
• anaconda-client from 1.6.0 to 1.6.3
• anaconda-navigator from 1.5.0 to 1.6.2
• anaconda-project from 0.4.1 to 0.6.0
• astropy from 1.3 to 1.3.2
• babel from 2.3.4 to 2.4.0
• beautifulsoup4 from 4.5.3 to 4.6.0
• bokeh from 0.12.4 to 0.12.5
• boto from 2.45.0 to 2.46.1
• bottleneck from 1.2.0 to 1.2.1
• cffi from 1.9.1 to 1.10.0
• chardet from 2.3.0 to 3.0.3
• colorama from 0.3.7 to 0.3.9
• conda from 4.3.14 to 4.3.21
• contextlib2 from 0.5.4 to 0.5.5
• cryptography from 1.7.1 to 1.8.1
• dask from 0.13.0 to 0.14.3
• flask from 0.12 to 0.12.2
• futures from 3.0.5 to 3.1.1
• greenlet from 0.4.11 to 0.4.12
• h5py from 2.6.0 to 2.7.0
• hdf5 from 1.8.15.1 to 1.8.17
• idna from 2.2 to 2.5
• ipykernel from 4.5.2 to 4.6.1
• ipython from 5.1.0 to 5.3.0
• ipython_genutils from 0.1.0 to 0.2.0
• ipywidgets from 5.2.2 to 6.0.0
• jedi from 0.9.0 to 0.10.2
• jinja2 from 2.9.4 to 2.9.6
• jsonschema from 2.5.1 to 2.6.0
• jupyter_client from 4.4.0 to 5.0.1
• jupyter_console from 5.0.0 to 5.1.0
• jupyter_core from 4.2.1 to 4.3.0

• llvmlite from 0.15.0 to 0.18.0

• lxml from 3.7.2 to 3.7.3
• matplotlib from 2.0.0 to 2.0.2
• menuinst from 1.4.4 to 1.4.7
• mistune from 0.7.3 to 0.7.4
• nbconvert from 4.2.0 to 5.1.1
• nbformat from 4.2.0 to 4.3.0
• nltk from 3.2.2 to 3.2.3
• notebook from 4.3.1 to 5.0.0
• numba from 0.30.1 to 0.33.0
• numpy from 1.11.3 to 1.12.1
• numexpr from 2.6.1 to 2.6.2
• openpyxl from 2.4.1 to 2.4.7
• openssl from 1.0.2k to 1.0.2l
• pandas from 0.19.2 to 0.20.1
• partd from 0.3.7 to 0.3.8
• path.py from 10.0 to 10.3.1
• pathlib2 from 2.2.0 to 2.2.1
• pillow from 4.0.0 to 4.1.1
• ply from 3.9 to 3.10
• prompt_toolkit from 1.0.9 to 1.0.14
• psutil from 5.0.1 to 5.2.2
• py from 1.4.32 to 1.4.33
• pycosat from 0.6.1 to 0.6.2
• pygments from 2.1.3 to 2.2.0
• pyopenssl from 16.2.0 to 17.0.0
• pytables from 3.2.2 to 3.3.0
• pytest from 3.0.5 to 3.0.7
• python 3.5 from 3.5.2 to 3.5.3
• python 3.6 from 3.6.0 to 3.6.1
• pytz from 2016.10 to 2017.2
• qtawesome from 0.4.3 to 0.4.4
• qtconsole from 4.2.1 to 4.3.0
• requests from 2.12.4 to 2.14.2
• scandir from 1.4 to 1.5
• scikit-image from 0.12.3 to 0.13.0

• scipy from 0.18.1 to 0.19.0

• sphinx from 1.5.1 to 1.5.6
• spyder from 3.1.2 to 3.1.4
• sqlalchemy from 1.1.5 to 1.1.9
• statsmodels from 0.6.1 to 0.8.0
• tornado from 4.4.2 to 4.5.1
• traitlets from 4.3.1 to 4.3.2
• werkzeug from 0.11.15 to 0.12.2
• widgetsnbextension from 1.2.6 to 2.0.0
• wrapt from 1.10.8 to 1.10.10
• xlwings from 0.10.2 to 0.10.4
Added:
• bleach 1.5.0
• html5lib 0.999
• navigator-updater 0.1.0
• olefile 0.44
• packaging 16.8
• pyodbc 4.0.16
• tblib 1.3.2
• testpath 0.3
• zict 0.1.2
Removed (from installers only):
• argcomplete
• chest
• configobj
• dill
• pyasn1
• redis
• redis-py

• sockjs-tornado
2017-03-10 4.3.1:
This patch release fixes problems with Anaconda Navigator not starting correctly on some versions of Mac OS X when
using the GUI installers.
Fixes:
• removed creation of ~/.continuum folder during install process on all platforms
• fixed ‘//’ showing up in prefix when installing system wide on Mac OS using the GUI installer
• fixed OpenSSL not being installable into a path which contains spaces
• allow Unicode characters in install path on Windows (cp_acp fix)
Updates:
• conda from 4.3.8 to 4.3.14
Added:
2017-02-03 4.3.0.1:
In this “mirco” patch release, we fixed a problem with the Windows installers which was causing problems with Qt
applications when the install prefix exceeds 30 characters. No new Anaconda meta-packages correspond to this release
(only new Windows installers).
2017-01-31 4.3.0:
Highlights:
• The Anaconda3 installers are based on Python 3.6. Anaconda 4.3 supports Python 2.7, 3.4, 3.5 and 3.6.
Anaconda 4.3 will be the last release which supports Python 3.4. We will discontinue regular Python 3.4
package updates in the next release.
• The Intel Math Kernel Library (MKL) is updated from 11.3.3 to 2017.0.1.
• Over 90 packages are updated.
• seaborn is now installed by default.
Other changes:
• Updates jpeg and libpng to increase compatibility with conda-forge.
• Warns about possible errors if installing on Windows into an install path with spaces, and does not allow
installation if the install path contains unicode characters.
• Fixes many Windows menu uninstallation issues and some other often reported uninstallation issues on
Windows.
• Anaconda 4.2 is the last release that supports macOS 10.7 and macOS 10.8. Anaconda 4.3 supports macOS
versions from 10.9 through the current version 10.12.

• conda-build, anaconda-clean and the Jupyter Notebook extensions are no longer installed by default but
can be installed with a single conda command.
Updates:
• astroid from 1.4.7 to 1.4.9
• astropy from 1.2.1 to 1.3
• backports_abc from 0.4 to 0.5
• bokeh from 0.12.2 to 0.12.4
• boto from 2.42.0 to 2.45.0
• cairo from 1.12.18 to 1.14.8
• cffi from 1.7.0 to 1.9.1
• click from 6.6 to 6.7
• cloudpickle from 0.2.1 to 0.2.2
• conda from 4.2.9 to 4.3.8
• contextlib2 from 0.5.3 to 0.5.4
• cryptography from 1.5 to 1.7.1
• curl from 7.49.0 to 7.52.1
• cython from 0.24.1 to 0.25.2
• cytoolz from 0.8.0 to 0.8.2
• dask from 0.11.0 to 0.13.0
• datashape from 0.5.2 to 0.5.4
• decorator from 4.0.10 to 4.0.11
• docutils from 0.12 to 0.13.1
• flask from 0.11.1 to 0.12
• flask-cors from 2.1.2 to 3.0.2
• fontconfig from 2.11.1 to 2.12.1
• gevent from 1.1.2 to 1.2.1
• glib from 2.43.0 to 2.50.2
• hdf5 from 1.8.15.1 to 1.8.17
• ipaddress from 1.0.16 to 1.0.18

• jdcal from 1.2 to 1.3

• jinja2 from 2.8 to 2.9.4
• jpeg from 8d to 9b
• lazy-object-proxy from 1.2.1 to 1.2.2
• libpng from 1.6.22 to 1.6.27
• libxml2 from 2.9.2 to 2.9.4
• libxslt from 1.1.28 to 1.1.29
• lxml from 3.6.4 to 3.7.2
• mkl from 11.3.3 to 2017.0.1
• multipledispatch from 0.4.8 to 0.4.9
• nltk from 3.2.1 to 3.2.2
• numba from 0.28.1 to 0.30.1
• numpy from 1.11.1 to 1.11.3
• openssl from 1.0.2j to 1.0.2k
• path.py from 8.2.1 to 10.0
• pathlib2 from 2.1.0 to 2.2.0
• pexpect from 4.0.1 to 4.2.1
• pip from 8.1.2 to 9.0.1
• pixman from 0.32.6 to 0.34.0
• prompt_toolkit from 1.0.3 to 1.0.9
• py from 1.4.31 to 1.4.32
• pycparser from 2.14 to 2.17
• pyflakes from 1.3.0 to 1.5.0
• pylint from 1.5.4 to 1.6.4


• python from 2.7.12 to 2.7.13
• python-dateutil from 2.5.3 to 2.6.0
• pytz from 2016.6.1 to 2016.10
• pyzmq from 15.4.0 to 16.0.2
• qt from 5.6.0 to 5.6.2
• qtawesome from 0.3.3 to 0.4.3
• qtpy from 1.1.2 to 1.2.1
• scikit-learn from 0.17.1 to 0.18.1
• toolz from 0.8.0 to 0.8.2
• wrapt from 1.10.6 to 1.10.8
• xlsxwriter from 0.9.3 to 0.9.6
• xlwt from 1.1.2 to 1.2.0
• zeromq from 4.1.4 to 4.1.5
Added:
• chardet 2.3.0
• isort 4.2.5
• libiconv 1.14
• numpydoc 0.6.0
• pcre 8.39 (on Linux)
• scandir 1.4
• seaborn 0.7.1
• subprocess32 3.2.7 (Python 2)
Removed (from installer only):
• anaconda-clean
• dynd-python
• filelock

• libdynd
• nb_anacondacloud
• nb_conda
• nb_conda_kernels
• nbpresent
• patchelf
• pkginfo
2016-09-28 4.2.0:
Highlights:
• updated Qt from major version 4 to 5
• updated IPython from 4.2 to 5.1
• added anaconda-clean, a tool for cleaning up Anaconda related configuration files and directories
Fixes:
• fixed Windows Outlook crash in silent install mode
• updated OpenSSL to 1.0.2j which contains important security fixes
Updates:
• bokeh from 0.12.0 to 0.12.2
• boto from 2.40.0 to 2.42.0
• cffi from 1.6.0 to 1.7.0
• conda-build form 1.21.2 to 2.0.2
• configparser from 3.5.0b2 to 3.5.0
• cryptography from 1.4 to 1.5
• cython from 0.24 to 0.24.1
• dask from 0.10.0 to 0.11.0
• hdf5 from 1.8.15.1 to 1.8.17


• lxml from 3.6.0 to 3.6.4
• nb_anacondacloud from 1.1.0 to 1.2.0
• nb_conda from 1.1.0 to 2.0.0
• nb_conda_kernels from 1.0.3 to 2.0.0
• numba from 0.26.0 to 0.28.1
• openssl from 1.0.2h to 1.0.2j
• pickleshare from 0.7.2 to 0.7.4
• pyqt from 4.11.4 to 5.6.0
• pytables from 3.2.2 to 3.2.3.1
• pytz from 2016.4 to 2016.6.1
• pyyaml from 3.11 to 3.12
• pyzmq from 15.2.0 to 15.4.0
• qt from 4.8.7 to 5.6.0
• qtpy from 1.0.2 to 1.1.2
• ruamel_yaml from 0.11.7 to 0.11.14
• scipy from 0.17.1 to 0.18.1
• setuptools from 23.0.0 to 27.2.0
• sip from 4.16.9 to 4.18

• tornado from 4.3 to 4.4.1

Added:
• anaconda-clean 1.0.0
• astroid 1.4.7
• dbus 1.10.10 (Linux)
• expat 2.1.0 (Linux)
• filelock 2.0.6
• glib 2.43.0 (Linux)
• gst-plugins-base 1.8.0 (Linux)
• gstreamer 1.8.0 (Linux)
• harfbuzz 0.9.39 (Linux)
• icu 57.1
• libgcc 4.8.5 (Linux)
• libxcb 1.12 (Linux)
• pkginfo 1.3.2
• pylint 1.5.4
• qtawesome 0.3.3
• wcwidth 0.1.7
• win_unicode_console 0.5 (Windows)
• wrapt 1.10.6
Removed (from installer only):
• pyreadline
• sphinx_rtd_theme
• conda-env (now part of conda itself)
2016-07-08 4.1.1:
Fixes:
• Running the shell installer on some older system, would print out (harmless) tracebacks during the install
process, see: https://github.com/ContinuumIO/anaconda-issues/issues/860

• We added blaze 0.10.1 back into the installer, which was accidentally missing in 4.1.0
Updates:
• bokeh from 0.11.1 to 0.12.0
• conda-build from 1.21.2 to 1.21.3
• numpy from 1.11.0 to 1.11.1
• Python 2.7 from 2.7.11 to 2.7.12
• Python 3.4 from 3.4.4 to 3.4.5
• Python 3.5 from 3.5.1 to 3.5.2
2016-06-28 4.1.0:
Highlights:
• added Jupyter Notebook Extensions
• Windows installation: silent mode fixes & now compatible with SCCM (System Center Configuration
Manager)
• updated MKL to 11.3.3, numpy to 1.11.0, as well as over 80 other updates, see below
• update Navigator from 1.1 to 1.2, in particular it no longer installs a desktop shortcut on macOS
• conda-recipes used to build the vast majority of the packages in the Anaconda installer have been published
at: https://github.com/ContinuumIO/anaconda-recipes
Updates:
• astropy from 1.1.2 to 1.2.1
• boto from 2.39.0 to 2.40.0
• cffi from 1.5.2 to 1.6.0
• cloudpickle from 0.1.1 to 0.2.1
• clyent from 1.2.1 to 1.2.2
• conda-env from 2.4.5 to 2.5.1
• cryptography from 1.3 to 1.4
• curl from 7.45.0 to 7.49.0
• cython from 0.23.4 to 0.24

• dask from 0.8.1 to 0.10.0

• dill from 0.2.4 to 0.2.5
• enum34 from 1.1.2 to 1.1.6
• flask from 0.10.1 to 0.11.1
• funcsigs from 0.4 to 1.0.2
• h5py from 2.5.0 to 2.6.0
• hdf5 from 1.8.15.1 to 1.8.16
• jsonschema from 2.4.0 to 2.5.1
• libffi from 3.0.13 to 3.2.1
• libgfortran from 3.0 to 3.0.0
• libsodium from 1.0.3 to 1.0.10
• mkl from 11.3.1 to 11.3.3
• nltk from 3.2 to 3.2.1
• numba from 0.24.0 to 0.26.0
• numexpr from 2.5 to 2.6.0
• numpy from 1.10.4 to 1.11.0
• odo from 0.4.2 to 0.5.0
• openssl from 1.0.2g to 1.0.2h
• patchelf from 0.8 to 0.9
• path.py from 8.1.2 to 8.2.1

• patsy from 0.4.0 to 0.4.1

• pickleshare from 0.5 to 0.7.2
• pip from 8.1.1 to 8.1.2
• ptyprocess from 0.5 to 0.5.1
• pycurl from 7.19.5.3 to 7.43.0
• pygments from 2.1.1 to 2.1.3
• pyparsing from 2.0.3 to 2.1.4
• pytz from 2016.2 to 2016.4
• qtpy from 1.0 to 1.0.2
• redis from 2.6.9 to 3.2.0
• redis-py from 2.10.3 to 2.10.5
• scipy from 0.17.0 to 0.17.1
• setuptools from 20.3 to 23.0.0
• sockjs-tornado from 1.0.1 to 1.0.3
• sqlite from 3.9.2 to 3.13.0
• terminado from 0.5 to 0.6
• xlrd from 0.9.4 to 1.0.0
• xlwt from 1.0.0 to 1.1.2
• xz from 5.0.5 to 5.2.2
Added:

• click 6.6
• configparser 3.5.0b2
• contextlib2 0.5.3
• entrypoints 0.2.2
• functools32 3.2.3.2
• imagesize 0.7.1
• nb_anacondacloud 1.1.0
• nb_conda 1.1.0
• nb_conda_kernels 1.0.3
• nbpresent 3.0.2
• pathlib2 2.1.0
Removed:
• conda-manager
• qtawesome
2016-03-29 4.0.0:
The reason for jumping the Anaconda version from 2.5 to 4.0 is to avoid any possible confusion with the versions of
Python included in Anaconda.
Highlights:
• this release of Anaconda includes the new Navigator, which is a graphical tool developed by Continuum
Analytics to manage conda environments, applications and much more.
Enhancements:
• much improved package resolving in the new conda 4.0
Fixes:
• updated OpenSSL to 1.0.2g which contains important security fixes
Updates:
• blaze from 0.9.0 to 0.9.1
• bokeh from 0.11.0 to 0.11.1
• cffi from 1.2.1 to 1.5.2
• conda from 3.19.1 to 4.0.5


• cryptography from 1.0.2 to 1.3
• cycler from 0.9.0 to 0.10.0
• dynd-python from 0.7.1 to 0.7.2
• libdynd from 0.7.1 to 0.7.2
• libgfortran from 1.0 to 3.0
• lxml from 3.5.0 to 3.6.0
• nltk from 3.1 to 3.2
• numba from 0.23.1 to 0.24.0
• numexpr from 2.4.6 to 2.5
• odo from 0.4.0 to 0.4.2
• openssl from 1.0.2f to 1.0.2g
• pexpect from 3.3 to 4.0.1
• pip from 8.0.2 to 8.1.1
• pygments from 2.1 to 2.1.1
• pytz from 2015.7 to 2016.2
• pywin32 from 219 to 220
• scikit-learn from 0.17 to 0.17.1
• setuptools from 19.6.2 to 20.3


• sympy from 0.7.6.1 to 1.0
• wheel from 0.26.0 to 0.29.0
Added:
• anaconda-navigator 1.1.0
• chest 0.2.3
• conda-manager 0.3.1
• dask 0.8.1
• dill 0.2.4
• flask-cors 2.1.2
• heapdict 1.0.0
• locket 0.2.0
• mpmath 0.19
• partd 0.3.2
• qtawesome 0.3.2
• qtpy 1.0
Removed (from installer only, the packages are still available):
• abstract-rendering
• gevent-websocket
• launcher
• node-webkit
2016-02-05 2.5.0:
Highlights:
• add MKL (runtime, version 11.3.1) and make it the default backend for numpy, scipy, scikit-learn and
numexpr on all platforms
Enhancements:
• added Windows debug information files, more precisely program database (.pdb files) files for Python by
default
• added NoRegistry option to Windows installers, passing /NoRegistry=1 makes the installer not touch the
registry
Fixes:

• in some cases start menu items were not created on Windows, due to a race condition, which we fixed in
menuinst
• fixed the -f option of the Unix bash installers
• updated OpenSSL to 1.0.2f which contains important security fixes
Updates:
• blaze-core from 0.8.3 to 0.9.0
• bokeh from 0.10.0 to 0.11.0
• boto from 2.38.0 to 2.39.0
• conda from 3.18.8 to 3.19.1
• dynd-python from 0.7.0 to 0.7.1
• enum34 from 1.0.4 to 1.1.2
• gevent-websocket from 0.9.3 to 0.9.5
• jdcal from 1.0 to 1.2
• libdynd from 0.7.0 to 0.7.1
• lxml from 3.4.4 to 3.5.0
• networkx from 1.10 to 1.11
• numba from 0.22.1 to 0.23.1

• numpy from 1.10.1 to 1.10.4

• odo from 0.3.4 to 0.4.0
• openssl from 1.0.2d to 1.0.2f
• patchelf from 0.6 to 0.8
• pep8 from 1.6.2 to 1.7.0
• pip from 7.1.2 to 8.0.2
• py from 1.4.30 to 1.4.31
• pycurl from 7.19.5.1 to 7.19.5.3
• pygments from 2.0.2 to 2.1
• python 3.4 from 3.4.3 to 3.4.4
• pyzmq from 14.7.0 to 15.2.0
• scipy from 0.16.0 to 0.17.0
• snowballstemmer from 1.2.0 to 1.2.1
• sphinx_rtd_theme from 0.1.7 to 0.1.9
• sqlite from 3.8.4.1 to 3.9.2
Added:
• futures 3.0.3
• mkl 11.3.1
• mkl-service 1.1.1
Removed (from installer only, the packages are still maintained and available):
• openblas 0.2.14 (Linux)
• theano 0.7.0 (Linux)
• ujson 1.33

2015-12-08 2.4.1:
Fixes:
• added missing Windows process elevation when creating menu items
• added libdynd and dynd-python, which was missing in the last release
• fixed Cython on Mac OS X reporting missing libgcc_s.10.5.dylib
• fixed default channels being shown correctly in “conda list” after installing using Anaconda installer
Updates:
• conda from 3.18.3 to 3.18.8
• conda-build 1.18.1 to 1.18.2
• numba from 0.21.0 to 0.22.1
• pixman from 0.26.2 to 0.32.6
• python 2.7 from 2.7.10 to 2.7.11
• python 3.5 from 3.5.0 to 3.5.1
• pytz from 2015.6 to 2015.7
• scikit-learn from 0.16.1 to 0.17
• setuptools from 18.4 to 18.5
• tornado from 4.2.1 to 4.3
Added:
• backports_abc 0.4
• cycler 0.9.0
• libdynd and dynd-python 0.7.0
• jbig 2.1

• pycairo 1.10.0
2015-11-02 2.4.0:
Highlights:
• add Python 3.5 support
• updated NumPy to 1.10
• added OpenBLAS support on Linux
• made drastic speed improvements to conda
• moved from IPython to Jupyter
• improved Start Menus on Windows
• updated Qt to 4.8.7 on all platforms
• updates to more than 60 other packages
Known issues:
• numba and llvmlite are missing for Python 3.5 (because they don’t support this Python version yet)
• numpy 1.10 has performance regression for record array access, see https://github.com/numpy/numpy/
issues/6467
• Python 3.5 does not work on Windows XP
Updates:
• argcomplete from 0.8.9 to 1.0.0
• babel from 1.3 to 2.1.1
• bokeh from 0.9.0 to 0.10.0
• cffi from 1.1.0 to 1.2.1
• cryptography from 0.9.1 to 1.0.2
• curl from 7.43.0 to 7.45.0
• conda from 3.14.1 to 3.18.3
• freetype from 2.5.2 to 2.5.5


• ipython-notebook from 3.2.0 to 4.0.4
• ipython-qtconsole from 3.2.0 to 4.0.1
• jedi from 0.8.1 to 0.9.0
• jinja2 from 2.7.3 to 2.8
• libsodium from 0.4.5 to 1.0.3
• libtiff from 4.0.2 to 4.0.6
• networkx from 1.9.1 to 1.10
• nltk from 3.0.3 to 3.1
• numba from 0.19.1 to 0.21.0
• numpy from 1.9.2 to 1.10.1
• odo from 0.3.2 to 0.3.4
• openssl from 1.0.1k to 1.0.2d
• pip from 7.0.3 to 7.1.2
• ptyprocess from 0.4 to 0.5
• py from 1.4.27 to 1.4.30
• pyasn1 from 0.1.7 to 0.1.9
• pyqt from 4.11.3 to 4.11.4
• pytz from 2015.4 to 2015.6
• qt from 4.8.6 to 4.8.7


• scipy from 0.15.1 to 0.16.0
• setuptools from 17.1.1 to 18.4
• sip from 4.16.5 to 4.16.9
• six from 1.9.0 to 1.10.0
• spyder from 2.3.5.2 to 2.3.7
• spyder-app from 2.3.5.2 to 2.3.7
• sympy from 0.7.6 to 0.7.6.1
• unicodecsv from 0.9.4 to 0.14.1
• xlrd from 0.9.3 to 0.9.4
Added:
• ipykernel 4.1.1
• jupyter 1.0.0
• libgfortran 1.0
• nbconvert 4.0.0
• nbformat 4.0.1
• notebook 4.0.6
• openblas 0.2.14
• patchelf 0.6
• path.py 8.1.2
• pexpect 3.3
• pickleshare 0.5
• qtconsole 4.1.0

• singledispatch 3.4.0.3
• traitlets 4.0.0
• wheel 0.26.0
• bcolz
• blz
• certifi
• dynd-python
• libdynd
• mock
• runipy
2015-07-02 2.3.0:
Highlights:
• updates to 60 packages, including Python 2.7.10 and Pandas 0.16.2
• support for signed packages in conda
Fixes:
• fixed the extra space in IPython terminal being created when typing the tab key on Linux
• added missing zope.interface.common sub-package
• fixed Sphinx package being included in Spyder package
Enhancements:
• added support for signed packages in conda
• added curl on Windows, and kerberos authentication support
• added Windows support for libnetcdf and hdf5
• split gdal into libgdal and gdal (python-bindings)
Known issues:
• when opening some HDF5 files, pytables will crash on Windows and Python 3
Updates:
• bcolz from 0.8.1 to 0.9.0
• binstar from 0.10.1 to 0.11.0
• bokeh from 0.8.1 to 0.9.0
• boto from 2.36.0 to 2.38.0

• cffi from 0.9.2 to 1.1.0

• cryptography from 0.8 to 0.9.1
• conda from 3.10.0 to 3.14.1
• curl from 7.38.0 to 7.43.0
• h5py from 2.4.0 to 2.5.0
• hdf5 from 1.8.14 to 1.8.15.1
• libxml2 from 2.9.0 to 2.9.2
• lxml from 3.4.2 to 3.4.4
• nltk from 3.0.2 to 3.0.3
• nose from 1.3.4 to 1.3.7
• numba from 0.17.0 to 0.19.1
• odo from 0.3.1 to 0.3.2
• pip from 6.0.8 to 7.0.3
• py from 1.4.26 to 1.4.27
• pycparser from 2.10 to 2.14
• pyopenssl from 0.14 to 0.15.1
• pytz from 2015.2 to 2015.4

• pyzmq from 14.5.0 to 14.7.0

• spyder from 2.3.4 to 2.3.5.2
• theano from 0.6.0 to 0.7.0
• tornado from 4.1 to 4.2
• xlwt from 0.7.5 to 1.0.0
• yaml from 0.1.4 to 0.1.6
Added to Anaconda installers:
• alabaster 0.7.3
• babel 1.3
• idna 2.0
• ipaddress 1.0.7
• sphinx_rtd_theme 0.1.7
• futures
Added (repository) support for:
• ansi2html
• azure
• blockspring
• boost
• btrees
• cloudpickle
• chest
• cligj
• csvkit

• dbf
• dill
• essbasepy
• flask-login
• heapdict
• holoviews
• ldap3
• line_profiler
• locket
• lockfile
• markdown
• markdown2
• meld3
• msgpack-python
• mysql-connector-python
• nano (Unix)
• param
• partd
• plac
• pyopengl
• pywget
• rasterio
• sas7bdat
• seaborn
• semantic_version
• snuggs
• spacy
• stripe
• supervisor (Unix)
• thinc
• unxutils (Windows)
• xray

2015-03-31 2.2.0:
Highlights:
• updates to 61 packages, including: Python, NumPyBokeh, pandas and blaze
• added 16 new packages
• added HTTPS support for default conda packages repo
Fixes:
• fixed cython command on Windows
• fixed untgz NSIS plugin to install files with exactly 100 characters
Enhancements:
• added https support for default conda packages repo
• renamed dateutil to python-dateutil to reflect the offical name
• added HDF5 and netcdf support for GDAL
• switched to using Pillow instead of PIL
• changed ipython-notebook to start directory to home directory on Windows
Updates:
• boto from 2.32.1 to 2.36.0
• cairo from 1.12.2 to 1.12.18
• cffi from 0.8.6 to 0.9.2
• conda from 3.7.0 to 3.10.0
• cryptography from 0.5.4 to 0.8
• cython from 0.21 to 0.22
• freetype from 2.4.10 to 2.5.2
• h5py from 2.3.1 to 2.4.0
• hdf5 from 1.8.13 to 1.8.14

• ipython-notebook from 2.2.0 to 3.0.0

• ipython-qtconsole from 2.2.0 to 3.0.0
• lxml from 3.4.0 to 3.4.2
• nltk from 3.0.0 to 3.0.2
• numba from 0.14.0 to 0.17.0
• numpy from 1.9.0 to 1.9.2
• openssl from 1.0.1h to 1.0.1k
• pep8 from 1.5.7 to 1.6.2
• pip from 1.5.6 to 6.0.8
• py from 1.4.25 to 1.4.26
• pycurl from 7.19.5 to 7.19.5.1
• pygments from 1.6 to 2.0.2
• pyqt from 4.10.4 to 4.11.3
• python-dateutil from 2.1 to 2.4.1
• pytz from 2014.7 to 2015.2
• pyzmq from 14.3.1 to 14.5.0
• qt from 4.8.5 to 4.8.6
• runipy from 0.1.1 to 0.1.3
• scipy from 0.14.0 to 0.15.1
• sip from 4.15.5 to 4.16.5
• six from 1.8.0 to 1.9.0
• spyder-app from 2.3.1 to 2.3.4
• sympy from 0.7.5 to 0.7.6

• tk from 8.5.15 to 8.5.18

• zlib from 1.2.7 to 1.2.8
Added:
• bcolz 0.8.1
• certifi 14.05.14
• clyent 0.3.4
• enum34 1.0.4 (on Python 2.6, 2.7 and 3.3)
• fastcache 1.0.2
• funcsigs 0.4
• jedi 0.8.1
• llvmlite 0.2.2
• mistune 0.5.1
• odo 0.3.1
• pillow 2.7.0
• ptyprocess 0.4
• pyasn1 0.1.7
• terminado 0.5
• atom
• casuarius
• chaco
• enable
• enaml
• future
• kiwisolver
• llvmpy
• mingw (on Windows)
• mpi4py
• pil (in favor of pillow)
• pyface

• traits
• traitsui
2014-09-30 2.1.0:
Fixes:
• fixed the ability to compile C extensions in Python 3 using MinGW
• added missing lzma module to Python 3.3 and 3.4 (links to xz)
• added missing werkzeug/debug/shared package data to Werkzeug package
Enhancements:
• added statsmodel support for Python 3.4
• added LZO support for pytables on Linux
• added scikit-learn support for Python 3.4
• added Windows cffi support (in repository)
• added bsddb conda package on Linux to support Berkeley DB
Updates:
• atom from 0.3.7 to 0.3.9
• beautiful-soup from 4.3.1 to 4.3.2
• boto from 0.28.0 to 2.32.1
• configobj from 5.0.5 to 5.0.6
• curl from 7.30.0 to 7.38.0
• docutils from 0.11 to 0.12
• dynd from 0.6.2 to 0.6.5
• enaml from 0.9.1 to 0.9.8
• future from 0.12.1 to 0.13.1
• h5py from 2.3.0 to 2.3.1

• hdf5 from 1.8.9 to 1.8.13

• jinja2 from 2.7.2 to 2.7.3
• kiwisolver from 0.1.2 to 0.1.3
• launcher from 0.1.5 to 1.0.0
• libnetcdf from 4.2.1.1 to 4.3.2
• llvmpy from 0.12.6 to 0.12.7
• lxml from 3.3.5 to 3.4.0
• markupsafe from 0.18 to 0.23
• networkx from 1.8.1 to 1.9.1
• nltk from 2.0.4 to 3.0.0
• nose from 1.3.3 to 1.3.4
• numba from 0.13.2 to 0.14.0
• pep8 from 1.5.6 to 1.5.7
• py from 1.4.20 to 1.4.25
• pycurl from 7.19.3.1 to 7.19.5
• pytz from 2014.3 to 2014.7
• pyzmq from 14.3.0 to 14.3.1
• runipy from 0.1.0 to 0.1.1
• six 1.6.1 to 1.8.0
• spyder from 2.3.0rc1 to 2.3.1

Added:
• abstract-rendering 0.5.1 (on Unix and Python 2)
• cffi 0.8.6
• cytoolz 0.7.0
• decorator 3.4.0
• futures-2.1.6 (for Python 2)
• pyopenssl 0.14
• sockjs-tornado 1.0.1
• toolz 0.7.0
• xz 5.0.5
2014-06-12 2.0.1:
Fixes:
• added missing libpython (the so-called MinGW import library) for Python 3.4
• in order to make pandas.io.excel work, we downgraded openpyxl from 2.0.2 to 1.8.5
• added missing idle script on Windows
Updates:
• numba from 0.13.1 to 0.13.2
• openssl from 1.0.1g to 1.0.1h
2014-05-28: 2.0.0:
Fixes:
• on Windows the /D option of the executable installer is now working
• added missing TkAgg matplotlib backend on Windows
• added missing osgeo._gdal_array extension to GDAL
• fixed rope on Python 3
Known issues:

• even though the matplotlib tkagg backend is now supported on all platforms and with all Python versions
now, there might be problems on Windows with Python 3.4
• the Windows file association (‘.py’-files being executed by the Anaconda Python interpreter) is not working
Enhancements:
• switched from using PySide to PyQt as the default Qt binding
• added lcms to PIL on Unix
• added ability to copy files upon install when filesystem fails to create hard links
• added netCDF4 support on 64-bit Windows
• on macOS, Tk in now linked to Cocoa (instead of X11)
Updated:
• blz from 0.6.1 to 0.6.2
• boto from 2.25.0 to 2.28.0
• configobj from 4.7.2 to 5.0.5
• dynd-python gtom 0.6.1 to 0.6.2
• future from 0.11.2 to 0.12.1
• gevent from 1.0 to 1.0.1
• h5py from 2.2.1 to 2.3.0
• itsdangerous from 0.23 to 0.24
• launcher from 0.1.2 to 0.1.5
• lxml from 3.3.1 to 3.3.5
• nose from 1.3.0 to 1.3.3
• numba from 0.12.1 to 0.13.1
• openpyxl 1.8.2 to 2.0.2
• openssl from 1.0.1c to 1.0.1g
• pep8 gtom 1.4.6 to 1.5.6
• pip from 1.5.2 to 1.5.6


• pycosat from 0.6.0 to 0.6.1
• pycurl from 7.19.0 to 7.19.3.1
• pytz from 2013b to 2014.3
• pyyaml 3.10 to 3.11
• pyzmq from 2.2.0.1 to 14.3.0
• scipy from 0.13.3 to 0.14.0
• six from 1.5.2 to 1.6.1
• sphinx form 1.2.1 to 1.2.2
• spyder from 2.2.5 to 2.3.0rc1
• sqlite from 3.7.13 to 3.8.4.1
• sympy from 0.7.4.1 to 0.7.5
• tk from 8.5.13 to 8.5.15
• xlrd from 0.9.2 to 0.9.3
Added:
• conda-launch 0.1
• jdcal 1.0
• python 3.4.1
• pyqt 4.10.4
• runipy 0.1.0
• sip 4.15.5
• xlwings 0.1.0 (Windows only)
Removed (from installer, packages are still supported and available in repo):
• apptools
• biopython
• envisage
• disco and erlang (from 64-bit Linux)

• gevent_zeromq
• keyring
• mayavi
• mdp
• netcdf4
• pykit
• pysal
• pysam
• vtk
2014-04-09: 1.9.2:
Fixes:
• updated to openssl 1.0.1g on Unix to fix the “Heartbleed bug” of the TLS Heartbeat Extension problem
(reported in the news)
• fixed /D option in silent mode for Windows installer
Updates:
• openssl from 1.0.1c to 1.0.1g
2014-02-20: 1.9.1:
Fixes:
• openpyxl to depend on up-to-date version of lxml
• added missing MSVCP (both for 2008 and 2010) DLLs to Windows installers which fixes issues with the
user install mode on some systems
Updates:
• atom from 0.3.6 to 0.3.7
• bokeh from 0.4 to 0.4.1
• boto 2.24.0 to 2.25.0
• dynd-python 0.6.0 to 0.6.1


• lxml from 3.2.3 to 3.3.1
• netcdf4 from 1.0.7 to 1.0.8
• numba from 0.12.0 to 0.12.1
• pykit from 0.1.0 to 0.2.0
Added:
• added Py3k support for h5py
• netcdf4 on 32-bit Windows
2014-02-10: 1.9.0:
Highlights:
• NumPy updated to version 1.8
• updates to about 35 packages, including Bokeh and Blaze
• added 10 new packages
Enhancements:
• use MSVC 2010 to compile Python 3 and C extensions on Windows
• remove distribute in favor of setuptools
• enable threadsafe when building HDF5 on Linux
• renamed the Python Imaging Library (PIL) from imaging to pil
• updated EULA
Fixes:
• ssl bindings in Python standard library on macOS
• Windows installers not working properly when PYTHONHOME is set
Updated:
• apptools from 4.2.0 to 4.2.1
• atom from 0.3.4 to 0.3.6
• biopython from 1.62 to 1.63
• boto from 2.15.0 to 2.24.0

• bokeh from 0.2 to 0.4

• chaco from 4.3.0 to 4.4.1
• dynd-python 0.5.0 to 0.6.0
• envisage from 4.3.0 to 4.4.1
• gevent from 0.13.8 to 1.0
• h5py from 2.2.0 to 2.2.1
• jinja2 from 2.7.1 to 2.7.2
• keyring from 3.2 to 3.3
• llvmmath from 0.1.1 to 0.1.2
• numba from 0.11.0 to 0.12.0
• pip from 1.4.1 to 1.5.2
• py from 1.4.17 to 1.4.20
• pycparser from 2.9.1 to 2.10
• pyface from 4.3.0 to 4.4.0
• pyreadline from 2.0.dev to 2.0
• python from 2.7.5 to 2.7.6, and 3.3.2 to 3.3.3
• requests 1.2.3 to 2.2.1
• scipy from 0.13.0 to 0.13.2
• six from 1.4.1 to 1.5.2


• sympy from 0.7.3 to 0.7.4.1
• theano from 0.5.0 to 0.6.0
• traits from 4.3.0 to 4.4.0
• traitsui from 4.3.0 to 4.4.0
Added:
• argcomplete 0.6.7
• blz 0.6.1
• cdecimal 2.3
• datashape 0.1.0
• future 0.11.2
• mock 1.0.1
• setuptools 2.1
• ssl_match_hostname 3.4.0.2
• ujson 1.33
• scikit-learn and redis-py support for Python 3
• added traits and unittest2 support for Python 2.6
Removed:
• distribute
• llvmmath
• meta
2013-11-05: 1.8.0:
Enhancements:
• on Windows the installer now allows installing in user mode without having system administrator privi-
leges
• use RPATH (instead of RUNPATH) on Linux, which fixes link problems when LD_LIBRARY_PATH is
set
• added ipython-notebook meta package for all supported Python versions
• removed curl binary on macOS, to avoid superseding system curl
Fixes:
• wrong location of VTK libraries in VTKTargets-debug.cmake on Linux
• fix python.app problem related to adding the symlink to lib, which also appears to create problems with
%%cython magic in ipython

• apply patch to Mayavi, which foxes running mlab scripts

Updated:
• atom from 0.3.2 to 0.3.4
• boto from 2.12.0 t 2.15.0
• bokeh from 0.1.1 to 0.2
• dynd from 0.4.2 to 0.5.0
• enaml from 0.7.19 to 0.8.3
• ipython 1.0.0 to 1.1.0
• keyring from 3.0.1 to 3.2
• numba from 0.10.2 to 0.11.0
• pycrypto from 2.6 to 2.6.1
• python 2.6.8 to 2.6.9
• scipy from 0.12.0 to 0.13.0
• sypder from 2.2.4 to 2.2.5
Added:
• blaze 0.3
• pykit 0.1
• beautiful-soup 4.3.1
• openpyxl 1.6.2
2013-09-10: 1.7.0:
Highlights:
• added VTK, Mayavi and Bokeh
• updated to new ipython 1.0 and matplotlib 1.3, and llvm 3.3

• many improvements and bug fixes to conda

Enhancements:
• removed conda as a direct anaconda dependency
• add MinGW runtime DLLs to Scripts directory on Windows
• fixed python-dateutil for Python 2
Updated:
• atom from 0.2.3 to 0.3.2
• boto from 2.9.6 to 2.12.0
• docutils from 0.10 to 0.11
• enaml from 0.7.6 to 0.7.19
• h5py from 2.1.1 to 2.2.0
• itsdangerous from 0.21 to 0.23
• jinja2 from 2.6 to 2.7.1
• libdynd and dynd-python from 0.4.0 to 0.4.2
• llvm from 3.2 to 3.3
• llvmmath from 0.1.0 to 0.1.1
• lxml from 3.2.1 to 3.2.3
• keyring from 1.4 to 3.0.1
• networkx fomr 1.7 to 1.8.1
• numba from 0.9.0 to 0.10.2
• opencv from 2.4.2 to 2.4.6
• pep8 from 1.4.5 to 1.4.6
• pip from 1.3.1 to 1.4.1
• pysal 1.5.0 to 1.6.0
• pyside from 1.1.2 to 1.2.1 (not macOS)
• qt from 4.7.4 to 4.8.5 (not macOS)


• six from 1.3.0 to 1.4.1
• sqlalchemy 0.8.1 to 0.8.2
• tornado form 3.1 to 3.1.1
Added:
• bokeh 0.1.1
• chaco 4.3.0
• configobj 4.7.2
• markupsafe 0.18
• mayavi 4.3.0
• patsy 0.2.1
• traits 4.3.0
• vtk 5.10.1
2013-07-09: 1.6.2: (Windows only)
• Fixed path being incorrectly appended on Windows during install
2013-07-03: 1.6.1:
• fixed .pkg installer

• updated binstar from 0.1.1 to 0.1.2 (fixes upload on Windows)
• updated conda from 1.7.1 to 1.7.2 (fixes updating python.app on macOS)
• updated dynd from 0.3.0 to 0.4.0
• updated launcher from 0.1.1 to 0.1.2
• added missing pydoc command on Unix
• macOS: fix hard coded build prefix in .dylib files for may other libraries
• Windows: append instead of prepend path on Windows
2013-06-21: 1.6.0:
Highlights:
• the “Launcher”, which allows users to start up applications
• conda has now the ability to build conda packages, which can be uploaded to binstar.org

• conda now uses a SAT solver to solve the install dependency problem
Enhancements:
• added a .pkg installer for macOS, such that installing Anaconda does not require command line access
• create copy of .bashrc (.bash_profile on macOS) before appending the PATH setting upon install
• Windows Menu items should are now installed system wide
Fixes:
• removed Lib/test/testbz2_bigmem.bz2 from Windows, this (harmless) file was triggering Trojan-
ArcBomb.BZip.Agent warning, see: http://bugs.python.org/issue17843
• json.decoder in Python 2.7 standard library not using .decode(‘hex’), this was (mysteriously) causing in-
stall problems on macOS
• fixed PIL._imagetk on Linux
Updated:
• boto from 2.9.2 to 2.9.6
• distribute from 0.6.36 to 0.6.45
• flask from 0.9 to 0.10.1
• lxml form 3.2.0 to 3.2.1
• numba from 0.8.1 to 0.9.0
• py from 1.4.12 to 1.4.14
Added:
• launcher 0.1.1
• binstar 0.1.1
• itsdangerous 0.21
• keyring 1.4
• llvmmath 0.1.0
• pep8 1.4.5
• pywin32 218.4 on Windows

2013-05-09: 1.5.1: (macOS only)
• fixed pip command

• replace spaces by underscore in user install location
• shared libraries now link to /usr/lib/libgcc_s.1.dylib (instead of /usr/local/lib/libgcc_s.1.dylib)
2013-05-08: 1.5.0:
Highlights:
• updates to all important packages: python, numpy, scipy, ipython, matplotlib, pandas, cython
• added netCDF4 (with OpenDAP support) on Linux and macOS
Fixed:
• Cython on macOS on Python 2.6, due to a problem with Pyhton’s config/Makefile
• py.test command (all platforms)
• python-config command not using correct interpreter on macOS
• added missing MSVC 2008 and 2010 runtime to Windows installers
• removed hard-coded build location from identification name of dynamic shared libraries on macOS, to
allow easier building against libraries in Anaconda
Enhancements:
• The Windows installers has a new dialog box with the following options:
– “Add Anaconda to the System Path”
– “Register Anaconda as default Python version of the system”
• The Unix installers have an option to add Anaconda to the path in the ~/.bashrc (on Linux) or
~/.bash_profile (on macOS). On macOS the default is ‘yes’, on Linux the default is ‘no’.
• added armv6l supports (only Python 2.7 and selected packages)
• link pycurl and libnetcdf dynamically against curl library on Unix
• add configure option –with-pgm for zeromq on Unix
Added:
• netCDF4 (with OpenDAP support) 1.0.4 on Linux and macOS
• ordereddict 1.1 (on Python 2.6)
• pycosat 0.6.0
• atom 0.2.3
• enaml 0.7.6
• casuarius 1.1
• dynd-python 0.3.0
• rope 0.9.4
Updates:


• scipy from 0.11.0 to 0.12.0
• astropy from 0.2 to 0.2.1
• bitarray from 0.8.0 to 0.8.1
• boto from 2.8.0 to 2.9.2
• curl from 7.26.0 to 7.30.0
• cython from 0.18 to 0.19
• distribute from 0.6.34 to 0.6.36
• lxml from 3.0.2 to 3.2.0
• nose from 1.2.1 to 1.3.0
• pytz from 2012j to 2013b
• six from 1.2.0 to 1.3.0
• xlrd from 0.9.0 to 0.9.2
• xlwt from 0.7.4 to 0.7.5
Removed (from installer only, still available with conda):
• bitey
• gdata (conflicts with atom (which is required by enaml))
• googlecl (requires gdata)

2013-03-12: 1.4.0:
Many more packages are now supported on Python 3.3. In addition, we have added Python 3 support on Windows,
such that now Python 2.6, 2.7 and 3.3 is supported across all platforms. In addition, we have redesigned the Windows
installer, which was suffering from a number of problems, in particular the lack of uninstall functionality and the GUI
not working on some systems.
added:
• astropy 0.2
• lxml 3.0.2
• pycparser 2.9.1
• six 1.2.0
• xlrd 0.9.0
• xlwt 0.7.4
updated:
• boto from 2.7.0 to 2.8.0
• cubes from 0.10.1 to 0.10.2
• dateutil from 1.5 to 2.1
• numpy from 1.7rc1 to 1.7.0
• pygments from 1.5 to 1.6
• pysal from 1.4.0 to 1.5.0
• pyreadline from 1.7.1 to 2.0.dev
• pytz from 2012d to 2012j
fixed:
• pytables on Windows
other notes:
• Linux: a ATLAS package is now available (conda install atlas). In addition the site.cfg in the
numpy.distutils has been updated, such that other packages (e.g. scipy) which use the atlas build con-
figuration can be build against the (non-MKL linked) numpy in Anaconda.
2013-02-06: 1.3.1:
added:
• Python 2.6 support for iopro, numba and numbapro

• Python 2.6 support on Windows (Python 2.6 is now supported on all platforms)
• added pythonw (the command to run Python GUI applications) on macOS
• added chaco on Windows
updates:
• iopro from 1.3.0 to 1.3.2
• numbapro from 0.8.1 to 0.8.1
other changes:
• removed anaconda-launcher
2013-01-23: 1.3.0:
fixes:
• fixed missing Grammar.txt in Sphinx
• recompiled llvm and llvmpy using gcc 4.4.6 on Linux, this fixes a problem with the mandel.py example in
numba
• made Windows installer dialog box resizeable
• fixed problem that importing numbapro or iopro removed sys from the namespace
updates:
• LLVM from 3.1 to 3.2
• llvmpy from 0.9 to 0.10.0
• numbapro from 0.7.3 to 0.8.0
• spyder form 2.1.11 to 2.1.13
• h5py from 2.1.0 to 2.1.1
• distribute form 0.6.30 to 0.6.34
• nose from 1.1.2 to 1.2.1
• docutils form 0.9.1 to 0.10
• nltk from 2.0.3 to 2.0.4


• numpy from 1.7.0b2 to 1.7.0rc1
• boto from 2.6.0 to 2.7.0
• scikits-image from 0.6.1 to 0.7.1
• pyaudio from 0.2.6 to 0.2.7
• redis from 2.4.15 to 2.6.9
• disco from 0.4.2 to 0.4.4
added:
• Tkinter support on all platforms
• redis support on macOS
• cubes 0.10.1
• ply 3.4
• pycrypto 2.6
• pyparsing 1.5.6
• googlecl 0.9.12
• gdata 2.0.17
• biopython 1.60
2012-11-21: 1.2.1:
• pucurl on macOS
• anaconda-launcher envs by updating to conda 1.2.1
• add missing pyodbc numpy_tests in iopro/tests/pyodbc
• updated wiseRF to version 1.1
• add creation of .continuum directory (if not created yet) on Windows
• minor fixes in numba, numbapro, and iopro
• fixed version of “py” package
• add missing Windows manifest to Windows executable installer
• fixed Windows Menu install and making Anaconda the default Python
• on 2012-12-06 we released a 32-bit Linux version

2012-11-13: 1.2.0:
• performance and feature enhancements to Numba Pro

• performance and feature enhancements to IOPro
• improved conda command (package management)
• added Qt to the Linux Version (Qt is now on all platforms)
• added MDP, NLTK and py, pytest
• update matplotlib from 1.1.1 to 1.2.0
• update h5py from 2.0.1 to 2.1.0
• update IOPro to 1.2.1
• update libpng to 1.5.13
2012-10-05: 1.1.0:
• add GUI to Windows installer

• IDE Spyder (Qt) for Mac Version
• add conda 1.0
• update llvmpy to 0.8.3
• add MinGW on Windows
2012-09-06: 1.0.0:
• add Windows support

• installer can now install into different locations
• enable building free and permium version
• enable termcap in erlang
• add MKL support to permium version
• add networkx, pysal, pycurl, gevent_zeromq, requests, pip, distribute
• add iopro to permium version
• update scipy from 0.11.0b1 to 0.11.0rc2
• update scikits-image form 0.6 to 0.6.1
• update pytables from 2.4.0b1 to 2.4.0
• update pandas from 0.8.0 to 0.8.1
• add patch to disco to always use the anaconda erl
• remove useless files (Python) from being installed

2012-08-21: 0.9.0:
• add macOS (x86_64 10.5 or higher) support

• add bitey and other packages
• update several other packages
2012-07-18: 0.8.3:
• update changes to etc/init.d/disco script

• add patch, fixes disco and ddfs listdir misfeature
• add –packages option to anaconda command
• add missing h5py
• improve ease of testing
2012-07-18: 0.8.2:
• fixed theano.sparse
• removed (broken) scikits namespace
• add disco config and setup files
• add anaconda command, for version information
2012-07-17: 0.8.1:
• fixed libm.so ctypes error in scipy tests

• added import tests to all C extension modules
• fixed lzo support in pytables
2012-07-17: 0.8.0:
• initial release
Help and support
The following resources are available to help you:

• Free community support is available from the Anaconda Support Group.
• Anaconda offers support and training.
• Package creators or maintainers may be able to help you with installing a package or building and publishing an
updated version. Package creators may also contact Anaconda to submit their package for consideration to be
included in Anaconda.
• Report bugs on the Anaconda GitHub issue tracker.

Security practices
Anaconda maintains the following security and provenance/chain-of-custody practices:

• The engineers whose purpose is to build and maintain the Anaconda Distribution have curated the packages
contained within based on their relevance to the data science community. These open-source packages are
vetted for their widespread adoption and community support, which allows any security vulnerabilities to be
addressed quickly and completely in a transparent manner.
• Source code and built artifacts are maintained with strict chain-of-control and are built, scanned, and hashed on
a separate secure network within Anaconda. Only a small number of developers and IT team members have
access to this network and the associated servers.
• All versions of the Anaconda Distribution and all packages that are made available at https://repo.anaconda.com/
have published SHA256 checksums. We recommend you verify your install.
• A Quality Assurance team performs exhaustive testing on each release of Anaconda and Miniconda, including
all installers and packages. This includes the use of multiple commercial anti-malware products, as well as
custom in-house security tools, for all supported operating systems - Windows, macOS, and Linux. When there
are issues, they are followed up on for remediation or noted in the documentation.
• Anaconda maintains a team of IT leaders that works with software engineers to monitor all active security events
through various channels of information, which results in fast response times and, whenever necessary, direct
communication to our customers through Customer Support.
• Developers use controlled machines with the latest security patches.
• Especially security-minded customers may implement the functionality of the Anaconda Repository as part of an
Anaconda Enterprise subscription to only allow a small set of packages to come onto their site at their control and
block all others from entering their network. Due to the open-source nature of the enclosed packages, they may
perform advanced code reviews or other associated activities to ensure their desired level of risk management
and/or compliance.
Troubleshooting
If you have a troubleshooting issue that is not listed here, obtain free support for Anaconda through the Anaconda
mailing list. For Anaconda installation or technical support options, visit our support offerings page.
You may also wish to see the Anaconda Navigator Troubleshooting guide.
• 403 error
• HTTP 000 CONNECTION FAILED
• Anaconda installer download problems
• Cannot open Anaconda Prompt after installation
• Cannot see Anaconda menu shortcuts after installation on Windows
• Windows error: Failed to create Anaconda menus or Failed to add Anaconda to the system PATH
• I’m having trouble with the Anaconda installer on Windows. How can I debug my issue?
• Cannot get conda to run after installing
• Recovering your Anaconda installation
• Using Anaconda behind a firewall or proxy

• .zshrc not updated under macOS Catalina

• Insecure Platform Warning
• Conda: command not found on macOS or Linux
• Conda: Channel is unavailable/missing or package itself is missing
• Collecting package metadata (repodata.json): - Killed
• Anaconda interfering with other software on Windows
• Windows error: no environment named “search” exists
• MKL Trial warning is displayed even though MKL-linked packages are now free and installed by default
• Error message: Permission denied, when loading MKL shared libraries
• Error message on Miniconda install: Already installed
• Conda update anaconda command does not install the latest version of Anaconda
• Linking problems when Python extensions are compiled with gcc
• Error message: Unable to remove files
• Files left behind after uninstalling Anaconda on Windows
• Spyder errors or failure to launch on Windows
• Problems running Anaconda on macOS 10.12.2
• “execution error: localhost doesn’t understand the “open location” message. (-1708)” when opening a
Jupyter notebook on macOS 10.12.5
• Missing libgfortran on Power8
• Missing libgomp on Power8
• Anaconda on Power8 reports “can not execute binary file”
• Uninstaller requests admin privileges on Windows
• Windows permission errors when installing from Favorites folder
• Trouble with activation on PowerShell on Windows
• Cannot install Distribution 2019.07 on a webfaction server
• Segmentation fault on package import with macOS Python 3.7 intepreter
• Using 32- and 64-bit libraries and CONDA_FORCE_32BIT
403 error
Cause
A 403 errors is a generic Forbidden error issued by a web server in the event the client is forbidden from accessing a
resource.
The 403 error you are receiving may look like the following:

Collecting package metadata (current_repodata.json): failed
UnavailableInvalidChannel: The channel is not accessible or is invalid.

channel name: pkgs/main
channel url: https://repo.anaconda.com/pkgs/main
error code: 403
You will need to adjust your conda configuration to proceed.

Use `conda config --show channels` to view your configuration's current state,
and use `conda config --show-sources` to view config file locations.
There are several reasons a 403 error could be received:
• The user has misconfigured their channels in their configuration (most common)
• A firewall or other security device or system is preventing user access (second most common)
• We are blocking their access because of a potential terms of service violation (third most common)
Solution
1. First, run the following to undo your configuration of Commercial Edition:
conda config --remove-key default_channels
2. Next, install or upgrade the conda-token tool:
conda install --freeze-installed conda-token
3. Lastly, re-apply the token and configuration settings:
# Replace <TOKEN> with your token

conda token set <TOKEN>
If this doesn’t resolve the issue, we recommend consulting our Terms of Service error page.
HTTP 000 CONNECTION FAILED
If you receive this error message, run the following command:
conda config --set ssl_verify false
Anaconda installer download problems
Cause
The Anaconda installer files are large (over 300 MB), and some users have problems with errors and interrupted
downloads when downloading large files.
Solution
One option is to download and install the smaller Miniconda (under 60MB) and then use the command conda
install anaconda to download and install all the remaining packages in Anaconda. If the package downloads

are interrupted, just run conda install anaconda again. Conda only downloads the packages that were not
finished in any previous attempts.
A second option is to download the large Anaconda installer file, and restart it if the download is interrupted or you
need to pause it.
Windows
If you use Internet Explorer:
1. Click the Settings icon.
2. Click “View Downloads” to open the Download Manager.
3. Click on the “Resume” button next to the stopped download to restart downloading. The download resumes at
the point where it stopped.
If you use Edge browser:
1. In Windows Explorer, open your downloads folder. There will be temporary files there associated with the
partial downloads. Delete all of the temporary files except for the download you want to resume.
2. In Edge, click the file to download it again. Pause the download but do not cancel it.
3. In Windows Explorer, open your downloads folder. You will see two files: the partially downloaded file from
earlier, and the paused download you just started. Copy the name of the file you just started, delete this file, and
rename the other file with the copied name.
4. In Edge, resume the download.
If you use Chrome browser:
Download the plugin for Chrome called Chrono Download manager. In your Chrome browser, go to https://chrome.
google.com/webstore/category/extensions, search on “Chrono Download” and select, “Add to Chrome.”
To resume the download using Chrono Download, from your top browser menu, click on the Chrome menu button,
then click “Downloads.” Select the filename, then click “Resume” to restart your download.
macOS and Linux
• In your terminal window, download the file with the command curl -O FILENAME.
Note: Replace FILENAME with the full path and name of the file, including http:// or https://.
• To pause the download, use CTRL-c.
Note: While a download is paused, you can shut down or restart your computer.
• When ready to resume your download, use curl -O -C FILENAME.

Where “-C” is the option for “continue”. You can pause and restart a download as many times as you wish.
Cannot open Anaconda Prompt after installation
I get an error message that says “activate.bat is not a recognized file or command”.
Cause
Anaconda 5.0.1 sometimes does not install completely on Windows.

Solution
Until a new version is released, you can install Miniconda, and then use conda to install the rest of the packages in
Anaconda with these instructions:
Open the command prompt (Windows key + the R key on your keyboard) which brings up the Run. . . dialog box.
Enter cmd.exe and then press enter)
Copy the following text:
cd %UserProfile%
powershell -command "& { (New-Object Net.WebClient).DownloadFile('https://repo.
˓→anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe', 'mc3.exe') }"
start /wait "" mc3.exe /InstallationType=JustMe /AddToPath=0 /RegisterPython=0 /

˓→NoRegistry=0 /S /D=%UserProfile%\anaconda3
%UserProfile%\anaconda3\Scripts\activate.bat
conda install -y anaconda=5.0.1 conda-build _ipyw_jlab_nb_ext_conf
Then paste it into the command prompt window.
Note: This installs to a subdirectory in your User directory named anaconda3. If you use a different directory,
replace anaconda3 with the actual name.
Cannot see Anaconda menu shortcuts after installation on Windows
After installing on Windows, in the Windows Start menu I cannot see Anaconda prompt, anaconda.org, or Navigator
shortcuts.
Cause
This may be caused by the way Windows updates the Start menu, or by having multiple versions of Python installed,
where they are interfering with one another. Existing Python installations, installations of Python modules in global
locations, or libraries that have the same names as Anaconda libraries can all prevent Anaconda from working properly.
Solution
If start menu shortcuts are missing, Microsoft recommends rebooting your computer or restarting Windows Explorer.
If that doesn’t work, clear $PYTHONPATH and re-install Anaconda. Other potential solutions are covered in the
“Conflicts with system state” section of this blog post.
Windows error: Failed to create Anaconda menus or Failed to add Anaconda to the system PATH
During installation on a Windows system, a dialog box appears that says “Failed to create Anaconda menus, Abort
Retry Ignore” or “Failed to add Anaconda to the system PATH.” There are many possible Windows causes for this.
Solution
Try these solutions, in order:

• Do not install on a PATH longer than 1024 characters.

• Turn off anti-virus programs during install, then turn back on.
• Uninstall all previous Python installations.
• Clear all PATHs related to Python in sysdm.cpl file.
• Delete any previously set up Java PATHs.
• If JDK is installed, uninstall it.
I’m having trouble with the Anaconda installer on Windows. How can I debug my issue?
Cause
The cause could be any number of issues.
Solution
Anaconda 4.4 added a feature to the Windows installer so that the “verbose” install information is printed out to a
special debug stream via the Win32 API function OutputDebugStream. To see these messages, during installation you
need to run the Microsoft utility https://technet.microsoft.com/en-us/sysinternals/debugview.aspx. This may provide
useful clues for troubleshooting or submitting bug reports.
Cannot get conda to run after installing
You may get “conda not found” or “conda is not recognized as an internal or external command” or a similar message,
and you cannot execute conda in a terminal window regardless of what path you are on.
Cause
Most likely when you were installing Anaconda or Miniconda, you answered “NO” to the question whether or not to
prepend the conda prompt to your path.
Solution
Uninstall and then reinstall Anaconda or Miniconda, answering “YES” to the question about prepending the conda
prompt.
Or, you can manually edit your .bashrc file to prepend the Anaconda or Miniconda install location. Open a text editor
and in your home directory, locate the hidden file .bashrc. Add this line to it and save:
export PATH=/Users/your-username/anaconda3/bin:$PATH
Close your terminal window and re-open before running a conda command.
Recovering your Anaconda installation
If your Anaconda installation is in a state where normal conda commands are not functioning, use the following steps
to repair Anaconda and preserve your installed packages and environments.

Step 1
Download a new installer, then follow the instructions for your system Windows, macOS, or Linux.
Note: Use the actual path, filename, and directory name for your installation.
Windows
Change your original installer’s name so you do not overwrite it:

move Anaconda Anaconda_old
Run the Anaconda.exe installer as usual and use robocopy to sync the directories:
robocopy Anaconda_old Anaconda /S

rd /s Anaconda_old
macOS

mv anaconda anaconda_orig
Install to same directory as your original installer:
bash Anaconda3-4.0.0-MacOSX-x86_64.sh
rsync -a anaconda_orig/ anaconda/
rm -rf anaconda_orig
Linux

mv anaconda anaconda_orig
Install to same directory as your original installer:
bash Anaconda3-4.0.0-Linux-x86_64.sh
rsync -a anaconda_orig/ anaconda/
Step 2
Run conda list to view the packages from the previous installation.
Run conda info -e to list the environments created in the previous installation which are now available in the
new installation.

Using Anaconda behind a firewall or proxy
Corporate security policies may prevent a new Anaconda installation from downloading packages and other func-
tionality that requires connecting to an external server. To make external connections you may need to con-
nect to a firewall/proxy. Additionally, your IT team may need to allow connections to https://anaconda.org and
https://repo.anaconda.com as these are the main package repositories.
Solution
To add the proxy information you will need to add two entries to your .condarc file located in the user’s home directory.
This information should be made available by your IT team and may contain a username and password that is included
in the URL. Read more about the .condarc configuration.
Example configuration:
channels:
- defaults
proxy_servers:
- http: http://username:password@proxyurl.com:8080
- https: https://username:password@proxyurl.com:8443
In some situations it may be necessary to export the HTTP_PROXY and HTTPS_PROXY environment variables.
MacOS/Linux
export HTTP_PROXY=http://username:password@proxyurl.com:8080
export HTTPS_PROXY=https://username:password@proxyurl.com:8443
Windows
set HTTP_PROXY=http://username:password@proxyurl.com:8080
set HTTPS_PROXY=https://username:password@proxyurl.com:8443
If these steps have not allowed connections you should speak to your IT team to verify that security policies are not
blocking connections to https://anaconda.com and https://repo.continuum.io.
.zshrc not updated under macOS Catalina
Cause
MacOS Catalina changed the default shell from Bash to zsh.
Solution
Run bash -c "conda init zsh" and then restart your shell to initialize conda for zsh.
Insecure Platform Warning

Cause
“InsecurePlatformWarning” appears only when the installed version of Python is older than version 2.7.9. This mes-
sage warns only that the validity of the SSL connection is not being verified. It should not affect your package
downloads.
Solution
To resolve this on Windows, install the updated package ndg-httpsclient:
conda install ndg-httpsclient
Note: When initially installing this package, you receive the SSL warning again. Once it is installed, the package
will prevent the warnings.
Conda: command not found on macOS or Linux
Cause
The conda shell function is not available, or is not working properly. Some causes:
• You have set conda_auto_activate_base to false. You need to run conda activate [env]. Env
is optional, the default if not provided is base.
• You haven’t started a new shell after installing Anaconda/Miniconda (assuming you allow it to modify your
startup script)
• You didn’t allow the installer to modify your startup script
• Conda has been corrupted, usually by a change in the Python package (e.g. 3.6->3.7)
Solution
Run /full/path/to/bin/conda init to modify ~/.bashrc.

Either start a new shell or source the modified ~/.bash_profile (Windows/MSYS2, Windows/Cygwin and macOS) or
~/.bashrc (Linux and Windows Subsystem for Linux). Source them via . ~/.bash_profile.
You may prefer that conda not automatically activate your base environment when a new shell is started. This behavior
shadows your system Python, and some users prefer to have their conda environment be inactive until they need it. To
achieve this, you can set a .condarc setting:
conda config --set auto_activate_base false
If you have this set, the conda command will still be available as a shell function, but your base environment will not
be active when a new shell is started. To activate your base environment, run conda activate.
Conda: Channel is unavailable/missing or package itself is missing

Cause
After a user has configured their .condarc for either Team Edition or Commercial Edition, in some cases they are
unable to install packages. They may receive an error message that the channel or package is unavailable or missing.
Solution
One potential fix for all of these is to run the following command:
conda clean -i
This will clear the “index cache” and force conda to sync metadata from the repo server.
Collecting package metadata (repodata.json): - Killed
Cause
When installing or searching for a package, you may see the process end abruptly with a “Killed” message:
$ conda install numpy

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): - Killed
This may be because your system lacks the sufficient disk space or memory to complete the process.
Solution
Verify that you have enough disk space and memory on your system to install and use Anaconda packages. The
minimum system requirements for Miniconda and Anaconda installers can be found in the conda user guide.
Anaconda interfering with other software on Windows
Cause
If a user chooses to add Anaconda to the Windows PATH, this can cause programs to use the new Anaconda versions
of software such as Python and not the versions that were already in place. In some cases this can cause incompatibility
and errors.
Solution
We recommend not adding Anaconda to the Windows PATH. Instead, use Anaconda software by opening Anaconda
Navigator or the Anaconda Prompt from the Start Menu.

Windows error: no environment named “search” exists
If anaconda-client is not installed and you search for a package on anaconda.org using the Anaconda search command:
anaconda search -t conda packagename
You will receive the following error message:
C:\Users\username>anaconda search -t conda packagename

No environment named "search" exists in C:\Anaconda\envs
Solution
Anaconda on Windows contains an anaconda.bat file, which is used for setting environment paths and switching
environments. If anaconda-client is not installed, this batch file is called instead and produces the error.
To resolve the error, install anaconda-client:
conda install anaconda-client
And then search for a package:
anaconda search -t conda packagename
MKL Trial warning is displayed even though MKL-linked packages are now free and installed by
default
See Dismissing MKL Trial warnings.
Error message: Permission denied, when loading MKL shared libraries
See Resolving MKL shared library permission denied errors.
Error message on Miniconda install: Already installed
Cause
This situation can occur if you are getting a conda error and you want to reinstall Miniconda to fix it.
Solution
For macOS and Linux, download and install the appropriate Miniconda for your operating system from the Miniconda
download page using the force or -f option:
bash Miniconda3-latest-MacOSX-x86_64.sh -f
Note: For Miniconda3-latest-MacOSX-x86_64, substitute the appropriate filename and version for your
operating system.
Be sure that you install to the same location as your existing install so it overwrites the core conda files and does not
install a duplicate in a new folder.

Conda update anaconda command does not install the latest version of Anaconda
Cause
For users who have installed packages that are not compatible with the latest version of the Anaconda metapackage,
running conda update anaconda updates the Anaconda metapackage to the latest compatible version, but this
may not be the latest version.
Solution
Obtain a list of the conflicting packages by running conda update anaconda or conda install
anaconda=5.2.
Note: Replace 5.2 with the latest version number.
Once you know which packages are conflicting, you can update all current packages without upgrading to the latest
version of Anaconda, or you can remove the conflicting packages and then upgrade to the latest version of Anaconda.
To update all current packages without upgrading to the latest version of Anaconda:
1. Use conda remove anaconda to remove the Anaconda metapackage itself. (This will not remove any of
the packages included with Anaconda.)
2. Use conda update --all to update all currently installed packages.
To remove the conflicting packages and upgrade to the latest version of Anaconda:
1. Remove the conflicting packages by running conda remove package-name for each one.
Note: Replace package-name with the name of the package.
2. Run conda update anaconda.
Linking problems when Python extensions are compiled with gcc
Cause
When compiling Python extensions with gcc on Windows, linking problems may result.
Solution
To resolve these linking problems, use the mingw import library–the conda package libpython–which Anaconda builds
and includes with the Anaconda Distribution.
Error message: Unable to remove files
When trying to update or install packages with conda, you may see an error message such as:
Error: Unable to remove files for package: <package-name>
Please close all processes running code from conda and try again.

Cause
This may be caused by a file lock issue.
Solution
Before updating or installing any packages with conda, be sure to terminate any running Anaconda processes such as
Spyder or IPython.
You can also force the installation of the package: conda install -f package-name.
Note: Replace package-name with the name of the package that you want to install.
Files left behind after uninstalling Anaconda on Windows
Cause
Some users may need to keep settings files and other users may need to delete them, so Anaconda leaves some set-
tings files in place when it is uninstalled. Specifically, the directories .spyder2, .ipython, .matplotlib,
and .astropy remain. Depending on your version of Windows these may be in C:\Documents and
Settings\Your_User_Name or in C:\Users\Your_User_Name.
Note: Replace Your_User_Name with your Windows user name as it appears in the Documents and
Settings or Users folder.
Solution
Manually delete any unneeded settings files.
Spyder errors or failure to launch on Windows
Cause
This may be caused by errors in the Spyder setting and configuration files.
Solution
1. Close and relaunch Spyder and see if the problem remains.

2. On the menu, select Start, then select Reset Spyder Settings and see if the problem remains.
3. Close Spyder and relaunch it from the Anaconda Prompt:
1. From the Start menu, open the Anaconda Prompt.
2. At the Anaconda Prompt, enter Spyder.
3. See if the problem remains.

4. Delete the directory .spyder2 and then repeat the previous steps from Step 1. Depending on your ver-
sion of Windows, .spyder2 may be in C:\Documents and Settings\Your_User_Name or in
C:\Users\Your_User_Name.
Note: Replace Your_User_Name, with your Windows user name as it appears in the Documents and Settings
folder.
Problems running Anaconda on macOS 10.12.2
Cause
Some installations of Anaconda on macOS 10.12.2 experienced incorrect file and directory permissions, which caused
a range of errors with Navigator and other parts of Anaconda.
Solution
We recommend that any users with Anaconda on macOS 10.12.2 follow these steps:
1. Uninstall Anaconda. Open the Terminal.app or iTerm2 terminal application and remove your Anaconda direc-
tory, which will have a name such as “anaconda2” or “anaconda3”, by entering a command such as this: rm
-rf ~/anaconda3
2. Use a text editor such as TextEdit to open the file named .bash_profile in your home directory. If you see
a line that adds Anaconda or Miniconda to your PATH environment variable, remove this line, and then save
and close the file. For example, if you see a line such as export PATH="/Users/jsmith/anaconda3/
bin:$PATH", remove that line.
3. Update to macOS 10.12.3 or later.
4. Reinstall Anaconda.
“execution error: localhost doesn’t understand the “open location” message. (-1708)” when open-
ing a Jupyter notebook on macOS 10.12.5
Cause
This version of macOS seems to have a bug affecting some of the ways for a program to open a web page in a browser.
Solution
Several possible workarounds have been found for this bug.

You can explicitly set the browser in ~/.jupyter/jupyter_notebook_config.py with a line such as this:
c.NotebookApp.browser = u'Safari'
Or you can copy the Jupyter notebook URL from the log messages on the command line and paste it into your browser.
Or you can set the BROWSER environment variable: export BROWSER=/Applications/Google\
Chrome.app/Contents/MacOS/Google\ Chrome
Further information is available at the Jupyter bug tracker, the Python bug tracker, and this blog post.

Missing libgfortran on Power8
Cause
Anaconda 4.4.0.0 for Power8 did not include libgfortran.
Solution
Anaconda 4.4.0.1 and later for Power8 do include libgfortran.

Upgrade to the latest version of Anaconda:
conda update anaconda
Anaconda 4.4.0.0 users who do not wish to upgrade may instead install libgfortran with this command:
conda install libgfortran
Missing libgomp on Power8
If the Python command “import numpy” fails, the system is likely missing the libgomp system library.
Cause
Most Power8 Linux distributions include libgomp, but some may not.
Solution
Check whether the system is missing libgomp with this command:
conda inspect linkages -n root numpy
If libgomp.so.1 is listed in the “not found:” section, it must be installed.

Install libgomp on Ubuntu with this command:
apt install libgomp1
Install libgomp on Red Hat Enterprise Linux (RHEL) or CentOS with this command:
yum install libgomp
Anaconda on Power8 reports “can not execute binary file”
Cause
Anaconda on Power8 only supports little endian mode. The little endian Python binary will not execute on a big endian
operating system.

Solution
Install Anaconda on Power8 on a little endian Linux installation or VM.
Uninstaller requests admin privileges on Windows
Cause
After installing Anaconda or Miniconda as a non-administrative user on Windows, uninstalling may prompt for ad-
ministrative privileges.
This occurs when running the uninstaller by choosing Control Panel, System, Apps & features, Python x.x.x (Mini-
conda3 4.3.xx 64-bit), Uninstall.
Solution
Open the Anaconda or Miniconda installation folder and run the .exe file uninstaller from that location. Uninstalla-
tion will complete without prompting for administrative privileges.
EXAMPLE: If you installed Miniconda3, the uninstall file will be Uninstall-Miniconda3.exe. Users who
installed Miniconda2 or Anaconda will find a similar file with the appropriate name.
Windows permission errors when installing from Favorites folder
Cause
The Windows Favorites folder has unusual permissions and may cause permission errors with installers of any soft-
ware. If you try launching the installer from the Favorites folder you may see errors such as “Setup was unable to
create the directory”, “Access is denied”, or “Error opening file for writing”.
Solution
Move the installer to a different folder and run the installer from the new folder.
Trouble with activation on PowerShell on Windows
Solution
If you run into the following backtrace on Windows:
File "C:\Users\damia\Miniconda3\lib\site-packages\conda\activate.py", line 550, in _

˓→replace_prefix_in_path
assert last_idx is not None

AssertionError
Open a cmd.exe prompt. cd to where you installed conda and run:
python -m conda init

Close the cmd.exe prompt and the Anaconda Prompt or the Anaconda PowerShell Prompt as usual.
If this doesn’t work, try running:
conda update conda
Cannot install Distribution 2019.07 on a webfaction server
You may receive an error when trying to install Distribution 2019.07 for Linux on a webfaction server:
PREFIX=/home/myname/anaconda3
Unpacking payload ...
[13822] Error loading Python lib '/tmp/_MEI<randomstring>/libpython3.6m.so.1.0':
˓→dlopen /tmp_MEI<randomstring>/libpython3.6m.so.1.0: failed to map segment from
˓→shared object: Operation not permitted
ERROR: could not extract tar starting at offset 00000000000020980+9231072+2
Cause
This is caused by having TMP as a noexec.
Solution
To enable installation, you can temporarily set TMP to somewhere else from which you can execute software.
For example:
cd
mkdir TMPconda
TMP=~/TMPconda bash Anaconda3-2019.07-Linux-x86_64.sh
After installing, set the TMP folder back to its initial location.
Segmentation fault on package import with macOS Python 3.7 intepreter
In CPython < 3.8, using python3-config to determine a linking command line to compile an extension module
will cause that extension module to segfault upon import. python3-config does provide command-line flags but
for the different purpose of embedding a Python interpreter.
Cause
This is because of the command-line flags returned by python3-config. Before Python 3.8, those are needed to
embed the core Python interpreter into a different project altogether and not those that should be used when linking a
Python extension module.
Python modules should never link to the core Python interpreter library directly, either statically at build time or
dynamically at runtime. This is because the Python executable itself provides all the necessary functions and symbols.

Solution
You should only use python*-config --ldflags when linking to an interpreter library (either static or shared).
Action Python < 3.8 Python >= 3.8

Get command line to link to ex- python -c "import python3-config --ldflags
tension module sysconfig;
print(sysconfig.
get_config_var('LDSHARED'))"
Get command line to embed python3-config --ldflags python3-config --ldflags
Python interpreter --embed
python3-config doesn’t include the command/compiler name whereas the sysconfig way does. This works pro-
vided none of your arguments have spaces:
python -c "import sysconfig; print(' '.join(sysconfig.get_config_var('LDSHARED').

˓→split(' ')[1:]))"
Using 32- and 64-bit libraries and CONDA_FORCE_32BIT
To work with both 32- and 64-bit libraries, we recommend that you have two separate installs: Anaconda32 and
Anaconda64 or Miniconda32 and Miniconda64.
When working with both versions, add the path to your installer files to the PATH.
Note: Always specify which version you want to work with because mixing 32- and 64-bit packages can cause
problems in your environment.
To get the information about conda including your PATH, run: conda info -a
Using CONDA_FORCE_32BIT is not recommended because it forces 32-bit packages to be installed in the environ-
ment, but does not force 32-bit libraries to load at runtime.
CONDA_FORCE_32BIT should be used only when running conda-build to build 32-bit packages on a 64-bit system.
Packages
Anaconda package lists
All packages available in the latest release of Anaconda are listed on the pages linked below. These packages may be
installed with the command conda install PACKAGENAME and are located in the package repository.
Click the links below to see which packages are available for each version of Python (3.8, 3.7, or 3.9) and each
operating system and architecture.
Anaconda is available for 64 and 32 bit Windows, macOS, and 64 Linux on the Intel and AMD x86, x86-64 CPU,
AWS Graviton 2 / ARM 64, IBM Z and IBM Power CPU architectures.
An RSS feed is updated each time a new package is added to the Anaconda package repository.
To request a package not listed on this page, please create an issue on the Anaconda issues page.

Python 3.8 Python 3.7 Python 3.9

64-bit Windows 64-bit Windows, Py3.8 64-bit Windows, Py3.7 64-bit Windows, Py3.9
32-bit Windows 32-bit Windows, Py3.8 32-bit Windows, Py3.7 32-bit Windows, Py3.9
macOS macOS, Py3.8 macOS, Py3.7 macOS, Py3.9
64-bit Linux 64-bit Linux, Py3.8 64-bit Linux, Py3.7 64-bit Linux, Py3.9
64-bit Linux Graviton2 Linux on ARM64, Py3.8 Linux on ARM64, Py3.7 Linux on ARM64, Py3.9
ARM64
64-bit Linux on IBM Z Linux on IBM Z, Py3.8 Linux on IBM Z, Py3.7 Linux on IBM Z, Py3.9
64-bit Linux on IBM Power Linux on IBM Power, Linux on IBM Power, Linux on IBM Power,
CPUs Py3.8 Py3.7 Py3.9
Packages for 64-bit Windows with Python 3.7
Packages for macOS on x86_64 with Python 3.7
Packages for 64-bit Linux on x86_64 CPUs with Python 3.7
Packages for 64-bit Linux on ARMv8 CPUs with Python 3.7
Packages for 64-bit Linux on IBM Z CPUs with Python 3.7

Packages for 64-bit Linux on IBM Power CPUs with Python 3.7
R language packages for Anaconda
• R Essentials bundle
• More resources
• List of R packages for Anaconda
The R language packages are available to install with conda at http://repo.anaconda.com/pkgs/r/. You can install any
of these R language packages into your current environment with the conda command conda install -c r
package-name.
Note: Replace package-name with the name of the package. For example, you can install the package‘‘r-acepack‘‘
with the command conda install -c r r-acepack.
Many Comprehensive R Archive Network (CRAN) packages are available as conda packages. Anaconda does not
provide builds of the entire CRAN repository, so there are some packages in CRAN that are not available as conda
packages.
Tip: You can also search for any R package if you know the name, such as conda search -f r-EXACTNAME.
Replace EXACTNAME with the desired CRAN or MRAN R package name. For example, for rbokeh, you would use
conda search -f r-rbokeh.
R Essentials bundle
Rather than install each R language package individually, you can get the R Essentials bundle. It includes approxi-
mately 80 of the most popular scientific packages for the R programming language.
You can install the R Essentials bundle with this command:
conda install -c r r-essentials
More resources
• Using R language with Anaconda

• Latest index of R packages built by Anaconda, Inc. on repo.anaconda.com
• Latest index of R packages built by Anaconda, Inc. on Anaconda Cloud

List of R packages for Anaconda
Number of supported packages: 6993

ABCDEFGHIJKLMNOPQRST UV WXY Z
Table 3: Misc
Name Version
Summary/License Platforms
_r-mutex 1.0.0 A mutex package to ensure environment exclusivity between Anaconda R and linux-
MRO. / BSD 32,
linux-
64,
osx-
64,
win-
32,
win-
64
_r-xgboost- 2.0 None / None linux-
mutex 64,
osx-
64,
win-
64

Table 4: A
Name Version
abind 1.4_5 Combine multidimensional arrays into a single array. This is a generalization linux-
of ‘cbind’ and ‘rbind’. Works with vectors, matrices, and higher-dimensional 32,
arrays. Also provides functions ‘adrop’, ‘asub’, and ‘afill’ for manipulating, linux-
extracting and replacing data in arrays. / LGPL (>= 2) 64,
noarch,
osx-
64,
win-
32,
win-
64
acepack 1.4.1 Two nonparametric methods for multiple regression transform selection are linux-
provided. The first, Alternative Conditional Expectations (ACE), is an al- 32,
gorithm to find the fixed point of maximal correlation, i.e. it finds a set of linux-
transformed response variables that maximizes R^2 using smoothing functions 64,
[see Breiman, L., and J.H. Friedman. 1985. Estimating Optimal Transforma- osx-
tions for Multiple Regression and Correlation. Journal of the American Sta- 64,
tistical Association. 80:580-598. <doi:10.1080/01621459.1985.10478157>]. win-
Also included is the Additivity Variance Stabilization (AVAS) method which 32,
works better than ACE when correlation is low [see Tibshirani, R.. 1986. win-
Estimating Transformations for Regression via Additivity and Variance Sta- 64
bilization. Journal of the American Statistical Association. 83:394-405.
<doi:10.1080/01621459.1988.10478610>]. A good introduction to these two
methods is in chapter 16 of Frank Harrel’s Regression Modeling Strategies in
the Springer Series in Statistics. / MIT file LICENSE
adgoftest 0.3 Anderson-Darling GoF test with p-value calculation based on Marsaglia’s linux-
2004 paper Evaluating the Anderson-Darling Distribution / GPL 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
aer 1.2_6 Functions, data sets, examples, demos, and vignettes for the book Christian linux-
Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer- 32,
Verlag, New York. ISBN 978-0-387-77316-2. (See the vignette AER for a linux-
package overview.) / GPL-2 | GPL-3 64,
noarch,
osx-
64,
win-
32,
win-
64
afex 0.23_0Convenience functions for analyzing factorial experiments using ANOVA or linux-
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of be- 32,
tween, within (i.e., repeated-measures), or mixed (i.e., split-plot) ANOVAs for linux-
data in long format (i.e., one observation per row), automatically aggregating 64,
multiple observations per individual and cell of the design. mixed() fits mixed noarch,
models using lme4::lmer() and computes p-values for all fixed effects using osx-
524 Chapter
either Kenward-Roger or Satterthwaite approximation for degrees of 5. Anaconda.org
freedom 64,
(LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio win-
tests (LMMs and GLMMs). afex_plot() provides a high-level interface for 32,
interaction or one-way plots using ggplot2, combining raw data and model es- win-
Table 5: B
Name Version
backports 1.1.4 Functions introduced or changed since R v3.0.0 are re-implemented in this linux-
package. The backports are conditionally exported in order to let R resolve 32,
the function name to either the implemented backport, or the respective base linux-
version, if available. Package developers can make use of new functions or 64,
arguments by selectively importing specific backports to support older instal- osx-
lations. / GPL-2 64,
win-
32,
win-
64
base64enc 0.1_3 This package provides tools for handling base64 encoding. It is more flexible linux-
than the orphaned base64 package. / GPL-2 | GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64
bcp 4.0.3 Provides an implementation of the Barry and Hartigan (1993) product partition linux-
model for the normal errors change point problem using Markov Chain Monte 32,
Carlo. It also extends the methodology to regression models on a connected linux-
graph (Wang and Emerson, 2015); this allows estimation of change point mod- 64,
els with multivariate responses. Parallel MCMC, previously available in bcp osx-
v.3.0.0, is currently not implemented. / GPL (>= 2) 64,
win-
32,
win-
64
bdsmatrix 1.3_3 This is a special case of sparse matrices, used by coxme. / LGPL-2 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
bestglm 0.37 Best subset glm using information criteria or cross-validation. Implements linux-
PCR and PLS using AIC/BIC. Implements one-standard deviation rule for use 32,
with the caret package. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
bh 1.69.0_1
Boost provides free peer-reviewed portable C source libraries. A large part of linux-
Boost is provided as C template code which is resolved entirely at compile- 32,
time without linking. This package aims to provide the most useful subset of linux-
5.1. Anaconda Individual Edition
Boost libraries for template use among CRAN package. By placing these li- 64, 525
braries in this package, we offer a more efficient distribution system for CRAN noarch,
as replication of this code in the sources of other packages is avoided. As of re- osx-
lease 1.69.0-1, the following Boost libraries are included: ‘algorithm’ ‘align’ 64,
Table 6: C
Name Version
cairo 1.5_10R graphics device using cairographics library that can be used to cre- linux-
ate high-quality vector (PDF, PostScript and SVG) and bitmap output 32,
(PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). linux-
Since it uses the same back-end for all output, copying across formats is 64,
WYSIWYG. Files are created without the dependence on X11 or other exter- osx-
nal programs. This device supports alpha channel (semi-transparent drawing) 64,
and resulting images can contain transparent and semi-transparent regions. It win-
is ideal for use in server environments (file output) and as a replacement for 32,
other devices that don’t have Cairo’s capabilities such as alpha support or anti- win-
aliasing. Backends are modular such that any subset of backends is supported. 64
/ GPL-2
callr 3.2.0 It is sometimes useful to perform a computation in a separate R process, with- linux-
out affecting the current R process at all. This packages does exactly that. / 32,
MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
car 3.0_2 Functions to Accompany J. Fox and S. Weisberg, An R Companion to Applied linux-
Regression, Third Edition, Sage, in press. / GPL (>= 2) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
cardata 3.0_2 Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied linux-
Regression, Third Edition, Sage (forthcoming). / GPL (>= 2) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
caret 6.0_83Misc functions for training and plotting classification and regression models. / linux-
GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
catools 1.17.1.2
Contains several basic utility functions including: moving (rolling, running) linux-
window statistic functions, read/write for GIF and ENVI binary files, fast cal- 32,
culation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off- linux-
Table 7: D
Name Version
data.table 1.12.2Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast linux-
add/modify/delete of columns by group using no copies at all, list columns, 32,
friendly and fast character-separated-value read/write. Offers a natural and linux-
flexible syntax, for faster development. / MPL-2.0 | file LICENSE 64,
osx-
64,
win-
32,
win-
64
dbi 1.0.0 A database interface definition for communication between R and relational linux-
database management systems. All classes in this package are virtual and need 32,
to be extended by the various R/DBMS implementations. / LGPL (>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
dbplyr 1.4.0 A ‘dplyr’ back end for databases that allows you to work with remote database linux-
tables as if they are in-memory data frames. Basic features works with any 32,
database that has a ‘DBI’ back end; more advanced features require ‘SQL’ linux-
translation to be provided by the package author. / MIT file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
ddalpha 1.3.9 Contains procedures for depth-based supervised learning, which are entirely linux-
non-parametric, in particular the DDalpha-procedure (Lange, Mosler and 32,
Mozharovskyi, 2014 <doi:10.1007/s00362-012-0488-4>). The training data linux-
sample is transformed by a statistical depth function to a compact low- 64,
dimensional space, where the final classification is done. It also offers an osx-
extension to functional data and routines for calculating certain notions of sta- 64,
tistical depth functions. 50 multivariate and 5 functional classification prob- win-
lems are included. / GPL-2 32,
win-
64
debugme 1.1.0 Specify debug messages as special string constants, and control debugging of linux-
packages via environment variables. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
5.1. Anaconda Individual
deoptimr Edition Evolution (DE) stochastic algorithms for global optimization of
1.0_8 Differential 527
linux-
problems with and without constraints. The aim is to curate a collection of 32,
its state-of-the-art variants that (1) do not sacrifice simplicity of design, (2) linux-
are essentially tuning-free, and (3) can be efficiently implemented directly in 64,
Table 8: E
Name Version
e1071 1.7_1 Functions for latent class analysis, short time Fourier transform, fuzzy clus- linux-
tering, support vector machines, shortest path computation, bagged clustering, 32,
naive Bayes classifier, . . . / GPL-2 linux-
64,
osx-
64,
win-
32,
win-
64
ellipsis 0.1.0 In S3 generics, it’s useful to take . . . so that methods can have additional linux-
argument. But this flexibility comes at a cost: misspelled arguments will be 64,
silently ignored. The ellipsis packages is an experiment that allows a generic osx-
to warn if any arguments passed in . . . are not used. / GPL-3 64,
win-
32,
win-
64
emmeans 1.3.4 Obtain estimated marginal means (EMMs) for many linear, generalized linear, linux-
and mixed models. Compute contrasts or linear functions of EMMs, trends, 32,
and comparisons of slopes. Plots and compact letter displays. Least-squares linux-
means are discussed, and the term estimated marginal means is suggested, 64,
in Searle, Speed, and Milliken (1980) Population marginal means in the linear noarch,
model: An alternative to least squares means, The American Statistician 34(4), osx-
216-221 <doi:10.1080/00031305.1980.10483031>. / GPL-2 | GPL-3 64,
win-
32,
win-
64
essentials 3.6.0 Some essential packages for working with R / Various linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
essentials- 3.4.3 Essential R packages including MS R Client and MS Machine Learning / Var- linux-
mrclient ious 64,
win-
64
estimability 1.3 Provides tools for determining estimability of linear functions of regression linux-
coefficients, and ‘epredict’ methods that handle non-estimable cases correctly. 32,
Estimability theory is discussed in many linear-models textbooks including linux-
Chapter 3 of Monahan, JF (2008), A Primer on Linear Models, Chapman and 64,
Hall (ISBN 978-1-4200-6201-4). / GPL (>= 3) noarch,
osx-
64,
win-
32,
win-
64
evaluate 0.13 Parsing and evaluation tools that make it easy to recreate the command line linux-
behaviour of R. / MIT file LICENSE 32,
linux-
Table 9: F
Name Version
fansi 0.4.0 Counterparts to R string manipulation functions that account for the effects of linux-
ANSI text formatting control sequences. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64
fastica 1.2_1 Implementation of FastICA algorithm to perform Independent Component linux-
Analysis (ICA) and Projection Pursuit. / GPL-2 | GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64
fbasics 3042.89
Provides a collection of functions to explore and to investigate basic prop- linux-
erties of financial returns and related quantities. The covered fields include 32,
techniques of explorative data analysis and the investigation of distributional linux-
properties, including parameter estimation and hypothesis testing. Even more 64,
there are several utility functions for data handling and management. / GPL osx-
(>= 2) 64,
win-
32,
win-
64
feather 0.3.3 Read and write feather files, a lightweight binary columnar data store designed linux-
for maximum speed. / Apache License 2.0 32,
linux-
64,
osx-
64,
win-
32,
win-
64
fftw 1.0_5 Provides a simple and efficient wrapper around the fastest Fourier transform linux-
in the west (FFTW) library <http://www.fftw.org/>. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
fgarch 3042.83.1
Provides a collection of functions to analyze and model heteroskedastic be- linux-
havior in financial time series models. / GPL (>= 2) 32,
linux-
64,
osx-
5.1. Anaconda Individual Edition 64, 529
win-
32,
win-
Table 10: G
Name Version
gdata 2.18.0Various R programming tools for data manipulation, including: - medical unit linux-
conversions (‘ConvertMedUnits’, ‘MedUnits’), - combining objects (‘bind- 32,
Data’, ‘cbindX’, ‘combine’, ‘interleave’), - character vector operations (‘cen- linux-
terText’, ‘startsWith’, ‘trim’), - factor manipulation (‘levels’, ‘reorder.factor’, 64,
‘mapLevels’), - obtaining information about R objects (‘object.size’, ‘elem’, noarch,
‘env’, ‘humanReadable’, ‘is.what’, ‘ll’, ‘keep’, ‘ls.funs’, ‘Args’,’nPairs’, osx-
‘nobs’), - manipulating MS-Excel formatted files (‘read.xls’, ‘installXLSX- 64,
support’, ‘sheetCount’, ‘xlsFormats’), - generating fixed-width format files win-
(‘write.fwf’), - extricating components of date & time objects (‘getYear’, ‘get- 32,
Month’, ‘getDay’, ‘getHour’, ‘getMin’, ‘getSec’), - operations on columns win-
of data frames (‘matchcols’, ‘rename.vars’), - matrix operations (‘unmatrix’, 64
‘upperTriangle’, ‘lowerTriangle’), - operations on vectors (‘case’, ‘unknown-
ToNA’, ‘duplicated2’, ‘trimSum’), - operations on data frames (‘frameApply’,
‘wideByFactor’), - value of last evaluated expression (‘ans’), and - wrapper for
‘sample’ that ensures consistent behavior for both scalar and vector arguments
(‘resample’). / GPL-2
generics 0.0.2 In order to reduce potential package dependencies and conflicts, generics pro- linux-
vides a number of commonly used S3 generics. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
64
geometry 0.4.1 Makes the ‘Qhull’ library <http://www.qhull.org> available in R, in a simi- linux-
lar manner as in Octave and MATLAB. Qhull computes convex hulls, Delau- 32,
nay triangulations, halfspace intersections about a point, Voronoi diagrams, linux-
furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It 64,
runs in 2D, 3D, 4D, and higher dimensions. It implements the Quickhull al- osx-
gorithm for computing the convex hull. Qhull does not support constrained 64,
Delaunay triangulations, or mesh generation of non-convex objects, but the win-
package does include some R functions that allow for this. / GPL (>= 3) 32,
win-
64
getopt 1.20.3Package designed to be used with Rscript to write ‘‘#!” shebang scripts that linux-
accept short and long flags/options. Many users will prefer using instead the 32,
packages optparse or argparse which add extra features like automatically gen- linux-
erated help option and usage, support for default values, positional argument 64,
support, etc. / GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64
ggplot2 3.1.1 A system for ‘declaratively’ creating graphics, based on The Grammar of linux-
Graphics. You provide the data, tell ‘ggplot2’ how to map variables to aes- 32,
thetics, what graphical primitives to use, and it takes care of the details. / linux-
GPL-2 | file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
Table 11: H
Name Version
haven 2.1.0 Import foreign statistical formats into R via the embedded ‘ReadStat’ C library, linux-
<https://github.com/WizardMac/ReadStat>. / MIT file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
hexbin 1.27.2Binning and plotting functions for hexagonal bins. / GPL-2 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
highcharter 0.7.0 A wrapper for the ‘Highcharts’ library including shortcut functions to plot linux-
R objects. ‘Highcharts’ <http://www.highcharts.com/> is a charting library 32,
offering numerous chart types with a simple configuration syntax. / MIT file linux-
LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
highr 0.8 Provides syntax highlighting for R source code. Currently it supports LaTeX linux-
and HTML output. Source code of other languages is supported via Andre 32,
Simon’s highlight package (<http://www.andre-simon.de>). / GPL linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
hmisc 4.2_0 Contains many functions useful for data analysis, high-level graphics, utility linux-
operations, functions for computing sample size and power, importing and 32,
annotating datasets, imputing missing values, advanced table making, variable linux-
clustering, character string manipulation, conversion of R objects to LaTeX 64,
and html code, and recoding variables. / GPL (>= 2) osx-
64,
win-
32,
win-
64
hms 0.4.2 Implements an S3 class for storing and formatting time-of-day values, based linux-
5.1. Anaconda Individual
on Edition
the ‘difftime’ class. / GPL-3 32, 531
linux-
64,
noarch,
Table 12: I
Name VersionSummary/License Platforms
igraph 1.2.4.1Routines for simple graphs and network analysis. It can handle large graphs linux-
very well and provides functions for generating random and regular graphs, 32,
graph visualization, centrality methods and much more. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
implyr 0.2.4 ‘SQL’ back-end to ‘dplyr’ for Apache Impala, the massively parallel process- linux-
ing query engine for Apache ‘Hadoop’. Impala enables low-latency ‘SQL’ 32,
queries on data stored in the ‘Hadoop’ Distributed File System ‘(HDFS)’, linux-
Apache ‘HBase’, Apache ‘Kudu’, Amazon Simple Storage Service ‘(S3)’, 64,
Microsoft Azure Data Lake Store ‘(ADLS)’, and Dell ‘EMC’ ‘Isilon’. See noarch,
<https://impala.apache.org> for more information about Impala. / Apache Li- osx-
cense 2.0 | file LICENSE 64,
win-
32,
win-
64
influencer 0.1.0 Provides functionality to compute various node centrality measures on net- linux-
works. Included are functions to compute betweenness centrality (by utilizing 32,
Madduri and Bader’s SNAP library), implementations of Burt’s constraint and linux-
effective network size (ENS) metrics, Borgatti’s algorithm to identify key play- 64,
ers, and Valente’s bridging metric. On Unix systems, the betweenness, Key osx-
Players, and bridging implementations are parallelized with OpenMP, which 64,
may run faster on systems which have OpenMP configured. / GPL-2 win-
32,
win-
64
ini 0.3.1 Parse simple ‘.ini’ configuration files to an structured list. Users can manipu- noarch
late this resulting list with lapply() functions. This same structured list can be
used to write back to file after modifications. / GPL-3
inline 0.3.15Functionality to dynamically define R functions and S4 methods with ‘inlined’ linux-
C, C or Fortran code supporting the .C and .Call calling conventions. / LGPL 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
ipred 0.9_8 Improved predictive models by indirect classification and bagging for classifi- linux-
cation, regression and survival problems as well as resampling based estima- 32,
tors of prediction error. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
irdisplay 0.7.0 An interface to the rich display capabilities of ‘Jupyter’ front-ends (e.g. linux-
‘Jupyter Notebook’) <https://jupyter.org>. Designed to be used from a run- 32,
Table 13: J
Name Version
janeaustenr 0.1.5 Full texts for Jane Austen’s 6 completed novels, ready for text analysis. These linux-
novels are Sense and Sensibility, Pride and Prejudice, Mansfield Park, Emma, 32,
Northanger Abbey, and Persuasion. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
jpeg 0.1_8 This package provides an easy and simple way to read, write and display linux-
bitmap images stored in the JPEG format. It can read and write both files 32,
and in-memory raw vectors. / GPL-2 | GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64
jsonlite 1.6 A fast JSON parser and generator optimized for statistical data and the web. linux-
Started out as a fork of ‘RJSONIO’, but has been completely rewritten in re- 32,
cent versions. The package offers flexible, robust, high performance tools for linux-
working with JSON in R and is particularly powerful for building pipelines 64,
and interacting with a web API. The implementation is based on the mapping osx-
described in the vignette (Ooms, 2014). In addition to converting JSON data 64,
from/to R objects, ‘jsonlite’ contains functions to stream, validate, and prettify win-
JSON data. The unit tests included with the package verify that all edge cases 32,
are encoded and decoded consistently for use with dynamic data in systems win-
and applications. / MIT file LICENSE 64

Table 14: K
keras 2.2.4.1Interface to ‘Keras’ <https://keras.io>, a high-level neural networks ‘API’. linux-
‘Keras’ was developed with a focus on enabling fast experimentation, supports 32,
both convolution based networks and recurrent networks (as well as combina- linux-
tions of the two), and runs seamlessly on both ‘CPU’ and ‘GPU’ devices. / 64,
MIT file LICENSE noarch,
osx-
64,
win-
64
kernlab 0.9_27Kernel-based machine learning methods for classification, regression, clus- linux-
tering, novelty detection, quantile regression and dimensionality reduction. 32,
Among other methods ‘kernlab’ includes Support Vector Machines, Spectral linux-
Clustering, Kernel PCA, Gaussian Processes and a QP solver. / GPL-2 64,
osx-
64,
win-
32,
win-
64
kernsmooth 2.23_15
Functions for kernel smoothing (and density estimation) corresponding to the linux-
book: Wand, M.P. and Jones, M.C. (1995) Kernel Smoothing. / Unlimited 32,
linux-
64,
osx-
64,
win-
32,
win-
64
knitr 1.22 Provides a general-purpose tool for dynamic report generation in R using Lit- linux-
erate Programming techniques. / GPL 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
kohonen 3.0.8 Functions to train self-organising maps (SOMs). Also interrogation of the linux-
maps and prediction using trained maps are supported. The name of the pack- 32,
age refers to Teuvo Kohonen, the inventor of the SOM. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64

Table 15: L
Name Version
labeling 0.3 Provides a range of axis labeling algorithms / MIT file LICENSE | Unlimited linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
lahman 6.0_0 Provides the tables from the ‘Sean Lahman Baseball Database’ as a set of R linux-
data.frames. It uses the data on pitching, hitting and fielding performance and 32,
other tables from 1871 through 2015, as recorded in the 2016 version of the linux-
database. / GPL 64,
noarch,
osx-
64,
win-
32,
win-
64
lars 1.2 Efficient procedures for fitting an entire lasso sequence with the cost of a single linux-
least squares fit. Least angle regression and infinitesimal forward stagewise 32,
regression are related to the lasso, as described in the paper below. / GPL-2 linux-
64,
osx-
64,
win-
32,
win-
64
later 0.8.0 Executes arbitrary R or C functions some time after the current time, after the linux-
R execution stack has emptied. / GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
lattice 0.20_38
A powerful and elegant high-level data visualization system inspired by Trel- linux-
lis graphics, with an emphasis on multivariate data. Lattice is sufficient for 32,
typical graphics needs, and is also flexible enough to handle most nonstandard linux-
requirements. See ?Lattice for an introduction. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64
latticeextra 0.6_28Building on the infrastructure provided by the lattice package, this package linux-
5.1. Anaconda Individual Edition
provides several new high-level functions and methods, as well as additional 32, 535
utilities such as panel and axis annotation functions. / GPL (>= 2) linux-
64,
noarch,
Table 16: M
Name Version
magic 1.5_9 A collection of efficient, vectorized algorithms for the creation and investiga-linux-
tion of magic squares and hypercubes, including a variety of functions for the 32,
manipulation and analysis of arbitrarily dimensioned arrays. The package in- linux-
cludes methods for creating normal magic squares of any order greater than 64,
2. The ultimate intention is for the package to be a computerized embodiment noarch,
all magic square knowledge, including direct numerical verification of proper- osx-
ties of magic squares (such as recent results on the determinant of odd-ordered 64,
semimagic squares). Some antimagic functionality is included. The package win-
also serves as a rebuttal to the often-heard comment I thought R was just for 32,
statistics. / GPL-2 win-
64
magrittr 1.5 Provides a mechanism for chaining commands with a new forward-pipe oper- linux-
ator, %>%. This operator will forward a value, or the result of an expression, 32,
into the next function call/expression. There is flexible support for the type of linux-
right-hand side expressions. For more information, see package vignette. To 64,
quote Rene Magritte, Ceci n’est pas un pipe. / MIT file LICENSE noarch,
osx-
64,
win-
32,
win-
64
manipulate 1.0.1 Interactive plotting functions for use within RStudio. The manipulate func- linux-
tion accepts a plotting expression and a set of controls (e.g. slider, picker, 32,
checkbox, or button) which are used to dynamically change values within the linux-
expression. When a value is changed using its corresponding control the ex- 64,
pression is automatically re-executed and the plot is redrawn. / GPL-2 noarch,
osx-
64,
win-
32,
win-
64
manipulatewidget 0.10.0Like package ‘manipulate’ does for static graphics, this package helps to easily linux-
add controls like sliders, pickers, checkboxes, etc. that can be used to modify 32,
the input data or the parameters of an interactive chart created with package linux-
‘htmlwidgets’. / GPL (>= 2) | file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
Continued on next page


Name Version
mapproj 1.2.6 Converts latitude/longitude into projected coordinates. / Lucent Public License
linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
maps 3.3.0 Display of maps. Projection code and larger maps are in separate packages linux-
(‘mapproj’ and ‘mapdata’). / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
maptools 0.9_5 Set of tools for manipulating geographic data. It includes binary access to linux-
‘GSHHG’ shoreline files. The package also provides interface wrappers for 32,
exchanging spatial objects with packages such as ‘PBSmapping’, ‘spatstat’, linux-
‘maps’, ‘RArcInfo’, and others. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64
markdown 0.9 Provides R bindings to the ‘Sundown’ ‘Markdown’ rendering library (<https: linux-
//github.com/vmg/sundown>). ‘Markdown’ is a plain-text formatting syntax 32,
that can be converted to ‘XHTML’ or other formats. See <http://en.wikipedia. linux-
org/wiki/Markdown> for more information about ‘Markdown’. / GPL-2 64,
osx-
64,
win-
32,
win-
64
mass 7.3_51.3
Functions and datasets to support Venables and Ripley, Modern Applied Statis- linux-
tics with S (4th edition, 2002). / GPL-2 | GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
matrix 1.2_17A rich hierarchy of matrix classes, including triangular, symmetric, and di- linux-
agonal matrices, both dense and sparse and with pattern, logical and numeric 32,
entries. Numerous methods for and operations on these matrices, using ‘LA- linux-
PACK’ and ‘SuiteSparse’ libraries. / GPL (>= 2) | file LICENCE 64,
osx-
64,
win-
32,
win-
64
matrixcalc 1.0_3 A collection of functions to support matrix calculations for probability, econo- linux-
metric and numerical analysis. There are additional functions that are compa- 64,
rable to APL functions which are useful for actuarial models such as pension win-
mathematics. This package is used for teaching and research purposes at the 64
Department of Finance and Risk Engineering, New York University, Polytech-
nic Institute, Brooklyn, NY 11201. / GPL (>= 2)
matrixmodels 0.4_1 Modelling with sparse and dense ‘Matrix’ matrices, using modular prediction linux-
and response module classes. / GPL (>= 2) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
matrixstats 0.54.0High-performing functions operating on rows and columns of matrices, e.g. linux-
col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized 64,
per data type and for subsetted calculations such that both memory usage and osx-
processing time is minimized. There are also optimized vector-based methods, 64,
e.g. binMeans(), madDiff() and weightedMedian(). / Artistic-2.0 win-
32,
win-
64
maxlik 1.3_4 Functions for Maximum Likelihood (ML) estimation and non-linear optimiza- linux-
tion, and related tools. It includes a unified way to call different optimizers, 32,
and classes and methods to handle the results from the ML viewpoint. It also linux-
includes a number of convenience tools for testing and developing your own 64,
models. / GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64


Name Version
memoise 1.1.0 Cache the results of a function so that when you call it again with the same linux-
arguments it returns the pre-computed value. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
mgcv 1.8_28Generalized additive (mixed) models, some of their extensions and other gen- linux-
eralized ridge regression with multiple smoothing parameter estimation by 32,
(Restricted) Marginal Likelihood, Generalized Cross Validation and similar, linux-
or using iterated nested Laplace approximation for fully Bayesian inference. 64,
See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a osx-
gam() function, a wide variety of smoothers, ‘JAGS’ support and distributions 64,
beyond the exponential family. / GPL (>= 2) win-
32,
win-
64
microbenchmark 1.4_6 Provides infrastructure to accurately measure and compare the execution time linux-
of R expressions. / BSD_2_clause file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
microsoftr 3.5.0.108
Umbrella package with licenses and notices for all Microsoft R packages / file linux-
LICENSE 64,
osx-
64,
win-
64
mime 0.6 Guesses the MIME type from a filename extension using the data derived from linux-
/etc/mime.types in UNIX-type systems. / GPL 32,
linux-
64,
osx-
64,
win-
32,
win-
64


miniui 0.1.1.1Provides UI widget and layout functions for writing Shiny apps that work well linux-
on small screens. / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
minqa 1.2.4 Derivative-free optimization by quadratic approximation based on an interface linux-
to Fortran implementations by M. J. D. Powell. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
misctools 0.6_22Miscellaneous small tools and utilities. Many of them facilitate the work linux-
with matrices, e.g. inserting rows or columns, creating symmetric matrices, 32,
or checking for semidefiniteness. Other tools facilitate the work with regres- linux-
sion models, e.g. extracting the standard errors, obtaining the number of (esti- 64,
mated) parameters, or calculating R-squared values. / GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64
mkl_fft 1.0.14NumPy-based implementation of Fast Fourier Transform using Intel (R) Math linux-
Kernel Library. / BSD 3-Clause 64,
osx-
64,
win-
32,
win-
64
mkl_random 1.0.4 Intel (R) MKL-powered package for sampling from common probability dis- linux-
tributions into NumPy arrays. / BSD 3-Clause 64,
osx-
64,
win-
32,
win-
64


Name Version
mlmrev 1.0_7 Data and examples from a multilevel modelling software review as well as linux-
other well-known data sets from the multilevel modelling literature. / GPL 32,
(>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
mnormt 1.5_5 Functions are provided for computing the density and the distribution func- linux-
tion of multivariate normal and t random variables, and for generating random 32,
vectors sampled from these distributions. Probabilities are computed via non- linux-
Monte Carlo methods; different routines are used in the case d=1, d=2, d>2, if 64,
d denotes the number of dimensions. / GPL-2 | GPL-3 osx-
64,
win-
32,
win-
64
modelmetrics 1.2.2 Collection of metrics for evaluating models written in C using ‘Rcpp’. Popular linux-
metrics include area under the curve, log loss, root mean square error, etc. / 32,
GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
modelr 0.1.4 Functions for modelling that help you seamlessly integrate modelling into a linux-
pipeline of data manipulation and visualisation. / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
modeltools 0.2_22A collection of tools to deal with statistical models. The functionality is ex- linux-
perimental and the user interface is likely to change in the future. The docu- 32,
mentation is rather terse, but packages ‘coin’ and ‘party’ have some working linux-
examples. However, if you find the implemented ideas interesting we would 64,
be very interested in a discussion of this proposal. Contributions are more than noarch,
welcome! / GPL-2 osx-
64,
win-
32,
win-
64
mongolite 2.0.1 High-performance MongoDB client based on ‘mongo-c-driver’ and ‘jsonlite’. linux-
Includes support for aggregation, indexing, map-reduce, streaming, encryp- 32,
tion, enterprise authentication, and GridFS. The online user manual provides linux-
an overview of the available methods in the package: <https://jeroen.github.io/ 64,
mongolite/>. / Apache License 2.0 osx-
64,
win-
32,
win-
64
mrclient 3.4.3 A free, community-supported, data science tool for high performance analytics linux-
/ Proprietary 64,
win-
64
mrclient-mlm 3.4.3 Pre-trained machine learning models for sentiment analysis and image detec- noarch
tion / Proprietary
mrclient-mml 3.4.3 Provides state-of-the-art fast, scalable machine learning algorithms and trans- linux-
forms for R / Proprietary 64,
win-
64
mro 0.1.1 Computes multiple correlation coefficient when the data matrix is given and linux-
tests its significance. / GPL-2 64,
win-
64
mro-base 3.5.1 R is a free software environment for statistical computing and graphics. / GPL- linux-
2 | GPL-3 64,
osx-
64,
win-
64
mro-base_impl 3.5.1 R is a free software environment for statistical computing and graphics. / GPL- linux-
2 | GPL-3 64,
win-
64
mro-basics 3.5.1 None / None linux-
64,
osx-
64,
win-
64


Name Version
multcomp 1.4_10Simultaneous tests and confidence intervals for general linear hypotheses in linux-
parametric models, including linear, generalized linear, linear mixed effects, 32,
and survival models. The package includes demos reproducing analyzes pre- linux-
sented in the book Multiple Comparisons Using R (Bretz, Hothorn, Westfall, 64,
2010, CRC Press). / GPL-2 noarch,
osx-
64,
win-
32,
win-
64
munsell 0.5.0 Provides easy access to, and manipulation of, the Munsell colours. Provides linux-
a mapping between Munsell’s original notation (e.g. 5R 5/10) and hexadec- 32,
imal strings suitable for use directly in R graphics. Also provides utilities to linux-
explore slices through the Munsell colour tree, to transform Munsell colours 64,
and display colour palettes. / MIT file LICENSE noarch,
osx-
64,
win-
32,
win-
64
mvtnorm 1.0_10Computes multivariate normal and t probabilities, quantiles, random deviates linux-
and densities. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64

Table 17: N
Name Version
networkd3 0.4 Creates ‘D3’ ‘JavaScript’ network, tree, dendrogram, and Sankey graphs from linux-
‘R’. / GPL (>= 3) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
nlme 3.1_139
Fit and compare Gaussian linear and nonlinear mixed-effects models. / GPL linux-
(>= 2) | file LICENCE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
nlopt-static 2.4.2 nonlinear optimization library / GNU Lesser General Public License (LGPL) linux-
32,
linux-
64,
osx-64
nloptr 1.2.1 Solve optimization problems using an R interface to NLopt. NLopt is a linux-
free/open-source library for nonlinear optimization, providing a common in- 32,
terface for a number of different free optimization routines available on- linux-
line as well as original implementations of various other algorithms. See 64,
<http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction> for more infor- osx-
mation on the available algorithms. During installation of nloptr on Unix- 64,
based systems, the installer checks whether the NLopt library is installed on win-
the system. If the NLopt library cannot be found, the code is compiled using 32,
the NLopt source included in the nloptr package. / LGPL-3 win-
64
nlp 0.2_0 Basic classes and methods for Natural Language Processing. / GPL-3 linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
nmf 0.21.0Provides a framework to perform Non-negative Matrix Factorization (NMF). linux-
The package implements a set of already published algorithms and seeding 32,
methods, and provides a framework to test, develop and plug new/custom al- linux-
gorithms. Most of the built-in algorithms have been optimized in C, and the 64,
main interface function provides an easy way of performing parallel computa- osx-
tions on multicore machines. / GPL (>= 2) 64,
win-
32,
win-
64
Table 18: O
Name Version
oce 1.0_1 Supports the analysis of Oceanographic data, including ‘ADCP’ measure- linux-
ments, measurements made with ‘argo’ floats, ‘CTD’ measurements, sectional 32,
data, sea-level time series, coastline and topographic data, etc. Provides spe- linux-
cialized functions for calculating seawater properties such as potential tem- 64,
perature in either the ‘UNESCO’ or ‘TEOS-10’ equation of state. Produces osx-
graphical displays that conform to the conventions of the Oceanographic liter- 64,
ature. / GPL (>= 2) win-
32,
win-
64
odbc 1.1.6 A DBI-compatible interface to ODBC databases. / MIT file LICENSE linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
openssl 1.3 Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Sup- linux-
ports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic sig- 32,
natures can either be created and verified manually or via x509 certificates. linux-
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for 64,
asymmetric (public key) encryption or EC for Diffie Hellman. High-level en- osx-
velope functions combine RSA and AES for encrypting arbitrary sized data. 64,
Other utilities include key generators, hash functions (md5, sha1, sha256, etc), win-
base64 encoder, a secure random number generator, and ‘bignum’ math meth- 32,
ods for manually performing crypto calculations on large multibyte integers. / win-
MIT file LICENSE 64
openxlsx 4.1.0 Simplifies the creation of Excel .xlsx files by providing a high level interface to linux-
writing, styling and editing worksheets. Through the use of ‘Rcpp’, read/write 32,
times are comparable to the ‘xlsx’ and ‘XLConnect’ packages with the added linux-
benefit of removing the dependency on Java. / MIT file LICENSE 64,
osx-
64,
win-
32,
win-
64

Table 19: P
Name Version
packrat 0.5.0 Manage the R packages your project depends on in an isolated, portable, and linux-
reproducible way. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
pbdzmq 0.3_3 ‘ZeroMQ’ is a well-known library for high-performance asynchronous mes- linux-
saging in scalable, distributed applications. This package provides high level 32,
R wrapper functions to easily utilize ‘ZeroMQ’. We mainly focus on inter- linux-
active client/server programming frameworks. For convenience, a minimal 64,
‘ZeroMQ’ library (4.2.2) is shipped with ‘pbdZMQ’, which can be used if no osx-
system installation of ‘ZeroMQ’ is available. A few wrapper functions com- 64,
patible with ‘rzmq’ are also provided. / GPL-3 win-
32,
win-
64
pbivnorm 0.6.0 Provides a vectorized R function for calculating probabilities from a standard linux-
bivariate normal CDF. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64
pbkrtest 0.4_7 Test in mixed effects models. Attention is on mixed effects models as imple- linux-
mented in the ‘lme4’ package. This package implements a parametric boot- 32,
strap test and a Kenward Roger modification of F-tests for linear mixed effects linux-
models and a parametric bootstrap test for generalized linear mixed models. / 64,
GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64
pcapp 1.9_73Provides functions for robust PCA by projection pursuit. The methods are linux-
described in Croux et al. (2006) <doi:10.2139/ssrn.968376>, Croux et al. 32,
(2013) <doi:10.1080/00401706.2012.727746>, Todorov and Filzmoser (2013) linux-
<doi:10.1007/978-3-642-33042-1_31>. / GPL (>= 3) 64,
osx-
64,
win-
32,
win-
64


Name Version
pdftools 2.2 Utilities based on ‘libpoppler’ for extracting text, fonts, attachments and meta-linux-
data from a PDF file. Also supports high quality rendering of PDF documents 64,
into PNG, JPEG, TIFF format, or into raw bitmap vectors for further process- osx-
ing in R. / MIT file LICENSE 64,
win-
32,
win-
64
perm 1.0_0.0
Perform Exact or Asymptotic permutation tests / GPL linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
pillar 1.3.1 Provides a ‘pillar’ generic designed for formatting columns of data using the linux-
full range of colours provided by modern terminals. / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
pkgbuild 1.0.3 Provides functions used to build R packages. Locates compilers needed to linux-
build R packages on various platforms and ensures the PATH is configured 64,
appropriately so R can use them. / GPL-3 noarch,
osx-
64,
win-
32,
win-
64
pkgconfig 2.0.2 Set configuration options on a per-package basis. Options set by a given pack- linux-
age only apply to that package, other packages are unaffected. / MIT file 32,
LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
pkgload 1.0.2 Simulates the process of installing a package and then attaching it. This is linux-
a key part of the ‘devtools’ package as it allows you to rapidly iterate while 64,
developing a package. / GPL-3 osx-
64,
win-
32,
win-
64
pkgmaker 0.27 Provides some low-level utilities to use for package development. It currently linux-
provides managers for multiple package specific options and registries, vi- 32,
gnette, unit test and bibtex related utilities. It serves as a base package for linux-
packages like NMF, RcppOctave, doRNG, and as an incubator package for 64,
other general purposes utilities, that will eventually be packaged separately. It noarch,
is still under heavy development and changes in the interface(s) are more than osx-
likely to happen. / GPL (>= 2) 64,
win-
32,
win-
64
pki 0.1_5.1
PKI functions such as verifying certificates, RSA encription and signing which linux-
can be used to build PKI infrastructure and perform cryptographic tasks. / 32,
GPL-2 | GPL-3 | file LICENSE linux-
64,
osx-
64,
win-
32,
win-
64
plm 1.7_0 A set of estimators and tests for panel data econometrics. / GPL (>= 2) linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
plogr 0.2.0 A simple header-only logging library for C. Add ‘LinkingTo: plogr’ to ‘DE- linux-
SCRIPTION’, and ‘#include <plogr.h>’ in your C modules to use it. / MIT file 32,
LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
plotly 4.9.0 Create interactive web graphics from ‘ggplot2’ graphs and/or a custom inter- linux-
face to the (MIT-licensed) JavaScript library ‘plotly.js’ inspired by the gram-32,
mar of graphics. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
pls 2.7_1 Multivariate regression methods Partial Least Squares Regression (PLSR), linux-
Principal Component Regression (PCR) and Canonical Powered Partial Least 64,
Squares (CPPLS). / GPL-2 noarch,
osx-
64,
win-
32,
win-
64
plumber 0.4.6 Gives the ability to automatically generate and serve an HTTP API from R linux-
functions using the annotations in the R documentation around your functions. 32,
/ MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
plyr 1.8.4 A set of tools that solves a common set of problems: you need to break a linux-
big problem down into manageable pieces, operate on each piece and then put 32,
all the pieces back together. For example, you might want to fit a model to linux-
each spatial location or time point in your study, summarise data by panels or 64,
collapse high-dimensional arrays to simpler summary statistics. The develop- osx-
ment of ‘plyr’ has been generously supported by ‘Becton Dickinson’. / MIT 64,
file LICENSE win-
32,
win-
64
png 0.1_7 This package provides an easy and simple way to read, write and display linux-
bitmap images stored in the PNG format. It can read and write both files and 32,
in-memory raw vectors. / GPL-2 | GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
polspline 1.1.14Routines for the polynomial spline fitting routines hazard regression, hazard linux-
estimation with flexible tails, logspline, lspec, polyclass, and polymars, by C.32,
Kooperberg and co-authors. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
pool 0.1.4.2Enables the creation of object pools, which make it less computationally ex- linux-
pensive to fetch a new object. Currently the only supported pooled objects are 32,
‘DBI’ connections. / GPL-3 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
praise 1.0.0 Build friendly R packages that praise their users if they have done something linux-
good, or they just need it to feel better. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
prettyunits 1.0.2 Pretty, human readable formatting of quantities. Time intervals: 1337000 -> linux-
15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 32,
1337 -> 1.34 kB. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
proc 1.14.0Tools for visualizing, smoothing and comparing receiver operating character- linux-
istic (ROC curves). (Partial) area under the curve (AUC) can be compared with 32,
statistical tests based on U-statistics or bootstrap. Confidence intervals can be linux-
computed for (p)AUC or ROC curves. / GPL (>= 3) 64,
osx-
64,
win-
32,
win-
64
processx 3.3.0 Tools to run system processes in the background. It can check if a background linux-
process is running; wait on a background process to finish; get the exit status of 32,
finished processes; kill background processes. It can read the standard output linux-
and error of the processes, using non-blocking connections. ‘processx’ can 64,
poll a process for standard output or error, with a timeout. It can also poll osx-
several processes at once. / MIT file LICENSE 64,
win-
32,
win-
64
prodlim 2018.04.18
Fast and user friendly implementation of nonparametric estimators for cen- linux-
sored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen 32,
method. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
profilemodel 0.6.0 Provides tools that can be used to calculate, evaluate, plot and use for infer- linux-
ence the profiles of arbitrary inference functions for arbitrary ‘glm’-like fitted 32,
models with linear predictors. More information on the methods that are im- linux-
plemented can be found in Kosmidis (2008) <https://www.r-project.org/doc/ 64,
Rnews/Rnews_2008-2.pdf>. / GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64
profvis 0.3.5 Interactive visualizations for profiling R code. / GPL-3 | file LICENSE linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
progress 1.2.0 Configurable Progress bars, they may include percentage, elapsed time, and/or noarch
the estimated completion time. They work in terminals, in ‘Emacs’ ‘ESS’,
‘RStudio’, ‘Windows’ ‘Rgui’ and the ‘macOS’ ‘R.app’. The package also
provides a ‘C’ ‘API’, that works with or without ‘Rcpp’. / MIT file LICENSE
promises 1.0.1 Provides fundamental abstractions for doing asynchronous programming in R linux-
using promises. Asynchronous programming is useful for allowing a single R 32,
process to orchestrate multiple tasks in the background while also attending
linux-
to something else. Semantics are similar to ‘JavaScript’ promises, but with a
64,
syntax that is idiomatic R. / MIT file LICENSE osx-
64,
win-
32,
win-
64
proto 1.0.0 An object oriented system using object-based, also called prototype-based, linux-
rather than class-based object oriented ideas. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
pryr 0.1.4 Useful tools to pry back the covers of R and understand the language at a linux-
deeper level. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
ps 1.3.0 List, query and manipulate all system processes, on ‘Windows’, ‘Linux’ and linux-
‘macOS’. / BSD_3_clause file LICENSE 64,
osx-
64,
win-
32,
win-
64


Name Version
pspline 1.0_18Smoothing splines with penalties on order m derivatives. / Unlimited linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
psych 1.8.12A general purpose toolbox for personality, psychometric theory and experi- linux-
mental psychology. Functions are primarily for multivariate analysis and scale 32,
construction using factor analysis, principal component analysis, cluster anal- linux-
ysis and reliability analysis, although others provide basic descriptive statis- 64,
tics. Item Response Theory is done using factor analysis of tetrachoric and noarch,
polychoric correlations. Functions for analyzing data at multiple levels in- osx-
clude within and between group statistics, including correlations and factor 64,
analysis. Functions for simulating and testing particular item and test struc- win-
tures are included. Several functions serve as a useful front end for struc- 32,
tural equation modeling. Graphical displays of path diagrams, factor anal- win-
ysis and structural equation models are created using basic graphics. Some 64
of the functions are written to support a book on psychometric theory as
well as publications in personality research. For more information, see the
<https://personality-project.org/r> web page. / GPL (>= 2)
purrr 0.3.2 A complete and consistent functional programming toolkit for R. / GPL-3 | file linux-
LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64

Table 20: Q
Name Version
qpdf 1.1 Content-preserving transformations transformations of PDF files such as split, linux-
combine, and compress. This package interfaces directly to the ‘qpdf’ C API 64,
and does not require any command line utilities. Note that ‘qpdf’ does not read osx-
actual content from PDF files: to extract text and data you need the ‘pdftools’ 64,
package. / Apache License 2.0 win-
32,
win-
64
qrm 0.4_13Accompanying package to the book Quantitative Risk Management: Con- linux-
cepts, Techniques and Tools by Alexander J. McNeil, RÃ¼diger Frey, and 64,
Paul Embrechts. / GPL (>= 2) osx-
64,
win-
32,
win-
64
quadprog 1.5_5 This package contains routines and documentation for solving quadratic pro- linux-
gramming problems. / GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
quantmod 0.4_14Specify, build, trade, and analyse quantitative financial trading strategies. / linux-
GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
quantreg 5.38 Estimation and inference methods for models of conditional quantiles: Lin- linux-
ear and nonlinear parametric and non-parametric (total variation penalized) 32,
models for conditional quantiles of a univariate response and several meth- linux-
ods for handling censored survival data. Portfolio selection methods based on 64,
expected shortfall risk are also included. / GPL (>= 2) osx-
64,
win-
32,
win-
64
qvcalc 0.9_1 Functions to compute quasi variances and associated measures of approxima- linux-
tion error. / GPL-2 | GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
Table 21: R
Name Version
r 3.6.0 R is a free software environment for statistical computing and graphics. / GPL- linux-
3.0 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-abc.data 1.0 Contains data which are used by functions of the ‘abc’ package. / GPL (>= 3) noarch
r-abc.rap 0.9.0 It aims to identify candidate genes that are “differentially methylated” between noarch
cases and controls. It applies Student’s t-test and delta beta analysis to identify
candidate genes containing multiple “CpG sites”. / GPL-3
r-abcoptim 0.15.0An implementation of Karaboga (2005) Artificial Bee Colony Optimization linux-
algorithm <http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf>. This (working) 64,
version is a Work-in-progress, which is why it has been implemented using osx-
pure R code. This was developed upon the basic version programmed in C and 64,
distributed at the algorithm’s official website. / MIT file LICENSE win-
64
r-abcp2 1.2 Tests the goodness of fit of a distribution of offspring to the Normal, Poisson, noarch
and Gamma distribution and estimates the proportional paternity of the second
male (P2) based on the best fit distribution. / GPL-2
r-abe 3.0.1 Performs augmented backward elimination and checks the stability of the ob- noarch
tained model. Augmented backward elimination combines significance or in-
formation based criteria with the change in estimate to either select the optimal
model for prediction purposes or to serve as a tool to obtain a practically sound,
highly interpretable model. More details can be found in Dunkler et al. (2014)
<doi:10.1371/journal.pone.0113677>. / GPL (>= 2)
r-abf2 0.7_1 Loads ABF2 files containing gap-free data from electrophysiological record- noarch
ings, as created by Axon Instruments/Molecular Devices software such as
pClamp 10. / Artistic-2.0
r-abind 1.4_5 Combine multidimensional arrays into a single array. This is a generalization linux-
of ‘cbind’ and ‘rbind’. Works with vectors, matrices, and higher-dimensional 32,
arrays. Also provides functions ‘adrop’, ‘asub’, and ‘afill’ for manipulating, linux-
extracting and replacing data in arrays. / LGPL (>= 2) 64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-abnormality 0.1.0 Contains the functions to implement the methodology and considerations laid noarch
out by Marks et al. in the manuscript Measuring Abnormality in High Dimen-
sional Spaces: Applications in Biomechanical Gait Analysis. As of 2/27/2018
this paper has been submitted and is under scientific review. Using high-
dimensional datasets to measure a subjectâ C™s overall level of abnormality
as compared to a reference population is often needed in outcomes research.
Utilizing applications in instrumented gait analysis, that article demonstrates
how using data that is inherently non-independent to measure overall abnor-
mality may bias results. A methodology is introduced to address this bias to
accurately measure overall abnormality in high dimensional spaces. While this
methodology is in line with previous literature, it differs in two major ways.
Advantageously, it can be applied to datasets in which the number of observa-
tions is less than the number of features/variables, and it can be abstracted to
practically any number of domains or dimensions. After applying the proposed
methodology to the original data, the researcher is left with a set of uncorre-
lated variables (i.e. principal components) with which overall abnormality can
be measured without bias. Different considerations are discussed in that article
in deciding the appropriate number of principal components to keep and the
aggregate distance measure to utilize. / MIT file LICENSE
r-abodoutlier 0.1 Performs angle-based outlier detection on a given dataframe. Three methods noarch
are available, a full but slow implementation using all the data that has cubic
complexity, a fully randomized one which is way more efficient and another
using k-nearest neighbours. These algorithms are specially well suited for high
dimensional data outlier detection. / MIT file LICENSE
r-abps 0.3 An implementation of the Abnormal Blood Profile Score (ABPS, part noarch
of the Athlete Biological Passport program of the World Anti-Doping
Agency), which combines several blood parameters into a single score in
order to detect blood doping (Sottas et al. (2006) <doi:10.2202/1557-
4679.1011>). The package also contains functions to calculate other scores
used in anti-doping programs, such as the OFF-score (Gore et al. (2003)
<http://www.haematologica.org/content/88/3/333>), as well as example data.
/ GPL (>= 2)
r-ac3net 1.2.2 Infers directional conservative causal core (gene) networks. It is an advanced noarch
version of the algorithm C3NET by providing directional network. Gokmen
Altay (2018) <doi:10.1101/271031>, bioRxiv. / GPL (>= 3)
r-aca 1.1 Offers an interactive function for the detection of breakpoints in series. / GPL noarch
r- 1.0_6 Provides functionality for creating and evaluating acceptance sampling plans. noarch
acceptancesampling Sampling plans can be single, double or multiple. / GPL (>= 3)
r-acclma 1.0 The main function is plotLMA(sourcefile,header) that takes a data set and plots noarch
the appropriate LMA and ACC graphs. If no sourcefile (a string) was passed,
a manual data entry window is opened. The header parameter indicates by
TRUE/FALSE (false by default) if the source CSV file has a head row or not.
The data set should contain only one independent variable (X) and one depen-
dent varialbe (Y) and can contain a weight for each observation / GPL-2
r-accrued 1.4.1 Package for visualizing data quality of partially accruing data. / GPL-3 noarch
r-acd 1.5.3 Categorical data analysis with complete or missing responses / GPL (>= 2) noarch


Name Version
r-ace2fastq 0.6.0 The ACE file format is used in genomics to store contigs from sequencing noarch
machines. This tools converts it into FASTQ format. Both formats contain the
sequence characters and their corresponding quality information. Unlike the
FASTQ file, the ace file stores the quality values numerically. The conversion
algorithm uses the standard Sanger formula. The package facilitates insertion
into pipelines, and content inspection. / GPL-3
r-acepack 1.4.1 Two nonparametric methods for multiple regression transform selection are linux-
provided. The first, Alternative Conditional Expectations (ACE), is an al- 32,
gorithm to find the fixed point of maximal correlation, i.e. it finds a set of linux-
transformed response variables that maximizes R^2 using smoothing functions 64,
[see Breiman, L., and J.H. Friedman. 1985. Estimating Optimal Transforma- osx-
tions for Multiple Regression and Correlation. Journal of the American Sta- 64,
tistical Association. 80:580-598. <doi:10.1080/01621459.1985.10478157>]. win-
Also included is the Additivity Variance Stabilization (AVAS) method which 32,
works better than ACE when correlation is low [see Tibshirani, R.. 1986. win-
Estimating Transformations for Regression via Additivity and Variance Sta- 64
bilization. Journal of the American Statistical Association. 83:394-405.
<doi:10.1080/01621459.1988.10478610>]. A good introduction to these two
methods is in chapter 16 of Frank Harrel’s Regression Modeling Strategies in
the Springer Series in Statistics. / MIT file LICENSE
r-acet 1.8.0 Twin models that are able to estimate the dynamic behaviour of the variance linux-
components in the classical twin models with respect to age using B-splines 64,
and P-splines. / GPL (>= 2) osx-
64,
win-
64
r-acfmperiod 1.0.0 Non-robust and robust computations of the sample autocovariance (ACOVF) noarch
and sample autocorrelation functions (ACF) of univariate and multivari-
ate processes. The methodology consists in reversing the diagonaliza-
tion procedure involving the periodogram or the cross-periodogram and
the Fourier transform vectors, and, thus, obtaining the ACOVF or the
ACF as discussed in Fuller (1995) <doi:10.1002/9780470316917>. The ro-
bust version is obtained by fitting robust M-regressors to obtain the M-
periodogram or M-cross-periodogram as discussed in Reisen et al. (2017)
<doi:10.1016/j.jspi.2017.02.008>. / GPL (>= 2)
r-acm4r 1.0 Fragment lengths or molecular weights from pairs of lanes are compared, and a noarch
number of matching bands are calculated using the Align-and-Count Method.
/ GPL
r-acmer 1.1.0 Implementation of estimator ACME, described in Wolpert (2015), ACME: noarch
A Partially Periodic Estimator of Avian & Chiropteran Mortality at Wind
Turbines (submitted). Unlike most other models, this estimator supports
decreasing-hazard Weibull model for persistence; decreasing search profi-
ciency as carcasses age; variable bleed-through at successive searches; and
interval mortality estimates. The package provides, based on search data, func-
tions for estimating the mortality inflation factor in Frequentist and Bayesian
settings. / MIT file LICENSE
r-acnr 1.0.0 Provides SNP array data from different types of copy-number regions. These noarch
regions were identified manually by the authors of the package and may be
used to generate realistic data sets with known truth. / LGPL (>= 2.1)


Name Version
r-acopula 0.9.3 Archimax copulas are mixture of Archimedean and EV copulas. The package noarch
provides definitions of several parametric families of generator and depen-
dence function, computes CDF and PDF, estimates parameters, tests for good-
ness of fit, generates random sample and checks copula properties for custom
constructs. In 2-dimensional case explicit formulas for density are used, in the
contrary to higher dimensions when all derivatives are linearly approximated.
Several non-archimax families (normal, FGM, Plackett) are provided as well.
/ GPL-2
r-acp 2.1 Analysis of count data exhibiting autoregressive properties, using the Autore- noarch
gressive Conditional Poisson model (ACP(p,q)) proposed by Heinen (2003). /
GPL-2
r-acrt 1.0.1 Functions for testing affine hypotheses on the regression coefficient vector in linux-
regression models with autocorrelated errors. / GPL-2 64,
osx-
64,
win-
64
r-acs 2.1.4 Provides a general toolkit for downloading, managing, analyzing, and pre- noarch
senting data from the U.S. Census (<https://www.census.gov/data/developers/
data-sets.html>), including SF1 (Decennial short-form), SF3 (Decennial long-
form), and the American Community Survey (ACS). Confidence intervals pro-
vided with ACS data are converted to standard errors to be bundled with es-
timates in complex acs objects. Package provides new methods to conduct
standard operations on acs objects and present/plot data in statistically appro-
priate ways. / GPL-3
r-acss 0.2_5 Main functionality is to provide the algorithmic complexity for short strings, noarch
an approximation of the Kolmogorov Complexity of a short string using the
coding theorem method (see ?acss). The database containing the complexity
is provided in the data only package acss.data, this package provides functions
accessing the data such as prob_random returning the posterior probability
that a given string was produced by a random process. In addition, two tra-
ditional (but problematic) measures of complexity are also provided: entropy
and change complexity. / GPL (>= 2)
r-acss.data 1.0 Data only package providing the algorithmic complexity of short strings, com- noarch
puted using the coding theorem method. For a given set of symbols in a string,
all possible or a large number of random samples of Turing machines (TM)
with a given number of states (e.g., 5) and number of symbols corresponding
to the number of symbols in the strings were simulated until they reached a
halting state or failed to end. This package contains data on 4.5 million strings
from length 1 to 12 simulated on TMs with 2, 4, 5, 6, and 9 symbols. The
complexity of the string corresponds to the distribution of the halting states of
the TMs. / GPL (>= 2)
r-acswr 1.0 A book designed to meet the requirements of masters students. Tattar, P.N., noarch
Suresh, R., and Manjunath, B.G. A Course in Statistics with R, J. Wiley, ISBN
978-1-119-15272-9. / GPL-2


Name Version
r-activedriver 1.0.0 A mutation analysis tool that discovers cancer driver genes with frequent muta- noarch
tions in protein signalling sites such as post-translational modifications (phos-
phorylation, ubiquitination, etc). The Poisson generalised linear regression
model identifies genes where cancer mutations in signalling sites are more fre-
quent than expected from the sequence of the entire gene. Integration of mu-
tations with signalling information helps find new driver genes and propose
candidate mechanisms to known drivers. Reference: Systematic analysis of
somatic mutations in phosphorylation signaling predicts novel cancer drivers.
Juri Reimand and Gary D Bader. Molecular Systems Biology (2013) 9:637
<doi:10.1038/msb.2012.68>. / GPL (>= 2)
r-activityindex 0.3.6 Read raw accelerometry from ‘GT3X’ data and plain table data to calculate noarch
Activity Index from Bai et al. (2016) <doi:10.1371/journal.pone.0160644>. /
GPL-3
r- 1.0.2 Performs estimation of physical activity and sedentary behavior variables from noarch
activpalprocessing activPAL (PAL Technologies, Glasgow, Scotland) events files. See <http://
paltechnologies.com> for more information on the activPAL. / GPL-2 | GPL-3
r-ada 2.0_5 Performs discrete, real, and gentle boost under both exponential and logistic noarch
loss on a given data set. The package ada provides a straightforward, well-
documented, and broad boosting routine for classification, ideally suited for
small to moderate-sized data sets. / GPL
r-adagio 0.7.1 The R package ‘adagio’ will provide methods and algorithms for discrete op- linux-
timization, e.g. knapsack and subset sum procedures, derivative-free Nelder- 64,
Mead and Hooke-Jeeves minimization, and some (evolutionary) global opti- osx-
mization functions. / GPL (>= 3) 64,
win-
64
r- 1.6 Implements Figueiredo EM algorithm for adaptive sparsity (Jeffreys prior) linux-
adaptivesparsity (see Figueiredo, M.A.T.; , Adaptive sparseness for supervised learning, Pat- 64,
tern Analysis and Machine Intelligence, IEEE Transactions on , vol.25, no.9, osx-
pp. 1150- 1159, Sept. 2003) and Wong algorithm for adaptively sparse gaus- 64,
sian geometric models (see Wong, Eleanor, Suyash Awate, and P. Thomas win-
Fletcher. Adaptive Sparsity in Gaussian Graphical Models. In Proceedings of 64
the 30th International Conference on Machine Learning (ICML-13), pp. 311-
319. 2013.) / LGPL (>= 3.0)
r-adaptivetau 2.2_3 Implements adaptive tau leaping to approximate the trajectory of a continuous- linux-
time stochastic process as described by Cao et al. (2007) The Journal of Chem- 64,
ical Physics <doi:10.1063/1.2745299> (aka. the Gillespie stochastic simula- osx-
tion algorithm). This package is based upon work supported by NSF DBI- 64,
0906041 and NIH K99-GM104158 to Philip Johnson and NIH R01-AI049334 win-
to Rustom Antia. / GPL (>= 3) 64
r-adaptmcmc 1.3 Enables sampling from arbitrary distributions if the log density is known noarch
up to a constant; a common situation in the context of Bayesian infer-
ence. The implemented sampling algorithm was proposed by Vihola (2012)
<DOI:10.1007/s11222-011-9269-5> and achieves often a high efficiency by
tuning the proposal distributions to a user defined acceptance rate. / GPL (>=
2)
r-adaptmt 1.0.0 Implementation of adaptive p-value thresholding (AdaPT), including both a noarch
framework that allows the user to specify any algorithm to learn local false
discovery rate and a pool of convenient functions that implement specific al-
gorithms. See Lei, Lihua and Fithian, William (2016) <arXiv:1609.06035>. /
MIT file LICENSE


Name Version
r-adapttest 1.0 The functions defined in this program serve for implementing adaptive two- noarch
stage tests. Currently, four tests are included: Bauer and Koehne (1994),
Lehmacher and Wassmer (1999), Vandemeulebroecke (2006), and the hori-
zontal conditional error function. User-defined tests can also be implemented.
Reference: Vandemeulebroecke, An investigation of two-stage tests, Statistica
Sinica 2006. / GPL (>= 2)
r-adct 0.1.0 Existing adaptive design methods in clinical trials. The package includes noarch
power, stopping boundaries (sample size) calculation functions for two-
group group sequential designs, adaptive design with coprimary endpoints,
biomarker-informed adaptive design, etc. / GPL (>= 2)
r-addhaz 0.5 Functions to fit the binomial and multinomial additive hazard models and to noarch
estimate the contribution of diseases/conditions to the disability prevalence,
as proposed by Nusselder and Looman (2004) and extended by Yokota et al
(2017). / GPL-3
r-additivitytests 1.1_4 Implementation of the Tukey, Mandel, Johnson-Graybill, LBI, Tusell and noarch
modified Tukey non-additivity tests. / GPL-3
r-addt 2.0 Accelerated destructive degradation tests (ADDT) are often used to collect noarch
necessary data for assessing the long-term properties of polymeric materials.
Based on the collected data, a thermal index (TI) is estimated. The TI can be
useful for material rating and comparison. This package implements the tradi-
tional method based on the least-squares method, the parametric method based
on maximum likelihood estimation, and the semiparametric method based on
spline methods, and the corresponding methods for estimating TI for poly-
meric materials. The traditional approach is a two-step approach that is cur-
rently used in industrial standards, while the parametric method is widely used
in the statistical literature. The semiparametric method is newly developed.
Both the parametric and semiparametric approaches allow one to do statistical
inference such as quantifying uncertainties in estimation, hypothesis testing,
and predictions. Publicly available datasets are provided illustrations. More
details can be found in Jin et al. (2017). / GPL-2
r-ade4 1.7_13Tools for multivariate data analysis. Several methods are provided for the anal- linux-
ysis (i.e., ordination) of one-table (e.g., principal component analysis, corre- 64,
spondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), osx-
three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia 64,
analysis). The philosophy of the package is described in Dray and Dufour win-
(2007) <doi:10.18637/jss.v022.i04>. / GPL (>= 2) 64
r-ade4tkgui 0.2_9 A Tcl/Tk GUI for some basic functions in the ‘ade4’ package. / GPL (>= 2) noarch
r-adegraphics 1.0_15Graphical functionalities for the representation of multivariate data. It is a noarch
complete re-implementation of the functions available in the ‘ade4’ package. /
GPL (>= 2)
r-adeptdata 1.0.1 Created to host raw accelerometry data sets and their derivatives which are noarch
used in the corresponding ‘adept’ package. / GPL-3
r- 2.0.0 The main application concerns to a new robust optimization package with noarch
adequacymodel two major contributions. The first contribution refers to the assessment of
the adequacy of probabilistic models through a combination of several statis-
tics, which measure the relative quality of statistical models for a given data
set. The second one provides a general purpose optimization method based on
meta-heuristics functions for maximizing or minimizing an arbitrary objective
function. / GPL (>= 2)


Name Version
r-adfexplorer 0.1.4 Amiga Disk Files (ADF) are virtual representations of 3.5 inch floppy disks noarch
for the Commodore Amiga. Most disk drives from other systems (including
modern drives) are not able to read these disks. To be able to emulate this
system, the ADF format was created. This package enables you to read ADF
files and import and export files from and to such virtual DOS-formatted disks.
/ GPL-3
r-adgoftest 0.3 Anderson-Darling GoF test with p-value calculation based on Marsaglia’s linux-
2004 paper Evaluating the Anderson-Darling Distribution / GPL 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-adimpro 0.9.0 Implements tools for manipulation of digital images and the Propagation linux-
Separation approach by Polzehl and Spokoiny (2006) <DOI:10.1007/s00440- 64,
005-0464-1> for smoothing digital images, see Polzehl and Tabelow (2007) osx-
<DOI:10.18637/jss.v019.i01>. / GPL (>= 2) 64,
win-
64
r-adjclust 0.5.7 Implements a constrained version of hierarchical agglomerative clustering, in linux-
which each observation is associated to a position, and only adjacent clusters 64,
can be merged. Typical application fields in bioinformatics include Genome- osx-
Wide Association Studies or Hi-C data analysis, where the similarity be- 64,
tween items is a decreasing function of their genomic distance. Taking ad- win-
vantage of this feature, the implemented algorithm is time and memory ef- 64
ficient. This algorithm is described in Chapter 4 of Alia Dehman (2015)
<https://hal.archives-ouvertes.fr/tel-01288568v1>. / GPL-3
r-adklakedata 0.6.1 Package for the access and distribution of Long-term lake datasets from lakes noarch
in the Adirondack Park, northern New York state. Includes a wide variety of
physical, chemical, and biological parameters from 28 lakes. Data are from
multiple collection organizations and have been harmonized in both time and
space for ease of reuse. / MIT file LICENSE
r-admisc 0.3 Contains functions used across packages ‘QCA’, ‘DDIwR’, and ‘venn’. In- noarch
terprets and translates DNF - Disjunctive Normal Form expressions, for both
binary and multi-value crisp sets, and extracts information (set names, set val-
ues) from those expressions. Other functions perform various other checks if
possibly numeric (even if all numbers reside in a character vector) and coerce
to numeric, or check if the numbers are whole. It also offers, among many
others, a highly flexible recoding function. / GPL (>= 2)
r-admit 2.1.3 Provides functions to perform the fitting of an adaptive mixture of Student- linux-
t distributions to a target density through its kernel function as described in 64,
Ardia et al. (2009) <doi:10.18637/jss.v029.i03>. The mixture approximation osx-
can then be used as the importance density in importance sampling or as the 64,
candidate density in the Metropolis-Hastings algorithm to obtain quantities of win-
interest for the target density itself. / GPL (>= 2) 64


Name Version
r-admmnet 0.1 Fit linear and cox models regularized with net (L1 and Laplacian), elastic-net linux-
(L1 and L2) or lasso (L1) penalty, and their adaptive forms, such as adaptive 64,
lasso and net adjusting for signs of linked coefficients. In addition, it treats osx-
the number of non-zero coefficients as another tuning parameter and simulta- 64,
neously selects with the regularization parameter. The package uses one-step win-
coordinate descent algorithm and runs extremely fast by taking into account 64
the sparsity structure of coefficients. / GPL (>= 2)
r-adoptr 0.2.2 Optimize one or two-arm, two-stage designs for clinical trials with respect to noarch
several pre-implemented objective criteria or implement custom objectives.
Optimization under uncertainty and conditional (given stage-one outcome)
constraints are supported. See Pilz M, Kunzmann K, Herrmann C, Rauch G,
Kieser M. A variational approach to optimal two-stage designs. Statistics in
Medicine. 2019;1â C“13. <doi:10.1002/sim.8291> for details. / MIT file LI-
CENSE
r-adpf 0.0.1 This function takes a vector or matrix of data and smooths the data with noarch
an improved Savitzky Golay transform. The Savitzky-Golay method for
data smoothing and differentiation calculates convolution weights using Gram
polynomials that exactly reproduce the results of least-squares polynomial re-
gression. Use of the Savitzky-Golay method requires specification of both
filter length and polynomial degree to calculate convolution weights. For max-
imum smoothing of statistical noise in data, polynomials with low degrees are
desirable, while a high polynomial degree is necessary for accurate reproduc-
tion of peaks in the data. Extension of the least-squares regression formalism
with statistical testing of additional terms of polynomial degree to a heuris-
tically chosen minimum for each data window leads to an adaptive-degree
polynomial filter (ADPF). Based on noise reduction for data that consist of
pure noise and on signal reproduction for data that is purely signal, ADPF
performed nearly as well as the optimally chosen fixed-degree Savitzky-Golay
filter and outperformed sub-optimally chosen Savitzky-Golay filters. For syn-
thetic data consisting of noise and signal, ADPF outperformed both optimally
chosen and sub-optimally chosen fixed-degree Savitzky-Golay filters. See
Barak, P. (1995) <doi:10.1021/ac00113a006> for more information. / GPL-
3
r-adpss 0.1.1 Provides the functions for planning and conducting a clinical trial with adap- linux-
tive sample size determination. Maximal statistical efficiency will be exploited 64,
even when dramatic or multiple adaptations are made. Such a trial consists of osx-
adaptive determination of sample size at an interim analysis and implementa- 64,
tion of frequentist statistical test at the interim and final analysis with a prefixed win-
significance level. The required assumptions for the stage-wise test statistics 64
are independent and stationary increments and normality. Predetermination of
adaptation rule is not required. / GPL (>= 2)
r-advdif4 0.7.18This software solves an Advection Bi-Flux Diffusive Problem using the Fi- noarch
nite Difference Method FDM. Vasconcellos, J.F.V., Marinho, G.M., Zanni,
J.H., 2016, Numerical analysis of an anomalous diffusion with a bimodal flux
distribution. <doi:10.1016/j.rimni.2016.05.001>. Silva, L.G., Knupp, D.C.,
Bevilacqua, L., Galeao, A.C.N.R., Silva Neto, A.J., 2014, Formulation and
solution of an Inverse Anomalous Diffusion Problem with Stochastic Tech-
niques. <doi:10.5902/2179460X13184>. In this version, it is possible to in-
clude a source as a function depending on space and time, that is, s(x,t). /
GPL-3


Name Version
r-adwordsr 0.3.1 Allows access to selected services that are part of the ‘Google Adwords’ API noarch
<https://developers.google.com/adwords/api/docs/guides/start>. ‘Google Ad-
words’ is an online advertising service by ‘Google’, that delivers Ads to users.
This package offers a authentication process using ‘OAUTH2’. Currently,
there are two methods of data of accessing the API, depending on the type of
request. One method uses ‘SOAP’ requests which require building an ‘XML’
structure and then sent to the API. These are used for the ‘ManagedCustom-
erService’ and the ‘TargetingIdeaService’. The second method is by building
‘AWQL’ queries for the reporting side of the ‘Google Adwords’ API. / MIT
file LICENSE
r-aer 1.2_6 Functions, data sets, examples, demos, and vignettes for the book Christian linux-
Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer- 32,
Verlag, New York. ISBN 978-0-387-77316-2. (See the vignette AER for a linux-
package overview.) / GPL-2 | GPL-3 64,
noarch,
osx-
64,
win-
32,
win-
64
r-afc 1.4.0 This is an implementation of the Generalized Discrimination Score (also noarch
known as Two Alternatives Forced Choice Score, 2AFC) for various repre-
sentations of forecasts and verifying observations. The Generalized Discrimi-
nation Score is a generic forecast verification framework which can be applied
to any of the following verification contexts: dichotomous, polychotomous
(ordinal and nominal), continuous, probabilistic, and ensemble. A compre-
hensive description of the Generalized Discrimination Score, including all
equations used in this package, is provided by Mason and Weigel (2009)
<doi:10.1175/MWR-D-10-05069.1>. / GPL-3
r-afex 0.23_0Convenience functions for analyzing factorial experiments using ANOVA or linux-
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of be- 32,
tween, within (i.e., repeated-measures), or mixed (i.e., split-plot) ANOVAs for linux-
data in long format (i.e., one observation per row), automatically aggregating 64,
multiple observations per individual and cell of the design. mixed() fits mixed noarch,
models using lme4::lmer() and computes p-values for all fixed effects using osx-
either Kenward-Roger or Satterthwaite approximation for degrees of freedom 64,
(LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio win-
tests (LMMs and GLMMs). afex_plot() provides a high-level interface for 32,
interaction or one-way plots using ggplot2, combining raw data and model es- win-
timates. afex uses type 3 sums of squares as default (imitating commercial 64
statistical software). / GPL (>= 2)
r-affluenceindex 1.0 Computes the statistical indices of affluence (richness) and constructs boot- noarch
strap confidence intervals for these indices. Also computes the Wolfson polar-
ization index. / GPL-2


Name Version
r-afpt 1.0.0 Allows estimation and modelling of flight costs in animal (vertebrate) flight, noarch
implementing the aerodynamic power model described in Klein Heerenbrink
et al. (2015) <doi:10.1098/rspa.2014.0952>. Taking inspiration from the pro-
gram ‘Flight’, developed by Colin Pennycuick (Pennycuick (2008) Modelling
the flying bird. Amsterdam: Elsevier. ISBN 0-19-857721-4), flight perfor-
mance is estimated based on basic morphological measurements such as body
mass, wingspan and wing area. ‘afpt’ can be used to make predictions on
how animals should adjust their flight behaviour and wingbeat kinematics to
varying flight conditions. / GPL (>= 3)
r-aggregater 0.0.2 Convenience functions for aggregating data frame. Currently mean, sum and noarch
variance are supported. For Date variables, recency and duration are sup-
ported. There is also support for dummy variables in predictive contexts. /
GPL-2
r-aggregation 1.0.1 Contains functionality for performing the following methods of p-value ag- noarch
gregation: Fisher’s method [Fisher, RA (1932, ISBN: 9780028447308)],
the Lancaster method (weighted Fisher’s method) [Lancaster, HO (1961,
<doi:10.1111/j.1467-842X.1961.tb00058.x>)], and Sidak correction [Sidak,
Z (1967, <doi:10.1080/01621459.1967.10482935>)]. Please cite Yi et
al., the manuscript corresponding to this package [Yi, L et al., (2017),
<doi:10.1101/190199>]. / GPL-3
r-aghmatrix 1.0.2 Computation of A (pedigree), G (genomic-base), and H (A corrected by G) linux-
relationship matrices for diploid and autopolyploid species. Several methods 64,
are implemented considering additive and non-additive models. / GPL-3 osx-
64,
win-
64
r-agop 0.2_2 Tools supporting multi-criteria and group decision making, including variable linux-
number of criteria, by means of aggregation operators, spread measures, fuzzy 64,
logic connectives, fusion functions, and preordered sets. Possible applications osx-
include, but are not limited to, quality management, scientometrics, software 64,
engineering, etc. / LGPL (>= 3) win-
64
r- 0.1.1 A tool for calculating agreement interval of two measurement methods (Ja- noarch
agreementinterval son Liao (2015) <DOI:10.1515/ijb-2014-0030>) and present results in plots
with discordance rate and/or clinically meaningful limit to quantify agreement
quality. / MIT file LICENSE
r-agridat 1.16 Datasets from books, papers, and websites related to agriculture. Example noarch
graphics and analyses are included. Data come from small-plot trials, multi-
environment trials, uniformity trials, yield monitors, and more. / CC BY-SA
4.0
r-agrmt 1.40.4Calculate agreement or consensus in ordered rating scales. The package im- noarch
plements van der Eijk’s (2001) <DOI: 10.1023/A:1010374114305> measure
of agreement A, which can be used to describe agreement, consensus, or po-
larization among respondents. It also implements measures of consensus (dis-
persion) by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth, Berry and
Mielke, and Garcia-Montalvo and Reynal-Querol. Furthermore, an implemen-
tation of Galtungs AJUS-system is provided to classify distributions, as well
as a function to identify the position of multiple modes. / GPL-3
r-agsemisc 1.3_1 High-featured panel functions for bwplot and xyplot, some plot management noarch
helpers, various convenience functions / GPL-2


Name Version
r-ahaz 1.14 Computationally efficient procedures for regularized estimation with the semi- linux-
parametric additive hazards regression model. / GPL-2 64,
osx-
64,
win-
64
r-ahocorasicktrie 0.1.0 Aho-Corasick is an optimal algorithm for finding many keywords in a text. linux-
It can locate all matches in a text in O(NM) time; i.e., the time needed scales 64,
linearly with the number of keywords (N) and the size of the text (M). Compare osx-
this to the naive approach which takes O(N*M) time to loop through each 64,
pattern and scan for it in the text. This implementation builds the trie (the win-
generic name of the data structure) and runs the search in a single function 64
call. If you want to search multiple texts with the same trie, the function will
take a list or vector of texts and return a list of matches to each text. By
default, all 128 ASCII characters are allowed in both the keywords and the
text. A more efficient trie is possible if the alphabet size can be reduced. For
example, DNA sequences use at most 19 distinct characters and usually only
4; protein sequences use at most 26 distinct characters and usually only 20.
UTF-8 (Unicode) matching is not currently supported. / Apache License 2.0
r-aidar 1.0.5 Read objects from the AIDA (<http://aida.freehep.org/>) file and make them noarch
available as dataframes in R. / LGPL (>= 2)
r-aim 1.01 R functions for adaptively constructing index models for continuous, binary noarch
and survival outcomes. Implementation requires loading R-pacakge survival /
LGPL-2
r-airgr 1.3.2.23
Hydrological modelling tools developed at Irstea-Antony (HYCAR Research linux-
Unit, France). The package includes several conceptual rainfall-runoff mod- 64,
els (GR4H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and osx-
melt model (CemaNeige) and the associated functions for their calibration and 64,
evaluation. Use help(airGR) for package description and references. / GPL-2 win-
64
r-airthermo 1.2.1 Deals with many computations related to the thermodynamics of atmospheric linux-
processes. It includes many functions designed to consider the density of air 64,
with varying degrees of water vapour in it, saturation pressures and mixing osx-
ratios, conversion of moisture indices, computation of atmospheric states of 64,
parcels subject to dry or pseudoadiabatic vertical evolutions and atmospheric win-
instability indices that are routinely used for operational weather forecasts or 64
meteorological diagnostics. / GPL-3
r-ake 1.0 Continuous and discrete (count or categorical) estimation of density, probabil- noarch
ity mass function (p.m.f.) and regression functions are performed using associ-
ated kernels. The cross-validation technique and the local Bayesian procedure
are also implemented for bandwidth selection. / GPL (>= 2)
r-akima 0.6_2 Several cubic spline interpolation methods of H. Akima for irregular and reg- linux-
ular gridded data are available through this package, both for the bivariate 64,
case (irregular data: ACM 761, regular data: ACM 760) and univariate case osx-
(ACM 433 and ACM 697). Linear interpolation of irregular gridded data is 64,
also covered by reusing D. J. Renkas triangulation code which is part of Aki- win-
mas Fortran code. A bilinear interpolator for regular grids was also added 64
for comparison with the bicubic interpolator on regular grids. / ACM | file
LICENSE (Restricts use)


Name Version
r-akmeans 1.1 Adaptive K-means algorithm with various threshold settings. It support two noarch
distance metric: Euclidean distance, Cosine distance (1 - cosine similarity) In
version 1.1, it contains one more threshold condition. / GPL-2
r-alabama 2015.3_1
Augmented Lagrangian Adaptive Barrier Minimization Algorithm for opti- noarch
mizing smooth nonlinear objective functions with constraints. Linear or non-
linear equality and inequality constraints are allowed. / GPL (>= 2)
r-albopictus 0.5 Implements discrete time deterministic and stochastic age-structured noarch
population dynamics models described in Erguler and others (2016)
<doi:10.1371/journal.pone.0149282> and Erguler and others (2017)
<doi:10.1371/journal.pone.0174293>. / GPL (>= 3)
r-ald 1.2 It provides the density, distribution function, quantile function, random num- noarch
ber generator, likelihood function, moments and Maximum Likelihood es-
timators for a given sample, all this for the three parameter Asymmetric
Laplace Distribution defined in Koenker and Machado (1999). This is a spe-
cial case of the skewed family of distributions available in Galarza et.al. (2017)
<doi:10.1002/sta4.140> useful for quantile regression. / GPL (>= 2)
r-alfr 1.2.1 Allows you to connect to an ‘Alfresco’ content management repository and noarch
interact with its contents using simple and intuitive functions. You will be able
to establish a connection session to the ‘Alfresco’ repository, read and upload
content and manage folder hierarchies. For more details on the ‘Alfresco’
content management repository see <https://www.alfresco.com/ecm-software/
document-management>. / GPL-3 | file LICENSE
r-algaeclassify 0.1.0 Functions designed to facilitate the assignment of morpho-functional group noarch
(MFG) classifications to phytoplankton species based on a combination of
taxonomy (Class,Order) and a suite of 7 binomial functional traits. Classifica-
tions can also be made using only a species list and a database of trait-derived
classifications included in the package. MFG classifications are derived from
Salmaso et al. (2015) <doi:10.1111/fwb.12520> and this reference should be
cited when using the package. The ‘algaeClassify’ package is a product of the
GEISHA (Global Evaluation of the Impacts of Storms on freshwater Habitat
and Structure of phytoplankton Assemblages), funded by CESAB (Centre for
Synthesis and Analysis of Biodiversity) and the USGS John Wesley Powell
Center, with data and other support provided by members of GLEON (Global
Lake Ecology Observation Network). This software is preliminary or provi-
sional and is subject to revision. It is being provided to meet the need for
timely best science. The software has not received final approval by the U.S.
Geological Survey (USGS). No warranty, expressed or implied, is made by
the USGS or the U.S. Government as to the functionality of the software and
related material nor shall the fact of release constitute any such warranty. The
software is provided on the condition that neither the USGS nor the U.S. Gov-
ernment shall be held liable for any damages resulting from the authorized on
unauthorized use of the software. / GPL (>= 3)
r-algdesign 1.1_7.3
Algorithmic experimental designs. Calculates exact and approximate theory linux-
experimental designs for D,A, and I criteria. Very large designs may be cre- 64,
ated. Experimental designs may be blocked or blocked designs created from osx-
a candidate list, using several criteria. The blocking can be done when whole 64,
and within plot factors interact. / GPL (>= 2) win-
64
r- 1.2 Two unordered pairs of data of two different snips positions is haplotyped by noarch
algebraichaplopackage resolving a small number ob closed equations. / GPL-2


Name Version
r-algorithmia 0.2.0 The company, Algorithmia, houses the largest marketplace of online algo- noarch
rithms. This package essentially holds a bunch of REST wrappers that make it
very easy to call algorithms in the Algorithmia platform and access files and di-
rectories in the Algorithmia data API. To learn more about the services they of-
fer and the algorithms in the platform visit <http://algorithmia.com>. More in-
formation for developers can be found at <http://developers.algorithmia.com>.
/ MIT file LICENSE
r-aliner 1.1.4 Functions are provided to calculate the ‘ALINE’ Distance between words as linux-
per (Kondrak 2000) and (Downey, Hallmark, Cox, Norquest, & Lansing, 2008, 64,
<doi:10.1080/09296170802326681>). The score is based on phonetic fea- osx-
tures represented using the Unicode-compliant International Phonetic Alpha- 64,
bet (IPA). Parameterized features weights are used to determine the optimal win-
alignment and functions are provided to estimate optimum values using a ge- 64
netic algorithm and supervised learning. See (Downey, Sun, and Norquest
2017, <https://journal.r-project.org/archive/2017/RJ-2017-005/index.html>. /
GPL-3
r-allan 1.01 Automated fitting of linear regression models and a stepwise routine / GPL-3 noarch
r-allanvar 1.1 A collection of tools for stochastic sensor error characterization using the Al- noarch
lan Variance technique originally developed by D. Allan. / GPL-2
r-allehap 0.9.9 Tools to simulate alphanumeric alleles, impute genetic missing data and recon- noarch
struct non-recombinant haplotypes from pedigree databases in a deterministic
way. Allelic simulations can be implemented taking into account many factors
(such as number of families, markers, alleles per marker, probability and pro-
portion of missing genotypes, recombination rate, etc). Genotype imputation
can be used with simulated datasets or real databases (previously loaded in
.ped format). Haplotype reconstruction can be carried out even with missing
data, since the program firstly imputes each family genotype (without a refer-
ence panel), to later reconstruct the corresponding haplotypes for each family
member. All this considering that each individual (due to meiosis) should un-
equivocally have two alleles per marker (one inherited from each parent) and
thus imputation and reconstruction results can be deterministically calculated.
/ GPL (>= 2)
r-allelematch 2.5.1 Tools for the identification of unique of multilocus genotypes when both geno- noarch
typing error and missing data may be present. The package is targeted at
those working with large datasets and databases containing multiple samples
of each individual, a situation that is common in conservation genetics, and
particularly in non-invasive wildlife sampling applications. Functions explic-
itly incorporate missing data, and can tolerate allele mismatches created by
genotyping error. If you use this tool, please cite the package using the jour-
nal article in Molecular Ecology Resources (Galpern et al., 2012). Please use
citation(‘allelematch’) to call the full citation. For users with access to the
associated journal article, tutorial material is also available as supplementary
material to the article describing this software, the citation for which can be
called using citation(‘allelematch’). / GPL-3
r-alleleretain 2.0.2 Simulate the effect of management or demography on allele retention and in- noarch
breeding accumulation in bottlenecked populations of animals with overlap-
ping generations. / GPL (>= 2)


Name Version
r-allelic 0.1 This is the implementation in RC of a new association test described in A linux-
fast, unbiased and exact allelic exact test for case-control association studies 64,
(Submitted). It appears that in most cases the classical chi-square test used for osx-
testing for allelic association on genotype data is biased. Our test is unbiased, 64,
exact but fast throught careful optimization. / GPL (>= 2) win-
64
r- 1.1 Contains functions possSpells.fnc and batch.possSpells.fnc. / GPL-2 noarch
allpossiblespellings
r-alluvial 0.1_2 Creating alluvial diagrams (also known as parallel sets plots) for multivariate noarch
and time series-like data. / MIT file LICENSE
r-alpaca 0.3.1 Provides a routine to concentrate out factors with many levels during the linux-
optimization of the log-likelihood function of the corresponding general- 64,
ized linear model (glm). The package is based on the algorithm proposed osx-
by Stammann (2018) <arXiv:1707.01815> and is restricted to glm’s that 64,
are based on maximum likelihood estimation and non-linear. It also offers win-
an efficient algorithm to recover estimates of the fixed effects in a post- 64
estimation routine and includes robust and multi-way clustered standard er-
rors. Further the package provides an analytical bias-correction for binary
choice models (logit and probit) derived by Fernandez-Val and Weidner (2016)
<doi:10.1016/j.jeconom.2015.12.014>. / GPL-3
r-alphasimr 0.10.0The successor to the ‘AlphaSim’ software for breeding program simulation linux-
[Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for 64,
stochastic simulations of breeding programs to the level of DNA sequence for osx-
every individual. Contained is a wide range of functions for modeling common 64,
tasks in a breeding program, such as selection and crossing. These functions win-
allow for constructing simulations of highly complex plant and animal breed- 64
ing programs via scripting in the R software environment. Such simulations
can be used to evaluate overall breeding program performance and conduct
research into breeding program design, such as implementation of genomic
selection. Included is the ‘Markovian Coalescent Simulator’ (‘MaCS’) for fast
simulation of biallelic sequences according to a population demographic his-
tory [Chen et al. (2009) <doi:10.1101/gr.083634.108>]. / MIT file LICENSE
r- 0.0.1 Download data from the Alpha Vantage API (<https://www.alphavantage. noarch
alphavantageclient co/>). Alpha Vantage is a RESTful API which provides various financial
data, including stock prices and technical indicators. There is documenta-
tion for the underlying API available here: <https://www.alphavantage.co/
documentation/>. To get access to this API, the user needs to first claim an
API key: <https://www.alphavantage.co/support/>. / MIT file LICENSE
r-alscpc 1.0 Using of the accelerated line search algorithm for simultaneously diagonalize noarch
a set of symmetric positive definite matrices. / GPL (>= 2)
r-alterryx 0.5.0 A tool to access each of the ‘Alteryx’ Gallery ‘API’ endpoints. Users can queue noarch
jobs, poll job status, and retrieve application output as a data frame. You will
need an ‘Alteryx’ Server license and have ‘Alteryx’ Gallery running to utilize
this package. The ‘API’ is accessed through the ‘URL’ that you setup for the
server running ‘Alteryx’ Gallery and more information on the endpoints can
be found at <https://gallery.alteryx.com/api-docs/>. / GPL-2
r-altmeta 2.2 Provides alternative statistical methods for meta-analysis, including new het- noarch
erogeneity tests and measures that are robust to outliers. / GPL (>= 2)


Name Version
r-altopt 0.1.1 Creates the optimal (D, U and I) designs for the accelerated life testing with noarch
right censoring or interval censoring. It uses generalized linear model (GLM)
approach to derive the asymptotic variance-covariance matrix of regression
coefficients. The failure time distribution is assumed to follow Weibull distri-
bution with a known shape parameter and log-linear link functions are used
to model the relationship between failure time parameters and stress variables.
The acceleration model may have multiple stress factors, although most ALTs
involve only two or less stress factors. ALTopt package also provides several
plotting functions including contour plot, Fraction of Use Space (FUS) plot
and Variance Dispersion graphs of Use Space (VDUS) plot. / GPL-3
r-amap 0.8_17Tools for Clustering and Principal Component Analysis (With robust methods, linux-
and parallelized functions). / GPL 64,
osx-
64,
win-
64
r-amap.seq 1.0 An Approximated Most Average Powerful Test with Optimal FDR Control noarch
with Application to RNA-seq Data / GPL (>= 2)
r-ambient 0.1.0 Generation of natural looking noise has many application within simulation, linux-
procedural generation, and art, to name a few. The ‘ambient’ package provides 64,
an interface to the ‘FastNoise’ C library and allows for efficient generation of osx-
perlin, simplex, worley, cubic, value, and white noise with optional pertubation 64,
in either 2, 3, or 4 (in case of simplex and white noise) dimensions. / MIT file win-
LICENSE 64
r-amcp 0.0.4 Accompanies Designing experiments and analyzing data: A model com- noarch
parison perspective (3rd ed.) by Maxwell, Delaney, & Kelley (forthcom-
ing from Routledge). Contains all of the data sets in the book’s chapters
and end-of-chapter exercises. Information about the book is available at
<http://www.DesigningExperiments.com>. / GPL (>= 3)
r-amctestmaker 1.0.0 Generate code for use with the Optical Mark Recognition free software Auto noarch
Multiple Choice (AMC). More specifically, this package provides functions
that use as input the question and answer texts, and output the LaTeX code for
AMC. / GPL-3
r-ameco 0.2.9 Annual macro-economic database provided by the European Commission. / noarch
CC0
r-amelia 1.7.5 A tool that multiply imputes missing data in a single cross-section (such as a linux-
survey), from a time series (like variables collected for each year in a coun- 64,
try), or from a time-series-cross-sectional data set (such as collected by years osx-
for each of several countries). Amelia II implements our bootstrapping-based 64,
algorithm that gives essentially the same answers as the standard IP or EMis win-
approaches, is usually considerably faster than existing approaches and can 64
handle many more variables. Unlike Amelia I and other statistically rigorous
imputation software, it virtually never crashes (but please let us know if you
find to the contrary!). The program also generalizes existing approaches by
allowing for trends in time series across observations within a cross-sectional
unit, as well as priors that allow experts to incorporate beliefs they have about
the values of missing cells in their data. Amelia II also includes useful diag-
nostics of the fit of multiple imputation models. The program works from the
R command line or via a graphical user interface that does not require users to
know R. / GPL (>= 2)


Name Version
r-amelie 0.2.1 Implements anomaly detection as binary classification for cross-sectional noarch
data. Uses maximum likelihood estimates and normal probability functions
to classify observations as anomalous. The method is presented in the fol-
lowing lecture from the Machine Learning course by Andrew Ng: <https:
//www.coursera.org/learn/machine-learning/lecture/C8IJp/algorithm/>, and is
also described in: Aleksandar Lazarevic, Levent Ertoz, Vipin Kumar, Aysel
Ozgur, Jaideep Srivastava (2003) <doi:10.1137/1.9781611972733.3>. / GPL
(>= 3)
r-amen 1.3 Analysis of dyadic network and relational data using additive and mul- noarch
tiplicative effects (AME) models. The basic model includes regression
terms, the covariance structure of the social relations model (Warner,
Kenny and Stoto (1979) <DOI:10.1037/0022-3514.37.10.1742>, Wong (1982)
<DOI:10.2307/2287296>), and multiplicative factor models (Hoff(2009)
<DOI:10.1007/s10588-008-9040-4>). Four different link functions ac-
commodate different relational data structures, including binary/network
data (bin), normal relational data (nrm), ordinal relational data (ord) and
data from fixed-rank nomination schemes (frn). Several of these link
functions are discussed in Hoff, Fosdick, Volfovsky and Stovel (2013)
<DOI:10.1017/nws.2013.17>. Development of this software was supported
in part by NIH grant R01HD067509. / GPL-3
r- 0.95 This package includes a set of pricing functions for American call options. noarch
americancallopt The following cases are covered: Pricing of an American call using the stan-
dard binomial approximation; Hedge parameters for an American call with a
standard binomial tree; Binomial pricing of an American call with continuous
payout from the underlying asset; Binomial pricing of an American call with
an underlying stock that pays proportional dividends in discrete time; Pricing
of an American call on futures using a binomial approximation; Pricing of a
currency futures American call using a binomial approximation; Pricing of a
perpetual American call. The user should kindly notice that this material is
for educational purposes only. The codes are not optimized for computational
efficiency as they are meant to represent standard cases of analytical and nu-
merical solution. / GPL-3
r-amerika 0.1.0 A color palette generator inspired by American politics, with colors ranging noarch
from blue on the left to gray in the middle and red on the right. A variety of
palettes allow for a range of applications from brief discrete scales (e.g., three
colors for Democrats, Independents, and Republicans) to continuous interpo-
lated arrays including dozens of shades graded from blue (left) to red (right).
This package greatly benefitted from building on the source code (with per-
mission) from Ram and Wickham (2015). / MIT file LICENSE
r-amget 1.0 AMGET allows to simply and rapidly creates highly informative diagnostic noarch
plots for ADAPT 5 models. Features include data analysis prior any model-
ing form either NONMEM or ADAPT shaped dataset, goodness-of-fit plots
(GOF), posthoc-fits plots (PHF), parameters distribution plots (PRM) and vi-
sual predictive check plots (VPC) based on ADAPT output. / GPL (>= 2)
r-aml 0.1_1 This package implements the adaptive mixed lasso (AML) method proposed noarch
by Wang et al.(2011). AML applies adaptive lasso penalty to a large number
of predictors, thus producing a sparse model, while accounting for the pop-
ulation structure in the linear mixed model framework. The package here is
primarily designed for application to genome wide association studies or ge-
nomic prediction in plant breeding populations, though it could be applied to
other settings of linear mixed models. / GPL (>= 2)


Name Version
r- 0.1 Provides a function to calculate the concentration of un-ionized ammonia in noarch
ammoniaconcentration the total ammonia in aqueous solution using the pH and temperature values. /
MIT file LICENSE
r-amore 0.2_15This package was born to release the TAO robust neural network algorithm to linux-
the R users. It has grown and I think it can be of interest for the users wanting 64,
to implement their own training algorithms as well as for those others whose osx-
needs lye only in the user space. / GPL (>= 2) 64,
win-
64
r-ampd 0.2 A method for automatic detection of peaks in noisy periodic and quasi- noarch
periodic signals. This method, called automatic multiscale-based peak de-
tection (AMPD), is based on the calculation and analysis of the local maxima
scalogram, a matrix comprising the scale-dependent occurrences of local max-
ima. For further information see <doi:10.3390/a5040588>. / GPL
r-anacoda 0.1.3.0Is a collection of models to analyze genome scale codon data using a Bayesian linux-
framework. Provides visualization routines and checkpointing for model fit- 64,
tings. Currently published models to analyze gene data for selection on codon osx-
usage based on Ribosome Overhead Cost (ROC) are: ROC (Gilchrist et al. 64,
(2015) <doi:10.1093/gbe/evv087>), and ROC with phi (Wallace & Drum- win-
mond (2013) <doi:10.1093/molbev/mst051>). In addition ‘AnaCoDa’ con- 64
tains three currently unpublished models. The FONSE (First order approxi-
mation On NonSense Error) model analyzes gene data for selection on codon
usage against of nonsense error rates. The PA (PAusing time) and PANSE
(PAusing time NonSense Error) models use ribosome footprinting data to an-
alyze estimate ribosome pausing times with and without nonsense error rate
from ribosome footprinting data. / GPL (>= 2)
r-analogsea 0.7.2 Provides a set of functions for interacting with the ‘Digital Ocean’ API at noarch
<https://developers.digitalocean.com/documentation/v2>, including creating
images, destroying them, rebooting, getting details on regions, and available
images. / MIT
r-analyz 1.4 Class with methods to read and execute R commands described as steps in a noarch
CSV file. / GPL (>= 2)
r-anapuce 2.3 Functions for normalisation, differentially analysis of microarray data and lo- noarch
cal False Discovery Rate. / GPL-2
r-ande 1.0 AODE achieves highly accurate classification by averaging over all of a small noarch
space. / GPL-3
r-andrews 1.0 Andrews curves for visualization of multidimensional data / GPL (>= 2) noarch
r-anfis 0.99.1The package implements ANFIS Type 3 Takagi and Sugeno’s fuzzy if-then noarch
rule network with the following features: (1) Independent number of member-
ship functions(MF) for each input, and also different MF extensible types. (2)
Type 3 Takagi and Sugeno’s fuzzy if-then rule (3) Full Rule combinations, e.g.
2 inputs 2 membership funtions -> 4 fuzzy rules (4) Hibrid learning, i.e. De-
scent Gradient for precedents and Least Squares Estimation for consequents
(5) Multiple outputs. / GPL (>= 2)
r-anmc 0.2.1 Computationally efficient method to estimate orthant probabilities of high- linux-
dimensional Gaussian vectors. Further implements a function to compute con- 64,
servative estimates of excursion sets under Gaussian random field priors. / osx-
GPL-3 64,
win-
64
r-annotlists 1.2 Annotate multiple lists from a specific annotation file. / GPL noarch


Name Version
r-anocva 0.1.1 Provides ANOCVA (ANalysis Of Cluster VAriability), a non-parametric sta- noarch
tistical test to compare clustering structures with applications in functional
magnetic resonance imaging data (fMRI). The ANOCVA allows us to com-
pare the clustering structure of multiple groups simultaneously and also to
identify features that contribute to the differential clustering. / GPL (>= 3)
r-anoint 1.4 The tools in this package are intended to help researchers assess multiple noarch
treatment-covariate interactions with data from a parallel-group randomized
controlled clinical trial. / GPL (>= 2)
r- 1.0 A technique for detecting anomalies in seasonal univariate time series. / linux-
anomalydetection Apache License 2.0 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r- 1.1.4 Allows for the computation of a prior predictive p-value to test replication noarch
anovareplication of relevant features of original ANOVA studies. Relevant features are cap-
tured in informative hypotheses. The package also allows for the computa-
tion of sample sizes for new studies, post-hoc power calculations, and comes
with a Shiny application in which all calculations can be conducted as well.
The statistical underpinnings are described in Zondervan-Zwijnenburg (2019)
<doi:10.31234/osf.io/6myqh>. / GPL (>= 3)
r- 0.1.7 Edit an ‘Antares’ simulation before running it : create new areas, links, thermal noarch
antareseditobject clusters or binding constraints or edit existing ones. Update ‘Antares’ general
& optimization settings. ‘Antares’ is an open source power system generator,
more information available here : <https://antares-simulator.org/>. / GPL (>=
2) | file LICENSE
r- 0.17.0Process results generated by ‘Antares’, a powerful open source software devel- noarch
antaresprocessing oped by RTE (Réseau de Transport d’Électricité) to simulate and study elec-
tric power systems (more information about ‘Antares’ here: <https://github.
com/AntaresSimulatorTeam/Antares_Simulator>). You can see the results of
several ANTARES studies here : <http://bpnumerique.rte-france.com/>. This
package provides functions to create new columns like net load, load factors,
upward and downward margins or to compute aggregated statistics like eco-
nomic surpluses of consumers, producers and sectors. / GPL (>= 2) | file
LICENSE
r-antaresread 2.2.4 Import, manipulate and explore results generated by ‘Antares’, a powerful noarch
open source software developed by RTE (Réseau de Transport d’Électricité) to
simulate and study electric power systems (more information about ‘Antares’
here : <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). You
can see the results of several ANTARES studies here : <http://bpnumerique.
rte-france.com/>. / GPL (>= 2) | file LICENSE
r-antiword 1.3 Wraps the ‘AntiWord’ utility to extract text from Microsoft Word documents. linux-
The utility only supports the old ‘doc’ format, not the new xml based ‘docx’ 64,
format. Use the ‘xml2’ package to read the latter. / GPL-2 osx-
64,
win-
64


Name Version
r-anylib 1.0.5 Made to make your life simpler with packages, by installing and loading a noarch
list of packages, whether they are on CRAN, Bioconductor or github. For
github, if you do not have the full path, with the maintainer name in it (e.g.
achateigner/topReviGO), it will be able to load it but not to install it. / CC
BY-SA 4.0
r-anytime 0.3.5 Convert input in any one of character, integer, numeric, factor, or ordered type linux-
into ‘POSIXct’ (or ‘Date’) objects, using one of a number of predefined for- 64,
mats, and relying on Boost facilities for date and time parsing. / GPL (>= osx-
2) 64,
win-
64
r-aod 1.3.1 Provides a set of functions to analyse overdispersed counts or proportions. noarch
Most of the methods are already available elsewhere but are scattered in differ-
ent packages. The proposed functions should be considered as complements to
more sophisticated methods such as generalized estimating equations (GEE)
or generalized linear mixed effect models (GLMM). / GPL (>= 2)
r-aods3 0.4_1.1
Provides functions to analyse overdispersed counts or proportions. These func- noarch
tions should be considered as complements to more sophisticated methods
such as generalized estimating equations (GEE) or generalized linear mixed
effect models (GLMM). aods3 is an S3 re-implementation of the deprecated
S4 package aod. / GPL (>= 2)
r-aoos 0.5.0 Another implementation of object-orientation in R. It provides syntactic sugar noarch
for the S4 class system and two alternative new implementations. One is an ex-
perimental version built around S4 and the other one makes it more convenient
to work with lists as objects. / MIT file LICENSE
r-aoptbdtvc 0.0.2 A collection of functions to construct A-optimal block designs for compar- noarch
ing test treatments with one or more control(s). Mainly A-optimal balanced
treatment incomplete block designs, weighted A-optimal balanced treatment
incomplete block designs, A-optimal group divisible treatment designs and
A-optimal balanced bipartite block designs can be constructed using the pack-
age. The designs are constructed using algorithms based on linear integer
programming. To the best of our knowledge, these facilities to construct A-
optimal block designs for comparing test treatments with one or more con-
trols are not available in the existing R packages. For more details on designs
for tests versus control(s) comparisons, please see Hedayat, A. S. and Ma-
jumdar, D. (1984) <doi:10.1080/00401706.1984.10487989> A-Optimal In-
complete Block Designs for Control-Test Treatment Comparisons, Techno-
metrics, 26, 363-370 and Mandal, B. N. , Gupta, V. K., Parsad, Rajen-
der. (2017) <doi:10.1080/03610926.2015.1071394> Balanced treatment in-
complete block designs through integer programming. Communications in
Statistics - Theory and Methods 46(8), 3728-3737. / GPL (>= 2)
r- 0.2.3 Provides capabilities to process Apache HTTPD Log files.The main function- noarch
apachelogprocessor alities are to extract data from access and error log files to data frames. /
LGPL-3 | file LICENSE
r-apc 1.3 Functions for age-period-cohort analysis. The data can be organised in ma- noarch
trices indexed by age-cohort, age-period or cohort-period. The data can in-
clude dose and response or just doses. The statistical model is a generalized
linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort fac-
tors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008)
<DOI:10.1093/biomet/asn026> is used. Thus, the analysis does not rely on ad
hoc identification. / GPL-3


Name Version
r-apcanalysis 1.0 Analysis of data from unreplicated orthogonal experiments / GPL-3 noarch
r-apcf 0.1.3 The adapted pair correlation function transfers the concept of the pair cor- win-
relation function from point patterns to patterns of objects of finite size and 64
irregular shape (e.g. lakes within a country). This is a reimplementation of the
method suggested by Nuske et al. (2009) <doi:10.1016/j.foreco.2009.09.050>
using the libraries ‘GEOS’ and ‘GDAL’ directly instead of through ‘PostGIS’.
/ GPL (>= 3)
r-apcluster 1.4.7 Implements Affinity Propagation clustering introduced by Frey and Dueck linux-
(2007) <DOI:10.1126/science.1136800>. The algorithms are largely analo- 64,
gous to the ‘Matlab’ code published by Frey and Dueck. The package further osx-
provides leveraged affinity propagation and an algorithm for exemplar-based 64,
agglomerative clustering that can also be used to join clusters obtained from win-
affinity propagation. Various plotting functions are available for analyzing 64
clustering results. / GPL (>= 2)
r-apdesign 1.0.0 An implementation of the additive polynomial (AP) design matrix. It con- noarch
structs and appends an AP design matrix to a data frame for use with longitu-
dinal data subject to seasonality. / GPL-3
r-ape 5.3 Functions for reading, writing, plotting, and manipulating phylogenetic trees, linux-
analyses of comparative data in a phylogenetic framework, ancestral charac- 32,
ter analyses, analyses of diversification and macroevolution, computing dis- linux-
tances from DNA sequences, reading and writing nucleotide sequences as 64,
well as importing from BioConductor, and several tools such as Mantel’s test, osx-
generalized skyline plots, graphical exploration of phylogenetic data (alex, 64,
trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees win-
using mean path lengths and penalized likelihood, dating trees with non- 32,
contemporaneous sequences, translating DNA into AA sequences, and as- win-
sessing sequence alignments. Phylogeny estimation can be done with the NJ, 64
BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling
incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding
triangle method). Some functions call external applications (PhyML, Clustal,
T-Coffee, Muscle) whose results are returned into R. / GPL (>= 2)
r-apercu 0.2.3 The goal is to print an aperÃ§u, a short view of a vector, a matrix, a data.frame, noarch
a list or an array. By default, it prints the first 5 elements of each dimension.
By default, the number of columns is equal to the number of lines. If you want
to control the selection of the elements, you can pass a list, with each element
being a vector giving the selection for each dimension. / CC BY-SA 4.0
r-apfr 1.0.2 Implements a multiple testing approach to the choice of a threshold gamma on noarch
the p-values using the Average Power Function (APF) and Bayes False Dis-
covery Rate (FDR) robust estimation. Function apf_fdr() estimates both quan-
tities from either raw data or p-values. Function apf_plot() produces smooth
graphs and tables of the relevant results. Details of the methods can be found
in Quatto P, Margaritella N, et al. (2019) <doi:10.1177/0962280219844288>.
/ GPL-3
r-aplore3 0.9 An unofficial companion to Applied Logistic Regression by D.W. Hosmer, S. noarch
Lemeshow and R.X. Sturdivant (3rd ed., 2013) containing the dataset used in
the book. / GPL-3


Name Version
r-aplpack 1.3.3 Some functions for drawing some special plots: The function ‘bagplot’ plots noarch
a bagplot, ‘faces’ plots chernoff faces, ‘iconplot’ plots a representation of a
frequency table or a data matrix, ‘plothulls’ plots hulls of a bivariate data set,
‘plotsummary’ plots a graphical summary of a data set, ‘puticon’ adds icons
to a plot, ‘skyline.hist’ combines several histograms of a one dimensional data
set in one plot, ‘slider’ functions supports some interactive graphics, ‘spin3R’
helps an inspection of a 3-dim point cloud, ‘stem.leaf’ plots a stem and leaf
plot, ‘stem.leaf.backback’ plots back-to-back versions of stem and leaf plot. /
GPL (>= 2)
r-apml0 0.9 Fit linear, logistic and Cox models regularized with L0, lasso (L1), elastic- linux-
net (L1 and L2), or net (L1 and Laplacian) penalty, and their adaptive forms, 64,
such as adaptive lasso / elastic-net and net adjusting for signs of linked coeffi- osx-
cients. It solves L0 penalty problem by simultaneously selecting regularization 64,
parameters and the number of non-zero coefficients. This augmented and pe- win-
nalized minimization method provides an approximation solution to the L0 64
penalty problem, but runs as fast as L1 regularization problem. The package
uses one-step coordinate descent algorithm and runs extremely fast by taking
into account the sparsity structure of coefficients. It could deal with very high
dimensional data and has superior selection performance. / GPL (>= 2)
r-apng 1.0 Convert several png files into an animated png file. This package exports only noarch
a single function ‘apng’. Call the apng function with a vector of file names
(which should be png files) to convert them to a single animated png file. /
GPL-3 | file LICENSE
r-appestimation 0.1.1 Calculating predictive model performance measures adjusted for predic- noarch
tor distributions using density ratio method (Sugiyama et al., (2012,
ISBN:9781139035613)). L1 and L2 error for continuous outcome and C-
statistics for binomial outcome are computed. / GPL-2
r-apple 0.3 Approximate Path for Penalized Likelihood Estimators for Generalized Linear linux-
Models penalized by LASSO or MCP / GPL-2 64,
osx-
64,
win-
64
r- 1.1_7 A few functions and several data set for the Springer book ‘Applied Predictive noarch
appliedpredictivemodelingModeling’. / GPL-2
r-appnn 1.0_0 Amyloid propensity prediction neural network (APPNN) is an amyloidogenic- noarch
ity propensity predictor based on a machine learning approach through recur-
sive feature selection and feed-forward neural networks, taking advantage of
newly published sequences with experimental, in vitro, evidence of amyloid
formation. / GPL-3
r-approximator 1.2_7 Performs Bayesian prediction of complex computer codes when fast approx- noarch
imations are available. It uses a hierarchical version of the Gaussian process,
originally proposed by Kennedy and O’Hagan (2000), Biometrika 87(1):1. /
GPL-2
r-approxmatch 1.0 Tools for constructing a matched design with multiple comparison groups. noarch
Further specifications of refined covariate balance restriction and exact match
on covariate can be imposed. Matches are approximately optimal in the
sense that the cost of the solution is at most twice the optimal cost, Crama
and Spieksma (1992) <doi:10.1016/0377-2217(92)90078-N>. / MIT file LI-
CENSE


Name Version
r-aprean3 1.0.1 An unofficial companion to the textbook Applied Regression Analysis by N.R. noarch
Draper and H. Smith (3rd Ed., 1998) including all the accompanying datasets.
/ GPL-3
r-aprof 0.4.1 Assists the evaluation of whether and where to focus code optimization, us- noarch
ing Amdahl’s law and visual aids based on line profiling. Amdahl’s profiler
organizes profiling output files (including memory profiling) in a visually ap-
pealing way. It is meant to help to balance development vs. execution time by
helping to identify the most promising sections of code to optimize and pro-
jecting potential gains. The package is an addition to R’s standard profiling
tools and is not a wrapper for them. / GPL (>= 2)
r-apsimbatch 0.1.0.2374
Run APSIM in Batch mode / GPL-3 noarch
r-apsrtable 0.8_8 Formats latex tables from one or more model objects side-by-side with stan- noarch
dard errors below, not unlike tables found in such journals as the American
Political Science Review. / GPL (>= 2)
r-aptools 6.8.8 We provide tools to estimate two prediction accuracy metrics, the average pos- noarch
itive predictive values (AP) as well as the well-known AUC (the area under
the receiver operator characteristic curve) for risk scores. The outcome of in-
terest is either binary or censored event time. Note that for censored event
time, our functions’ estimates, the AP and the AUC, are time-dependent for
pre-specified time interval(s). A function that compares the APs of two risk
scores/markers is also included. Optional outputs include positive predictive
values and true positive fractions at the specified marker cut-off values, and a
plot of the time-dependent AP versus time (available for event time data). /
LGPL-3
r-aqr 0.4 This R extension provides methods to use a standalone ActiveQuant Master linux-
Server from within R. Currently available features include fetching and storing 64,
historical data, receiving and sending live data. Several utility methods for osx-
simple data transformations are included, too. For support requests, please join 64,
the mailing list at https://r-forge.r-project.org/mail/?group_id=1518 / GPL (>= win-
2) 64
r-ar 1.1 In mathematics, ‘rejection sampling’ is a basic technique used to generate ob- noarch
servations from a distribution. It is also commonly called ‘the Acceptance-
Rejection method’ or ‘Accept-Reject algorithm’ and is a type of Monte Carlo
method. ‘Acceptance-Rejection method’ is based on the observation that to
sample a random variable one can perform a uniformly random sampling of
the 2D cartesian graph, and keep the samples in the region under the graph of
its density function. Package ‘AR’ is able to generate/simulate random data
from a probability density function by Acceptance-Rejection method. More-
over, this package is a useful teaching resource for graphical presentation of
Acceptance-Rejection method. From the practical point of view, the user needs
to calculate a constant in Acceptance-Rejection method, which package ‘AR’
is able to compute this constant by optimization tools. Several numerical ex-
amples are provided to illustrate the graphical presentation for the Acceptance-
Rejection Method. / LGPL-3
r-arabicstemr 1.2 Allows users to stem Arabic texts for text analysis. / GPL (>= 2) noarch


Name Version
r-ararredux 1.0 Processes noble gas mass spectrometer data to determine the isotopic compo- noarch
sition of argon (comprised of Ar36, Ar37, Ar38, Ar39 and Ar40) released from
neutron-irradiated potassium-bearing minerals. Then uses these compositions
to calculate precise and accurate geochronological ages for multiple samples
as well as the covariances between them. Error propagation is done in matrix
form, which jointly treats all samples and all isotopes simultaneously at ev-
ery step of the data reduction process. Includes methods for regression of the
time-resolved mass spectrometer signals to t=0 (‘time zero’) for both single-
and multi-collector instruments, blank correction, mass fractionation correc-
tion, detector intercalibration, decay corrections, interference corrections, in-
terpolation of the irradiation parameter between neutron fluence monitors, and
(weighted mean) age calculation. All operations are performed on the logs of
the ratios between the different argon isotopes so as to properly treat them as
‘compositional data’, sensu Aitchison [1986, The Statistics of Compositional
Data, Chapman and Hall]. / GPL-2
r-arc 1.2 Implements the Classification-based on Association Rules (CBA) (Bing Liu, noarch
Wynne Hsu, Yiming Ma (1999) <http://dl.acm.org/citation.cfm?id=3000292.
3000305>) algorithm for association rule classification (ARC). The package
also contains several convenience methods that allow to automatically set CBA
parameters (minimum confidence, minimum support) and it also natively han-
dles numeric attributes by integrating a pre-discretization step. The rule gener-
ation phase is handled by the ‘arules’ package. To further decrease the size of
the CBA models produced by the ‘arc’ package, postprocessing by the ‘qCBA’
package is suggested. / AGPL-3
r-archdata 1.2 The archdata package provides several types of data that are typically used in noarch
archaeological research. It provides all of the data sets used in Quantitative
Methods in Archaeology Using R by David L Carlson, one of the Cambridge
Manuals in Archaeology. / GPL
r-arco 0.3_1 Set of functions to analyse and estimate Artificial Counterfactual models from noarch
Carvalho, Masini and Medeiros (2016) <DOI:10.2139/ssrn.2823687>. / MIT
file LICENSE
r-ardec 2.0 Package ArDec implements autoregressive-based decomposition of a time se- noarch
ries based on the constructive approach in West (1997). Particular cases in-
clude the extraction of trend and seasonal components. / GPL (>= 2)
r-areaplot 1.2_1 Plot stacked areas and confidence bands as filled polygons, or add polygons noarch
to existing plots. A variety of input formats are supported, including vectors,
matrices, data frames, formulas, etc. / GPL (>= 2)
r-arf3ds4 2.5_10Activated Region Fitting (ARF) is an analysis method for fMRI data. / GPL-2 linux-
64,
osx-
64,
win-
64
r-argo 2.0.0 Augmented Regression with General Online data (ARGO) for accurate estima- noarch
tion of influenza epidemics in United States on both national level and regional
level. It replicates the method introduced in paper Yang, S., Santillana, M. and
Kou, S.C. (2015) <doi:10.1073/pnas.1515373112> and Ning, S., Yang, S. and
Kou, S.C. (2019) <doi:10.1038/s41598-019-41559-6>. / GPL-2


Name Version
r-argon2 0.2_0 Utilities for secure password hashing via the argon2 algorithm. It is a rel- linux-
atively new hashing algorithm and is believed to be very secure. The ‘ar- 64,
gon2’ implementation included in the package is the reference implementa- osx-
tion. The package also includes some utilities that should be useful for di- 64,
gest authentication, including a wrapper of ‘blake2b’. For similar R pack- win-
ages, see sodium and ‘bcrypt’. See <https://en.wikipedia.org/wiki/Argon2> or 64
<https://eprint.iacr.org/2015/430.pdf> for more information. / BSD 2-clause
License file LICENSE
r-argondash 0.1.0 Create awesome ‘Bootstrap 4’ dashboards powered by ‘Argon’. See more here noarch
<https://rinterface.github.io/argonDash/>. / GPL-2
r-argonr 0.1.0 R wrapper around the argon HTML library. More at <https://demos. noarch
creative-tim.com/argon-design-system/>. / GPL-2
r-argosfilter 0.63 Functions to filters animal satellite tracking data obtained from Argos. It is noarch
especially indicated for telemetry studies of marine animals, where Argos lo-
cations are predominantly of low-quality. / GPL (>= 2)
r-argparse 2.0.1 A command line parser to be used with Rscript to write #! shebang scripts that linux-
gracefully accept positional and optional arguments and automatically gener- 32,
ate usage. / GPL (>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-argparser 0.4 Cross-platform command-line argument parser written purely in R with no noarch
external dependencies. It is useful with the Rscript front-end and facilitates
turning an R script into an executable script. / GPL (>= 3)
r-argumentcheck 0.10.2The typical process of checking arguments in functions is iterative. In this noarch
process, an error may be returned and the user may fix it only to receive another
error on a different argument. ‘ArgumentCheck’ facilitates a more helpful way
to perform argument checks allowing the programmer to run all of the checks
and then return all of the errors and warnings in a single message. / GPL-3
r-arht 0.1.0 Perform the Adaptable Regularized Hotelling’s T^2 test (ARHT) proposed by noarch
Li et al., (2016) <arXiv:1609.08725>. Both one-sample and two-sample mean
test are available with various probabilistic alternative prior models. It contains
a function to consistently estimate higher order moments of the population co-
variance spectral distribution using the spectral of the sample covariance ma-
trix (Bai et al. (2010) <doi:10.1111/j.1467-842X.2010.00590.x>). In addition,
it contains a function to sample from 3-variate chi-squared random vectors ap-
proximately with a given correlation matrix when the degrees of freedom are
large. / GPL (>= 2)
r-aricode 0.1.2 Implements an efficient O(n) algorithm based on bucket-sorting for fast com- linux-
putation of standard clustering comparison measures. Available measures in- 64,
clude adjusted Rand index (ARI), normalized information distance (NID), nor- osx-
malized mutual information (NMI), adjusted mutual information (AMI), nor- 64,
malized variation information (NVI) and entropy, as described in Vinh et al win-
(2009) <doi:10.1145/1553374.1553511>. / GPL (>= 3) 64


Name Version
r-arm 1.10_1Functions to accompany A. Gelman and J. Hill, Data Analysis Using Regres- noarch
sion and Multilevel/Hierarchical Models, Cambridge University Press, 2007. /
GPL (>= 3)
r-armspp 0.0.2 An efficient ‘Rcpp’ implementation of the Adaptive Rejection Metropolis linux-
Sampling (ARMS) algorithm proposed by Gilks, W. R., Best, N. G. and Tan, 64,
K. K. C. (1995) <doi:10.2307/2986138>. This allows for sampling from a osx-
univariate target probability distribution specified by its (potentially unnor- 64,
malised) log density. / MIT file LICENSE win-
64
r-arnie 0.1.2 Arnold Schwarzenegger movie weekend box office records from 1982-2014 / noarch
CC BY-SA 4.0
r-arpobservation 1.2.0 Tools for simulating data generated by direct observation recording. Behavior noarch
streams are simulated based on an alternating renewal process, given specified
distributions of event durations and interim times. Different procedures for
recording data can then be applied to the simulated behavior streams. Func-
tions are provided for the following recording methods: continuous duration
recording, event counting, momentary time sampling, partial interval record-
ing, whole interval recording, and augmented interval recording. / GPL-3
r-arpr 0.1.1 Provides convenience functions for programming with magrittr pipes. Con- noarch
ditional pipes, a string prefixer and a function to pipe the given object into a
specific argument given by character name are currently supported. It is named
after the dadaist Hans Arp, a friend of Rene Magritte. / GPL (>= 3)
r-arpsdca 1.1.1 Functions for Arps decline-curve analysis on oil and gas data. Includes expo- noarch
nential, hyperbolic, harmonic, and hyperbolic-to-exponential models as well
as the preceding with initial curtailment or a period of linear rate buildup.
Functions included for computing rate, cumulative production, instantaneous
decline, EUR, time to economic limit, and performing least-squares best fits. /
LGPL-2.1
r-arrangements 1.1.5 Fast generators and iterators for permutations, combinations and partitions. linux-
The iterators allow users to generate arrangements in a memory efficient man- 64,
ner and the generated arrangements are in lexicographical (dictionary) order. osx-
Permutations and combinations can be drawn with/without replacement and 64,
support multisets. It has been demonstrated that ‘arrangements’ outperforms win-
most of the existing packages of similar kind. Some benchmarks could be 64
found at <https://randy3k.github.io/arrangements/articles/benchmark.html>. /
MIT file LICENSE
r-arrapply 2.1 High performance variant of apply() for a fixed set of functions. Considerable linux-
speedup is a trade-off for universality, user defined functions cannot be used 64,
with this package. However, 21 most currently employed functions are avail- osx-
able for usage. They can be divided in three types: reducing functions (like 64,
mean(), sum() etc., giving a scalar when applied to a vector), mapping func- win-
tion (like normalise(), cumsum() etc., giving a vector of the same length as the 64
input vector) and finally, vector reducing function (like diff() which produces
result vector of a length different from the length of input vector). Optional or
mandatory additional arguments required by some functions (e.g. norm type
for norm() or normalise() functions) can be passed as named arguments in
‘. . . ’. / GPL (>= 2)


Name Version
r-arrow 0.14.1.1
‘Apache’ ‘Arrow’ <https://arrow.apache.org/> is a cross-language develop- linux-
ment platform for in-memory data. It specifies a standardized language- 64
independent columnar memory format for flat and hierarchical data, organized
for efficient analytic operations on modern hardware. This package provides
an interface to the ‘Arrow C’ library. / Apache License (>= 2.0)
r-ars 0.6 Adaptive Rejection Sampling, Original version. / GPL (>= 2) linux-
64,
osx-
64,
win-
64
r-arsenal 3.2.0 An Arsenal of ‘R’ functions for large-scale statistical summaries, which are noarch
streamlined to work within the latest reporting tools in ‘R’ and ‘RStudio’ and
which use formulas and versatile summary statistics for summary tables and
models. The primary functions include tableby(), a Table-1-like summary of
multiple variable types ‘by’ the levels of one or more categorical variables;
paired(), a Table-1-like summary of multiple variable types paired across two
time points; modelsum(), which performs simple model fits on one or more
endpoints for many variables (univariate or adjusted for covariates); freqlist(),
a powerful frequency table across many categorical variables; comparedf(), a
function for comparing data.frames; and write2(), a function to output tables
to a document. / GPL (>= 2)
r-artiva 1.2.3 Reversible Jump MCMC (RJ-MCMC)sampling for approximating the poste- noarch
rior distribution of a time varying regulatory network, under the Auto Regres-
sive TIme VArying (ARTIVA) model (for a detailed description of the algo-
rithm, see Lebre et al. BMC Systems Biology, 2010). Starting from time-
course gene expression measurements for a gene of interest (referred to as
target gene) and a set of genes (referred to as parent genes) which may explain
the expression of the target gene, the ARTIVA procedure identifies temporal
segments for which a set of interactions occur between the parent genes and
the target gene. The time points that delimit the different temporal segments
are referred to as changepoints (CP). / GPL (>= 2)
r-artp 2.0.5 For calculating gene and pathway p-values using the Adaptive Rank Truncated linux-
Product test. / GPL-2 64,
osx-
64,
win-
64
r-artp2 0.9.45Pathway and gene level association test using raw data or summary statistics. linux-
/ GPL-2 | GPL-3 64,
osx-
64,
win-
64
r-arules 1.6_3 Provides the infrastructure for representing, manipulating and analyzing trans- linux-
action data and patterns (frequent itemsets and association rules). Also pro- 64,
vides C implementations of the association mining algorithms Apriori and osx-
Eclat. / GPL-3 64,
win-
64


Name Version
r-arulescba 1.1.4 Provides a function to build an association rule-based classifier for data frames, linux-
and to classify incoming data frames using such a classifier. / GPL-3 64,
osx-
64,
win-
64
r-arulesnbminer 0.1_5 NBMiner is an implementation of the model-based mining algorithm for min- noarch
ing NB-frequent itemsets presented in Michael Hahsler. A model-based fre-
quency constraint for mining associations from transaction data. Data Mining
and Knowledge Discovery, 13(2):137-166, September 2006. In addition an
extension for NB-precise rules is implemented. / GPL-2
r- 0.2_22Add-on for arules to handle and mine frequent sequences. Provides interfaces linux-
arulessequences to the C implementation of cSPADE by Mohammed J. Zaki. / GPL-2 64,
osx-
64,
win-
64
r-arxiv 0.5.19An interface to the API for ‘arXiv’ (<https://arxiv.org>), a repository of elec- noarch
tronic preprints for computer science, mathematics, physics, quantitative biol-
ogy, quantitative finance, and statistics. / MIT file LICENSE
r-asaur 0.50 Data sets are referred to in the text Applied Survival Analysis Using R by Dirk noarch
F. Moore, Springer, 2016, ISBN: 978-3-319-31243-9, <DOI:10.1007/978-3-
319-31245-3>. / CC0
r-asciiruler 0.2 An ASCII ruler is for measuring text and is especially useful for sequence noarch
analysis. Included in this package are methods to create ASCII rulers and
associated GenBank sequence blocks, multi-column text displays that make it
easy for viewers to locate nucleotides by position. / GPL-3 | file LICENSE
r-asd 2.2 Package runs simulations for adaptive seamless designs with and without early noarch
outcomes for treatment selection and subpopulation type designs. / GPL-3
r-asdreader 0.1_3 A simple driver that reads binary data created by the ASD Inc. portable noarch
spectrometer instruments, such as the FieldSpec (for more information, see
<http://www.asdi.com/products/fieldspec-spectroradiometers>). Spectral data
can be extracted from the ASD files as raw (DN), white reference, radiance, or
reflectance. Additionally, the metadata information contained in the ASD file
header can also be accessed. / GPL-3
r-asgs.foyer 0.2.1 The Australian Statistical Geography Standard (‘ASGS’) is a set of shapefiles noarch
by the Australian Bureau of Statistics. This package provides an interface to
those shapefiles, as well as methods for converting coordinates to shapefiles. /
MPL
r-ash 1.0_15David Scott’s ASH routines ported from S-PLUS to R. / GPL (>= 2) linux-
64,
osx-
64,
win-
64
r-asioheaders 1.12.1_1
‘Asio’ is a cross-platform C library for network and low-level I/O program- noarch
ming that provides developers with a consistent asynchronous model using a
modern C approach. It is also included in Boost but requires linking when
used with Boost. Standalone it can be used header-only (provided a recent
compiler). ‘Asio’ is written and maintained by Christopher M. Kohlhoff, and
released under the ‘Boost Software License’, Version 1.0. / BSL-1.0


Name Version
r-askpass 1.0 Cross-platform utilities for prompting the user for credentials or a passphrase, linux-
for example to authenticate with a server or read a protected key. Includes 64,
native programs for MacOS and Windows, hence no ‘tcltk’ is required. Pass- osx-
word entry can be invoked in two different ways: directly from R via the 64,
askpass() function, or indirectly as password-entry back-end for ‘ssh-agent’ win-
or ‘git-credential’ via the SSH_ASKPASS and GIT_ASKPASS environment 32,
variables. Thereby the user can be prompted for credentials or a passphrase if win-
needed when R calls out to git or ssh. / MIT file LICENSE 64
r-asnipe 1.1.11Implements several tools that are used in animal social network analysis. In noarch
particular, this package provides the tools to infer groups and generate net-
works from observation data, perform permutation tests on the data, calculate
lagged association rates, and performed multiple regression analysis on social
network data. / GPL-2
r-aspbay 1.2 This package allows to make inference on the properties of causal genetic linux-
variants in linkage disequilibrium with genotyped markers. In a first step, 64,
we select a subset of variants using a score statistic for affected sib-pairs. In osx-
a second step, on the selected subset, we make inference on causal genetic 64,
variants in the considered region. / GPL-2 win-
64
r-aspc 0.1.2 The aSPC test is designed to test global association between two groups of noarch
variables potentially with moderate to high dimension (e.g. in hundreds). The
aSPC is particularly useful when the association signals between two groups
of variables are sparse. / GPL-3
r-aspect 1.0_5 Contains various functions for optimal scaling. One function performs opti- linux-
mal scaling by maximizing an aspect (i.e. a target function such as the sum of 64,
eigenvalues, sum of squared correlations, squared multiple correlations, etc.) osx-
of the corresponding correlation matrix. Another function performs imple- 64,
ments the LINEALS approach for optimal scaling by minimization of an as- win-
pect based on pairwise correlations and correlation ratios. The resulting corre- 64
lation matrix and category scores can be used for further multivariate methods
such as structural equation models. / GPL-2
r-aspi 0.2.0 Tools for the analysis and visualization of bilateral asymmetry in parasitic in- noarch
fections. / GPL-3
r-assa 1.0 Functions to model and decompose time series into principal compo- linux-
nents using singular spectrum analysis (de Carvalho and Rua (2017) 64,
<doi:10.1016/j.ijforecast.2015.09.004>; de Carvalho et al (2012) osx-
<doi:10.1016/j.econlet.2011.09.007>). / GPL (>= 3) 64,
win-
64
r-assertable 0.2.5 Simple, flexible, assertions on data.frame or data.table objects with verbose noarch
output for vetting. While other assertion packages apply towards more general
use-cases, assertable is tailored towards tabular data. It includes functions to
check variable names and values, whether the dataset contains all combina-
tions of a given set of unique identifiers, and whether it is a certain length. In
addition, assertable includes utility functions to check the existence of target
files and to efficiently import multiple tabular data files into one data.table. /
GPL-3
r-assertive 0.3_5 Lots of predicates (is_* functions) to check the state of your variables, and noarch
assertions (assert_* functions) to throw errors if they aren’t in the right form.
/ GPL-3


Name Version
r-assertive.base 0.0_7 A minimal set of predicates and assertions used by the assertive package. This noarch
is mainly for use by other package developers who want to include run-time
testing features in their own packages. End-users will usually want to use
assertive directly. / GPL (>= 3)
r-assertive.code 0.0_3 A set of predicates and assertions for checking the properties of code. This noarch
assertive directly. / GPL-3
r-assertive.data 0.0_3 A set of predicates and assertions for checking the properties of (country in- noarch
dependent) complex data types. This is mainly for use by other package de-
velopers who want to include run-time testing features in their own packages.
End-users will usually want to use assertive directly. / GPL-3
r- 0.0_2 A set of predicates and assertions for checking the properties of UK-specific noarch
assertive.data.uk complex data types. This is mainly for use by other package developers who
want to include run-time testing features in their own packages. End-users will
usually want to use assertive directly. / GPL-3
r- 0.0_2 A set of predicates and assertions for checking the properties of US-specific noarch
assertive.data.us complex data types. This is mainly for use by other package developers who
want to include run-time testing features in their own packages. End-users will
usually want to use assertive directly. / GPL-3
r- 0.0_2 A set of predicates and assertions for checking the properties of dates and noarch
assertive.datetimes times. This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually want
to use assertive directly. / GPL-3
r-assertive.files 0.0_2 A set of predicates and assertions for checking the properties of files and con- noarch
nections. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will usu-
ally want to use assertive directly. / GPL (>= 3)
r- 0.0_2 A set of predicates and assertions for checking the properties of matrices. This noarch
assertive.matrices is mainly for use by other package developers who want to include run-time
r- 0.0_2 A set of predicates and assertions for checking the properties of models. This noarch
assertive.models is mainly for use by other package developers who want to include run-time
r- 0.0_2 A set of predicates and assertions for checking the properties of numbers. This noarch
assertive.numbers is mainly for use by other package developers who want to include run-time
r- 0.0_4 A set of predicates and assertions for checking the properties of variables, such noarch
assertive.properties as length, names and attributes. This is mainly for use by other package de-
velopers who want to include run-time testing features in their own packages.
End-users will usually want to use assertive directly. / GPL (>= 3)
r- 0.0_4 A set of predicates and assertions for checking the state and capabilities of noarch
assertive.reflection R, the operating system it is running on, and the IDE being used. This is
mainly for use by other package developers who want to include run-time test-
ing features in their own packages. End-users will usually want to use assertive
directly. / GPL (>= 3)


Name Version
r-assertive.sets 0.0_3 A set of predicates and assertions for checking the properties of sets. This noarch
r- 0.0_3 A set of predicates and assertions for checking the properties of strings. This noarch
assertive.strings is mainly for use by other package developers who want to include run-time
assertive directly. / GPL-3
r-assertive.types 0.0_3 A set of predicates and assertions for checking the types of variables. This noarch
r-assertthat 0.2.1 An extension to stopifnot() that makes it easy to declare the pre and post con- linux-
ditions that you code should satisfy, while also producing friendly error mes- 32,
sages so that your users know what’s gone wrong. / GPL-3 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-assist 3.1.5 A comprehensive package for fitting various non-parametric/semi-parametric linux-
linear/nonlinear fixed/mixed smoothing spline models. / GPL (>= 2) 64,
osx-
64,
win-
64
r-assocafc 1.0.2 When doing association analysis one does not always have the genotypes for noarch
the control population. In such cases it may be necessary to fall back on fre-
quency based tests using well known sources for the frequencies in the control
population, for instance, from the 1000 Genomes Project. The Allele Fre-
quency Comparison (‘AssocAFC’) package performs multiple rare variant as-
sociation analyses in both population and family-based GWAS (Genome-Wide
Association Study) designs. It includes three score tests that are based on
the difference of the sum of allele frequencies between cases and controls.
Two of these tests, Wcorrected() and Wqls(), are collapsing-based tests and
suffer from having protective and risk variants. The third test, afcSKAT(),
is a score test that overcomes the mix of SNP (Single-Nucleotide Polymor-
phism) effect directions. For more details see Saad M and Wijsman EM (2017)
<doi:10.1093/bib/bbx107>. / GPL-3
r-assocind 1.0.1 Implements several new association indices that can control for various types noarch
of errors. Also includes existing association indices and functions for simulat-
ing the effects of different rates of error on estimates of association strength
between individuals using each method. / GPL-2
r-assortnet 0.12 Functions to calculate the assortment of vertices in social networks. This can noarch
be measured on both weighted and binary networks, with discrete or continu-
ous vertex values. / GPL-2


Name Version
r-assotester 0.1_10R package with statistical tests and methods for genetic association studies linux-
with emphasis on rare variants and binary (dichotomous) traits / GPL (>= 3) 64,
osx-
64,
win-
64
r-ast 0.1.0 Fits a model to adjust and consider additional variations in three dimensions noarch
of age groups, time, and space on residuals excluded from a prediction model
that have residual such as: linear regression, mixed model and so on. Details
are given in Foreman et al. (2015) <doi:10.1186/1478-7954-10-1>. / GPL-2 |
GPL-3
r-aster2 0.3 Aster models are exponential family regression models for life history anal- linux-
ysis. They are like generalized linear models except that elements of the re- 64,
sponse vector can have different families (e. g., some Bernoulli, some Poisson, osx-
some zero-truncated Poisson, some normal) and can be dependent, the depen- 64,
dence indicated by a graphical structure. Discrete time survival analysis, zero- win-
inflated Poisson regression, and generalized linear models that are exponential 64
family (e. g., logistic regression and Poisson regression with log link) are spe-
cial cases. Main use is for data in which there is survival over discrete time
periods and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the exponential family canonical parameter-
ization (aster transform of usual parameterization). Unlike the aster package,
this package does dependence groups (nodes of the graph need not be condi-
tionally independent given their predecessor node), including multinomial and
two-parameter normal as families. Thus this package also generalizes mark-
capture-recapture analysis. / GPL (>= 2)
r-astrodatr 0.1 A collection of 19 datasets from contemporary astronomical research. They noarch
are described the textbook ‘Modern Statistical Methods for Astronomy with
R Applications’ by Eric D. Feigelson and G. Jogesh Babu (Cambridge Uni-
versity Press, 2012, Appendix C) or on the website of Penn State’s Center for
Astrostatistics (http://astrostatistics.psu.edu/datasets). These datasets can be
used to exercise methodology involving: density estimation; heteroscedastic
measurement errors; contingency tables; two-sample hypothesis tests; spatial
point processes; nonlinear regression; mixture models; censoring and trunca-
tion; multivariate analysis; classification and clustering; inhomogeneous Pois-
son processes; periodic and stochastic time series analysis. / GPL
r-astrofns 4.1_0 Miscellaneous astronomy functions, utilities, and data. / GPL (>= 2) noarch
r-astrolibr 0.1 Several dozen low-level utilities and codes from the Interactive Data Lan- noarch
guage (IDL) Astronomy Users Library (http://idlastro.gsfc.nasa.gov) are im-
plemented in R. They treat: time, coordinate and proper motion transforma-
tions; terrestrial precession and nutation, atmospheric refraction and aberra-
tion, barycentric corrections, and related effects; utilities for astrometry, pho-
tometry, and spectroscopy; and utilities for planetary, stellar, Galactic, and
extragalactic science. / GPL
r-astsa 1.9 Data sets and scripts to accompany Time Series Analysis and Its Applications: noarch
With R Examples (4th ed), by R.H. Shumway and D.S. Stoffer. Springer
Texts in Statistics, 2017, <DOI:10.1007/978-3-319-52452-8>, and Time Se-
ries: A Data Analysis Approach Using R. Chapman-Hall, 2019, <ISBN: 978-
0367221096>. / GPL-3


Name Version
r-asyk 0.1.0 Density estimation by using symmetrical kernels and to calculate mean square noarch
error. See Scaillet (2004) <doi:10.1080/10485250310001624819> and Khan
and Akbar (2019). / GPL-2
r-asymld 0.1 Computes asymmetric LD measures (ALD) for multi-allelic genetic data. noarch
These measures are identical to the correlation measure (r) for bi-allelic data.
/ GPL-2
r-asymptest 0.1.4 One and two sample mean and variance tests (differences and ratios) are con- noarch
sidered. The test statistics are all expressed in the same form as the Student
t-test, which facilitates their presentation in the classroom. This contribution
also fills the gap of a robust (to non-normality) alternative to the chi-square
single variance test for large samples, since no such procedure is implemented
in standard statistical software. / GPL (>= 2)
r-asynchlong 2.0 Estimation of regression models for sparse asynchronous longitudinal obser- noarch
vations, where time-dependent response and covariates are mismatched and
observed intermittently within subjects. Kernel weighted estimating equa-
tions are used for generalized linear models with either time-invariant or time-
dependent coefficients. / GPL-2
r-asypow 2015.6.25
A set of routines written in the S language that calculate power and related noarch
quantities utilizing asymptotic likelihood ratio methods. / ACM | file LI-
CENSE (Restricts use)
r-ate 0.2.0 Nonparametric estimation and inference for average treatment effects based on noarch
covariate balancing. / GPL (>= 2)
r-atlas 1.0.0 Stanford ‘ATLAS’ (Advanced Temporal Search Engine) is a powerful tool that noarch
allows constructing cohorts of patients extremely quickly and efficiently. This
package is designed to interface directly with an instance of ‘ATLAS’ search
engine and facilitates API queries and data dumps. Prerequisite is a good
knowledge of the temporal language to be able to efficiently construct a query.
More information available at <https://shahlab.stanford.edu/start>. / GPL-3
r-atmcmc 1.0 Uses adaptive diagnostics to tune and run a random walk Metropolis MCMC noarch
algorithm, to converge to a specified target distribution and estimate means of
functionals. / GPL (>= 2)
r-atmray 1.31 Calculates acoustic traveltimes and ray paths in 1-D, linear atmospheres. Later linux-
versions will support arbitrary 1-D atmospheric models, such as radiosonde 64,
measurements and standard reference atmospheres. / GPL osx-
64,
win-
64
r-atsa 3.1.2 Contains some tools for testing, analyzing time series data and fitting popular noarch
time series models such as ARIMA, Moving Average and Holt Winters, etc.
Most functions also provide nice and clear outputs like SAS does, such as iden-
tify, estimate and forecast, which are the same statements in PROC ARIMA in
SAS. / GPL-2 | GPL-3
r-atsd 1.2.0 Provides functions for retrieving time-series and related meta-data such as noarch
entities, metrics, and tags from the Axibase Time-Series Database (ATSD).
ATSD is a non-relational clustered database used for storing performance mea-
surements from IT infrastructure resources: servers, network devices, storage
systems, and applications. / Apache License 2.0


Name Version
r-attachment 0.0.9 Tools to help manage dependencies during package development. This can noarch
retrieve all dependencies that are used in R files in the R directory, in Rmd files
in vignettes directory and in ‘roxygen2’ documentation of functions. There is
a function to update the Description file of your package and a function to
create a file with the R commands to install all dependencies of your package.
All functions to retrieve dependencies of R scripts and Rmd files can be used
independently of a package development. / GPL-3
r-attempt 0.3.0 Tools for defensive programming, inspired by ‘purrr’ mappers and based on noarch
‘rlang’.’attempt’ extends and facilitates defensive programming by providing
a consistent grammar, and provides a set of easy to use functions for common
tests and conditions. ‘attempt’ only depends on ‘rlang’, and focuses on speed,
so it can be easily integrated in other functions and used in data analysis. /
MIT file LICENSE
r-attrcusum 0.1.0 An implementation of tools for design of attribute variable sampling inter- linux-
val cumulative sum chart. It currently provides information for monitoring of 64,
mean increase such as average number of sample to signal, average time to osx-
signal, a matrix of transient probabilities, suitable control limits when the data 64,
are (zero inflated) Poisson/binomial distribution. Functions in the tools can win-
be easily applied to other count processes. Also, tools might be extended to 64
more complicated cumulative sum control chart. We leave these issues as our
perpetual work. / GPL (>= 2)
r-atus 0.2 Abridged data from the American Time Use Survey (ATUS) for years 2003- noarch
2016. The ATUS is an annual survey conducted on a sample of individuals
across the United States studying how individuals spent their time over the
course of a day. Individual respondents were interviewed about what activi-
ties they did, during what times (rounded to 15 minute increments), at what
locations, and in the presence of which individuals. The activities are subse-
quently encoded based on 3 separate tier codes for classification. This package
includes data from the multi-year ATUS Activities, ATUS-CPS, and ATUS
Respondents files were included. Columns were selected based on complete-
ness of data as well as presence on the Frequently Used Variables list provided
by the ATUS website. All activity codes (other than code ‘50’ for ‘Unable
to Code’) were included. Permission was obtained from the Bureau of Labor
Statistics for inclusion in this package. The full data can be obtained from
<http://www.bls.gov/tus/>. / GPL (>= 2)
r-auc 0.3.0 This package includes functions to compute the area under the curve of se- noarch
lected measures: The area under the sensitivity curve (AUSEC), the area under
the specificity curve (AUSPC), the area under the accuracy curve (AUACC),
and the area under the receiver operating characteristic curve (AUROC). The
curves can also be visualized. Support for partial areas is provided. / GPL (>=
2)
r-aucrf 1.1 Variable selection using Random Forest based on optimizing the area-under- noarch
the ROC curve (AUC) of the Random Forest. / GPL (>= 2)
r-audio 0.1_6 Interfaces to audio devices (mainly sample-based) from R to allow recording linux-
and playback of audio. Built-in devices include Windows MM, Mac OS X 64,
AudioUnits and PortAudio (the last one is very experimental). / MIT file LI- osx-
CENSE 64,
win-
64
r-audit 0.1_1 Two Bayesian methods for Accounting Populations / MIT noarch


Name Version
r-auth0 0.1.1 Uses Auth0 API (see <https://auth0.com> for more information) to use a sim- noarch
ple and secure authentication system. It provides tools to log in and out a shiny
application using social networks or a list of e-mails. / MIT file LICENSE
r-auto.pca 0.3 PCA done by eigenvalue decomposition of a data correlation matrix, here it au- noarch
tomatically determines the number of factors by eigenvalue greater than 1 and
it gives the uncorrelated variables based on the rotated component scores, Such
that in each principal component variable which has the high variance are se-
lected. It will be useful for non-statisticians in selection of variables. For more
information, see the <http://www.ijcem.org/papers032013/ijcem_032013_06.
pdf> web page. / GPL-2
r-autodeskr 0.1.3 An interface to the ‘AutoDesk’ ‘API’ Platform including the Authentication noarch
‘API’ for obtaining authentication to the ‘AutoDesk’ Forge Platform, Data
Management ‘API’ for managing data across the platform’s cloud services,
Design Automation ‘API’ for performing automated tasks on design files in
the cloud, Model Derivative ‘API’ for translating design files into different for-
mats, sending them to the viewer app, and extracting design data, and Viewer
for rendering 2D and 3D models (see <https://developer.autodesk.com> for
more information). / Apache License | file LICENSE
r-autoencoder 1.1 Implementation of the sparse autoencoder in R environment, following the noarch
notes of Andrew Ng (http://www.stanford.edu/class/archive/cs/cs294a/cs294a.
1104/sparseAutoencoder.pdf). The features learned by the hidden layer of the
autoencoder (through unsupervised learning of unlabeled data) can be used in
constructing deep belief neural networks. / GPL-2
r-automl 1.2.8 Fits from simple regression to highly customizable deep neural networks either noarch
with gradient descent or metaheuristic, using automatic hyper parameters tun-
ing and custom cost function. A mix inspired by the common tricks on Deep
Learning and Particle Swarm Optimization. / GNU General Public License
r- 2.0.0 Fits the autologistic model described in Besag’s famous 1974 paper on auto- noarch
automultinomial models <http://www.jstor.org/stable/2984812>. Fits a multicategory general-
ization of the autologistic model when there are more than 2 response cate-
gories. Provides support for both asymptotic and bootstrap confidence inter-
vals. For full model descriptions and a guide to the use of this package, please
see the vignette. / GPL-2
r-autopls 1.3 Some convenience functions for pls regression, including backward variable noarch
selection and validation procedures, image based predictions and plotting. /
GPL-2
r- 1.0 Consider autoregressive model of order p where the distribution function of noarch
autoregressionmde innovation is unknown, but innovations are independent and symmetrically
distributed. The package contains a function named ARMDE which takes X
(vector of n observations) and p (order of the model) as input argument and
returns minimum distance estimator of the parameters in the model. / GPL-2
r-autoshiny 0.0.2 Static code compilation of a ‘shiny’ app given an R function (into ‘ui.R’ and noarch
‘server.R’ files or into a ‘shiny’ app object). See examples at <https://github.
com/alekrutkowski/autoshiny>. / GPL-2


Name Version
r-autovarcore 1.0_4 Automatically find the best vector autoregression models and networks for a linux-
given time series data set. ‘AutovarCore’ evaluates eight kinds of models: 64,
models with and without log transforming the data, lag 1 and lag 2 models, osx-
and models with and without weekday dummy variables. For each of these 8 64,
model configurations, ‘AutovarCore’ evaluates all possible combinations for win-
including outlier dummies (at 2.5x the standard deviation of the residuals) and 64
retains the best model. Model evaluation includes the Eigenvalue stability test
and a configurable set of residual tests. These eight models are further reduced
to four models because ‘AutovarCore’ determines whether adding weekday
dummies improves the model fit. / MIT file LICENSE
r-av 0.2 Bindings to ‘FFmpeg’ <http://www.ffmpeg.org/> AV library for working with linux-
audio and video in R. Generate high quality videos files by capturing images 64,
from the R graphics device combined with custom audio stream. This pack- osx-64
age interfaces directly to the C API and does not require any command line
utilities. / MIT file LICENSE
r-averisk 1.0.3 Average population attributable fractions are calculated for a set of risk factors noarch
(either binary or ordinal valued) for both prospective and case- control designs.
Confidence intervals are found by Monte Carlo simulation. The method can
be applied to either prospective or case control designs, provided an estimate
of disease prevalence is provided. In addition to an exact calculation of AF, an
approximate calculation, based on randomly sampling permutations has been
implemented to ensure the calculation is computationally tractable when the
number of risk factors is large. / CC0
r-aweek 1.0.0 Which day a week starts depends heavily on the either the local or profes- noarch
sional context. This package is designed to be a lightweight solution to easily
switching between week-based date definitions. / MIT file LICENSE
r-awr 1.11.189
Installs the compiled Java modules of the Amazon Web Services (‘AWS’) noarch
‘SDK’ to be used in downstream R packages interacting with ‘AWS’. See
<https://aws.amazon.com/sdk-for-java> for more information on the ‘AWS’
‘SDK’ for Java. / AGPL-3
r-awr.athena 2.0.7_0
‘RJDBC’ based ‘DBI’ driver to Amazon Athena, which is an interactive query noarch
service to analyze data in Amazon ‘S3’ using standard ‘SQL’. / AGPL-3
r-awr.kms 0.1 Encrypt plain text and ‘decrypt’ cipher text using encryption keys hosted at noarch
Amazon Web Services (‘AWS’) Key Management Service (‘KMS’), on which
see <https://aws.amazon.com/kms> for more information. / AGPL-3
r-aws 2.2_1 We provide a collection of R-functions implementing adaptive smoothing pro- linux-
cedures in 1D, 2D and 3D. This includes the Propagation-Separation Ap- 64,
proach to adaptive smoothing as described in J. Polzehl and V. Spokoiny osx-
(2006) <DOI:10.1007/s00440-005-0464-1>, J. Polzehl and V. Spokoiny 64,
(2004) <DOI:10.20347/WIAS.PREPRINT.998> and J. Polzehl, K. Papafit- win-
soros, K. Tabelow (2018) <DOI:10.20347/WIAS.PREPRINT.2520>, the In- 64
tersecting Confidence Intervals (ICI), variational approaches and a non-local
means filter. / GPL (>= 2)
r-aws.cloudtrail 0.1.5 A simple client package for the Amazon Web Services (‘AWS’) ‘CloudTrail’ noarch
‘API’ <https://aws.amazon.com/cloudtrail/>. / GPL-2
r- 0.1.2 Client for ‘AWS Comprehend’ <https://aws.amazon.com/comprehend>, a noarch
aws.comprehend cloud natural language processing service that can perform a number of quan-
titative text analyses, including language detection, sentiment analysis, and
feature extraction. / GPL (>= 2)
r- 0.2.0 Retrieve Amazon EC2 instance metadata from within the running instance. / noarch
aws.ec2metadata GPL (>= 2)


Name Version
r-aws.iam 0.1.7 A simple client for the Amazon Web Services (‘AWS’) Identity and Access noarch
Management (‘IAM’) ‘API’ <https://aws.amazon.com/iam/>. / GPL (>= 2)
r-aws.kms 0.1.2 Client package for the ‘AWS Key Management Service’ <https://aws.amazon. noarch
com/kms/>, a cloud service for managing encryption keys. / GPL (>= 2)
r-aws.lambda 0.1.6 A simple client package for the Amazon Web Services (‘AWS’) Lambda ‘API’ noarch
<https://aws.amazon.com/lambda/>. / GPL (>= 2)
r-aws.s3 0.3.12A simple client package for the Amazon Web Services (‘AWS’) Simple Stor- noarch
age Service (‘S3’) ‘REST’ ‘API’ <https://aws.amazon.com/s3/>. / GPL (>=
2)
r-aws.ses 0.1.4 A simple client package for the Amazon Web Services (AWS) Simple Email noarch
Service (SES) <http://aws.amazon.com/ses/> REST API. / GPL (>= 2)
r-aws.signature 0.5.2 Generates version 2 and version 4 request signatures for Amazon Web Ser- noarch
vices (‘AWS’) <https://aws.amazon.com/> Application Programming Inter-
faces (‘APIs’) and provides a mechanism for retrieving credentials from en-
vironment variables, ‘AWS’ credentials files, and ‘EC2’ instance metadata.
For use on ‘EC2’ instances, users will need to install the suggested package
‘aws.ec2metadata’ <https://cran.r-project.org/package=aws.ec2metadata>. /
GPL (>= 2)
r-aws.sns 0.1.7 A simple client package for the Amazon Web Services (‘AWS’) Simple No- noarch
tification Service (‘SNS’) ‘API’ <https://aws.amazon.com/sns/>. / GPL (>=
2)
r-aws.sqs 0.1.10A simple client package for the Amazon Web Services (‘AWS’) Simple Queue noarch
Service (‘SQS’) <https://aws.amazon.com/sqs/> ‘API’. / GPL (>= 2)
r-aws.transcribe 0.1.2 Client for ‘AWS Transcribe’ <https://aws.amazon.com/documentation/ noarch
transcribe>, a cloud transcription service that can convert an audio media file
in English and other languages into a text transcript. / GPL (>= 2)
r-aws.translate 0.1.3 A client for ‘AWS Translate’ <https://aws.amazon.com/documentation/ noarch
translate>, a machine translation service that will convert a text input in one
language into a text output in another language. / GPL (>= 2)
r-awsjavasdk 0.2.0 Provides boilerplate access to all of the classes included in the Amazon Web noarch
Services (‘AWS’) Java Software Development Kit (SDK) via package:’rJava’.
According to Amazon, the ‘SDK helps take the complexity out of coding by
providing Java APIs for many AWS services including Amazon S3, Amazon
EC2, DynamoDB, and more’. You can read more about the included Java code
on Amazon’s website: <https://aws.amazon.com/sdk-for-java/>. / GPL-2
r-awsmethods 1.1_1 Defines the method extract and provides ‘openMP’ support as needed in sev- linux-
eral packages. / GPL (>= 2) 64,
osx-
64,
win-
64
r- 1.0.0 A simple interface to the instance metadata for a virtual machine running in noarch
azurevmmetadata Microsoft’s ‘Azure’ cloud. This provides information about the VM’s config-
uration, such as its processors, memory, networking, storage, and so on. Part
of the ‘AzureR’ family of packages. / MIT
r-b2z 1.4 This package fits the Bayesian two-Zone Models. / GPL-2 noarch
r-b6e6rl 1.1 This package contains b6e6rl algorithm, adaptive differential evolution for noarch
global optimization. / GPL-2


Name Version
r-babar 1.0 Babar is designed to use nested sampling (a Bayesian analysis technique) to noarch
compare possible models for bacterial growth curves, as well as extracting
parameters. It allows model evidence and parameter likelihood values to be
extracted, and also contains helper functions for comparing distributions as
well as direct access to the underlying nested sampling code. / GPL-2
r-backpipe 0.2.3 Provides a backward-pipe operator for ‘magrittr’ (%<%) or ‘pipeR’ (%<<%) noarch
that allows for a performing operations from right-to-left. This allows writing
more legible code where right-to-left ordering is natural. This is common with
hierarchies and nested structures such as trees, directories or markup languages
(e.g. HTML and XML). The package also includes a R-Studio add-in that can
be bound to a keyboard shortcut. / GPL-2 | file LICENSE
r-backports 1.1.4 Implementations of functions which have been introduced in R since version linux-
3.0.0. The backports are conditionally exported which results in R resolving 32,
the function names to the version shipped with R (if available) and uses the linux-
implemented backports as fallback. This way package developers can make 64,
use of the new functions without worrying about the minimum required R osx-
version. / GPL-2 64,
win-
32,
win-
64
r-backtest 0.3_4 The backtest package provides facilities for exploring portfolio-based conjec- noarch
tures about financial instruments (stocks, bonds, swaps, options, et cetera). /
GPL (>= 2)
r-bacprior 2.0 The BACprior package provides an approximate sensitivity analysis of the noarch
Bayesian Adjustment for Confounding (BAC) algorithm (Wang et al., 2012)
with regards to the hyperparameter omega. The package also provides func-
tions to guide the user in their choice of an appropriate omega value. The
method is based on Lefebvre, Atherton and Talbot (2014). / GPL (>= 2)
r-badgecreatr 0.2.0 Tired of copy and pasting almost identical markdown for badges in every new noarch
R-package that you create, on Github or other code-sharing sites? This pack-
age allows you to easily paste badges. If you want to, it will also search your
DESCRIPTION file and extract the package name, license, R-version, and
current projectversion and transform that into badges. It will also search for a
.travis.yml file and create a Travis badge, if you use Codecov.io to check your
code coverage after a Travis build this package will also build a Codecov.io-
badge. All the badges can be placed individually or can be placed below the
top YAML content of your RMarkdown file (Readme.Rmd) or README.md
file. Currently creates badges for Projectstatus (Repostatus.org), license Travis
Build Status, Codecov, Minimal R version, CRAN status, CRAN downloads,
Github stars and forks, Package rank, rdocumentation, current version of your
package and last change of README.Rmd. / GPL-3
r-baessd 1.0.1 Implements sample size calculations following the approach described in noarch
Bayesian Average Error Based Approach to Hypothesis Testing and Sample
Size Determination. / GPL-2


Name Version
r-bagrboostr 0.0.2 bagRboostR is a set of ensemble classifiers for multinomial classification. The noarch
bagging function is the implementation of Breiman’s ensemble as described
by Opitz & Maclin (1999). The boosting function is the implementation of
Stagewise Additive Modeling using a Multi-class Exponential loss function
(SAMME) created by Zhu et al (2006). Both bagging and SAMME implemen-
tations use randomForest as the weak classifier and expect a character outcome
variable. Each ensemble classifier returns a character vector of predictions for
the test set. / MIT file LICENSE
r-bain 0.2.1 Computes approximated adjusted fractional Bayes factors for equality, in- linux-
equality, and about equality constrained hypotheses. S3 methods are available 64,
for specific types of lm() models, namely ANOVA, ANCOVA, and multiple osx-
regression, and for the t_test(). The statistical underpinnings are described 64,
in Hoijtink, Mulder, van Lissa, and Gu, (2018) <doi:10.31234/osf.io/v3shc>, win-
Gu, Mulder, and Hoijtink, (2018) <doi:10.1111/bmsp.12110>, Hoijtink, Gu, 64
and Mulder, (2018) <doi:10.1111/bmsp.12145>, and Hoijtink, Gu, Mulder,
and Rosseel, (2018) <doi:10.1037/met0000187>. / GPL (>= 3)
r-bairt 0.1.2 Bayesian estimation of the two and three parameter models of item response noarch
theory (IRT). Also, it is possible to use a web interactive application intended
for the making of an MCMC estimation and model-fit of the IRT models. /
GPL (>= 2)
r-balancecheck 0.2 Two practical tests are provided for assessing whether multiple covariates in noarch
a treatment group and a matched control group are balanced in observational
studies. / GPL (>= 2)
r-bammtools 2.1.6 Provides functions for analyzing and visualizing complex macroevolutionary linux-
dynamics on phylogenetic trees. It is a companion package to the command 64,
line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and osx-
is entirely oriented towards the analysis, interpretation, and visualization of 64,
evolutionary rates. Functionality includes visualization of rate shifts on phylo- win-
genies, estimating evolutionary rates through time, comparing posterior distri- 64
butions of evolutionary rates across clades, comparing diversification models
using Bayes factors, and more. / GPL (>= 2)
r-bamp 2.0.7 Bayesian Age-Period-Cohort Modeling and Prediction using efficient Markov linux-
Chain Monte Carlo Methods. This is the R version of the previous 64,
BAMP software as described in Volker Schmid and Leonhard Held (2007) osx-
<DOI:10.18637/jss.v021.i08> Bayesian Age-Period-Cohort Modeling and 64,
Prediction - BAMP, Journal of Statistical Software 21:8. This package in- win-
cludes checks of convergence using Gelman’s R. / GPL-3 64
r- 0.1.1 A convenience package for use while drafting code. It facilitates making stand- noarch
bannercommenter out comment lines decorated with bands of characters. The input text strings
are converted into R comment lines, suitably formatted. These are then dis-
played in a console window and, if possible, automatically transferred to a clip-
board ready for pasting into an R script. Designed to save time when drafting
R scripts that will need to be navigated and maintained by other programmers.
/ GPL (>= 2)
r-banxicor 0.9.0 Provides functions to scrape IQY calls to Bank of Mexico, downloading and noarch
ordering the data conveniently. / CC0
r-baprestopro 0.1 Bayesian estimation and prediction for stochastic processes based on the Eu- noarch
ler approximation. Considered processes are: jump diffusion, (mixed) dif-
fusion models, hidden (mixed) diffusion models, non-homogeneous Poisson
processes (NHPP), (mixed) regression models for comparison and a regres-
sion model including a NHPP. / GPL (>= 2)


Name Version
r-barborgradient 1.0.5 Tool to find where a function has its lowest value(minimum). The functions noarch
can be any dimensions. Recommended use is with eps=10^-10, but can be run
with 10^-20, although this depends on the function. Two more methods are in
this package, simple gradient method (Gradmod) and Powell method (Powell).
These are not recommended for use, their purpose are purely for comparison.
/ GPL-3
r-barcode 1.1 This package includes the function code{barcode()}, which produces a noarch
histogram-like plot of a distribution that shows granularity in the data. / GPL
(>= 2)
r-barcodingr 1.0_2 To perform species identification using DNA barcodes. / GPL-2 noarch
r-barnard 1.8 Barnard’s unconditional test for 2x2 contingency tables. / GPL-2 linux-
64,
osx-
64,
win-
64
r-barsurf 0.3.1 Produces heat maps, contour plots, bar plots (in 3D) and surface plots (also, in noarch
3D). Is designed for plotting functions of two variables, however, can plot rel-
atively arbitrary matrices. Uses HCL color space, extensively. Also, supports
triangular plots and nested matrices. / GPL (>= 2)
r-bart 2.5 Bayesian Additive Regression Trees (BART) provide flexible nonparametric linux-
modeling of covariates for continuous, binary, categorical and time-to-event 64,
outcomes. For more information on BART, see Chipman, George and McCul- osx-
loch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch 64,
and Laud (2016) <doi:10.1002/sim.6893>. / GPL (>= 2) win-
64
r- 1.1 These are bartMachine’s Java dependency libraries. Note: this package has no noarch
bartmachinejars functionality of its own and should not be installed as a standalone package
without bartMachine. / GPL-3
r-barycenter 1.3.1 Computations of entropy regularized Wasserstein Distances, a.k.a. dual- linux-
Sinkhorn divergences, and entropy regularized Wasserstein Barycenters. Rele- 64,
vant papers are Marco Cuturi (2013) <arXiv:1306.0895>, Marco Cuturi (2014) osx-
<arXiv:1310.4375> and Jason Altschuler et al. <arXiv:1705.09634>. / GPL-2 64,
win-
64


Name Version
r-bas 1.5.3 Package for Bayesian Variable Selection and Model Averaging in linear mod- linux-
els and generalized linear models using stochastic or deterministic sampling 64,
without replacement from posterior distributions. Prior distributions on co- osx-
efficients are from Zellner’s g-prior or mixtures of g-priors corresponding to 64,
the Zellner-Siow Cauchy Priors or the mixture of g-priors from Liang et al win-
(2008) <DOI:10.1198/016214507000001337> for linear models or mixtures 64
of g-priors in GLMs of Li and Clyde (2018) <arXiv:1503.06913>. Other
model selection criteria include AIC, BIC and Empirical Bayes estimates of
g. Sampling probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an efficient MCMC algorithm sam-
ples models using the BAS tree structure as an efficient hash table. Uni-
form priors over all models or beta-binomial prior distributions on model
size are allowed, and for large p truncated priors on the model space may
be used. The user may force variables to always be included. Details be-
hind the sampling algorithm are provided in Clyde, Ghosh and Littman (2010)
<DOI:10.1198/jcgs.2010.09049>. This material is based upon work supported
by the National Science Foundation under Grant DMS-1106891. Any opin-
ions, findings, and conclusions or recommendations expressed in this material
are those of the author(s) and do not necessarily reflect the views of the Na-
tional Science Foundation. / GPL (>= 3)
r-base 3.6.1 R is a free software environment for statistical computing and graphics. / GPL- linux-
3.0 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-base64 2.0 Compatibility wrapper to replace the orphaned package by Romain Francois. noarch
New applications should use the ‘openssl’ or ‘base64enc’ package instead. /
MIT file LICENSE
r-base64enc 0.1_3 This package provides tools for handling base64 encoding. It is more flexible linux-
than the orphaned base64 package. / GPL-2 | GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-base64url 1.4 In contrast to RFC3548, the 62nd character () is replaced with -, the 63rd linux-
character (/) is replaced with _. Furthermore, the encoder does not fill the 64,
string with trailing =. The resulting encoded strings comply to the regular osx-
expression pattern [A-Za-z0-9_-] and thus are safe to use in URLs or for file 64,
names. The package also comes with a simple base32 encoder/decoder suited win-
for case insensitive file systems. / GPL-3 64


Name Version
r-baseline 1.2_1 Collection of baseline correction algorithms, along with a framework and a noarch
GUI for optimising baseline algorithm parameters. Typical use of the pack-
age is for removing background effects from spectra originating from various
types of spectroscopy and spectrometry, possibly optimizing this with regard
to regression or classification results. Correction methods include polynomial
fitting, weighted local smoothers and many more. / GPL-2
r-basetheme 0.1.1 Functions to create and select graphical themes for the base plotting system. noarch
Contains: 1) several custom pre-made themes 2) mechanism for creating new
themes by making persistent changes to the graphical parameters of base plots.
/ GPL-2
r- 0.2.2 Provides a function for examining posterior MCMC samples from a single noarch
basicmcmcplots chain using trace plots and density plots, and from multiple chains by compar-
ing posterior medians and credible intervals from each chain. These plotting
functions have a variety of options, such as figure sizes, legends, parameters to
plot, and saving plots to file. Functions interface with the NIMBLE software
package, see de Valpine, Turek, Paciorek, Anderson-Bergman, Temple Lang
and Bodik (2017) <doi:10.1080/10618600.2016.1172487>. / GPL-3
r-basicspace 0.20 Conducts Aldrich-McKelvey and Blackbox Scaling (Poole et al 2016) linux-
<doi:10.18637/jss.v069.i07> to recover latent dimensions of judgment. / GPL- 64,
2 osx-
64,
win-
64
r-basix 1.1 BASIX provides some efficient C/C implementations to speed up calculations linux-
in R. / GPL-2 64,
osx-
64,
win-
64
r-bass 0.2.2 Bayesian fitting and sensitivity analysis methods for adaptive spline surfaces. linux-
Built to handle continuous and categorical inputs as well as functional or scalar 64,
output. An extension of the methodology in Denison, Mallick and Smith osx-
(1998) <doi:10.1023/A:1008824606259>. / GPL-3 64,
win-
64
r-batch 1.1_5 Functions to allow you to easily pass command-line arguments into R, and noarch
functions to aid in submitting your R code in parallel on a cluster and joining
the results afterward (e.g. multiple parameter values for simulations running
in parallel, splitting up a permutation test in parallel, etc.). See ‘parseCom-
mandArgs(. . . )’ for the main example of how to use this package. / GPL
r-batchmeans 1.0_3 Provides consistent batch means estimation of Monte Carlo standard errors. / noarch
GPL (>= 2)
r-batchscr 0.1.0 Handy frameworks, such as error handling and log generation, for batch noarch
scripts. Use case: in scripts running in remote servers, set error handling
mechanism for downloading and uploading and record operation log. / MIT
file LICENSE


Name Version
r-batman 0.1.0 Survey systems and other third-party data sources commonly use non-standard linux-
representations of logical values when it comes to qualitative data - Yes, No 64,
and N/A, say. batman is a package designed to seamlessly convert these into osx-
logicals. It is highly localised, and contains equivalents to boolean values in 64,
languages including German, French, Spanish, Italian, Turkish, Chinese and win-
Polish. / MIT file LICENSE 64
r-bayesbio 1.0.0 A hodgepodge of hopefully helpful functions. Two of these perform shrinkage noarch
estimation: one using a simple weighted method where the user can specify the
degree of shrinkage required, and one using James-Stein shrinkage estimation
for the case of unequal variances. / GPL-3
r-bayescombo 1.0 Combine diverse evidence across multiple studies to test a high level scientific noarch
theory. The methods can also be used as an alternative to a standard meta-
analysis. / GPL-3
r-bayescomm 0.1_2 Bayesian multivariate binary (probit) regression models for analysis of eco- linux-
logical communities. / GPL (>= 2) 64,
osx-
64,
win-
64
r-bayesda 2012.04_1
Functions for Bayesian Data Analysis, with datasets from the book Bayesian noarch
data Analysis (second edition) by Gelman, Carlin, Stern and Rubin. Not all
datasets yet, hopefully completed soon. / GPL (>= 2)
r-bayesdccgarch 2.0 Bayesian estimation of dynamic conditional correlation GARCH model for linux-
multivariate time series volatility (Fioruci, J.A., Ehlers, R.S. and Andrade- 64,
Filho, M.G., (2014), DOI:10.1080/02664763.2013.839635). / GPL (>= 2) osx-
64,
win-
64
r-bayesdistreg 0.1.0 Implements Bayesian Distribution Regression methods. This package contains noarch
functions for three estimators (non-asymptotic, semi-asymptotic and asymp-
totic) and related routines for Bayesian Distribution Regression in Huang and
Tsyawo (2018) <doi:10.2139/ssrn.3048658> which is also the recommended
reference to cite for this package. The functions can be grouped into three
(3) categories. The first computes the logit likelihood function and posterior
densities under uniform and normal priors. The second contains Independence
and Random Walk Metropolis-Hastings Markov Chain Monte Carlo (MCMC)
algorithms as functions and the third category of functions are useful for semi-
asymptotic and asymptotic Bayesian distribution regression inference. / GPL-
2
r-bayesgarch 2.1.3 Provides the bayesGARCH() function which performs the Bayesian estimation linux-
of the GARCH(1,1) model with Student’s t innovations as described in Ardia 64,
(2008) <doi:10.1007/978-3-540-78657-3>. / GPL (>= 2) osx-
64,
win-
64


Name Version
r-bayesianetas 1.0.3 The Epidemic Type Aftershock Sequence (ETAS) model is one of the best- linux-
performing methods for modeling and forecasting earthquake occurrences. 64,
This package implements Bayesian estimation routines to draw samples from osx-
the full posterior distribution of the model parameters, given an earthquake cat- 64,
alog. The paper on which this package is based is Gordon J. Ross - Bayesian win-
Estimation of the ETAS Model for Earthquake Occurrences (2016), available 64
from the below URL. / GPL-3
r-bayesianpower 0.1.6 A collection of methods to determine the required sample size for the evalua- noarch
tion of inequality constrained hypotheses by means of a Bayes factor. Alter-
natively, for a given sample size, the unconditional error probabilities or the
expected conditional error probabilities can be determined. Additional mate-
rial on the methods in this package is available in Klaassen, F., Hoijtink, H. &
Gu, X. (2019) <doi:10.31219/osf.io/d5kf3>. / LGPL-3
r-bayesimages 0.6_0 Various algorithms for segmentation of 2D and 3D images, such as com- linux-
puted tomography and satellite remote sensing. This package implements 64,
Bayesian image analysis using the hidden Potts model with external field osx-
prior of Moores et al. (2015) <doi:10.1016/j.csda.2014.12.001>. Latent labels 64,
are sampled using chequerboard updating or Swendsen-Wang. Algorithms win-
for the smoothing parameter include pseudolikelihood, path sampling, the 64
exchange algorithm, approximate Bayesian computation (ABC-MCMC and
ABC-SMC), and the parametric functional approximate Bayesian (PFAB) al-
gorithm. Refer to <doi:10.1007/s11222-014-9525-6> and <doi:10.1214/18-
BA1130> for further details. / GPL (>= 2) | file LICENSE
r-bayesloglin 1.0.1 The function MC3() searches for log-linear models with the highest posterior linux-
probability. The function gibbsSampler() is a blocked Gibbs sampler for sam- 64,
pling from the posterior distribution of the log-linear parameters. The func- osx-
tions findPostMean() and findPostCov() compute the posterior mean and co- 64,
variance matrix for decomposable models which, for these models, is available win-
in closed form. / GPL (>= 2) 64
r-bayesm 3.1_3 Covers many important models used in marketing and micro-econometrics ap- linux-
plications. The package includes: Bayes Regression (univariate or multivari- 64,
ate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Or- osx-
dinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), Mul- 64,
tivariate Probit, Negative Binomial (Poisson) Regression, Multivariate Mix- win-
tures of Normals (including clustering), Dirichlet Process Prior Density Esti- 64
mation with normal base, Hierarchical Linear Models with normal prior and
covariates, Hierarchical Linear Models with a mixture of normals prior and
covariates, Hierarchical Multinomial Logits with a mixture of normals prior
and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
analysis of choice-based conjoint data, Bayesian treatment of linear instrumen-
tal variables models, Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as in Rossi et al, JASA (01)), Bayesian Analysis of Ag-
gregate Random Coefficient Logit Models as in BLP (see Jiang, Manchanda,
Rossi 2009) For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non-
and Semi-Parametric Methods and Applications (Princeton U Press 2014). /
GPL (>= 2)
r-bayesmams 0.1 Calculating Bayesian sample sizes for multi-arm trials where several experi- noarch
mental treatments are compared to a common control, perhaps even at multiple
stages. / GPL (>= 2)


Name Version
r-bayesmixsurv 0.9.1 Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Haz- noarch
ards, with Lasso Shrinkage and Stratification. As a Bayesian dynamic survival
model, it relaxes the proportional-hazard assumption. Lasso shrinkage con-
trols overfitting, given the increase in the number of free parameters in the
model due to presence of two Weibull components in the hazard function. /
GPL (>= 2)
r-bayesni 0.1 A Bayesian testing procedure for noninferiority trials with binary endpoints. noarch
The prior is constructed based on Bernstein polynomials with options for both
informative and non-informative prior. The critical value of the test statistic
(Bayes factor) is determined by minimizing total weighted error (TWE) crite-
ria / GPL-2
r- 1.1.0 Fits a piecewise exponential hazard to survival data using a Hierarchical noarch
bayespiecehazselect Bayesian model with an Intrinsic Conditional Autoregressive formulation for
the spatial dependency in the hazard rates for each piece. This function uses
Metropolis- Hastings-Green MCMC to allow the number of split points to vary
and also uses Stochastic Search Variable Selection to determine what covari-
ates drive the risk of the event. This function outputs trace plots depicting the
number of split points in the hazard and the number of variables included in
the hazard. The function saves all posterior quantities to the desired path. /
GPL-2
r- 0.2.1 Fits a piecewise exponential hazard to survival data using a Hierarchical noarch
bayespiecewiseicar Bayesian model with an Intrinsic Conditional Autoregressive formulation for
the spatial dependency in the hazard rates for each piece. This function uses
Metropolis- Hastings-Green MCMC to allow the number of split points to
vary. This function outputs graphics that display the histogram of the number
of split points and the trace plots of the hierarchical parameters. The function
outputs a list that contains the posterior samples for the number of split points,
the location of the split points, and the log hazard rates corresponding to these
splits. Additionally, this outputs the posterior samples of the two hierarchical
parameters, Mu and Sigma^2. / GPL-2
r-bayesqr 2.3 Bayesian quantile regression using the asymmetric Laplace distribution, linux-
both continuous as well as binary dependent variables are supported. The 64,
package consists of implementations of the methods of Yu & Moyeed osx-
(2001) <doi:10.1016/S0167-7152(01)00124-9>, Benoit & Van den Poel 64,
(2012) <doi:10.1002/jae.1216> and Al-Hamzawi, Yu & Benoit (2012) win-
<doi:10.1177/1471082X1101200304>. To speed up the calculations, the 64
Markov Chain Monte Carlo core of all algorithms is programmed in Fortran
and called from R. / GPL (>= 2)
r-bayess 1.4 bayess contains a collection of functions that allows the reenactment of the R noarch
programs used in the book Bayesian Essentials with R (revision of Bayesian
Core) without further programming. R code being available as well, they can
be modified by the user to conduct one’s own simulations. / GPL-2
r-bayessae 1.0_2 Provides a variety of methods from Rao (2003, ISBN:0-471-41374-7) and linux-
some other research articles to deal with several specific small area area- level 64,
models in Bayesian framework. Models provided range from the basic Fay- osx-
Herriot model to its improvement such as You-Chapman models, unmatched 64,
models, spatial models and so on. Different types of priors for specific param- win-
eters could be chosen to obtain MCMC posterior draws. The main sampling 64
function is written in C with GSL lab so as to facilitate the computation. Model
internal checking and model comparison criteria are also involved. / GPL-2


Name Version
r-bayest 1.0 Provides an Markov-Chain-Monte-Carlo algorithm for Bayesian t-tests on the noarch
effect size. The underlying Gibbs sampler is based on a two-component Gaus-
sian mixture and approximates the posterior distributions of the effect size, the
difference of means and difference of standard deviations. A posterior analysis
of the effect size via the region of practical equivalence is provided, too. For
more details about the Gibbs sampler see Kelter (2019) <arXiv:1906.07524>.
/ GPL-2
r-bayestree 0.3_1.4
This is an implementation of BART:Bayesian Additive Regression Trees, by linux-
Chipman, George, McCulloch (2010). / GPL (>= 2) 64,
osx-
64,
win-
64
r-bayestreeprior 1.0.1 Provides a way to simulate from the prior distribution of Bayesian trees noarch
by Chipman et al. (1998) <DOI:10.2307/2669832>. The prior distri-
bution of Bayesian trees is highly dependent on the design matrix X,
therefore using the suggested hyperparameters by Chipman et al. (1998)
<DOI:10.2307/2669832> is not recommended and could lead to unexpected
prior distribution. This work is part of my master thesis (expected 2016). /
GPL-3
r-bayesvalidate 0.0 BayesValidate implements the software validation method described in the noarch
paper Validation of Software for Bayesian Models using Posterior Quantiles
(Cook, Gelman, and Rubin, 2005). It inputs a function to perform Bayesian
inference as well as functions to generate data from the Bayesian model be-
ing fit, and repeatedly generates and analyzes data to check that the Bayesian
inference program works properly. / GPL (>= 2)
r-bayesvarsel 1.8.0 Conceived to calculate Bayes factors in linear models and then to pro- linux-
vide a formal Bayesian answer to testing and variable selection prob- 64,
lems. From a theoretical side, the emphasis in this package is placed osx-
on the prior distributions and it allows a wide range of them: Jef- 64,
freys (1961); Zellner and Siow(1980)<DOI:10.1007/bf02888369>; Zell- win-
ner and Siow(1984); Zellner (1986)<DOI:10.2307/2233941>; Fernan- 64
dez et al. (2001)<DOI:10.1016/s0304-4076(00)00076-2>; Liang et
al. (2008)<DOI:10.1198/016214507000001337> and Bayarri et al.
(2012)<DOI:10.1214/12-aos1013>. The interaction with the package is
through a friendly interface that syntactically mimics the well-known lm()
command of R. The resulting objects can be easily explored providing the user
very valuable information (like marginal, joint and conditional inclusion prob-
abilities of potential variables; the highest posterior probability model, HPM;
the median probability model, MPM) about the structure of the true -data
generating- model. Additionally, this package incorporates abilities to handle
problems with a large number of potential explanatory variables through paral-
lel and heuristic versions of the main commands, Garcia-Donato and Martinez-
Beneito (2013)<DOI:10.1080/01621459.2012.742443>. / GPL-2
r-bayesxsrc 3.0_1 BayesX performs Bayesian inference in structured additive regression (STAR) linux-
models. The R package BayesXsrc provides the BayesX command line 64,
tool for easy installation. A convenient R interface is provided in package osx-
R2BayesX. / GPL-2 | GPL-3 64,
win-
64


Name Version
r-bayfoxr 0.0.1 A Bayesian, global planktic foraminifera core top calibration to modern sea- noarch
surface temperatures. Includes four calibration models, considering species-
specific calibration parameters and seasonality. / GPL (>= 3)
r-bayhap 1.0.1 The package BayHap performs simultaneous estimation of uncertain haplo- linux-
type frequencies and association with haplotypes based on generalized lin- 64,
ear models for quantitative, binary and survival traits. Bayesian statistics and osx-
Markov Chain Monte Carlo techniques are the theoretical framework for the 64,
methods of estimation included in this package. Prior values for model param- win-
eters can be included by the user. Convergence diagnostics and statistical and 64
graphical analysis of the sampling output can be also carried out. / GPL-2
r-bayhaz 0.1_3 A suite of R functions for Bayesian estimation of smooth hazard rates via noarch
Compound Poisson Process (CPP) and Bayesian Penalized Spline (BPS) pri-
ors. / GPL (>= 2)
r-bayloredpsych 0.5 Functions and data used for Baylor University Educational Psychology Quan- noarch
titative Courses / GPL (>= 2)
r-baystar 0.2_9 The manuscript introduces the BAYSTAR package, which provides the func- noarch
tionality for Bayesian estimation in autoregressive threshold models. / GPL
(>= 2)
r-bb 2014.10_1
Barzilai-Borwein spectral methods for solving nonlinear system of equations, noarch
and for optimizing nonlinear objective functions subject to simple constraints.
A tutorial style introduction to this package is available in a vignette on the
CRAN download page or, when the package is loaded in an R session, with
vignette(BB). / GPL-3
r-bbefkr 4.2 Estimating optimal bandwidths for the regression mean function approximated noarch
by the functional Nadaraya-Watson estimator and the error density approxi-
mated by a kernel density of residuals simultaneously in a scalar-on-function
regression. As a by-product of Markov chain Monte Carlo, the optimal choice
of semi-metric is selected based on largest marginal likelihood. / GPL (>= 2)
r-bbemkr 2.0 Bayesian bandwidth estimation for Nadaraya-Watson type multivariate kernel noarch
regression with Gaussian error density / GPL (>= 2)
r-bbl 0.1.5 Supervised learning using Boltzmann Bayes model inference, which extends linux-
naive Bayes model to include interactions. Enables classification of data into 64,
multiple response groups based on a large number of discrete predictors that osx-
can take factor values of heterogeneous levels. Either pseudo-likelihood and 64,
mean field inference can be used with L2 regularization, cross-validation, and win-
prediction on new data. Woo et al. (2016) <doi:10.1186/s12864-016-2871-3>. 64
/ GPL-2
r-bbmisc 1.11 Miscellaneous helper functions for and from B. Bischl and some other guys, linux-
mainly for package development. / BSD_2_clause file LICENSE 64,
osx-
64,
win-
64
r-bbmle 1.0.20Methods and functions for fitting maximum likelihood models in R. This pack- noarch
age modifies and extends the ‘mle’ classes in the ‘stats4’ package. / GPL
r-bbmm 3.0 The model provides an empirical estimate of a movement path using discrete noarch
location data obtained at relatively short time intervals. / GNU General Public
License


Name Version
r-bbmv 2.1 Provides a set of functions to fit general macroevolutionary models for contin- noarch
uous traits evolving in adaptive landscapes of any shape. This package imple-
ments the Fokker-Planck-Kolmogorov model (FPK), in which the trait evolves
under random diffusion but is also subject to a force that pulls it towards spe-
cific values - this force can be of any shape. FPK has a version in which hard
reflective bounds exist at the extremes of the trait interval: this second model
is called BBMV. / GPL-2
r-bbo 0.2 This package provides an R implementation of Biogeography-Based Opti- noarch
mization (BBO), originally invented by Prof. Dan Simon, Cleveland State
University, Ohio. This method is an application of the concept of biogeogra-
phy, a study of the geographical distribution of biological organisms, to opti-
mization problems. More information about this method can be found here:
http://academic.csuohio.edu/simond/bbo/. / GPL (>= 3)
r-bcaboot 0.2_1 Computation of bootstrap confidence intervals in an almost automatic fashion. noarch
/ GPL (>= 2)
r-bcbcsf 1.0_1 Fully Bayesian Classification with a subset of high-dimensional features, such linux-
as expression levels of genes. The data are modeled with a hierarchical 64,
Bayesian models using heavy-tailed t distributions as priors. When a large osx-
number of features are available, one may like to select only a subset of fea- 64,
tures to use, typically those features strongly correlated with the response in win-
training cases. Such a feature selection procedure is however invalid since 64
the relationship between the response and the features has be exaggerated by
feature selection. This package provides a way to avoid this bias and yield
better-calibrated predictions for future cases when one uses F-statistic to se-
lect features. / GPL (>= 2)
r-bcc1997 0.1.1 Calculates the prices of European options based on the universal so- noarch
lution provided by Bakshi, Cao and Chen (1997) <doi:10.1111/j.1540-
6261.1997.tb02749.x>. This solution considers stochastic volatility, stochastic
interest and random jumps. Please cite their work if this package is used. /
GPL (>= 2)
r-bcdating 0.9.8 Tools for Dating Business Cycles using Harding-Pagan (Quarterly Bry- noarch
Boschan) method and various plotting features. / GPL-2
r-bcf 1.2.1 Causal inference for a binary treatment and continuous outcome us- linux-
ing Bayesian Causal Forests. See Hahn, Murray and Carvalho (2017) 64,
<arXiv:1706.09523> for additional information. This implementation relies osx-
on code originally accompanying Pratola et. al. (2013) <arXiv:1309.1906>. / 64,
GPL-3 win-
64
r-bcgee 0.1 Provides bias-corrected estimates for the regression coefficients of a marginal noarch
model estimated with generalized estimating equations. Details about
the bias formula used are in Lunardon, N., Scharfstein, D. (2017)
<doi:10.1002/sim.7366>. / GPL-2
r-bclust 1.5 Builds a dendrogram using log posterior as a natural distance defined by the linux-
model and meanwhile waits the clustering variables. It is also capable to com- 64,
puting equivalent Bayesian discrimination probabilities. The adopted method osx-
suites small sample large dimension setting. The model parameter estimation 64,
maybe difficult, depending on data structure and the chosen distribution fam- win-
ily. / GPL (>= 2) 64


Name Version
r-bcp 4.0.3 Provides an implementation of the Barry and Hartigan (1993) product partition linux-
model for the normal errors change point problem using Markov Chain Monte 32,
Carlo. It also extends the methodology to regression models on a connected linux-
graph (Wang and Emerson, 2015); this allows estimation of change point mod- 64,
els with multivariate responses. Parallel MCMC, previously available in bcp osx-
v.3.0.0, is currently not implemented. / GPL (>= 2) 64,
win-
32,
win-
64
r-bcpa 1.1 The Behavioral Change Point Analysis (BCPA) is a method of identifying hid- linux-
den shifts in the underlying parameters of a time series, developed specifically 64,
to be applied to animal movement data which is irregularly sampled. The osx-
method is based on: E. Gurarie, R. Andrews and K. Laidre A novel method 64,
for identifying behavioural changes in animal movement data (2009) Ecology win-
Letters 12:5 395-408. / Unlimited 64
r-bcpmeta 1.0 A Bayesian approach to detect mean shifts in AR(1) time series while ac- noarch
commodating metadata (if available). In addition, a linear trend component is
allowed. / GPL (>= 2)
r-bcra 2.1 Functions provide risk projections of invasive breast cancer based on Gail noarch
model according to National Cancer Institute’s Breast Cancer Risk Assess-
ment Tool algorithm for specified race/ethnic groups and age intervals. / GPL
(>= 2)
r-bcrypt 1.1 Bindings to the ‘blowfish’ password hashing algorithm derived from the linux-
‘OpenBSD’ implementation. / BSD_2_clause file LICENSE 64,
osx-
64,
win-
64
r-bcv 1.0.1 Methods for choosing the rank of an SVD approximation via cross valida- linux-
tion. The package provides both Gabriel-style block holdouts and Wold-style 64,
speckled holdouts. It also includes an implementation of the SVDImpute al- osx-
gorithm. For more information about Bi-cross-validation, see Owen & Perry’s 64,
2009 AoAS article (at http://arxiv.org/abs/0908.2062) and Perry’s 2009 PhD win-
thesis (at http://arxiv.org/abs/0909.3052). / BSD_3_clause file LICENSE 64
r-bda 10.1.9Functions for density estimation based on grouped data, and next-generation linux-
gene expression data. / Unlimited 64,
osx-
64,
win-
64
r-bdgraph 2.60 Statistical tools for Bayesian structure learning in undirected graphical models linux-
for continuous, discrete, and mixed data. The package is implemented the 64,
recent improvements in the Bayesian graphical models literature, including osx-
Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Mohammadi and Wit 64,
(2019) <doi:10.18637/jss.v089.i03>. / GPL (>= 2) win-
64
r-bdots 0.1.19Analyze differences among time series curves with p-value adjust- noarch
ment for multiple comparisons introduced in Oleson et al (2015)
<DOI:10.1177/0962280215607411>. / GPL-3


Name Version
r-bdp2 0.1.3 Tools and workflow to choose design parameters in Bayesian adaptive single- noarch
arm phase II trial designs with binary endpoint (response, success) with possi-
ble stopping for efficacy and futility at interim analyses. Also contains routines
to determine and visualize operating characteristics. See Kopp-Schneider et al.
(2018) <doi:10.1002/bimj.201700209>. / GPL-2
r-bdpv 1.3 Computation of asymptotic confidence intervals for negative and positive pre- noarch
dictive values in binary diagnostic tests in case-control studies. Experimental
design for hypothesis tests on predictive values. / GPL (>= 2)
r-bdsmatrix 1.3_3 This is a special case of sparse matrices, used by coxme. / LGPL-2 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-beanplot 1.2 Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin noarch
plot. / GPL-2
r-beast 1.1 Assume that a temporal process is composed of contiguous segments with noarch
differing slopes and replicated noise-corrupted time series measurements are
observed. The unknown mean of the data generating process is modelled as a
piecewise linear function of time with an unknown number of change-points.
The package infers the joint posterior distribution of the number and posi-
tion of change-points as well as the unknown mean parameters per time-series
by MCMC sampling. A-priori, the proposed model uses an overfitting num-
ber of mean parameters but, conditionally on a set of change-points, only a
subset of them influences the likelihood. An exponentially decreasing prior
distribution on the number of change-points gives rise to a posterior distri-
bution concentrating on sparse representations of the underlying sequence,
but also available is the Poisson distribution. See Papastamoulis et al (2017)
<arXiv:1709.06111> for a detailed presentation of the method. / GPL-2
r-bedmatrix 1.6.1 A matrix-like data structure that allows for efficient, convenient, and scalable linux-
subsetting of binary genotype/phenotype files generated by PLINK (<https: 64,
//www.cog-genomics.org/plink2>), the whole genome association analysis osx-
toolset, without loading the entire file into memory. / MIT 64,
win-
64
r-beepr 1.3 The main function of this package is beep(), with the purpose to make it easy noarch
to play notification sounds on whatever platform you are on. It is intended to
be useful, for example, if you are running a long analysis in the background
and want to know when it is ready. / GPL-3
r-beeswarm 0.2.3 The bee swarm plot is a one-dimensional scatter plot like stripchart, but with noarch
closely-packed, non-overlapping points. / Artistic-2.0
r-beginr 0.1.7 Useful functions for R beginners, including hints for the arguments of the noarch
‘plot()’ function, self-defined functions for error bars, user-customized pair
plots and hist plots, enhanced linear regression figures, etc.. This package
could be helpful to R experts as well. / MIT
r-behavr 0.3.2 Implements an S3 class based on ‘data.table’ to store and process efficiently noarch
ethomics (high-throughput behavioural) data. / GPL-3


Name Version
r-belex 0.1.0 Tools for downloading historical financial data from the www.belex.rs. / GPL- noarch
3
r-belg 0.2.3 Calculates the Boltzmann entropy of a landscape gradient. This package linux-
uses the analytical method created by Gao, P., Zhang, H. and Li, Z., 2018 64,
(<doi:10.1111/tgis.12315>). It also extend the original idea by allowing cal- osx-
culations on data with missing values. / MIT file LICENSE 64,
win-
64
r-benchden 1.0.5 Full implementation of the 28 distributions introduced as benchmarks for non- noarch
parametric density estimation by Berlinet and Devroye (1994). Includes den-
sities, cdfs, quantile functions and generators for samples as well as additional
information on features of the densities. Also contains the 4 histogram densi-
ties used in Rozenholc/Mildenberger/Gather (2010). / GPL (>= 2)
r-benchr 0.2.3_1
Provides infrastructure to accurately measure and compare the execution time linux-
of R expressions. / GPL (>= 2) 64,
osx-
64,
win-
64
r-bender 0.1.1 R client for Bender Hyperparameters optimizer : <https://bender.dreem.com> noarch
The R client allows you to communicate with the Bender API and therefore
submit some new trials within your R script itself. / MIT file LICENSE
r- 0.1.5 Provides tools that make it easier to validate data using Benford’s Law. / GPL- noarch
benford.analysis 3
r-benfordtests 1.2.0 Several specialized statistical tests and support functions for determining if linux-
numerical data could conform to Benford’s law. / GPL-3 64,
osx-
64,
win-
64
r-bentcablear 0.3.0 Included are two main interfaces for fitting and diagnosing bent-cable regres- noarch
sions for autoregressive time-series data or independent data (time series or
otherwise): ‘bentcable.ar()’ and ‘bentcable.dev.plot()’. Some components in
the package can also be used as stand-alone functions. The bent cable (linear-
quadratic-linear) generalizes the broken stick (linear-linear), which is also han-
dled by this package. Version 0.2 corrects a glitch in the computation of confi-
dence intervals for the CTP. References that were updated from Versions 0.2.1
and 0.2.2 appear in Version 0.2.3 and up. Version 0.3.0 improves robustness
of the error-message producing mechanism. It is the author’s intention to dis-
tribute any future updates via GitHub. / GPL (>= 3)
r-beqi2 2.0_0 Tool for analysing benthos data. It estimates several quality indices like the noarch
total abundance of species, species richness, Margalef’s d, AZTI Marine Bi-
otic Index (AMBI), and the BEQI-2 index. Furthermore, additional (optional)
features are provided that enhance data preprocessing: (1) genus to species
conversion, i.e.,taxa counts at the taxonomic genus level can optionally be
converted to the species level and (2) pooling: small samples are combined
to bigger samples with a standardized size to (a) meet the data requirements
of the AMBI, (b) generate comparable species richness values and (c) give a
higher benthos signal to noise ratio. / GPL (>= 3)


Name Version
r-ber 4.0 The functions in this package remove batch effects from microarrary normal- noarch
ized data. The expression levels of the genes are represented in a matrix where
rows correspond to independent samples and columns to genes (variables).
The batches are represented by categorical variables (objects of class factor).
When further covariates of interest are available they can be used to remove
efficiently the batch effects and adjust the data. / GPL-2
r-berryfunctions 1.18.2Draw horizontal histograms, color scattered points by 3rd dimension, enhance noarch
date- and log-axis plots, zoom in X11 graphics, trace errors and warnings, use
the unit hydrograph in a linear storage cascade, convert lists to data.frames and
arrays, fit multiple functions. / GPL (>= 2)
r-bess 1.0.6 An implementation of best subset selection in generalized linear model linux-
and Cox proportional hazard model via the primal dual active set algo- 64,
rithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2017) osx-
<arXiv:1709.06254>. The algorithm formulates coefficient parameters and 64,
residuals as primal and dual variables and utilizes efficient active set selection win-
strategies based on the complementarity of the primal and dual variables. / 64
GPL-3
r-bestglm 0.37 Best subset glm using information criteria or cross-validation. / GPL (>= 2) linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-bestree 0.5.2 Decision tree algorithm with a major feature added. Allows for users noarch
to define an ordering on the partitioning process. Resulting in Branch-
Exclusive Splits Trees (BEST). Cedric Beaulac and Jeffrey S. Rosentahl
(2019) <arXiv:1804.10168>. / MIT file LICENSE
r-betabit 1.3 Three games: proton, frequon and regression. Each one is a console-based noarch
data-crunching game for younger and older data scientists. Act as a data-
hacker and find Slawomir Pietraszko’s credentials to the Proton server. In pro-
ton you have to solve four data-based puzzles to find the login and password.
There are many ways to solve these puzzles. You may use loops, data filtering,
ordering, aggregation or other tools. Only basics knowledge of R is required
to play the game, yet the more functions you know, the more approaches you
can try. In frequon you will help to perform statistical cryptanalytic attack on
a corpus of ciphered messages. This time seven sub-tasks are pushing the bar
much higher. Do you accept the challenge? In regression you will test your
modeling skills in a series of eight sub-tasks. Try only if ANOVA is your close
friend. It’s a part of Beta and Bit project. You will find more about the Beta
and Bit project at <http://betabit.wiki>. / GPL-2
r-betacal 0.1.0 Fit beta calibration models and obtain calibrated probabilities from them. / noarch
MIT file LICENSE
r-betafam 1.0 To detecting rare variants for quantitative traits using nuclear families, the lin- noarch
ear combination methods are proposed using the estimated regression coeffi-
cients from the multiple regression and regularized regression as the weights.
/ GPL (>= 2)


Name Version
r-betalink 2.2.1 Measures of beta-diversity in networks, and easy visualization of why two noarch
networks are different. / BSD_2_clause file LICENSE
r-betategarch 3.3 Simulation, estimation and forecasting of first-order Beta-Skew-t-EGARCH linux-
models with leverage (one-component, two-component, skewed versions). / 64,
GPL-2 osx-
64,
win-
64
r-bethel 0.2 The sample size according to the Bethel’s procedure. / GPL (>= 2) noarch
r-bevimed 5.3 A fast integrative genetic association test for rare diseases based on a model linux-
for disease status given allele counts at rare variant sites. Probability of as- 64,
sociation, mode of inheritance and probability of pathogenicity for individual osx-
variants are all inferred in a Bayesian framework - ‘A Fast Association Test for 64,
Identifying Pathogenic Variants Involved in Rare Diseases’, Greene et al 2017 win-
<doi:10.1016/j.ajhg.2017.05.015>. / GPL (>= 2) 64
r-beyondbenford 1.1 Allows to compare the goodness of fit of Benford’s and Blondeau Da Silva’s noarch
digit distributions in a dataset. It is used to check whether the data distribution
is consistent with theoretical distributions highlighted by Blondeau Da Silva
or not (through the dat.distr() function): this ideal theoretical distribution must
be at least approximately followed by the data for the use of Blondeau Da
Silva’s model to be well-founded. It also enables to plot histograms of digit
distributions, both observed in the dataset and given by the two theoretical
approaches (with the digit.ditr() function). Finally, it proposes to quantify the
goodness of fit via Pearson’s chi-squared test (with the chi2() function). /
GPL-2
r-bezier 1.1.2 The bezier package is a toolkit for working with Bezier curves and splines. noarch
The package provides functions for point generation, arc length estimation,
degree elevation and curve fitting. / GPL (>= 2)
r-bfa 0.4 Provides model fitting for several Bayesian factor models including Gaussian, linux-
ordinal probit, mixed and semiparametric Gaussian copula factor models under 64,
a range of priors. / GPL-3 osx-
64,
win-
64
r-bfp 0.0_40Implements the Bayesian paradigm for fractional polynomial models under linux-
the assumption of normally distributed error terms, see Sabanes Bove, D. and 64,
Held, L. (2011) <doi:10.1007/s11222-010-9170-7>. / GPL (>= 2) osx-
64,
win-
64
r-bfsl 0.1.0 Provides the solution from York (1968) <doi:10.1016/S0012-821X(68)80059- noarch
7> for fitting a straight line to bivariate data with errors in both coordinates.
It gives unbiased estimates of the intercept, slope and standard errors of the
best-fit straight line to independent points with (possibly correlated) normally
distributed errors in both x and y. Other commonly used errors-in-variables
methods, such as orthogonal distance regression, geometric mean regression
or Deming regression are special cases of YorkâC™s solution. / GPL-3


Name Version
r-bgge 0.6.5 Application of genome prediction for a continuous variable, focused on geno- noarch
type by environment (GE) genomic selection models (GS). It consists a group
of functions that help to create regression kernels for some GE genomic mod-
els proposed by Jarquín et al. (2014) <doi:10.1007/s00122-013-2243-1> and
Lopez-Cruz et al. (2015) <doi:10.1534/g3.114.016097>. Also, it computes
genomic predictions based on Bayesian approaches. The prediction function
uses an orthogonal transformation of the data and specific priors present by
Cuevas et al. (2014) <doi:10.1534/g3.114.013094>. / GPL-3
r-bgmfiles 0.0.6 A collection of box-geometry model (BGM) files for the Atlantis ecosys- noarch
tem model. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem
model (see <http://atlantis.cmar.csiro.au/> for more information). / CC0
r-bgphazard 1.2.3 Computes the hazard rate estimate as described by Nieto-Barajas and Walker noarch
(2002) and Nieto-Barajas (2003). / GPL (>= 2)
r-bgsimd 1.0 Implement an efficient block Gibbs sampler with incomplete data from a multi- noarch
nomial distribution taking values from the k categories 1,2,. . . ,k, where data
are assumed to miss at random and each missing datum belongs to one and
only one of m distinct non-empty proper subsets A1, A2,. . . , Am of 1,2,. . . ,k
and the k categories are labelled such that only consecutive A’s may overlap. /
GPL (>= 2)
r-bh 1.69.0_1
Boost provides free peer-reviewed portable C source libraries. A large part of linux-
Boost is provided as C template code which is resolved entirely at compile- 32,
time without linking. This package aims to provide the most useful subset of linux-
Boost libraries for template use among CRAN package. By placing these li- 64,
braries in this package, we offer a more efficient distribution system for CRAN noarch,
as replication of this code in the sources of other packages is avoided. As of re- osx-
lease 1.69.0-1, the following Boost libraries are included: ‘algorithm’ ‘align’ 64,
‘any’ ‘atomic’ ‘bimap’ ‘bind’ ‘circular_buffer’ ‘compute’ ‘concept’ ‘config’ win-
‘container’ ‘date_time’ ‘detail’ ‘dynamic_bitset’ ‘exception’ ‘filesystem’ ‘fly- 32,
weight’ ‘foreach’ ‘functional’ ‘fusion’ ‘geometry’ ‘graph’ ‘heap’ ‘icl’ ‘inte- win-
ger’ ‘interprocess’ ‘intrusive’ ‘io’ ‘iostreams’ ‘iterator’ ‘math’ ‘move’ ‘mpl’ 64
‘multiprcecision’ ‘numeric’ ‘pending’ ‘phoenix’ ‘preprocessor’ ‘propery_tree’
‘random’ ‘range’ ‘scope_exit’ ‘smart_ptr’ ‘sort’ ‘spirit’ ‘tuple’ ‘type_traits’
‘typeof’ ‘unordered’ ‘utility’ ‘uuid’. / BSL-1.0
r-bhat 0.9_10Functions for MLE, MCMC, CIs (originally in Fortran) / GPL (>= 2) noarch
r-bhh2 2016.05.31
Functions and data sets reproducing some examples in Box, Hunter and Hunter noarch
II. Useful for statistical design of experiments, especially factorial experi-
ments. / GPL (>= 2)
r-bhm 1.15 Contains tools to fit both predictive and prognostic biomarker effects using noarch
biomarker threshold models. Evaluate the treatment effect, biomarker ef-
fect and treatment-biomarker interaction using probability index measurement.
Test for treatment-biomarker interaction using residual bootstrap method. /
GPL (>= 2)
r-bhsbvar 1.0.4 Provides a function for estimating the parameters of Structural Bayesian linux-
Vector Autoregression models with the method developed by Baumeister 64,
and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamil- osx-
ton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) 64,
<doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse re- win-
sponses, historical decompositions, and posterior distributions of model pa- 64
rameters are also provided. / GPL (>= 3)


Name Version
r-biasedurn 1.07 Statistical models of biased sampling in the form of univariate and multivariate linux-
noncentral hypergeometric distributions, including Wallenius’ noncentral hy- 64,
pergeometric distribution and Fisher’s noncentral hypergeometric distribution osx-
(also called extended hypergeometric distribution). See vignette(UrnTheory) 64,
for explanation of these distributions. / GPL-3 win-
64
r-bibplots 0.0.6 Currently, the package provides four functions for plotting and analyzing bib- noarch
liometric data (JIF, Journal Impact Factor, and paper percentile values), beam-
plots with citations, and two plot function to visualize the result of a reference
publication year spectroscopy (RPYS) analysis performed in the free software
‘CRExplorer’ (see <http://crexplorer.net>). Further extension to more plot
variants is planned. / EUPL
r-bibtex 0.4.2 Utility to parse a bibtex file. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
r-biclique 1.0.3 A tool for enumerating maximal complete bipartite graphs. The input should linux-
be a edge list file or a binary matrix file. The output are maximal complete 64,
bipartite graphs. Algorithms used can be found in this paper Y Zhang et al. osx-
BMC Bioinformatics 2014 15:110 <doi:10.1186/1471-2105-15-110>. / GPL- 64,
2 win-
64
r-bicorn 0.1.0 Prior transcription factor binding knowledge and target gene expression data noarch
are integrated in a Bayesian framework for functional cis-regulatory module
inference. Using Gibbs sampling, we iteratively estimate transcription factor
associations for each gene, regulation strength for each binding event and the
hidden activity for each transcription factor. / GPL-2
r- 2.0.0 Calculates the bidimensional regression between two 2D configurations fol- noarch
bidimregression lowing the approach by Tobler (1965). / GPL-3
r-bife 0.6 Estimates fixed effects binary choice models (logit and probit) with potentiallylinux-
many individual fixed effects and computes average partial effects. Incidental64,
parameter bias can be reduced with an asymptotic bias-correction proposed by osx-
Fernandez-Val (2009) <doi:10.1016/j.jeconom.2009.02.007>. / GPL-2 64,
win-
64
r-bigalgebra 0.8.4.1This package provides arithmetic functions for R matrix and big.matrix ob- linux-
jects. / LGPL-3 64,
osx-
64,
win-
64
r-biganalytics 1.1.14Extend the ‘bigmemory’ package with various analytics. Functions ‘bigk- linux-
means’ and ‘binit’ may also be used with native R objects. For ‘tapply’-like 64,
functions, the bigtabulate package may also be helpful. For linear algebra osx-
support, see ‘bigalgebra’. For mutex (locking) support for advanced shared- 64,
memory usage, see ‘synchronicity’. / LGPL-3 win-
64


Name Version
r-bigintegeralgos 0.1.2 Features the multiple polynomial quadratic sieve algorithm for factoring large linux-
integers and a vectorized factoring function that returns the complete factor- 64,
ization of an integer. Utilizes the C library GMP (GNU Multiple Precision osx-
Arithmetic) and classes created by Antoine Lucas et al. found in the ‘gmp’ 64,
package. / GPL-2 win-
64
r-biglm 0.9_1 Regression for data too large to fit in memory / GPL-3 linux-
64,
osx-
64,
win-
64
r-biglmm 0.9_1 Regression for data too large to fit in memory. This package functions exactly linux-
like the ‘biglm’ package, but works with later versions of R. / GPL-3 64,
osx-
64,
win-
64
r-bigmap 2.1.0 Unsupervised clustering protocol for large scale structured data, based linux-
on a low dimensional representation of the data. Dimensionality reduc- 64,
tion is performed using a parallelized implementation of the t-Stochastic osx-64
Neighboring Embedding algorithm (Garriga J. and Bartumeus F. (2018),
<arXiv:1812.09869>). / GPL-3
r-bigmemory 4.5.33Create, store, access, and manipulate massive matrices. Matrices are allocated linux-
to shared memory and may use memory-mapped files. Packages ‘biganalyt- 64,
ics’, ‘bigtabulate’, ‘synchronicity’, and ‘bigalgebra’ provide advanced func- osx-
tionality. / LGPL-3 64,
win-
64
r-bigmemory.sri 0.1.3 This package provides a shared resource interface for the bigmemory and syn- noarch
chronicity packages. / LGPL-3
r-bigml 0.1.2 The ‘bigml’ package contains bindings for the BigML API. The package in- noarch
cludes methods that provide straightforward access to basic API functionality,
as well as methods that accommodate idiomatic R data types and concepts. /
LGPL-3
r-bigreadr 0.1.9 Read large text files by splitting them in smaller files. Package bigreadr also
linux-
provides some convenient wrappers of fread/fwrite. / GPL-3 64,
osx-
64,
win-
64


Name Version
r-bigreg 0.1.2 Allows the user to carry out GLM on very large data sets. Data can be cre- linux-
ated using the data_frame() function and appended to the object with ob- 64,
ject$append(data); data_frame and data_matrix objects are available that al- osx-64
low the user to store large data on disk. The data is stored as doubles in binary
format and any character columns are transformed to factors and then stored as
numeric (binary) data while a look-up table is stored in a separate .meta_data
file in the same folder. The data is stored in blocks and GLM regression algo-
rithm is modified and carries out a MapReduce- like algorithm to fit the model.
The functions bglm(), and summary() and bglm_predict() are available for cre-
ating and post-processing of models. The library requires Armadillo installed
on your system. It probably won’t function on windows since multi-core pro-
cessing is done using mclapply() which forks R on Unix/Linux type operating
systems. / GPL-2
r-bigsplines 1.1_1 Fits smoothing spline regression models using scalable algorithms designed linux-
for large samples. Seven marginal spline types are supported: linear, cubic, 64,
different cubic, cubic periodic, cubic thin-plate, ordinal, and nominal. Random osx-
effects and parametric effects are also supported. Response can be Gaussian 64,
or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative win-
Binomial. / GPL-2 64
r-bigtabulate 1.1.5 Extend the bigmemory package with ‘table’, ‘tapply’, and ‘split’ support for linux-
‘big.matrix’ objects. The functions may also be used with native R matrices 64,
for improving speed and memory-efficiency. / LGPL-3 osx-
64,
win-
64
r-bigtcr 1.1 For studying recurrent disease and death with competing risks, comparisons linux-
based on the well-known cumulative incidence function can be confounded by 64,
different prevalence rates of the competing events. Alternatively, comparisons osx-
of the conditional distribution of the survival time given the failure event type 64,
are more relevant for investigating the prognosis of different patterns of re- win-
currence disease. This package implements a nonparametric estimator for the 64
conditional cumulative incidence function and a nonparametric conditional bi-
variate cumulative incidence function for the bivariate gap times proposed in
Huang et al. (2016) <doi:10.1111/biom.12494>. / GPL-3
r-bigtime 0.1.0 Estimation of large Vector AutoRegressive (VAR), Vector AutoRegressive linux-
with Exogenous Variables X (VARX) and Vector AutoRegressive Moving Av- 64,
erage (VARMA) Models with Structured Lasso Penalties, see Nicholson, Bien osx-
and Matteson (2017) <arXiv:1412.5250v2> and Wilms, Basu, Bien and Mat- 64,
teson (2017) <arXiv:1707.09208>. / GPL-2 win-
64
r-bigvar 1.0.4 Estimates VAR and VARX models with structured Lasso Penalties. / GPL-2 linux-
64,
osx-
64,
win-
64
r-bikeshare14 0.1.2 Anonymised Bay Area bike share trip data for the year 2014. Also contains noarch
additional metadata on stations and weather. / CC0


Name Version
r-bild 1.1_5 Performs logistic regression for binary longitudinal data, allowing for serial linux-
dependence among observations from a given individual and a random inter- 64,
cept term. Estimation is via maximization of the exact likelihood of a suitably osx-
defined model. Missing values and unbalanced data are allowed, with some 64,
restrictions. / GPL-2 win-
64
r-bimetallic 1.0 A power calculator for Genome-wide association studies (GWAs) with com- noarch
bined gold (error-free) and silver (erroneous) phenotyping per McDavid A,
Crane PK, Newton KM, Crosslin DR, et al. (2011) / GPL-2
r-bimets 1.4.0 Time series analysis, (dis)aggregation and manipulation, e.g. time series ex- noarch
tension, merge, projection, lag, lead, delta, moving and cumulative average
and product, selection by index, date and year-period, conversion to daily,
monthly, quarterly, (semi)annually. Simultaneous equation models definition,
estimation, simulation and forecasting with coefficient restrictions, error au-
tocorrelation, exogenization, add-factors, impact and interim multipliers anal-
ysis, conditional equation evaluation, endogenous targeting and model renor-
malization. / EUPL
r-bimixt 1.0 Estimates non-Gaussian mixture models of case-control data. The four types noarch
of models supported are binormal, two component constrained, two compo-
nent unconstrained, and four component. The most general model is the four
component model, under which both cases and controls are distributed accord-
ing to a mixture of two unimodal distributions. In the four component model,
the two component distributions of the control mixture may be distinct from
the two components of the case mixture distribution. In the two component
unconstrained model, the components of the control and case mixtures are the
same; however the mixture probabilities may differ for cases and controls. In
the two component constrained model, all controls are distributed according
to one of the two components while cases follow a mixture distribution of the
two components. In the binormal model, cases and controls are distributed ac-
cording to distinct unimodal distributions. These models assume that Box-Cox
transformed case and control data with a common lambda parameter are dis-
tributed according to Gaussian mixture distributions. Model parameters are es-
timated using the expectation-maximization (EM) algorithm. Likelihood ratio
test comparison of nested models can be performed using the lr.test function.
AUC and PAUC values can be computed for the model-based and empirical
ROC curves using the auc and pauc functions, respectively. The model-based
and empirical ROC curves can be graphed using the roc.plot function. Finally,
the model-based density estimates can be visualized by plotting a model object
created with the bimixt.model function. / GPL-3
r-binarize 1.3 Provides methods for the binarization of one-dimensional data and some visu- linux-
alization functions. / Artistic-2.0 64,
osx-
64,
win-
64
r-binaryemvs 0.1 Implements variable selection for high dimensional datasets with a binary re- noarch
sponse variable using the EM algorithm. Both probit and logit models are
supported. Also included is a useful function to generate high dimensional
data with correlated variables. / GPL-3


Name Version
r-binarylogic 0.3.9 Provides the binary S3 class. The instance of binary is used to convert a dec- noarch
imal number (Base10) to a binary number (Base2). The Class provides some
features e.G. shift(), rotate(), summary(). Based on logical vectors. / GPL-3
r-binb 0.0.4 A collection of ‘LaTeX’ styles using ‘Beamer’ customization for pdf-based noarch
presentation slides in ‘RMarkdown’. At present it contains ‘RMarkdown’
adaptations of the LaTeX themes ‘Metropolis’ (formerly ‘mtheme’) theme by
Matthias Vogelgesang and others (now included in ‘TeXLive’), the ‘IQSS’ by
Ista Zahn (which is included here), and the ‘Monash’ theme by Rob J Hynd-
man. Additional (free) fonts may be needed: ‘Metropolis’ prefers ‘Fira’, and
‘IQSS’ requires ‘Libertinus’. / GPL-2
r-binda 1.0.3 The binda package implements functions for multi-class discriminant analy- noarch
sis using binary predictors, for corresponding variable selection, and for di-
chotomizing continuous data. / GPL-3
r-bindata 0.9_19Generation of correlated artificial binary data. / GPL-2 noarch
r-bindr 0.1.1 Provides a simple interface for creating active bindings where the bound func- linux-
tion accepts additional arguments. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-bindrcpp 0.2.2 Provides an easy way to fill an environment with active bindings that call a C linux-
function. / MIT file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-binford 0.1.0 Binford’s hunter-gatherer data includes more than 200 variables coding as- noarch
pects of hunter-gatherer subsistence, mobility, and social organization for 339
ethnographically documented groups of hunter-gatherers. / GPL-3
r-binmto 0.0_7 Asymptotic simultaneous confidence intervals for comparison of many treat- noarch
ments with one control, for the difference of binomial proportions, allows
for Dunnett-like-adjustment, Bonferroni or unadjusted intervals. Simulation
of power of the above interval methods, approximate calculation of any-pair-
power, and sample size iteration based on approximate any-pair power. Exact
conditional maximum test for many-to-one comparisons to a control. / GPL-2
r-binnonnor 1.5.1 Generation of multiple binary and continuous non-normal variables simultane- noarch
ously given the marginal characteristics and association structure based on the
methodology proposed by Demirtas et al. (2012) <DOI:10.1002/sim.5362>. /
GPL-2 | GPL-3


Name Version
r-binnor 2.3.1 Generating multiple binary and normal variables simultaneously noarch
given marginal characteristics and association structure based
on the methodology proposed by Demirtas and Doganay (2012)
<DOI:10.1080/10543406.2010.521874>. / GPL-2
r-binom 1.1_1 Constructs confidence intervals on the probability of success in a binomial linux-
experiment via several parameterizations / GPL-3 64,
osx-
64,
win-
64
r-binomialcftp 1.0 Binomial random numbers are generated via the perfect sampling algorithm. noarch
At each iteration dual markov chains are generated and coalescence is checked.
In case coalescence occurs, the resulting number is outputted. In case not, then
the algorithm is restarted from T(t)=2*T(t) until coalescence occurs. / GPL-2
r-binomlogit 1.2 The R package contains different MCMC schemes to estimate the regression noarch
coefficients of a binomial (or binary) logit model within a Bayesian frame-
work: a data-augmented independence MH-sampler, an auxiliary mixture
sampler and a hybrid auxiliary mixture (HAM) sampler. All sampling pro-
cedures are based on algorithms using data augmentation, where the regres-
sion coefficients are estimated by rewriting the logit model as a latent variable
model called difference random utility model (dRUM). / GPL-3
r-binomsamsize 0.1_5 A suite of functions to compute confidence intervals and necessary sample linux-
sizes for the parameter p of the Bernoulli B(p) distribution under simple ran- 64,
dom sampling or under pooled sampling. Such computations are e.g. of inter- osx-
est when investigating the incidence or prevalence in populations. The package 64,
contains functions to compute coverage probabilities and coverage coefficients win-
of the provided confidence intervals procedures. Sample size calculations are 64
based on expected length. / GPL-3
r-binostics 0.1.2 Calculates graph theoretic scagnostics. Scagnostics describe various measures linux-
of interest for pairs of variables, based on their appearance on a scatterplot. 64,
They are useful tool for discovering interesting or unusual scatterplots from a osx-
scatterplot matrix, without having to look at every individual plot. / GPL-3 64,
win-
64
r-binr 1.1 Implementation of algorithms for cutting numerical values exhibiting a po- noarch
tentially highly skewed distribution into evenly distributed groups (bins). This
functionality can be applied for binning discrete values, such as counts, as well
as for discretization of continuous values, for example, during generation of
features used in machine learning algorithms. / Apache License (== 2.0)
r-binseqtest 1.0.3 For a series of binary responses, create stopping boundary with exact results noarch
after stopping, allowing updating for missing assessments. / GPL-3
r-binst 0.2.1 Various supervised and unsupervised binning tools including using entropy, noarch
recursive partition methods and clustering. / MIT
r-bio.infer 1.3_3 Imports benthic count data, reformats this data, and computes environmental noarch
inferences from this data. / GPL-2


Name Version
r-bio3d 2.3_4 Utilities to process, organize and explore protein structure, sequence and dy- linux-
namics data. Features include the ability to read and write structure, se- 64,
quence and dynamic trajectory data, perform sequence and structure database osx-
searches, data summaries, atom selection, alignment, superposition, rigid core 64,
identification, clustering, torsion analysis, distance matrix analysis, structure win-
and sequence conservation analysis, normal mode analysis, principal compo- 64
nent analysis of heterogeneous structure data, and correlation network analysis
from normal mode and molecular dynamics data. In addition, various utility
functions are provided to enable the statistical and graphical power of the R
environment to work with biological sequence and structural data. Please refer
to the URLs below for more information. / GPL-2
r-biocircos 0.3.4 Implement in ‘R’ interactive Circos-like visualizations of genomic data, to noarch
map information such as genetic variants, genomic fusions and aberrations to a
circular genome, as proposed by the ‘JavaScript’ library ‘BioCircos.js’, based
on the ‘JQuery’ and ‘D3’ technologies. The output is by default displayed
in stand-alone HTML documents or in the ‘RStudio’ viewer pane. Moreover
it can be integrated in ‘R Markdown’ documents and ‘Shiny’ applications. /
GPL-2
r-biocmanager 1.30.4A convenient tool to install and update Bioconductor packages. / Artistic-2.0 noarch
r-biodem 0.4 The Biodem package provides a number of functions for Biodemographic noarch
analysis. / GPL-2
r-biodry 0.6 Multilevel ecological data series (MEDS) are sequences of observations or- noarch
dered according to temporal/spatial hierarchies that are defined by sample de-
signs, with sample variability confined to ecological factors. Dendroclimatic
MEDS of tree rings and climate are modeled into normalized fluctuations of
tree growth and aridity. Modeled fluctuations (model frames) are compared
with Mantel correlograms on multiple levels defined by sample design. Pack-
age implementation can be understood by running examples in modelFrame(),
and muleMan() functions. / GPL-3
r-bioftf 1.2_0 The main drawback of the most common biodiversity indices is that different noarch
measures may lead to different rankings among communities. This instrument
overcomes this limit using some functional tools with the diversity profiles. In
particular, the derivatives, the curvature, the radius of curvature, the arc length,
and the surface area are proposed. The goal of this method is to interpret in
detail the diversity profiles and obtain an ordering between different ecological
communities on the basis of diversity. In contrast to the typical indices of
diversity, the proposed method is able to capture the multidimensional aspect
of biodiversity, because it takes into account both the evenness and the richness
of the species present in an ecological community. / GPL-2


Name Version
r-biogas 1.10.3High- and low-level functions for processing biogas data and predicting bio- noarch
gas production. Molar mass and calculated oxygen demand (COD’) can be
determined from a chemical formula. Measured gas volume can be corrected
for water vapor and to (possibly user-defined) standard temperature and pres-
sure. Gas quantity can be converted between volume, mass, and moles. Gas
composition, cumulative production, or other variables can be interpolated to
a specified time. Cumulative biogas and methane production (and rates) can
be calculated using volumetric, manometric, or gravimetric methods for any
number of reactors. With cumulative methane production data and data on
reactor contents, biochemical methane potential (BMP) can be calculated and
summarized, including subtraction of the inoculum contribution and normal-
ization by substrate mass. Cumulative production and production rates can
be summarized in several different ways (e.g., omitting normalization) using
the same function. Biogas quantity and composition can be predicted from
substrate composition and additional, optional data. Lastly, inoculum and sub-
strate mass can be determined for planning BMP experiments. / GPL-2
r-biom.utils 0.9 Provides utilities to facilitate import, export and computation with the noarch
BIOM (Biological Observation Matrix) format (http://biom-format.org). /
BSD_2_clause
r-bionetdata 1.0.1 Data Package that includes several examples of chemical and biological data noarch
networks, i.e. data graph structured. / GPL-2
r-biopn 1.2.0 bioPN is a package suited to perform simulation of deterministic and stochastic linux-
systems of biochemical reaction networks. Models are defined using a subset 64,
of Petri Nets, in a way that is close at how chemical reactions are defined. osx-
For deterministic solutions, bioPN creates the associated system of differen- 64,
tial equations on the fly, and solves it with a Runge Kutta Dormand Prince 45 win-
explicit algorithm. For stochastic solutions, bioPN offers variants of Gillespie 64
algorithm, or SSA. For hybrid deterministic/stochastic, it employs the Hasel-
tine and Rawlings algorithm, that partitions the system in fast and slow reac-
tions. bioPN algorithms are developed in C to achieve adequate performance.
/ GPL-2
r-bios2cor 1.2 Utilities for computation and analysis of correlation/co-variation in multi- noarch
ple sequence alignments and in side chain motions during molecular dynam-
ics simulations. Features include the computation of correlation/co-variation
scores using a variety of scoring functions between either sequence positions
in alignments or side chain dihedral angles in molecular dynamics simulations
and to analyze the correlation/co-variation matrix through a variety of tools
including network representation and principal components analysis. In ad-
dition, several utility functions are based on the R graphical environment to
provide friendly tools for help in data interpretation. Examples of sequence
co-variation analysis and utility tools are provided in: Pele J, Moreau M, Abdi
H, Rodien P, Castel H, Chabbert M. (2014) <doi:10.1002/prot.24570>. This
work was supported by the French National Research Agency (Grant number:
ANR-11-BSV2-026). / GPL-2
r-biotic 0.1.2 Calculates a range of UK freshwater invertebrate biotic indices including noarch
BMWP, Whalley, WHPT, Habitat-specific BMWP, AWIC, LIFE and PSI. /
GPL-3
r-birk 2.1.2 Collection of tools to make R more convenient. Includes tools to summarize noarch
data using statistics not available with base R and manipulate objects for anal-
yses. / GPL-3


Name Version
r-birtr 1.0.0 R functions for The Basics of Item Response Theory Using R by Frank B. noarch
Baker and Seock-Ho Kim (Springer, 2017, ISBN-13: 978-3-319-54204-1) in-
cluding iccplot(), icccal(), icc(), iccfit(), groupinv(), tcc(), ability(), tif(), and
rasch(). For example, iccplot() plots an item characteristic curve under the
two-parameter logistic model. / GPL-2
r-bisect 0.9.0 An implementation of Bisect, a method for inferring cell type composition noarch
of samples based on methylation sequencing data (Whole Genome Bisulfite
Sequencing and Reduced Representation Sequencing). The method is specif-
ically tailored for sequencing data, and therefore works better than methods
developed for methylation arrays. It contains a supervised mode that requires
a reference (the methylation probabilities in the pure cell types), and a semi-
supervised mode, that requires cell counts for a subset of the samples, but does
not require a reference. / GPL-3
r-bisectr 0.1.0 Tools to find bad commits with git bisect. See https://github.com/wch/bisectr noarch
for examples and test script templates. / GPL-2
r-bisrna 0.2.2 Bisulfite-treated RNA non-conversion in a set of samples is analysed as fol- noarch
lows : each sample’s non-conversion distribution is identified to a Poisson
distribution. P-values adjusted for multiple testing are calculated in each sam-
ple. Combined non-conversion P-values and standard errors are calculated
on the intersection of the set of samples. For further details, see C Legrand,
F Tuorto, M Hartmann, R Liebers, D Jakob, M Helm and F Lyko (2017)
<doi:10.1101/gr.210666.116>. / GPL-2
r-bit 1.1_14bitmapped vectors of booleans (no NAs), coercion from and to logicals, inte- linux-
gers and integer subscripts; fast boolean operators and fast summary statistics. 32,
With ‘bit’ vectors you can store true binary booleans {FALSE,TRUE} at the linux-
expense of 1 bit only, on a 32 bit architecture this means factor 32 less RAM 64,
and ~ factor 32 more speed on boolean operations. Due to overhead of R calls, osx-
actual speed gain depends on the size of the vector: expect gains for vectors 64,
of size > 10000 elements. Even for one-time boolean operations it can pay-off win-
to convert to bit, the pay-off is obvious, when such components are used more 32,
than once. Reading from and writing to bit is approximately as fast as ac- win-
cessing standard logicals - mostly due to R’s time for memory allocation. The 64
package allows to work with pre-allocated memory for return values by call-
ing .Call() directly: when evaluating the speed of C-access with pre-allocated
vector memory, coping from bit to logical requires only 70% of the time for
copying from logical to logical; and copying from logical to bit comes at a
performance penalty of 150%. the package now contains further classes for
representing logical selections: ‘bitwhich’ for very skewed selections and ‘ri’
for selecting ranges of values for chunked processing. All three index classes
can be used for subsetting ‘ff’ objects (ff-2.1-0 and higher). / GPL-2
r-bit64 0.9_7 Package ‘bit64’ provides serializable S3 atomic 64bit (signed) integers. These linux-
are useful for handling database keys and exact counting in -2^63. WARN- 32,
ING: do not use them as replacement for 32bit integers, integer64 are not linux-
supported for subscripting by R-core and they have different semantics when 64,
combined with double, e.g. integer64 double => integer64. Class integer64 osx-
can be used in vectors, matrices, arrays and data.frames. Methods are avail- 64,
able for coercion from and to logicals, integers, doubles, characters and factors win-
as well as many elementwise and summary functions. Many fast algorithmic 32,
operations such as ‘match’ and ‘order’ support interactive data exploration win-
and manipulation and optionally leverage caching. / GPL-2 64


Name Version
r-bitops 1.0_6 Functions for bitwise operations on integer vectors. / GPL (>= 2) linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-bitrina 1.3 Provides methods for the binarization and trinarization of one-dimensional linux-
data and some visualization functions. / Artistic-2.0 64,
osx-
64,
win-
64
r-bitrugs 0.1 MCMC methods to estimate transmission dynamics and infection routes in linux-
hospitals using genomic sampling data. / GPL-3 64,
osx-
64,
win-
64
r-bitsqueezr 0.1.0 Provides a implementation of floating-point quantization algorithms for use linux-
in precision-preserving compression, similar to the approach taken in the 64,
‘netCDF operators’ (NCO) software package and described in Zender (2016) osx-
<doi:10.5194/gmd-2016-63>. / GPL-3 64,
win-
64
r-bivariate.pareto 1.0.2 Perform competing risks analysis under bivariate Pareto models. See Shih et noarch
al. (2018) <doi:10.1080/03610926.2018.1425450> for details. / GPL-2
r-bivarp 1.0 Parameter estimation of bivariate distribution functions modeled as a noarch
Archimedean copula function. The input data may contain values from right
censored. Used marginal distributions are two-parameter. Methods for density,
distribution, survival, random sample generation. / GPL-3
r-bivarripower 1.2 Implements sample size calculations for bivariate random intercept regression noarch
model that are described in Comulada and Weiss (2010) / GPL-2
r-bivgeo 2.0.1 Computes the joint probability mass function (pmf), the joint cumulative func- noarch
tion (cdf), the joint survival function (sf), the correlation coefficient, the covari-
ance, the cross-factorial moment and generate random deviates for the Basu-
Dhar bivariate geometric distribution as well the joint probability mass, cumu-
lative and survival function assuming the presence of a cure fraction given by
the standard bivariate mixture cure fraction model. The package also computes
the estimators based on the method of moments. / GPL-2
r-bivgeom 1.0 Implements Roy’s bivariate geometric model (Roy (1993) noarch
<doi:10.1006/jmva.1993.1065>): joint probability mass function, distri-
bution function, survival function, random generation, parameter estimation,
and more. / GPL-3


Name Version
r-bivrec 1.0.0 Alternating recurrent event data arise frequently in biomedical and social sci- linux-
ences where 2 types of events such as hospital admissions and discharge occur 64,
alternatively over time. As such we implement a collection of non-parametric osx-
and semiparametric methods to analyze such data. The main functions are 64,
biv.rec.fit() and biv.rec.np(). Use biv.rec.fit() for estimation of covariate ef- win-
fects on the two alternating event gap times (xij and yij) using semiparametric 64
methods. The method options are Lee.et.al and Chang. Use biv.rec.np() for
estimation of the joint cumulative distribution function (cdf) for the two alter-
nating events gap times (xij and yij) as well as the marginal survival function
for type I gap times (xij) and the conditional cdf of the type II gap times (yij)
given an interval of type I gap times (xij) in a non-parametric fashion. The
package also provides options to simulate and visualize the data and results of
analysis. / GPL-3
r-bizdays 1.0.6 Business days calculations based on a list of holidays and nonworking week- noarch
days. Quite useful for fixed income and derivatives pricing. / MIT
r-bkpc 1.0.1 Bayesian kernel projection classifier is a nonlinear multicategory classifier linux-
which performs the classification of the projections of the data to the prin- 64,
cipal axes of the feature space. A Gibbs sampler is implemented to find the osx-
posterior distributions of the parameters. / GPL-2 64,
win-
64
r-blakerci 1.0_6 Fast and accurate calculation of Blaker’s binomial and Poisson confidence lim- noarch
its (and some related stuff). / GPL-3
r-blandaltmanleh 0.3.1 Bland-Altman Plots using either base graphics or ggplot2, augmented with noarch
confidence intervals, with detailed return values and a sunflowerplot option
for data with ties. / GPL-3
r-blatr 1.0.1 A wrapper around the ‘Blat’ command line SMTP mailer for Windows. ‘Blat’ win-
is public domain software, but be sure to read the license before use. It can be 64
found at the Blat website http://www.blat.net. / MIT
r-blendedlink 1.0 A new link function that equals one specified link function up to a cutover then noarch
a linear rescaling of another specified link function. For use in glm() or glm2().
The intended use is in binary regression, in which case the first link should
be set to log and the second to logit. This ensures that fitted probabilities
are between 0 and 1 and that exponentiated coefficients can be interpreted as
relative risks for probabilities up to the cutoff. / GPL-2 | GPL-3
r-blendstat 1.0.2 Performs a joint analysis of experiments with mixtures and random effects, noarch
taking on a process variable represented by a covariable. / GPL-2
r-blin 0.0.1 Estimate influence networks from longitudinal bipartite relational data, where noarch
the longitudinal relations are continuous. The outputs are estimates of
weighted influence networks among each actor type in the data set. The gen-
erative model is the Bipartite Longitudinal Influence Network (BLIN) model,
a linear autoregressive model for these type of data. The supporting paper is
‘‘Inferring Influence Networks from Longitudinal Bipartite Relational Data”,
which is in preparation by the same authors. The model may be estimated us-
ing maximum likelihood methods and Bayesian methods. For more detail on
methods, see Marrs et. al. <arXiv:1809.03439>. / MIT
r-blm 2013.2.4.4
Implements regression models for binary data on the absolute risk scale. These noarch
models are applicable to cohort and population-based case-control data. /
GPL-2


Name Version
r-blme 1.0_4 Maximum a posteriori estimation for linear and generalized linear mixed- noarch
effects models in a Bayesian setting. Extends ‘lme4’ by Douglas Bates, Martin
Maechler, Ben Bolker, and Steve Walker. / GPL-2
r-blmodel 1.0.2 Posterior distribution in the Black-Litterman model is computed from a prior noarch
distribution given in the form of a time series of asset returns and a continuous
distribution of views provided by the user as an external function. / GNU
General Public License version 3
r-blob 1.1.1 R’s raw vector is useful for storing a single binary object. What if you want linux-
to put a vector of them in a data frame? The ‘blob’ package provides the blob 32,
object, a list of raw vectors, suitable for use as a column in data frame. / GPL-3 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-blockfest 1.6 An R implementation of an extension of the ‘BayeScan’ software (Foll, 2008) linux-
<DOI:10.1534/genetics.108.092221> for codominant markers, adding the op- 64,
tion to group individual SNPs into pre-defined blocks. A typical application osx-
of this new approach is the identification of genomic regions, genes, or gene 64,
sets containing one or more SNPs that evolved under directional selection. / win-
GPL-2 64
r-blockforest 0.2.3 A random forest variant ‘block forest’ (‘BlockForest’) tailored to the predic- linux-
tion of binary, survival and continuous outcomes using block-structured co- 64,
variate data, for example, clinical covariates plus measurements of a certain osx-
omics data type or multi-omics data, that is, data for which measurements of 64,
different types of omics data and/or clinical data for each patient exist. Ex- win-
amples of different omics data types include gene expression measurements, 64
mutation data and copy number variation measurements. Block forest are pre-
sented in Hornung & Wright (2019). The package includes four other ran-
dom forest variants for multi-omics data: ‘RandomBlock’, ‘BlockVarSel’,
‘VarProb’, and ‘SplitWeights’. These were also considered in Hornung &
Wright (2019), but performed worse than block forest in their comparison
study based on 20 real multi-omics data sets. Therefore, we recommend to use
block forest (‘BlockForest’) in applications. The other random forest variants
can, however, be consulted for academic purposes, for example, in the context
of further methodological developments. Reference: Hornung, R. & Wright,
M. N. (2019) Block Forests: random forests for blocks of clinical and omics
covariate data. BMC Bioinformatics 20:358. <doi:10.1186/s12859-019-2942-
y>. / GPL-3
r-blockmatrix 1.0 Some elementary matrix algebra tools are implemented to manage block ma- noarch
trices or partitioned matrix, i.e. matrix of matrices (http://en.wikipedia.org/
wiki/Block_matrix). The block matrix is here defined as a new S3 object. In
this package, some methods for matrix object are rewritten for blockmatrix
object. New methods are implemented. This package was created to solve
equation systems with block matrices for the analysis of environmental vector
time series . Bugs/comments/questions/collaboration of any kind are warmly
welcomed. / GPL-2
r-blockmessage 1.0 Creates strings that show a text message in 8 by 8 block letters / GPL-2 noarch


Name Version
r-blockmodeling 0.3.4 This is primarily meant as an implementation of generalized block- linux-
modeling for valued networks. In addition, measures of similarity 64,
or dissimilarity based on structural equivalence and regular equiva- osx-
lence (REGE algorithms) can be computed and partitioned matrices 64,
can be plotted: Žiberna (2007)<doi:10.1016/j.socnet.2006.04.002>, win-
Žiberna (2008)<doi:10.1080/00222500701790207>, Žiberna 64
(2014)<doi:10.1016/j.socnet.2014.04.002>. / GPL-2
r-blockmodels 1.1.1 Latent and Stochastic Block Model estimation by a Variational EM algorithm. linux-
Various probability distribution are provided (Bernoulli, Poisson. . . ), with or 64,
without covariates. / LGPL-2.1 osx-
64,
win-
64
r-blockrand 1.3 Create randomizations for block random clinical trials. Can also produce a pdf noarch
file of randomization cards. / GPL-2
r-blocksdesign 3.5 Constructs D-optimal or near D-optimal nested and crossed block designs for noarch
unstructured or general factorial treatment designs. The treatment design, if
required, is found from a model matrix design formula and can be added se-
quentially, if required. The block design is found from a defined set of block
factors and is conditional on the defined treatment design. The block factors
are added in sequence and each added block factor is optimized conditional
on all previously added block factors. The block design can have repeated
nesting down to any required depth of nesting with either simple nested blocks
or a crossed blocks design at each level of nesting. Outputs include a table
showing the allocation of treatments to blocks and tables showing the achieved
D-efficiency factors for each block and treatment design. / GPL-2
r-blr 1.5 Bayesian Linear Regression. / GPL-2 linux-
64,
osx-
64,
win-
64
r-blrpm 1.0 Due to a limited availability of observed high-resolution precipitation records noarch
with adequate length, simulations with stochastic precipitation models are
used to generate series for subsequent studies [e.g. Khaliq and Cun-
mae, 1996, <doi:10.1016/0022-1694(95)02894-3>, Vandenberghe et al., 2011,
<doi:10.1029/2009WR008388>]. This package contains an R implementation
of the original Bartlett-Lewis rectangular pulse model (BLRPM), developed
by Rodriguez-Iturbe et al. (1987) <doi:10.1098/rspa.1987.0039>. It contains
a function for simulating a precipitation time series based on storms and cells
generated by the model with given or estimated model parameters. Addition-
ally BLRPM parameters can be estimated from a given or simulated precipi-
tation time series. The model simulations can be plotted in a three-layer plot
including an overview of generated storms and cells by the model (which can
also be plotted individually), a continuous step-function and a discrete precip-
itation time series at a chosen aggregation level. / GPL-2
r-blsapi 0.2.1 Allows users to request data for one or multiple series through the U.S. noarch
Bureau of Labor Statistics API. Users provide parameters as specified in
<https://www.bls.gov/developers/api_signature.htm> and the function returns
a JSON string. / GPL-2


Name Version
r-blsm 0.1.0 Provides a Bayesian latent space model for complex networks, either weighted linux-
or unweighted. Given an observed input graph, the estimates for the latent co- 64,
ordinates of the nodes are obtained through a Bayesian MCMC algorithm. The osx-
overall likelihood of the graph depends on a fundamental probability equation, 64,
which is defined so that ties are more likely to exist between nodes whose win-
latent space coordinates are close. The package is mainly based on the model 64
by Hoff, Raftery and Handcock (2002) <doi:10.1198/016214502388618906>
and contains some extra features (e.g., removal of the Procrustean
step, weights implemented as coefficients of the latent distances, 3D
plots). The original code related to the above model was retrieved from
<https://www.stat.washington.edu/people/pdhoff/Code/hoff_raftery_handcock_2002_jasa/>.
Users can inspect the MCMC simulation, create and customize insightful
graphical representations or apply clustering techniques. / GPL-2
r-bmamevt 1.0.3 Toolkit for Bayesian estimation of the dependence structure in multivariate linux-
extreme value parametric models. / GPL-2 64,
osx-
64,
win-
64
r-bmass 1.0.3 Multivariate tool for analyzing genome-wide association study results in the noarch
form of univariate summary statistics. The goal of ‘bmass’ is to com-
prehensively test all possible multivariate models given the phenotypes and
datasets provided. Multivariate models are determined by assigning each
phenotype to being either Unassociated (U), Directly associated (D) or In-
directly associated (I) with the genetic variant of interest. Test results for
each model are presented in the form of Bayes factors, thereby allowing di-
rect comparisons between models. The underlying framework implemented
here is based on the modeling developed in A Unified Framework for As-
sociation Analysis with Multiple Related Phenotypes, M. Stephens (2013)
<doi:10.1371/journal.pone.0065245>. / GPL-3
r-bmix 0.6 This is a bare-bones implementation of sampling algorithms for a variety of linux-
Bayesian stick-breaking (marginally DP) mixture models, including particle 64,
learning and Gibbs sampling for static DP mixtures, particle learning for dy- osx-
namic BAR stick-breaking, and DP mixture regression. The software is de- 64,
signed to be easy to customize to suit different situations and for experimen- win-
tation with stick-breaking models. Since particles are repeatedly copied, it is 64
not an especially efficient implementation. / GPL-2
r-bmixture 1.3 Provides statistical tools for Bayesian estimation for finite mixture of distri- linux-
butions, mainly mixture of Gamma, Normal and t-distributions. The pack- 64,
age is implemented the recent improvements in Bayesian literature for the osx-
finite mixture of distributions, including Mohammadi and et al. (2013) 64,
<doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) win-
<doi:10.1080/03610918.2011.588358>. / GPL-2 64
r-bmk 1.0 MCMC diagnostic package that contains tools to diagnose convergence as well noarch
as to evaluate sensitivity studies, Includes summary functions which output
mean, median, 95percentCI, Gelman & Rubin diagnostics and the Hellinger
distance based diagnostics, Also contains functions to determine when an
MCMC chain has converged via Hellinger distance, A function is also pro-
vided to compare outputs from identically dimensioned chains for determining
sensitivy to prior distribution assumptions / GPL-2


Name Version
r-bmp 0.3 Reads Windows BMP format images. Currently limited to 8 bit greyscale im- noarch
ages and 24,32 bit (A)RGB images. Pure R implementation without external
dependencies. / GPL-2
r-bmrbr 0.2.0 Nuclear magnetic resonance (NMR) is a highly versatile analytical technique noarch
for studying molecular configuration, conformation, and dynamics, especially
those of biomacromolecules such as proteins. Biological Magnetic Resonance
Data Bank (‘BMRB’) is a repository for Data from NMR Spectroscopy on Pro-
teins, Peptides, Nucleic Acids, and other Biomolecules. Currently, ‘BMRB’
offers an R package ‘RBMRB’ to fetch data, however, it doesn’t easily offer
individual data file downloading and storing in a local directory. When using
‘RBMRB’, the data will stored as an R object, which fundamentally hinders
the NMR researches to access the rich information from raw data, for example,
the metadata. Here, ‘BMRBr’ File Downloader (‘BMRBr’) offers a more fun-
damental, low level downloader, which will download original deposited .str
format file. This type of file contains information such as entry title, authors,
citation, protein sequences, and so on. Many factors affect NMR experiment
outputs, such as temperature, resonance sensitivity and etc., approximately
40% of the entries in the ‘BMRB’ have chemical shift accuracy problems [1,2]
Unfortunately, current reference correction methods are heavily dependent on
the availability of assigned protein chemical shifts or protein structure. This
is my current research project is going to solve, which will be included in
the future release of the package. The current version of the package is suffi-
cient and robust enough for downloading individual ‘BMRB’ data file from the
‘BMRB’ database <http://www.bmrb.wisc.edu>. The functionalities of this
package includes but not limited: * To simplifies NMR researches by com-
bine data downloading and results analysis together. * To allows NMR data
reaches a broader audience that could utilize more than just chemical shifts
but also metadata. * To offer reference corrected data for entries without as-
signment or structure information (future release). Reference: [1] E.L. Ulrich,
H. Akutsu, J.F. Doreleijers, Y. Harano, Y.E. Ioannidis, J. Lin, et al., BioMa-
gResBank, Nucl. Acids Res. 36 (2008) D402–8. <doi:10.1093/nar/gkm957>.
[2] L. Wang, H.R. Eghbalnia, A. Bahrami, J.L. Markley, Linear analysis of
carbon-13 chemical shift differences and its application to the detection and
correction of errors in referencing and spin system identifications, J. Biomol.
NMR. 32 (2005) 13–22. <doi:10.1007/s10858-005-1717-0>. / GPL-3
r-bmrv 1.32 Provides two Bayesian models for detecting the association between rare ge- linux-
netic variants and a trait that can be continuous, ordinal or binary. Bayesian 64,
latent variable collapsing model (BLVCM) detects interaction effect and is osx-
dedicated to twin design while it can also be applied to independent samples. 64,
Hierarchical Bayesian multiple regression model (HBMR) incorporates geno- win-
type uncertainty information and can be applied to either independent or fam- 64
ily samples. Furthermore, it deals with continuous, binary and ordinal traits. /
GPL-2
r-bms 0.3.4 Bayesian model averaging for linear models with a wide choice of (customiz- noarch
able) priors. Built-in priors include coefficient priors (fixed, flexible and hyper-
g priors), 5 kinds of model priors, moreover model sampling by enumeration or
various MCMC approaches. Post-processing functions allow for inferring pos-
terior inclusion and model probabilities, various moments, coefficient and pre-
dictive densities. Plotting functions available for posterior model size, MCMC
convergence, predictive and coefficient densities, best models representation,
BMA comparison. / Artistic-2.0


Name Version
r-bnclassify 0.4.2 State-of-the art algorithms for learning discrete Bayesian network classifiers linux-
from data, including a number of those described in Bielza & Larranaga (2014) 64,
<doi:10.1145/2576868>, with functions for prediction, model evaluation and osx-
inspection. / GPL-2 64,
win-
64
r- 1.0 Data generator based on Bayesian network model / GPL-2 noarch
bndatagenerator
r-bnlearn 4.5 Bayesian network structure learning, parameter learning and inference. This linux-
package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast- 64,
IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score- osx-
based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, 64,
H2PC) structure learning algorithms for discrete, Gaussian and conditional win-
Gaussian networks, along with many score functions and conditional indepen- 64
dence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN)
classifiers are also implemented. Some utility functions (model comparison
and manipulation, random data generation, arc orientation testing, simple and
advanced plots) are included, as well as support for parameter estimation
(maximum likelihood and Bayesian) and inference, conditional probability
queries, cross-validation, bootstrap and model averaging. Development snap-
shots with the latest bugfixes are available from <http://www.bnlearn.com>. /
GPL-2
r-bnn 1.0.2 Perform Bayesian variable selection for high-dimensional nonlinear systems linux-
and also can be used to test nonlinearity for a general regression problem. 64,
The computation can be accelerated using multiple CPUs. You can refer to osx-
<doi:10.1080/01621459.2017.1409122> for more detail. / GPL-2 64,
win-
64
r-bnormnlr 1.0 Implementation of Bayesian estimation in normal heteroscedastic nonlinear noarch
regression Models following Cepeda-Cuervo, (2001). / GPL-2
r-bnpmr 1.2 Implements the Bayesian nonparametric monotonic regression method de- linux-
scribed in Bornkamp & Ickstadt (2009), Biometrics, 65, 198-205. / GPL-3 64,
osx-
64,
win-
64
r-bnpsd 1.1.1 The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate noarch
subpopulations from which n individuals draw their alleles dictated by their
individual-specific admixture proportions. The BN-PSD model additionally
imposes the Balding-Nichols (BN) allele frequency model to the intermediate
populations, which therefore evolved independently from a common ancestral
population T with subpopulation-specific FST (Wright’s fixation index) pa-
rameters. The BN-PSD model can be used to yield complex population struc-
tures. Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
/ GPL-3
r-bnptsclust 2.0 Performs the algorithm for time series clustering described in Nieto-Barajas noarch
and Contreras-Cristan (2014). / GPL-2


Name Version
r-bnsl 0.1.4 From a given data frame, this package learns its Bayesian network structure linux-
based on a selected score. / GPL-2 64,
osx-
64,
win-
64
r-bnstruct 1.0.6 Bayesian Network Structure Learning from Data with Missing Values. The linux-
package implements the Silander-Myllymaki complete search, the Max-Min 64,
Parents-and-Children, the Hill-Climbing, the Max-Min Hill-climbing heuristic osx-
searches, and the Structural Expectation-Maximization algorithm. Available 64,
scoring functions are BDeu, AIC, BIC. The package also implements methods win-
for generating and using bootstrap samples, imputed data, inference. / GPL-2 64
r-bnviewer 0.1.4 Bayesian networks provide an intuitive framework for probabilistic reasoning noarch
and its graphical nature can be interpreted quite clearly. Graph based methods
of machine learning are becoming more popular because they offer a richer
model of knowledge that can be understood by a human in a graphical format.
The ‘bnviewer’ is an R Package that allows the interactive visualization of
Bayesian Networks. The aim of this package is to improve the Bayesian Net-
works visualization over the basic and static views offered by existing pack-
ages. / MIT
r-boa 1.1.8_2
A menu-driven program and library of functions for carrying out convergence noarch
diagnostics and statistical and graphical analysis of Markov chain Monte Carlo
sampling output. / GPL-2
r-boardgames 1.0.0 Tools for constructing board/grid based games, as well as readily available noarch
game(s) for your entertainment. / GPL-2
r-bodenmiller 0.1 This data package contains a subset of the Bodenmiller et al, Nat Biotech noarch
2012 dataset for testing single cell, high dimensional analysis and visualization
methods. / CC0
r-boilerpiper 1.3 Generic Extraction of main text content from HTML files; removal of noarch
ads, sidebars and headers using the boilerpipe (http://code.google.com/p/
boilerpipe/) Java library. The extraction heuristics from boilerpipe show a ro-
bust performance for a wide range of web site templates. / Apache License
(== 2.0)
r-bolstad 0.2_40A set of R functions and data sets for the book Introduction to Bayesian Statis- noarch
tics, Bolstad, W.M. (2017), John Wiley & Sons ISBN 978-1-118-09156-2. /
GPL-2
r-bolstad2 1.0_28A set of R functions and data sets for the book Understanding Computational noarch
Bayesian Statistics, Bolstad, W.M. (2009), John Wiley & Sons ISBN 978-
0470046098 / GPL-2
r-boltzmm 0.1.4 Provides probability computation, data generation, and model estimation for linux-
fully-visible Boltzmann machines. It follows the methods described in Nguyen 64,
and Wood (2016a) <doi:10.1162/NECO_a_00813> and Nguyen and Wood osx-
(2016b) <doi:10.1109/TNNLS.2015.2425898>. / GPL-3 64,
win-
64
r-bondvaluation 0.1.0 Analysis of large datasets of fixed coupon bonds, allowing for irregular first linux-
and last coupon periods and various day count conventions. With this package 64,
you can compute the yield to maturity, the modified and MacAulay durations osx-
and the convexity of fixed-rate bonds. It provides the function AnnivDates, 64,
which can be used to evaluate the quality of the data and return time-invariant win-
properties and temporal structure of a bond. / GPL-3 64


Name Version
r-bookdown 0.13 Output formats and utilities for authoring books and technical documents with noarch
R Markdown. / GPL-3
r-boolnet 2.1.5 Provides methods to reconstruct and generate synchronous, asynchronous, linux-
probabilistic and temporal Boolean networks, and to analyze and visualize 64,
attractors in Boolean networks. / Artistic-2.0 osx-
64,
win-
64
r-boom 0.9.1 A C library for Bayesian modeling, with an emphasis on Markov chain Monte linux-
Carlo. Although boom contains a few R utilities (mainly plotting functions), 64,
its primary purpose is to install the BOOM C library on your system so that osx-
other packages can link against it. / LGPL-2.1 64,
win-
64
r-boomspikeslab 1.1.1 Spike and slab regression a la McCulloch and George (1997). / LGPL-2.1 linux-
64,
osx-
64,
win-
64
r-boostr 1.0.0 boostr provides a modular framework that return the focus of ensemble learn- noarch
ing back to ‘learning’ (instead of programming). / GPL-2
r-boot 1.3_20Functions and datasets for bootstrapping from the book Bootstrap Methods and linux-
Their Application by A. C. Davison and D. V. Hinkley (1997, CUP), originally 32,
written by Angelo Canty for S. / Unlimited linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-bootes 1.2 Calculate robust measures of effect sizes using the bootstrap. / GPL-2 noarch
r-bootlr 1.0.2 Computes appropriate confidence intervals for the likelihood ratio tests com- noarch
monly used in medicine/epidemiology, using the method of Marill et al. (2015)
<doi:10.1177/0962280215592907>. It is particularly useful when the sensitiv-
ity or specificity in the sample is 100%. Note that this does not perform the
test on nested models–for that, see ‘epicalc::lrtest’. / LGPL-2.1
r-bootmrmr 0.1 Selection of informative features like genes, transcripts, RNA seq, etc. using noarch
Bootstrap Maximum Relevance and Minimum Redundancy technique from a
given high dimensional genomic dataset. Informative gene selection involves
identification of relevant genes and removal of redundant genes as much as
possible from a large gene space. Main applications in high-dimensional ex-
pression data analysis (e.g. microarray data, NGS expression data and other
genomics and proteomics applications). / GPL-2
r-bootpr 0.60 Bias-Corrected Forecasting and Bootstrap Prediction Intervals for Autoregres- noarch
sive Time Series / GPL-2


Name Version
r-bootres 1.2.4 Bootstrapped correlation and response functions are widely used in den- noarch
drochronology to calibrate tree-ring proxy data against multiple instru-
mental time series of climatic variables. With this package, we provide
functionality similar to DENDROCLIM2002 (Biondi and Waikul (2004)
<10.1016/j.cageo.2003.11.004>). A full description with examples is given
in Zang and Biondi (2013) <10.1016/j.dendro.2012.08.001>. / GPL-3
r-bootruin 1.2_4 We provide a framework for testing the probability of ruin in the classical linux-
(compound Poisson) risk process. It also includes some procedures for as- 64,
sessing and comparing the performance between the bootstrap test and the test osx-
using asymptotic normality. / AGPL-3 64,
win-
64
r-bootspecdens 3.0 Bootstrap for testing the hypothesis that the spectral densities of a number m, noarch
m>=2, not necessarily independent time series are equal / GPL-2
r-bootstepaic 1.2_0 Model selection by bootstrapping the stepAIC() procedure. / GPL-2 noarch
r-bootstrap 2019.6Software (bootstrap, cross-validation, jackknife) and data for the book An In- linux-
troduction to the Bootstrap by B. Efron and R. Tibshirani, 1993, Chapman and 64,
Hall. This package is primarily provided for projects already based on it, and osx-
for support of the book. New projects should preferentially use the recom- 64,
mended package boot. / BSD_3_clause win-
64
r-boottol 2.0 Used to create bootstrap tolerance levels for the Kolmogorov-Smirnov (KS) noarch
statistic, the area under receiver operator characteristic curve (AUROC) statis-
tic, and the Gini coefficient for each score cutoff. Also provides a bootstrap
alternative to the Vasicek test. / GPL-2
r-bor 0.1.0 Transforms focal observations’ data, where different types of social interac- noarch
tions can be recorded by multiple observers, into asymmetric data matrices.
Each cell in these matrices provides counts on the number of times a specific
type of social interaction was initiated by the row subject and directed to the
column subject. / GPL-3
r-borrowr 0.1.0 Estimate population average treatment effects from a primary data source with linux-
borrowing from supplemental sources. Causal estimation is done with either 64,
a Bayesian linear model or with Bayesian additive regression trees (BART) to osx-
adjust for confounding. Borrowing is done with multisource exchangeability 64,
models (MEMs). For information on BART, see Chipman, George, & Mc- win-
Culloch (2010) <doi:10.1214/09-AOAS285>. For information on MEMs, see 64
Kaizer, Koopmeiners, & Hobbs (2018) <doi10.1093/biostatistics/kxx031>. /
GPL-3
r-boruta 6.0.0 An all relevant feature selection wrapper algorithm. It finds relevant featureslinux-
by comparing original attributes’ importance with importance achievable at 32,
random, estimated using their permuted copies (shadows). / GPL (>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-bosonsampling 0.1.1 Classical Boson Sampling using the algorithm of Clifford and Clifford (2017) linux-
<arXiv:1706.01260>. Also provides functions for generating random unitary 64,
matrices, evaluation of matrix permanents (both real and complex) and evalu- osx-
ation of complex permanent minors. / GPL-2 64,
win-
64
r-boussinesq 1.0.3 This package is a collection of R functions implemented from published noarch
and available analytic solutions for the One-Dimensional Boussinesq Equa-
tion (ground-water). In particular, the function beq.lin is the analytic so-
lution of the linearized form of Boussinesq Equation between two differ-
ent head-based boundary (Dirichlet) conditions; beq.song is the non-linear
power-series analytic solution of the motion of a wetting front over a dry
bedrock (Song at al, 2007, see complete reference on function documentation).
Bugs/comments/questions/collaboration of any kind are warmly welcomed. /
GPL-2
r-boxoffice 1.2.2 Download daily box office information (how much each movie earned in the- noarch
aters) using data from either Box Office Mojo (<http://www.boxofficemojo.
com/>) or The Numbers (<http://www.the-numbers.com/>). / GPL-3
r-boxplotdbl 1.3.0 Correlation chart of two set (x and y) of data. Using Quartiles with boxplot noarch
style. Visualize the effect of factor. / MIT (FOSS)
r-bpa 0.1.1 Run basic pattern analyses on character sets, digits, or combined input con- noarch
taining both characters and numeric digits. Useful for data cleaning and for
identifying columns containing multiple or nonstandard formats. / GPL-2
r-bpbounds 0.1.3 Implementation of the nonparametric bounds for the average causal effect un- noarch
der an instrumental variable model by Balke and Pearl (Bounds on Treatment
Effects from Studies with Imperfect Compliance, JASA, 1997, 92, 439, 1171-
1176). The package can calculate bounds for a binary outcome, a binary treat-
ment/phenotype, and an instrument with either 2 or 3 categories. The package
implements bounds for situations where these 3 variables are measured in the
same dataset (trivariate data) or where the outcome and instrument are mea-
sured in one study and the treatment/phenotype and instrument are measured
in another study (bivariate data). / GPL-3
r-bpcp 1.3.4 Calculates nonparametric pointwise confidence intervals for the survival dis- noarch
tribution for right censored data. Has two-sample tests for dissimilarity (e.g.,
difference, ratio or odds ratio) in survival at a fixed time. Especially important
for small sample sizes or heavily censored data. Includes mid-p options. /
GPL-2
r-bpeaks 1.2 bPeaks is a simple approach to identify transcription factor binding sites from noarch
ChIP-seq data. Our general philosophy is to provide an easy-to-use tool, well-
adapted for small eukaryotic genomes (< 20 Mb). bPeaks uses a combination
of 4 cutoffs (T1, T2, T3 and T4) to mimic good peak properties as described by
biologists who visually inspect the ChIP-seq data on a genome browser. For
yeast genomes, bPeaks calculates the proportion of peaks that fall in promoter
sequences. These peaks are good candidates as transcription factor binding
sites. / GPL-3
r-bpkde 1.0_7 Nonparametric multivariate kernel density estimation using a back-projected linux-
kernel. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-bpp 1.0.0 Implements functions to update Bayesian Predictive Power Computations after noarch
not stopping a clinical trial at an interim analysis. Such an interim analysis
can either be blinded or unblinded. Code is provided for Normally distributed
endpoints with known variance, with a prominent example being the hazard
ratio. / GPL-2
r-bqtl 1.0_32QTL mapping toolkit for inbred crosses and recombinant inbred lines. In- linux-
cludes maximum likelihood and Bayesian tools. / GPL-2 64,
osx-
64,
win-
64
r-bracer 1.0.1 Performs brace expansions on strings. Made popular by Unix shells, brace noarch
expansion allows users to quickly generate certain character vectors by tak-
ing a single string and (recursively) expanding the comma-separated lists
and double-period-separated integer and character sequences enclosed within
braces in that string. The double-period-separated numeric integer expansion
also supports padding the resulting numbers with zeros. / MIT
r-bradleyterry2 1.0_9 Specify and fit the Bradley-Terry model, including structured versions in linux-
which the parameters are related to explanatory variables through a linear pre- 32,
dictor and versions with contest-specific effects, such as a home advantage. / linux-
GPL (>= 2) 64,
noarch,
osx-
64,
win-
32,
win-
64
r-braidrm 0.71 Contains functions for evaluating, analyzing, and fitting combined action dose noarch
response surfaces with the Bivariate Response to Additive Interacting Dose
(BRAID) model of combined action. / GPL-3
r-branching 0.9.4 Simulation and parameter estimation of multitype Bienayme - Galton - Watson linux-
processes. / GPL-2 64,
osx-
64,
win-
64
r-brandwatchr 0.3.0 Interact with the ‘Brandwatch’ API <https://developers.brandwatch.com/ noarch
docs>. Allows you to authenticate to the API and obtain data for projects,
queries, query groups tags and categories. Also allows you to directly obtain
mentions and aggregate data for a specified query or query group. / MIT
r-brant 0.2_0 Tests the parallel regression assumption for ordinal logit models generated noarch
with the function polr() from the package ‘MASS’. / GPL-2
r-brea 0.2.0 A function to produce MCMC samples for posterior inference in semiparamet- noarch
ric Bayesian discrete time competing risks recurrent events models. / GPL-3


Name Version
r-breakaway 3.0 Species richness estimation is an important problem in biodiversity analysis. noarch
This package provides methods for total species richness estimation (observed
plus unobserved) and a method for modelling total diversity with covariates.
breakaway() estimates total (observed plus unobserved) species richness. Mi-
crobial diversity datasets are characterized by a large number of rare species
and a small number of highly abundant species. The class of models im-
plemented by breakaway() is flexible enough to model both these features.
breakaway_nof1() implements a similar procedure however does not require a
singleton count. betta() provides a method for modelling total diversity with
covariates in a way that accounts for its estimated nature and thus accounts
for unobserved taxa, and betta_random() permits random effects modelling. /
GPL-2
r-breakfast 1.0.0 The breakfast package performs multiple change-point detection in data se- noarch
quences, or sequence segmentation, using computationally efficient multiscale
methods. This version of the package implements the Tail-Greedy Unbal-
anced Haar, Wild Binary Segmentation and Adaptive Wild Binary Segmen-
tation change-point detection and segmentation methodologies. To start with,
see the function segment.mean. / GPL-3
r-breeze 0.4_3 A collection of functions to analyse, visualize and interpret wind data and to noarch
calculate the potential energy production of wind turbines. / MIT
r-bretigea 1.0.0 Analysis of relative cell type proportions in bulk gene expression data. noarch
Provides a well-validated set of brain cell type-specific marker genes de-
rived from multiple types of experiments, as described in McKenzie (2018)
<doi:10.1038/s41598-018-27293-5>. For brain tissue data sets, there are
marker genes available for astrocytes, endothelial cells, microglia, neurons,
oligodendrocytes, and oligodendrocyte precursor cells, derived from each of
human, mice, and combination human/mouse data sets. However, if you have
access to your own marker genes, the functions can be applied to bulk gene
expression data from any tissue. Also implements multiple options for relative
cell type proportion estimation using these marker genes, adapting and ex-
panding on approaches from the ‘CellCODE’ R package described in Chikina
(2015) <doi:10.1093/bioinformatics/btv015>. The number of cell type marker
genes used in a given analysis can be increased or decreased based on your
preferences and the data set. Finally, provides functions to use the estimates
to adjust for variability in the relative proportion of cell types across samples
prior to downstream analyses. / MIT
r-brew 1.0_6 brew implements a templating framework for mixing text and R code for report linux-
generation. brew template syntax is similar to PHP, Ruby’s erb module, Java 32,
Server Pages, and Python’s psp module. / GPL-2 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-brglm 0.6.2 Fit generalized linear models with binomial responses using either an adjusted- linux-
score approach to bias reduction or maximum penalized likelihood where pe- 32,
nalization is by Jeffreys invariant prior. These procedures return estimates with linux-
improved frequentist properties (bias, mean squared error) that are always fi- 64,
nite even in cases where the maximum likelihood estimates are infinite (data osx-
separation). Fitting takes place by fitting generalized linear models on iter- 64,
atively updated pseudo-data. The interface is essentially the same as ‘glm’. win-
More flexibility is provided by the fact that custom pseudo-data representa- 32,
tions can be specified and used for model fitting. Functions are provided for win-
the construction of confidence intervals for the reduced-bias estimates. / GPL 64
(>= 2)
r-bridgedist 0.1.0 An implementation of the bridge distribution with logit-link in R. In Wang and noarch
Louis (2003) <DOI:10.1093/biomet/90.4.765>, such a univariate bridge dis-
tribution was derived as the distribution of the random intercept that ‘bridged’
a marginal logistic regression and a conditional logistic regression. The condi-
tional and marginal regression coefficients are a scalar multiple of each other.
Such is not the case if the random intercept distribution was Gaussian. / GPL-2
r-brlrmr 0.1.5 Provides two main functions, il() and fil(). The il() function im- noarch
plements the EM algorithm developed by Ibrahim and Lipsitz (1996)
<DOI:10.2307/2533068> to estimate the parameters of a logistic regression
model with the missing response when the missing data mechanism is nonig-
norable. The fil() function implements the algorithm proposed by Maity et.
al. (2017) <https://github.com/arnabkrmaity/brlrmr> to reduce the bias pro-
duced by the method of Ibrahim and Lipsitz (1996) <DOI:10.2307/2533068>.
/ GPL-3
r-brm 1.0 Fits novel models for the conditional relative risk, risk difference and odds noarch
ratio. / MIT
r-brnn 0.7 Bayesian regularization for feed-forward neural networks. / GPL-2 linux-
64,
osx-
64,
win-
64
r-brobdingnag 1.2_6 Handles very large numbers in R. Real numbers are held using their natural noarch
logarithms, plus a logical flag indicating sign. The package includes a vignette
that gives a step-by-step introduction to using S4 methods. / GPL-3
r-broom 0.5.2 Summarizes key information about statistical objects in tidy tibbles. This linux-
makes it easy to report results, create plots and consistently work with large 32,
numbers of models at once. Broom provides three verbs that each provide linux-
different types of information about a model. tidy() summarizes information 64,
about model components such as coefficients of a regression. glance() re- noarch,
ports information about an entire model, such as goodness of fit measures like osx-
AIC and BIC. augment() adds information about individual observations to a 64,
dataset, such as fitted values or influence measures. / MIT file LICENSE win-
32,
win-
64


Name Version
r-brotli 1.2 A lossless compressed data format that uses a combination of the LZ77 al- linux-
gorithm and Huffman coding. Brotli is similar in speed to deflate (gzip) but 64,
offers more dense compression. / MIT osx-
64,
win-
64
r-browndog 0.2.1 An R interface for the Brown Dog which allows researchers to leverage Brown noarch
Dog Services that provides modules to identify the conversion options for a
file, to convert file to appropriate format, or to extract data from a file. See
<http://browndog.ncsa.illinois.edu/> for more information. / FreeBSD | file
LICENSE
r-brq 2.5 Bayesian estimation and variable selection for quantile regression models. / noarch
GPL-2
r-brunnermunzel 1.3.5 Provides the functions for Brunner-Munzel test and permuted Brunner-Munzel linux-
test, which enable to use formula, matrix, and table as argument. These 64,
functions are based on Brunner and Munzel (2000) <doi:10.1002/(SICI)1521- osx-
4036(200001)42:1%3C17::AID-BIMJ17%3E3.0.CO;2-U> and Neubert and 64,
Brunner (2007) <doi:10.1016/j.csda.2006.05.024>, and are written with FOR- win-
TRAN. / GPL-2 | GPL-3 64
r-bs4dash 0.4.0 Make ‘Bootstrap 4’ dashboards. Use the full power of ‘AdminLTE3’, noarch
a dashboard template built on top of ‘Bootstrap 4’ <https://github.com/
almasaeed2010/AdminLTE/tree/v3-dev>. / GPL-2
r-bsda 1.2.0 Data sets for book Basic Statistics and Data Analysis by Larry J. Kitchens. / noarch
GPL-2
r-bsearchtools 0.0.61Exposes the binary search functions of the C standard library linux-
(std::lower_bound, std::upper_bound) plus other convenience functions, 64,
allowing faster lookups on sorted vectors. / GPL-2 osx-
64,
win-
64
r-bsmd 2013.0718_1
Bayes screening and model discrimination follow-up designs. / GPL-2 linux-
64,
osx-
64,
win-
64
r-bspec 1.5 Bayesian inference on the (discrete) power spectrum of time series. / GPL-2 noarch
r-bsplinepsd 0.6.0 Implementation of a Metropolis-within-Gibbs MCMC algorithm to flexibly linux-
estimate the spectral density of a stationary time series. The algorithm up- 64,
dates a nonparametric B-spline prior using the Whittle likelihood to pro- osx-
duce pseudo-posterior samples and is based on the work presented in Ed- 64,
wards, M.C., Meyer, R. and Christensen, N., Statistics and Computing (2018). win-
<doi.org/10.1007/s11222-017-9796-9>. / GPL-3 64
r-bsplus 0.1.1 The Bootstrap framework lets you add some JavaScript functionality to your noarch
web site by adding attributes to your HTML tags - Bootstrap takes care of
the JavaScript <https://getbootstrap.com/javascript>. If you are using R Mark-
down or Shiny, you can use these functions to create collapsible sections, ac-
cordion panels, modals, tooltips, popovers, and an accordion sidebar frame-
work (not described at Bootstrap site). / MIT
r-bspmma 0.1_2 The main functions carry out Gibbs’ sampler routines for nonparametric and noarch
semiparametric Bayesian models for random effects meta-analysis. / GPL-2


Name Version
r-bsts 0.9.1 Time series regression using dynamic linear models fit using MCMC. linux-
See Scott and Varian (2014) <DOI:10.1504/IJMMNO.2014.059942>, among 64,
many other sources. / LGPL-2.1 osx-
64,
win-
64
r-btm 0.2.1 Biterm Topic Models find topics in collections of short texts. It is a word co- linux-
occurrence based topic model that learns topics by modeling word-word co- 64,
occurrences patterns which are called biterms. This in contrast to traditional osx-
topic models like Latent Dirichlet Allocation and Probabilistic Latent Seman- 64,
tic Analysis which are word-document co-occurrence topic models. A biterm win-
consists of two words co-occurring in the same short text window. This con- 64
text window can for example be a twitter message, a short answer on a survey,
a sentence of a text or a document identifier. The techniques are explained in
detail in the paper ‘A Biterm Topic Model For Short Text’ by Xiaohui Yan, Ji-
afeng Guo, Yanyan Lan, Xueqi Cheng (2013) <https://github.com/xiaohuiyan/
xiaohuiyan.github.io/blob/master/paper/BTM-WWW13.pdf>. / Apache Li-
cense 2.0
r-bucky 1.0.5 Provides functions for various statistical techniques commonly used in the so- noarch
cial sciences, including functions to compute clustered robust standard errors,
combine results across multiply-imputed data sets, and simplify the addition
of robust and clustered robust standard errors. The package was originally de-
veloped, in part, to assist porting of replication code from ‘Stata’ and attempts
to replicate default options from ‘Stata’ where possible. / GPL-3
r-bucss 1.1.0 Implements a method of correcting for publication bias and uncertainty when noarch
planning sample sizes in a future study from an original study. See Anderson,
Kelley, & Maxwell (2017; Psychological Science, 28, 1547-1562). / GPL-3
r-buddle 1.0 Statistical classification has been popular among various fields and stayed in linux-
the limelight of scientists of those fields. Examples of the fields include clinical 64,
trials where the statistical classification of patients is indispensable to predict osx-
the clinical courses of diseases. Considering the negative impact of diseases 64,
on performing daily tasks, correctly classifying patients based on the clinical win-
information is vital in that we need to identify patients of the high-risk group to 64
develop a severe state and arrange medical treatment for them at an opportune
moment. Deep learning - a part of artificial intelligence - has gained much
attention, and research on it burgeons during past decades. It is a veritable
technique which was originally designed for the classification, and hence, the
EzDL package can provide sublime solutions to various challenging classifi-
cation problems encountered in the clinical trials. The EzDL package is based
on the back-propagation algorithm which performs a multi-layer feed-forward
neural network. This package contains two functions: Buddle_Main() and
Buddle_Predict(). Buddle_Main() builds a feed-forward neural network model
and trains the model. Buddle_Predict() provokes the trained model which is
the output of Buddle_Main(), classifies given data, and make a final prediction
for the data. / GPL-2
r-buildmer 1.2 Finds the largest possible regression model that will still converge for various noarch
types of regression analyses (including mixed models and generalized addi-
tive models) and then optionally performs stepwise elimination similar to the
forward and backward effect selection methods in SAS, based on the change
in log-likelihood or its significance, Akaike’s Information Criterion, or the
Bayesian Information Criterion. / FreeBSD


Name Version
r-bullwhipgame 0.1.0 The bullwhipgame is an educational game that has as purpose the illustration noarch
and exploration of the bullwhip effect,i.e, the increase in demand variability
along the supply chain. Marchena Marlene (2010) <arXiv:1009.3977>. / GPL-
3
r-bunchr 1.2.0 View and analyze data where bunching is expected. Estimate counter- fac- noarch
tual distributions. For earnings data, estimate the compensated elasticity of
earnings w.r.t. the net-of-tax rate. / MIT
r-bundesbank 0.1_9 Download data from the time-series databases of the Bundesbank, the German noarch
central bank. See the overview at the Bundesbank website (<https://www.
bundesbank.de/en/statistics/time-series-databases>) for available series. The
package provides only a single function, getSeries(), which supports both tra-
ditional and real-time datasets; it will also download meta data if available.
Downloaded data can automatically be arranged in various formats, such as
data frames or ‘zoo’ series. The data may optionally be cached, so as to avoid
repeated downloads of the same series. / GPL-3
r-bundesligr 0.1.0 All final tables of Germany’s highest football (soccer!) league, the Bundesliga. noarch
Contains data from 1964 to 2016. / GPL-3
r-burstfin 1.02 A suite of functions for finance, including the estimation of variance matrices noarch
via a statistical factor model or Ledoit-Wolf shrinkage. / Unlimited
r-burstmisc 1.1 Script search, corner, genetic optimization, permutation tests, write expect test. noarch
/ Unlimited
r-bursts 1.0_1 An implementation of Jon Kleinberg’s burst detection algorithm. Uses an infi- noarch
nite Markov model to detect periods of increased activity in a series of discrete
events with known times, and provides a simple visualization of the results. /
MIT
r-busdater 0.2.0 Get a current financial year, start of current month, End of current month, start noarch
of financial year and end of it. Allow for offset from the date. / MIT
r- 0.2.0 Calculates business duration between two dates. This excluding weekends, noarch
businessduration public holidays and non-business hours. / AGPL-3
r-buysetest 1.7 Implementation of the Generalized Pairwise Comparisons (GPC). GPC com- linux-
pare two groups of observations (intervention vs. control group) regarding 64,
several prioritized endpoints. The net benefit and win ratio statistics can then osx-
be estimated and corresponding confidence intervals and p-values can be es- 64,
timated using resampling methods or the asymptotic U-statistic theory. The win-
software enables the use of thresholds of minimal importance difference, strat- 64
ification, and corrections to deal with right-censored endpoints or missing val-
ues. / GPL-3
r-bvar 0.1.5 Toolkit for the estimation of hierarchical Bayesian vector autoregressions. Im- noarch
plements hierarchical prior selection for conjugate priors in the fashion of Gi-
annone, Lenza & Primiceri (2015) <doi:10.1162/REST_a_00483>. Allows for
the computation of impulse responses and forecasts and provides functionality
for assessing results. / GPL-3
r-bvarsv 1.1 R/C implementation of the model proposed by Primiceri (Time Varying Struc- linux-
tural Vector Autoregressions and Monetary Policy, Review of Economic Stud- 64,
ies, 2005), with functionality for computing posterior predictive distributions osx-
and impulse responses. / GPL-2 64,
win-
64


Name Version
r-bvartools 0.0.2 Assists in the set-up of algorithms for Bayesian inference of vector au- linux-
toregressive (VAR) models. Functions for posterior simulation, forecast- 64,
ing, impulse response analysis and forecast error variance decomposition osx-
are largely based on the introductory texts of Koop and Korobilis (2010) 64,
<doi:10.1561/0800000013> and Luetkepohl (2007, ISBN: 9783540262398). win-
/ GPL-2 64
r-bvenn 0.1 This package implements a simple alternative to the traditional Venn diagram. noarch
It depicts each overlap as a separate bubble with area proportional to the over-
lap size. Relation of the bubbles to input sets is shown by their their arrange-
ment. / GPL-2
r-bvls 1.4 An R interface to the Stark-Parker implementation of an algorithm for linux-
bounded-variable least squares / GPL-2 64,
osx-
64,
win-
64
r-bwd 0.1.0 Implements a backward procedure for single and multiple change point detec- linux-
tion proposed by Shin et al. <arXiv:1812.10107>. The backward approach is 64,
particularly useful to detect short and sparse signals which is common in copy osx-
number variation (CNV) detection. / GPL-2 64,
win-
64
r-bwgr 1.6.5 Whole-genome regression methods on Bayesian framework fitted via EM or linux-
Gibbs sampling, univariate and multivariate, with optional kernel term and 64,
sampling techniques. / GPL-3 osx-
64,
win-
64
r-bwimage 1.0 A computational tool to describe patterns in black and white images from natu- noarch
ral structures. ‘bwimage’ implemented functions for exceptionally broad sub-
ject. For instance, ‘bwimage’ provide examples that range from calculation
of canopy openness, description of patterns in vertical vegetation structure, to
patterns in bird nest structure. / GPL-2
r-bwstest 0.2.2 Performs the ‘Baumgartner-Weiss-Schindler’ two-sample test of linux-
equal probability distributions, <doi:10.2307/2533862>. Also per- 64,
forms similar rank-based tests for equal probability distributions osx-
due to Neuhauser <doi:10.1080/10485250108832874> and Murakami 64,
<doi:10.1080/00949655.2010.551516>. / LGPL-3 win-
64
r-bytescircle 1.1 Shows statistics about bytes contained in a file as a circle graph of deviations linux-
from mean in sigma increments. The function can be useful for statistically an- 64,
alyze the content of files in a glimpse: text files are shown as a green centered osx-
crown, compressed and encrypted files should be shown as equally distributed 64,
variations with a very low CV (sigma/mean), and other types of files can be win-
classified between these two categories depending on their text vs binary con- 64
tent, which can be useful to quickly determine how information is stored inside
them (databases, multimedia files, etc). / GPL-3


Name Version
r-bzinb 1.0.3 Provides a maximum likelihood estimation of Bivariate Zero-Inflated Negative linux-
Binomial (BZINB) model or the nested model parameters. Also estimates 64,
the underlying correlation of the a pair of count data. See Cho, H., Liu, C., osx-
Preisser, J., and Wu, D. (In preparation) for details. / GPL-2 64,
win-
64
r-c212 0.95 Methods for detecting safety signals in clinical trials using groupings of ad- linux-
verse events by body-system or system organ class.The package title c212 is 64,
in reference to the original Engineering and Physical Sciences Research Coun- osx-
cil (UK) funded project which was named CASE 2/12. / GPL-2 64,
win-
64
r-c2c 0.1.0 Compare two classifications or clustering solutions that may or may not have noarch
the same number of classes, and that might have hard or soft (fuzzy, prob-
abilistic) membership. Calculate various metrics to assess how the clusters
compare to each other. The calculations are simple, but provide a handy tool
for users unfamiliar with matrix multiplication. This package is not geared to-
wards traditional accuracy assessment for classification/ mapping applications
- the motivating use case is for comparing a probabilistic clustering solution to
a set of reference or existing class labels that could have any number of classes
(that is, without having to degrade the probabilistic clustering to hard classes).
/ GPL-3
r-c3net 1.1.1 This package allows inferring gene regulatory networks with direct physical noarch
interactions from microarray expression data using C3NET. / GPL-3
r-ca 0.71 Computation and visualization of simple, multiple and joint correspondence noarch
analysis. / GPL-3
r-cabootcrs 1.0 Performs correspondence analysis on a two-way contingency table and pro- noarch
duces bootstrap-based elliptical confidence regions around the projected coor-
dinates for the category points. Includes routines to plot the results in a variety
of styles. Also reports the standard numerical output for correspondence anal-
ysis. / GPL-2
r-cacirt 1.4 Computes classification accuracy and consistency indices under Item Re- noarch
sponse Theory. Implements the total score IRT-based methods in Lee, Hanson
& Brennen (2002) and Lee (2010), the IRT-based methods in Rudner (2001,
2005), and the total score nonparametric methods in Lathrop & Cheng (2014).
For dichotomous and polytomous tests. / GPL-2
r-caic4 0.8 Provides functions for the estimation of the conditional Akaike information in noarch
generalized mixed-effect models fitted with (g)lmer() from ‘lme4’. / GPL-2
r-cairo 1.5_10Cairo graphics device that can be use to create high-quality vector (PDF, linux-
PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality 32,
rendering in displays (X11 and Win32). Since it uses the same back-end for linux-
all output, copying across formats is WYSIWYG. Files are created without the 64,
dependence on X11 or other external programs. This device supports alpha osx-
channel (semi-transparent drawing) and resulting images can contain transpar- 64,
ent and semi-transparent regions. It is ideal for use in server environments (file win-
output) and as a replacement for other devices that don’t have Cairo’s capabil- 32,
ities such as alpha support or anti-aliasing. Backends are modular such that win-
any subset of backends is supported. / GPL-2 64


Name Version
r-calacs 2.2.2 Implements several string comparison algorithms, including calACS (count noarch
all common subsequences), lenACS (calculate the lengths of all common sub-
sequences), and lenLCS (calculate the length of the longest common subse-
quence). Some algorithms differentiate between the more strict definition of
subsequence, where a common subsequence cannot be separated by any other
items, from its looser counterpart, where a common subsequence can be inter-
rupted by other items. This difference is shown in the suffix of the algorithm
(-Strict vs -Loose). For example, q-w is a common subsequence of q-w-e-
r and q-e-w-r on the looser definition, but not on the more strict definition.
calACSLoose Algorithm from Wang, H. All common subsequences (2007) IJ-
CAI International Joint Conference on Artificial Intelligence, pp. 635-640. /
GPL-3
r-calculator.lr.fns 1.3 Arithmetic operations scalar multiplication, addition, subtraction, multiplica- noarch
tion and division of LR fuzzy numbers (which are on the basis of extension
principle) have a complicate form for using in fuzzy Statistics, fuzzy Mathe-
matics, machine learning, fuzzy data analysis and etc. Calculator for LR Fuzzy
Numbers package relieve and aid applied users to achieve a simple and closed
form for some complicated operator based on LR fuzzy numbers and also the
user can easily draw the membership function of the obtained result by this
package. / LGPL-3
r-calibrate 1.7.2 Package for drawing calibrated scales with tick marks on (non-orthogonal) noarch
variable vectors in scatterplots and biplots. / GPL-2
r-calibrator 1.2_8 Performs Bayesian calibration of computer models as per Kennedy and noarch
O’Hagan 2001. The package includes routines to find the hyperparameters
and parameters; see the help page for stage1() for a worked example using the
toy dataset. A tutorial is provided in the calex.Rnw vignette; and a suite of
especially simple one dimensional examples appears in inst/doc/one.dim/. /
GPL-2
r-callr 3.2.0 It is sometimes useful to perform a computation in a separate R process, with- linux-
out affecting the current R process at all. This packages does exactly that. / 32,
64,
noarch,
osx-
64,
win-
32,
win-
64
r-caman 0.74 Tools for the analysis of finite semiparametric mixtures. These are useful when linux-
data is heterogeneous, e.g. in pharmacokinetics or meta-analysis. The NPMLE 64,
and VEM algorithms (flexible support size) and EM algorithms (fixed support osx-
size) are provided for univariate and bivariate data. / GPL-2 64,
win-
64


Name Version
r-camsrad 0.3.0 Copernicus Atmosphere Monitoring Service (CAMS) radiations service pro- noarch
vides time series of global, direct, and diffuse irradiations on horizontal sur-
face, and direct irradiation on normal plane for the actual weather condi-
tions as well as for clear-sky conditions. The geographical coverage is the
field-of-view of the Meteosat satellite, roughly speaking Europe, Africa, At-
lantic Ocean, Middle East. The time coverage of data is from 2004-02-
01 up to 2 days ago. Data are available with a time step ranging from 15
min to 1 month. For license terms and to create an account, please see
<http://www.soda-pro.com/web-services/radiation/cams-radiation-service>. /
MIT
r-canprot 0.1.2 Datasets are collected here for differentially (up- and down-) expressed pro- noarch
teins identified in proteomic studies of cancer and in cell culture experiments.
Tables of amino acid compositions of proteins are used for calculations of
chemical composition, projected into selected basis species. Plotting func-
tions are used to visualize the compositional differences and thermodynamic
potentials for proteomic transformations. / GPL-3
r-canvasxpress 1.24.8Enables creation of visualizations using the CanvasXpress framework in R. noarch
CanvasXpress is a standalone JavaScript library for reproducible research with
complete tracking of data and end-user modifications stored in a single PNG
image that can be played back. See <http://canvasxpress.org> for more infor-
mation. / GPL-3
r-caper 1.0.1 Functions for performing phylogenetic comparative analyses. / GPL-2 noarch
r-capitalr 1.2.0 Provides Capital Budgeting Analysis functionality and the essential Annuity noarch
loan functions. Also computes Loan Amortization Schedules including sched-
ules with irregular payments. / GPL-3
r-capn 1.0.0 Implements approximation methods for natural capital asset prices suggested noarch
by Fenichel and Abbott (2014) <doi:10.1086/676034> in Journal of the As-
sociations of Environmental and Resource Economists (JAERE), Fenichel et
al. (2016) <doi:10.1073/pnas.1513779113> in Proceedings of the National
Academy of Sciences (PNAS), and Yun et al. (2017) in PNAS (accepted), and
their extensions: creating Chebyshev polynomial nodes and grids, calculating
basis of Chebyshev polynomials, approximation and their simulations for: V-
approximation (single and multiple stocks, PNAS), P-approximation (single
stock, PNAS), and Pdot-approximation (single stock, JAERE). Development
of this package was generously supported by the Knobloch Family Founda-
tion. / GPL-2
r-captioner 2.2.3 Provides a method for automatically numbering figures, tables, or other ob- noarch
jects. Captions can be displayed in full, or as citations. This is especially
useful for adding figures and tables to R markdown documents without having
to numbering them manually. / MIT
r-captr 0.3.0 Get text from images of text using Captricity Optical Character Recognition noarch
(OCR) API. Captricity allows you to get text from handwritten forms — think
surveys — and other structured paper documents. And it can output data in
form a delimited file keeping field information intact. For more information,
read <https://shreddr.captricity.com/developer/overview/>. / MIT
r-capushe 1.1.1 Calibration of penalized criteria for model selection. The calibration methods noarch
available are based on the slope heuristics. / GPL (>= 2.0)


Name Version
r-capwire 1.1.4 Fits models from Miller et al. 2005 to estimate population sizes from natural noarch
populations. Several models are implemented. Package also includes func-
tions to perform a likelihood ratio test to choose between models, perform
parametric bootstrapping to obtain confidence intervals and multiple functions
to simulate data. / GPL-2
r-car 3.0_2 Functions to Accompany J. Fox and S. Weisberg, An R Companion to Applied linux-
Regression, Third Edition, Sage, in press. / GPL (>= 2) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-cardata 3.0_2 Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied linux-
Regression, Third Edition, Sage (forthcoming). / GPL (>= 2) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-cardiomodel 1.4 Includes over 100 mixed-effects model structures describing the relationship noarch
between drug concentration and QT interval, heart rate/pulse rate or blood
pressure. Given an exposure-response dataset, the tool fits each model struc-
ture to the observed data. / GPL-3
r-care 1.1.10Implements the regression approach of Zuber and Strimmer (2011) High- noarch
dimensional regression and variable selection using CAR scores SAGMB 10:
34, <DOI:10.2202/1544-6115.1730>. CAR scores measure the correlation be-
tween the response and the Mahalanobis-decorrelated predictors. The squared
CAR score is a natural measure of variable importance and provides a canoni-
cal ordering of variables. This package provides functions for estimating CAR
scores, for variable selection using CAR scores, and for estimating correspond-
ing regression coefficients. Both shrinkage as well as empirical estimators are
available. / GPL-3
r-care1 1.1.0 The R package CARE1, the first part of the program CARE (Capture- noarch
Recapture) in http://chao.stat.nthu.edu.tw/softwareCE.html, can be used to an-
alyze epidemiological data via sample coverage approach (Chao et al. 2001a).
Based on the input of records from several incomplete lists (or samples) of in-
dividuals, the R package CARE1 provides output of population size estimate
and related statistics. / GPL-3


Name Version
r-careless 1.1.3 When taking online surveys, participants sometimes respond to items without noarch
regard to their content. These types of responses, referred to as careless or
insufficient effort responding, constitute significant problems for data quality,
leading to distortions in data analysis and hypothesis testing, such as spurious
correlations. The ‘R’ package ‘careless’ provides solutions designed to de-
tect such careless / insufficient effort responses by allowing easy calculation
of indices proposed in the literature. It currently supports the calculation of
longstring, even-odd consistency, psychometric synonyms/antonyms, Maha-
lanobis distance, and intra-individual response variability (also termed inter-
item standard deviation). For a review of these methods, see Curran (2016)
<doi:10.1016/j.jesp.2015.07.006>. / MIT
r-caret 6.0_83Misc functions for training and plotting classification and regression models. / linux-
GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-caribou 1.1 This is a package for estimating the population size of migratory caribou herds noarch
based on large scale aggregations monitored by radio telemetry. It imple-
ments the methodology found in the article by Rivest et al. (1998) about cari-
bou abundance estimation. It also includes a function based on the Lincoln-
Petersen Index as applied to radio telemetry data by White and Garrott (1990).
/ GPL-2
r-carletonstats 2.0 Includes commands for bootstrapping and permutation tests, a command for noarch
created grouped bar plots, and a demo of the quantile-normal plot for data
drawn from different distributions. / GPL-2
r-carlit 1.0 Functions to calculate and plot ecological quality ratios (EQR) as specified by noarch
Ballesteros et al. 2007. / GPL-2
r-caroline 0.7.6 The caroline R library contains dozens of functions useful for: database mi- noarch
gration (dbWriteTable2), database style joins & aggregation (nerge, groupBy
& bestBy), data structure conversion (nv, tab2df), legend table making (sstable
& leghead), plot annotation (labsegs & mvlabs), data visualization (violins,
pies & raPlot), character string manipulation (m & pad), file I/O (write.delim),
batch scripting and more. The package’s greatest contributions lie in the
database style merge, aggregation and interface functions as well as in it’s
extensive use and propagation of row, column and vector names in most func-
tions. / Artistic-2.0
r-carrier 0.1.0 Sending functions to remote processes can be wasteful of resources because noarch
they carry their environments with them. With the carrier package, it is easy
to create functions that are isolated from their environment. These isolated
functions, also called crates, print at the console with their total size and can
be easily tested locally before being sent to a remote. / GPL-3


Name Version
r-cascadedata 1.2 These experimental expression data (5 leukemic ‘CLL’ B-lymphocyte of ag- noarch
gressive form from ‘GSE39411’, <doi:10.1073/pnas.1211130110>), after B-
cell receptor stimulation, are used as examples by packages such as the ‘Cas-
cade’ one, a modeling tool allowing gene selection, reverse engineering, and
prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat,
L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>. /
GPL-2
r-casematch 1.0.7 Allows users to identify similar cases for qualitative case studies using statis- noarch
tical matching methods. / GPL-2
r-casmap 0.6.0 A significant pattern mining-based toolbox for region-based genome- linux-
wide association studies and higher-order epistasis analyses, imple- 64,
menting the methods described in Llinares-López et al. (2017) osx-
<doi:10.1093/bioinformatics/btx071>. / GPL-2 64,
win-
64
r-cat 0.0_6.5
Analysis of categorical-variable with missing values / file LICENSE linux-
64,
osx-
64,
win-
64
r-catchr 0.2.1 R has a unique way of dealing with warnings, errors, messages, and other noarch
conditions, but it can often be troublesome to users coming from different pro-
gramming backgrounds. The purpose of this package is to provide flexible
and useful tools for handling R conditions with less hassle. In order to lower
the barrier of entry, keep code clean and readable, and reduce the amount of
typing required, catchr uses a very simple domain-specific language that sim-
plifies things on the front-end. This package aims to maintain a continuous
learning curve that lets new users jump straight in to condition-handling, while
simultaneously offering depth and complexity for more advanced users. / MIT
r-catdap 1.3.4 Categorical data analysis by AIC. The methodology is described in Sakamoto linux-
(1992) <ISBN 978-0-7923-1429-5>. / GPL-2 64,
osx-
64,
win-
64
r-catdata 1.2.1 This R-package contains examples from the book Regression for Categorical noarch
Data, Tutz 2011, Cambridge University Press. The names of the examples
refer to the chapter and the data set that is used. / GPL-2
r-catencoders 0.1.1 Contains some commonly used categorical variable encoders, such as ‘La- noarch
belEncoder’ and ‘OneHotEncoder’. Inspired by the encoders implemented
in Python ‘sklearn.preprocessing’ package (see <http://scikit-learn.org/stable/
modules/preprocessing.html>). / GPL-2 | GPL-3
r-cateselection 1.0 A multi-factor dimensionality reduction based forward selection method for noarch
genetic association mapping. / GPL-2
r-catirt 0.5_0 Functions designed to simulate data that conform to basic unidimensional IRT linux-
models (for now 3-parameter binary response models and graded response 64,
models) along with Post-Hoc CAT simulations of those models with various osx-
item selection methods, ability estimation methods, and termination criteria. / 64,
GPL-2 win-
64


Name Version
r-catnet 1.15.5Structure learning and parameter estimation of discrete Bayesian networks linux-
using likelihood-based criteria. Exhaustive search for fixed node orders and 64,
stochastic search of optimal orders via simulated annealing algorithm are im- osx-
plemented. / GPL-2 64,
win-
64
r-catools 1.17.1.2
Contains several basic utility functions including: moving (rolling, running) linux-
window statistic functions, read/write for GIF and ENVI binary files, fast cal- 32,
culation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off- linux-
error-free sum and cumsum, etc. / GPL-3 64,
osx-
64,
win-
32,
win-
64
r-catr 3.16 Provides routines for the generation of response patterns under unidimensional noarch
dichotomous and polytomous computerized adaptive testing (CAT) frame-
work. It holds many standard functions to estimate ability, select the first
item(s) to administer and optimally select the next item, as well as several
stopping rules. Options to control for item exposure and content balancing
are also available (Magis and Barrada (2017) <doi:10.18637/jss.v076.c01>). /
GPL-2
r-catseyes 0.2.3 Provides the tools to produce catseye plots, principally by catseyesplot() func- noarch
tion which calls R’s standard plot() function internally, or alternatively by the
catseyes() function to overlay the catseye plot onto an existing R plot window.
Catseye plots illustrate the normal distribution of the mean (picture a normal
bell curve reflected over its base and rotated 90 degrees), with a shaded confi-
dence interval; they are an intuitive way of illustrating and comparing normally
distributed estimates, and are arguably a superior alternative to standard confi-
dence intervals, since they show the full distribution rather than fixed quantile
bounds. The catseyesplot and catseyes functions require pre-calculated means
and standard errors (or standard deviations), provided as numeric vectors; this
allows the flexibility of obtaining this information from a variety of sources,
such as direct calculation or prediction from a model. Catseye plots, as illustra-
tions of the normal distribution of the means, are described in Cumming (2013
& 2014). Cumming, G. (2013). The new statistics: Why and how. Psycholog-
ical Science, 27, 7-29. <doi:10.1177/0956797613504966> pmid:24220629. /
GPL-3
r-catspec 0.97 ‘ctab’ creates (multiway) percentage tables. ‘sqtab’ contains a set of functions noarch
for estimating models for square tables such as quasi-independence, symmetry,
uniform association. Examples show how to use these models in a loglinear
model using glm or in a multinomial logistic model using mlogit or clogit /
GPL-2
r-catt 2.0 This function conducts the Cochran-Armitage trend test to a 2 by k contin- noarch
gency table. It will report the test statistic (Z) and p-value.A linear trend in
the frequencies will be calculated, because the weights (0,1,2) will be used by
default. / GPL-3


Name Version
r-cattexact 0.1.0 Provides functions for computing the one-sided p-values of the Cochran- noarch
Armitage trend test statistic for the asymptotic and the exact conditional test.
The computation of the p-value for the exact test is performed using an algo-
rithm following an idea by Mehta, et al. (1992) <doi:10.2307/1390598>. /
GPL-2 | GPL-3
r-causalmgm 0.1.1 Allows users to learn undirected and directed (causal) graphs over mixed noarch
data types (i.e., continuous and discrete variables). To learn a directed graph
over mixed data, it first calculates the undirected graph (Sedgewick et al,
2016) and then it uses local search strategies to prune-and-orient this graph
(Sedgewick et al, 2017). AJ Sedgewick, I Shi, RM Donovan, PV Benos (2016)
<doi:10.1186/s12859-016-1039-0>. AJ Sedgewick, JD Ramsey, P Spirtes, C
Glymour, PV Benos (2017) <arXiv:1704.02621>. / GPL-2
r-causalsens 0.1.2 The causalsens package provides functions to perform sensitivity analyses and noarch
to study how various assumptions about selection bias affects estimates of
causal effects. / GPL-2
r-cbanalysis 0.2.0 A set of functions that helps you to generate descriptive statistics based on the noarch
variable types. / GPL-2
r-cbinom 1.3 Implementation of the d/p/q/r family of functions for a continuous analog to linux-
the standard discrete binomial with continuous size parameter and continuous 64,
support with x in [0, size 1], following Ilienko (2013) <arXiv:1303.5990>. / osx-
GPL-2 64,
win-
64
r-cbird 1.0 The clustering of binary data with reducing the dimensional- linux-
ity (CLUSBIRD) proposed by Yamamoto and Hayashi (2015) 64,
<doi:10.1016/j.patcog.2015.05.026>. / GPL-2 osx-
64,
win-
64
r-cblasr 1.0.0 Provides the ‘cblas.h’ header file as C interface to the underlying internal linux-
‘BLAS’ library in R. ‘CBLAS’ <https://www.netlib.org/blas/cblas.h> is a col- 64,
lection of wrappers originally written by Keita Teranishi and provides a C in- osx-
terface to the FORTRAN ‘BLAS’ library <https://www.netlib.org/blas/>. Note 64,
that as internal ‘BLAS’ library provided by R <https://svn.r-project.org/R/ win-
trunk/src/include/R_ext/BLAS.h> is used and only the double precision / dou- 64
ble complex ‘BLAS’ routines are supported. / GPL-2
r-cbsem 1.0.0 The composites are linear combinations of their indicators in composite based noarch
structural equation models. Structural models are considered consisting of
two blocks. The indicators of the exogenous composites are named by X, the
indicators of the endogenous by Y. Reflective relations are given by arrows
pointing from the composite to their indicators. Their values are called load-
ings. In a reflective-reflective scenario all indicators have loadings. Arrows
are pointing to their indicators only from the endogenous composites in the
formative-reflective scenario. There are no loadings at all in the formative-
formative scenario. The covariance matrices are computed for these three sce-
narios. They can be used to simulate these models. These models can also be
estimated and a segmentation procedure is included as well. / GPL-3
r-cbsodatar 0.3.4 The data and meta data from Statistics Netherlands (<https://www.cbs.nl>) can noarch
be browsed and downloaded. The client uses the open data API of Statistics
Netherlands. / GPL-2


Name Version
r-cbt 1.0 The Confidence Bound Target (CBT) algorithm is designed for infinite arms noarch
bandit problem. It is shown that CBT algorithm achieves the regret lower
bound for general reward distributions. Reference: Hock Peng Chan and
Shouri Hu (2018) <arXiv:1805.11793>. / GPL-2
r-cc 1.0 Tools for creating and visualizing statistical process control charts. Control noarch
charts are used for monitoring measurement processes, such as those occur-
ring in manufacturing. The objective is to monitor the history of such pro-
cesses and flag outlying measurements: out-of-control signals. Montgomery,
D. (2009, ISBN:978-0-470-16992-6) contains an extensive discussion of the
methodology. / GPL-2
r-ccagfa 1.0.8 Variational Bayesian algorithms for learning canonical correlation analysis noarch
(CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA).
Inference with several random initializations can be run with the functions
CCAexperiment() and GFAexperiment(). / GPL-2
r-ccapp 0.3.2 Canonical correlation analysis and maximum correlation via projection pur- linux-
suit, as well as fast implementations of correlation estimators, with a focus on 64,
robust and non-parametric methods. / GPL-2 osx-
64,
win-
64
r-ccchooser 0.2.6 ccChooser can be used to developing and evaluation of core collections for noarch
germplasm collections (entire collection). This package used to develop a core
collection for biological resources like genbanks. A core collection is defined
as a sample of accessions that represent, with the lowest possible level of re-
dundancy, the genetic diversity (the richness of gene or genotype categories) of
the entire collection. The establishing a core collection that represents genetic
diversity of the entire collection with minimum loss of its original diversity
and minimum redundancies is an important problem for gene-banks curators
and crop breeders. ccChooser establish core collection base on phenotypic
data (agronomic, morphological, phenological). / GPL-2
r-cccp 0.2_4 Routines for solving convex optimization problems with cone constraints by linux-
means of interior-point methods. The implemented algorithms are partially 64,
ported from CVXOPT, a Python module for convex optimization (see <http: osx-
//cvxopt.org> for more information). / GPL-3 64,
win-
64
r-cccrm 1.2.1 Estimates the Concordance Correlation Coefficient to assess agreement. The noarch
scenarios considered are non-repeated measures, non-longitudinal repeated
measures (replicates) and longitudinal repeated measures. The estimation ap-
proaches implemented are variance components and U-statistics approaches. /
GPL-2
r-ccda 1.1 This package implements the combined cluster and discriminant analysis noarch
method for finding homogeneous groups of data with known origin as de-
scribed in Kovacs et. al (2014): Classification into homogeneous groups
using combined cluster and discriminant analysis (CCDA). Environmental
Modelling & Software. DOI: http://dx.doi.org/10.1016/j.envsoft.2014.01.010
/ GPL-2
r-cchs 0.4.1 Contains a function, also called ‘cchs’, that calculates Estimator III of Borgan noarch
et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting
a Cox proportional hazards model to data from a case-cohort study where the
subcohort was selected by stratified simple random sampling. / GPL-3


Name Version
r-cclust 0.6_21Convex Clustering methods, including K-means algorithm, On-line Update linux-
algorithm (Hard Competitive Learning) and Neural Gas algorithm (Soft Com- 64,
petitive Learning), and calculation of several indexes for finding the number osx-
of clusters in a data set. / GPL-2 64,
win-
64
r-ccm 1.2 Classification method described in Dancik et al (2011) <doi:10.1158/0008- noarch
5472.CAN-11-2427> that classifies a sample according to the class with the
maximum mean (or any other function of) correlation between the test and
training samples with known classes. / GPL-2
r-ccmm 1.0 Estimate the direct and indirect (mediation) effects of treatment on the out- noarch
come when intermediate variables (mediators) are compositional and high-
dimensional. Sohn, M.B. and Li, H. (2017). Compositional Mediation Analy-
sis for Microbiome Studies. (AOAS: In revision). / GPL-2
r-ccp 1.1 Significance tests for canonical correlation analysis, including asymptotic tests noarch
and a Monte Carlo method / GPL-3
r-ccpop 1.0 Tests of association between SNPs or pairs of SNPs and binary phenotypes, in noarch
case-control / case-population / case-control-population studies. / GPL-2
r-ccremover 1.0.4 Implements a method for identifying and removing the cell-cycle effect from noarch
scRNA-Seq data. The description of the method is in Barron M. and Li J.
(2016) <doi:10.1038/srep33892>. Identifying and removing the cell-cycle ef-
fect from single-cell RNA-Sequencing data. Submitted. Different from previ-
ous methods, ccRemover implements a mechanism that formally tests whether
a component is cell-cycle related or not, and thus while it often thoroughly re-
moves the cell-cycle effect, it preserves other features/signals of interest in the
data. / GPL-3
r-cdb 0.0.1 A constant database is a data structure created by Daniel J. Bernstein in his cdb noarch
package. Its format consists on a sequence of (key,value)-pairs. This R pack-
age replicates the basic utilities for reading (cdbget) and writing (cdbdump)
constant databases. / GPL-2
r-cde 0.4.1 Facilitates searching, download and plotting of Water Framework Direc- noarch
tive (WFD) reporting data for all waterbodies within the UK Environment
Agency area. The types of data that can be downloaded are: WFD sta-
tus classification data, Reasons for Not Achieving Good (RNAG) status, ob-
jectives set for waterbodies, measures put in place to improve water qual-
ity and details of associated protected areas. The site accessed is <https:
//environment.data.gov.uk/catchment-planning/>. The data are made available
under the Open Government Licence v3.0 <https://www.nationalarchives.gov.
uk/doc/open-government-licence/version/3/>. This package has been peer-
reviewed by rOpenSci (v. 0.4.0). / GPL-3
r-cdft 1.0.1 This package proposes a statistical downscaling method for cumulative distri- noarch
bution functions (CDF), as well as the computation of the Cram‘er-von Mises
statistics U, and the Kolmogorov-Smirnov statistics KS. / GPL-2
r-cdlasso 1.1 Coordinate Descent Algorithms for Lasso Penalized L1, L2, and Logistic Re- linux-
gression / GPL-2 64,
osx-
64,
win-
64


Name Version
r-cdltools 0.14 Downloads USDA National Agricultural Statistics Service (NASS) cropscape linux-
data for a specified state. Utilities for fips, abbreviation, and name conversion 64,
are also provided. Full functionality requires an internet connection, but data osx-
sets can be cached for later off-line use. / Unlimited 64,
win-
64
r-cdnmoney 2012.4_2
Components of Canadian Credit Aggregates and Monetary Aggregates with noarch
continuity adjustments. / GPL-2
r-cdrom 1.1 Classification is based on the recently developed phylogenetic approach by noarch
Assis and Bachtrog (2013). The method classifies the evolutionary mecha-
nisms retaining pairs of duplicate genes (conservation, neofunctionalization,
subfunctionalization, or specialization) by comparing gene expression profiles
of duplicate genes in one species to those of their single- copy ancestral genes
in a sister species. / GPL-2
r-cdvine 1.4 Functions for statistical inference of canonical vine (C-vine) and D-vine cop- linux-
ulas. Tools for bivariate exploratory data analysis and for bivariate as well as 64,
vine copula selection are provided. Models can be estimated either sequen- osx-
tially or by joint maximum likelihood estimation. Sampling algorithms and 64,
plotting methods are also included. Data is assumed to lie in the unit hyper- win-
cube (so-called copula data). / GPL-2 64
r-cec 0.10.2CEC divides data into Gaussian type clusters. The implementation allows the linux-
simultaneous use of various type Gaussian mixture models, performs the re- 64,
duction of unnecessary clusters and it’s able to discover new groups. Based on osx-
Spurek, P. and Tabor, J. (2014) <doi:10.1016/j.patcog.2014.03.006>. / GPL-3 64,
win-
64
r- 1.0.4 This package is a wrapper for the C implementation of the 25 benchmark func- linux-
cec2005benchmark tions for the CEC 2005 Special Session on Real-Parameter Optimization. The 64,
original C code by Santosh Tiwari and related documentation are available osx-
at http://www.ntu.edu.sg/home/EPNSugan/index_files/CEC-05/CEC05.htm. / 64,
GPL-3 win-
64
r-cec2013 0.1_5 This package provides R wrappers for the C implementation of 28 benchmark linux-
functions defined for the Special Session and Competition on Real-Parameter 64,
Single Objective Optimization at CEC-2013. The focus of this package is to osx-
provide an open-source and multi-platform implementation of the CEC2013 64,
benchmark functions, in order to make easier for researchers to test the per- win-
formance of new optimization algorithms in a reproducible way. The original 64
C code (Windows only) was provided by Jane Jing Liang, while GNU/Linux
comments were made by Janez Brest. This package was gently authorised
for publication on CRAN by Ponnuthurai Nagaratnam Suganthan. The of-
ficial documentation is available at http://www.ntu.edu.sg/home/EPNSugan/
index_files/CEC2013/CEC2013.htm. Bugs reports/comments/questions are
very welcomed (in English, Spanish or Italian). / GPL-3


Name Version
r-cellranger 1.1.0 Helper functions to work with spreadsheets and the A1:D10 style of cell range linux-
specification. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-cengam 0.5.3 Implementation of Tobit type I and type II families for censored regres- noarch
sion using the ‘mgcv’ package, based on methods detailed in Woods (2016)
<doi:10.1080/01621459.2016.1180986>. / GPL-2
r-censcov 1.0_0 Implementations of threshold regression approaches for linear regression mod- noarch
els with a covariate subject to random censoring, including deletion threshold
regression and completion threshold regression. Reverse survival regression,
which flip the role of response variable and the covariate, is also considered. /
GPL-3
r-censnid 0_0_1Implements AS138, AS139. / GPL-2 linux-
64,
osx-
64,
win-
64
r-censorcopula 2.0 Implement an interval censor method to break ties when using data with ties noarch
to fitting a bivariate copula. / GPL-2
r-censregmod 1.0 Fits univariate censored linear regression model under Normal or Student-t noarch
distribution / GPL (>= 3.0)
r-census2016 0.2.0 Contains selected variables from the time series profiles for statistical areas noarch
level 2 from the 2006, 2011, and 2016 censuses of population and housing,
Australia. Also provides methods for viewing the questions asked for conve-
nience during analysis. / CC BY 4.0
r-censusapi 0.6.0 A wrapper for the U.S. Census Bureau APIs that returns data frames of Census noarch
data and metadata. Available datasets include the Decennial Census, American
Community Survey, Small Area Health Insurance Estimates, Small Area In-
come and Poverty Estimates, Population Estimates and Projections, and more.
/ GPL-3
r-censys 0.1.0 The ‘Censys’ public search engine enables researchers to quickly ask questions noarch
about the hosts and networks that compose the Internet. Details on how ‘Cen-
sys’ was designed and how it is operated are available at <https://www.censys.
io/about>. Both basic and extended research access queries are made avail-
able. More information on the SQL dialect used by the ‘Censys’ engine can
be found at <https://cloud.google.com/bigquery/docs/reference/legacy-sql>. /
AGPL-3
r-centiserve 1.0.0 Calculates centrality indices additional to the ‘igraph’ package centrality func- noarch
tions. / GPL-2


Name Version
r-cents 0.1_41Fit censored time series / GPL-2 linux-
64,
osx-
64,
win-
64
r-cepreader 1.1_3 Read Condensed Cornell Ecology Program (‘CEP’) and legacy ‘CANOCO’ linux-
files into R data frames. / MIT 64,
osx-64
r- 1.1.9 Implements the iterated RMCD method of Cerioli (2010) for multivariate noarch
ceriolioutlierdetection outlier detection via robust Mahalanobis distances. Also provides the finite-
sample RMCD method discussed in the paper, as well as the methods provided
in Hardin and Rocke (2005) <doi:10.1198/106186005X77685> and Green and
Martin (2017). / GPL-2
r-cernaseek 2.1 Provides several functions to identify and analyse miRNA sponge, includ- noarch
ing popular methods for identifying miRNA sponge interactions, two types of
global ceRNA regulation prediction methods and four types of context-specific
prediction methods( Li Y et al.(2017) <doi:10.1093/bib/bbx137>), which are
based on miRNA-messenger RNA regulation alone, or by integrating hetero-
geneous data, respectively. In addition, For predictive ceRNA relationship
pairs, this package provides several downstream analysis algorithms, includ-
ing regulatory network analysis and functional annotation analysis, as well
as survival prognosis analysis based on expression of ceRNA ternary pair. /
GPL-3
r-cernn 0.1 An implementation of the covariance estimation method proposed in Chi and noarch
Lange (2014), Stable estimation of a covariance matrix guided by nuclear
norm penalties, Computational Statistics and Data Analysis 80:117-128. / MIT
r-cetcolor 0.2.0 Collection of perceptually uniform colour maps made by Peter Kovesi (2015) noarch
Good Colour Maps: How to Design Them <arXiv:1509.03700> at the Centre
for Exploration Targeting (CET). / CC BY-SA 4.0
r-cfa 0.10_0Analysis of configuration frequencies for simple and repeated measures, linux-
multiple-samples CFA, hierarchical CFA, bootstrap CFA, functional CFA, 64,
Kieser-Victor CFA, and Lindner’s test using a conventional and an accelerated osx-
algorithm. / GPL-2 64,
win-
64
r-cfc 1.1.2 Numerical integration of cause-specific survival curves to arrive at cause- linux-
specific cumulative incidence functions, with three usage modes: 1) Conve- 64,
nient API for parametric survival regression followed by competing-risk anal- osx-
ysis, 2) API for CFC, accepting user-specified survival functions in R, and 3) 64,
Same as 2, but accepting survival functions in C. / GPL-2 win-
64
r- 1.0 Estimate quantiles using formula (18) from http://www.jaschke-net.de/papers/ noarch
cfestimatequantiles CoFi.pdf (Yaschke; 2001) / GPL-2
r-cfma 1.0 Performs causal functional mediation analysis (CFMA) for functional treat- noarch
ment, functional mediator, and functional outcome. This package includes
two functional mediation model types: (1) a concurrent mediation model and
(2) a historical influence mediation model. See Zhao et al. (2018), Functional
Mediation Analysis with an Application to Functional Magnetic Resonance
Imaging Data, <arXiv:1805.06923> for details. / GPL-2


Name Version
r-cgauc 1.2.1 The cgAUC can calculate the AUC-type measure of Obuchowski(2006) when linux-
gold standard is continuous, and find the optimal linear combination of vari- 64,
ables with respect to this measure. / GPL-2 osx-
64,
win-
64
r-cgdsr 1.3.0 Provides a basic set of R functions for querying the Cancer Genomics Data noarch
Server (CGDS), hosted by the Computational Biology Center at Memorial-
Sloan-Kettering Cancer Center (MSKCC) at <www.cbioportal.org>. / LGPL-
3
r-cge 0.1.9 Developing general equilibrium models, computing general equilibrium and noarch
simulating economic dynamics with structural dynamic models in LI (2019,
ISBN: 9787521804225) General Equilibrium and Structural Dynamics: Per-
spectives of New Structural Economics. Beijing: Economic Science Press. /
GPL-2 | GPL-3
r-cggp 1.0.1 Run computer experiments using the adaptive composite grid algorithm with linux-
a Gaussian process model. The algorithm works best when running an ex- 64,
periment that can evaluate thousands of points from a deterministic computer osx-
simulation. This package is an implementation of a forthcoming paper by 64,
Plumlee, Erickson, Ankenman, et al. For a preprint of the paper, contact the win-
maintainer of this package. / GPL-3 64
r-cgh 1.0_7.1
Functions to analyze microarray comparative genome hybridization data using linux-
the Smith-Waterman algorithm / GPL-2 64,
osx-
64,
win-
64
r-cglasso 1.1.1 The l1-penalized censored Gaussian graphical model is an extension of the linux-
graphical lasso estimator developed to handle datasets with censored observa- 64,
tions. An EM-like algorithm is implemented to estimate the parameters of the osx-
censored Gaussian graphical models. / GPL-2 64,
win-
64
r-cgp 2.1_1 Fit composite Gaussian process (CGP) models as described in Ba and Joseph noarch
(2012) Composite Gaussian Process Models for Emulating Expensive Func-
tions, Annals of Applied Statistics. The CGP model is capable of approximat-
ing complex surfaces that are not second-order stationary. Important functions
in this package are CGP, print.CGP, summary.CGP, predict.CGP and plotCGP.
/ LGPL-2.1
r-cgraph 4.0.3 Allows to create, evaluate, and differentiate computational graphs in R. A linux-
computational graph is a graph representation of a multivariate function de- 64,
composed by its (elementary) operations. Nodes in the graph represent arrays osx-
while edges represent dependencies among the arrays. An advantage of ex- 64,
pressing a function as a computational graph is that this enables to differentiate win-
the function by automatic differentiation. The ‘cgraph’ package supports vari- 64
ous operations including basic arithmetic, trigonometry operations, and linear
algebra operations. It differentiates computational graphs by reverse automatic
differentiation. The flexible architecture of the package makes it applicable to
solve a variety of problems including local sensitivity analysis, gradient-based
optimization, and machine learning. / Apache License 2.0


Name Version
r-cgwtools 3.0.1 Functions for performing quick observations or evaluations of data, includ- noarch
ing a variety of ways to list objects by size, class, etc. In addition, func-
tions which mimic Unix shell commands, including ‘head’, ‘tail’ ,’pushd’ ,and
‘popd’. The functions ‘seqle’ and ‘reverse.seqle’ mimic the base ‘rle’ but can
search for linear sequences. The function ‘splatnd’ allows the user to gener-
ate zero-argument commands without the need for ‘makeActiveBinding’ . /
LGPL-3
r-chandwich 1.1.2 Performs adjustments of a user-supplied independence loglikelihood noarch
function using a robust sandwich estimator of the parameter covari-
ance matrix, based on the methodology in Chandler and Bate (2007)
<doi:10.1093/biomet/asm015>. This can be used for cluster correlated data
when interest lies in the parameters of the marginal distributions or for per-
forming inferences that are robust to certain types of model misspecification.
Functions for profiling the adjusted loglikelihoods are also provided, as are
functions for calculating and plotting confidence intervals, for single model
parameters, and confidence regions, for pairs of model parameters. Nested
models can be compared using an adjusted likelihood ratio test. / GPL-2
r-changepoint 2.2.2 Implements various mainstream and specialised changepoint methods for linux-
finding single and multiple changepoints within data. Many popular non- 64,
parametric and frequentist methods are included. The cpt.mean(), cpt.var(), osx-
cpt.meanvar() functions should be your first point of call. / GPL-3 64,
win-
64
r- 0.3.1 This implements the methods developed in, L. Bybee and Y. Atchade. (2018). linux-
changepointshd Contains a series of methods for estimating change-points given user speci- 64,
fied black-box models. The methods include binary segmentation for multi- osx-
ple change-point estimation. For estimating each individual change-point the 64,
package includes simulated annealing, brute force, and, for Gaussian graphical win-
models, an applications specific rank-one update implementation. Addition- 64
ally, code for estimating Gaussian graphical models is included. The goal of
this package is to allow for the efficient estimation of change-points in com-
plicated models with high dimensional data. / GPL-2
r- 0.1.0 Detection of change-points for variance of heteroscedastic Gaussian vari- noarch
changepointsvar ables with piecewise constant variance function. Adelfio, G. (2012),
Change-point detection for variance piecewise constant models, Com-
munications in Statistics, Simulation and Computation, 41:4, 437-448,
<doi:10.1080/03610918.2011.592248>. / GPL-2
r- 1.0 A multiple testing procedure for clustered alternative hypotheses. It is assumed noarch
changepointtesting that the p-values under the null hypotheses follow U(0,1) and that the distri-
butions of p-values from the alternative hypotheses are stochastically smaller
than U(0,1). By aggregating information, this method is more sensitive to
detecting signals of low magnitude than standard methods. Additionally, spo-
radic small p-values appearing within a null hypotheses sequence are avoided
by averaging on the neighboring p-values. / GPL-2


Name Version
r- 1.16 Advertisers use a variety of online marketing channels to reach consumers and linux-
channelattribution they want to know the degree each channel contributes to their marketing suc- 64,
cess. This is called the online multi-channel attribution problem. This pack- osx-
age contains a probabilistic algorithm for the attribution problem. The model 64,
uses a k-order Markov representation to identify structural correlations in the win-
customer journey data. The package also contains three heuristic algorithms 64
(first-touch, last-touch and linear-touch approach) for the same problem. The
algorithms are implemented in C. / GPL-2
r-chaos01 1.2.1 Computes and visualize the results of the 0-1 test for chaos proposed by linux-
Gottwald and Melbourne (2004) <DOI:10.1137/080718851>. The algorithm 64,
is available in parallel for the independent values of parameter c. Additionally, osx-
fast RQA is added to distinguish chaos from noise. / GPL-3 64,
win-
64
r-chargetransport 1.0.2 This package provides functions to compute Marcus, Marcus-Levich-Jortner linux-
or Landau-Zener charge transfer rates. These rates can then be used to per- 64,
form kinetic Monte Carlo simulations to estimate charge carrier mobilities in osx-
molecular materials. The preparation of this package was supported by the the 64,
Fondazione Cariplo (PLENOS project, ref. 2011-0349). / GPL-3 win-
64
r-chcn 1.5 A compilation of historical through contemporary climate measurements noarch
scraped from the Environment Canada Website Including tools for scraping
data, creating metadata and formating temperature files. / GPL-2
r-cheb 0.3 Discrete Linear Chebyshev Approximation / GPL-3 linux-
64,
osx-
64,
win-
64
r-checkarg 0.1.0 Utility functions that allow checking the basic validity of a function argument noarch
or any other value, including generating an error and assigning a default in a
single line of code. The main purpose of the package is to provide simple and
easily readable argument checking to improve code robustness. / GPL-2
r-checkdigit 0.1_1 A set of functions to calculate check digits according to various algorithms and noarch
to verify whether a string ends in a valid check digit / GPL-3
r-checkmate 1.9.1 Tests and assertions to perform frequent argument checks. A substantial part linux-
of the package was written in C to minimize any worries about execution time 32,
overhead. / BSD_3_clause file LICENSE linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
r-checkpoint 0.4.6 The goal of checkpoint is to solve the problem of package reproducibility linux-
in R. Specifically, checkpoint allows you to install packages as they existed 64,
on CRAN on a specific snapshot date as if you had a CRAN time machine. noarch,
To achieve reproducibility, the checkpoint() function installs the packages re- osx-
quired or called by your project and scripts to a local library exactly as they 64,
existed at the specified point in time. Only those packages are available to win-
your project, thereby avoiding any package updates that came later and may 64
have altered your results. In this way, anyone using checkpoint’s checkpoint()
can ensure the reproducibility of your scripts or projects at any time. To
create the snapshot archives, once a day (at midnight UTC) Microsoft re-
freshes the Austria CRAN mirror on the Microsoft R Archived Network server
(<https://mran.microsoft.com/>). Immediately after completion of the rsync
mirror process, the process takes a snapshot, thus creating the archive. Snap-
shot archives exist starting from 2014-09-17. / GPL-2
r-cheddar 0.1_633
Provides a flexible, extendable representation of an ecological community and linux-
a range of functions for analysis and visualisation, focusing on food web, body 64,
mass and numerical abundance data. Allows inter-web comparisons such as osx-
examining changes in community structure over environmental, temporal or 64,
spatial gradients. / BSD_2_clause win-
64
r-chemcal 0.2.1 Simple functions for plotting linear calibration functions and estimating stan- noarch
dard errors for measurements according to the Handbook of Chemometrics
and Qualimetrics: Part A by Massart et al. There are also functions estimating
the limit of detection (LOD) and limit of quantification (LOQ). The functions
work on model objects from - optionally weighted - linear regression (lm) or
robust linear regression (‘rlm’ from the ‘MASS’ package). / GPL-2
r- 0.1.13Functions and scripts used in the book Chemometrics with R - Multivariate noarch
chemometricswithr Data Analysis in the Natural Sciences and Life Sciences by Ron Wehrens,
Springer (2011). Data used in the package are available from github. / GPL-2
r-chemospec 5.1.48A collection of functions for top-down exploratory data analysis of spectral noarch
data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-
ray fluorescence (XRF) and other similar types of spectroscopy. Includes func-
tions for plotting and inspecting spectra, peak alignment, hierarchical cluster
analysis (HCA), principal components analysis (PCA) and model-based clus-
tering. Robust methods appropriate for this type of high-dimensional data
are available. ChemoSpec is designed for structured experiments, such as
metabolomics investigations, where the samples fall into treatment and con-
trol groups. Graphical output is formatted consistently for publication quality
plots. ChemoSpec is intended to be very user friendly and to help you get
usable results quickly. A vignette covering typical operations is available. /
GPL-3


Name Version
r-chemospec2d 0.3.166
A collection of functions for exploratory chemometrics of 2D spectroscopic noarch
data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear
single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra.
‘ChemoSpec2D’ deploys methods aimed primarily at classification of sam-
ples and the identification of spectral features which are important in distin-
guishing samples from each other. Each 2D spectrum (a matrix) is treated
as the unit of observation, and thus the physical sample in the spectrometer
corresponds to the sample from a statistical perspective. In addition to chemo-
metric tools, a few tools are provided for plotting 2D spectra, but these are not
intended to replace the functionality typically available on the spectrometer.
‘ChemoSpec2D’ takes many of its cues from ‘ChemoSpec’ and tries to create
consistent graphical output and to be very user friendly. / GPL-3
r-chemospecutils 0.3.39Functions supporting the common needs of packages ‘ChemoSpec’ and noarch
‘ChemoSpec2D’. / GPL-3
r-cherry 0.6_12Provides an alternative approach to multiple testing by calculating a simulta- noarch
neous upper confidence bounds for the number of true null hypotheses among
any subset of the hypotheses of interest, using the methods of Goeman and
Solari (2011) <doi:10.1214/11-STS356>. / GPL-2
r-chff 0.1.0 The software matches the current history to the closest history in a time series noarch
to build a forecast. / GPL-3
r-chi 0.1 Light weight implementation of the standard distribution functions for the chi noarch
distribution, wrapping those for the chi-squared distribution in the stats pack-
age. / GPL-2
r-chi2x3way 1.1 Provides two index partitions for three-way contingency tables: partition of the noarch
association measure chi-squared and of the predictability index tau under sev-
eral representative hypotheses about the expected frequencies (hypothesized
probabilities). / GPL (> 2)
r-chillmodels 1.0.0 Calculates the chilling and heat accumulation for studies of the temper- noarch
ate fruit trees. The models in this package are: Utah (Richardson et al.,
1974, ISSN:0018-5345), Positive Chill Units - PCU (Linsley-Noaks et al.,
1995, ISSN:1017-0316), GDH-A - Growing Degree Hours by Anderson et
al.(1986, ISSN:0567-7572), GDH-R - Growing Degree Hours by Richard-
son et al.(1975, ISSN:0018-5345), North Carolina (Shaltout e Unrath, 1983,
ISSN:0003-1062), Landsberg Model (Landsberg, 1974, ISSN:0305-7364),
Q10 Model (Bidabe, 1967, ISSN:0031-9368), Jones Model (Jones et al.,
2013 <DOI:10.1111/j.1438-8677.2012.00590.x>), Low-Chill Model (Gilreath
and Buchanan, 1981, ISSN:0003-1062), Model for Cherry Sweetheart (Guak
and Nielsen, 2013 <DOI:10.1007/s13580-013-0140-9>), Model for apple
Gala (Guak and Nielsen, 2013 <DOI:10.1007/s13580-013-0140-9>), Taiwan
Model (Lu et al., 2012 <DOI:10.17660/ActaHortic.2012.962.35>), Dynamic
Model (Fishman et al., 1987, ISSN:0022-5193) adapted from the function
Dynamic_Model() of the ‘chillR’ package (Luedeling, 2018), Unified Model
(Chuine et al., 2016 <DOI:10.1111/gcb.13383>) and Heat Restriction model.
/ GPL-3
r-chiptest 1.0 Nonparametric Tests to identify the differential enrichment region for two con- linux-
ditions or time-course ChIP-seq data. It includes: data preprocessing func- 64,
tion, estimation of a small constant used in hypothesis testing, a kernel-based osx-
two sample nonparametric test, two assumption-free two sample nonparamet- 64,
ric test. / GPL (>= 2.15.1) win-
64


Name Version
r-chnosz 1.3.3 An integrated set of tools for thermodynamic calculations in aqueous geo- linux-
chemistry and geobiochemistry. Functions are provided for writing balanced 64,
reactions to form species from user-selected basis species and for calculating osx-
the standard molal properties of species and reactions, including the standard 64,
Gibbs energy and equilibrium constant. Calculations of the non-equilibrium win-
chemical affinity and equilibrium chemical activity of species can be portrayed 64
on diagrams as a function of temperature, pressure, or activity of basis species;
in two dimensions, this gives a maximum affinity or predominance diagram.
The diagrams have formatted chemical formulas and axis labels, and water sta-
bility limits can be added to Eh-pH, oxygen fugacity- temperature, and other
diagrams with a redox variable. The package has been developed to handle
common calculations in aqueous geochemistry, such as solubility due to com-
plexation of metal ions, mineral buffers of redox or pH, and changing the basis
species across a diagram (mosaic diagrams). CHNOSZ also has unique ca-
pabilities for comparing the compositional and thermodynamic properties of
different proteins. / GPL-2
r-choicedes 0.9_3 Design functions for DCMs and other types of choice studies (including noarch
MaxDiff and other tradeoffs). / GPL-2
r-choicemodelr 1.2 Implements an MCMC algorithm to estimate a hierarchical multinomial logit noarch
model with a normal heterogeneity distribution. The algorithm uses a hybrid
Gibbs Sampler with a random walk metropolis step for the MNL coefficients
for each unit. Dependent variable may be discrete or continuous. Independent
variables may be discrete or continuous with optional order constraints. Means
of the distribution of heterogeneity can optionally be modeled as a linear func-
tion of unit characteristics variables. / GPL-3
r-cholwishart 1.0.1 Sampling from the Cholesky factorization of a Wishart random variable, sam- linux-
pling from the inverse Wishart distribution, sampling from the Cholesky fac- 64,
torization of an inverse Wishart random variable, sampling from the pseudo osx-
Wishart distribution, sampling from the generalized inverse Wishart distribu- 64,
tion, computing densities for the Wishart and inverse Wishart distributions, win-
and computing the multivariate gamma and digamma functions. / GPL-3 64
r-choplump 1.0_0.4
Choplump Tests are Permutation Tests for Comparing Two Groups with Some noarch
Positive but Many Zero Responses / GPL-3
r-chopthin 0.2.2 Resampling is a standard step in particle filtering and in sequential Monte linux-
Carlo. This package implements the chopthin resampler, which keeps a bound 64,
on the ratio between the largest and the smallest weights after resampling. / osx-
GPL-3 64,
win-
64
r-chor 0.0_4 Learning the structure of graphical models from datasets with thousands of noarch
variables. More information about the research papers detailing the the-
ory behind Chordalysis is available at <http://www.francois-petitjean.com/
Research> (KDD 2016, SDM 2015, ICDM 2014, ICDM 2013). The R pack-
age development site is <https://github.com/HerrmannM/Monash-ChoR>. /
GPL-3
r-chords 0.95.4Maximum likelihood estimation in respondent driven samples. / GPL-2 noarch
r- 1.0.1 Contains 3 maps. 1) US States 2) US Counties 3) Countries of the world. / noarch
choroplethrmaps BSD_3_clause


Name Version
r-chromomap 0.2 Provides interactive, configurable and elegant graphics visualization of the noarch
chromosomes or chromosome regions of any living organism allowing users
to map chromosome elements (like genes, SNPs etc.) on the chromosome
plot. It introduces a special plot viz. the chromosome heatmap that, in ad-
dition to mapping elements, can visualize the data associated with chromo-
some elements (like gene expression) in the form of heat colors which can be
highly advantageous in the scientific interpretations and research work. Be-
cause of the large size of the chromosomes, it is impractical to visualize each
element on the same plot. However, the plot provides a magnified view for
each of chromosome locus to render additional information and visualization
specific for that location. You can map thousands of genes and can view all
mappings easily. Users can investigate the detailed information about the map-
pings (like gene names or total genes mapped on a location) or can view the
magnified single or double stranded view of the chromosome at a location
showing each mapped element in sequential order. The package provide mul-
tiple features like visualizing multiple sets, chromosome heat-maps, group an-
notations, adding hyperlinks, and labelling. The plots can be saved as HTML
documents that can be customized and shared easily. In addition, you can
include them in R Markdown or in R ‘Shiny’ applications. / GPL-3
r-chron 2.3_53Provides chronological objects which can handle dates and times. / GPL-2 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-chunkr 1.1.1 Read tables chunk by chunk using a C backend and a simple R interface. / linux-
GPL-2 64,
osx-
64,
win-
64
r- 1.3 Calculation of consensus values for atomic weights, isotope amount ratios, noarch
ciaawconsensus and isotopic abundances with the associated uncertainties using multivariate
meta-regression approach for consensus building. / Unlimited


r-ciee 0.1.1 In many studies across different disciplines, detailed measures of the variables noarch
of interest are available. If assumptions can be made regarding the direc-
tion of effects between the assessed variables, this has to be considered in
the analysis. The functions in this package implement the novel approach
CIEE (causal inference using estimating equations; Konigorski et al., 2018,
<DOI:10.1002/gepi.22107>) for estimating and testing the direct effect of an
exposure variable on a primary outcome, while adjusting for indirect effects
of the exposure on the primary outcome through a secondary intermediate
outcome and potential factors influencing the secondary outcome. The un-
derlying directed acyclic graph (DAG) of this considered model is described
in the vignette. CIEE can be applied to studies in many different fields, and
it is implemented here for the analysis of a continuous primary outcome and
a time-to-event primary outcome subject to censoring. CIEE uses estimating
equations to obtain estimates of the direct effect and robust sandwich standard
error estimates. Then, a large-sample Wald-type test statistic is computed for
testing the absence of the direct effect. Additionally, standard multiple regres-
sion, regression of residuals, and the structural equation modeling approach
are implemented for comparison. / GPL-2
r-cifsmry 1.0.1.1Estimate of cumulative incidence function in two samples. Provide weighted linux-
summary statistics based on various methods and weights. / GPL-2 64,
osx-
64,
win-
64
r-cim 1.0.0 Produces statistical indicators of the impact of migration on the socio- noarch
demographic composition of an area. Three measures can be used: ratios,
percentages and the Duncan index of dissimilarity. The input data files are
assumed to be in an origin-destination matrix format, with each cell repre-
senting a flow count between an origin and a destination area. Columns are
expected to represent origins, and rows are expected to represent destinations.
The first row and column are assumed to contain labels for each area. See
Rodriguez-Vignoli and Rowe (2018) <doi:10.1080/00324728.2017.1416155>
for technical details. / GPL-2
r-cin 0.1 Many experiments in neuroscience involve randomized and fast stimulation noarch
while the continuous outcome measures respond at much slower time scale,
for example event-related fMRI. This package provide valid statistical tools
with causal interpretation under these challenging settings, without imposing
model assumptions. / GPL-2
r-cinid 1.2 This package provides functions to compute a method for identifying the instar noarch
of Curculionid larvae from the observed distribution of the headcapsule size
of mature larvae. / GPL (>= 2.0)
r-cinterpolate 1.0.0 Simple interpolation methods designed to be used from C code. Supports con- linux-
stant, linear and spline interpolation. An R wrapper is included but this pack- 64,
age is primarily designed to be used from C code using ‘LinkingTo’. The osx-
spline calculations are classical cubic interpolation, e.g., Forsythe, Malcolm 64,
and Moler (1977) <ISBN: 9780131653320>. / MIT win-
64


Name Version
r-ciplot 1.0 Plot confidence interval from the objects of statistical tests such as t.test(), noarch
var.test(), cor.test(), prop.test() and fisher.test() (‘htest’ class), Tukey test
[TukeyHSD()], Dunnett test [glht() in ‘multcomp’ package], logistic regres-
sion [glm()], and Tukey or Games-Howell test [posthocTGH() in ‘user-
friendlyscience’ package]. Users are able to set the styles of lines and points.
This package contains the function to calculate odds ratios and their confidence
intervals from the result of logistic regression. / GPL-2
r-cir 2.0.0 Isotonic regression (IR), as well as a great small-sample improvement to IR noarch
called CIR, interval estimates for both, and additional utilities. / GPL-2
r-circmle 0.2.1 A series of wrapper functions to implement the 10 maximum likelihood noarch
models of animal orientation described by Schnute and Groot (1992)
<DOI:10.1016/S0003-3472(05)80068-5>. The functions also include the abil-
ity to use different optimizer methods and calculate various model selection
metrics (i.e., AIC, AICc, BIC). / GPL-2
r-circnntsr 2.2 Includes functions for the analysis of circular data using distributions based on noarch
Nonnegative Trigonometric Sums (NNTS). The package includes functions
for calculation of densities and distributions, for the estimation of parameters,
for plotting and more. / GPL-2
r-circoutlier 3.2.3 Detection of outliers in circular-circular regression models, modifying its and noarch
estimating of models parameters. / GPL-2
r-circstats 0.2_6 Circular Statistics, from Topics in Circular Statistics (2001) S. Rao Jammala- noarch
madaka and A. SenGupta, World Scientific. / GPL-2
r-circular 0.4_93Circular Statistics, from Topics in circular Statistics (2001) S. Rao Jammala-linux-
madaka and A. SenGupta, World Scientific. / GPL-2 64,
osx-
64,
win-
64
r-circularddm 0.1.0 Circular drift-diffusion model for continuous reports. / GPL-2 linux-
64,
osx-
64,
win-
64
r-cirt 1.3.0 Jointly model the accuracy of cognitive responses and item choices within linux-
a bayesian hierarchical framework as described by Culpepper and Balamuta 64,
(2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package contains osx-
the datasets used within the analysis of the paper. / GPL-2 64,
win-
64


Name Version
r-cit 2.2 A likelihood-based hypothesis testing approach is implemented for assessing linux-
causal mediation. For example, it could be used to test for mediation of a 64,
known causal association between a DNA variant, the ‘instrumental variable’, osx-
and a clinical outcome or phenotype by gene expression or DNA methylation, 64,
the potential mediator. Another example would be testing mediation of the win-
effect of a drug on a clinical outcome by the molecular target. The hypothe- 64
sis test generates a p-value or permutation-based FDR value with confidence
intervals to quantify uncertainty in the causal inference. The outcome can be
represented by either a continuous or binary variable, the potential mediator
is continuous, and the instrumental variable can be continuous or binary and
is not limited to a single variable but may be a design matrix representing
multiple variables. / Artistic-2.0
r-citbcmst 1.0.4 This package implements the approach to assign tumor gene expression dataset noarch
to the 6 CIT Breast Cancer Molecular Subtypes described in Guedj et al 2012.
/ GPL-2
r-citccmst 1.0.2 This package implements the approach to assign tumor gene expression dataset noarch
to the 6 CIT Colon Cancer Molecular Subtypes described in Marisa et al 2013.
/ GPL-2
r-cityplot 2.0 Input: a csv-file for each database table and a controlfile describing relations noarch
between tables. Output: An extended ER diagram / LGPL-3
r-cklrt 0.2.3 Composite Kernel Machine Regression based on Likelihood Ratio Test linux-
(CKLRT): in this package, we develop a kernel machine regression frame- 64,
work to model the overall genetic effect of a SNP-set, considering the possible osx-
GE interaction. Specifically, we use a composite kernel to specify the overall 64,
genetic effect via a nonparametric function and we model additional covariates win-
parametrically within the regression framework. The composite kernel is con- 64
structed as a weighted average of two kernels, one corresponding to the genetic
main effect and one corresponding to the GE interaction effect. We propose
a likelihood ratio test (LRT) and a restricted likelihood ratio test (RLRT) for
statistical significance. We derive a Monte Carlo approach for the finite sam-
ple distributions of LRT and RLRT statistics. (N. Zhao, H. Zhang, J. Clark, A.
Maity, M. Wu. Composite Kernel Machine Regression based on Likelihood
Ratio Test with Application for Combined Genetic and Gene-environment In-
teraction Effect (Submitted).) / GPL-3
r-ckmeans.1d.dp 4.2.2 Fast optimal univariate clustering and segementation by dynamic program- linux-
ming. Three types of problem including univariate k-means, k-median, and 64,
k-segments are solved with guaranteed optimality and reproducibility. The osx-
core algorithm minimizes the sum of within-cluster distances using respec- 64,
tive metrics. Its advantage over heuristic clustering algorithms in efficiency win-
and accuracy is increasingly pronounced as the number of clusters k increases. 64
Weighted k-means and unweighted k-segments algorithms can also optimally
segment time series and perform peak calling. An auxiliary function generates
histograms that are adaptive to patterns in data. In contrast to heuristic meth-
ods, this package provides a powerful set of tools for univariate data analysis
with guaranteed optimality. Use four spaces when indenting paragraphs within
the Description. / LGPL-3
r-cla 0.95_1Implements ‘Markovitz’ Critical Line Algorithm (‘CLA’) for clas- noarch
sical mean-variance portfolio optimization, see Markovitz (1952)
<doi:10.2307/2975974>. Care has been taken for correctness in light of
previous buggy implementations. / GPL-3


Name Version
r-cladorcpp 0.15.1Various cladogenesis-related calculations that are slow in pure R are imple- linux-
mented in C with Rcpp. These include the calculation of the probability of var- 64,
ious scenarios for the inheritance of geographic range at the divergence events osx-
on a phylogenetic tree, and other calculations necessary for models which are 64,
not continuous-time markov chains (CTMC), but where change instead occurs win-
instantaneously at speciation events. Typically these models must assess the 64
probability of every possible combination of (ancestor state, left descendent
state, right descendent state). This means that there are up to (# of states)^3
combinations to investigate, and in biogeographical models, there can easily
be hundreds of states, so calculation time becomes an issue. C implementation
plus clever tricks (many combinations can be eliminated a priori) can greatly
speed the computation time over naive R implementations. CITATION INFO:
This package is the result of my Ph.D. research, please cite the package if you
use it! Type: citation(package=cladoRcpp) to get the citation information. /
GPL-2
r-clam 2.3.2 Performs ‘classical’ age-depth modelling of dated sediment deposits - prior noarch
to applying more sophisticated techniques such as Bayesian age-depth mod-
elling. Any radiocarbon dated depths are calibrated. Age-depth models
are constructed by sampling repeatedly from the dated levels, each time
drawing age-depth curves. Model types include linear interpolation, lin-
ear or polynomial regression, and a range of splines. See Blaauw (2010).
<doi:10.1016/j.quageo.2010.01.002>. / GPL-2
r-clamr 2.1_1 Implementation of the Wilkinson and Ivany (2002) approach to paleoclimate noarch
analysis, applied to isotope data extracted from clams. / GPL-3
r-clarifai 0.4.2 Get description of images from Clarifai API. For more information, see <http: noarch
//clarifai.com>. Clarifai uses a large deep learning cloud to come up with
descriptive labels of the things in an image. It also provides how confident it
is about each of the labels. / MIT
r-class 7.3_15Various functions for classification, including k-nearest neighbour, Learning linux-
Vector Quantization and Self-Organizing Maps. / GPL-2 | GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-classifly 0.4 Given $p$-dimensional training data containing $d$ groups (the design space), noarch
a classification algorithm (classifier) predicts which group new data belongs to.
Generally the input to these algorithms is high dimensional, and the boundaries
between groups will be high dimensional and perhaps curvilinear or multi-
faceted. This package implements methods for understanding the division of
space between the groups. / MIT


Name Version
r-classint 0.3_1 Selected commonly used methods for choosing univariate class intervals for linux-
mapping or other graphics purposes. / GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-cld2 1.2 Bindings to Google’s C library Compact Language Detector 2 (see <https: linux-
//github.com/cld2owners/cld2#readme> for more information). Probabilisti- 64,
cally detects over 80 languages in plain text or HTML. For mixed-language osx-
input it returns the top three detected languages and their approximate propor- 64,
tion of the total classified text bytes (e.g. 80% English and 20% French out win-
of 1000 bytes). There is also a ‘cld3’ package on CRAN which uses a neural 64
network model instead. / Apache License 2.0
r-cld3 1.2 Google’s Compact Language Detector 3 is a neural network model for lan- linux-
guage identification and the successor of ‘cld2’ (available from CRAN). The 64,
algorithm is still experimental and takes a novel approach to language de- osx-
tection with different properties and outcomes. It can be useful to combine 64,
this with the Bayesian classifier results from ‘cld2’. See <https://github.com/ win-
google/cld3#readme> for more information. / Apache License 2.0 64
r-cleancall 0.1.0 Wrapper of .Call() that runs exit handlers to clean up C resources. Helps man- linux-
aging C (non-R) resources while using the R API. / MIT 64,
osx-
64,
win-
64
r-cleandata 0.3.0 Functions to work with data frames to prepare data for further analysis. The noarch
functions for imputation, encoding, partitioning, and other manipulation can
produce log files to keep track of process. / MIT
r-cleanerr 0.1.1 How to deal with missing data?Based on the concept of almost functional de- noarch
pendencies, a method is proposed to fill missing data, as well as help you see
what data is missing. The user can specify a measure of error and how many
combinations he wish to test the dependencies against, the closer to the length
of the dataset, the more precise. But the higher the number, the more time it
will take for the process to finish. If the program cannot predict with the accu-
racy determined by the user it shall not fill the data, the user then can choose
to increase the error or deal with the data another way. / MIT
r-cleanr 1.2.0 Check your R code for some of the most common layout flaws. Many tried to noarch
teach us how to write code less dreadful, be it implicitly as B. W. Kernighan
and D. M. Ritchie (1988) <ISBN:0-13-110362-8> in ‘The C Programming
Language’ did, be it explicitly as R.C. Martin (2008) <ISBN:0-13-235088-2>
in ‘Clean Code: A Handbook of Agile Software Craftsmanship’ did. So we
should check our code for files too long or wide, functions with too many lines,
too wide lines, too many arguments or too many levels of nesting. Note: This
is not a static code analyzer like pylint or the like. Checkout <https://cran.r-
project.org/package=lintr> instead. / BSD_2_clause


Name Version
r-cli 1.1.0 A suite of tools designed to build attractive command line interfaces (‘CLIs’). linux-
Includes tools for drawing rules, boxes, trees, and ‘Unicode’ symbols with 32,
‘ASCII’ alternatives. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-clickclust 1.1.5 Clustering categorical sequences by means of finite mixtures with Markov linux-
model components is the main utility of ClickClust. The package also allows 64,
detecting blocks of equivalent states by forward and backward state selection osx-
procedures. / GPL-2 64,
win-
64
r-clickclustcont 0.1.7 Provides an expectation maximization (EM) algorithm to fit a mixture of con- noarch
tinuous time Markov models for use with clickstream or other sequence type
data. Gallaugher, M.P.B and McNicholas, P.D. (2018) <arXiv:1802.04849>. /
GPL-2
r-clikcorr 1.0 A profile likelihood based method of estimation and inference on the correla- noarch
tion coefficient of bivariate data with different types of censoring and missing-
ness. / GPL-2
r-climatestability 0.1.1 Climate stability measures are not formalized in the literature and tools for noarch
generating stability metrics from existing data are nascent. This package pro-
vides tools for calculating climate stability from raster data encapsulating cli-
mate change as a series of time slices. The methods follow Owens and Gural-
nick. Submitted, Biodiversity Informatics. / GPL-3
r-clime 0.4.1 A robust constrained L1 minimization method for estimating a large sparse noarch
inverse covariance matrix (aka precision matrix), and recovering its support
for building graphical models. The computation uses linear programming. /
GPL-2
r-clinfun 1.0.15Utilities to make your clinical collaborations easier if not fun. It contains func- linux-
tions for designing studies such as Simon 2-stage and group sequential designs 64,
and for data analysis such as Jonckheere-Terpstra test and estimating survival osx-
quantiles. / GPL-2 64,
win-
64
r- 1.1.1 Provides estimates of several summary measures for clinical trials including linux-
clinicaltrialsummary the average hazard ratio, the weighted average hazard ratio, the restricted su- 64,
periority probability ratio, the restricted mean survival difference and the ratio osx-
of restricted mean times lost, based on the short-term and long-term hazard 64,
ratio model (Yang, 2005 <doi:10.1093/biomet/92.1.1>) which accommodates win-
various non-proportional hazards scenarios. The inference procedures and the 64
asymptotic results for the summary measures are discussed in Yang (2018,
<doi:10.1002/sim.7676>). / GPL-3


Name Version
r-clinpk 0.9.0 Calculates equations commonly used in clinical pharmacokinetics and clini- noarch
cal pharmacology, such as equations for dose individualization, compartmen-
tal pharmacokinetics, drug exposure, anthropomorphic calculations, clinical
chemistry, and conversion of common clinical parameters. Where possible and
relevant, it provides multiple published and peer-reviewed equations within the
respective R function. / MIT
r-clinsig 1.2 Functions for calculating clinical significance. / GPL-2 noarch
r-clinutidna 1.0 This package provides the estimation of an index measuring the clinical utility noarch
of DNA testing in the context of gene-environment interactions on a disease.
The corresponding gene-environment interaction effect on the additive scale
can also be obtained. The estimation is based on case-control or cohort data.
The method was developed by Nguyen et al. 2013. / GPL-3
r-clipr 0.6.0 Simple utility functions to read from and write to the Windows, OS X, and linux-
X11 clipboards. / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-clisymbols 1.2.0 A small subset of Unicode symbols, that are useful when building command noarch
line applications. They fall back to alternatives on terminals that do not support
Unicode. Many symbols were taken from the ‘figures’ ‘npm’ package (see
<https://github.com/sindresorhus/figures>). / MIT file LICENSE
r-clogitboost 1.1 A set of functions to fit a boosting conditional logit model. / GPL-2 linux-
64,
osx-
64,
win-
64
r-clogitl1 1.5 Tools for the fitting and cross validation of exact conditional logistic regression linux-
models with lasso and elastic net penalties. Uses cyclic coordinate descent and 64,
warm starts to compute the entire path efficiently. / GPL-2 osx-
64,
win-
64
r-cloneseeker 1.0.7 Defines the classes and functions used to simulate and to analyze data noarch
sets describing copy number variants and, optionally, sequencing muta-
tions in order to detect clonal subsets. See Zucker et al. (2019)
<doi:10.1093/bioinformatics/btz057>. / Apache License (== 2.0)
r-cloudml 0.6.1 Interface to the Google Cloud Machine Learning Platform <https://cloud. noarch
google.com/ml-engine>, which provides cloud tools for training machine
learning models. / Apache License 2.0
r-cloudutil 0.1.12Provides means of plots for comparing utilization data of compute systems. / noarch
GPL-2


Name Version
r-clrdag 0.6.0 Provides MLEdag() for constrained maximum likelihood estimation and linux-
likelihood ratio test of a large directed acyclic graph. The al- 64,
gorithms are described in the paper by Li, Shen, and Pan (2019) osx-
<doi:10.1080/01621459.2019.1623042>. / GPL-2 64,
win-
64
r-clsocp 1.0 This package provides and implementation of a one step smoothing newton noarch
method for the solution of second order cone programming problems, origi-
nally described by Xiaoni Chi and Sanyang Liu. / GPL-3
r-clttools 1.3 Central limit theorem experiments presented by data frames or plots. Func- noarch
tions include generating theoretical sample space, corresponding probability,
and simulated results as well. / GPL-2
r-clubsandwich 0.3.5 Provides several cluster-robust variance estimators (i.e., sandwich estima- noarch
tors) for ordinary and weighted least squares linear regression models, in-
cluding the bias-reduced linearization estimator introduced by Bell and
McCaffrey (2002) <http://www.statcan.gc.ca/pub/12-001-x/2002002/article/
9058-eng.pdf> and developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for
estimating the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression co-
efficients use Satterthwaite or saddle-point corrections. Tests of multiple- con-
trast hypotheses use an approximation to Hotelling’s T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), ivreg() (from package ‘AER’), plm() (from package ‘plm’),
gls() and lme() (from ‘nlme’), robu() (from ‘robumeta’), and rma.uni() and
rma.mv() (from ‘metafor’). / GPL-3
r-clue 0.3_57CLUster Ensembles. / GPL-2 linux-
64,
osx-
64,
win-
64
r-cluer 1.4 CLUster Evaluation (CLUE) is a computational method for identifying op- noarch
timal number of clusters in a given time-course dataset clustered by cmeans
or kmeans algorithms and subsequently identify key kinases or pathways
from each cluster. Its implementation in R is called ClueR. See README
on <https://github.com/PengyiYang/ClueR> for more details. P Yang et al.
(2015) <doi:10.1371/journal.pcbi.1004403>. / GPL-3
r-clues 0.5.9 We developed the clues R package to provide functions for automatically esti- linux-
mating the number of clusters and getting the final cluster partition without any
64,
input parameter except the stopping rule for convergence. The package also osx-
provides functions to evaluate and compare the performances of partitions of 64,
a data set both numerically and graphically. / GPL-2 win-
64
r-cluscov 1.1.0 Clustered covariate regression enables estimation and inference in both linear linux-
and non-linear models with linear predictor functions even when the design 64,
matrix is column rank deficient. Routines in this package implement algo- osx-
rithms in Soale and Tsyawo (2019) <doi:10.13140/RG.2.2.32355.81441>. / 64,
GPL-2 win-
64


Name Version
r-clusrank 0.6_2 Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) linux-
for clustered data. / GPL-3 64,
osx-
64,
win-
64
r-clust.bin.pair 0.1.2 Tests, utilities, and case studies for analyzing significance in clustered noarch
binary matched-pair data. The central function clust.bin.pair uses one
of several tests to calculate a Chi-square statistic. Implemented are
the tests Eliasziw (1991) <doi:10.1002/sim.4780101211>, Obuchowski
(1998) <doi:10.1002/(SICI)1097-0258(19980715)17:13%3C1495::AID-
SIM863%3E3.0.CO;2-I>, Durkalski (2003) <doi:10.1002/sim.1438>,
and Yang (2010) <doi:10.1002/bimj.201000035> with McNemar (1947)
<doi:10.1007/BF02295996> included for comparison. The utility functions
nested.to.contingency and paired.to.contingency convert data between various
useful formats. Thyroids and psychiatry are the canonical datasets from
Obuchowski and Petryshen (1989) <doi:10.1016/0165-1781(89)90196-0>
respectively. / MIT
r-cluster 2.0.8 Methods for Cluster analysis. Much extended the original from Peter linux-
Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw 32,
(1990) Finding Groups in Data. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
r-cluster.datasets 1.0_1 A collection of data sets for teaching cluster analysis. / GPL-2 noarch
r- 1.0.0 Provides functionality for the analysis of clustered data using the cluster boot- noarch
clusterbootstrap strap. / GPL-3
r-clustercrit 1.2.8 Compute clustering validation indices. / GPL-2 linux-
64,
osx-
64,
win-
64
r- 1.3.4 We developed the clusterGeneration package to provide functions for generat- noarch
clustergeneration ing random clusters, generating random covariance/correlation matrices, cal-
culating a separation index (data and population version) for pairs of clusters
or cluster distributions, and 1-D and 2-D projection plots to visualize clusters.
The package also contains a function to generate random clusters based on
factorial designs with factors such as degree of separation, number of clusters,
number of variables, number of noisy variables. / GPL-2
r- 1.0 The Partitioning Algorithm based on Recursive Thresholding (PART) is used noarch
clustergenomics to recursively uncover clusters and subclusters in the data. Functionality is
also available for visualization of the clustering. / Artistic-2.0


Name Version
r-clusterhap 0.1 One haplotype is a combination of SNP (Single Nucleotide Polymorphisms) noarch
within the QTL (Quantitative Trait Loci). clusterhap groups together all indi-
viduals of a population with the same haplotype. Each group contains indi-
vidual with the same allele in each SNP, whether or not missing data. Thus,
clusterhap groups individuals, that to be imputed, have a non-zero probability
of having the same alleles in the entire sequence of SNP’s. Moreover, cluster-
hap calculates such probability from relative frequencies. / GPL-3
r- 1.0 A dynamic programming algorithm for optimal clustering multidimensional linux-
clustering.sc.dp data with sequential constraint. The algorithm minimizes the sum of squares 64,
of within-cluster distances. The sequential constraint allows only subsequent osx-
items of the input data to form a cluster. The sequential constraint is typically 64,
required in clustering data streams or items with time stamps such as video win-
frames, GPS signals of a vehicle, movement data of a person, e-pen data, etc. 64
The algorithm represents an extension of Ckmeans.1d.dp to multiple dimen-
sional spaces. Similarly to the one-dimensional case, the algorithm guarantees
optimality and repeatability of clustering. Method clustering.sc.dp can find
the optimal clustering if the number of clusters is known. Otherwise, methods
findwithinss.sc.dp and backtracking.sc.dp can be used. / LGPL-3
r-clusternomics 0.1.1 Integrative context-dependent clustering for heterogeneous biomedical noarch
datasets. Identifies local clustering structures in related datasets, and a global
clusters that exist across the datasets. / MIT
r-clusternor 0.0_3 The clustering ‘NUMA’ Optimized Routines package or ‘clusternor’ is a linux-
highly optimized package for performing clustering in parallel with ac- 64,
celerations specifically targeting multi-core Non-Uniform Memory Access osx-
(‘NUMA’) hardware architectures. Disa Mhembere, Da Zheng, Carey E. 64,
Priebe, Joshua T. Vogelstein, Randal Burns (2019) <arXiv:1902.09527>. / win-
Apache License 2.0 64
r-clusterpower 0.6.111
Calculate power for cluster randomized trials (CRTs) that compare two noarch
means, two proportions, or two counts using closed-form solutions. In
addition, calculate power for cluster randomized crossover trials using
Monte Carlo methods. For more information, see Reich et al. (2012)
<doi:10.1371/journal.pone.0035564>. / GPL-2
r-clusterranktest 1.0 Nonparametric rank based tests (rank-sum tests and signed-rank tests) for clus- noarch
tered data, especially useful for clusters having informative cluster size and
intra-cluster group size. / GPL-2 | GPL-3
r-clusterrepro 0.9 This is a function for validating microarray clusters via reproducibility, based noarch
on the paper referenced below. / GPL-2
r-clustertend 1.4 Calculate some statistics aiming to help analyzing the clustering tendency of noarch
given data. In the first version, Hopkins’ statistic is implemented. / GPL-2
r-clusteval 0.1 An R package that provides a suite of tools to evaluate clustering algorithms, linux-
clusterings, and individual clusters. / MIT 64,
osx-
64,
win-
64
r-clustmixtype 0.2_1 Functions to perform k-prototypes partitioning clustering for mixed variable- noarch
type data according to Z.Huang (1998): Extensions to the k-Means Algo-
rithm for Clustering Large Data Sets with Categorical Variables, Data Mining
and Knowledge Discovery 2, 283-304, <DOI:10.1023/A:1009769707641>. /
GPL-2


Name Version
r-clustmmdd 1.0.4 An implementation of a variable selection procedure in clustering by mixture linux-
models for discrete data (clustMMDD). Genotype data are examples of such 64,
data with two unordered observations (alleles) at each locus for diploid indi- osx-
vidual. The two-fold problem of variable selection and clustering is seen as 64,
a model selection problem where competing models are characterized by the win-
number of clusters K, and the subset S of clustering variables. Competing 64
models are compared by penalized maximum likelihood criteria. We consid-
ered asymptotic criteria such as Akaike and Bayesian Information criteria, and
a family of penalized criteria with penalty function to be data driven calibrated.
/ GPL-2
r-clustsig 1.1 A complimentary package for use with hclust; simprof tests to see which (if noarch
any) clusters are statistically different. The null hypothesis is that there is
no a priori group structure. See Clarke, K.R., Somerfield, P.J., and Gorley
R.N. 2008. Testing of null hypothesis in exploratory community analyses:
similarity profiles and biota-environment linkage. J. Exp. Mar. Biol. Ecol.
366, 56-69. / GPL-2
r-clustvarlv 2.0.0 Functions for the clustering of variables around Latent Variables, for 2-way linux-
or 3-way data. Each cluster of variables, which may be defined as a local or 64,
directional cluster, is associated with a latent variable. External variables mea- osx-
sured on the same observations or/and additional information on the variables 64,
can be taken into account. A noise cluster or sparse latent variables can also win-
be defined. / GPL-3 64
r-clv 0.3_2.1
Package contains most of the popular internal and external cluster validation linux-
methods ready to use for the most of the outputs produced by functions coming 64,
from package cluster. Package contains also functions and examples of usage osx-
for cluster stability approach that might be applied to algorithms implemented 64,
in cluster package as well as user defined clustering algorithms. / GPL-2 win-
64
r-clvalid 0.6_6 Statistical and biological validation of clustering results. / LGPL-3 noarch
r-cmaes 1.0_11Single objective optimization using a CMA-ES. / GPL-2 noarch
r-cmc 1.0 Calculation and plot of the stepwise Cronbach-Mesbah Curve / GPL-2 noarch
r-cmce 0.1.0 Implements the Bayesian calibration model described in Pratola and Chkrebtii noarch
(2018) <DOI:10.5705/ss.202016.0403> for stochastic and deterministic sim-
ulators. Additive and multiplicative discrepancy models are currently sup-
ported. See <http://www.matthewpratola.com/software> for more information
and examples. / AGPL-3
r-cmf 1.0 Collective matrix factorization (CMF) finds joint low-rank representations for linux-
a collection of matrices with shared row or column entities. This code learns 64,
variational Bayesian approximation for CMF, supporting multiple likelihood osx-
potentials and missing data, while identifying both factors shared by multiple 64,
matrices and factors private for each matrix. / GPL-2 win-
64


Name Version
r-cmls 1.0_0 Solves multivariate least squares (MLS) problems subject to constraints on noarch
the coefficients, e.g., non-negativity, orthogonality, equality, inequality, mono-
tonicity, unimodality, smoothness, etc. Includes flexible functions for solv-
ing MLS problems subject to user-specified equality and/or inequality con-
straints, as well as a wrapper function that implements 24 common constraint
options. Also does k-fold or generalized cross-validation to tune constraint
options for MLS problems. See ten Berge (1993, ISBN:9789066950832)
for an overview of MLS problems, and see Goldfarb and Idnani (1983)
<doi:10.1007/BF02591962> for a discussion of the underlying quadratic pro-
gramming algorithm. / GPL-2
r-cmm 0.12 Quite extensive package for maximum likelihood estimation and weighted noarch
least squares estimation of categorical marginal models (CMMs; e.g., Bergsma
and Rudas, 2002, <http://www.jstor.org/stable/2700006?; Bergsma, Croon and
Hagenaars, 2009, <DOI:10.1007/b12532>. / GPL-2
r-cmna 1.0.2 Provides the source and examples for James P. Howard, II, Computational noarch
Methods for Numerical Analysis with R, <http://howardjp.github.io/cmna/>, a
book on numerical methods in R. / BSD_2_clause
r-cmocean 0.2 Perceptually uniform palettes for commonly used variables in oceanography noarch
as functions taking an integer and producing character vectors of colours. See
Thyng, K.M., Greene, C.A., Hetland, R.D., Zimmerle, H.M. and S.F. DiMarco
(2016) <doi:10.5670/oceanog.2016.66> for the guidelines adhered to when
creating the palettes. / MIT
r-cmpcontrol 1.0 The main purpose of this package is to juxtapose the different control limits noarch
obtained by modelling a data set through the COM-Poisson distribution vs. the
classical Poisson distribution. Accordingly, this package offers the ability to
compute the COM-Poisson parameter estimates and plot associated Shewhart
control charts for a given data set. / GPL-2 | GPL-3
r-cmplot 3.3.3 Manhattan plot, a type of scatter plot, was widely used to display the asso- noarch
ciation results. However, it is usually time-consuming and laborious for a
non-specialist user to write scripts and adjust parameters of an elaborate plot.
Moreover, the ever-growing traits measured have necessitated the integration
of results from different Genome-wide association study researches. Circle
Manhattan Plot is the first open R package that can lay out Genome-wide as-
sociation study P-value results in both traditional rectangular patterns, QQ-plot
and novel circular ones. United in only one bull’s eye style plot, association
results from multiple traits can be compared interactively, thereby to reveal
both similarities and differences between signals. / GPL-2
r-cmpprocess 1.0 A toolkit for flexible modeling of count processes where data (over- or under-) noarch
dispersion exists. Estimations can be obtained under two data constructs where
one has: (1) data on number of events in an s-unit time interval, or (2) only
wait-time data. This package is supplementary to the work set forth in Zhu et
al. (2016) <doi:10.1080/00031305.2016.1234976>. / GPL-3
r-cmprsk 2.2_8 Estimation, testing and regression modeling of subdistribution functions in linux-
competing risks, as described in Gray (1988), A class of K-sample tests for 64,
comparing the cumulative incidence of a competing risk, Ann. Stat. 16:1141- osx-
1154 <DOI:10.1214/aos/1176350951>, and Fine JP and Gray RJ (1999), A 64,
proportional hazards model for the subdistribution of a competing risk, JASA, win-
94:496-509, <DOI:10.1080/01621459.1999.10474144>. / GPL-2 64


Name Version
r-cmprskqr 0.9.1 Estimation, testing and regression modeling of subdistribution functions in linux-
competing risks using quantile regressions, as described in Peng and Fine 64,
(2009) <DOI:10.1198/jasa.2009.tm08228>. / GPL-2 osx-
64,
win-
64
r-cmrutils 1.3.1 A collection of useful helper routines developed by students of the Center for noarch
Mathematical Research, Stankin, Moscow. / GPL-3
r-cmvnorm 1.0_6 Various utilities for the complex multivariate Gaussian distribution. / GPL-2 noarch
r-cna 2.2.0 Provides comprehensive functionalities for causal modeling with Coinci- linux-
dence Analysis (CNA), which is a configurational comparative method 64,
of causal data analysis that was first introduced in Baumgartner (2009) osx-
<doi:10.1177/0049124109339369>, and generalized in Baumgartner & Am- 64,
buehl (2018) <doi:10.1017/psrm.2018.45>. CNA is related to Qualitative win-
Comparative Analysis (QCA), but contrary to the latter, it is custom-built 64
for uncovering causal structures with multiple outcomes and it builds causal
models from the bottom up by gradually combining single factors to com-
plex dependency structures until the requested thresholds of model fit are met.
The new functionalities provided by this package version include functions for
evaluating and benchmarking the correctness of CNA’s output, a function de-
termining whether a solution is an INUS model, a function bringing non-INUS
expressions into INUS form, and a function for identifying cyclic models. The
package vignette has been updated accordingly. / GPL-2
r-cnorm 1.2.0 Conventional methods for producing standard scores in psychometrics or noarch
biometrics are often plagued with jumps or gaps (i.e., discontinuities)
in norm tables and low confidence for assessing extreme scores. The
continuous norming method introduced by A. Lenhard et al. (2016),
<doi:10.1177/1073191116656437>, generates continuous test norm scores on
the basis of the raw data from standardization samples, without requiring as-
sumptions about the distribution of the raw data: Norm scores are directly
established from raw data by modeling the latter ones as a function of both per-
centile scores and an explanatory variable (e.g., age). The method minimizes
bias arising from sampling and measurement error, while handling marked de-
viations from normality, addressing bottom or ceiling effects and capturing
almost all of the variance in the original norm data sample. / AGPL-3
r-cobiclust 0.1.0 Implementation of a probabilistic method for biclustering adapted to overdis- noarch
persed count data. It is a Gamma-Poisson Latent Block Model. It also im-
plements two selection criteria in order to select the number of biclusters. /
GPL-2
r-cobra 0.99.4This package performs prediction for regression-oriented problems, aggregat- linux-
ing in a nonlinear scheme any basic regression machines suggested by the 64,
context and provided by the user. If the user has no valuable knowledge on osx-
the data, four defaults machines wrappers are implemented so as to cover a 64,
minimal spectrum of prediction methods. If necessary, the computations may win-
be parallelized. The method is described in Biau, Fischer, Guedj and Malley 64
(2013), COBRA: A Nonlinear Aggregation Strategy. / GPL-2


Name Version
r-cobs 1.3_3 Qualitatively Constrained (Regression) Smoothing Splines via Linear Pro- linux-
gramming and Sparse Matrices. / GPL-2 64,
osx-
64,
win-
64
r-coclust 0.3_2 A copula based clustering algorithm that finds clusters according to the com- noarch
plex multivariate dependence structure of the data generating process. The
updated version of the algorithm is described in Di Lascio, F.M.L. and Gian-
nerini, S. (2016). Clustering dependent observations with copula functions.
Statistical Papers, p.1-17. <doi:10.1007/s00362-016-0822-3>. / GPL-2
r-coconut 1.0.2 Allows for pooled analysis of microarray data by batch-correcting control sam- noarch
ples, and then applying the derived correction parameters to non-control sam-
ples to obtain bias-free, inter-dataset corrected data. / GPL-3
r-cocor 1.1_3 Statistical tests for the comparison between two correlations based on ei- noarch
ther independent or dependent groups. Dependent correlations can either be
overlapping or nonoverlapping. A web interface is available on the website
http://comparingcorrelations.org. A plugin for the R GUI and IDE RKWard is
included. Please install RKWard from https://rkward.kde.org to use this fea-
ture. The respective R package ‘rkward’ cannot be installed directly from a
repository, as it is a part of RKWard. / GPL-3
r-cocron 1.0_1 Statistical tests for the comparison between two or more alpha coefficients noarch
based on either dependent or independent groups of individuals. A web in-
terface is available at http://comparingcronbachalphas.org. A plugin for the R
GUI and IDE RKWard is included. Please install RKWard from https:// rk-
ward.kde.org to use this feature. The respective R package ‘rkward’ cannot be
installed directly from a repository, as it is a part of RKWard. / GPL-3
r-coda 0.19_2Provides functions for summarizing and plotting the output from Markov linux-
Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of con- 32,
vergence to the equilibrium distribution of the Markov chain. / GPL (>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-coda.base 0.2.1 A minimum set of functions to perform compositional data analysis using the linux-
log-ratio approach introduced by John Aitchison (1982) <http://www.jstor.org/ 64,
stable/2345821>. Main functions have been implemented in c for better per- osx-
formance. / GPL-3 64,
win-
64
r-codadiags 1.0 Markov chain Monte Carlo burn-in based on bridge statistics, in the way of linux-
coda::heidel.diag, but including non asymptotic tabulated statistics. / GPL-3 64,
osx-
64,
win-
64


Name Version
r-codatags 1.43 Computes genomic breeding values using external information on the mark- noarch
ers. The package fits a linear mixed model with heteroscedastic random ef-
fects, where the random effect variance is fitted using a linear predictor and a
log link. The method is described in Mouresan, Selle and Ronnegard (2019)
<doi:10.1101/636746>. / GPL-3
r-code 1.0.0 Generates all necessary C functions allowing the user to work with the noarch
compiled-code interface of ode() and bvptwp(). The implementation supports
forcings and events. Also provides functions to symbolically compute Jaco-
bians, sensitivity equations and adjoint sensitivities being the basis for sensi-
tivity analysis. / GPL-2
r-codep 0.9_1 Computation of Multiscale Codependence Analysis and spatial eigenvector linux-
maps, as an additional feature. / GPL-3 64,
osx-
64,
win-
64
r-codetools 0.2_16Code analysis tools for R. / GPL linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-codina 1.1.1 Categorize links and nodes from multiple networks in 3 categories: Common noarch
links (alpha) specific links (gamma), and different links (beta). Also catego-
rizes the links into sub-categories and groups. The package includes a visual-
ization tool for the networks. More information about the methodology can be
found at: Gysi et. al., 2018 <arXiv:1802.00828>. / GPL-2
r-coenocliner 0.2_2 Simulate species occurrence and abundances (counts) along gradients. / GPL- noarch
2
r-coenoflex 2.2_0 Simulates the composition of samples of vegetation according to gradient- linux-
based vegetation theory. Features a flexible algorithm incorporating compe- 64,
tition and complex multi-gradient interaction. / GPL-2 osx-
64,
win-
64
r-coexist 1.0 species coexistence modeling under asymmetric dispersal and fluctuating noarch
source-sink dynamics;testing the proportion of coexistence scenarios driven
by neutral and niche processes / GPL (>= 2.0)
r-cofad 0.1.0 Contrast analysis for factorial designs is an alternative to the classical noarch
ANOVA approach with the advantage of testing focused hypothesis. The
method is mainly based on Rosenthal, Rosnow and Rubin (2000, ISBN:978-
0521659802) and Sedlmeier and Renkewitz (2018, ISBN:978-3868943214). /
GPL-2


Name Version
r-cofra 0.1002Calculates complete functional regulation analysis and visualize the results noarch
in a single heatmap. The provided example data is for biological data but
the methodology can be used for large data sets to compare quantitative en-
tities that can be grouped. For example, a store might divide entities into
cloth, food, car products etc and want to see how sales changes in the groups
after some event. The theoretical background for the calculations are pro-
vided in New insights into functional regulation in MS-based drug profiling,
Ana Sofia Carvalho, Henrik Molina & Rune Matthiesen, Scientific Reports
<doi:10.1038/srep18826>. / GPL-2
r-coin 1.3_0 Conditional inference procedures for the general independence problem in- linux-
cluding two-sample, K-sample (non-parametric ANOVA), correlation, cen- 32,
sored, ordered and multivariate problems. / GPL-2 linux-
64,
osx-
64,
win-
32,
win-
64
r-coindeskr 0.1.0 Extract real-time Bitcoin price details by accessing ‘CoinDesk’ Bitcoin price noarch
Index API <https://www.coindesk.com/api/>. / CC0
r-cointmonitor 0.1.0 We propose a consistent monitoring procedure to detect a structural change noarch
from a cointegrating relationship to a spurious relationship. The proce-
dure is based on residuals from modified least squares estimation, using ei-
ther Fully Modified, Dynamic or Integrated Modified OLS. It is inspired
by Chu et al. (1996) <DOI:10.2307/2171955> in that it is based on pa-
rameter estimation on a pre-break calibration period only, rather than being
based on sequential estimation over the full sample. See the discussion paper
<DOI:10.2139/ssrn.2624657> for further information. This package provides
the monitoring procedures for both the cointegration and the stationarity case
(while the latter is just a special case of the former one) as well as printing and
plotting methods for a clear presentation of the results. / GPL-3


Name Version
r-cointreg 0.2.0 Cointegration methods are widely used in empirical macroeconomics and em- noarch
pirical finance. It is well known that in a cointegrating regression the or-
dinary least squares (OLS) estimator of the parameters is super-consistent,
i.e. converges at rate equal to the sample size T. When the regressors
are endogenous, the limiting distribution of the OLS estimator is contami-
nated by so-called second order bias terms, see e.g. Phillips and Hansen
(1990) <DOI:10.2307/2297545>. The presence of these bias terms ren-
ders inference difficult. Consequently, several modifications to OLS that
lead to zero mean Gaussian mixture limiting distributions have been pro-
posed, which in turn make standard asymptotic inference feasible. These
methods include the fully modified OLS (FM-OLS) approach of Phillips
and Hansen (1990) <DOI:10.2307/2297545>, the dynamic OLS (D-OLS)
approach of Phillips and Loretan (1991) <DOI:10.2307/2298004>, Saikko-
nen (1991) <DOI:10.1017/S0266466600004217> and Stock and Watson
(1993) <DOI:10.2307/2951763> and the new estimation approach called
integrated modified OLS (IM-OLS) of Vogelsang and Wagner (2014)
<DOI:10.1016/j.jeconom.2013.10.015>. The latter is based on an augmented
partial sum (integration) transformation of the regression model. IM-OLS is
similar in spirit to the FM- and D-OLS approaches, with the key difference
that it does not require estimation of long run variance matrices and avoids
the need to choose tuning parameters (kernels, bandwidths, lags). However,
inference does require that a long run variance be scaled out. This package
provides functions for the parameter estimation and inference with all three
modified OLS approaches. That includes the automatic bandwidth selection
approaches of Andrews (1991) <DOI:10.2307/2938229> and of Newey and
West (1994) <DOI:10.2307/2297912> as well as the calculation of the long
run variance. / GPL-3
r-cold 2.0_0 Performs regression analysis for longitudinal count data, allowing for se- linux-
rial dependence among observations from a given individual and two di- 64,
mensional random effects on the linear predictor. Estimation is via maxi- osx-
mization of the exact likelihood of a suitably defined model. Missing val- 64,
ues and unbalanced data are allowed; M. Helena Goncalves et al.(2007) win-
<doi:10.1016/j.csda.2007.03.002>. / GPL-2 64
r-collectargs 0.4.0 We often want to take all (or most) of the objects in one environment (such noarch
as the parameter values of a function) and pass them to another. This might
be calling a second function, or iterating over a list, calling the same function.
These functions wrap often repeated code. Current stable version (committed
on October 14, 2017). / MIT
r-collections 0.1.6 Provides high performance container data types such as Queue, Stack, Deque, linux-
Dict and OrderedDict. Benchmarks <https://randy3k.github.io/collections/ 64,
articles/benchmark.html> have shown that these containers are asymptotically osx-
more efficient than those offered by other packages. / MIT 64,
win-
64
r-collesslike 1.0 Computation of Colless-Like, Sackin and cophenetic balance indices noarch
of a phylogenetic tree and study of the distribution of these bal-
ance indices under the alpha-gamma model. For more details see A.
Mir, F. Rossello, L. Rotger (2013) <doi:10.1016/j.mbs.2012.10.005>, M.
J. Sackin (1972) <doi:10.1093/sysbio/21.2.225>, D. H. Colless (1982)
<doi:10.2307/2413420>. / GPL-2


Name Version
r-collutils 1.0.5 Provides some low level functions for processing PLINK input and output linux-
files. / GPL-3 64
r-colmozzie 1.1.1 Weekly notified dengue cases and climate variables in Colombo district Sri noarch
Lanka from 2008/ week-52 to 2014/ week-21. / CC0
r-coloredica 1.0.0 It implements colored Independent Component Analysis (Lee et al., 2011) and noarch
spatial colored Independent Component Analysis (Shen et al., 2014). They are
two algorithms to perform ICA when sources are assumed to be temporal or
spatial stochastic processes, respectively. / GPL-2
r- 2.4 Given 2-,3- or 4-dimensional data, plots a Venn diagram, i.e. ‘crossing circles’. noarch
colorfulvennplot The user can specify values, labels for each circle-group and unique colors for
each plotted part. Here is what it would look like for a 3-dimensional plot:
http://elliotnoma.files.wordpress.com/2011/02/venndiagram.png. To see what
the 4-dimensional plot looks like, go to http://elliotnoma.files.wordpress.com/
2013/03/4dplot.png. / GPL-2
r-colorhcplot 1.3.1 Build dendrograms with sample groups highlighted by different colors. Visu- noarch
alize results of hierarchical clustering analyses as dendrograms whose leaves
and labels are colored according to sample grouping. Assess whether data
point grouping aligns to naturally occurring clusters. / GPL-2
r-colorpalette 1.0_1 Different methods to generate a color palette based on a specified base color noarch
and a number of colors that should be created. / MIT
r-colorr 1.0.0 Color palettes for EPL, MLB, NBA, NHL, and NFL teams. / MIT noarch
r-colorramps 2.3 Builds gradient color maps / GPL-3 noarch
r-colorspace 1.4_1 Carries out mapping between assorted color spaces including RGB, HSV, linux-
HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar 32,
CIELAB. Qualitative, sequential, and diverging color palettes based on HCL linux-
colors are provided along with an interactive palette picker (with either a 64,
Tcl/Tk or a shiny GUI). / BSD_3_clause file LICENSE osx-
64,
win-
32,
win-
64
r-colortools 0.1.5 R package with handy functions to help users select and play with color noarch
schemes in an HSV color model / GPL-3
r-colourlovers 0.3.5 Provides access to the COLOURlovers <http://www.colourlovers.com/> API, noarch
which offers color inspiration and color palettes. / GPL-2
r-colourvalues 0.2.2 Maps one of the viridis colour palettes, or a user-specified palette to val- linux-
ues. Viridis colour maps are created by StÃ©fan van der Walt and Nathaniel 64,
Smith. They were set as the default palette for the ‘Python’ ‘Matplotlib’ osx-
library, introduced at SciPy 2015 conference <http://scipy2015.scipy.org/ 64,
ehome/index.php?eventid=115969&>. Other palettes available in this li- win-
brary have been derived from ‘RColorBrewer’ <https://CRAN.R-project. 64
org/package=RColorBrewer> and ‘colorspace’ <https://CRAN.R-project.org/
package=colorspace> packages. / GPL-3
r-colr 0.1.900
Powerful functions to select and rename columns in dataframes, lists and nu- noarch
meric types by ‘Perl’ regular expression. Regular expression (‘regex’) are a
very powerful grammar to match strings, such as column names. / GPL-2
r-colt 0.1.1 A collection of command-line color styles based on the ‘crayon’ package. noarch
‘Colt’ styles are defined in themes that can easily be switched, to ensure com-
mand line output looks nice on dark as well as light consoles. / MIT


Name Version
r-comat 0.3.0 Builds co-occurrence matrices based on spatial raster data. It includes creation linux-
of weighted co-occurrence matrices (wecoma) and integrated co-occurrence 64,
matrices (incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>). osx-
/ MIT 64,
win-
64
r-combat 0.0.4 Genome-wide association studies (GWAS) have been widely used for identi- noarch
fying common variants associated with complex diseases. Due to the small
effect sizes of common variants, the power to detect individual risk variants is
generally low. Complementary to SNP-level analysis, a variety of gene-based
association tests have been proposed. However, the power of existing gene-
based tests is often dependent on the underlying genetic models, and it is not
known a priori which test is optimal. Here we proposed COMBined Associ-
ation Test (COMBAT) to incorporate strengths from multiple existing gene-
based tests, including VEGAS, GATES and simpleM. Compared to individual
tests, COMBAT shows higher overall performance and robustness across a
wide range of genetic models. The algorithm behind this method is described
in Wang et al (2017) <doi:10.1534/genetics.117.300257>. / GPL-2
r-combinat 0.0_8 routines for combinatorics / GPL-2 noarch
r- 0.4 Estimation of optimal portfolio weights as combination of simple portfolio noarch
combineportfolio strategies, like the tangency, global minimum variance (GMV) or naive (1/N)
portfolio. It is based on a utility maximizing 8-fund rule. Popular special
cases like the Kan-Zhou(2007) 2-fund and 3-fund rule or the Tu-Zhou(2011)
estimator are nested. / GPL-2
r-combinepvalue 1.0 We offer two statistical tests to combine p-values: selfcontained.test vs com- noarch
petitive.test. The goal is to test whether a vector of pvalues are jointly signifi-
cant when we combine them together. / GPL-3
r-combins 1.1_1 Series of partially balanced incomplete block designs (PBIB) based on noarch
the combinatory method (S) introduced in (Imane Rezgui et al, 2014)
<doi:10.3844/jmssp.2014.45.48>; and it gives their associated U-type design.
/ GPL-3
r-combmsc 1.4.2.1Functions for computing optimal convex combinations of model selection cri- noarch
teria based on ranks, along with utility functions for constructing model lists,
MSCs, and priors on model lists. / GPL-2
r-comclim 0.9.5 Computes community climate statistics for volume and mismatch using noarch
species’ climate niches either unscaled or scaled relative to a regional species
pool. These statistics can be used to describe biogeographic patterns and infer
community assembly processes. Includes a vignette outlining usage. / GPL-3
r-comf 0.1.9 Functions to calculate various common and less common thermal comfort noarch
indices, convert physical variables, and evaluate the performance of thermal
comfort indices. / GPL-2
r-comics 1.0.4 Provided are Computational methods for Immune Cell-type Subsets, includ- noarch
ing:(1) DCQ (Digital Cell Quantifier) to infer global dynamic changes in im-
mune cell quantities within a complex tissue; and (2) VoCAL (Variation of
Cell-type Abundance Loci) a deconvolution-based method that utilizes tran-
scriptome data to infer the quantities of immune-cell types, and then uses these
quantitative traits to uncover the underlying DNA loci. / GPL-2


Name Version
r-commandr 1.0.1 An S4 representation of the Command design pattern. The Operation class noarch
is a simple implementation using closures and supports forward and reverse
(undo) evaluation. The more complicated Protocol framework represents each
type of command (or analytical protocol) by a formal S4 class. Commands
may be grouped and consecutively executed using the Pipeline class. Example
use cases include logging, do/undo, analysis pipelines, GUI actions, parallel
processing, etc. / Artistic-2.0
r-commentr 1.0.4 Functions to produce nicely formatted comments to use in R-scripts (or La- noarch
tex/HTML/markdown etc). A comment with formatting is printed to the con-
sole and can then be copied to a script. / GPL-2
r- 1.0_6 Useful libraries for building a Java based GUI under R are provided. / GPL-2 noarch
commonjavajars
r-commonmark 1.7 The CommonMark specification defines a rationalized version of markdown linux-
syntax. This package uses the ‘cmark’ reference implementation for convert- 32,
ing markdown text into various formats including html, latex and groff man. linux-
In addition it exposes the markdown parse tree in xml format. The latest ver- 64,
sion of this package also adds support for Github extensions including tables, osx-
autolinks and strikethrough text. / BSD_2_clause file LICENSE 64,
win-
32,
win-
64
r-commonsmath 1.2.4 Java JAR files for the Apache Commons Mathematics Library for use by users noarch
and other packages. / Apache License 2.0 | file LICENSE
r-commontrend 0.7_1 Directly extract and plot stochastic common trends from a cointegration sys- noarch
tem using different approaches, currently including Kasa (1992) and Gonzalo
and Granger (1995). The approach proposed by Gonzalo and Granger, also
known as Permanent-Transitory Decomposition, is widely used in macroeco-
nomics and market microstructure literature. Kasa’s approach, on the other
hand, has a nice property that it only uses the super consistent estimator: the
cointegration vector ‘beta’. This package also provides functions calculate
P-value from Johansen Statistics according to the approximation method pro-
posed by Doornik (1998). Update: 0.7-1: Fix bugs in calculation alpha. Add
formulas and more explanations. 0.6-1: Rewrite the description file. 0.5-1:
Add functions to calculate P-value from Johansen statistic, and vice versa. /
GPL-2
r-comorbidity 0.5.0 Computing comorbidity scores such as the weighted Charlson score noarch
(Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elix-
hauser comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-
199801000-00004>) using ICD-9-CM or ICD-10 codes (Quan, 2005
<doi:10.1097/01.mlr.0000182534.19832.83>). / GPL-3
r-comp2roc 1.1.4 Comparison of two ROC curves through the methodology proposed by Ana C. noarch
Braga. / GPL-2
r-compactr 0.1 Creates empty plots with compact axis notation to which users can add what- noarch
ever they like (points, lines, text, etc.) The notation is more compact in the
sense that the axis-labels and tick-labels are closer to the axis and the tick-
marks are shorter. Also, if the plot appears as part of a matrix, the x-axis
notation is suppressed unless the plot appears along the bottom row and the
y-axis notation is suppress unless the plot appears along the left column. /
GPL-2


Name Version
r-compare 0.2_6 Functions to compare a model object to a comparison object. If the objects noarch
are not identical, the functions can be instructed to explore various modifica-
tions of the objects (e.g., sorting rows, dropping names) to see if the modified
versions are identical. / GPL-2
r-comparec 1.3.1 Proposed by Harrell, the C index or concordance C, is considered an over- linux-
all measure of discrimination in survival analysis between a survival outcome 64,
that is possibly right censored and a predictive-score variable, which can repre- osx-
sent a measured biomarker or a composite-score output from an algorithm that 64,
combines multiple biomarkers. This package aims to statistically compare two win-
C indices with right-censored survival outcome, which commonly arise from 64
a paired design and thus resulting two correlated C indices. / GPL (>= 2.0)
r-compareodm 1.2 Input: 2 ODM files (ODM version 1.3) Output: list of identical, matching, noarch
similar and differing data items / GPL-3
r-comparer 0.2.0 Quickly run experiments to compare the run time and output of code blocks. noarch
The function mbc() can make fast comparisons of code, and will calculate
statistics comparing the resulting outputs. It can be used to compare model
fits to the same data or see which function runs faster. The function ffexp()
runs a function using all possible combinations of selected inputs. This is
useful for comparing the effect of different parameter values. It can also run in
parallel and automatically save intermediate results, which is very useful for
long computations. / GPL-3
r-comparetests 1.2 A standard test is observed on all specimens. We treat the second test (or noarch
sampled test) as being conducted on only a stratified sample of specimens.
Verification Bias is this situation when the specimens for doing the second
(sampled) test is not under investigator control. We treat the total sample as
stratified two-phase sampling and use inverse probability weighting. We es-
timate diagnostic accuracy (category-specific classification probabilities; for
binary tests reduces to specificity and sensitivity, and also predictive values)
and agreement statistics (percent agreement, percent agreement by category,
Kappa (unweighted), Kappa (quadratic weighted) and symmetry tests (reduces
to McNemar’s test for binary tests)). See: Katki HA, Li Y, Edelstein DW, Cas-
tle PE. Estimating the agreement and diagnostic accuracy of two diagnostic
tests when one test is conducted on only a subsample of specimens. Stat Med.
2012 Feb 28; 31(5) <doi:10.1002/sim.4422>. / GPL-3
r-compas 0.1 Manipulate and analyze 3-D structural geometry of Protein Data Bank (PDB) linux-
files. / GPL-3 64,
osx-
64,
win-
64
r-compboost 0.1.0 C implementation of component-wise boosting implementation of component- linux-
wise boosting written in C to obtain high runtime performance and full mem- 64,
ory control. The main idea is to provide a modular class system which can osx-
be extended without editing the source code. Therefore, it is possible to use 64,
R functions as well as C functions for custom base-learners, losses, logging win-
mechanisms or stopping criteria. / MIT 64


Name Version
r-compglm 2.0 A function (which uses a similar interface to the ‘glm’ function) for the linux-
fitting of a Conway-Maxwell-Poisson GLM. There are also various meth- 64,
ods for analysis of the model fit. The package also contains functions for osx-
the Conway-Maxwell-Poisson distribution in a similar interface to functions 64,
‘dpois’, ‘ppois’ and ‘rpois’. The functions are generally quick, since the win-
workhorse functions are written in C (thanks to the Rcpp package). / GPL- 64
2
r-comphclust 1.0_3 Performs the complementary hierarchical clustering procedure and returns X’ linux-
(the expected residual matrix) and a vector of the relative gene importances. / 64,
GPL-2 osx-
64,
win-
64
r-complexity 1.1.1 Allows for the easy computation of complexity: the proportion of the param- noarch
eter space in line with the hypothesis by chance. The package comes with a
Shiny application in which the calculations can be conducted as well. / GPL-2
r- 3.0 Computes the probability density function, cumulative distribution function, noarch
complognormal quantile function, random numbers of any composite model based on the log-
normal distribution. / GPL-2
r-compoisson 0.3 Provides routines for density and moments of the Conway-Maxwell-Poisson noarch
distribution as well as functions for fitting the COM-Poisson model for
over/under-dispersed count data. / BSD
r-compoissonreg 0.6.1 Fit Conway-Maxwell Poisson (COM-Poisson or CMP) regression mod- linux-
els to count data (Sellers & Shmueli, 2010) <doi:10.1214/09-AOAS306>. 64,
The package provides functions for model estimation, dispersion testing, osx-
and diagnostics. Zero-inflated CMP regression (Sellers & Raim, 2016) 64,
<doi:10.1016/j.csda.2016.01.007> is also supported. / GPL-2 | GPL-3 win-
64
r-compound.cox 3.18 Univariate feature selection and compound covariate methods under noarch
the Cox model with high-dimensional features (e.g., gene expres-
sions). Available are survival data for non-small-cell lung cancer pa-
tients with gene expressions (Chen et al 2007 New Engl J Med)
<DOI:10.1056/NEJMoa060096>, statistical methods in Emura et al (2012
PLoS ONE) <DOI:10.1371/journal.pone.0047627>, Emura & Chen (2016
Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al.
(2019)<DOI:10.1016/j.cmpb.2018.10.020>. Algorithms for generating corre-
lated gene expressions are also available. / GPL-2
r-compquadform 1.4.3 Computes the distribution function of quadratic forms in normal variables us- linux-
ing Imhof’s method, Davies’s algorithm, Farebrother’s algorithm or Liu et al.’s 64,
algorithm. / GPL-2 osx-
64,
win-
64
r-compr 1.0 Different tools for describing and analysing paired comparison data are pre- noarch
sented. Main methods are estimation of products scores according Bradley
Terry Luce model. A segmentation of the individual could be conducted on
the basis of a mixture distribution approach. The number of classes can be
tested by the use of Monte Carlo simulations. This package deals also with
multi-criteria paired comparison data. / GPL-2


Name Version
r-comprehenr 0.6.7 Provides ‘Python’-style list comprehensions. List comprehension expressions noarch
use usual loops (for(), while() and repeat()) and usual if() as list producers. In
many cases it gives more concise notation than standard *apply filter strategy.
/ GPL-2
r-compute.es 0.2_4 This package contains several functions for calculating the most widely used noarch
effect sizes (ES), along with their variances, confidence intervals and p-values.
The output includes ES’s of d (mean difference), g (unbiased estimate of d),
r (correlation coefficient), z’ (Fisher’s z), and OR (odds ratio and log odds
ratio). In addition, NNT (number needed to treat), U3, CLES (Common Lan-
guage Effect Size) and Cliff’s Delta are computed. This package uses recom-
mended formulas as described in The Handbook of Research Synthesis and
Meta-Analysis (Cooper, Hedges, & Valentine, 2009). / GPL-2
r-comtradr 0.2.2 Interface with and extract data from the United Nations Comtrade API <https: noarch
//comtrade.un.org/data/>. Comtrade provides country level shipping data for
a variety of commodities, these functions allow for easy API query and data
returned as a tidy data frame. / GPL-3
r-con2aqi 0.1.0 To calculate the AQI (Air Quality Index) from pollutant concentration noarch
data. O3, PM2.5, PM10, CO, SO2, and NO2 are available cur-
rently. The method can be referenced at Environmental Protection Agency,
United States as follows: EPA (2016) <https://www3.epa.gov/airnow/
aqi-technical-assistance-document-may2016.pdf>. / GPL-3
r-conake 1.0 Continuous smoothing of probability density function on a compact or semi- noarch
infinite support is performed using four continuous associated kernels: ex-
tended beta, gamma, lognormal and reciprocal inverse Gaussian. The cross-
validation technique is also implemented for bandwidth selection. / GPL-2
r-concatenate 1.0.0 Simple functions for joining strings. Construct human-friendly messages noarch
whose elements aren’t known in advance, like in stop, warning, or message,
from clean code. / GPL (>= 3.2)
r-conclust 1.1 There are 4 main functions in this package: ckmeans(), lcvqe(), mpckm() and noarch
ccls(). They take an unlabeled dataset and two lists of must-link and cannot-
link constraints as input and produce a clustering as output. / GPL-3
r-conconpiwifun 0.4.6 Continuous convex piecewise linear (ccpl) resp. quadratic (ccpq) functions can linux-
be implemented with sorted breakpoints and slopes. This includes functions 64,
that are ccpl (resp. ccpq) on a convex set (i.e. an interval or a point) and osx-
infinite out of the domain. These functions can be very useful for a large class 64,
of optimisation problems. Efficient manipulation (such as log(N) insertion) of win-
such data structure is obtained with map standard template library of C (that 64
hides balanced trees). This package is a wrapper on such a class based on Rcpp
modules. / GPL-2
r-concor 1.0_0.1
The four functions svdcp (cp for column partitioned), svdbip or svdbip2 (bip noarch
for bi-partitioned), and svdbips (s for a simultaneous optimization of one set
of r solutions), correspond to a SVD by blocks notion, by supposing each
block depending on relative subspaces, rather than on two whole spaces as
usual SVD does. The other functions, based on this notion, are relative to two
column partitioned data matrices x and y defining two sets of subsets xi and yj
of variables and amount to estimate a link between xi and yj for the pair (xi,
yj) relatively to the links associated to all the other pairs. / GPL-3


Name Version
r-concordance 1.6 A set of utilities for matching products in different classification codes used in noarch
international trade research. It supports concordance between HS (Combined),
ISIC Rev. 2,3, and SITC1,2,3,4 product classification codes, as well as BEC,
NAICS, and SIC classifications. It also provides code nomenclature / descrip-
tions look-up, Rauch classification look-up (via concordance to SITC2) and
trade elasticity look-up (via concordance to SITC2/3 or HS3.ss). / GPL-2
r-concreg 0.6 Implements concordance regression which can be used to estimate general- linux-
ized odds of concordance. Can be used for non- and semi-parametric survival 64,
analysis with non-proportional hazards, for binary and for continuous outcome osx-
data. / GPL-3 64,
win-
64
r-conditionz 0.1.0 Provides ability to control how many times in function calls conditions are noarch
thrown (shown to the user). Includes control of warnings and messages. / MIT
r-condmvnorm 2015.2_1
Computes conditional multivariate normal probabilities, random deviates and noarch
densities. / GPL-2
r-condreg 0.20 Based on url{http://statistics.stanford.edu/~ckirby/techreports/GEN/2012/ noarch
2012-10.pdf} / GPL-3
r-condvis 0.5_1 Exploring fitted models by interactively taking 2-D and 3-D sections in data noarch
space. / GPL-2
r-coneproj 1.14 Routines doing cone projection and quadratic programming, as well linux-
as doing estimation and inference for constrained parametric regres- 64,
sion and shape-restricted regression problems. See Mary C. Meyer osx-
(2013)<doi:10.1080/03610918.2012.659820> for more details. / GPL-2 64,
win-
64
r-conf.design 2.0.0 This small library contains a series of simple tools for constructing and manip- noarch
ulating confounded and fractional factorial designs. / GPL-2
r-config 0.3 Manage configuration values across multiple environments (e.g. development, linux-
test, production). Read values using a function that determines the current 32,
environment and returns the appropriate value. / GPL-3 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-configparser 1.0.0 Enhances the ‘ini’ package by adding the ability to interpolate variables. The noarch
INI configuration file is read into an R6 ConfigParser object (loosely inspired
by Pythons ConfigParser module) and the keys can be read, where ‘%(. . . .)s’
instances are interpolated by other included options or outside variables. /
GPL-3
r-confinterpret 1.0.0 Produces descriptive interpretations of confidence intervals. Includes (extensi- noarch
ble) support for various test types, specified as sets of interpretations dependent
on where the lower and upper confidence limits sit. Provides plotting functions
for graphical display of interpretations. / AGPL-3


Name Version
r-confintvariance 1.0.2 Surrounds the usual sample variance of a univariate numeric sample with a noarch
confidence interval for the population variance. This has been done so far
only under the assumption that the underlying distribution is normal. Under
the hood, this package implements the unique least-variance unbiased esti-
mator of the variance of the sample variance, in a formula that is equiva-
lent to estimating kurtosis and square of the population variance in an un-
biased way and combining them according to the classical formula into an
estimator of the variance of the sample variance. Both the sample vari-
ance and the estimator of its variance are U-statistics. By the theory of
U-statistic, the resulting estimator is unique. See Fuchs, Krautenbacher
(2016) <doi:10.1080/15598608.2016.1158675> and the references therein for
an overview of unbiased estimation of variances of U-statistics. / GPL-3
r-conflicted 1.0.4 R’s default conflict management system gives the most recently loaded pack- noarch
age precedence. This can make it hard to detect conflicts, particularly when
they arise because a package update creates ambiguity that did not previously
exist. ‘conflicted’ takes a different approach, making every conflict an error
and forcing you to choose which function to use. / GPL-3
r-confreq 1.5.4_3
Offers several functions for Configural Frequencies Analysis (CFA), which is noarch
a useful statistical tool for the analysis of multiway contingency tables. CFA
was introduced by G. A. Lienert as ‘Konfigurations Frequenz Analyse - KFA’.
Lienert, G. A. (1971). Die Konfigurationsfrequenzanalyse: I. Ein neuer Weg
zu Typen und Syndromen. Zeitschrift für Klinische Psychologie und Psy-
chotherapie, 19(2), 99–115. / GPL-3
r-confsam 0.2 For multiple testing. Computes estimates and confidence bounds for the False noarch
Discovery Proportion (FDP), the fraction of false positives among all rejected
hypotheses. The methods in the package use permutations of the data. Doing
so, they take into account the dependence structure in the data. / GPL-3
r-conics 0.3 plot conics (ellipses, hyperbolas, parabolas) / GPL-2 noarch
r-conjointchecks 0.0.9 Implementation of a procedure (Domingue, 2012; see also Karabatsos, 2001 noarch
and Kyngdon, 2011) to test the single and double cancellation axioms of con-
joint measure in data that is dichotomously coded and measured with error. /
GPL-2
r-connmattools 0.3.3 Collects several different methods for analyzing and working with connectivity noarch
data in R. Though primarily oriented towards marine larval dispersal, many of
the methods are general and useful for terrestrial systems as well. / GPL-2
r-conover.test 1.1.5 Computes the Conover-Iman test (1979) for stochastic dominance and reports noarch
the results among multiple pairwise comparisons after a Kruskal-Wallis test
for stochastic dominance among k groups (Kruskal and Wallis, 1952). The
interpretation of stochastic dominance requires an assumption that the CDF of
one group does not cross the CDF of the other. conover.test makes k(k-1)/2
multiple pairwise comparisons based on Conover-Iman t-test-statistic of the
rank differences. The null hypothesis for each pairwise comparison is that the
probability of observing a randomly selected value from the first group that
is larger than a randomly selected value from the second group equals one
half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney
rank-sum test. Like the rank-sum test, if the data can be assumed to be con-
tinuous, and the distributions are assumed identical except for a difference in
location, Conover-Iman test may be understood as a test for median difference.
conover.test accounts for tied ranks. The Conover-Iman test is strictly valid if
and only if the corresponding Kruskal-Wallis null hypothesis is rejected. /
GPL-2


Name Version
r-conquestr 0.3.7 Extends ‘ACER ConQuest’ by allowing R users to call ‘ACER ConQuest’ from noarch
within R. The user can also access ‘ACER ConQuest’ data objects by reading
‘ACER ConQuest’ System Files (generated by the ‘ACER ConQuest’ com-
mand ‘put’). This is of particular use to those who are parsing text file output
(e.g., ‘show’ files) as this is not consistent across releases of ‘ACER Con-
Quest’. Requires ‘ACER ConQuest’ version 4.29.3 or later. A demonstration
version can be downloaded from <https://shop.acer.edu.au/acer-conquest-4>.
/ GPL-3
r-conspline 1.2 Given response y, continuous predictor x, and covariate matrix, the relation- noarch
ship between E(y) and x is estimated with a shape constrained regression
spline. Function outputs fits and various types of inference. / GPL-2 | GPL-3
r-constants 0.0.2 CODATA internationally recommended values of the fundamental physical noarch
constants, provided as symbols for direct use within the R language. Op-
tionally, the values with errors and/or the values with units are also pro-
vided if the ‘errors’ and/or the ‘units’ packages are installed. The Commit-
tee on Data for Science and Technology (CODATA) is an interdisciplinary
committee of the International Council for Science which periodically pro-
vides the internationally accepted set of values of the fundamental physi-
cal constants. This package contains the 2014 CODATA version, published
on 25 June 2015: Mohr, P. J., Newell, D. B. and Taylor, B. N. (2016)
<DOI:10.1103/RevModPhys.88.035009>, <DOI:10.1063/1.4954402>. / MIT
r-constellation 0.2.0 Examine any number of time series data frames to identify instances in which noarch
various criteria are met within specified time frames. In clinical medicine,
these types of events are often called constellations of signs and symptoms,
because a single condition depends on a series of events occurring within a
certain amount of time of each other. This package was written to work with
any number of time series data frames and is optimized for speed to work well
with data frames with millions of rows. / GPL-2
r-container 0.3.0 Common container data structures deque, set and dict (resembling ‘Python’s noarch
dict type) with typical member functions to insert, delete and access container
elements. Provides iterators and reference semantics. / GPL-3
r-contfrac 1.1_12Various utilities for evaluating continued fractions. / GPL-2 linux-
64,
osx-
64,
win-
64
r-conting 1.7 Bayesian analysis of complete and incomplete contingency tables. / GPL-2 noarch
r- 0.1.1 Provides functions for making contour plots. The contour plot can be created noarch
contourfunctions from grid data, a function, or a data set. If non-grid data is given, then a
Gaussian process is fit to the data and used to create the contour plot. / GPL-3
r-controltest 1.1.0 Nonparametric two-sample procedure for comparing survival quantiles. / noarch
GPL-3
r- 1.4.3 Functions for clustering regions that form convergence clubs, according to the noarch
convergenceclubs definition of Phillips and Sul (2009) <doi:10.1002/jae.1080>. / GPL-3


Name Version
r- 1.2.1 This is a pedagogical package, designed to help students understanding con- noarch
convergenceconcepts vergence of random variables. It provides a way to investigate interactively
various modes of convergence (in probability, almost surely, in law and in
mean) of a sequence of i.i.d. random variables. Visualisation of simulated
sample paths is possible through interactive plots. The approach is illustrated
by examples and exercises through the function ‘investigate’, as described in
Lafaye de Micheaux and Liquet (2009) <http://dx.doi.org/10.1198/tas.2009.
0032>. The user can study his/her own sequences of random variables. / GPL-
2
r-convertgraph 0.1 Converts graphical file formats (SVG, PNG, JPEG, BMP, GIF, PDF, etc) to one noarch
another. The exceptions are the SVG file format that can only be converted to
other formats and in contrast, PDF format, which can only be created from
others graphical formats. The main purpose of the package was to provide
a solution for converting SVG file format to PNG which is often needed for
exporting graphical files produced by R widgets. / MIT
r-coop 0.6_2 Fast implementations of the co-operations: covariance, correlation, and cosine linux-
similarity. The implementations are fast and memory-efficient and their use 64,
is resolved automatically based on the input data, handled by R’s S3 meth- osx-
ods. Full descriptions of the algorithms and benchmarks are available in the 64,
package vignettes. / BSD_2_clause win-
64
r-coppecosenzar 0.1.3 The program implements the COPPE-Cosenza Fuzzy Hierarchy Model. The noarch
model was based on the evaluation of local alternatives, representing regional
potentialities, so as to fulfill demands of economic projects. After defining
demand profiles in terms of their technological coefficients, the degree of im-
portance of factors is defined so as to represent the productive activity. The
method can detect a surplus of supply without the restriction of the distance
of classical algebra, defining a hierarchy of location alternatives. In COPPE-
Cosenza Model, the distance between factors is measured in terms of the dif-
ference between grades of memberships of the same factors belonging to two
or more sets under comparison. The required factors are classified under the
following linguistic variables: Critical (CR); Conditioning (C); Little Condi-
tioning (LC); and Irrelevant (I). And the alternatives can assume the following
linguistic variables: Excellent (Ex), Good (G), Regular (R), Weak (W), Empty
(Em), Zero (Z) and Inexistent (In). The model also provides flexibility, allow-
ing different aggregation rules to be performed and defined by the Decision
Maker. Such feature is considered in this package, allowing the user to de-
fine other aggregation matrices, since it considers the same linguistic variables
mentioned. / GPL-2
r-copula 0.999_19.1
Classes (S4) of commonly used elliptical, Archimedean, extreme-value and linux-
other copula families, as well as their rotations, mixtures and asymmetriza- 32,
tions. Nested Archimedean copulas, related tools and special functions. Meth- linux-
ods for density, distribution, random number generation, bivariate dependence 64,
measures, Rosenblatt transform, Kendall distribution function, perspective and osx-
contour plots. Fitting of copula models with potentially partly fixed parame- 64,
ters, including standard errors. Serial independence tests, copula specification win-
tests (independence, exchangeability, radial symmetry, extreme-value depen- 32,
dence, goodness-of-fit) and model selection based on cross-validation. Empir- win-
ical copula, smoothed versions, and non-parametric estimators of the Pickands 64
dependence function. / GPL (>= 3) | file LICENCE


Name Version
r-copula.markov 2.4 Estimation and statistical process control are performed under copula- noarch
based time-series models. Available are statistical methods in Long
and Emura (2014 JCSA), Emura et al. (2017 Commun Stat-Simul)
<DOI:10.1080/03610918.2015.1073303>, Huang and Emura(2019, in revi-
sion) and Huang, Chen and Emura (2019-, in revision). / GPL-2
r-copula.surv 1.0 Perform association analysis of bivariate survival data based on copula models. noarch
Two different ways to estimate the association parameter in copula models are
implemented. A goodness-of-fit test for a given copula model is implemented.
See Emura, Lin and Wang (2010) <doi.org/10.1016/j.csda.2010.03.013> for
details. / GPL-2
r-copuladata 0.0_1 Data sets used for copula modeling in addition to those in the package ‘cop- noarch
ula’. These include a random subsample from the US National Education
Longitudinal Study (NELS) of 1988 and nursing home data from Wisconsin. /
GPL-3
r-coranking 0.1.4 Calculates the co-ranking matrix to assess the quality of a dimensionality re- linux-
duction. / GPL-3 64,
osx-
64,
win-
64
r-corbin 0.3.1 We design algorithms with linear time complexity with respect to the dimen- noarch
sion for three commonly studied correlation structures, including exchange-
able, decaying-product and K-dependent correlation structures, and extend the
algorithms to generate binary data of general non-negative correlation matri-
ces with quadratic time complexity. Jiang, W., Song, S., Hou, L. and Zhao, H.
CorBin: An efficient R package to generate high-dimensional binary data with
correlation structures. Submitted to Journal of Statistical Software. / GPL-3
r-corclass 0.1.1 Perform a correlational class analysis of the data, resulting in a partition of the noarch
data into separate modules. / GPL-2
r-cord 0.1.1 Partition data points (variables) into communities/clusters, similar to clus- linux-
tering algorithms, such as k-means and hierarchical clustering. This pack- 64,
age implements a clustering algorithm based on a new metric CORD, de- osx-
fined for high dimensional parametric or semi-parametric distributions. Read 64,
http://arxiv.org/abs/1508.01939 for more details. / GPL-3 win-
64
r-core 3.0 given a collection of intervals with integer start and end positions, find recur- noarch
rently targeted regions and estimate the significance of finding. Randomiza-
tion is implemented by parallel methods, either using local host machines, or
submitting grid engine jobs. / GPL-2


Name Version
r-corelearn 1.53.1A suite of machine learning algorithms written in C with the R interface con- linux-
tains several learning techniques for classification and regression. Predictive 64,
models include e.g., classification and regression trees with optional construc- osx-
tive induction and models in the leaves, random forests, kNN, naive Bayes, and 64,
locally weighted regression. All predictions obtained with these models can be win-
explained and visualized with the ‘ExplainPrediction’ package. This package 64
is especially strong in feature evaluation where it contains several variants of
Relief algorithm and many impurity based attribute evaluation functions, e.g.,
Gini, information gain, MDL, and DKM. These methods can be used for fea-
ture selection or discretization of numeric attributes. The OrdEval algorithm
and its visualization is used for evaluation of data sets with ordinal features and
class, enabling analysis according to the Kano model of customer satisfaction.
Several algorithms support parallel multithreaded execution via OpenMP. The
top-level documentation is reachable through ?CORElearn. / GPL-3
r-corenlp 0.4_2 Provides a minimal interface for applying annotators from the ‘Stanford noarch
CoreNLP’ java library. Methods are provided for tasks such as tokenisation,
part of speech tagging, lemmatisation, named entity recognition, coreference
detection and sentiment analysis. / GPL-2
r-coretdt 1.0 Use to analysis case-parent trio sequencing studies. Test the compound het- noarch
erozygous and recessive disease models / GPL-3
r-corlink 1.0.0 A matrix of agreement patterns and counts for record pairs is the input for the noarch
procedure. An EM algorithm is used to impute plausible values for missing
record pairs. A second EM algorithm, incorporating possible correlations be-
tween per-field agreement, is used to estimate posterior probabilities that each
pair is a true match - i.e. constitutes the same individual. / CC0
r-coroica 1.0.1 Contains an implementation of a confounding robust independent component noarch
analysis (ICA) for noisy and grouped data. The main function coroICA()
performs a blind source separation, by maximizing an independence across
sources and allows to adjust for varying confounding based on user-specified
groups. Additionally, the package contains the function uwedge() which can
be used to approximately jointly diagonalize a list of matrices. For more de-
tails see the project website <https://sweichwald.de/coroICA/>. / AGPL-3
r-corpcor 1.6.9 Implements a James-Stein-type shrinkage estimator for the covariance ma- noarch
trix, with separate shrinkage for variances and correlations. The details of the
method are explained in Schafer and Strimmer (2005) <DOI:10.2202/1544-
6115.1175> and Opgen-Rhein and Strimmer (2007) <DOI:10.2202/1544-
6115.1252>. The approach is both computationally as well as statistically very
efficient, it is applicable to small n, large p data, and always returns a positive
definite and well-conditioned covariance matrix. In addition to inferring the
covariance matrix the package also provides shrinkage estimators for partial
correlations and partial variances. The inverse of the covariance and correla-
tion matrix can be efficiently computed, as well as any arbitrary power of the
shrinkage correlation matrix. Furthermore, functions are available for fast sin-
gular value decomposition, for computing the pseudoinverse, and for checking
the rank and positive definiteness of a matrix. / GPL-3
r-corpora 0.5 Utility functions for the statistical analysis of corpus frequency data. This noarch
package is a companion to the open-source course Statistical Inference:
A Gentle Introduction for Computational Linguists and Similar Creatures
(‘SIGIL’). / GPL-3
r-corporacoco 1.1_0 A set of functions used to compare co-occurrence between two corpora. / noarch
GPL-3


Name Version
r-corpus 0.10.0Text corpus data analysis, with full support for international text (Unicode). linux-
Functions for reading data from newline-delimited ‘JSON’ files, for normaliz- 64,
ing and tokenizing text, for searching for term occurrences, and for computing osx-
term occurrence frequencies, including n-grams. / Apache License (== 2.0) | 64,
file LICENSE win-
64
r-corrcoverage 1.0.0 Using a computationally efficient method, the package can be used to find linux-
the corrected coverage estimate of a credible set of putative causal variants 64,
from Bayesian genetic fine-mapping. The package can also be used to ob- osx-64
tain a corrected credible set if required; that is, the smallest set of variants
required such that the corrected coverage estimate of the resultant credible set
is within some user defined accuracy of the desired coverage. Maller et al.
(2012) <doi:10.1038/ng.2435>, Wakefield (2009) <doi:10.1002/gepi.20359>,
Fortune and Wallace (2018) <doi:10.1093/bioinformatics/bty898>. / MIT
r-corrdna 1.0.1 Can be useful for finding associations among different positions in a position- noarch
wise aligned sequence dataset. The approach adopted for finding associations
among positions is based on the latent multivariate normal distribution. / GPL-
2
r-correctedfdr 1.0 There are many estimators of false discovery rate. In this package we com- noarch
pute the Nonlocal False Discovery Rate (NFDR) and the estimators of lo-
cal false discovery rate: Corrected False discovery Rate (CFDR), Re-ranked
False Discovery rate (RFDR) and the blended estimator. Bickel, D. R. (2016)
<http://hdl.handle.net/10393/34277>. / LGPL-3
r- 1.2.17Analyzes and modifies metabolomics raw data (generated using GC-APCI- noarch
correctoverloadedpeaks MS, Gas Chromatography-Atmospheric Pressure Chemical Ionization-Mass
Spectrometry) to correct overloaded signals, i.e. ion intensities exceeding de-
tector saturation leading to a cut-off peak. Data in xcmsRaw format are ac-
cepted as input and mzXML files can be processed alternatively. Overloaded
signals are detected automatically and modified using an Gaussian or Isotopic-
Ratio approach, QC plots are generated and corrected data are stored within
the original xcmsRaw or mzXML respectively to allow further processing. /
GPL-3
r-correlplot 1.0_2 Correlplot contains diverse routines for the construction of different plots for noarch
representing correlation matrices. / GPL-2
r-corrmixed 0.1_13In clinical practice and research settings in medicine and the behavioral sci- noarch
ences, it is often of interest to quantify the correlation of a continuous end-
point that was repeatedly measured (e.g., test-retest correlations, ICC, etc.).
This package allows for estimating these correlations based on mixed-effects
models. Part of this software has been developed using funding provided from
the European Union’s 7th Framework Programme for research, technological
development and demonstration under Grant Agreement no 602552. / GPL-2
r-corrplot 0.84 A graphical display of a correlation matrix or general matrix. It also contains noarch
some algorithms to do matrix reordering. In addition, corrplot is good at de-
tails, including choosing color, text labels, color labels, layout, etc. / GPL-3
r-corrsieve 1.6_8 Statistical summary of Structure output. / GPL-3 noarch
r-corset 0.1_4 Set of methods to constrain numerical series and time series within arbitrary noarch
boundaries. / GPL-3


Name Version
r-cortest 0.9.8 There are 6 novel robust tests for equal correlation. They are all based on logis- noarch
tic regressions. U are proportion to different types of correlation in 6 methods.
The ST1() is based on Pearson correlation. ST2() improved ST1() by using
median absolute deviation. ST3() utilized type M correlation and ST4() used
Spearman correlation. ST5() and ST6() used two different ways to combine
ST3() and ST4(). We highly recommend ST5() according to the passage New
Statistical Methods for Constructing Robust Differential Correlation Networks
to characterize the interactions among microRNAs published in Scientific Re-
ports. / GPL-2
r-cortools 1.0 Designed for analysis of the results of a Genome Wide Association Study. noarch
Includes tools to pull lists of Chromosome number and SNP position below
a certain significance threshold, refine gene networks (including data I/O for
Cytoscape), and check SNP base pair changes. / Artistic-2.0
r-cosmofns 1.0_1 Package encapsulates standard expressions for distances, times, luminosities, noarch
and other quantities useful in observational cosmology, including molecular
line observations. Currently coded for a flat universe only. / GPL-2
r-cost 0.1.0 Parameter estimation, one-step ahead forecast and new location prediction noarch
methods for spatio-temporal data. / GPL-3
r-costsensitive 0.1.2.10
Reduction-based techniques for cost-sensitive multi-class classification, in linux-
which each observation has a different cost for classifying it into one class, 64,
and the goal is to predict the class with the minimum expected cost for osx-
each new observation. Implements Weighted All-Pairs (Beygelzimer, A., 64,
Langford, J., & Zadrozny, B., 2008, <doi:10.1007/978-0-387-79361-0_1>), win-
Weighted One-Vs-Rest (Beygelzimer, A., Dani, V., Hayes, T., Langford, J., & 64
Zadrozny, B., 2005, <https://dl.acm.org/citation.cfm?id=1102358>) and Re-
gression One-Vs-Rest. Works with arbitrary classifiers taking observation
weights, or with regressors. Also implements cost-proportionate rejection
sampling for working with classifiers that don’t accept observation weights.
/ BSD_2_clause
r-cotrend 1.0.1 Implements cointegration/cotrending rank selection algorithm in noarch
Guo and Shintani (2013) Consistant cotrending rank selection
when both stochastic and nonlinear deterministic trends are present.
The Econometrics Journal 16: 473-483 <doi:10.1111/j.1368-
423X.2012.00392.x>. Numbered examples correspond to Feb
2011 preprint <http://www.fas.nus.edu.sg/ecs/events/seminar/seminar-
papers/05Apr11.pdf>. / GPL-3
r-couchdb 1.4.1 Interface to the couchDB document database <http://couchdb.apache.org>. / noarch
AGPL-3
r-countgmifs 0.0.1 Provides a function for fitting Poisson and negative binomial regression mod- noarch
els when the number of parameters exceeds the sample size, using the the
generalized monotone incremental forward stagewise method. / GPL-2
r-counthmm 0.1.0 Provides tools for penalized estimation of flexible hidden Markov models for noarch
time series of counts w/o the need to specify a (parametric) family of distri-
butions. These include functions for model fitting, model checking, and state
decoding. For details, see Adam, T., Langrock, R., and WeiÃŸ, C.H. (2019):
Penalized Estimation of Flexible Hidden Markov Models for Time Series of
Counts. <arXiv:1901.03275>. / GPL-3
r-countrycode 1.1.0 Standardize country names, convert them into one of eleven coding schemes, noarch
convert between coding schemes, and assign region descriptors. / GPL-3


Name Version
r-covafillr 0.4.3 Facilitates local polynomial regression for state dependent covariates in state- linux-
space models. The functionality can also be used from ‘C’ based model builder 64,
tools such as ‘Rcpp’/’inline’, ‘TMB’, or ‘JAGS’. / BSD_2_clause osx-
64,
win-
64
r-covbm 0.1.0 Allows Brownian motion, fractional Brownian motion, and integrated linux-
Ornstein-Uhlenbeck process components to be added to linear and non-linear 64,
mixed effects models using the structures and methods of the ‘nlme’ package. osx-
/ GPL-3 64,
win-
64
r-covfefe 0.1.0 Converts any word, sentence or speech into Trump’s infamous cov- noarch
fefe format. Reference: <https://www.nytimes.com/2017/05/31/us/politics/
covfefe-trump-twitter.html>. Inspiration thanks to: <https://codegolf.
stackexchange.com/questions/123685/covfefify-a-string>. / GPL-3
r-covr 3.3.1 Track and report code coverage for your package and (optionally) upload the linux-
results to a coverage service like ‘Codecov’ <http://codecov.io> or ‘Coveralls’ 64,
<http://coveralls.io>. Code coverage is a measure of the amount of code be- osx-
ing exercised by a set of tests. It is an indirect measure of test quality and 64,
completeness. This package is compatible with any testing methodology or win-
framework and tracks coverage of both R code and compiled C/C/FORTRAN 64
code. / GPL-3
r-covreg 1.0 This package fits a simultaneous regression model for the mean vectors and noarch
covariance matrices of multivariate response variables, as described in Hoff
and Niu (2012). The explanatory variables can be continuous or discrete. The
current version of the package provides the Bayesian estimates. / GPL-2
r-covrobust 1.1_3 The cov.nnve() function implements robust covariance estimation by the near- noarch
est neighbor variance estimation (NNVE) method of Wang and Raftery (2002)
<DOI:10.1198/016214502388618780>. / GPL-2
r-covsep 1.1.0 Functions for testing if the covariance structure of 2-dimensional data (e.g. noarch
samples of surfaces X_i = X_i(s,t)) is separable, i.e. if covariance(X) =
C_1 x C_2. A complete descriptions of the implemented tests can be found
in the paper Aston, John A. D.; Pigoli, Davide; Tavakoli, Shahin. Tests
for separability in nonparametric covariance operators of random surfaces.
Ann. Statist. 45 (2017), no. 4, 1431–1461. <doi:10.1214/16-AOS1495>
<https://projecteuclid.org/euclid.aos/1498636862> <arXiv:1505.02023>. /
GPL-2
r-covtestr 0.1.4 Testing functions for Covariance Matrices. These tests include high- linux-
dimension homogeneity of covariance matrix testing described by Schott 64,
(2007) <doi:10.1016/j.csda.2007.03.004> and high-dimensional one-sample osx-
tests of covariance matrix structure described by Fisher, et al. (2010) 64,
<doi:10.1016/j.jmva.2010.07.004>. Covariance matrix tests use C to speed win-
performance and allow larger data sets. / GPL-2 64
r-coxboost 1.4 This package provides routines for fitting Cox models by likelihood based linux-
boosting for a single endpoint or in presence of competing risks / GPL-2 64,
osx-
64,
win-
64


Name Version
r-coxme 2.2_14This package fits Cox proportional hazards models containing both fixed and linux-
random effects. The random effects can have a general form, of which famil- 64,
ial interactions (a kinship matrix) is a particular special case. Note that the osx-
simplest case of a mixed effects Cox model, i.e. a single random per-group 64,
intercept, is also called a frailty model. The approach is based on Rippatti and win-
Palgren, Biometrics 2002. / LGPL-2 64
r-coxphf 1.13 Implements Firth’s penalized maximum likelihood bias reduction method for linux-
Cox regression which has been shown to provide a solution in case of mono- 64,
tone likelihood (nonconvergence of likelihood function). The program fits pro- osx-
file penalized likelihood confidence intervals which were proved to outperform 64,
Wald confidence intervals. / GPL-3 win-
64
r-coxphlb 1.2.0 Performs analysis of right-censored length-biased data using Cox model. It noarch
contains model fitting and checking, and the stationarity assumption test. The
model fitting and checking methods are described in Qin and Shen (2010)
<doi:10.1111/j.1541-0420.2009.01287.x> and Lee, Ning, and Shen (2018)
<doi:10.1007/s10985-018-9422-y>. / GPL-2
r-coxphmic 0.1.0 Sparse estimation for Cox PH models is done via Minimum approximated noarch
Information Criterion (MIC) by Su, Wijayasinghe, Fan, and Zhang (2016)
<DOI:10.1111/biom.12484>. MIC mimics the best subset selection using a
penalized likelihood approach yet with no need of a tuning parameter. The
problem is further reformulated with a re-parameterization step so that it re-
duces to one unconstrained non-convex yet smooth programming problem,
which can be solved efficiently. Furthermore, the re-parameterization tactic
yields an additional advantage in terms of circumventing post-selection infer-
ence. / GPL-2
r-coxphsgd 0.2.1 Estimate coefficients of Cox proportional hazards model using stochastic gra- noarch
dient descent algorithm for batch data. / GPL-2
r-coxphw 4.0.1 Implements weighted estimation in Cox regression as proposed by Schemper, linux-
Wakounig and Heinze (Statistics in Medicine, 2009, <doi:10.1002/sim.3623>) 64,
and as described in Dunkler, Ploner, Schemper and Heinze (Journal of Sta- osx-
tistical Software, 2018, <doi:10.18637/jss.v084.i02>). Weighted Cox regres- 64,
sion provides unbiased average hazard ratio estimates also in case of non- win-
proportional hazards. Approximated generalized concordance probability an 64
effect size measure for clear-cut decisions can be obtained. The package pro-
vides options to estimate time-dependent effects conveniently by including in-
teractions of covariates with arbitrary functions of time, with or without mak-
ing use of the weighting option. / GPL-2
r-coxplus 1.1.1 A high performance package estimating Cox Model when an even has more linux-
than one causes. It also supports random and fixed effects, tied events, and 64,
time-varying variables. / GPL-3 osx-
64,
win-
64


Name Version
r-coxridge 0.9.2 A package for fitting Cox models with penalized ridge-type partial likelihood. noarch
The package includes functions for fitting simple Cox models with all covari-
ates controlled by a ridge penalty. The weight of the penalty is optimised
by using a REML type-algorithm. Models with time varying effects of the
covariates can also be fitted. Some of the covariates may be allowed to be
fixed and thus not controlled by the penalty. There are three different penalty
functions, ridge, dynamic and weighted dynamic. Time varying effects can be
fitted without the need of an expanded dataset. / GPL-2
r-coxrobust 1.0 Fit robustly proportional hazards regression model / GPL-2 linux-
64,
osx-
64,
win-
64
r-coxsei 0.1 It fits a CoxSEI (Cox type Self-Exciting Intensity) model to right-censored linux-
counting process data. / GPL-2 64,
osx-
64,
win-
64
r-cp 1.6 Functions for calculating the conditional power for different models in survival noarch
time analysis within randomized clinical trials with two different treatments to
be compared and survival as an endpoint. / GPL-3
r-cpa 1.0 The package includes functions to test and compare causal models. / GPL-2 noarch
r-cpca 0.1.2 This package contains methods to perform Common Principal Component noarch
Analysis (CPCA). The stepwise method by Trendafilov is published in the
current version. Please see Trendafilov (2010). Stepwise estimation of com-
mon principal components. Computational Statistics & Data Analysis, 54(12),
3446-3457. doi:10.1016/j.csda.2010.03.010 / GPL-3
r-cpcg 1.0 Solves system of linear equations using (preconditioned) conjugate gradient linux-
algorithm, with improved efficiency using Armadillo templated ‘C’ linear al- 64,
gebra library, and flexibility for user-specified preconditioning method. Please osx-
check <https://github.com/styvon/cPCG> for latest updates. / GPL-2 64,
win-
64
r-cpgassoc 2.60 Is designed to test for association between methylation at CpG sites across the noarch
genome and a phenotype of interest, adjusting for any relevant covariates. The
package can perform standard analyses of large datasets very quickly with no
need to impute the data. It can also handle mixed effects models with chip
or batch entering the model as a random intercept. Also includes tools to
apply quality control filters, perform permutation tests, and create QQ plots,
manhattan plots, and scatterplots for individual CpG sites. / GPL-2
r-cpgfilter 1.1 Filter CpGs based on Intra-class Correlation Coefficients (ICCs) when repli- noarch
cates are available. ICCs are calculated by fitting linear mixed effects models
to all samples including the un-replicated samples. Including the large number
of un-replicated samples improves ICC estimates dramatically. The method
accommodates any replicate design. / GPL-3


Name Version
r-cpk 1.3_1 The package cpk provides simplified clinical pharmacokinetic functions for noarch
dose regimen design and modification at the point-of-care. Currently, the fol-
lowing functions are available: (1) ttc.fn for target therapeutic concentration,
(2) dr.fn for dose rate, (3) di.fn for dosing interval, (4) dm.fn for maintenance
dose, (5) bc.ttc.fn for back calculation, (6) ar.fn for accumulation ratio, (7)
dpo.fn for orally administered dose, (8) cmax.fn for peak concentration, (9)
css.fn for steady-state concentration, (10) cmin.fn for trough,(11) ct.fn for
concentration-time predictions, (12) dlcmax.fn for calculating loading dose
based on drug’s maximum concentration, (13) dlar.fn for calculating loading
dose based on drug’s accumulation ratio, and (14) R0.fn for calculating drug
infusion rate. Reference: Linares O, Linares A. Computational opioid pre-
scribing: A novel application of clinical pharmacokinetics. J Pain Palliat Care
Pharmacother 2011;25:125-135. / GPL-2
r-cplots 0.4_0 Provides functions to produce some circular plots for circular data, in a noarch
height- or area-proportional manner. They include barplots, smooth density
plots, stacked dot plots, histograms, multi-class stacked smooth density plots,
and multi-class stacked histograms. The new methodology for general area-
proportional circular visualization is described in an article submitted (after
revision) to Journal of Computational and Graphical Statistics. / GPL-2
r-cpm 2.2 Sequential and batch change detection for univariate data streams, using the linux-
change point model framework. Functions are provided to allow nonparamet- 64,
ric distribution-free change detection in the mean, variance, or general dis- osx-
tribution of a given sequence of observations. Parametric change detection 64,
methods are also provided for Gaussian, Bernoulli and Exponential sequences. win-
Both the batch (Phase I) and sequential (Phase II) settings are supported, and 64
the sequences may contain either a single or multiple change points. / GPL-3
r-cpmcglm 1.2 We propose to determine the correction of the significance level after multiple noarch
coding of an explanatory variable in Generalized Linear Model. The different
methods of correction of the p-value are the Single step Bonferroni procedure,
and resampling based methods developed by P.H.Westfall in 1993. Resam-
pling methods are based on the permutation and the parametric bootstrap pro-
cedure. If some continuous, and dichotomous transformations are performed
this package offers an exact correction of the p-value developed by B.Liquet &
D.Commenges in 2005. The naive method with no correction is also available.
/ GPL (> 2)
r-cpprouting 1.1 Calculation of distances, shortest paths and isochrones on weighted graphs linux-
using several variants of Dijkstra algorithm. Proposed algorithms are unidi- 64,
rectional Dijkstra (Dijkstra, E. W. (1959) <doi:10.1007/BF01386390>), bidi- osx-
rectional Dijkstra (Goldberg, Andrew & Fonseca F. Werneck, Renato (2005) 64,
<https://pdfs.semanticscholar.org/0761/18dfbe1d5a220f6ac59b4de4ad07b50283ac.pdf>), win-
A* search (P. E. Hart, N. J. Nilsson et B. Raphael (1968) 64
<doi:10.1109/TSSC.1968.300136>), new bidirectional A* (Pijls & Post
(2009) <http://repub.eur.nl/pub/16100/ei2009-10.pdf>). / GPL-2
r-cprr 0.2.0 Calculate date of birth, age, and gender, and generate anonymous sequence noarch
numbers from CPR numbers. <https://en.wikipedia.org/wiki/Personal_
identification_number_(Denmark)>. / GPL-3
r-cpt 1.0.2 Non-parametric test for equality of multivariate distributions. Trains a classi- noarch
fier to classify (multivariate) observations as coming from one of several dis-
tributions. If the classifier is able to classify the observations better than would
be expected by chance (using permutation inference), then the null hypothesis
that the distributions are equal is rejected. / GPL-3


Name Version
r-cptcity 1.0.4 Incorporates colour gradients from the ‘cpt-city’ web archive available at noarch
<http://soliton.vm.bytemark.co.uk/pub/cpt-city/>. / GPL-3
r-cptec 0.1.0 Allows to retrieve data from the ‘CPTEC/INPE’ weather forecast API. noarch
‘CPTEC’ stands for ‘Centro de Previsão de Tempo e Estudos Climáticos’ and
‘INPE’ for ‘Instituto Nacional de Pesquisas Espaciais’. ‘CPTEC’ is the most
advanced numerical weather and climate forecasting center in Latin Amer-
ica, with high-precision short and medium-term weather forecasting since the
beginning of 1995. See <http://www.cptec.inpe.br/> for more information. /
GPL-3
r-cqrreg 1.2 Estimate quantile regression(QR) and composite quantile regression (cqr) linux-
and with adaptive lasso penalty using interior point (IP), majorize and mini- 64,
mize(MM), coordinate descent (CD), and alternating direction method of mul- osx-
tipliers algorithms(ADMM). / GPL-2 64,
win-
64
r-cr 1.0 This package contains R-functions to perform power calculation in a group se- noarch
quential clinical trial with censored survival data and possibly unequal patient
allocation between treatment and control groups. The fuctions can also be
used to determine the study duration in a clinical trial with censored survival
data as the sum of the accrual duration, which determines the sample size in a
traditional sense, and the follow-up duration, which more or less controls the
number of events to be observed. This package also contains R functions and
methods to display the computed results. / GPL-2
r-crac 1.0 R functions for cosmological research. The main functions are similar to the noarch
python library, cosmolopy. / GPL-2
r-cramer 0.9_3 Provides R routine for the so called two-sample Cramer-Test. This nonpara- noarch
metric two-sample-test on equality of the underlying distributions can be ap-
plied to multivariate data as well as univariate data. It offers two possibilities
to approximate the critical value both of which are included in this package. /
GPL-2
r-crank 1.1_2 Functions for completing and recalculating rankings and sorting. / GPL-2 noarch
r-cranlogs 2.1.1 ‘API’ to the database of ‘CRAN’ package downloads from the ‘RStudio’ noarch
‘CRAN mirror’. The database itself is at <http://cranlogs.r-pkg.org>, see
<https://github.com/r-hub/cranlogs.app> for the raw ‘API’. / MIT
r-crantastic 0.1 Various R tools for http://crantastic.org/ / GPL-2 noarch
r-crayon 1.3.4 Colored terminal output on terminals that support ‘ANSI’ color and highlight linux-
codes. It also works in ‘Emacs’ ‘ESS’. ‘ANSI’ color support is automatically 32,
detected. Colors and highlighting can be combined and nested. New styles can linux-
also be created easily. This package was inspired by the ‘chalk’ ‘JavaScript’ 64,
project. / MIT file LICENSE noarch,
osx-
64,
win-
32,
win-
64
r-crblocks 1.0_0 Implements a statistical test for comparing bar plots or histograms of categor- noarch
ical data derived from a randomized block repeated measures layout. / GPL-3


Name Version
r-cream 1.1.1 Provides a new method for identification of clusters of genomic regions within noarch
chromosomes. Primarily, it is used for calling clusters of cis-regulatory el-
ements (COREs). ‘CREAM’ uses genome-wide maps of genomic regions in
the tissue or cell type of interest, such as those generated from chromatin-based
assays including DNaseI, ATAC or ChIP-Seq. ‘CREAM’ considers proximity
of the elements within chromosomes of a given sample to identify COREs
in the following steps: 1) It identifies window size or the maximum allowed
distance between the elements within each CORE, 2) It identifies number of
elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters
the COREs with lowest order which does not pass the threshold considered in
the approach. / GPL-3
r-credentials 1.1 Setup and retrieve HTTPS and SSH credentials for use with ‘git’ and other noarch
services. For HTTPS remotes the package interfaces the ‘git-credential’ utility
which ‘git’ uses to store HTTP usernames and passwords. For SSH remotes
we provide convenient functions to find or generate appropriate SSH keys.
The package both helps the user to setup a local git installation, and also pro-
vides a back-end for git/ssh client libraries to authenticate with existing user
credentials. / MIT
r-creditmetrics 0.0_2 A set of functions for computing the CreditMetrics risk model / Unlimited noarch
r-credsubs 1.0.1 Functions for constructing simultaneous credible bands and identifying subsets noarch
via the credible subsets (also called credible subgroups) method. / GPL-3
r-credule 0.1.3 It provides functions to bootstrap Credit Curves from market quotes (Credit linux-
Default Swap - CDS - spreads) and price Credit Default Swaps - CDS. / MIT 64,
osx-
64,
win-
64
r-crf 0.4_2 Implements modeling and computational tools for conditional random fields linux-
(CRF) model as well as other probabilistic undirected graphical models of 64,
discrete data with pairwise and unary potentials. / GPL-2 osx-
64,
win-
64
r-crfsuite 0.3 Wraps the ‘CRFsuite’ library <https://github.com/chokkan/crfsuite> allowing linux-
users to fit a Conditional Random Field model and to apply it on existing data. 64,
The focus of the implementation is in the area of Natural Language Processing osx-
where this R package allows you to easily build and apply models for named 64,
entity recognition, text chunking, part of speech tagging, intent recognition or win-
classification of any category you have in mind. Next to training, a small web 64
application is included in the package to allow you to easily construct training
data. / BSD_3_clause
r-crimcv 0.9.6 A finite mixture of Zero-Inflated Poisson (ZIP) models for analyzing criminal linux-
trajectories. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-crisp 1.0.0 Implements convex regression with interpretable sharp partitions (CRISP), noarch
which considers the problem of predicting an outcome variable on the ba-
sis of two covariates, using an interpretable yet non-additive model. CRISP
partitions the covariate space into blocks in a data-adaptive way, and fits a
mean model within each block. Unlike other partitioning methods, CRISP
is fit using a non-greedy approach by solving a convex optimization prob-
lem, resulting in low-variance fits. More details are provided in Petersen,
A., Simon, N., and Witten, D. (2016). Convex Regression with Interpretable
Sharp Partitions. Journal of Machine Learning Research, 17(94): 1-31 <http:
//jmlr.org/papers/volume17/15-344/15-344.pdf>. / GPL-2
r-crm 1.2.4 Functions for phase I clinical trials using the continual reassessment method. linux-
/ GPL-2 64,
osx-
64,
win-
64
r-crn 1.1 The crn package provides the core functions required to download and format noarch
data from the Climate Reference Network. Both daily and hourly data are
downloaded from the ftp, a consolidated file of all stations is created, station
metadata is extracted. In addition functions for selecting individual variables
and creating R friendly datasets for them is provided. / GPL-2
r-crochet 2.2.0 Functions to help implement the extraction / subsetting / indexing function ‘[’ noarch
and replacement function ‘[<-’ of custom matrix-like types (based on S3, S4,
etc.), modeled as closely to the base matrix class as possible (with tests to
prove it). / MIT
r-crone 0.1.1 Functions to carry out the most important crystallographic calculations for noarch
crystal structures made of 1d Gaussian-shaped atoms, especially useful for
methods development. Main reference: E. Smith, G. Evans, J. Foadi (2017)
<doi:10.1088/1361-6404/aa8188>. / GPL-2
r-cronr 0.4.0 Create, edit, and remove ‘cron’ jobs on your unix-alike system. The package noarch
provides a set of easy-to-use wrappers to ‘crontab’. It also provides an RStudio
add-in to easily launch and schedule your scripts. / MIT
r-crop 0.0_2 A device closing function which is able to crop graphics (e.g., PDF, PNG files) noarch
on Unix-like operating systems with the required underlying command-line
tools installed. / GPL-2 | GPL-3
r-cropdatape 1.0.0 Provides peruvian agricultural production data from the Agriculture Minestry noarch
of Peru (MINAGRI). The first version includes 6 crops: rice, quinoa, potato,
sweet potato, tomato and wheat; all of them across 24 departments. Initially,
in excel files which has been transformed and assembled using tidy data prin-
ciples, i.e. each variable is in a column, each observation is a row and each
value is in a cell. The variables variables are sowing and harvest area per crop,
yield, production and price per plot, every one year, from 2004 to 2014. / MIT
r-crossdes 1.1_1 Contains functions for the construction of carryover balanced crossover de- noarch
signs. In addition contains functions to check given designs for balance. /
GPL-2
r-crossreg 1.0 This package provides functions to calculate confidence intervals for crossover noarch
points of two simple linear regression lines using the non-linear regression, the
delta method, the Fieller method, and the bootstrap methods. / GPL-2


Name Version
r-crosstalk 1.0.0 Provides building blocks for allowing HTML widgets to communicate with linux-
each other, with Shiny or without (i.e. static .html files). Currently supports 32,
linked brushing and filtering. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-crossva 0.9.9 Enables transformation of Verbal Autopsy data collected with the WHO noarch
2016 questionnaire (versions 1.4.1 & 1.5.1) or the WHO 2014 questionnaire
for automated coding of Cause of Death using the InSilicoVA (data.type =
WHO2016) and InterVA5 algorithms. Previous versions of this package sup-
ported user-supplied mappings (via the map_records function), but this func-
tionality has been removed. This package is made available by WHO and the
Bloomberg Data for Health Initiative. / GPL-3
r-crossval 1.0.3 Contains generic functions for performing cross validation and for computing noarch
diagnostic errors. / GPL-3
r-crov 0.1.3 Fits a constrained regression model for an ordinal response with ordinal pre- noarch
dictors and possibly others, Espinosa and Hennig (2018) <arXiv:1804.08715>.
The parameter estimates associated with an ordinal predictor are constrained
to be monotonic. If a monotonicity direction (isotonic or antitonic) is not spec-
ified for an ordinal predictor by the user, then the monotonicity direction clas-
sification procedure establishes it. A monotonicity test is also available to test
the null hypothesis of monotonicity over a set of parameters associated with
an ordinal predictor. / GPL-2
r-crp.csfp 2.0.2 Modelling credit risks based on the concept of CreditRisk, First Boston Fi- noarch
nancial Products, 1997 and CreditRisk in the Banking Industry, Gundlach &
Lehrbass, Springer, 2003. / GPL-2
r-crrp 1.0 In competing risks regression, the proportional subdistribution hazards(PSH) linux-
model is popular for its direct assessment of covariate effects on the cumula- 64,
tive incidence function. This package allows for penalized variable selection osx-
for the PSH model. Penalties include LASSO, SCAD, MCP, and their group 64,
versions. / GPL-2 win-
64
r-crrsc 1.1 Extension of cmprsk to Stratified and Clustered data. Goodness of fit test for linux-
Fine-Gray model. / GPL-2 64,
osx-
64,
win-
64
r-crrstep 2015_2.1
Performs forward and backwards stepwise regression for the Proportional sub- noarch
distribution hazards model in competing risks (Fine & Gray 1999). Procedure
uses AIC, BIC and BICcr as selection criteria. BICcr has a penalty of k =
log(n*), where n* is the number of primary events. / GPL-2


Name Version
r-crseeventstudy 1.2 Based on Dutta et al. (2018) <doi:10.1016/j.jempfin.2018.02.004>, this pack- noarch
age provides their standardized test for abnormal returns in long-horizon event
studies. The methods used improve the major weaknesses of size, power,
and robustness of long-run statistical tests described in Kothari/Warner (2007)
<doi:10.1016/B978-0-444-53265-7.50015-9>. Abnormal returns are weighted
by their statistical precision (i.e., standard deviation), resulting in abnormal
standardized returns. This procedure efficiently captures the heteroskedas-
ticity problem. Clustering techniques following Cameron et al. (2011)
<10.1198/jbes.2010.07136> are adopted for computing cross-sectional corre-
lation robust standard errors. The statistical tests in this package therefore
accounts for potential biases arising from returns’ cross-sectional correlation,
autocorrelation, and volatility clustering without power loss. / BSD_3_clause
r-crskdiag 1.0.1 Provides the implementation of analytical and graphical approaches for check- linux-
ing the assumptions of the Fine and Gray model. / GPL-2 64,
osx-
64,
win-
64
r-crsnls 0.2 Functions for nonlinear regression parameters estimation by algorithms based noarch
on Controlled Random Search algorithm. Both functions (crs4hc(), crs4hce())
adapt current search strategy by four heuristics competition. In addition,
crs4hce() improves adaptability by adaptive stopping condition. / GPL-2
r-crso 0.1.1 An algorithm for identifying candidate driver combinations in cancer. CRSO noarch
is based on a theoretical model of cancer in which a cancer rule is defined to
be a collection of two or more events (i.e., alterations) that are minimally suffi-
cient to cause cancer. A cancer rule set is a set of cancer rules that collectively
are assumed to account for all of ways to cause cancer in the population. In
CRSO every event is designated explicitly as a passenger or driver within each
patient. Each event is associated with a patient-specific, event-specific passen-
ger penalty, reflecting how unlikely the event would have happened by chance,
i.e., as a passenger. CRSO evaluates each rule set by assigning all samples to
a rule in the rule set, or to the null rule, and then calculating the total statistical
penalty from all unassigned event. CRSO uses a three phase procedure find
the best rule set of fixed size K for a range of Ks. A core rule set is then iden-
tified from among the best rule sets of size K as the rule set that best balances
rule set size and statistical penalty. Users should consult the ‘crso’ vignette
for an example walk through of a full CRSO run. The full description, of the
CRSO algorithm is presented in: Klein MI, Cannataro V, Townsend J, Stern
DF and Zhao H. Identifying combinations of cancer driver in individual pa-
tients. BioRxiv 674234 [Preprint]. June 19, 2019. <doi:10.1101/674234>.
Please cite this article if you use ‘crso’. / GPL-2
r-crtsize 1.0 Sample size estimation in cluster (group) randomized trials. Contains tra- noarch
ditional power-based methods, empirical smoothing (Rotondi and Donner,
2009), and updated meta-analysis techniques (Rotondi and Donner, 2012). /
GPL-2
r-crwrm 0.0.1 To re-calculate the coefficients and the standard deviation when changing the noarch
reference group. / GPL-3
r-cseqpat 0.1.2 Mines contiguous sequential patterns in text. / MIT noarch
r-cshapes 0.6 Package for CShapes, a GIS dataset of country boundaries (1946-today). In- noarch
cludes functions for data extraction and the computation of distance matrices
and -lists. / GPL-2


Name Version
r-csn 1.1.3 Provides functions for computing the density and the log-likelihood function noarch
of closed-skew normal variates, and for generating random vectors sampled
from this distribution. See Gonzalez-Farias, G., Dominguez-Molina, J., and
Gupta, A. (2004). The closed skew normal distribution, Skew-elliptical dis-
tributions and their applications: a journey beyond normality, Chapman and
Hall/CRC, Boca Raton, FL, pp. 25-42. / GPL-2
r-csp 0.1.0 Provides the Correlates of State Policy data set for easy use in R. / CC0 noarch
r-csrplus 1.03_0Includes two functions to evaluate the hypothesis of complete spatial random- noarch
ness (csr) in point processes. The function ‘mwin’ calculates quadrat counts
to estimate the intensity of a spatial point process through the moving window
approach proposed by Bailey and Gatrell (1995). Event counts are computed
within a window of a set size over a fine lattice of points within the region of
observation. The function ‘pielou’ uses the nearest neighbor test statistic and
asymptotic distribution proposed by Pielou (1959) to compare the observed
point process to one generated under csr. The value can be compared to that
given by the more widely used test proposed by Clark and Evans (1954). /
GPL-2
r-cssam 1.2.4 Cell-type specific differential expression of a microarray experiment of het- noarch
erogeneous tissue samples, using SAM. / LGPL-3
r-cstar 1.0 Functions that allow a researcher to examine the robustness of the substantive noarch
significance of their findings. Implements ideas set out in Esarey and Danne-
man (2014). / GPL-2
r-csv 0.5.3 Reads and writes CSV with selected conventions. Uses the same generic func- noarch
tion for reading and writing to promote consistent formats. / GPL-3
r-csvread 1.2.1 Functions for loading large (10M lines) CSV and other delimited files, sim- linux-
ilar to read.csv, but typically faster and using less memory than the standard 64,
R loader. While not entirely general, it covers many common use cases when osx-
the types of columns in the CSV file are known in advance. In addition, the 64,
package provides a class ‘int64’, which represents 64-bit integers exactly when win-
reading from a file. The latter is useful when working with 64-bit integer iden- 64
tifiers exported from databases. The CSV file loader supports common column
types including ‘integer’, ‘double’, ‘string’, and ‘int64’, leaving further type
transformations to the user. / Apache License (== 2.0)
r-csvy 0.3.0 Support for import from and export to the CSVY file format. CSVY is a file noarch
format that combines the simplicity of CSV (comma-separated values) with
the metadata of other plain text and binary formats (JSON, XML, Stata, etc.)
by placing a YAML header on top of a regular CSV. / GPL-2
r-cthresher 1.1.0 Estimation and inference methods for the continuous threshold expectile re- noarch
gression. It can fit the continuous threshold expectile regression and test the
existence of change point, for the paper, Feipeng Zhang and Qunhua Li (2016).
A continuous threshold expectile regression, submitted. / GPL (>= 2.0)
r-ctrdata 0.18.2Provides functions for querying, retrieving and analysing protocol- and results- noarch
related information on clinical trials from two public registers, the European
Union Clinical Trials Register (EUCTR, <https://www.clinicaltrialsregister.
eu/>) and ClinicalTrials.gov (CTGOV, <https://clinicaltrials.gov/>). The in-
formation is transformed and then stored in a database (mongo). Functions
are provided for accessing and analysing the locally stored information on the
clinical trials, as well as for identifying duplicate records. The package is mo-
tivated by the need for aggregating and trend-analysing the design, conduct
and outcomes across clinical trials. / MIT


Name Version
r-ctrlgene 1.0.1 A simple way to assess the stability of candidate housekeeping genes is imple- noarch
mented in this package. / GPL-2
r-cts 1.0_22Functions to fit continuous time autoregressive models with the Kalman filter linux-
(Wang (2013) <doi:10.18637/jss.v053.i05>). / GPL-2 64,
osx-
64,
win-
64
r-ctt 2.3.3 A collection of common test and item analyses from a classical test theory noarch
(CTT) framework. Analyses can be applied to both dichotomous and poly-
tomous data. Functions provide reliability analyses (alpha), item statistics,
disctractor analyses, disattenuated correlations, scoring routines, and empiri-
cal ICCs. / GPL-2
r-cttinshiny 0.1.0 A Shiny interface developed in close coordination with the CTT package, pro- noarch
viding a GUI that guides the user through CTT analyses. / GPL-2
r-ctv 0.8_5 Infrastructure for task views to CRAN-style repositories: Querying task views linux-
and installing the associated packages (client-side tools), generating HTML 32,
pages and storing task view information in the repository (server-side tools). / linux-
GPL-2 | GPL-3 64,
noarch,
osx-
64,
win-
32,
win-
64
r-cub 1.1.3 For ordinal rating data, estimate and test models within the family of CUB noarch
models and their extensions (where CUB stands for Combination of a discrete
Uniform and a shifted Binomial distributions). Simulation routines, plotting
facilities and fitting measures are also provided. / GPL-2 | GPL-3
r-cubature 2.0.3 R wrappers around the cubature C library of Steven G. Johnson for adaptive linux-
multivariate integration over hypercubes and the Cuba C library of Thomas 64,
Hahn for deterministic and Monte Carlo integration. Scalar and vector inter- osx-
faces for cubature and Cuba routines are provided; the vector interfaces are 64,
highly recommended as demonstrated in the package vignette. / GPL-3 win-
64
r-cubeview 0.1.0 Creates a 3D data cube view of a RasterStack/Brick, typically a collec- noarch
tion/array of RasterLayers (along z-axis) with the same geographical extent (x
and y dimensions) and resolution, provided by package ‘raster’. Slices through
each dimension (x/y/z), freely adjustable in location, are mapped to the visible
sides of the cube. The cube can be freely rotated. Zooming and panning can
be used to focus on different areas of the cube. / MIT
r-cubfits 0.1_3 Estimating mutation and selection coefficients on synonymous codon bias us- linux-
age based on models of ribosome overhead cost (ROC). Multinomial logistic 64,
regression and Markov Chain Monte Carlo are used to estimate and predict osx-
protein production rates with/without the presence of expressions and mea- 64,
surement errors. Work flows with examples for simulation, estimation and win-
prediction processes are also provided with parallelization speedup. The whole 64
framework is tested with yeast genome and gene expression data of Yassour,
et al. (2009) <doi:10.1073/pnas.0812841106>. / Mozilla Public License 2.0


Name Version
r-cubist 0.2.2 Regression modeling using rules with added instance-based corrections. / linux-
GPL-3 64,
osx-
64,
win-
64
r-cump 2.0 Combining Univariate Association Test Results of Multiple Phenotypes for noarch
Detecting Pleiotropy. / GPL-2
r-cumplyr 0.1_1 Extends ddply to allow calculation of cumulative quantities. / MIT noarch
r-cumseg 1.2 Estimation of number and location of change points in mean-shift (piecewise noarch
constant) models. Particularly useful to model genomic sequences of continu-
ous measurements. / GPL-3
r-cumstats 1.0 Cumulative descriptive statistics for (arithmetic, geometric, harmonic) mean, noarch
median, mode, variance, skewness and kurtosis. / GPL-3
r-curl 3.3 The curl() and curl_download() functions provide highly configurable drop-in linux-
replacements for base url() and download.file() with better performance, sup- 32,
port for encryption (https, ftps), gzip compression, authentication, and other linux-
‘libcurl’ goodies. The core of the package implements a framework for per- 64,
forming fully customized requests where data can be processed either in mem- osx-
ory, on disk, or streaming via the callback or connection interfaces. Some 64,
knowledge of ‘libcurl’ is recommended; for a more-user-friendly web client win-
see the ‘httr’ package which builds on this package with http specific tools and 32,
logic. / MIT file LICENSE win-
64
r-currentsurvival 1.0 The currentSurvival package contains functions for the estimation of the noarch
current cumulative incidence (CCI) and the current leukaemia-free survival
(CLFS). The CCI is the probability that a patient is alive and in any disease re-
mission (e.g. complete cytogenetic remission in chronic myeloid leukaemia)
after initiating his or her therapy (e.g. tyrosine kinase therapy for chronic
myeloid leukaemia). The CLFS is the probability that a patient is alive and in
any disease remission after achieving the first disease remission. / GPL-2
r-curry 0.1.1 Partial application is the process of reducing the arity of a function by fixing noarch
one or more arguments, thus creating a new function lacking the fixed argu-
ments. The curry package provides three different ways of performing partial
function application by fixing arguments from either end of the argument list
(currying and tail currying) or by fixing multiple named arguments (partial
application). This package provides this functionality through the %<%, %-
<%, and %><% operators which allows for a programming style comparable
to modern functional languages. Compared to other implementations such a
purrr::partial() the operators in curry composes functions with named argu-
ments, aiding in autocomplete etc. / GPL-2
r-curstatci 0.1.1 Computes the maximum likelihood estimator, the smoothed maximum likeli- linux-
hood estimator and pointwise bootstrap confidence intervals for the distribu- 64,
tion function under current status data. Groeneboom and Hendrickx (2017) osx-
<doi:10.1214/17-EJS1345>. / GPL-3 64,
win-
64


Name Version
r-curvecomp 0.1.0 Performs multiple comparison procedures on curve observations among noarch
different treatment groups. The methods are applicable in a va-
riety of situations (such as independent groups with equal or un-
equal sample sizes, or repeated measures) by using parametric boot-
strap. References to these procedures can be found at Konietschke, Gel,
and Brunner (2014) <doi:10.1090/conm/622/12431> and Westfall (2011)
<doi:10.1080/10543406.2011.607751>. / GPL-2
r-cusp 2.3.3 Cobb’s maximum likelihood method for cusp-catastrophe modeling (Grasman, linux-
van der Maas, & Wagenmakers, 2009, JSS, 32:8; Cobb, L, 1981, Behavioral 64,
Science, 26:1, 75–78). Includes a cusp() function for model fitting, and several osx-
utility functions for plotting, and for comparing the model to linear regression 64,
and logistic curve models. / GPL-2 win-
64
r- 1.0.0 Functions for evaluating and visualizing predictive model performance noarch
customerscoringmetrics (specifically: binary classifiers) in the field of customer scoring. These met-
rics include lift, lift index, gain percentage, top-decile lift, F1-score, expected
misclassification cost and absolute misclassification cost. See Berry & Linoff
(2004, ISBN:0-471-47064-3), Witten and Frank (2005, 0-12-088407-0) and
Blattberg, Kim & Neslin (2008, ISBN:978–0–387–72578–9) for details. Vi-
sualization functions are included for lift charts and gain percentage charts.
All metrics that require class predictions offer the possibility to dynamically
determine cutoff values for transforming real-valued probability predictions
into class predictions. / GPL-2
r-cusum 0.4.0 Provides functions for constructing and evaluating CUSUM charts and RA- linux-
CUSUM charts with focus on false signal probability. / GPL-2 64,
osx-
64,
win-
64
r-cusumdesign 1.1.3 Computation of decision intervals (H) and average run lengths (ARL) for linux-
CUSUM charts. / GPL-2 64,
osx-
64,
win-
64
r-cutpointsoehr 0.1.2 Use optimal equal-HR method to determine two optimal cutpoints of a contin- noarch
uous predictor that has a U-shaped relationship with survival outcomes based
on Cox regression model. The optimal equal-HR method estimates two op-
timal cut-points that have approximately the same log hazard value based on
Cox regression model and divides individuals into different groups according
to their HR values. / GPL-3
r- 1.0 This package can be used to standardize abundance indices using the delta- noarch
cuttlefish.model GLM method and to model the English Channel cuttlefish stock using a two-
stage biomass model / GPL-3


Name Version
r-cvauc 1.1.0 This package contains various tools for working with and evaluating cross- noarch
validated area under the ROC curve (AUC) estimators. The primary func-
tions of the package are ci.cvAUC and ci.pooled.cvAUC, which report cross-
validated AUC and compute confidence intervals for cross-validated AUC es-
timates based on influence curves for i.i.d. and pooled repeated measures data,
respectively. One benefit to using influence curve based confidence intervals is
that they require much less computation time than bootstrapping methods. The
utility functions, AUC and cvAUC, are simple wrappers for functions from the
ROCR package. / Apache License (== 2.0)
r-cvcalibration 1.0_1 Statistical inferences for estimating the calibration equation with error-in ob- noarch
servations / GPL-2
r-cvd 1.0.2 Methods for color vision deficiencies (CVD), to help understanding and miti- noarch
gating issues with CVDs and to generate tests for diagnosis and interpretation.
/ GPL-3
r-cvequality 0.2.0 Contains functions for testing for significant differences between noarch
multiple coefficients of variation. Includes Feltz and Miller’s
(1996) <DOI:10.1002/(SICI)1097-0258(19960330)15:6%3C647::AID-
SIM184%3E3.0.CO;2-P> asymptotic test and Krishnamoorthy and Lee’s
(2014) <DOI:10.1007/s00180-013-0445-2> modified signed-likelihood ratio
test. See the vignette for more, including full details of citations. / MIT
r-cvgee 0.3_0 Calculates predictions from generalized estimating equations and inter- noarch
nally cross-validates them using the logarithmic, quadratic and spheri-
cal proper scoring rules; Kung-Yee Liang and Scott L. Zeger (1986)
<doi:10.1093/biomet/73.1.13>. / GPL-3
r-cvmgof 1.0.0 It is devoted to Cramer-von Mises goodness-of-fit tests. It implements three noarch
statistical methods based on Cramer-von Mises statistics to estimate and test a
regression model. / CeCILL
r-cvq2 1.2.0 The external prediction capability of quantitative structure-activity relation- noarch
ship (QSAR) models is often quantified using the predictive squared correla-
tion coefficient. This value can be calculated with an external data set or by
cross validation. / GPL-3
r-cvst 0.2_2 The fast cross-validation via sequential testing (CVST) procedure is an im- linux-
proved cross-validation procedure which uses non-parametric testing coupled 32,
with sequential analysis to determine the best parameter set on linearly increas- linux-
ing subsets of the data. By eliminating under-performing candidates quickly 64,
and keeping promising candidates as long as possible, the method speeds up noarch,
the computation while preserving the capability of a full cross-validation. Ad- osx-
ditionally to the CVST the package contains an implementation of the ordinary 64,
k-fold cross-validation with a flexible and powerful set of helper objects and win-
methods to handle the overall model selection process. The implementations 32,
of the Cochran’s Q test with permutations and the sequential testing frame- win-
work of Wald are generic and can therefore also be used in other contexts. / 64
GPL (>= 2.0)


Name Version
r-cvtools 0.3.2 Tools that allow developers to write functions for cross-validation with min- linux-
imal programming effort and assist users with model selection. / GPL (>= 32,
2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-cvtuningcov 1.0 This is a package for selecting tuning parameters based on cross-validation noarch
(CV) in regularized estimators of large covariance matrices. Four regular-
ized methods are implemented: banding, tapering, hard-thresholding and soft-
thresholding. Two types of matrix norms are applied: Frobenius norm and
operator norm. Two types of CV are considered: K-fold CV and random CV.
Usually K-fold CV use K-1 folds to train a model and the rest one fold to val-
idate the model. The reverse version trains a model with 1 fold and validates
with the rest with K-1 folds. Random CV randomly splits the data set to two
parts, a training set and a validation set with user-specified sizes. / GPL-2
r-cvxbiclustr 0.0.1 An iterative algorithm for solving a convex formulation of the biclustering linux-
problem. / MIT 64,
osx-
64,
win-
64
r-cvxclustr 1.1.1 Alternating Minimization Algorithm (AMA) and Alternating Direction linux-
Method of Multipliers (ADMM) splitting methods for convex clustering. / 64,
CC BY-NC-SA 4.0 osx-
64,
win-
64
r-cwhmisc 6.6 Miscellaneous useful or interesting functions. / GPL-2 noarch
r-cxhull 0.2.0 Computes the convex hull in arbitrary dimension, based on the Qhull library linux-
(<http://www.qhull.org>). The package provides a complete description of the 64,
convex hull: edges, ridges, facets, adjacencies. Triangulation is optional. / osx-
GPL-3 64,
win-
64
r-cxxfunplus 1.0 extend cxxfunction by saving the dynamic shared objects for reusing across R noarch
sessions / GPL-3
r-cyclertools 1.1.1 A suite of functions for analysing cycling data. / MIT linux-
64,
osx-
64,
win-
64
r-cyclocomp 1.1.0 Cyclomatic complexity is a software metric (measurement), used to indicate noarch
the complexity of a program. It is a quantitative measure of the number of
linearly independent paths through a program’s source code. It was developed
by Thomas J. McCabe, Sr. in 1976. / MIT


r-cycloids 1.0 Tools for calculating coordinate representations of hypocycloids, epicyloids, noarch
hypotrochoids, and epitrochoids (altogether called ‘cycloids’ here) with dif-
ferent scaling and positioning options. The cycloids can be visualised with
any appropriate graphics function in R. / GPL-3
r-cytobankapi 1.3.0 Tools to interface with Cytobank’s API via R, organized by various endpoints noarch
that represent various areas of Cytobank functionality. Learn more about Cy-
tobank at <https://www.cytobank.org>. / Artistic-2.0
r- 1.0.0 A collection of tools that leverage the CytobankAPI R pack- noarch
cytobankbridger age <https://cran.r-project.org/web/packages/CytobankAPI/vignettes/
cytobank-quickstart.html> to complete more complex workflows, and
add/extend various Cytobank features. / Artistic-2.0
r-d3network 0.5.2.1This packages is intended to make it easy to create D3 JavaScript network, noarch
tree, dendrogram, and Sankey graphs from R using data frames. !!! NOTE:
Active development has moved to the networkD3 package. !!! / GPL-3
r-d3plus 0.1.0 Provides functions that offer seamless ‘D3Plus’ integration. The examples noarch
provided here are taken from the official ‘D3Plus’ website <http://d3plus.org>.
/ MIT
r-daag 1.22.1Various data sets used in examples and exercises in the book Maindonald, J.H. noarch
and Braun, W.J. (2003, 2007, 2010) Data Analysis and Graphics Using R. /
GPL-3
r-daagxtras 0.8_4 various data sets used in additional exercises for the book Maindonald, J.H. noarch
and Braun, W.J. (3rd edn 2010) Data Analysis and Graphics Using R, and for
a ‘Data Mining’ course. Note that a number of datasets that were in earlier
versions of this package have been transferred to the DAAG package. / Un-
limited
r-daarem 0.3 Implements the DAAREM method for accelerating the convergence of slow, noarch
monotone sequences from smooth, fixed-point iterations such as the EM algo-
rithm. For further details about the DAAREM method. see Henderson, N.C.
and Varadhan, R. (2018) <arXiv:1803.06673>. / GPL-2
r-dacf 1.0.0 An implementation of data analytic methods in R for analyses for data noarch
with ceiling/floor effects. The package currently includes functions for
mean/variance estimation and mean comparison tests. Implemented methods
are from Aitkin (1964) <doi:10.1007/BF02289723> and Liu & Wang (in prep).
/ GPL-2
r-dagr 1.1.3 Functions to draw, manipulate, evaluate directed acyclic graphs and simulate noarch
corresponding data. / GPL-2
r-daime 1.1 Reverse and model the effects of changing deposition rates on geological data noarch
and rates. Based on Hohmann (2018) <doi:10.13140/RG.2.2.23372.51841> .
/ CC BY 4.0
r-dalex2 0.9 Machine Learning models are widely used and have various applications in noarch
classification or regression tasks. Due to increasing computational power,
availability of new data sources and new methods, ML models are more and
more complex. Models created with techniques like boosting, bagging of neu-
ral networks are true black boxes. It is hard to trace the link between input
variables and model outcomes. They are used because of high performance,
but lack of interpretability is one of their weakest sides. In many applications
we need to know, understand or prove how input variables are used in the
model and what impact do they have on final model prediction. DALEX2 is
a collection of tools that help to understand how complex predictive models
are working. DALEX2 is a part of DrWhy universe for tools for Explanation,
Exploration and Visualisation for Predictive Models. / GPL-3


Name Version
r-daly 1.5.0 The DALY Calculator is a free, open-source Graphical User Interface (GUI) linux-
for stochastic disability-adjusted life year (DALY) calculation. / GPL-2 64,
osx-
64,
win-
64
r-dam 0.0.1 A collection of functions which aim to assist common computational workflow noarch
for analysis of matabolomic data.. / CC0
r-dams 0.2 The single largest source of dams in the United States is the National Inven- noarch
tory of Dams (NID) <http://nid.usace.army.mil> from the US Army Corps of
Engineers. Entire data from the NID cannot be obtained all at once and NID’s
website limits extraction of more than a couple of thousand records at a time.
Moreover, selected data from the NID’s user interface cannot not be saved to
a file. In order to make the analysis of this data easier, all the data from NID
was extracted manually. Subsequently, the raw data was checked for potential
errors and cleaned. This package provides sample cleaned data from the NID
and provides functionality to access the entire cleaned NID data. / GPL-2
r-dang 0.0.10A collection of utility functions. / GPL-2 noarch
r-dap 1.0 An implementation of Discriminant Analysis via Projections (DAP) method linux-
for high-dimensional binary classification in the case of unequal co- 64,
variance matrices. See Irina Gaynanova and Tianying Wang (2018) osx-
<arXiv:1711.04817v2>. / GPL-2 64,
win-
64
r-dapr 0.0.3 An easy-to-use, dependency-free set of functions for iterating over ele- noarch
ments of various input objects. Functions are wrappers around base ap-
ply()/lapply()/vapply() functions but designed to have similar functionality
to the mapping functions in the ‘purrr’ package <https://purrr.tidyverse.org/>.
Specifically, function names more explicitly communicate the expected class
of the output and functions also allow for the convenient shortcut of ‘~ .x’
instead of the more verbose ‘function(.x) .x’. / GPL-3
r-dark 0.9.8 The recovery of visual sensitivity in a dark environment is known as dark adap- noarch
tation. In a clinical or research setting the recovery is typically measured af-
ter a dazzling flash of light and can be described by the Mahroo, Lamb and
Pugh (MLP) model of dark adaptation. The functions in this package take
dark adaptation data and use nonlinear regression to find the parameters of the
model that ‘best’ describe the data. They do this by firstly, generating rapid
initial objective estimates of data adaptation parameters, then a multi-start al-
gorithm is used to reduce the possibility of a local minimum. There is also a
bootstrap method to calculate parameter confidence intervals. The functions
rely upon a ‘dark’ list or object. This object is created as the first step in the
workflow and parts of the object are updated as it is processed. / GPL-3
r-darts 1.0 Are you aiming at the right spot in darts? Maybe not! Use this pack- linux-
age to find your optimal aiming location. For a better explanation, go to 64,
http://www-stat.stanford.edu/~ryantibs/darts/ or see the paper A Statistician osx-
Plays Darts. / GPL-3 64,
win-
64


Name Version
r-dashboard 0.1.0 The dashboard package allows users to create web pages which display inter- noarch
active data visualizations working in a standard modern browser. It displays
them locally using the Rook server. Nor knowledge about web technologies
nor Internet connection are required. D3.js is a JavaScript library for manipu-
lating documents based on data. D3 helps the dashboard package bring data to
life using HTML, SVG and CSS. / GPL-2
r-dasst 0.3.3 Provides methods for reading, displaying, processing and writing files origi- noarch
nally arranged for the ‘DSSAT-CSM’ fixed width format. The ‘DSSAT-CSM’
cropping system model is described at J.W. Jones, G. Hoogenboomb, C.H.
Porter, K.J. Boote, W.D. Batchelor, L.A. Hunt, P.W. Wilkens, U. Singh, A.J.
Gijsman, J.T. Ritchie (2003) <doi:10.1016/S1161-0301(02)00107-7>. / GPL-
2
r-data.table 1.12.2Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast linux-
add/modify/delete of columns by group using no copies at all, list columns, a 32,
fast friendly file reader and parallel file writer. Offers a natural and flexible linux-
syntax, for faster development. / MPL-2.0 | file LICENSE 64,
osx-
64,
win-
32,
win-
64
r- 1.1.0 Provides external JAR dependencies for the ‘DatabaseConnector’ package. / noarch
databaseconnectorjars Apache License
r-dataclean 1.0 Includes functions that researchers or practitioners may use to clean raw data, noarch
transferring html, xlsx, txt data file into other formats. And it also can be
used to manipulate text variables, extract numeric variables from text variables
and other variable cleaning processes. It is originated from a author’s project
which focuses on creative performance in online education environment. The
resulting paper of that study will be published soon. / GPL-3
r-dataframes2xls 0.4.7 Writes data frames to xls files. It supports multiple sheets and basic formatting. noarch
/ BSD_3_clause
r-datagraph 1.0.1 Functions to save either ‘.dtable’ or ‘.dtbin’ files that can be read by Data- linux-
Graph, a graphing and analysis application for macOS. Can save a data frame, 64,
collection of data frames and sequences of data frames and individual vectors. osx-
For more information see <https://www.visualdatatools.com/DataGraph/Help/ 64,
DataFiles/R/index.html>. / GPL-2 win-
64
r-datamap 0.1_1 datamap utilizes variable bindings and objects of class UserDefinedDatabase linux-
to provide a simple mapping system to foreign objects. Maps can be used as 64,
environments or attached to the search path, and changes to either are persis- osx-
tent. Mapped foreign objects are fetched in real-time and are never cached by 64,
the mapping system. / GPL-2 win-
64
r-datamaps 0.0.3 Easily create interactive choropleth maps then add bubbles and arcs by coordi- noarch
nates or region name. These maps can be used directly from the console, from
‘RStudio’, in ‘Shiny’ apps and ‘R Markdown’ documents. ‘Shiny’ proxies al-
low to interactively add arcs and bubbles, change choropleth values, or change
labels. / MIT


Name Version
r-dataqualityr 1.0 The package performs variable level data quality checks including missing noarch
values, unique values, frequency tables, and generates summary statistics /
MIT
r-datarium 0.1.0 Contains data organized by topics: categorical data, regression model, means noarch
comparisons, independent and repeated measures ANOVA, mixed ANOVA
and ANCOVA. / GPL-2
r-datarobot 2.14.2For working with the ‘DataRobot’ predictive modeling platform’s API <https: noarch
//www.datarobot.com/>. / MIT
r-datasaurus 0.1.4 The Datasaurus Dozen is a set of datasets with the same summary statis- noarch
tics. They retain the same summary statistics despite having radically dif-
ferent distributions. The datasets represent a larger and quirkier object les-
son that is typically taught via Anscombe’s Quartet (available in the ‘datasets’
package). Anscombe’s Quartet contains four very different distributions with
the same summary statistics and as such highlights the value of visualisa-
tion in understanding data, over and above summary statistics. As well as
being an engaging variant on the Quartet, the data is generated in a novel
way. The simulated annealing process used to derive datasets from the original
Datasaurus is detailed in Same Stats, Different Graphs: Generating Datasets
with Varied Appearance and Identical Statistics through Simulated Annealing
<doi:10.1145/3025453.3025912>. / MIT
r-dataseries 0.2.0 Download and import time series from <http://www.dataseries.org>, a com- noarch
prehensive and up-to-date collection of open data from Switzerland. / GPL-3
r-datassim 1.0 For estimation of a variable of interest using Kalman filter by incorporat- linux-
ing results from previous assessments, i.e. through development weighted 64,
estimates where weights are assigned inversely proportional to the variance osx-
of existing and new estimates. For reference see Ehlers et al. (2017) 64,
<doi:10.20944/preprints201710.0098.v1>. / GPL-2 win-
64
r-datastructures 0.2.8 Implementation of advanced data structures such as hashmaps, heaps, or linux-
queues. Advanced data structures are essential in many computer science and 64,
statistics problems, for example graph algorithms or string analysis. The pack- osx-
age uses ‘Boost’ and ‘STL’ data types and extends these to R with ‘Rcpp’ 64,
modules. / GPL-3 win-
64
r-datautils 0.1.5 Contains facilities such as getting the current timestamp in decimal seconds, linux-
computing interval w.r.t. a reference timestamp, and custom plotting with error 64,
bars. / LGPL-3 osx-
64,
win-
64
r-dataverse 0.2.0 Provides access to Dataverse version 4 APIs <https://dataverse.org/>, enabling noarch
data search, retrieval, and deposit. For Dataverse versions <= 4.0, use the
deprecated ‘dvn’ package <https://cran.r-project.org/package=dvn>. / GPL-2
r-date 1.2_38Functions for handling dates. / GPL-2 linux-
64,
osx-
64,
win-
64


Name Version
r-datetime 0.1.4 Provides methods for working with nominal dates, times, and durations. Base noarch
R has sophisticated facilities for handling time, but these can give unexpected
results if, for example, timezone is not handled properly. This package pro-
vides a more casual approach to support cases which do not require rigorous
treatment. It systematically deconstructs the concepts origin and timezone,
and de-emphasizes the display of seconds. It also converts among nominal
durations such as seconds, hours, days, and weeks. See ‘?datetime’ and ‘?du-
ration’ for examples. Adapted from ‘metrumrg’ <http://r-forge.r-project.org/
R/?group_id=1215>. / GPL-3
r-datetimeutils 0.3_0 Utilities for handling dates and times, such as selecting particular days of the noarch
week or month, formatting timestamps as required by RSS feeds, or converting
timestamp representations of other software (such as ‘MATLAB’ and ‘Excel’)
to R. The package is lightweight (no dependencies, pure R implementations)
and relies only on R’s standard classes to represent dates and times (‘Date’
and ‘POSIXt’); it aims to provide efficient implementations, through vectori-
sation and the use of R’s native numeric representations of timestamps where
possible. / GPL-3
r-datr 0.1.0 Interface with the ‘Dat’ p2p network protocol <https://datproject.org>. Clone noarch
archives from the network, share your own files, and install packages from the
network. / GPL-3
r-davies 1.1_9 Various utilities for the Davies distribution. / GPL-2 noarch
r-dbemplikegof 1.2.4 Goodness-of-fit and two sample comparison tests using sample entropy / GPL- noarch
2
r- 1.0.0 Test for joint assessment of normality / GPL-2 noarch
dbemplikenorm
r-dbest 1.8 A program for analyzing vegetation time series, with two algorithms: 1) noarch
change detection algorithm that detects trend changes, determines their type
(abrupt or non-abrupt), and estimates their timing, magnitude, number, and
direction; 2) generalization algorithm that simplifies the temporal trend into
main features. The user can set the number of major breakpoints or magnitude
of greatest changes of interest for detection, and can control the generaliza-
tion process by setting an additional parameter of generalization-percentage. /
GPL-2
r-dbhydror 0.2_7 Client for programmatic access to the South Florida Water Management noarch
District’s ‘DBHYDRO’ database at <https://www.sfwmd.gov/science-data/
dbhydro>, with functions for accessing hydrologic and water quality data. /
GPL-3
r-dbi 1.0.0 A database interface definition for communication between R and relational linux-
database management systems. All classes in this package are virtual and need 32,
to be extended by the various R/DBMS implementations. / LGPL (>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-dblcens 1.1.7 Use EM algorithm to compute the NPMLE of CDF and also the two censor- linux-
ing distributions. For doubly censored data (as described in Chang and Yang 64,
(1987) Ann. Stat. 1536-47). You can also specify a constraint, it will return osx-
the constrained NPMLE and the -2 log empirical likelihood ratio. This can be 64,
used to test the hypothesis about the constraint and find confidence intervals win-
for probability or quantile via empirical likelihood ratio theorem. Influence 64
function of hat F may also be calculated (but may be slow). / GPL-2
r-dbplyr 1.4.0 A ‘dplyr’ back end for databases that allows you to work with remote database linux-
tables as if they are in-memory data frames. Basic features works with any 32,
database that has a ‘DBI’ back end; more advanced features require ‘SQL’ linux-
translation to be provided by the package author. / MIT file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-dbscan 1.1_4 A fast reimplementation of several density-based algorithms of the DBSCAN linux-
family for spatial data. Includes the DBSCAN (density-based spatial clus- 64,
tering of applications with noise) and OPTICS (ordering points to identify osx-
the clustering structure) clustering algorithms HDBSCAN (hierarchical DB- 64,
SCAN) and the LOF (local outlier factor) algorithm. The implementations win-
use the kd-tree data structure (from library ANN) for faster k-nearest neigh- 64
bor search. An R interface to fast kNN and fixed-radius NN search is also
provided. / GPL-2
r-dbstats 1.0.5 Prediction methods where explanatory information is coded as a matrix of noarch
distances between individuals. Distances can either be directly input as a dis-
tances matrix, a squared distances matrix, an inner-products matrix or com-
puted from observed predictors. / GPL-2
r-dbx 0.2.5 Provides select, insert, update, upsert, and delete database operations. Sup- noarch
ports ‘PostgreSQL’, ‘MySQL’, ‘SQLite’, and more, and plays nicely with the
‘DBI’ package. / MIT
r-dcg 0.9.3 Data cloud geometry (DCG) applies random walks in finding community noarch
structures for social networks. Fushing, VanderWaal, McCowan, & Koehl
(2013) (<doi:10.1371/journal.pone.0056259>). / GPL-2
r-dchipio 0.1.5 Functions for reading DCP and CDF.bin files generated by the dChip software. noarch
/ LGPL-2.1
r-dcl 0.1.0 Statistical modelling and forecasting in claims reserving in non-life insurance noarch
under the Double Chain Ladder framework by Martinez-Miranda, Nielsen and
Verrall (2012). / GPL-2
r-dcovts 1.1 Computing and plotting the distance covariance and correlation function of a noarch
univariate or a multivariate time series. Both versions of biased and unbiased
estimators of distance covariance and correlation are provided. Test statistics
for testing pairwise independence are also implemented. Some data sets are
also included. / GPL-2


Name Version
r-dcurver 0.9.1 A Davidian curve defines a seminonparametric density, whose shape and flex- linux-
ibility can be tuned by easy to estimate parameters. Since a special case of a 64,
Davidian curve is the standard normal density, Davidian curves can be used for osx-
relaxing normality assumption in statistical applications (Zhang & Davidian, 64,
2001) <doi:10.1111/j.0006-341X.2001.00795.x>. This package provides the win-
density function, the gradient of the loglikelihood and a random generator for 64
Davidian curves. / GPL-3
r-dcv 0.1.1 This package performs several conventional Cross-validation statistical meth- noarch
ods for climate-growth model in the climate reconstruction from tree rings,
including Sign Test statistic, Reduction of Error statistic, Product Mean Test,
Durbin-Watson statistic etc. This package is at its primary stage, the functions
have not been tested exhaustively and more functions would be added in the
comming days. / GPL-2
r-ddalpha 1.3.9 Contains procedures for depth-based supervised learning, which are entirely linux-
non-parametric, in particular the DDalpha-procedure (Lange, Mosler and 32,
Mozharovskyi, 2014 <doi:10.1007/s00362-012-0488-4>). The training data linux-
sample is transformed by a statistical depth function to a compact low- 64,
dimensional space, where the final classification is done. It also offers an osx-
extension to functional data and routines for calculating certain notions of sta- 64,
tistical depth functions. 50 multivariate and 5 functional classification prob- win-
lems are included. / GPL-2 32,
win-
64
r-ddm 1.0_0 A set of three two-census methods to the estimate the degree of death regis- noarch
tration coverage for a population. Implemented methods include the General-
ized Growth Balance method (GGB), the Synthetic Extinct Generation method
(SEG), and a hybrid of the two, GGB-SEG. Each method offers automatic es-
timation, but users may also specify exact parameters or use a graphical inter-
face to guess parameters in the traditional way if desired. / GPL-2
r-ddrtree 0.1.5 Provides an implementation of the framework of reversed graph embedding linux-
(RGE) which projects data into a reduced dimensional space while constructs 64,
a principal tree which passes through the middle of the data simultaneously. osx-
DDRTree shows superiority to alternatives (Wishbone, DPT) for inferring the 64,
ordering as well as the intrinsic structure of the single cell genomics data. In win-
general, it could be used to reconstruct the temporal progression as well as 64
bifurcation structure of any datatype. / Artistic-2.0
r-deadband 0.1.0 Statistical deadband algorithms are based on the Send-On-Delta concept as in noarch
Miskowicz(2006,<doi:10.3390/s6010049>). A collection of functions com-
pare effectiveness and fidelity of sampled signals using statistical deadband
algorithms. / GPL-2
r-deal 1.2_39Bayesian networks with continuous and/or discrete variables can be learned linux-
and compared from data. The method is described in Boettcher and Dethlefsen 64,
(2003), <doi:10.18637/jss.v008.i20>. / GPL-2 osx-
64,
win-
64


Name Version
r-deamer 1.0 deamer provides deconvolution algorithms for the non-parametric estimation noarch
of the density f of an error-prone variable x with additive noise e. The model is
y = x e where the noisy variable y is observed, while x is unobserved. Estima-
tion may be performed for i) a known density of the error ii) with an auxiliary
sample of pure noise and iii) with an auxiliary sample of replicate (repeated)
measurements. Estimation is performed using adaptive model selection and
penalized contrasts. / GPL-3
r-debugme 1.1.0 Specify debug messages as special string constants, and control debugging of linux-
packages via environment variables. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-debugr 0.0.1 Tool to print out the value of R objects/expressions while running an R script. noarch
Outputs can be made dependent on user-defined conditions/criteria. Debug
messages only appear when a global option for debugging is set. This way,
‘debugr’ code can even remain in the debugged code for later use without any
negative effects during normal runtime. / GPL-3
r-decide 1.2 Calculates various estimates for measures of educational differentials, the rel- noarch
ative importance of primary and secondary effects in the creation of such dif-
ferentials and compares the estimates obtained from two datasets. / GPL-2
r-decido 0.2.0 Provides constrained triangulation of polygons. Ear cutting (or ear clipping) linux-
applies constrained triangulation by successively ‘cutting’ triangles from a 64,
polygon defined by path/s. Holes are supported by introducing a bridge seg- osx-
ment between polygon paths. This package wraps the ‘header-only’ library 64,
‘earcut.hpp’ <https://github.com/mapbox/earcut.hpp.git> which includes a win-
reference to the method used by Held, M. (2001) <doi:10.1007/s00453-001- 64
0028-4>. / MIT
r-decision 0.1.0 Contains a function called dmur() which accepts four parameters like possi- noarch
ble values, probabilities of the values, selling cost and preparation cost. The
dmur() function generates various numeric decision parameters like MEMV
(Maximum (optimum) expected monitory value), best choice, EPPI (Expected
profit with perfect information), EVPI (Expected value of the perfect infor-
mation), EOL (Expected opportunity loss), which facilitate effective decision-
making. / GPL-2
r-decode 1.2 Integrated differential expression (DE) and differential co-expression (DC) noarch
analysis on gene expression data based on DECODE (DifferEntial CO-
expression and Differential Expression) algorithm. / GPL-3
r-decoder 1.1.13Main function decode is used to decode coded key values to plain text. Func- noarch
tion code can be used to code plain text to code if there is a 1:1 relation between
the two. The concept relies on ‘keyvalue’ objects used for translation. There
are several ‘keyvalue’ objects included in the areas of geographical regional
codes, administrative health care unit codes, diagnosis codes and more. It is
also easy to extend the use by arbitrary code sets. / GPL-2


Name Version
r-decompr 4.5.0 Two global-value-chain decompositions are implemented. Firstly, the Wang- noarch
Wei-Zhu (Wang, Wei, and Zhu, 2013) algorithm splits bilateral gross exports
into 16 value-added components. Secondly, the Leontief decomposition (de-
fault) derives the value added origin of exports by country and industry, which
is also based on Wang, Wei, and Zhu (Wang, Z., S.-J. Wei, and K. Zhu. 2013.
Quantifying International Production Sharing at the Bilateral and Sector Lev-
els.). / GPL-3
r-decon 1.2_4 This package contains a collection of functions to deal with nonparametric linux-
measurement error problems using deconvolution kernel methods. We focus 64,
two measurement error models in the package: (1) an additive measurement osx-
error model, where the goal is to estimate the density or distribution func- 64,
tion from contaminated data; (2) nonparametric regression model with errors- win-
in-variables. The R functions allow the measurement errors to be either ho- 64
moscedastic or heteroscedastic. To make the deconvolution estimators com-
putationally more efficient in R, we adapt the Fast Fourier Transform (FFT)
algorithm for density estimation with error-free data to the deconvolution ker-
nel estimation. Several methods for the selection of the data-driven smoothing
parameter are also provided in the package. See details in: Wang, X.F. and
Wang, B. (2011). Deconvolution estimation in measurement error models:
The R package decon. Journal of Statistical Software, 39(10), 1-24. / GPL-3
r-deconvolver 1.1 Empirical Bayes methods for learning prior distributions from data. An un- noarch
known prior distribution (g) has yielded (unobservable) parameters, each of
which produces a data point from a parametric exponential family (f). The
goal is to estimate the unknown prior (g-modeling) by deconvolution and Em-
pirical Bayes methods. / GPL-2
r-deepboost 0.1.6 Provides deep boosting models training, evaluation, predicting and hyper pa- linux-
rameter optimising using grid search and cross validation. Based on Google’s 64,
Deep Boosting algorithm, and Google’s C implementation. Cortes, C., Mohri, osx-
M., & Syed, U. (2014) <http://machinelearning.wustl.edu/mlpapers/papers/ 64,
icml2014c2_cortesb14>. / Apache License (== 2.0) win-
64
r-deepgmm 0.1.56Deep Gaussian mixture models as proposed by Viroli and McLachlan (2019) noarch
<doi:10.1007/s11222-017-9793-z> provide a generalization of classical Gaus-
sian mixtures to multiple layers. Each layer contains a set of latent variables
that follow a mixture of Gaussian distributions. To avoid overparameterized
solutions, dimension reduction is applied at each layer by way of factor mod-
els. / GPL-3
r-deepnet 0.2 Implement some deep learning architectures and neural network algorithms, noarch
including BP,RBM,DBN,Deep autoencoder and so on. / GPL-3
r-deepnn 0.3 Implementation of some Deep Learning methods. Includes multilayer noarch
perceptron, different activation functions, regularisation strategies, stochas-
tic gradient descent and dropout. Thanks go to the following references
for helping to inspire and develop the package: Ian Goodfellow, Yoshua
Bengio, Aaron Courville, Francis Bach (2016, ISBN:978-0262035613)
Deep Learning. Terrence J. Sejnowski (2018, ISBN:978-0262038034)
The Deep Learning Revolution. Grant Sanderson (3brown1blue)
<https://www.youtube.com/playlist?list=PLZHQObOWTQDNU6R1_67000Dx_ZCJB-
3pi> Neural Networks YouTube playlist. Michael A. Nielsen
<http://neuralnetworksanddeeplearning.com/> Neural Networks and Deep
Learning. / GPL-3


Name Version
r-deepr 0.1 Tests for, and describe differences in event count profiles in groups of recon- noarch
structed cophylogenies / GPL-2
r-default 1.0.0 A simple syntax to change the default values for function arguments, whether noarch
they are in packages or defined locally. / MIT
r-deformula 0.1.1 Numerical quadrature of functions of one variable over a finite or infinite in- linux-
terval with double exponential formulas. / GPL-2 64,
osx-
64,
win-
64
r-deisotoper 0.0.7 Provides a low-level interface for a deisotoper container implemented in the linux-
‘Java’ programming language and means of S3 helper functions for plotting 64
and debugging isotopes of mass spectrometric data. The deisotoper algorithm
detects and aggregates peaks which belong to the same isotopic cluster of a
given mass spectrum. / GPL-3
r-delaporte 7.0.2 Provides probability mass, distribution, quantile, random-variate generation, linux-
and method-of-moments parameter-estimation functions for the Delaporte dis- 64,
tribution. The Delaporte is a discrete probability distribution which can be osx-
considered the convolution of a negative binomial distribution with a Poisson 64,
distribution. Alternatively, it can be considered a counting distribution with win-
both Poisson and negative binomial components. It has been studied in actu- 64
arial science as a frequency distribution which has more variability than the
Poisson, but less than the negative binomial. / BSD_2_clause
r-deldir 0.1_23Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation linux-
(with respect to the entire plane) of a planar point set. Plots triangulations 64,
and tessellations in various ways. Clips tessellations to sub-windows. Calcu- osx-
lates perimeters of tessellations. Summarises information about the tiles of the 64,
tessellation. / GPL-2 win-
64
r-delt 0.8.2 We implement methods for estimating multivariate densities. We include a linux-
discretized kernel estimator, an adaptive histogram (a greedy histogram and a 64,
CART-histogram), stagewise minimization, and bootstrap aggregation. / GPL- osx-
2 64,
win-
64
r-delta 0.2.0.2Measure of agreement delta was originally by MartÃn & Femia noarch
(2004) <DOI:10.1348/000711004849268>. Since then has been con-
sidered as agreement measure for different fields, since their behav-
ior is usually better than the usual kappa index by Cohen (1960)
<DOI:10.1177/001316446002000104>. The main issue with delta is that
can not be computed by hand contrary to kappa. The current algorithm is
based on the Version 5 of the delta windows program that can be found on
<https://www.ugr.es/~bioest/software/delta/cmd.php?seccion=downloads>. /
GPL-3
r-deltaplotr 1.6 The deltaPlotR package implements Angoff’s Delta Plot method to detect di- noarch
chotomous DIF. Several detection thresholds are included, either from multi-
variate normality assumption or by prior determination. Item purification is
supported (Magis and Facon (2014) <doi:10.18637/jss.v059.c01>). / GPL-2


Name Version
r-deltd 0.1.0 It plots densities by using asymmetrical kernels which belong to life time dis- noarch
tributions and calculate its related MSE. For details see Chen (2000), Jin and
Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>. /
GPL-2
r-demetics 0.8_7 This package allows to calculate the fixation index Gst (Nei, 1973) and the noarch
differentiation index D (Jost, 2008) pairwise between or averaged over several
populations. P-values, stating the significance of differentiation, and 95 per-
cent confidence intervals can be estimated using bootstrap resamplings. In the
case that more than two populations are compared pairwise, the p-values are
adjusted by bonferroni correction and in several other ways due to the multiple
comparison from one data set. / GPL-2
r-deming 1.4 Generalized Deming regression, Theil-Sen regression and Passing-Bablock re- noarch
gression functions. / LGPL-2
r-demogr 0.6.0 Construction and analysis of matrix population models in R. / GPL-2 noarch
r-demokde 0.9_4 Demonstration code showing how (univariate) kernel density estimates are noarch
computed, at least conceptually, and allowing users to experiment with dif-
ferent kernels, should they so wish. NOTE: the density function in the stats
package should be used for computational efficiency. / GPL-2
r-demova 1.0 Tool for the development of multi-linear QSPR/QSAR models (Quantitative noarch
structure-property/activity relationship). Theses models are used in chem-
istry, biology and pharmacy to find a relationship between the structure of a
molecule and its property (such as activity, toxicology but also physical prop-
erties). The various functions of this package allows: selection of descrip-
tors based of variances, intercorrelation and user expertise; selection of the
best multi-linear regression in terms of correlation and robustness; methods
of internal validation (Leave-One-Out, Leave-Many-Out, Y-scrambling) and
external using test sets. / GPL-2
r-dendroextras 0.2.3 Provides extra functions to manipulate dendrograms that build on the base noarch
functions provided by the ‘stats’ package. The main functionality it is de-
signed to add is the ability to colour all the edges in an object of class ‘den-
drogram’ according to cluster membership i.e. each subtree is coloured, not
just the terminal leaves. In addition it provides some utility functions to cut
‘dendrogram’ and ‘hclust’ objects and to set/get labels. / GPL-2
r-dendsort 0.3.3 An implementation of functions to optimize ordering of nodes in a dendro- noarch
gram, without affecting the meaning of the dendrogram. A dendrogram can
be sorted based on the average distance of subtrees, or based on the smallest
distance value. These sorting methods improve readability and interpretability
of tree structure, especially for tasks such as comparison of different distance
measures or linkage types and identification of tight clusters and outliers. As
a result, it also introduces more meaningful reordering for a coupled heatmap
visualization. / GPL-2 | GPL-3
r-denoiseq 0.1.1 Given count data from two conditions, it determines which transcripts are dif- noarch
ferentially expressed across the two conditions using Bayesian inference of
the parameters of a bottom-up model for PCR amplification. This model is
developed in Ndifon Wilfred, Hilah Gal, Eric Shifrut, Rina Aharoni, Nissan
Yissachar, Nir Waysbort, Shlomit Reich Zeliger, Ruth Arnon, and Nir Fried-
man (2012), <http://www.pnas.org/content/109/39/15865.full>, and results in
a distribution for the counts that is a superposition of the binomial and negative
binomial distribution. / GPL-2


Name Version
r-denpro 0.9.2 We provide tools to (1) visualize multivariate density functions and density es- linux-
timates with level set trees, (2) visualize level sets with shape trees, (3) visual- 64,
ize multivariate data with tail trees, (4) visualize scales of multivariate density osx-
estimates with mode graphs and branching maps, and (5) visualize anisotropic 64,
spread with 2D volume functions and 2D probability content functions. Level win-
set trees visualize mode structure, shape trees visualize shapes of level sets 64
of unimodal densities, and tail trees visualize connected data sets. The kernel
estimator is implemented but the package may also be applied for visualizing
other density estimates. / GPL-2
r-denseflmm 0.1.2 Estimation of functional linear mixed models for densely sampled data based noarch
on functional principal component analysis. / GPL-2
r-densparcorr 1.1 Provide a Dens-based method for estimating functional connection in large noarch
scale brain networks using partial correlation. / GPL-2
r-densratio 0.2.1 Density ratio estimation. The estimated density ratio function can be used noarch
in many applications such as anomaly detection, change-point detection,
covariate shift adaptation. The implemented methods are uLSIF (Hido
et al. (2011) <doi:10.1007/s10115-010-0283-2>), RuLSIF (Yamada et al.
(2011) <doi:10.1162/NECO_a_00442>), and KLIEP (Sugiyama et al. (2007)
<doi:10.1007/s10463-008-0197-x>). / MIT
r-denstrip 1.5.4 Graphical methods for compactly illustrating probability distributions, includ- noarch
ing density strips, density regions, sectioned density plots and varying width
strips. / GPL-2
r-denvax 0.1.1 Provides the mathematical model described by Serostatus Testing & Dengue noarch
Vaccine Cost-Benefit Thresholds in <doi:10.1098/rsif.2019.0234>. Using the
functions in the package, that analysis can be repeated using sample life his-
tories, either synthesized from local seroprevalence data using other functions
in this package (as in the manuscript) or from some other source. The pack-
age provides a vignette which walks through the analysis in the publication, as
well as a function to generate a project skeleton for such an analysis. / MIT
r-deoptim 2.2_4 Implements the differential evolution algorithm for global optimization of a linux-
real-valued function of a real-valued parameter vector. / GPL-2 64,
osx-
64,
win-
64
r-deoptimr 1.0_8 Differential Evolution (DE) stochastic algorithms for global optimization of linux-
problems with and without constraints. The aim is to curate a collection of 32,
its state-of-the-art variants that (1) do not sacrifice simplicity of design, (2) linux-
are essentially tuning-free, and (3) can be efficiently implemented directly in 64,
the R language. Currently, it only provides an implementation of the ‘jDE’ noarch,
algorithm by Brest et al. (2006) <doi:10.1109/TEVC.2006.872133>. / GPL osx-
(>= 2) 64,
win-
32,
win-
64


Name Version
r- 3.0 Estimation and testing methods for dependently truncated data. Semi- noarch
depend.truncation parametric methods are based on Emura et al. (2011)<Stat Sinica 21:349-67>,
Emura & Wang (2012)<doi:10.1016/j.jmva.2012.03.012>, and Emura &
Murotani (2015)<doi:10.1007/s11749-015-0432-8>. Parametric approaches
are based on Emura & Konno (2012)<doi:10.1007/s00362-014-0626-2>
and Emura & Pan (2017)<doi:10.1007/s00362-017-0947-z>. A regres-
sion approach is based on Emura & Wang (2016)<doi:10.1007/s10463-
015-0526-9>. Quasi-independence tests are based on Emura &
Wang (2010)<doi:10.1016/j.jmva.2009.07.006>. Right-truncated data
for Japanese male centenarians are given by Emura & Murotani
(2015)<doi:10.1007/s11749-015-0432-8>. / GPL-2
r-deplogo 1.0 Plots dependency logos from a set of input sequences. / GPL-3 noarch
r-deployrrserve 9.0.0 Rserve acts as a socket server (TCP/IP or local sockets) which allows binary linux-
requests to be sent to R. Every connection has a separate workspace and work- 64,
ing directory. Client-side implementations are available for popular languages win-
such as C/C and Java, allowing any application to use facilities of R without 64
the need of linking to R code. Rserve supports remote connection, user au-
thentication and file transfer. A simple R client is included in this package as
well. / GPL version 2
r-depmix 0.9.15Fits (multigroup) mixtures of latent or hidden Markov models on mixed cate- linux-
gorical and continuous (timeseries) data. The Rdonlp2 package can optionally 64,
be used for optimization of the log-likelihood and is available from R-forge. / osx-
GPL-3 64,
win-
64
r-depth.plot 0.1 Could be used to obtain spatial depths, spatial ranks and outliers of multivariatenoarch
random variables. Could also be used to visualize DD-plots (a multivariate
generalization of QQ-plots). / GPL-2
r-depthtools 0.4 depthTools is a package that implements different statistical tools for the de- noarch
scription and analysis of gene expression data based on the concept of data
depth, namely, the scale curves for visualizing the dispersion of one or various
groups of samples (e.g. types of tumors), a rank test to decide whether two
groups of samples come from a single distribution and two methods of super-
vised classification techniques, the DS and TAD methods. All these techniques
are based on the Modified Band Depth, which is a recent notion of depth with a
low computational cost, what renders it very appropriate for high dimensional
data such as gene expression data. / GPL-2
r-dequer 2.0_1 Queues, stacks, and ‘deques’ are list-like, abstract data types. These are meant linux-
to be very cheap to grow, or insert new objects into. A typical use case involves 64,
storing data in a list in a streaming fashion, when you do not necessarily know osx-
how may elements need to be stored. Unlike R’s lists, the new data structures 64,
provided here are not necessarily stored contiguously, making insertions and win-
deletions at the front/end of the structure much faster. The underlying imple- 64
mentation is new and uses a head/tail doubly linked list; thus, we do not rely on
R’s environments or hashing. To avoid unnecessary data copying, most opera-
tions on these data structures are performed via side-effects. / BSD_2_clause
r- 0.1.0 Modeling the zero coupon yield curve using the dynamic De Rezende and Fer- noarch
derezende.ferreira reira (2011) <doi:10.1002/for.1256> five factor model with variable or fixed
decaying parameters. For explanatory purposes, the package also includes
various short datasets of interest rates for the BRICS countries. / GPL-2


Name Version
r-deriv 3.8.5 R-based solution for symbolic differentiation. It admits user-defined function noarch
as well as function substitution in arguments of functions to be differentiated.
Some symbolic simplification is part of the work. / GPL-3
r-derivmkts 0.2.4 A set of pricing and expository functions that should be useful in teaching a noarch
course on financial derivatives. / MIT
r-des 1.0.0 Discrete event simulation (DES) involves modeling of systems having discrete, noarch
i.e. abrupt, state changes. For instance, when a job arrives to a queue, the
queue length abruptly increases by 1. This package is an R implementation of
the event-oriented approach to DES; see the tutorial in Matloff (2008) <http:
//heather.cs.ucdavis.edu/~matloff/156/PLN/DESimIntro.pdf>. / MIT
r-desc 1.2.0 Tools to read, write, create, and manipulate DESCRIPTION files. It is in- linux-
tended for packages that create or manipulate other packages. / MIT file LI- 32,
CENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-descomponer 1.5 Decompose a time series into seasonal, trend and irregular components using noarch
transformations to amplitude-frequency domain. / GPL-2
r-descr 1.1.4 Weighted frequency and contingency tables of categorical variables and of the linux-
comparison of the mean value of a numerical variable by the levels of a factor, 64,
and methods to produce xtable objects of the tables and to plot them. There osx-
are also functions to facilitate the character encoding conversion of objects, to 64,
quickly convert fixed width files into csv ones, and to export a data.frame to a win-
text file with the necessary R and SPSS codes to reread the data. / GPL-2 64
r-describer 0.2.0 Allows users to quickly and easily describe data using common descriptive noarch
statistics. / MIT
r-designgg 1.1 The package provides R scripts for designing genetical genomics experiments. noarch
/ GPL-3
r-designglmm 0.1.0 Use simulated annealing to find optimal designs for Poisson regression models noarch
with blocks. / GPL-3
r-desir 1.2.1 Functions for (1) ranking, selecting, and prioritising genes, proteins, and noarch
metabolites from high dimensional biology experiments, (2) multivariate hit
calling in high content screens, and (3) combining data from diverse sources.
/ GPL-3
r-desirability 2.1 S3 classes for multivariate optimization using the desirability function by Der- noarch
ringer and Suich (1980). / GPL-2
r-desnowball 1.0 This package implements a statistical data mining method to compare whole noarch
genome gene expression profiles, with respect to the presence of a recurrent
genetic disturbance event, to identify the affected target genes. / GPL-3


Name Version
r-desolve 1.24 Functions that solve initial value problems of a system of first-order ordinary linux-
differential equations (‘ODE’), of partial differential equations (‘PDE’), of dif- 64,
ferential algebraic equations (‘DAE’), and of delay differential equations. The osx-
functions provide an interface to the FORTRAN functions ‘lsoda’, ‘lsodar’, 64,
‘lsode’, ‘lsodes’ of the ‘ODEPACK’ collection, to the FORTRAN functions win-
‘dvode’, ‘zvode’ and ‘daspk’ and a C-implementation of solvers of the ‘Runge- 64
Kutta’ family with fixed or variable time steps. The package contains routines
designed for solving ‘ODEs’ resulting from 1-D, 2-D and 3-D partial differ-
ential equations (‘PDE’) that have been converted to ‘ODEs’ by numerical
differencing. / GPL-2
r-det 2.0.1 Builds both ROC (Receiver Operating Characteristic) and DET (Detection Er- noarch
ror Tradeoff) curves from a set of predictors, which are the results of a binary
classification system. The curves give a general vision of the performance of
the classifier, and are useful for comparing performance of different systems.
/ GPL-2
r-detector 0.1.0 Allows users to quickly and easily detect data containing Personally Identifi- noarch
able Information (PII) through convenience functions. / MIT
r-detestset 1.1.6 Solvers and test set for stiff and non-stiff differential equations, and differential linux-
algebraic equations. ‘Mazzia, F., Cash, J.R. and K. Soetaert, 2012. DOI: 64,
10.1016/j.cam.2012.03.014’. / GPL-3 osx-
64,
win-
64
r-detmcd 0.0.5 Implementation of DetMCD, a new algorithm for robust and deterministic linux-
estimation of location and scatter. The benefits of robust and determin- 64,
istic estimation are explained in Hubert, Rousseeuw and Verdonck (2012) osx-
<doi:10.1080/10618600.2012.672100>. / GPL-2 64,
win-
64
r-detpack 1.1.3 Density estimation for possibly large data sets and conditional/unconditional noarch
random number generation or bootstrapping with distribution element trees.
The function ‘det.construct’ translates a dataset into a distribution element
tree. To evaluate the probability density based on a previously com-
puted tree at arbitrary query points, the function ‘det.query’ is available.
The functions ‘det1’ and ‘det2’ provide density estimation and plotting for
one- and two-dimensional datasets. Conditional/unconditional smooth boot-
strapping from an available distribution element tree can be performed by
‘det.rnd’. For more details on distribution element trees, see: Meyer,
D.W. (2016) <arXiv:1610.00345> or Meyer, D.W., Statistics and Com-
puting (2017) <doi:10.1007/s11222-017-9751-9> and Meyer, D.W. (2017)
<arXiv:1711.04632> or Meyer, D.W., Journal of Computational and Graph-
ical Statistics (2018) <doi:10.1080/10618600.2018.1482768>. / GPL-2
r-detr 0.0.5 DetLTS, DetMM (and DetS) Algorithms for Deterministic, Robust Linear Re- linux-
gression. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-detsel 1.0.3 In the new era of population genomics, surveys of genetic polymorphism linux-
(genome scans) offer the opportunity to distinguish locus-specific from 64,
genome wide effects at many loci. Identifying presumably neutral regions osx-
of the genome that are assumed to be influenced by genome-wide effects only, 64,
and excluding presumably selected regions, is therefore critical to infer pop- win-
ulation demography and phylogenetic history reliably. Conversely, detecting 64
locus-specific effects may help identify those genes that have been, or still
are, targeted by natural selection. The software package DetSel has been de-
veloped to identify markers that show deviation from neutral expectation in
pairwise comparisons of diverging populations. / GPL-2
r-devemf 3.6_3 Output graphics to EMF/EMF. / GPL-3 linux-
64,
osx-
64,
win-
64
r-devfunc 0.1 A concise check of the format of one or multiple input arguments (data type, noarch
length or value) is provided. Since multiple input arguments can be tested
simultaneously, a lengthly list of checks at the beginning of your function can
be avoided, hereby enhancing the readability and maintainability of your code.
/ GPL-3
r-devoid 0.1.0 Provides a non-drawing graphic device for benchmarking purpose. In order to linux-
properly benchmark graphic drawing code it is necessary to factor out the de- 64,
vice implementation itself so that results are not related to the specific graphics osx-
device used during benchmarking. The ‘devoid’ package implements a graphic 64,
device that accepts all the required calls from R’s graphic engine but performs win-
no action. Apart from benchmarking it is unlikely that this device has any 64
practical use. / MIT
r-devore7 0.7.6 Data sets and sample analyses from Jay L. Devore (2008), Probability and noarch
Statistics for Engineering and the Sciences (7th ed), Thomson. / GPL-2
r-devrate 0.1.10A set of functions to quantify the relationship between development rate and noarch
temperature and to build phenological models. The package comprises a set
of models and estimated parameters borrowed from a literature review in ec-
totherms. The methods and literature review are described in Rebaudo et
al. (2018) <doi:10.1111/2041-210X.12935> and Rebaudo and Rabhi (2018)
<doi:10.1111/eea.12693>. An example can be found in Rebaudo et al. (2017)
<doi:10.1007/s13355-017-0480-5>. / GPL-2
r-devtools 2.0.2 Collection of package development tools. / GPL (>= 2) linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-df2json 0.0.2 It handles numerics, characters, factors, and logicals. / GPL-3 noarch


Name Version
r-dfadjust 1.0.0 Computes small-sample degrees of freedom adjustment for heteroskedasticity noarch
robust standard errors, and for clustered standard errors in linear regression.
See Imbens and Kolesár (1994) <doi:10.1162/REST_a_00552> for a discus-
sion of these adjustments. / MIT
r-dfcomb 3.0_0 Phase I/II adaptive dose-finding design for combination studies where toxicity linux-
rates are supposed to increase with both agents. / GPL-3 64,
osx-
64,
win-
64
r-dfcompare 1.0.0 Compares two dataframes with a common key and returns the delta records. noarch
The package will return three dataframes that contain the added, changed, and
deleted records. / GPL-3
r-dfcrm 0.2_2.1
Provides functions to run the CRM and TITE-CRM in phase I trials and cali- noarch
bration tools for trial planning purposes. / GPL-2
r-dfmta 1.7_0 Phase I/II adaptive dose-finding design for single-agent Molecularly Tar- linux-
geted Agent (MTA), according to the paper Phase I/II Dose-Finding 64,
Design for Molecularly Targeted Agent: Plateau Determination us- osx-
ing Adaptive Randomization, Riviere Marie-Karelle et al. (2016) 64,
<doi:10.1177/0962280216631763>. / GPL-3 win-
64
r-dfoptim 2018.2_1
Derivative-Free optimization algorithms. These algorithms do not require gra- noarch
dient information. More importantly, they can be used to solve non-smooth
optimization problems. / GPL-2
r-dfphase1 1.1.1 Statistical methods for retrospectively detecting changes in location and/or dis- linux-
persion of univariate and multivariate variables. Data values are assumed to be 64,
independent, can be individual (one observation at each instant of time) or sub- osx-
grouped (more than one observation at each instant of time). Control limits are 64,
computed, often using a permutation approach, so that a prescribed false alarm win-
probability is guaranteed without making any parametric assumptions on the 64
stable (in-control) distribution. / LGPL-2
r-dga 1.2 Performs Bayesian model averaging for capture-recapture. This includes code noarch
to stratify records, check the strata for suitable overlap to be used for capture-
recapture, and some functions to plot the estimated population size. / GPL-2
r-dglars 2.1.2 Differential geometric least angle regression method for fitting sparse gener- linux-
alized linear models. In this version of the package, the user can fit models 64,
specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian fam- osx-
ily. Furthermore, several link functions can be used to model the relationship 64,
between the conditional expected value of the response variable and the linear win-
predictor. The solution curve can be computed using an efficient predictor- 64
corrector or a cyclic coordinate descent algorithm, as described in the paper
linked to via the URL below. / GPL-2
r-dgmb 1.2 A set of functions have been implemented to generate random data to perform noarch
Monte Carlo simulations on structural models with formative constructs and
interaction and nonlinear effects (Two-Step PLS Mode B structural models).
The setup of the true model considers a simple structure with three formative
exogenous constructs related to one formative endogenous construct. The rou-
tines take into account the interaction and nonlinear effects of the exogenous
constructs on the endogenous construct. / GPL-2
r-dgodata 0.0.2 Provides data used by package ‘dgo’ in examples and vignettes. / GPL-3 noarch


Name Version
r-dgof 1.2 This package contains a proposed revision to the stats::ks.test() function and linux-
the associated ks.test.Rd help page. With one minor exception, it does not 64,
change the existing behavior of ks.test(), and it adds features necessary for osx-
doing one-sample tests with hypothesized discrete distributions. The package 64,
also contains cvm.test(), for doing one-sample Cramer-von Mises goodness- win-
of-fit tests. / GPL (>= 2.0) 64
r-dhh 0.0.1 The density, cumulative distribution, quantiles, and i.i.d random variables of noarch
a heavy-headed distribution. For more information, please see the vignette. /
GPL-2
r-dhsic 2.1 Contains an implementation of the d-variable Hilbert Schmidt independence linux-
criterion and several hypothesis tests based on it, as described in Pfister et al. 64,
(2017) <doi:10.1111/rssb.12235>. / GPL-3 osx-
64,
win-
64
r-di 1.1.4 A set of utilities for calculating the Deficit (frailty) Index (DI) in gerontological noarch
studies. The deficit index was first proposed by Arnold Mitnitski and Kenneth
Rockwood and represents a proxy measure of aging and also can be served as
a sensitive predictor of survival. For more information, see (i)Accumulation of
Deficits as a Proxy Measure of Aging by Arnold B. Mitnitski et al. (2001), The
Scientific World Journal 1, <DOI:10.1100/tsw.2001.58>; (ii) Frailty, fitness
and late-life mortality in relation to chronological and biological age by Arnold
B Mitnitski et al. (2001), BMC Geriatrics2002 2(1), <DOI:10.1186/1471-
2318-2-1>. / GPL-3
r-diagonals 0.4.0 Several tools for handling block-matrix diagonals and similar constructs are noarch
implemented. Block-diagonal matrices can be extracted or removed using two
small functions implemented here. In addition, non-square matrices are sup-
ported. Block diagonal matrices occur when two dimensions of a data set are
combined along one edge of a matrix. For example, trade-flow data in the
‘decompr’ and ‘gvc’ packages have each country-industry combination occur
along both edges of the matrix. / GPL-3
r-diagrammer 1.0.1 Build graph/network structures using functions for stepwise addition and dele- linux-
tion of nodes and edges. Work with data available in tables for bulk addition of 32,
nodes, edges, and associated metadata. Use graph selections and traversals to linux-
apply changes to specific nodes or edges. A wide selection of graph algorithms 64,
allow for the analysis of graphs. Visualize the graphs and take advantage of noarch,
any aesthetic properties assigned to nodes and edges. / MIT file LICENSE osx-
64,
win-
32,
win-
64
r-dialr 0.3.0 Parse, format, and validate international phone numbers using noarch
Google’s ‘libphonenumber’ java library, <https://github.com/googlei18n/
libphonenumber>. / GPL-3
r-dialrjars 8.10.14
Collects ‘libphonenumber’ jars required for the ‘dialr’ package. / GPL-3 noarch
r-diaplt 1.3.0 Visualize one-factor data frame. Beads plot consists of diamonds of each fac- noarch
tor of each data series. A diamond indicates average and range. Look over a
data frame with many numeric columns and a factor column. / MIT (FOSS)


Name Version
r-dice 1.2 This package provides utilities to calculate the probabilities of various dice- noarch
rolling events, such as the probability of rolling a four-sided die six times and
getting a 4, a 3, and either a 1 or 2 among the six rolls (in any order); the
probability of rolling two six-sided dice three times and getting a 10 on the
first roll, followed by a 4 on the second roll, followed by anything but a 7 on
the third roll; or the probabilities of each possible sum of rolling five six-sided
dice, dropping the lowest two rolls, and summing the remaining dice. / GPL-2
r-dicedesign 1.8_1 Space-Filling Designs and Uniformity Criteria. / GPL-3 linux-
64,
osx-
64,
win-
64
r-diceeval 1.4 Estimation, validation and prediction of models of different types : linear mod- noarch
els, additive models, MARS,PolyMARS and Kriging. / GPL-3
r-dicekriging 1.5.6 Estimation, validation and prediction of kriging models. Important functions : linux-
km, print.km, plot.km, predict.km. / GPL-2 | GPL-3 64,
osx-
64,
win-
64
r-dichromat 2.0_0 Collapse red-green or green-blue distinctions to simulate the effects of differ- linux-
ent types of color-blindness. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-dicionariosibge 1.6 This package contains the dictionaries for reading microdata from IBGE noarch
(Brazilian Institute of Geography and Statistics) surveys PNAD, PME and
POF. / GPL-2
r-didacticboost 0.1.1 A basic, clear implementation of tree-based gradient boosting designed to il- noarch
lustrate the core operation of boosting models. Tuning parameters (such as
stochastic subsampling, modified learning rate, or regularization) are not im-
plemented. The only adjustable parameter is the number of training rounds. If
you are looking for a high performance boosting implementation with tuning
parameters, consider the ‘xgboost’ package. / GPL-3
r-dielectric 0.2.3 Physical constants. Gold, silver and glass permittivities, together with spline noarch
interpolation functions. / GPL-3
r-diezeit 0.1_0 A wrapper for the ZEIT ONLINE Content API, available at <http://developer. noarch
zeit.de>. ‘diezeit’ gives access to articles and corresponding metadata from
the ZEIT archive and from ZEIT ONLINE. A personal API key is required for
usage. / MIT


Name Version
r-difconet 1.0_4 Estimation of DIFferential COexpressed NETworks using diverse and user noarch
metrics. This package is basically used for three functions related to the
estimation of differential coexpression. First, to estimate differential co-
expression where the coexpression is estimated, by default, by Spearman
correlation. For this, a metric to compare two correlation distributions is
needed. The package includes 6 metrics. Some of them needs a thresh-
old. A new metric can also be specified as a user function with specific
parameters (see difconet.run). The significance is be estimated by permu-
tations. Second, to generate datasets with controlled differential correlation
data. This is done by either adding noise, or adding specific correlation struc-
ture. Third, to show the results of differential correlation analyses. Please
see <http://bioinformatica.mty.itesm.mx/difconet> for further information. /
GPL-2
r-diffee 1.1.0 This is an R implementation of Fast and Scalable Learning of Sparse Changes noarch
in High-Dimensional Gaussian Graphical Model Structure (DIFFEE). The
DIFFEE algorithm can be used to fast estimate the differential network be-
tween two related datasets. For instance, it can identify differential gene
network from datasets of case and control. By performing data-driven net-
work inference from two high-dimensional data sets, this tool can help
users effectively translate two aggregated data blocks into knowledge of the
changes among entities between two Gaussian Graphical Model. Please run
demo(diffeeDemo) to learn the basic functions provided by this package. For
further details, please read the original paper: Beilun Wang, Arshdeep Sekhon,
Yanjun Qi (2018) <arXiv:1710.11223>. / GPL-2
r-diffmeshgp 0.1.0 This R function implements the nonstationary Kriging model proposed by noarch
Tuo, Wu and Yu (2014) <DOI:10.1080/00401706.2013.842935> for analyz-
ing multi-fidelity computer outputs. This function computes the maximum
likelihood estimates for the model parameters as well as the predictive means
and variances of the exact solution (i.e., the conceptually highest fidelity). /
GPL-2
r-diffobj 0.2.3 Generate a colorized diff of two R objects for an intuitive visualization of their linux-
differences. / GPL-2 64,
osx-
64,
win-
64
r-diffpriv 0.4.2 An implementation of major general-purpose mechanisms for privatizing noarch
statistics, models, and machine learners, within the framework of differential
privacy of Dwork et al. (2006) <doi:10.1007/11681878_14>. Example mech-
anisms include the Laplace mechanism for releasing numeric aggregates, and
the exponential mechanism for releasing set elements. A sensitivity sampler
(Rubinstein & Alda, 2017) <arXiv:1706.02562> permits sampling target non-
private function sensitivity; combined with the generic mechanisms, it permits
turn-key privatization of arbitrary programs. / MIT
r-diffr 0.1 An R interface to the ‘codediff’ JavaScript library (a copy of which is included noarch
in the package, see <https://github.com/danvk/codediff.js> for information).
Allows for visualization of the difference between 2 files, usually text files or
R scripts, in a browser. / GPL-2


Name Version
r-diffusr 0.1.4 Implementation of network diffusion algorithms such as heat diffusion or linux-
Markov random walks. Network diffusion algorithms generally spread in- 64,
formation in the form of node weights along the edges of a graph to other osx-
nodes. These weights can for example be interpreted as temperature, an initial 64,
amount of water, the activation of neurons in the brain, or the location of a win-
random surfer in the internet. The information (node weights) is iteratively 64
propagated to other nodes until a equilibrium state or stop criterion occurs. /
GPL-3
r-digest 0.6.18Implementation of a function ‘digest()’ for the creation of hash digests of ar- linux-
bitrary R objects (using the ‘md5’, ‘sha-1’, ‘sha-256’, ‘crc32’, ‘xxhash’ and 32,
‘murmurhash’ algorithms) permitting easy comparison of R language objects, linux-
as well as a function ‘hmac()’ to create hash-based message authentication 64,
code. Please note that this package is not meant to be deployed for crypto- osx-
graphic purposes for which more comprehensive (and widely tested) libraries 64,
such as ‘OpenSSL’ should be used. / GPL (>= 2) win-
32,
win-
64
r-digitalpcr 1.1.0 The assay sensitivity is the minimum number of copies that the digital PCR noarch
assay can detect. Users provide serial dilution results in the format of counts of
positive and total reaction wells. The output is the estimated assay sensitivity
and the copy number per well in the initial dilute. / GPL-2
r-dils 0.8.1 Combine multiple-relationship networks into a single weighted network. The linux-
approach is similar to factor analysis in the that contribution from each con- 64,
stituent network varies so as to maximize the information gleaned from the osx-
multiple-relationship networks. This implementation uses Principal Compo- 64,
nent Analysis calculated using ‘prcomp’ with bootstrap subsampling. Missing win-
links are imputed using the method of Chen et al. (2012). / MIT 64
r-dime 1.2 A robust differential identification method that considers an ensemble of finite linux-
mixture models combined with a local false discovery rate (fdr) to analyze 64,
ChIP-seq (high-throughput genomic)data comparing two samples allowing for osx-
flexible modeling of data. / GPL-2 64,
win-
64
r-dimred 0.2.2 A collection of dimensionality reduction techniques from R packages and pro- linux-
vides a common interface for calling the methods. / GPL-3 | file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-dinamic 1.0 This function implements the DiNAMIC procedure for assessing the statisti- noarch
cal significance of recurrent DNA copy number aberrations (Bioinformatics
(2011) 27(5) 678 - 685). / GPL-2
r-dint 2.1.0 S3 classes and methods to create and work with year-quarter, year-month and noarch
year-isoweek vectors. Basic arithmetic operations (such as adding and sub-
tracting) are supported, as well as formatting and converting to and from stan-
dard R date types. / MIT


Name Version
r-diphiseq 0.2.0 Implements the algorithm described in Jun Li and Alicia T. Lamere, DiPhiSeq: noarch
Robust comparison of expression levels on RNA-Seq data with large sam-
ple sizes (Unpublished). Detects not only genes that show different average
expressions (differential expression, DE), but also genes that show different
diversities of expressions in different groups (differentially dispersed, DD).
DD genes can be important clinical markers. ‘DiPhiSeq’ uses a redescend-
ing penalty on the quasi-likelihood function, and thus has superior robustness
against outliers and other noise. Updates from version 0.1.0: (1) Added the op-
tion of using adaptive initial value for phi. (2) Added a function for estimating
the proportion of outliers in the data. (3) Modified the input parameter names
for clarity, and modified the output format for the main function. / GPL-3
r-diptest 0.75_7Compute Hartigan’s dip test statistic for unimodality / multimodality and pro- linux-
vide a test with simulation based p-values, where the original public code has 64,
been corrected. / GPL-2 osx-
64,
win-
64
r-direct 1.0.1 A Bayesian clustering method for replicated time series or replicated mea- linux-
surements from multiple experimental conditions, e.g., time-course gene ex- 64,
pression data. It estimates the number of clusters directly from the data osx-
using a Dirichlet-process prior. See Fu, A. Q., Russell, S., Bray, S. and 64,
Tavare, S. (2013) Bayesian clustering of replicated time-course gene expres- win-
sion data with weak signals. The Annals of Applied Statistics. 7(3) 1334-1361. 64
<doi:10.1214/13-AOAS650>. / GPL-2
r- 0.1.1 Allows the computation of clustering coefficients for directed and weighted noarch
directedclustering networks by using different approaches. It allows to compute cluster-
ing coefficients that are not present in ‘igraph’ package. A descrip-
tion of clustering coefficients can be found in Directed clustering in
weighted networks: a new perspective, Clemente, G.P., Grassi, R. (2017),
<doi:10.1016/j.chaos.2017.12.007>. / GPL-3
r-directeffects 0.2 A set of functions to estimate the controlled direct effect of treat- noarch
ment fixing a potential mediator to a specific value. Implements
the sequential g-estimation estimator described in Vansteelandt (2009)
<doi:10.1097/EDE.0b013e3181b6f4c9> and Acharya, Blackwell, and Sen
(2016) <doi:10.1017/S0003055416000216>. / GPL-2
r-directlabels 2018.05.22
An extensible framework for automatically placing direct labels onto multi- noarch
color ‘lattice’ or ‘ggplot2’ plots. Label positions are described using Position-
ing Methods which can be re-used across several different plots. There are
heuristics for examining trellis and ggplot objects and inferring an appropriate
Positioning Method. / GPL-3
r- 1.2 Calculate adjusted means and proportions of a variable by groups defined by noarch
directstandardisation another variable by direct standardisation, standardised to the structure of the
dataset. / GPL-2
r-dirmult 0.1.3_4
Estimate parameters in Dirichlet-Multinomial and compute profile log- noarch
likelihoods. / GPL-2


Name Version
r-discfrail 0.1 Functions for fitting Cox proportional hazards models for grouped time-to- noarch
event data, where the shared group-specific frailties have a discrete nonpara-
metric distribution. The methods proposed in the package is described by
Gasperoni, F., Ieva, F., Paganoni, A. M., Jackson, C. H., Sharples, L. (2018)
<doi:10.1093/biostatistics/kxy071>. There are also functions for simulating
from these models, with a nonparametric or a parametric baseline hazard func-
tion. / GPL-3
r-disclap 1.5 Discrete Laplace exponential family for models such as a generalized linear noarch
model / GPL-2
r-disclapmix 1.7.3 Make inference in a mixture of discrete Laplace distributions using the EM linux-
algorithm. This can e.g. be used for modelling the distribution of Y chromo- 64,
somal haplotypes as described in [1, 2] (refer to the URL section). / GPL-2 osx-
64,
win-
64
r-discretefdr 1.3_1 Multiple testing procedures described in the paper Döhler, Durand and linux-
Roquain (2018) New FDR bounds for discrete and heterogeneous tests 64,
<doi:10.1214/18-EJS1441>. The main procedures of the paper (HSU and osx-
HSD), their adaptive counterparts (AHSU and AHSD), and the HBR variant 64,
are available and are coded to take as input a set of observed p-values and theirwin-
discrete support under the null. A function to compute such p-values and sup- 64
ports for Fisher’s exact tests is also provided, along with a wrapper allowing
to apply discrete procedures directly from contingency tables. / MIT
r-discretelaplace 1.1.1 Probability mass function, distribution function, quantile function, random noarch
generation and estimation for the skew discrete Laplace distributions. / GPL-3
r-discretemtp 0.1_2 Multiple testing procedures for discrete test statistics, that use the known dis- noarch
crete null distribution of the p-values for simultaneous inference. / GPL-2
r-discreterv 1.2.2 Create, manipulate, transform, and simulate from discrete random variables. noarch
The syntax is modeled after that which is used in mathematical statistics and
probability courses, but with powerful support for more advanced probability
calculations. This includes the creation of joint random variables, and the
derivation and manipulation of their conditional and marginal distributions. /
GPL-3
r-discretization 1.0_1 This package is a collection of supervised discretization algorithms. It can also noarch
be grouped in terms of top-down or bottom-up, implementing the discretiza-
tion algorithms. / GPL-3
r-discriminer 0.1_29Functions for Discriminant Analysis and Classification purposes covering var- noarch
ious methods such as descriptive, geometric, linear, quadratic, PLS, as well as
qualitative discriminant analyses / GPL-3
r-discsurv 1.4.0 Provides data transformations, estimation utilities, predictive evaluation mea- noarch
sures and simulation functions for discrete time survival analysis. / GPL-3
r- 1.4.6 Formatting of population and case data, calculation of Standardized Incidence noarch
diseasemapping Ratios, and fitting the BYM model using INLA. / GPL-3
r-dishet 1.0.0 Model cell type heterogeneity of bulk renal cell carcinoma. The observed gene noarch
expression in bulk tumor sample is modeled by a log-normal distribution with
the location parameter structured as a linear combination of the component-
specific gene expressions. / GPL-2


Name Version
r-dismo 1.1_4 Functions for species distribution modeling, that is, predicting entire geo- linux-
graphic distributions form occurrences at a number of sites and the environ- 64,
ment at these sites. / GPL-3 osx-
64,
win-
64
r-disparityfilter 2.2.3 The disparity filter algorithm is a network reduction technique to identify the noarch
‘backbone’ structure of a weighted network without destroying its multi-scale
nature. The algorithm is documented in M. Angeles Serrano, Marian Boguna
and Alessandro Vespignani in Extracting the multiscale backbone of complex
weighted networks, Proceedings of the National Academy of Sciences 106
(16), 2009. This implementation of the algorithm supports both directed and
undirected networks. / GPL-2
r-displayhts 1.0 A package containing R functions for displaying data and results from high- noarch
throughput screening experiments. / GPL-2
r-dispmod 1.2 Functions for estimating Gaussian dispersion regression models (Aitkin, 1987 noarch
<doi:10.2307/2347792>), overdispersed binomial logit models (Williams,
1987 <doi:10.2307/2347977>), and overdispersed Poisson log-linear models
(Breslow, 1984 <doi:10.2307/2347661>), using a quasi-likelihood approach. /
GPL-2
r-disposables 1.0.3 Create disposable R packages for testing. You can create, install and load noarch
multiple R packages with a single function call, and then unload, uninstall and
destroy them with another function call. This is handy when testing how some
R code or an R package behaves with respect to other packages. / MIT
r-dissutils 1.0 This package has extensible C code for computing dissimilarities between vec- linux-
tors. It also has a number of C functions for assembling collections of dissim- 64,
ilarities. In particular, it lets you find a matrix of dissimilarities between the osx-
rows of two input matrices. There are also functions for finding the nearest 64,
neighbors of each row of a matrix, either within the matrix itself or within win-
another matrix. / GPL-2 64
r- 0.0 Calculates the study size (either number of detections, or proportion of re- noarch
distance.sample.size gion that should be covered) to achieve a target precision for the estimated
abundance. The calculation allows for the penalty due to unknown detection
function, and for overdispersion. The user must specify a guess at the true
detection function. / GPL-2 | GPL-3
r-distances 0.1.7.2Provides tools for constructing, manipulating and using distance metrics. / linux-
GPL-3 64,
osx-
64,
win-
64
r-distcomp 1.0_1 Implementing algorithms and fitting models when sites (possibly remote) linux-
share computation summaries rather than actual data over HTTP with a mas- 64,
ter R process (using ‘opencpu’, for example). A stratified Cox model and a osx-
singular value decomposition are provided. The former makes direct use of 64,
code from the R ‘survival’ package. (That is, the underlying Cox model code win-
is derived from that in the R ‘survival’ package.) Sites may provide data via 64
several means: CSV files, Redcap API, etc. An extensible design allows for
new methods to be added in the future. Web applications are provided (via
‘shiny’) for the implemented methods to help in designing and deploying the
computations. / LGPL-2


Name Version
r-distcrete 1.0.3 Creates discretised versions of continuous distribution functions by map- noarch
ping continuous values to an underlying discrete grid, based on a (uni-
form) frequency of discretisation, a valid discretisation point, and an integra-
tion range. For a review of discretisation methods, see Chakraborty (2015)
<doi:10.1186/s40488-015-0028-6>. / MIT
r-distdrawr 0.1.3 Download data from the FlorKart database of the floristic field mapping in noarch
Germany in a convenient way. The database incorporates distribution data for
plants in Germany on the basis of quadrants on a topographical map with a res-
olution of 1 : 25000 (TK 25). The data is owned and provided by the German
Federal Agency for Nature Conservation (BfN) and the Network Phytodiver-
sity in Germany (NetPhyD). For further information please visit <http://www.
floraweb.de/pflanzenarten/hintergrundtexte_florkart_organisation.html>. The
author of this package is in no way associated with the BfN or NetPhyD. /
GPL-2
r-distfree.cr 1.5.1 Constructs confidence regions without the need to know the sampling distri- noarch
bution of bivariate data. The method was proposed by Zhiqiu Hu & Rong-cai
Yang (2013) <doi:10.1371/journal.pone.0081179.g001>. / GPL-2
r-distillery 1.0_6 Some very simple method functions for confidence interval calculation, boot- noarch
strap resampling, and to distill pertinent information from a potentially com-
plex object; primarily used in common with packages extRemes and Spa-
tialVx. / GPL-2
r-distory 1.4.3 Geodesic distance between phylogenetic trees and associated functions. / BSD linux-
64,
osx-
64,
win-
64
r-distrib 1.0 A different way for calculating pdf/pmf, cdf, quantile and random data such noarch
that the user is able to consider the name of related distribution as an argu-
ment and so easily can changed by a changing argument by user. It must be
mentioned that the core and computation base of package ‘DISTRIB’ is pack-
age ‘stats’. Although similar functions are introduced previously in package
‘stats’, but the package ‘DISTRIB’ has some special applications in some spe-
cial computational programs. / LGPL-3
r-distributions3 0.1.1 Tools to create and manipulate probability distributions using S3. Generics noarch
random(), pdf(), cdf() and quantile() provide replacements for base R’s r/d/p/q
style functions. Functions and arguments have been named carefully to mini-
mize confusion for students in intro stats courses. The documentation for each
distribution contains detailed mathematical notes. / MIT
r-distributiontest 1.0 Provides new types of omnibus tests which are generally much more pow- noarch
erful than traditional tests (including the Kolmogorov-Smirnov, Cramer-von
Mises and Anderson-Darling tests),see Zhang (2002) <doi:10.1111/1467-
9868.00337>. / GPL-3
r- 0.6_0 Utilities are provided which are of use in the packages I have developed linux-
distributionutils for dealing with distributions. Currently these packages are GeneralizedHy- 64,
perbolic, VarianceGamma, and SkewHyperbolic and NormalLaplace. Each osx-
of these packages requires DistributionUtils. Functionality includes sam- 64,
ple skewness and kurtosis, log-histogram, tail plots, moments by integration, win-
changing the point about which a moment is calculated, functions for testing 64
distributions using inversion tests and the Massart inequality. Also includes an
implementation of the incomplete Bessel K function. / GPL-2


Name Version
r-disttools 0.1.7 Provides convenient methods for accessing the data in ‘dist’ objects with mini- noarch
mal memory and computational overhead. ‘disttools’ can be used to extract the
distance between any pair or combination of points encoded by a ‘dist’ object
using only the indices of those points. This is an improvement over existing
functionality, which requires either coercing a ‘dist’ object into a matrix or
calculating the one dimensional index corresponding to a pair of observations.
Coercion to a matrix is undesirable because doing so doubles the amount of
memory required for storage. In contrast, there is no inherent downside to the
latter solution. However, in part due to several edge cases, correctly and effi-
ciently implementing such a solution can be challenging. ‘disttools’ abstracts
away these challenges and provides a simple interface to access the data in a
‘dist’ object using the latter approach. / MIT
r-divdyn 0.8.0 Functions to describe sampling and diversity dynamics of fossil occurrence linux-
datasets (e.g. from the Paleobiology Database). The package includes meth- 64,
ods to calculate range- and occurrence-based metrics of taxonomic richness, osx-
extinction and origination rates, along with traditional sampling measures. A 64,
powerful subsampling tool is also included that implements frequently used win-
sampling standardization methods in a multiple bin-framework. The plotting 64
of time series and the occurrence data can be simplified by the functions in-
corporated in the package, as well other calculations, such as environmental
affinities and extinction selectivity testing. Details can be found in: Kocsis,
A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
/ CC BY 4.0
r-divmelt 1.0.3 This package has tools for analyzing DNA melting data to generate HRM noarch
scores, the DNA diversity measure output of the HRM Diversity Assay. For
additional documentation visit http://code.google.com/p/divmelt/. / GPL-2
r-divo 1.0.0 A set of tools for empirical analysis of diversity (a number and frequency of linux-
different types in population) and similarity (a number and frequency of shared 64,
types in two populations) in biological or ecological systems. / GPL-3 osx-
64,
win-
64
r-dixontest 1.0.0 For outlier detection in small and normally distributed samples the ratio linux-
test of Dixon (Q-test) can be used. Density, distribution function, quan- 64,
tile function and random generation for Dixon’s ratio statistics are pro- osx-
vided as wrapper functions. The core applies McBane’s Fortran functions 64,
<doi:10.18637/jss.v016.i03> that use Gaussian quadrature for a numerical so- win-
lution. / GPL-3 64
r-dkdna 0.1.1 Compute diffusion kernels on DNA polymorphisms, including SNP and bi- linux-
allelic genotypes. / GPL-2 64,
osx-
64,
win-
64
r-dlasso 2.0.2 An implementation of the differentiable lasso (dlasso) and SCAD (dSCAD) noarch
using iterative ridge algorithm. This package allows selecting the tuning pa-
rameter by AIC, BIC, GIC and GIC. / GPL-2


Name Version
r-dlib 1.0.3 Interface for ‘Rcpp’ users to ‘dlib’ <http://dlib.net> which is a ‘C’ toolkit con- linux-
taining machine learning algorithms and computer vision tools. It is used in a 64,
wide range of domains including robotics, embedded devices, mobile phones, osx-
and large high performance computing environments. This package allows R 64,
users to use ‘dlib’ through ‘Rcpp’. / BSL-1.0 win-
64
r-dlm 1.1_5 Provides routines for Maximum likelihood, Kalman filtering and smoothing, linux-
and Bayesian analysis of Normal linear State Space models, also known as 64,
Dynamic Linear Models. / GPL-2 osx-
64,
win-
64
r-dma 1.4_0 Dynamic model averaging for binary and continuous outcomes. / GPL-2 noarch
r-dmrnet 0.2.0 Model selection algorithms for regression and classification, where the noarch
predictors can be numerical and categorical and the number of regressors
exceeds the number of observations. The selected model consists of a
subset of numerical regressors and partitions of levels of factors. Alek-
sandra Maj-Kańska, Piotr Pokarowski and Agnieszka Prochenka (2015)
<doi:10.1214/15-EJS1050>. Piotr Pokarowski and Jan Mielniczuk (2015)
<http://www.jmlr.org/papers/volume16/pokarowski15a/pokarowski15a.pdf>.
/ GPL-2
r-dmt 0.8.20Probabilistic dependency modeling toolkit. / BSD_2_clause noarch
r-dmwr 0.4.1 This package includes functions and data accompanying the book Data Mining noarch
with R, learning with case studies by Luis Torgo, CRC Press 2010. / GPL-2
r-dnaseqtest 1.0 Generates DNA sequences based on Markov model techniques for matched se- noarch
quences. This can be generalized to several sequences. The sequences (taxa)
are then arranged in an evolutionary tree (phylogenetic tree) depicting how
taxa diverge from their common ancestors. This gives the tests and estima-
tion methods for the parameters of different models. Standard phylogenetic
methods assume stationarity, homogeneity and reversibility for the Markov
processes, and often impose further restrictions on the parameters. / GPL-2
r-dne 2.1.0 The DnE package involves functions to analyse the distribution of a set of noarch
given data. The basic idea of the analysis is chi-squared test. Functions which
have the form as is.xxdistribution are used to analyse whether the data obeys
the xxdistrbution. If you do not know which distribution to judge, use function
is.dt(). / GPL-2
r-dng 0.2.1 Provides density, distribution function, quantile function and random gener- linux-
ation for the split normal and split-t distributions, and computes their mean, 64,
variance, skewness and kurtosis for the two distributions (Li, F, Villani, M. osx-
and Kohn, R. (2010) <doi:10.1016/j.jspi.2010.04.031>). / GPL-2 64,
win-
64


r-dnmf 1.3 Discriminant Non-Negative Matrix Factorization aims to extend the Non- noarch
negative Matrix Factorization algorithm in order to extract features that en-
force not only the spatial locality, but also the separability between classes
in a discriminant manner. It refers to three article, Zafeiriou, Stefanos, et al.
Exploiting discriminant information in nonnegative matrix factorization with
application to frontal face verification. Neural Networks, IEEE Transactions
on 17.3 (2006): 683-695. Kim, Bo-Kyeong, and Soo-Young Lee. Spectral
Feature Extraction Using dNMF for Emotion Recognition in Vowel Sounds.
Neural Information Processing. Springer Berlin Heidelberg, 2013. and Lee,
Soo-Young, Hyun-Ah Song, and Shun-ichi Amari. A new discriminant NMF
algorithm and its application to the extraction of subtle emotional differences
in speech. Cognitive neurodynamics 6.6 (2012): 525-535. / GPL-2
r-do 1.0.0.0Flexibly convert data between long and wide format using just two functions: noarch
reshape_toLong() and reshape_toWide(). / GPL-3
r-dobad 1.0.6 Provides Frequentist (EM) and Bayesian (MCMC) Methods for Inference of noarch
Birth-Death-Immigration Markov Chains. / GPL-2
r-dobson 0.4 Example datasets from the book An Introduction to Generalised Linear Models noarch
(Year: 2018, ISBN:9781138741515) by Dobson and Barnett. / GPL-2
r-dockerfiler 0.1.3 Build a Dockerfile straight from your R session. ‘dockerfiler’ allows you to noarch
create step by step a Dockerfile, and provide convenient tools to wrap R code
inside this Dockerfile. / MIT
r-docopt 0.6.1 Define a command-line interface by just giving it a description in the specific noarch
format. / MIT
r-docopulae 0.4.0 A direct approach to optimal designs for copula models based on the Fisher linux-
information. Provides flexible functions for building joint PDFs, evaluating 64,
the Fisher information and finding optimal designs. It includes an extensible osx-
solution to summation and integration called ‘nint’, functions for transforming, 64,
plotting and comparing designs, as well as a set of tools for common low-level win-
tasks. / MIT 64
r-docstring 1.0.0 Provides the ability to display something analogous to Python’s docstrings noarch
within R. By allowing the user to document their functions as comments at the
beginning of their function without requiring putting the function into a pack-
age we allow more users to easily provide documentation for their functions.
The documentation can be viewed just like any other help files for functions
provided by packages as well. / GPL-2
r-documair 0.6_0 Production of R packages from tagged comments introduced within the code linux-
and a minimum of additional documentation files. / GPL (>= 2.15) 64,
osx-
64,
win-
64
r-document 3.1.0 Have you ever been tempted to create ‘roxygen2’-style documentation com- noarch
ments for one of your functions that was not part of one of your packages (yet)?
This is exactly what this package is about: running ‘roxygen2’ on (chunks of)
a single code file. / BSD_2_clause
r-docusignr 0.0.3 Connect to the ‘DocuSign’ Rest API <https://www.docusign.com/p/ noarch
RESTAPIGuide/RESTAPIGuide.htm>, which supports embedded signing,
and sending of documents. / GPL-3
r-dodge 0.9_2 A variety of sampling plans are able to be compared using evaluations of their noarch
operating characteristics (OC), average outgoing quality (OQ), average total
inspection (ATI) etc. / GPL-3


Name Version
r-doestrare 0.2 Rare variant association test integrating variant position information. It aims linux-
to identify the presence of clusters of disease-risk variants in specific gene 64,
regions. For more details, please read the publication from Persyn et al. (2017) osx-
<doi:10.1371/journal.pone.0179364>. / GPL-2 64,
win-
64
r-doex 1.1 Contains several one-way heteroscedastic ANOVA tests such as Alexander- noarch
Govern test by Alexandern and Govern (1994) <doi:10.2307/1165140>,
Alvandi et al. Generalized F test by Alvandi et al. (2012)
<doi:10.1080/03610926.2011.573160>, Approximate F test by Asiribo
and Gurland (1990) <doi:10.1080/03610929008830427>, Box F test by Box
(1954) <doi:10.1214/aoms/1177728786>, Brown-Forsythe test by Brown
and Forsythe (1974) <do:10.2307/1267501>, B2 test by Ozdemir and Kurt
(2006) <http://sjam.selcuk.edu.tr/sjam/article/view/174>, Cochran F test by
Cochran (1937) <https://www.jstor.org/stable/pdf/2984123.pdf>, Fiducial
Approach test by Li et al. (2011) <doi:10.1016/j.csda.2010.12.009>, Gen-
eralized F test by Weerahandi (1995) <doi:10.2307/2532947>, Johansen F
test by Johansen (1980) <doi:10.1093/biomet/67.1.85>, Modified Brown-
Forsythe test by Mehrotra (1997) <doi:10.1080/03610919708813431>,
Modified Welch test by Hartung et al.(2002) <doi:10.1007/s00362-
002-0097-8>, One-Stage test by Chen and Chen (1998)
<doi:10.1080/03610919808813501>, One-Stage Range test by Chen and
Chen (2000) <doi:10.1080/01966324.2000.10737505>, Parametric Bootstrap
test by Krishnamoorhty et al.(2007) <doi:10.1016/j.csda.2006.09.039>, Per-
mutation F test by Berry and Mielke (2002) <doi:10.2466/pr0.2002.90.2.495>,
Scott-Smith test by Scott and Smith (1971) <doi:10.2307/2346757>, Welch
test by Welch(1951) <doi:10.2307/2332579>, and Welch-Aspin test by Aspin
(1948) <doi:10.1093/biomet/35.1-2.88>. These tests are used to test the
equality of group means under unequal variance. Furthermore, a modified
version of Generalized F-test is improved to test the equality of non-normal
group means under unequal variances and a revised version of Generalized
F-test is given to test the equality of non-normal group means caused by
skewness. / GPL-2
r-domc 1.3.5 Provides a parallel backend for the %dopar% function using the multicore linux-
functionality of the parallel package. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r- 1.0.0 Dominance analysis is a method that allows to compare the relative impor- noarch
dominanceanalysis tance of predictors in multiple regression models: ordinary least squares,
generalized linear models and hierarchical linear models. The main prin-
ciples and methods of dominance analysis are described in Budescu, D. V.
(1993) <doi:10.1037/0033-2909.114.3.542> and Azen, R., & Budescu, D. V.
(2003) <doi:10.1037/1082-989X.8.2.129> for ordinary least squares regres-
sion. Subsequently, the extensions for multivariate regression, logistic regres-
sion and hierarchical linear models were described in Azen, R., & Budescu,
D. V. (2006) <doi:10.3102/10769986031002157>, Azen, R., & Traxel, N.
(2009) <doi:10.3102/1076998609332754> and Luo, W., & Azen, R. (2013)
<doi:10.3102/1076998612458319>, respectively. / GPL-2
r-domino 0.3.1 A wrapper on top of the ‘Domino Command-Line Client’. It lets you run noarch
‘Domino’ commands (e.g., run, upload, download) directly from your R en-
vironment. Under the hood, it uses R’s system function to run the ‘Domino’
executable, which must be installed as a prerequisite. ‘Domino’ is a service
that makes it easy to run your code on scalable hardware, with integrated ver-
sion control and collaboration features designed for analytical workflows (see
<http://www.dominodatalab.com> for more information). / MIT
r-doparallel 1.0.14Provides a parallel backend for the %dopar% function using the parallel pack- linux-
age. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-dorng 1.7.1 Provides functions to perform reproducible parallel foreach loops, using in- noarch
dependent random streams as generated by L’Ecuyer’s combined multiple-
recursive generator [L’Ecuyer (1999), <DOI:10.1287/opre.47.1.159>]. It en-
ables to easily convert standard %dopar% loops into fully reproducible loops,
independently of the number of workers, the task scheduling strategy, or the
chosen parallel environment and associated foreach backend. / GPL-2
r-dos 1.0.0 Contains data sets, examples and software from the book Design of Observa- noarch
tional Studies by Paul R. Rosenbaum, New York: Springer, <doi:10.1007/978-
1-4419-1213-8>, ISBN 978-1-4419-1212-1. / GPL-2
r-dosearch 1.0.2 Identification of causal effects from arbitrary observational and experimen- linux-
tal probability distributions via do-calculus and standard probability manip- 64,
ulations using a search-based algorithm. Allows for the presence of mech- osx-
anisms related to selection bias (Bareinboim, E. and Tian, J. (2015) <http: 64,
//ftp.cs.ucla.edu/pub/stat_ser/r445.pdf>), transportability (Bareinboim, E. and win-
Pearl, J. (2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>), missing data 64
(Mohan, K. and Pearl, J. and Tian., J. (2013) <http://ftp.cs.ucla.edu/pub/stat_
ser/r410.pdf>) and arbitrary combinations of these. / GPL-2


Name Version
r-dosefinding 0.9_16The DoseFinding package provides functions for the design and analysis of linux-
dose-finding experiments (with focus on pharmaceutical Phase II clinical tri- 64,
als). It provides functions for: multiple contrast tests, fitting non-linear dose- osx-
response models (using Bayesian and non-Bayesian estimation), calculating 64,
optimal designs and an implementation of the MCPMod methodology. / GPL- win-
3 64
r-dostats 1.3.2 A small package containing helper utilities for creating function for computing noarch
statistics. / GPL-3
r-dotcall64 1.0_0 Provides .C64(), which is an enhanced version of .C() and .Fortran() from the linux-
foreign function interface. .C64() supports long vectors, arguments of type 64,
64-bit integer, and provides a mechanism to avoid unnecessary copies of read- osx-
only and write-only arguments. This makes it a convenient and fast interface 64,
to C/C and Fortran code. / GPL-2 win-
64
r-dotdot 0.1.0 Use ‘..’ on the right hand side of the ‘:=’ operator as a shorthand for the left noarch
hand side, so that ‘var := f(..) ..’ is equivalent to ‘var <- f(var) var’. This
permits the user to be explicit about growing an object or overwriting it using
its previous value, avoids repeating a variable name, and saves keystrokes,
time, visual space and cognitive load. / GPL-3
r-dotenv 1.0.2 Load configuration from a ‘.env’ file, that is in the current working directory, noarch
into environment variables. / MIT
r-doubcens 1.1 Contains the discrete nonparametric survivor function estimation algorithm of linux-
De Gruttola and Lagakos for doubly interval-censored failure time data and 64,
the discrete nonparametric survivor function estimation algorithm of Sun for osx-
doubly interval-censored left-truncated failure time data [Victor De Gruttola 64,
& Stephen W. Lagakos (1989) <doi:10.2307/2532030>] [Jianguo Sun (1995) win-
<doi:10.2307/2533008>]. / GPL-2 64
r- 1.4 Likelihood-based inference methods with doubly-truncated data are developed noarch
double.truncation under various models. Nonparametric models are based on Efron and Pet-
rosian (1999) <doi:10.1080/01621459.1999.10474187> and Emura, Konno,
and Michimae (2015) <doi:10.1007/s10985-014-9297-5>. Parametric mod-
els from the special exponential family (SEF) are based on Hu and Emura
(2015) <doi:10.1007/s00180-015-0564-z> and Emura, Hu and Konno (2017)
<doi:10.1007/s00362-015-0730-y>. / GPL-2
r-doublecone 1.1 Performs hypothesis tests concerning a regression function in a least-squares noarch
model, where the null is a parametric function, and the alternative is the union
of large-dimensional convex polyhedral cones. See Bodhisattva Sen and Mary
C Meyer (2016) <doi:10.1111/rssb.12178> for more details. / GPL-2 | GPL-3
r-doubleexpseq 1.1 Differential exon usage test for RNA-Seq data via an empirical Bayes shrink- noarch
age method for the dispersion parameter the utilizes inclusion-exclusion data
to analyze the propensity to skip an exon across groups. The input data consists
of two matrices where each row represents an exon and the columns represent
the biological samples. The first matrix is the count of the number of reads
expressing the exon for each sample. The second matrix is the count of the
number of reads that either express the exon or explicitly skip the exon across
the samples, a.k.a. the total count matrix. Dividing the two matrices yields
proportions representing the propensity to express the exon versus skipping
the exon for each sample. / GPL-3
r-dovalidation 1.1.0 Local linear hazard estimator and its multiplicatively bias correction, including noarch
three bandwidth selection methods: best one-sided cross-validation, double
one-sided cross-validation, and standard cross-validation. / GPL-2


Name Version
r-downloader 0.4 Provides a wrapper for the download.file function, making it possible to down- linux-
load files over HTTPS on Windows, Mac OS X, and other Unix-like platforms. 32,
The ‘RCurl’ package provides this functionality (and much more) but can be linux-
difficult to install because it must be compiled with external dependencies. 64,
This package has no external dependencies, so it is much easier to install. / noarch,
GPL-2 osx-
64,
win-
32,
win-
64
r-downsize 0.2.2 Toggles the test and production versions of a large workflow. / GPL-3 noarch
r-dparser 0.1.8 A Scannerless GLR parser/parser generator. Note that GLR standing for linux-
generalized LR, where L stands for left-to-right and R stands for rightmost 64,
(derivation). For more information see <https://en.wikipedia.org/wiki/GLR_ osx-
parser>. This parser is based on the Tomita (1987) algorithm. (Paper can be 64,
found at <http://acl-arc.comp.nus.edu.sg/archives/acl-arc-090501d3/data/pdf/ win-
anthology-PDF/J/J87/J87-1004.pdf>). The original ‘dparser’ package docu- 64
mentation can be found at <http://dparser.sourceforge.net/>. This allows you
to add mini-languages to R (like RxODE’s ODE mini-language Wang, Hal-
low, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages
like ‘NONMEM’ to automatically translate them to R code. To use this in your
code, add a LinkingTo dparser in your DESCRIPTION file and instead of using
#include <dparse.h> use #include <dparser.h>. This also provides a R-based
port of the make_dparser <http://dparser.sourceforge.net/d/make_dparser.cat>
command called mkdparser(). Additionally you can parse an arbitrary gram-
mar within R using the dparse() function, which works on most OSes and is
mainly for grammar testing. The fastest parsing, of course, occurs at the C
level, and is suggested. / BSD_3_clause
r-dpcid 1.0 Differential partial correlation identification with the ridge and the fusion linux-
penalties. / GPL-2 64,
osx-
64,
win-
64
r-dpglasso 1.0 fits the primal graphical lasso, via one-at-a-time block-coordinate descent. / linux-
GPL-2 64,
osx-
64,
win-
64


r-dplrcon 1.0 The concordance method is a non-parametric method based on bootstrapping noarch
that is used to test the hypothesis that two subsets of time series are similar
in terms of mean, variance or both. This method was developed to address a
concern within dendroclimatology that young trees may produce a differing
climate response to older more established trees. Details of this method are
available in Pirie, M. (2013). The Climate of New Zealand reconstructed from
kauri tree rings: Enhancement through the use of novel statistical methodol-
ogy. PhD. Dissertation, School of Environment and Department of Statistics,
University of Auckland, New Zealand. This package also produces a figure
with 3 panels, each panel is for a different climate variable. An example of
this figure in included in On the influence of tree size on the climate - growth
relationship of New Zealand kauri (Agathis australis): insights from annual,
monthly and daily growth patterns. J Wunder, AM Fowler, ER Cook, M Pirie,
SPJ McCloskey. Trees 27 (4), 937-948. For further R functions for loading
your own dendroclimatology datasets and performing dendrochronology anal-
ysis refer to the R package dplR: Dendrochronology Program Library in R.
The concordance procedure is intended to add to the standard dendrochronol-
ogy techniques provided in dplR. / GPL-3
r-dplyr 0.8.0.1A fast, consistent tool for working with data frame like objects, both in mem- linux-
ory and out of memory. / MIT file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-dpp 0.1.2 This MCMC method takes a data numeric vector (Y) and assigns the elements linux-
of Y to a (potentially infinite) number of normal distributions. The individual 64,
normal distributions from a mixture of normals can be inferred. Following the osx-
method described in Escobar (1994) <doi:10.2307/2291223> we use a Dirich- 64,
let Process Prior (DPP) to describe stochastically our prior assumptions about win-
the dimensionality of the data. / MIT 64
r-dprint 0.0.4 Provides a generalized method for printing tabular data within the R environ- noarch
ment in order to make the process of presenting high quality tabular output
seamless for the user. Output is directed to the R graphics device so that tables
can be exported to any file format supported by the graphics device. Utilizes a
formula interface to specify the contents of tables often found in manuscripts
or business reports. In addition, formula interface provides inline formatting
of the numeric cells of a table and renaming column labels. / GPL-2
r-dqshiny 0.0.3 Provides highly customizable modules to enhance your shiny apps. Includes noarch
layout independent collapsible boxes and value boxes, a very fast autocom-
plete input, rhandsontable extensions for filtering and paging and much more.
/ GPL-3


Name Version
r-dr 3.0.10Functions, methods, and datasets for fitting dimension reduction regression, noarch
using slicing (methods SAVE and SIR), Principal Hessian Directions (phd,
using residuals and the response), and an iterative IRE. Partial methods, that
condition on categorical predictors are also available. A variety of tests, and
stepwise deletion of predictors, is also included. Also included is code for
computing permutation tests of dimension. Adding additional methods of es-
timating dimension is straightforward. For documentation, see the vignette in
the package. With version 3.0.4, the arguments for dr.step have been modified.
/ GPL-2
r-dragonking 0.1.0 Statistical tests and test statistics to identify events in a dataset that are dragon noarch
kings (DKs). The statistical methods in this package were reviewed in Wheat-
ley & Sornette (2015) <doi:10.2139/ssrn.2645709>. / GPL-3
r-dragular 0.3.1 Move elements between containers in ‘Shiny’ without explicitly using noarch
‘JavaScript’. It can be used to build custom inputs or to change the positions
of user interface elements like plots or tables. / GPL-2
r-drat 0.1.5 Creation and use of R Repositories via helper functions to insert packages into noarch
a repository, and to add repository information to the current R session. Two
primary types of repositories are support: gh-pages at GitHub, as well as local
repositories on either the same machine or a local network. Drat is a recursive
acronym: Drat R Archive Template. / GPL-2
r-draw 1.0.0 A set of user-friendly wrapper functions for creating consistent graphics and noarch
diagrams with lines, common shapes, text, and page settings. Compatible with
and based on the R ‘grid’ package. / MIT
r-drawr 1.0.1 We present DRaWR, a network-based method for ranking genes or properties noarch
related to a given gene set. Such related genes or properties are identified from
among the nodes of a large, heterogeneous network of biological information.
Our method involves a random walk with restarts, performed on an initial net-
work with multiple node and edge types, preserving more of the original, spe-
cific property information than current methods that operate on homogeneous
networks. In this first stage of our algorithm, we find the properties that are
the most relevant to the given gene set and extract a subnetwork of the orig-
inal network, comprising only the relevant properties. We then rerank genes
by their similarity to the given gene set, based on a second random walk with
restarts, performed on the above subnetwork. / GPL-2
r- 0.1.3 Calculates the T-Statistic for the drift burst hypothesis from the working paper linux-
driftbursthypothesis Christensen, Oomen and Reno (2018) <DOI:10.2139/ssrn.2842535>. 64,
The authors’ MATLAB code is available upon request, see: osx-
<https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2842535>. / GPL- 64,
3 win-
64
r-drillr 0.1 Provides a R driver for Apache Drill<https://drill.apache.org>, which noarch
could connect to the Apache Drill cluster<https://drill.apache.org/docs/
installing-drill-on-the-cluster> or drillbit<https://drill.apache.org/docs/
embedded-mode-prerequisites> and get result(in data frame) from
the SQL query and check the current configuration status. This link
<https://drill.apache.org/docs> contains more information about Apache Drill.
/ GPL-3


Name Version
r-drimpute 1.0 R codes for imputing dropout events. Many statistical methods in cell type linux-
identification, visualization and lineage reconstruction do not account for 64,
dropout events (‘PCAreduce’, ‘SC3’, ‘PCA’, ‘t-SNE’, ‘Monocle’, ‘TSCAN’, osx-
etc). ‘DrImpute’ can improve the performance of such software by imputing 64,
dropout events. / GPL-3 win-
64
r-drmdel 1.3.1 Dual empirical likelihood (DEL) inference under semiparametric density ra- linux-
tio models (DRM) in the presence of multiple samples, including population 64,
cumulative distribution function estimation, quantile estimation and compar- osx-
ison, density estimation, composite hypothesis testing for DRM parameters 64,
which encompasses testing for changes in population distribution functions as win-
a special case, etc. / GPL-3 64
r-dropr 0.1 Drop out analysis for psychologists in a R based web application. Shiny is used noarch
to visualize and analyze drop outs tailored to the methods of online survey
methodology. Concept and app presented at the SCIP Conference in Long
Beach, California. / GPL-2
r-droptest 0.1.3 Generates simulated data representing the LOX drop testing process (also noarch
known as impact testing). A simulated process allows for accelerated study
of test behavior. Functions are provided to simulate trials, test series, and
groups of test series. Functions for creating plots specific to this process are
also included. Test attributes and criteria can be set arbitrarily. This work is
not endorsed by or affiliated with NASA. See ASTM G86-17, Standard Test
Method for Determining Ignition Sensitivity of Materials to Mechanical Im-
pact in Ambient Liquid Oxygen and Pressurized Liquid and Gaseous Oxygen
Environments <doi:10.1520/G0086-17>. / MIT
r-drr 0.0.3 An Implementation of Dimensionality Reduction via Regression using Kernel linux-
Ridge Regression. / GPL-3 | file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-ds 4.0 Performs various analyzes of descriptive statistics, including correlations, noarch
graphics and tables. / GPL-2
r-dsample 0.91.2.2
Two discretization-based Monte Carlo algorithms, namely the Fu-Wang algo- noarch
rithm and the Wang-Lee algorithm, are provided for random sample generation
from a high dimensional distribution of complex structure. The normalizing
constant of the target distribution needs not to be known. / GPL-2
r-dsbayes 1.1 Calculate posterior modes and credible intervals of parameters of the Dixon- noarch
Simon model for subgroup analysis (with binary covariates) in clinical trials. /
GPL-2
r-dsl 0.1_6.1
An abstract DList class helps storing large list-type objects in a distributed linux-
manner. Corresponding high-level functions and methods for handling dis- 64,
tributed storage (DStorage) and lists allows for processing such DLists on dis-osx-
tributed systems efficiently. In doing so it uses a well defined storage backend
64,
implemented based on the DStorage class. / GPL-3 win-
64


Name Version
r-dst 1.4.0 Using the Theory of Belief Functions for evidence calculus. Basic probability noarch
assignments, or mass functions, can be defined on the subsets of a set of possi-
ble values and combined. A mass function can be extended to a larger frame.
Marginalization, i.e. reduction to a smaller frame can also be done. These fea-
tures can be combined to analyze small belief networks and take into account
situations where information cannot be satisfactorily described by probability
distributions. / GPL-2
r-dstat 1.0.4 A d-statistic tests the null hypothesis of no treatment effect in a matched, noarch
nonrandomized study of the effects caused by treatments. A d-statistic fo-
cuses on subsets of matched pairs that demonstrate insensitivity to unmeasured
bias in such an observational study, correcting for double-use of the data by
conditional inference. This conditional inference can, in favorable circum-
stances, substantially increase the power of a sensitivity analysis (Rosenbaum
(2010) <doi:10.1007/978-1-4419-1213-8_14>). There are two examples, one
concerning unemployment from Lalive et al. (2006) <doi:10.1111/j.1467-
937X.2006.00406.x>, the other concerning smoking and periodontal disease
from Rosenbaum (2017) <doi:10.1214/17-STS621>. / GPL-2
r-dt 0.5 Data objects in R can be rendered as HTML tables using the JavaScript library linux-
‘DataTables’ (typically via R Markdown or Shiny). The ‘DataTables’ library 32,
has been included in this R package. The package name ‘DT’ is an abbrevia- linux-
tion of ‘DataTables’. / GPL-3 | file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-dtables 0.2.0 Towards automation of descriptive frequencies and statistics tables. / GPL-3 noarch
r-dtangle 0.3.1 Deconvolving cell types from high-throughput gene profiling data. / GPL-3 noarch
r-dtaxg 0.1.0 To calculate the sensitivity and specificity in the absence of gold standard us- noarch
ing the Bayesian method. The Bayesian method can be referenced at Haiyan
Gu and Qiguang Chen (1999) <doi:10.3969/j.issn.1002-3674.1999.04.004>. /
GPL-3
r-dtd 0.2.1 Provides fast methods to work with Merton’s distance to default model in- linux-
troduced in Merton (1974) <doi:10.1111/j.1540-6261.1974.tb03058.x>. The 64,
methods includes simulation and estimation of the parameters. / GPL-2 osx-
64,
win-
64
r-dtda 2.1_1 This package implements different algorithms for analyzing randomly trun- noarch
cated data, one-sided and two-sided (i.e. doubly) truncated data. Two real data
sets are included. / GPL-2
r-dtda.cif 1.0 Nonparametric estimator of the cumulative incidences of competing risks un- linux-
der double truncation. The estimator generalizes the Efron-Petrosian NPMLE 64,
(Non-Parametric Maximun Likelihood Estimator) to the competing risks set- osx-
ting. Efron, B. and Petrosian, V. (1999) <doi:10.2307/2669997>. / GPL-2 64,
win-
64


Name Version
r-dtda.ni 1.0 Non-iterative estimator for the cumulative distribution of a doubly truncated noarch
variable. de Uña-Álvarez J. (2018) <doi:10.1007/978-3-319-73848-2_37>. /
GPL-2
r-dtk 3.5 This package was created to analyze multi-level one-way experimental de- noarch
signs. It is designed to handle vectorized observation and factor data where
there are unequal sample sizes and population variance homogeneity can not
be assumed. To conduct the Dunnett modified Tukey-Kramer test (a.k.a. the
T3 Procedure), create two vectors: one for your observations and one for the
factor level of each observation. The function, gl.unequal, provides a means
to more conveniently produce a factor vector with unequal sample sizes. Next,
use the DTK.test function to conduct the test and save the output as an object
to input into the DTK.plot function, which produces a confidence interval plot
for each of the pairwise comparisons. Lastly, the function TK.test conducts
the original Tukey-Kramer test. / GPL-2
r-dtmcpack 0.1_2 A series of functions which aid in both simulating and determining the prop- noarch
erties of finite, discrete-time, discrete state markov chains. Two functions
(DTMC, MultDTMC) produce n iterations of a Markov Chain(s) based on
transition probabilities and an initial distribution. The function FPTime deter-
mines the first passage time into each state. The function statdistr determines
the stationary distribution of a Markov Chain. / GPL-2
r-dtp 0.1.0 Compute the dynamic threshold panel model suggested by (Stephanie Kre- noarch
mer, Alexander Bick and Dieter Nautz (2013) <doi:10.1007/s00181-012-
0553-9>) in which they extended the (Hansen (1999) <doi: 10.1016/S0304-
4076(99)00025-1>) original static panel threshold estimation and the Caner
and (Hansen (2004) <doi:10.1017/S0266466604205011>) cross-sectional in-
strumental variable threshold model, where generalized methods of moments
type estimators are used. / GPL-3
r-dtrlearn2 1.0 We provide a comprehensive software to estimate general K-stage DTRs from noarch
SMARTs with Q-learning and a variety of outcome-weighted learning meth-
ods. Penalizations are allowed for variable selection and model regularization.
With the outcome-weighted learning scheme, different loss functions - SVM
hinge loss, SVM ramp loss, binomial deviance loss, and L2 loss - are adopted
to solve the weighted classification problem at each stage; augmentation in the
outcomes is allowed to improve efficiency. The estimated DTR can be eas-
ily applied to a new sample for individualized treatment recommendations or
DTR evaluation. / GPL-2
r-dtrreg 1.4 Dynamic treatment regime estimation and inference via G-estimation, dy- noarch
namic weighted ordinary least squares (dWOLS) and Q-learning. Inference
via bootstrap and (for G-estimation) recursive sandwich estimation. Estima-
tion and inference for survival outcomes via Dynamic Weighted Survival Mod-
eling (DWSurv). / GPL-2
r-dtsg 0.1.3 Basic time series functionalities such as listing of missing values, application noarch
of arbitrary aggregation as well as rolling window functions and automatic
detection of periodicity. As it is mainly based on ‘data.table’, it is fast and - in
combination with the ‘R6’ package - offers reference semantics. In addition
to its native R6 interface, it provides an S3 interface inclusive an S3 wrapper
method generator for those who prefer the latter. / MIT
r-dtt 0.1_2 This package provides functions for 1D and 2D Discrete Cosine Trans- noarch
form (DCT), Discrete Sine Transform (DST) and Discrete Hartley Transform
(DHT). / GPL-2


Name Version
r-dub 0.2.0 Provides an operator for assigning nested components of a list to names via a noarch
concise pattern matching syntax. This is especially convenient for assigning
individual names to the multiple values that a function may return in the form
of a list, and for extracting deeply nested list components. / MIT
r-dummies 1.5.6 Expands factors, characters and other eligible classes into dummy/indicator noarch
variables. / GPL-2
r-dummy 0.1.3 Efficiently create dummies of all factors and character vectors in a data frame. noarch
Support is included for learning the categories on one data set (e.g., a training
set) and deploying them on another (e.g., a test set). / GPL-2
r-dunn.test 1.3.5 Computes Dunn’s test (1964) for stochastic dominance and reports the results noarch
among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic
dominance among k groups (Kruskal and Wallis, 1952). The interpretation of
stochastic dominance requires an assumption that the CDF of one group does
not cross the CDF of the other. ‘dunn.test’ makes k(k-1)/2 multiple pairwise
comparisons based on Dunn’s z-test-statistic approximations to the actual rank
statistics. The null hypothesis for each pairwise comparison is that the proba-
bility of observing a randomly selected value from the first group that is larger
than a randomly selected value from the second group equals one half; this null
hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test.
Like the rank-sum test, if the data can be assumed to be continuous, and the
distributions are assumed identical except for a difference in location, Dunn’s
test may be understood as a test for median difference. ‘dunn.test’ accounts
for tied ranks. / GPL-2
r-dunnetttests 2.0 For the implementation of the step-down or step-up Dunnett testing proce- noarch
dures, the package includes R functions to calculate critical constants and R
functions to calculate adjusted P-values of the test statistics. In addition, the
package also contains functions to evaluate testing powers and hence the nec-
essary sample sizes specially for the classical problem of comparisons of sev-
eral treatments with a control. / GPL-2
r-durmod 1.1_2 Estimation of piecewise constant mixed proportional hazard compet- linux-
ing risk model with NPMLE. The model is described in S. Gaure 64,
et al. (2007) <doi:10.1016/j.jeconom.2007.01.015>, J. Heckman and osx-
B. Singer (1984) <doi:10.2307/1911491>, and B.G. Lindsay (1983) 64,
<doi:10.1214/aos/1176346059>. / Artistic-2.0 win-
64
r-dwdlarger 0.1_0 Solving large scale distance weighted discrimination. The main algorithm is noarch
a symmetric Gauss-Seidel based alternating direction method of multipliers
(ADMM) method. See Lam, X.Y., Marron, J.S., Sun, D.F., and Toh, K.C.
(2018) <arXiv:1604.05473> for more details. / GPL-2
r-dwlm 0.1.0 This linear model solution is useful when both predictor and response have noarch
associated uncertainty. The doubly weights linear model solution is invari-
ant on which quantity is used as predictor or response. Based on the re-
sults by Reed(1989) <doi:10.1119/1.15963> and Ripley & Thompson(1987)
<doi:10.1039/AN9871200377>. / GPL-2
r-dyads 1.1.2 Contains functions for the MCMC simulation of dyadic network mod- noarch
els j2 (Zijlstra, 2017, <doi:10.1080/0022250X.2017.1387858>) and
p2 (Van Duijn, Snijders & Zijlstra, 2004, <doi: 10.1046/j.0039-
0402.2003.00258.x>) as described in Zijlstra, Van Duijn & Snijders
(2009) <doi: 10.1348/000711007X255336>. / GPL-2


r-dydea 0.1.0 Finds regular and chaotic intervals in the data using the 0-1 test for chaos noarch
proposed by Gottwald and Melbourne (2004) <DOI:10.1137/080718851>. /
GPL-3
r-dygraphs 1.1.1.6An R interface to the ‘dygraphs’ JavaScript charting library (a copy of which is linux-
included in the package). Provides rich facilities for charting time-series data 32,
in R, including highly configurable series- and axis-display and interactive linux-
features like zoom/pan and series/point highlighting. / MIT file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-dykstra 1.0_0 Solves quadratic programming problems using Richard L. Dyk- noarch
stra’s cyclic projection algorithm. Routine allows for a combina-
tion of equality and inequality constraints. See Dykstra (1983)
<doi:10.1080/01621459.1983.10477029> for details. / GPL-2
r-dym 0.2 Add a Did You Mean feature to the R interactive. With this package, error mes- noarch
sages for misspelled input of variable names or package names suggest what
you really want to do in addition to notification of the mistake. / BSD_3_clause
r-dyn 0.2_9.6
Time series regression. The dyn class interfaces ts, irts(), zoo() and zooreg() noarch
time series classes to lm(), glm(), loess(), quantreg::rq(), MASS::rlm(), MCM-
Cpack::MCMCregress(), quantreg::rq(), randomForest::randomForest() and
other regression functions allowing those functions to be used with time se-
ries including specifications that may contain lags, diffs and missing values. /
GPL-3
r-dynamac 0.1.8 While autoregressive distributed lag (ARDL) models allow for extremely flex- noarch
ible dynamics, interpreting substantive significance of complex lag structures
remains difficult. This package is designed to assist users in dynamically sim-
ulating and plotting the results of various ARDL models. It also contains post-
estimation diagnostics, including a test for cointegration when estimating the
error-correction variant of the autoregressive distributed lag model (Pesaran,
Shin, and Smith 2001 <doi:10.1002/jae.616>). / GPL-2
r- 1.1 The package is aimed at dynamically visualizing probability distributions and noarch
dynamicdistribution their moments and all the commonly used distributions are included. / GPL-2
r-dynamichazard 0.6.5 Contains functions that lets you fit dynamic hazard models using linux-
state space models. The first implemented model is described in 64,
Fahrmeir (1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir win-
(1994) <doi:10.1093/biomet/81.2.317>. Extensions hereof are available where 64
the Extended Kalman filter is replaced by an unscented Kalman filter and
other options including particle filters. The implemented particle filters sup-
port more general state space models. / GPL-2
r-dynamictreecut 1.63_1Contains methods for detection of clusters in hierarchical clustering dendro- noarch
grams. / GPL-2
r-dynatree 1.2_10Inference by sequential Monte Carlo for dynamic tree regression and classi- linux-
fication models with hooks provided for sequential design and optimization, 64,
fully online learning with drift, variable selection, and sensitivity analysis of
osx-
inputs. Illustrative examples from the original dynamic trees paper are facili- 64,
tated by demos in the package; see demo(package=dynaTree). / LGPL-3 win-
64


Name Version
r-dynclust 3.13 DynClust is a two-stage procedure for the denoising and clustering of stack of noarch
noisy images acquired over time. Clustering only assumes that the data contain
an unknown but small number of dynamic features. The method first denoises
the signals using local spatial and full temporal information. The clustering
step uses the previous output to aggregate voxels based on the knowledge of
their spatial neighborhood. Both steps use a single keytool based on the sta-
tistical comparison of the difference of two signals with the null signal. No
assumption is therefore required on the shape of the signals. The data are as-
sumed to be normally distributed (or at least follow a symmetric distribution)
with a known constant variance. Working pixelwise, the method can be time-
consuming depending on the size of the data-array but harnesses the power of
multicore cpus. / MIT
r-dyncomp 0.0.2_1
While there are many well-established measures for identifying critical fluc- noarch
tuations and phase transitions, these measures only work with many points
of measurement and thus are unreliable when studying short and coarse-
grained time series. This package provides a measure for complexity
in a time series that does not rely on long time series (Kaiser (2017),
<doi:10.17605/OSF.IO/GWTKX>). / MIT
r- 0.1.0 An anonymization algorithm to resist neighbor label attack in a dynamic net- noarch
dynetnlaresistance work. / MIT
r-dynia 0.2 Fit dynamic intervention model using the arima() function. / GPL-2 noarch
r-dynpanel 0.1.0 Computes the first stage GMM estimate of a dynamic linear model with p lags noarch
of the dependent variables. / GPL-3
r-dynpred 0.1.2 The dynpred package contains functions for dynamic prediction in survival linux-
analysis. / GPL-2 64,
osx-
64,
win-
64
r-dynprog 0.1.0 A domain-specific language for specifying translating recursions into noarch
dynamic-programming algorithms. See <https://en.wikipedia.org/wiki/
Dynamic_programming> for a description of dynamic programming. / GPL-3
r-dzexpm 2.0 MCMC method to estimate and predict skewed spatial processes. A real noarch
data set is included. Reference: Wang, Yang and Majumdar (2018)
<doi.org/10.1007/s00180-017-0741-3>. / GPL-2
r-e1071 1.7_1 Functions for latent class analysis, short time Fourier transform, fuzzy clus- linux-
tering, support vector machines, shortest path computation, bagged clustering, 32,
naive Bayes classifier, . . . / GPL-2 linux-
64,
osx-
64,
win-
32,
win-
64
r-eaf 1.8 Plots of the empirical attainment function for two objectives. / GPL-2 linux-
64,
osx-
64,
win-
64


Name Version
r-easyahp 0.1.1 Given the scores from decision makers, the analytic hierarchy process can be noarch
conducted easily. / GPL-3
r-easyanova 7.0 Perform analysis of variance and other important complementary analyses. noarch
The functions are easy to use. Performs analysis in various designs, with bal-
anced and unbalanced data. / GPL-2
r-easycsv 1.0.8 Allows users to easily read multiple comma separated tables and create a data noarch
frame under the same name. Is able to read multiple comma separated tables
from a local directory, a zip file or a zip file on a remote directory. / GPL-2
r-easynls 5.0 Fit and plot some nonlinear models. / GPL-2 noarch
r-easypubmed 2.13 Query NCBI Entrez and retrieve PubMed records in XML or text format. Pro- noarch
cess PubMed records by extracting and aggregating data from selected fields.
A large number of records can be easily downloaded via this simple-to-use
interface to the NCBI PubMed API. / GPL-2
r-easyreg 3.0 Performs analysis of regression in simple designs with quantitative treatments, noarch
including mixed models and non linear models. / GPL-2
r-easysvg 0.1.0 This SVG elements generator can easily generate SVG elements such as rect, noarch
line, circle, ellipse, polygon, polyline, text and group. Also, it can combine
and output SVG elements into a SVG file. / MIT
r-ebal 0.1_6 Package implements entropy balancing, a data preprocessing procedure that noarch
allows users to reweight a dataset such that the covariate distributions in the
reweighted data satisfy a set of user specified moment conditions. This can
be useful to create balanced samples in observational studies with a binary
treatment where the control group data can be reweighted to match the covari-
ate moments in the treatment group. Entropy balancing can also be used to
reweight a survey sample to known characteristics from a target population. /
GPL-2
r-ebass 0.1 We propose a new sample size calculation method for trial-based cost- noarch
effectiveness analyses. Our strategy is based on the value of perfect infor-
mation that would remain after the completion of the study. / GPL-3
r-ebdbnet 1.2.5 Infer the adjacency matrix of a network from time course data using an em- linux-
pirical Bayes estimation procedure based on Dynamic Bayesian Networks. / 64,
GPL-3 osx-
64,
win-
64
r-eben 4.6 Provides the Empirical Bayesian Elastic Net for handling multicollinearity in linux-
generalized linear regression models. As a special case of the ‘EBglmnet’ 64,
package (also available on CRAN), this package encourages a grouping effects osx-
to select relevant variables and estimate the corresponding non-zero effects. / 64,
GPL-3 win-
64
r-ebgenotyping 2.0.1 Genotyping the population using next generation sequencing data is essen- noarch
tially important for the rare variant detection. In order to distinguish the
genomic structural variation from sequencing error, we propose a statistical
model which involves the genotype effect through a latent variable to depict
the distribution of non-reference allele frequency data among different sam-
ples and different genome loci, while decomposing the sequencing error into
sample effect and positional effect. An ECM algorithm is implemented to es-
timate the model parameters, and then the genotypes and SNPs are inferred
based on the empirical Bayes method. / GPL-2


Name Version
r-ebglmnet 4.1 Provides empirical Bayesian lasso and elastic net algorithms for variable selec- linux-
tion and effect estimation. Key features include sparse variable selection and 64,
effect estimation via generalized linear regression models, high dimensionality osx-
with p>>n, and significance test for nonzero effects. This package outperforms 64,
other popular methods such as lasso and elastic net methods in terms of power win-
of detection, false discovery rate, and power of detecting grouping effects. / 64
GPL-3
r-ebprs 1.1.5 EB-PRS is a novel method that leverages information for effect sizes across noarch
all the markers to improve the prediction accuracy. No parameter tuning is
needed in the method, and no external information is needed. This R-package
provides the calculation of polygenic risk scores from the given training sum-
mary statistics and testing data. We can use EB-PRS to extract main infor-
mation, estimate Empirical Bayes parameters, derive polygenic risk scores for
each individual in testing data, and evaluate the PRS according to AUC and
predictive r2. / GPL-3
r-ebrank 1.0.0 Empirical Bayes ranking applicable to parallel-estimation settings where the noarch
estimated parameters are asymptotically unbiased and normal, with known
standard errors. A mixture normal prior for each parameter is estimated us-
ing Empirical Bayes methods, subsequentially ranks for each parameter are
simulated from the resulting joint posterior over all parameters (The marginal
posterior densities for each parameter are assumed independent). Finally, ex-
periments are ordered by expected posterior rank, although computations min-
imizing other plausible rank-loss functions are also given. / CC0
r-ebsnp 1.0 Genotyping and SNP calling tool for single-sample next generation sequenc- noarch
ing data analysis using an empirical Bayes method. / GPL-2
r-ecctmc 0.2.5 Draw sample paths for endpoint-conditioned continuous time Markov chains linux-
via modified rejection sampling or uniformization. / GPL-3 64,
osx-
64,
win-
64
r-ecfsup 0.1_2 Testing the equality of several covariance functions of functional data. Four linux-
different methods are implemented: L2-norm with W-S naive, L2-norm with 64,
W-S bias-reduced, L2-norm (Zhang 2013) <ISBN:9781439862735>, and sup- osx-
norm with resampling (Guo et al. 2017) <arXiv:1609.04232>. / LGPL-3 64,
win-
64
r-echarts2shiny 0.2.13Embed interactive charts to their Shiny applications. These charts will be gen- noarch
erated by ECharts library developed by Baidu (<http://echarts.baidu.com/>).
Current version supports line chart, bar chart, pie chart, scatter plot, gauge,
word cloud, radar chart, tree map, and heat map. / GPL-2
r-ecipex 1.0 Provides a function that quickly computes the fine structure isotope patterns noarch
of a set of chemical formulas to a given degree of accuracy (up to the limit set
by errors in floating point arithmetic). A data-set comprising the masses and
isotopic abundances of individual elements is also provided. / GPL-2


Name Version
r-eco 4.0_1 Implements the Bayesian and likelihood methods proposed in Imai, linux-
Lu, and Strauss (2008 <DOI: 10.1093/pan/mpm017>) and (2011 64,
<DOI:10.18637/jss.v042.i05>) for ecological inference in 2 by 2 tables osx-
as well as the method of bounds introduced by Duncan and Davis (1953). 64,
The package fits both parametric and nonparametric models using either the win-
Expectation-Maximization algorithms (for likelihood models) or the Markov 64
chain Monte Carlo algorithms (for Bayesian models). For all models, the
individual-level data can be directly incorporated into the estimation whenever
such data are available. Along with in-sample and out-of-sample predictions,
the package also provides a functionality which allows one to quantify the
effect of data aggregation on parameter estimation and hypothesis testing
under the parametric likelihood models. / GPL-2
r-ecodist 2.0.1 Dissimilarity-based analysis functions including ordination and Mantel test linux-
functions, intended for use with spatial and community data. / GPL-2 64,
osx-
64,
win-
64
r-ecohydmod 1.0.0 Simulates the soil water balance (soil moisture, evapotranspiration, leakage noarch
and runoff), rainfall series by using the marked Poisson process and the veg-
etation growth through the normalized difference vegetation index (NDVI).
Please see Souza et al. (2016) <doi:10.1002/hyp.10953>. / GPL-2
r-econdemand 1.0 Tools for general properties including price, quantity, elasticity, convexity, noarch
marginal revenue and manifold of various economics demand systems includ-
ing Linear, Translog, CES, LES and CREMR. / GNU General Public License
version 2
r-ecoreg 0.2.2 Estimating individual-level covariate-outcome associations using aggregate noarch
data (ecological inference) or a combination of aggregate and individual-level
data (hierarchical related regression). / GPL-2
r-ecosimr 0.1.0 Given a site by species interaction matrix, users can make inferences about noarch
species interactions by performance hypothesis comparing test statistics
against a null distribution. The current package provides algorithms and met-
rics for niche-overlap, body size ratios and species co-occurrence. Users can
also integrate their own algorithms and metrics within these frameworks or
completely novel null models. Detailed explanations about the underlying as-
sumptions of null model analysis in ecology can be found at http://ecosimr.org.
/ MIT
r-ecosolver 0.5.2 R interface to the Embedded COnic Solver (ECOS), an efficient and robust linux-
C library for convex problems. Conic and equality constraints can be speci- 64,
fied in addition to integer and boolean variable constraints for mixed-integerosx-
problems. This R interface is inspired by the python interface and has similar64,
calling conventions. / GPL-3 win-
64


Name Version
r-ecotoxicology 1.0.1 Implementation of the EPA’s Ecological Exposure Research Division (EERD) noarch
tools (discontinued in 1999) for Probit and Trimmed Spearman-Karber Analy-
sis. Probit and Spearman-Karber methods from Finney’s book Probit analysis
a statistical treatment of the sigmoid response curve with options for most ac-
curate results or identical results to the book. Probit and all the tables from
Finney’s book (code-generated, not copied) with the generating functions in-
cluded. Control correction: Abbott, Schneider-Orelli, Henderson-Tilton, Sun-
Shepard. Toxicity scales: Horsfall-Barratt, Archer, Gauhl-Stover, Fullerton-
Olsen, etc. / GPL-3
r-ecotroph 1.6 EcoTroph is an approach and software for modelling marine and freshwater noarch
ecosystems. It is articulated entirely around trophic levels. EcoTroph’s key
displays are bivariate plots, with trophic levels as the abscissa, and biomass
flows or related quantities as ordinates. Thus, trophic ecosystem function-
ing can be modelled as a continuous flow of biomass surging up the food
web, from lower to higher trophic levels, due to predation and ontogenic pro-
cesses. Such an approach, wherein species as such disappear, may be viewed
as the ultimate stage in the use of the trophic level metric for ecosystem mod-
elling, providing a simplified but potentially useful caricature of ecosystem
functioning and impacts of fishing. This version contains catch trophic spec-
trum analysis (CTSA) function and corrected versions of the mf.diagnosis and
create.ETmain functions. / GPL-3
r-ecovirtual 1.1 Computer simulations of classical ecological models as a learning resource. / noarch
GPL-2
r-ecp 3.1.1 Implements various procedures for finding multiple change-points. Two meth- linux-
ods make use of dynamic programming and pruning, with no distributional as- 64,
sumptions other than the existence of certain absolute moments in one method. osx-
Hierarchical and exact search methods are included. All methods return the set 64,
of estimated change- points as well as other summary information. / GPL-2 win-
64
r-ed50 0.1.1 Functions of five estimation method for ED50 (50 percent effective noarch
dose) are provided, and they are respectively Dixon-Mood method (1948)
<doi:10.2307/2280071>, Choi’s original turning point method (1990)
<doi:10.2307/2531453> and it’s modified version given by us, as well as lo-
gistic regression and isotonic regression. Besides, the package also supports
comparison between two estimation results. / GPL-3
r-edci 1.1_3 Detection of edge points in images based on the difference of two asymmet- linux-
ric M-kernel estimators. Linear and circular regression clustering based on 64,
redescending M-estimators. Detection of linear edges in images. / GPL-2 osx-
64,
win-
64
r-edesign 1.0_13An implementation of maximum entropy sampling for spatial data is pro- linux-
vided. An exact branch-and-bound algorithm as well as greedy and dual 64,
greedy heuristics are included. / GPL (>= 2.0) osx-
64,
win-
64
r-edf 1.0.0 Import physiologic data stored in the European Data Format (EDF and EDF) noarch
into R. Both EDF and EDF files are supported. Discontinuous EDF files are
not yet supported. / MIT


Name Version
r-edfreader 1.2.1 Reads European Data Format files EDF and EDF, see <http://www.edfplus. noarch
info>, BioSemi Data Format files BDF, see <http://www.biosemi.com/faq/
file_format.htm>, and BDF files, see <http://www.teuniz.net/edfbrowser/
bdfplus%20format%20description.html>. The files are read in two steps: first
the header is read and then the signals (using the header object as a parameter).
/ GPL-3
r-edfun 0.2.0 Easily creating empirical distribution functions from data: ‘dfun’, ‘pfun’, noarch
‘qfun’ and ‘rfun’. / GPL-2 | GPL-3
r-edgarwebr 1.0.0 A set of methods to access and parse live filing information from the U.S. Se- noarch
curities and Exchange Commission (SEC - <https://sec.gov>) including com-
pany and fund filings along with all associated metadata. / MIT
r-edgebundler 0.1.4 Generates interactive circle plots with the nodes around the circumference and noarch
linkages between the connected nodes using hierarchical edge bundling via
the D3 JavaScript library. See <http://d3js.org/> for more information on D3.
/ GPL-3
r-edgecorr 1.0 Facilitates basic spatial edge correction to point pattern data. / GPL-2 noarch
r-edison 1.1.1 Package EDISON (Estimation of Directed Interactions from Sequences Of noarch
Non-homogeneous gene expression) runs an MCMC simulation to reconstruct
networks from time series data, using a non-homogeneous, time-varying dy-
namic Bayesian network. Networks segments and changepoints are inferred
concurrently, and information sharing priors provide a reduction of the infer-
ence uncertainty. / GPL-2
r-edma 1.5_3 Perform dynamic model averaging with grid search as in Dangl and Halling linux-
(2012) <doi:10.1016/j.jfineco.2012.04.003> using parallel computing. / GPL- 64,
2 osx-
64,
win-
64
r-eegkitdata 1.0 Contains the example EEG data used in the package eegkit. Also contains noarch
code for easily creating larger EEG datasets from the EEG Database on the
UCI Machine Learning Repository. / GPL-2
r- 0.5 Functions to test for changes of a response to a stimulus grouping relative to a noarch
effectsrelbaseline background or baseline response. / GPL-3
r-effectstars 1.9 Notice: The package EffectStars2 provides a more up-to-date implementation noarch
of effect stars! EffectStars provides functions to visualize regression mod-
els with categorical response as proposed by Tutz and Schauberger (2013)
<doi:10.1080/10618600.2012.701379>. The effects of the variables are plot-
ted with star plots in order to allow for an optical impression of the fitted
model. / GPL-2
r-effectstars2 0.1_2 Provides functions for the method of effect stars as proposed by Tutz and noarch
Schauberger (2013) <doi:10.1080/10618600.2012.701379>. Effect stars can
be used to visualize estimates of parameters corresponding to different groups,
for example in multinomial logit models. Beside the main function ‘effect-
stars’ there exist methods for special objects, for example for ‘vglm’ objects
from the ‘VGAM’ package. / GPL-2


Name Version
r-effecttreat 0.4 In personalized medicine, one wants to know, for a given patient and his or noarch
her outcome for a predictor (pre-treatment variable), how likely it is that a
treatment will be more beneficial than an alternative treatment. This package
allows for the quantification of the predictive causal association (i.e., the as-
sociation between the predictor variable and the individual causal effect of the
treatment) and related metrics. Part of this software has been developed using
funding provided from the European Union’s 7th Framework Programme for
research, technological development and demonstration under Grant Agree-
ment no 602552. / GPL-2
r- 0.1.4 An implementation for using efficient initials to compute the maximal eigen- noarch
efficientmaxeigenpair pair in R. It provides three algorithms to find the efficient initials under two
cases: the tridiagonal matrix case and the general matrix case. Besides, it also
provides two algorithms for the next to the maximal eigenpair under these two
cases. / MIT
r-efflog 1.0 Fitting a causal loglinear model and calculating the causal effects for a causal noarch
loglinear model with the multiplicative interaction or without the multiplica-
tive interaction, obtaining the natural direct, indirect and the total effect. It
calculates also the cell effect, which is a new interaction effect. / GPL-2
r-effsize 0.7.6 A collection of functions to compute the standardized effect sizes for experi- noarch
ments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A). The computation
algorithms have been optimized to allow efficient computation even with very
large data sets. / GPL-2
r-egst 1.0.0 Genetic predisposition for complex traits is often manifested through multiple noarch
tissues of interest at different time points in the development. As an example,
the genetic predisposition for obesity could be manifested through inherited
variants that control metabolism through regulation of genes expressed in the
brain and/or through the control of fat storage in the adipose tissue by dysregu-
lation of genes expressed in adipose tissue. We present a method eGST (eQTL-
based genetic subtyper) that integrates tissue-specific eQTLs with GWAS data
for a complex trait to probabilistically assign a tissue of interest to the pheno-
type of each individual in the study. eGST estimates the posterior probability
that an individual’s phenotype can be assigned to a tissue based on individual-
level genotype data of tissue-specific eQTLs and marginal phenotype data in a
genome-wide association study (GWAS) cohort. Under a Bayesian framework
of mixture model, eGST employs a maximum a posteriori (MAP) expectation-
maximization (EM) algorithm to estimate the tissue-specific posterior proba-
bility across individuals. Methodology is available from: A Majumdar, C Gi-
ambartolomei, N Cai, MK Freund, T Haldar, T Schwarz, J Flint, B Pasaniuc
(2019) <doi:10.1101/674226>. / GPL-3
r-eha 2.6.0 Sampling of risk sets in Cox regression, selections in the Lexis diagram, boot- linux-
strapping. Parametric proportional hazards fitting with left truncation and right 64,
censoring for common families of distributions, piecewise constant hazards, osx-
and discrete models. Parametric accelerated failure time models for left trun- 64,
cated and right censored data. / GPL-2 win-
64
r-ehof 1.8 Extended and enhanced hierarchical logistic regression models (called noarch
Huisman-Olff-Fresco in biology, see Huisman et al. 1993 JVS
<doi:10.1111/jvs.12050>) models. Response curves along one-dimensional
gradients including no response, monotone, plateau, unimodal and bimodal
models. / GPL-2


Name Version
r-eiadata 0.0.5 An R wrapper to allow the user to query categories and Series IDs, and import noarch
data, from the EIA’s API <https://www.eia.gov/opendata/>. / GPL-2
r-eigeninv Solves the ‘‘inverse eigenvalue problem” which is to generate a real-valued noarch
2011.8_1
matrix that has the specified real eigenvalue spectrum. It can generate in-
finitely many dense matrices, symmetric or asymmetric, with the given set
of eigenvalues. Algorithm can also generate stochastic and doubly stochastic
matrices. / GPL-2
r-eigenmodel 1.11 Estimation of the parameters in a model for symmetric relational data (e.g., noarch
the above-diagonal part of a square matrix), using a model-based eigenvalue
decomposition and regression. Missing data is accommodated, and a poste-
rior mean for missing data is calculated under the assumption that the data
are missing at random. The marginal distribution of the relational data can
be arbitrary, and is fit with an ordered probit specification. See Hoff (2007)
<arXiv:0711.1146> for details on the model. / GPL-2
r-eigenprcomp 1.0 Computes confidence intervals for the proportion explained by the first 1,2,k noarch
principal components, and computes confidence intervals for each eigenvalue.
Both computations are done via nonparametric bootstrap. / GPL-2


Name Version
r-eikosograms 0.1.1 An eikosogram (ancient Greek for probability picture) divides the unit square noarch
into rectangular regions whose areas, sides, and widths, represent various
probabilities associated with the values of one or more categorical variates.
Rectangle areas are joint probabilities, widths are always marginal (though
possibly joint margins, i.e. marginal joint distributions of two or more vari-
ates), and heights of rectangles are always conditional probabilities. Eikoso-
grams embed the rules of probability and are useful for introducing elemen-
tary probability theory, including axioms, marginal, conditional, and joint
probabilities, and their relationships (including Bayes theorem as a com-
pletely trivial consequence). They are markedly superior to Venn diagrams
for this purpose, especially in distinguishing probabilistic independence, mu-
tually exclusive events, coincident events, and associations. They also are
useful for identifying and understanding conditional independence structure.
As data analysis tools, eikosograms display categorical data in a manner sim-
ilar to Mosaic plots, especially when only two variates are involved (the
only case in which they are essentially identical, though eikosograms pur-
posely disallow spacing between rectangles). Unlike Mosaic plots, eikoso-
grams do not alternate axes as each new categorical variate (beyond two) is
introduced. Instead, only one categorical variate, designated the response,
presents on the vertical axis and all others, designated the conditioning vari-
ates, appear on the horizontal. In this way, conditional probability appears
only as height and marginal probabilities as widths. The eikosogram is there-
fore much better suited to a response model analysis (e.g. logistic model)
than is a Mosaic plot. Mosaic plots are better suited to log-linear style mod-
elling as in discrete multivariate analysis. Of course, eikosograms are also
suited to discrete multivariate analysis with each variate in turn appearing
as the response. This makes it better suited than Mosaic plots to discrete
graphical models based on conditional independence graphs (i.e. Bayesian
Networks or BayesNets). The eikosogram and its superiority to Venn dia-
grams in teaching probability is described in W.H. Cherry and R.W. Oldford
(2003) <https://math.uwaterloo.ca/~rwoldfor/papers/eikosograms/paper.pdf>,
its value in exploring conditional independence structure and relation to graph-
ical and log-linear models is described in R.W. Oldford (2003) <https://math.
uwaterloo.ca/~rwoldfor/papers/eikosograms/independence/paper.pdf>, and a
number of problems, puzzles, and paradoxes that are easily explained with
eikosograms are given in R.W. Oldford (2003) <https://math.uwaterloo.ca/
~rwoldfor/papers/eikosograms/examples/paper.pdf>. / GPL-3
r-eila 0.1_2 Implementation of Efficient Inference of Local Ancestry using fused quantile noarch
regression and k-means classifier / GPL-2
r-eipartialid 0.1.2 Estimate district-level bounds for 2x2 ecological inference based on the ap- noarch
proach described in the forthcoming article Jiang et al. (2019), Ecological Re-
gression with Partial Identification, Political Analysis. Interval data regression
is used to bound the nonidentified regression parameter in a linear contextual
effects model, from which district-level bounds are derived. The approach
here can be useful as a baseline of comparison for future work on ecological
inference. / MIT


Name Version
r-eive 2.3 Performs a compact genetic algorithm search to reduce errors-in-variables bias linux-
in linear regression. The algorithm estimates the regression parameters with 64,
lower biases and higher variances but mean-square errors (MSEs) are reduced. osx-
/ GPL-3 64,
win-
64
r-eiwild 0.6.7 This package allows to use the hybrid Multinomial-Dirichlet-Model of Eco- linux-
logical Inference for estimating inner Cells of RxC-Tables. This was already 64,
implemented in the eiPack-package. eiwild-package now has the possibility to osx-
use individual level data to support the aggregate level data and using different 64,
Hyperpriori-Distributions. / GPL-3 win-
64
r-ekmcmc 0.1.0 Functions for estimating catalytic constant and Michaelis-Menten constant for noarch
enzyme kinetics model using Metropolis-Hasting algorithm within Gibbs sam-
pler based on the Bayesian framework. Additionally, a function to create plot
to identify the goodness-of-fit is included. / GPL-3
r-el 1.0 Empirical likelihood (EL) inference for two-sample problems. The follow- linux-
ing statistics are included: the difference of two-sample means, smooth Hu- 64,
ber estimators, quantile (qdiff) and cumulative distribution functions (ddiff), osx-64
probability-probability (P-P) and quantile-quantile (Q-Q) plots as well as re-
ceiver operating characteristic (ROC) curves. / GPL-2
r-el2surv 1.1 Functions for computing critical values and implementing the one-sided/two- noarch
sided EL tests. / GPL-2
r-elasth 0.3.1 O pacote desponibiliza funções para estimar modelos de componentes não ob- noarch
servados e determinar intervenções automaticamente. Com especial atenção
para a replicação dos modelos utilizados na metodologia de calculo do resul-
tado estrutural da SPE/MF. The package provides simple ways to estimates
general unobserved components models and automatically detects intervenc-
tions. It is specially useful to replicate Brazilian Ministry of Finance method-
ology to estimate income-output gap elasticities. / GPL-3
r-elasticnet 1.1.1 Provides functions for fitting the entire solution path of the Elastic-Net and also noarch
provides functions for estimating sparse Principal Components. The Lasso
solution paths can be computed by the same function. First version: 2005-10.
/ GPL-2
r-elec 0.1.2.1This is a bizarre collection of functions written to do various sorts of statistical noarch
election audits. There are also functions to generate simulated voting data,
and simulated truth so as to do simulations to check characteristics of these
methods. / GPL-2
r-elec.strat 0.1.1 An extension of the elec package intended for use on election audits using linux-
stratified random samples. Includes functions to obtain conservative and exact 64,
p-values, and functions that give sample sizes that may make election audits osx-
more efficient. / GPL-2 64,
win-
64
r-elections 1.0 This includes a dataset on the outcomes of the USA presidential elections since noarch
1920, and various predictors, as used in <http://vanderwalresearch.com/blog/
15-elections>. / GPL-2
r-electivity 1.0.2 Provides all electivity algorithms (including Vanderploeg and Scavia electiv- noarch
ity) that were examined in Lechowicz (1982) <doi:10.1007/BF00349007>,
plus the example data that were provided for moth resource utilisation. / MIT


Name Version
r-elemstatlearn 2015.6.26.2
Useful when reading the book above mentioned, in the documentation referred noarch
to as ‘the book’. / GPL-2
r-elexr 1.0 Provides R access to election results data. Wraps elex (https://github.com/ noarch
newsdev/elex/), a Python package and command line tool for fetching and
parsing Associated Press election results. / MIT
r-elhmc 1.1.0 A tool to draw samples from a Empirical Likelihood Bayesian posterior of noarch
parameters using Hamiltonian Monte Carlo. / GPL-2
r-elitism 1.0.4 Recently many new p-value based multiple test procedures have been pro- noarch
posed, and these new methods are more powerful than the widely used
Hochberg procedure. These procedures strongly control the familywise er-
ror rate (FWER). This is a comprehensive collection of p-value based FWER-
control stepwise multiple test procedures, including six procedure families and
thirty multiple test procedures. In this collection, the conservative Hochberg
procedure, linear time Hommel procedures, asymptotic Rom procedure, Gou-
Tamhane-Xi-Rom procedures, and Quick procedures are all developed in re-
cent five years since 2014. The package name elitism is an acronym of equip-
ment for logarithmic and linear time stepwise multiple hypothesis testing. Ver-
sion 1.0.0 was released on June 26, 2019. See Gou, J., and Zhang, F. (2020).
Quick multiple test procedures and p-value adjustments. Technical report. /
GPL-3
r-elliplot 1.2.0 Correlation chart of two set (x and y) of data. Using Quantiles. Visualize the noarch
effect of factor. / MIT (FOSS)
r-ellipse 0.4.1 Contains various routines for drawing ellipses and ellipse-like confidence re- noarch
gions, implementing the plots described in Murdoch and Chow (1996), A
graphical display of large correlation matrices, The American Statistician 50,
178-180. There are also routines implementing the profile plots described in
Bates and Watts (1988), Nonlinear Regression Analysis and its Applications.
/ GPL-2
r-ellipsis 0.1.0 In S3 generics, it’s useful to take . . . so that methods can have additional linux-
argument. But this flexibility comes at a cost: misspelled arguments will be 64,
silently ignored. The ellipsis packages is an experiment that allows a generic osx-
to warn if any arguments passed in . . . are not used. / GPL-3 64,
win-
32,
win-
64
r-elliptic 1.4_0 A suite of elliptic and related functions including Weierstrass and Jacobi noarch
forms. Also includes various tools for manipulating and visualizing complex
functions. / GPL-2
r-elmr 1.0 Training and prediction functions are provided for the Extreme Learning Ma- noarch
chine algorithm (ELM). The ELM use a Single Hidden Layer Feedforward
Neural Network (SLFN) with random generated weights and no gradient-
based backpropagation. The training time is very short and the online version
allows to update the model using small chunk of the training set at each it-
eration. The only parameter to tune is the hidden layer size and the learning
function. / GPL-2 | GPL-3


Name Version
r-elmso 1.0.0 An implementation of the algorithm described in Efficient Large- Scale Inter- noarch
net Media Selection Optimization for Online Display Advertising by Paulson,
Luo, and James (Journal of Marketing Research 2018; see URL below for jour-
nal text/citation and <http://www-bcf.usc.edu/~gareth/research/ELMSO.pdf>
for a full-text version of the paper). The algorithm here is designed to allo-
cate budget across a set of online advertising opportunities using a coordinate-
descent approach, but it can be used in any resource-allocation problem with
a matrix of visitation (in the case of the paper, website pageviews) and chan-
nels (in the paper, websites). The package contains allocation functions both
in the presence of bidding, when allocation is dependent on channel-specific
cost curves, and when advertising costs are fixed at each channel. / GPL-3
r-elo 2.0.0 A flexible framework for calculating Elo ratings and resulting rankings of any linux-
two-team-per-matchup system (chess, sports leagues, ‘Go’, etc.). This imple- 64,
mentation is capable of evaluating a variety of matchups, Elo rating updates, osx-
and win probabilities, all based on the basic Elo rating system. It also includes 64,
methods to benchmark performance, including logistic regression and Markov win-
chain models. / GPL-2 64
r-elrm 1.2.4 Implements a Markov Chain Monte Carlo algorithm to approximate exact linux-
conditional inference for logistic regression models. Exact conditional in- 64,
ference is based on the distribution of the sufficient statistics for the pa- osx-
rameters of interest given the sufficient statistics for the remaining nuisance 64,
parameters. Using model formula notation, users specify a logistic model win-
and model terms of interest for exact inference. See Zamar et al. (2007) 64
<doi:10.18637/jss.v021.i03> for more details. / GPL-2
r-elyp 0.7_5 Empirical likelihood ratio tests for the Yang and Prentice (short/long term haz-
linux-
ards ratio) models. Empirical likelihood tests within a Cox model, for param- 64,
eters defined via both baseline hazard function and regression parameters. / osx-
GPL-2 64,
win-
64
r-embc 2.0.2 Unsupervised, multivariate, binary clustering for meaningful annotation of linux-
data, taking into account the uncertainty in the data. A specific constructor 64,
for trajectory analysis in movement ecology yields behavioural annotation of osx-
trajectories based on estimated local measures of velocity and turning angle, 64,
eventually with solar position covariate as a daytime indicator, (Expectation- win-
Maximization Binary Clustering for Behavioural Annotation). / GPL-3 64
r-embedsom 1.9.1 Provides a smooth mapping of multidimensional points into low-dimensional linux-
space defined by a self-organizing map. Designed to work with ‘Flow- 64,
SOM’ and flow-cytometry use-cases. See Kratochvil et al. (2019) osx-
<doi:10.1101/496869>. / GPL-3 64,
win-
64
r-emc 1.3 random walk Metropolis, Metropolis Hasting, parallel tempering, evolutionary linux-
Monte Carlo, temperature ladder construction and placement / GPL-2 64,
osx-
64,
win-
64


Name Version
r-emcdf 0.1.2 Computes and visualizes empirical joint distribution of multivariate data with linux-
optimized algorithms and multi-thread computation. There is a faster algo- 64,
rithm using dynamic programming to compute the whole empirical joint dis- osx-
tribution of a bivariate data. There are optimized algorithms for computing 64,
empirical joint CDF function values for other multivariate data. Visualization win-
is focused on bivariate data. Levelplots and wireframes are included. / GPL-3 64
r-emcluster 0.2_12EM algorithms and several efficient initialization methods for model-based linux-
clustering of finite mixture Gaussian distribution with unstructured dispersion 64,
in both of unsupervised and semi-supervised learning. / Mozilla Public Li- osx-
cense 2.0 64,
win-
64
r-emdbook 1.3.11Auxiliary functions and data sets for Ecological Models and Data, a book noarch
presenting maximum likelihood estimation and related topics for ecologists
(ISBN 978-0-691-12522-0). / GPL-3
r-emdist 0.3_1 Package providing calculation of Earth Mover’s Distance (EMD). / MIT linux-
64,
osx-
64,
win-
64
r-emg 1.0.7 Provides basic distribution functions for a mixture model of a Gaussian and noarch
exponential distribution. / GPL-2
r-emhawkes 0.9.0 Simulate and fitting exponential multivariate Hawkes model. This pack- noarch
age simulates a multivariate Hawkes model, introduced by Hawkes (1971)
<doi:10.1093/biomet/58.1.83>, with an exponential kernel and fits the param-
eters from the data. Models with the constant parameters, as well as complex
dependent structures, can also be simulated and estimated. The estimation is
based on the maximum likelihood method, introduced by introduced by Ozaki
(1979) <doi:10.1007/BF02480272>, with ‘maxLik’ package. / GPL-2
r-emistatr 1.2.2.0Provides a fast and parallelised calculator to estimate combined wastewater noarch
emissions. It supports the planning and design of urban drainage systems,
without the requirement of extensive simulation tools. The ‘EmiStatR’ pack-
age implements modular R methods. This enables to add new functionalities
through the R framework. / GPL-3
r-emme2 0.9 This package includes functions to read and write to an EMME/2 databank / noarch
GPL-3
r-emmeans 1.3.4 Obtain estimated marginal means (EMMs) for many linear, generalized linear, linux-
and mixed models. Compute contrasts or linear functions of EMMs, trends, 32,
and comparisons of slopes. Plots and compact letter displays. Least-squares linux-
means are discussed, and the term estimated marginal means is suggested, 64,
in Searle, Speed, and Milliken (1980) Population marginal means in the linearnoarch,
model: An alternative to least squares means, The American Statistician 34(4),
osx-
216-221 <doi:10.1080/00031305.1980.10483031>. / GPL-2 | GPL-3 64,
win-
32,
win-
64


Name Version
r-emmixmfa 2.0.7 We provide functions to fit finite mixtures of multivariate normal or t- linux-
distributions to data with various factor analytic structures adopted for 64,
the covariance/scale matrices. The factor analytic structures available in- osx-
clude mixtures of factor analyzers and mixtures of common factor an- 64,
alyzers. The latter approach is so termed because the matrix of fac- win-
tor loadings is common to components before the component-specific ro- 64
tation of the component factors to make them white noise. Note that
the component-factor loadings are not common after this rotation. Max-
imum likelihood estimators of model parameters are obtained via the
Expectation-Maximization algorithm. See descriptions of the algorithms used
in McLachlan GJ, Peel D (2000) <doi:10.1002/0471721182.ch8> McLach-
lan GJ, Peel D (2000) <ISBN:1-55860-707-2> McLachlan GJ, Peel D, Bean
RW (2003) <doi:10.1016/S0167-9473(02)00183-4> McLachlan GJ, Bean
RW, Ben-Tovim Jones L (2007) <doi:10.1016/j.csda.2006.09.015> Baek J,
McLachlan GJ, Flack LK (2010) <doi:10.1109/TPAMI.2009.149> Baek J,
McLachlan GJ (2011) <doi:10.1093/bioinformatics/btr112> McLachlan GJ,
Baek J, Rathnayake SI (2011) <doi:10.1002/9781119995678.ch9>. / GPL-2
r-emmixskew 1.0.3 EM algorithm for Fitting Mixture of Multivariate Skew Normal and Skew t linux-
Distributions. An implementation of the algorithm described in Wang, Ng, 64,
and McLachlan (2009) <doi:10.1109/DICTA.2009.88>. / GPL-3 osx-
64,
win-
64
r-emmli 0.0.3 Fit models of modularity to morphological landmarks. Perform model selec- noarch
tion on results. Fit models with a single within-module correlation or with
separate within-module correlations fitted to each module. / MIT
r-emmreml 3.1 The main functions are ‘emmreml’, and ‘emmremlMultiKernel’. ‘emmreml’ noarch
solves a mixed model with known covariance structure using the ‘EMMA’
algorithm. ‘emmremlMultiKernel’ is a wrapper for ‘emmreml’ to handle
multiple random components with known covariance structures. The func-
tion ‘emmremlMultivariate’ solves a multivariate gaussian mixed model with
known covariance structure using the ‘ECM’ algorithm. / GPL-2
r-emoa 0.5_0 Collection of building blocks for the design and analysis of evolutionary mul- linux-
tiobjective optimization algorithms. / GPL-2 64,
osx-
64,
win-
64
r-emon 1.3.2 Statistical tools for environmental and ecological surveys. Simulation-based noarch
power and precision analysis; detection probabilities from different survey de-
signs; visual fast count estimation. / GPL-3
r-emov 0.1.1 Fixation and saccade detection in eye movement recordings. This package im- noarch
plements a dispersion-based algorithm (I-DT) proposed by Salvucci & Gold-
berg (2000) which detects fixation duration and position. / GPL-3
r-emp 2.0.5 Functions for estimating EMP (Expected Maximum Profit Measure) noarch
in Credit Risk Scoring and Customer Churn Prediction, accord-
ing to Verbraken et al (2013, 2014) <DOI:10.1109/TKDE.2012.50>,
<DOI:10.1016/j.ejor.2014.04.001>. / GPL-3


Name Version
r-empichar 1.0.0 Evaluates the empirical characteristic function of univariate and multivariate linux-
samples. This package uses ‘RcppArmadillo’ for fast evaluation. It is also 64,
possible to export the code to be used in other packages at ‘C’ level. / MIT osx-
64,
win-
64
r-emplik 1.0_4.3
Empirical likelihood ratio tests for means/quantiles/hazards from possibly cen- linux-
sored and/or truncated data. Now does regression too. This version contains 64,
some C code. / GPL-2 osx-
64,
win-
64
r-emplik2 1.21 Calculates the p-value for a mean-type hypothesis (or multiple mean-type hy- noarch
potheses) based on two samples with censored data. / GPL-2
r-ems 1.2.7 Collection of functions for data analysis and editing of clinical and epidemio- noarch
logical data. Most of them are related to benchmark with prediction models. /
GPL-2
r-emsaov 2.3 Provides the analysis of variance table including the expected mean squares noarch
(EMS) for various types of experimental design. When some variables are
random effects or we use special experimental design such as nested design,
repeated-measures design, or split-plot design, it is not easy to find the ap-
propriate test, especially denominator for F-statistic which depends on EMS. /
GPL-2
r-emsnm 1.0 It provides a method based on EM algorithm to estimate the parameter of a noarch
mixture model, Sigmoid-Normal Model, where the samples come from sev-
eral normal distributions (also call them subgroups) whose mean is determined
by co-variable Z and coefficient alpha while the variance are homogeneous.
Meanwhile, the subgroup each item belongs to is determined by co-variables
X and coefficient eta through Sigmoid link function which is the extension of
Logistic Link function. It uses bootstrap to estimate the standard error of pa-
rameters. When sample is indeed separable, removing estimation with abnor-
mal sigma, the estimation of alpha is quite well. I used this method to explore
the subgroup structure of HIV patients and it can be used in other domains
where exists subgroup structure. / GPL-2
r-emt 1.1 The package provides functions to carry out a Goodness-of-fit test for discrete noarch
multivariate data. It is tested if a given observation is likely to have occurred
under the assumption of an ab-initio model. A p-value can be calculated using
different distance measures between observed and expected frequencies. A
Monte Carlo method is provided to make the package capable of solving high-
dimensional problems. / GPL-3


Name Version
r-emulator 1.2_20Allows one to estimate the output of a computer program, as a function of noarch
the input parameters, without actually running it. The computer program
is assumed to be a Gaussian process, whose parameters are estimated using
Bayesian techniques that give a PDF of expected program output. This PDF
is conditional on a training set of runs, each consisting of a point in parameter
space and the model output at that point. The emphasis is on complex codes
that take weeks or months to run, and that have a large number of undeter-
mined input parameters; many climate prediction models fall into this class.
The emulator essentially determines Bayesian posterior estimates of the PDF
of the output of a model, conditioned on results from previous runs and a user-
specified prior linear model. A vignette is provided and the help pages include
examples. / GPL-3
r-emvs 1.0 An efficient expectation-maximization algorithm for fitting Bayesian spike- linux-
and-slab regularization paths for linear regression. Rockova and George 64,
(2014) <doi:10.1080/01621459.2013.869223>. / GPL-3 osx-
64,
win-
64
r-enc 0.2.1 Implements an S3 class for storing ‘UTF-8’ strings, based on regular character linux-
vectors. Also contains routines to portably read and write ‘UTF-8’ encoded 64,
text files, to convert all strings in an object to ‘UTF-8’, and to create character osx-
vectors with various encodings. / GPL-3 64,
win-
64
r-encode 0.3.6 Interconverts between ordered lists and compact string notation. Useful for noarch
capturing code lists, and pair-wise codes and decodes, for text storage. Anal-
ogous to factor levels and labels. Generics encode() and decode() perform
interconversion, while codes() and decodes() extract components of an encod-
ing. The function encoded() checks whether something is interpretable as an
encoding. If a vector has an encoded ‘guide’ attribute, as_factor() uses it to
coerce to factor. / GPL-3
r-endogenous 1.0 Likelihood-based approaches to estimate linear regression parameters and noarch
treatment effects in the presence of endogeneity. Specifically, this package in-
cludes James Heckman’s classical simultaneous equation models-the sample
selection model for outcome selection bias and hybrid model with structural
shift for endogenous treatment. For more information, see the seminal paper of
Heckman (1978) <DOI:10.3386/w0177> in which the details of these models
are provided. This package accommodates repeated measures on subjects with
a working independence approach. The hybrid model further accommodates
treatment effect modification. / GPL-2
r-endogmnp 0.2_1 endogMNP is an R package that fits a Bayesian multinomial probit model with linux-
endogenous selection, which is sometimes called an endogenous switching 64,
model. This can be used to model discrete choice data when respondents select osx-
themselves into one of several groups. This package is based on the MNP 64,
package by Kosuke Imai and David A. van Dyk. This package modifies their win-
code. / GPL-2 64


Name Version
r-endorse 1.6.1 Fit the hierarchical and non-hierarchical Bayesian measurement models pro- linux-
posed by Bullock, Imai, and Shapiro (2011) <DOI:10.1093/pan/mpr031> 64,
to analyze endorsement experiments. Endorsement experiments are a sur- osx-
vey methodology for eliciting truthful responses to sensitive questions. This 64,
methodology is helpful when measuring support for socially sensitive political win-
actors such as militant groups. The model is fitted with a Markov chain Monte 64
Carlo algorithm and produces the output containing draws from the posterior
distribution. / GPL-2
r-energy 1.7_6 E-statistics (energy) tests and statistics for multivariate and univariate in- linux-
ference, including distance correlation, one-sample, two-sample, and multi- 64,
sample tests for comparing multivariate distributions, are implemented. Mea- osx-
suring and testing multivariate independence based on distance correlation, 64,
partial distance correlation, multivariate goodness-of-fit tests, k-groups and win-
hierarchical clustering based on energy distance, testing for multivariate nor- 64
mality, distance components (disco) for non-parametric analysis of structured
data, and other energy statistics/methods are implemented. / GPL-2
r- 1.0 Provides a function for distribution free control chart based on the change point noarch
energyonlinecpm model, for multivariate statistical process control. The main constituent of the
chart is the energy test that focuses on the discrepancy between empirical char-
acteristic functions of two random vectors. This new control chart highlights
in three aspects. Firstly, it is distribution free, requiring no knowledge of the
random processes. Secondly, this control chart can monitor mean and vari-
ance simultaneously. Thirdly it is devised for multivariate time series which
is more practical in real data application. Fourthly, it is designed for online
detection (Phase II), which is central for real time surveillance of stream data.
For more information please refer to O. Okhrin and Y.F. Xu (2017) <https:
//github.com/YafeiXu/working_paper/raw/master/CPM102.pdf>. / GPL-3
r-english 1.2_3 Allow numbers to be presented in an English language version, one, two, three, noarch
. . . Ordinals are also available, first, second, third, . . . / GPL-2
r-engrexpt 0.1_8 Datasets from Nelson, Coffin and Copeland Introductory Statistics for Engi- noarch
neering Experimentation (Elsevier, 2003) with sample code. / GPL-2
r-enrichr 2.1 Provides an R interface to all ‘Enrichr’ databases. ‘Enrichr’ is a web-based noarch
tool for analysing gene sets and returns any enrichment of common annotated
biological features. Quoting from their website ‘Enrichment analysis is a com-
putational method for inferring knowledge about an input gene set by compar-
ing it to annotated gene sets representing prior biological knowledge.’ See
(<http://amp.pharm.mssm.edu/Enrichr/>) for further details. / GPL-2
r-enrichvs 0.0.5 These programs are used for calculating enrichment factors, drawing enrich- noarch
ment curves to evaluate virtual screening approaches. / BSD


Name Version
r-enrichwith 0.2 Provides the enrich method to enrich list-like R objects with new, relevant noarch
components. The current version has methods for enriching objects of class
‘family’, ‘link-glm’, ‘lm’, ‘glm’ and ‘betareg’. The resulting objects preserve
their class, so all methods associated with them still apply. The package also
provides the ‘enriched_glm’ function that has the same interface as ‘glm’ but
results in objects of class ‘enriched_glm’. In addition to the usual compo-
nents in a glm object, ‘enriched_glm’ objects carry an object-specific simulate
method and functions to compute the scores, the observed and expected infor-
mation matrix, the first-order bias, as well as model densities, probabilities,
and quantiles at arbitrary parameter values. The package can also be used to
produce customizable source code templates for the structured implementation
of methods to compute new components and enrich arbitrary objects. / GPL-2
| GPL-3
r-ensemblebma 5.1.5 Bayesian Model Averaging to create probabilistic forecasts from ensemble noarch
forecasts and weather observations. / GPL-2
r-ensemblepp 1.0_0 Data sets for the chapter Ensemble Postprocessing with R of the book Stephane noarch
Vannitsem, Daniel S. Wilks, and Jakob W. Messner (2018) Statistical Post-
processing of Ensemble Forecasts, Elsevier, 362pp. These data sets contain
temperature and precipitation ensemble weather forecasts and corresponding
observations at Innsbruck/Austria. Additionally, a demo with the full code of
the book chapter is provided. / GPL-2 | GPL-3
r-ensurer 1.1 Add simple runtime contracts to R values. These ensure that values fulfil cer- noarch
tain conditions and will raise appropriate errors if they do not. / MIT
r-entropy 1.2.1 This package implements various estimators of entropy, such as the shrinkage noarch
estimator by Hausser and Strimmer, the maximum likelihood and the Millow-
Madow estimator, various Bayesian estimators, and the Chao-Shen estimator.
It also offers an R interface to the NSB estimator. Furthermore, it provides
functions for estimating Kullback-Leibler divergence, chi-squared, mutual in-
formation, and chi-squared statistic of independence. In addition there are
functions for discretizing continuous random variables. / GPL-3
r- 1.2 Contains methods for the estimation of Shannon’s entropy, variants of Renyi’s linux-
entropyestimation entropy, mutual information, Kullback-Leibler divergence, and generalized 64,
Simpson’s indices. The estimators used have a bias that decays exponentially osx-
fast. / GPL-3 64,
win-
64
r- 1.1 Rows of two matrices are compared for Shannon entropy, coefficient of varia- noarch
entropyexplorer tion, and expression. P-values can be requested for all metrics. / GPL-3
r-envcpt 1.1.1 Tools for automatic model selection and diagnostics for Climate and Environ- linux-
mental data. In particular the envcpt() function does automatic model selection 64,
between a variety of trend, changepoint and autocorrelation models. The en- osx-
vcpt() function should be your first port of call. / GPL-3 64,
win-
64
r-envdocument 2.4.1 Prints out information about the R working environment (system, R ver- noarch
sion,loaded and attached packages and versions) from a single function
env_doc(). Optionally adds information on git repository, tags, commits and
remotes (if available). / GPL (>= 3.0)


Name Version
r-envipat 2.4 Fast and very memory-efficient calculation of isotope patterns, subse- linux-
quent convolution to theoretical envelopes (profiles) plus valley detection 64,
and centroidization or intensoid calculation. Batch processing, resolution osx-
interpolation, wrapper, adduct calculations and molecular formula pars- 64,
ing. Loos, M., Gerber, C., Corona, F., Hollender, J., Singer, H. (2015) win-
<doi:10.1021/acs.analchem.5b00941>. / GPL-2 64
r-envirostat 0.4_2 Functions and datasets to support the book by Nhu D Le and James V Zidek, linux-
Springer (2006). / AGPL-3 64,
osx-
64,
win-
64
r-envnames 0.4.0 Set of functions to keep track of user-defined environment names (which can- linux-
not be retrieved with the built-in function environmentName()). The package 64,
also provides functionality to search for objects in environments, deal with osx-
function calling chains, and retrieve an object’s memory address. / GPL-3 64,
win-
64
r-epandist 1.1.1 Analyzing censored variables usually requires the use of optimization algo- noarch
rithms. This package provides an alternative algebraic approach to the task of
determining the expected value of a random censored variable with a known
censoring point. Likewise this approach allows for the determination of the
censoring point if the expected value is known. These results are derived under
the assumption that the variable follows an Epanechnikov kernel distribution
with known mean and range prior to censoring. Statistical functions related to
the uncensored Epanechnikov distribution are also provided by this package. /
LGPL-3
r-epanet2toolkit 0.3.2 Enables simulation of water piping networks using ‘EPANET’. The package linux-
provides functions from the ‘EPANET’ programmer’s toolkit as R functions so 64,
that basic or customized simulations can be carried out from R. The package osx-
uses ‘EPANET’ version 2.1 from Open Water Analytics <https://github.com/ 64,
OpenWaterAnalytics/EPANET/releases/tag/v2.1>. / MIT win-
64
r-epanetreader 0.7.3 Reads water network simulation data in ‘Epanet’ text-based ‘.inp’ and ‘.rpt’ noarch
formats into R. Also reads results from ‘Epanet-msx’. Provides basic summary
information and plots. The README file has a quick introduction. See <http:
//www2.epa.gov/water-research/epanet> for more information on the Epanet
software for modeling hydraulic and water quality behavior of water piping
systems. / MIT
r-epibasix 1.5 Contains elementary tools for analysis of common epidemiological problems, noarch
ranging from sample size estimation, through 2x2 contingency table analysis
and basic measures of agreement (kappa, sensitivity/specificity). Appropriate
print and summary statements are also written to facilitate interpretation wher-
ever possible. Source code is commented throughout to facilitate modification.
The target audience includes advanced undergraduate and graduate students in
epidemiology or biostatistics courses, and clinical researchers. / GPL-2


Name Version
r-epicontacttrace 0.12.0Routines for epidemiological contact tracing and visualisation of network of linux-
contacts. / EUPL 64,
osx-
64,
win-
64
r-epidisplay 3.5.0.1Package for data exploration and result presentation. Full ‘epicalc’ pack- noarch
age with data management functions is available at ‘<http://medipe.psu.ac.th/
epicalc>’. / GPL-2
r-epiilm 1.4.2 Provides tools for simulating from discrete-time individual level models for in- linux-
fectious disease data analysis. This epidemic model class contains spatial and 64,
contact-network based models with two disease types: Susceptible-Infectious osx-
(SI) and Susceptible-Infectious-Removed (SIR). / GPL-2 64,
win-
64
r-epiilmct 1.1.3 Provides tools for simulating from continuous-time individual level models of linux-
disease transmission, and carrying out infectious disease data analyses with 64,
the same models. The epidemic models considered are distance-based and/or osx-
contact network-based models within Susceptible-Infectious-Removed (SIR) 64,
or Susceptible-Infectious-Notified-Removed (SINR) compartmental frame- win-
works. / GPL-2 64
r-epimdr 0.6_4 Functions, data sets and shiny apps for Epidemics: Models and Data in R by noarch
Ottar N. Bjornstad (ISBN 978-3-319-97487-3) <https://www.springer.com/gp/
book/9783319974866>. The package contains functions to study the S(E)IR
model, spatial and age-structured SIR models; time-series SIR and chain-
binomial stochastic models; catalytic disease models; coupled map lattice
models of spatial transmission and network models for social spread of in-
fection. The package is also an advanced quantitative companion to the cours-
era Epidemics Massive Online Open Course <https://www.coursera.org/learn/
epidemics>. / GPL-3
r-epir 1.0_4 Tools for the analysis of epidemiological data. Contains functions for directly noarch
and indirectly adjusting measures of disease frequency, quantifying measures
of association on the basis of single or multiple strata of count data presented
in a contingency table, and computing confidence intervals around incidence
risk and incidence rate estimates. Miscellaneous functions for use in meta-
analysis, diagnostic test interpretation, and sample size calculations. / GPL-2
r-episcan 0.0.1 Searching genomic interactions with linear/logistic regression in a high- noarch
dimensional dataset is a time-consuming task. This package provides some
efficient ways to scan epistasis in genome-wide interaction studies (GWIS).
Both case-control status (binary outcome) and quantitative phenotype (con-
tinuous outcome) are supported (the main references: 1. Kam-Thong, T.,
D. Czamara, K. Tsuda, K. Borgwardt, C. M. Lewis, A. Erhardt-Lehmann,
B. Hemmer, et al. (2011). <doi:10.1038/ejhg.2010.196>. 2. Kam-Thong,
T., B. Pütz, N. Karbalai, B. Müller-Myhsok, and K. Borgwardt. (2011).
<doi:10.1093/bioinformatics/btr218>.) / GPL-2
r- 0.1.2 Constructing an epistemic model such that, for every player i and for every noarch
epistemicgametheory choice c(i) which is optimal, there is one type that expresses common belief in
rationality. / GPL-3
r-epitools 0.5_10Tools for training and practicing epidemiologists including methods for two- noarch
way and multi-way contingency tables. / GPL-2


Name Version
r-eplot 1.0 Aim: Adjust the graphical parameters to create nicer longitudinal series plots. noarch
The default set of graphical parameters is very general, and can be improved
upon when we are interested in plotting data points observed over time. Func-
tions facilitate plotting those kind of series, univariate plots, bivariate plots
(with vertical axis on both left and right hand sides), multivariate plots and
plots which allow to examine whether a new observation is ‘unusual’ via con-
struction and visualization of prediction intervals around it. / GPL-2
r-eply 0.1.2 Evaluate a function over a data frame of expressions. / GPL-3 noarch
r-epsiwal 0.1.0 Implements the conditional estimation procedure of Lee, Sun, Sun and Taylor noarch
(2016) <doi:10.1214/15-AOS1371>. This procedure allows hypothesis testing
on the mean of a normal random vector subject to linear constraints. / LGPL-3
r-epxtor 0.3_0 Import data from ‘Epidata’ XML files ‘.epx’ and convert it to R data structures. noarch
/ GPL-3
r-eq5d 0.2.0 EQ-5D is a popular health related quality of life instrument used in the noarch
clinical and economic evaluation of health care. Developed by the Eu-
roQol group <https://www.euroqol.org>, the instrument consists of two
components: health state description and evaluation. For the descrip-
tion component a subject self-rates their health in terms of five di-
mensions; mobility, self-care, usual activities, pain/discomfort, and anxi-
ety/depression using either a three-level (EQ-5D-3L, <https://www.euroqol.
org/eq-5d-instruments/eq-5d-3l-about>) or a five-level (EQ-5D-5L, <https:
//www.euroqol.org/eq-5d-instruments/eq-5d-5l-about>) scale. Frequently the
scores on these five dimensions are converted to a single utility index using
country specific value sets, which can be used in the clinical and economic
evaluation of health care as well as in population health surveys. The eq5d
package provides methods to calculate index scores from a subject’s dimension
scores. 19 TTO and 9 VAS EQ-5D-3L value sets including those for countries
in Szende et al (2007) <doi:10.1007/1-4020-5511-0> and Szende et al (2014)
<doi:10.1007/978-94-007-7596-1>, 15 EQ-5D-5L EQ-VT value sets from the
EuroQol website, and the EQ-5D-5L crosswalk value sets developed by van
Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008> are included. Addition-
ally, a shiny web tool is included to enable the calculation and visualisation of
EQ-5D index values via a web browser using EQ-5D dimension scores stored
in CSV or Excel files. / MIT
r-eqs2lavaan 3.0 Transitioning from EQS to R for structural equation modeling (SEM) is made noarch
easier with a set of functions to convert .out files into R code. The EQS output
can be converted into lavaan syntax and run in the R environment. Other func-
tions parse descriptive statistics and the covariance matrix from an EQS .out
file. A heat map plot of a covariance matrix is also included. / GPL-2
r-equalcovs 1.0 Tests the equality of two covariance matrices, used in paper Two sam- linux-
ple tests for high dimensional covariance matrices. Li and Chen (2012) 64,
<arXiv:1206.0917>. / GPL-2 osx-
64,
win-
64
r-equalden.hd 1.2 The equality of a large number k of densities is tested by measuring the L2 dis- linux-
tance between the corresponding kernel density estimators and the one based 64,
on the pooled sample. The test even works for sample sizes as small as 2. / osx-
GPL-2 64,
win-
64


Name Version
r-equaltestmi 0.1.0 Functions for examining measurement invariance via equivalence testing along noarch
with adjusted RMSEA(root mean square error of approximation; Steiger &
Lind, 1980) cutoff values. In particular, a projection-based method is im-
plemented to test the equality of latent factor means across groups without
assuming the equality of intercepts. / GPL-3
r-equate 2.0.7 Contains methods for observed-score linking and equating under the single- noarch
group, equivalent-groups, and nonequivalent-groups with anchor test(s) de-
signs. Equating types include identity, mean, linear, general linear, equiper-
centile, circle-arc, and composites of these. Equating methods include syn-
thetic, nominal weights, Tucker, Levine observed score, Levine true score,
Braun/Holland, frequency estimation, and chained equating. Plotting and sum-
mary methods, and methods for multivariate presmoothing and bootstrap error
estimation are also provided. / GPL-3
r-equivnoninf 1.0 Making available in R the complete set of programs accompanying S. Wellek’s noarch
(2010) monograph ‘’Testing Statistical Hypotheses of Equivalence and Non-
inferiority. Second Edition” (Chapman&Hall/CRC). / CC0
r-equivump 0.1.1 Implementation of uniformly most powerful invariant equivalence tests noarch
for one- and two-sample problems (paired and unpaired) as described in
Wellek (2010, ISBN:978-1-4398-0818-4). Also one-sided alternatives (non-
inferiority and non-superiority tests) are supported. Basically a variant of a
t-test with (relaxed) null and alternative hypotheses exchanged. / GPL-2
r-erboost 1.3 Expectile regression is a nice tool for estimating the conditional expectiles linux-
of a response variable given a set of covariates. This package implements a 64,
regression tree based gradient boosting estimator for nonparametric multiple osx-
expectile regression. / GPL-2 64,
win-
64
r-ercv 1.0.0 Provides a methodology simple and trustworthy for the analysis of extreme noarch
values and multiple threshold tests for a generalized Pareto distribution, to-
gether with an automatic threshold selection algorithm. See del Castillo, J,
Daoudi, J and Lockhart, R (2014) <doi:10.1111/sjos.12037>. / GPL-2
r-ergmharris 1.0 Data for use with the Sage Introduction to Exponential Random Graph Mod- noarch
eling text by Jenine K. Harris. Network data set consists of 1283 local health
departments and the communication links among them along with several at-
tributes. / GPL-3
r-erm 1.0_0 Fits Rasch models (RM), linear logistic test models (LLTM), rating scale linux-
model (RSM), linear rating scale models (LRSM), partial credit models 64,
(PCM), and linear partial credit models (LPCM). Missing values are allowed osx-
in the data matrix. Additional features are the ML estimation of the person pa- 64,
rameters, Andersen’s LR-test, item-specific Wald test, Martin-Loef-Test, non- win-
parametric Monte-Carlo Tests, itemfit and personfit statistics including infit 64
and outfit measures, ICC and other plots, automated stepwise item elimina-
tion, simulation module for various binary data matrices. / GPL-3
r-erpr 0.2.0 This package is dedicated to the analysis of event-related potentials (ERPs). noarch
Event-related potentials are the measured brain responses associated with a
specific sensory, cognitive, or motor event and are obtained from electroen-
cephalographic (EEG) signal. The erpR package contains a series of functions
for importing ERP data, computing traditional ERP measures, exploratory
ERP analyses and plotting. / GPL-3


Name Version
r-err 0.2.0 Messages should provide users with readable information about R objects noarch
without flooding their console. ‘cc()’ concatenates vector and data frame val-
ues into a grammatically correct string using commas, an ellipsis and conjunc-
tion. ‘cn()’ allows the user to define a string which varies based on a count.
‘co()’ combines the two to produce a customizable object aware string. The
package further facilitates this process by providing five ‘sprintf’-like types
such as ‘%n’ for the length of an object and ‘%o’ for its name as well as wrap-
pers for pasting objects and issuing errors, warnings and messages. / MIT
r-errorizer 0.2.1 Provides a function to convert existing R functions into errorized versions with noarch
added logging and handling functionality when encountering errors or warn-
ings. The errorize function accepts an existing R function as its first argu-
ment and returns a R function with the exact same arguments and functionality.
However, if an error or warning occurs when running that errorized R function,
it will save a .Rds file to the current working directory with the relevant objects
and information required to immediately recreate the error. / BSD_2_clause
r-errors 0.3.2 Support for measurement errors in R vectors, matrices and arrays: automatic noarch
uncertainty propagation and reporting. Documentation about ‘errors’ is pro-
vided in the paper by Ucar, Pebesma & Azcorra (2018, <doi:10.32614/RJ-
2018-075>), included in this package as a vignette; see ‘citation(errors)’ for
details. / MIT
r-es 1.0 Implementation of the Edge Selection Algorithm / GPL-2 noarch
r-es.dif 1.0.1 Computes various effect sizes of the difference, their variance, and confidence noarch
interval. This package treats Cohen’s d, Hedges’ d, biased/unbiased c (an
effect size between a mean and a constant) and e (an effect size between means
without assuming the variance equality). / MIT
r-esc 0.5.0 Implementation of the web-based ‘Practical Meta-Analysis Effect Size Calcu- noarch
lator’ from David B. Wilson (<http://www.campbellcollaboration.org/escalc/
html/EffectSizeCalculator-Home.php>) in R. Based on the input, the effect
size can be returned as standardized mean difference, Cohen’s f, Hedges’ g,
Pearson’s r or Fisher’s transformation z, odds ratio or log odds, or eta squared
effect size. / GPL-3
r-esdesign 1.0.2 Software of ‘esDesign’ is developed to implement the adaptive enrich- noarch
ment designs with sample size re-estimation. In details, three-proposed
trial designs are provided, including the AED1-SSR (or ES1-SSR), AED2-
SSR (or ES2-SSR) and AED3-SSR (or ES3-SSR). In addition, this pack-
age also contains several widely used adaptive designs, such as the
Marker Sequential Test (MaST) design proposed Freidlin et al. (2014)
<doi:10.1177/1740774513503739>, the adaptive enrichment designs without
early stopping (AED or ES), the sample size re-estimation procedure (SSR)
based on the conditional power proposed by Proschan and Hunsberger (1995),
and some useful functions. In details, we can calculate the futility and/or effi-
cacy stopping boundaries, the sample size required, calibrate the value of the
threshold of the difference between subgroup-specific test statistics, conduct
the simulation studies in AED, SSR, AED1-SSR, AED2-SSR and AED3-SSR.
/ GPL-2
r-esg 0.1 The package presents a Scenarios class containing general parameters, risk noarch
parameters and projection results. Risk parameters are gathered together into
a ParamsScenarios sub-object. The general process for using this package is to
set all needed parameters in a Scenarios object, use the customPathsGeneration
method to proceed to the projection, then use xxx_PriceDistribution() methods
to get asset prices. / GPL-2


Name Version
r-eshrink 0.1.0 Computes shrinkage estimators for regression problems. Selects penalty pa- noarch
rameter by minimizing bias and variance in the effect estimate, where bias and
variance are estimated from the posterior predictive distribution. / GPL-2
r-esmprep 0.2.0 Support in preparing a raw ESM dataset for statistical analysis. Preparation linux-
includes the handling of errors (mostly due to technological reasons) and the 64,
generating of new variables that are necessary and/or helpful in meeting the osx-64
conditions when statistically analyzing ESM data. The functions in ‘esmprep’
are meant to hierarchically lead from bottom, i.e. the raw (separated) ESM
dataset(s), to top, i.e. a single ESM dataset ready for statistical analysis. This
hierarchy evolved out of my personal experience in working with ESM data. /
GPL-2
r-esreg 0.4.0 Simultaneous modeling of the quantile and the expected shortfall of a re- linux-
sponse variable given a set of covariates, see Dimitriadis and Bayer (2017) 64,
<arXiv:1704.02213>. / GPL-3 osx-64
r-essentials 3.6.0 Some essential packages for working with R / Various linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-essentials- 3.4.3 Essential R packages including MS R Client and MS Machine Learning / Var- linux-
mrclient ious 64,
win-
64
r-esshist 1.2.2 Provide an optimal histogram, in the sense of probability density estimation linux-
and features detection, by means of multiscale variational inference. In other 64,
words, the resulting histogram servers as an optimal density estimator, and osx-
meanwhile recovers the features, such as increases or modes, with both false 64,
positive and false negative controls. Moreover, it provides a parsimonious rep- win-
resentation in terms of the number of blocks, which simplifies data interpreta- 64
tion. The only assumption for the method is that data points are independent
and identically distributed, so it applies to fairly general situations, including
continuous distributions, discrete distributions, and mixtures of both. For de-
tails see Li, Munk, Sieling and Walther (2016) <arXiv:1612.07216>. / GPL-3
r-esther 1.0 Our method is a variable selection method to select active components in linux-
sparse linear mixed models in order to estimate the heritability. The selec- 64,
tion allows us to reduce the size of the data sets which improves the accuracy osx-
of the estimations. Our package also provides a confidence interval for the 64,
estimated heritability. / GPL-2 win-
64


Name Version
r-estimability 1.3 Provides tools for determining estimability of linear functions of regression linux-
coefficients, and ‘epredict’ methods that handle non-estimable cases correctly. 32,
Estimability theory is discussed in many linear-models textbooks including linux-
Chapter 3 of Monahan, JF (2008), A Primer on Linear Models, Chapman and 64,
Hall (ISBN 978-1-4200-6201-4). / GPL (>= 3) noarch,
osx-
64,
win-
32,
win-
64
r-estimatr 0.20.0Fast procedures for small set of commonly-used, design-appropriate estima- linux-
tors with robust standard errors and confidence intervals. Includes estimators 64,
for linear regression, instrumental variables regression, difference-in-means, osx-
Horvitz-Thompson estimation, and regression improving precision of experi- 64,
mental estimates by interacting treatment with centered pre-treatment covari- win-
ates introduced by Lin (2013) <doi:10.1214/12-AOAS583>. / MIT 64
r-estout 1.2 This package is intended to speedup the process of creating model-comparing noarch
tables common in Macroeconomics. The function collection stores the esti-
mates of several models and formats it to a table of the form estimate starred
and std.err. below. The default output is LaTeX but output to CSV for later
editing in a spreadsheet tool is possible as well. It works for linear models
(lm) and panel models from the plm-package (plm). Two further implemented
functions descsto and desctab enable you to export descriptive statistics of
data-frames and single variables to LaTeX and CSV. / GPL-2
r-estsimpdmp 1.2 This package deals with the estimation of the jump rate for piecewise- noarch
deterministic Markov processes (PDMPs), from only one observation of the
process within a long time. The main functions provide an estimate of this
function. The state space may be discrete or continuous. The associated paper
has been published in Scandinavian Journal of Statistics and is given in refer-
ences. Other functions provide a method to simulate random variables from
their (conditional) hazard rate, and then to simulate PDMPs. / GPL-2


Name Version
r-estudy2 0.9.0 An implementation of a most commonly used event study methodology, linux-
including both parametric and nonparametric tests. It contains variety 64,
aspects of the rate of return estimation (the core calculation is done in osx-
C), as well as three classical for event study market models: mean ad- 64,
justed returns, market adjusted returns and single-index market models. win-
There are 6 parametric and 6 nonparametric tests provided, which examine 64
cross-sectional daily abnormal return (see the documentation of the func-
tions for more information). Parametric tests include tests proposed by
Brown and Warner (1980) <DOI:10.1016/0304-405X(80)90002-1>, Brown
and Warner (1985) <DOI:10.1016/0304-405X(85)90042-X>, Boehmer
et al. (1991) <DOI:10.1016/0304-405X(91)90032-F>, Patell (1976)
<DOI:10.2307/2490543>, and Lamb (1995) <DOI:10.2307/253695>.
Nonparametric tests covered in estudy2 are tests described in Cor-
rado and Zivney (1992) <DOI:10.2307/2331331>, McConnell and
Muscarella (1985) <DOI:10.1016/0304-405X(85)90006-6>, Boehmer
et al. (1991) <DOI:10.1016/0304-405X(91)90032-F>, Cowan (1992)
<DOI:10.1007/BF00939016>, Corrado (1989) <DOI:10.1016/0304-
405X(89)90064-0>, Campbell and Wasley (1993) <DOI:10.1016/0304-
405X(93)90025-7>, Savickas (2003) <DOI:10.1111/1475-6803.00052>,
Kolari and Pynnonen (2010) <DOI:10.1093/rfs/hhq072>. Further-
more, tests for the cumulative abnormal returns proposed by Brown and
Warner (1985) <DOI:10.1016/0304-405X(85)90042-X> and Lamb (1995)
<DOI:10.2307/253695> are included. / GPL-3
r-esvis 0.2.0 A variety of methods are provided to estimate and visualize distributional noarch
differences in terms of effect sizes. Particular emphasis is upon evaluat-
ing differences between two or more distributions across the entire scale,
rather than at a single point (e.g., differences in means). For example,
Probability-Probability (PP) plots display the difference between two or more
distributions, matched by their empirical CDFs (see Ho and Reardon, 2012;
<doi:10.3102/1076998611411918>), allowing for examinations of where on
the scale distributional differences are largest or smallest. The area under
the PP curve (AUC) is an effect-size metric, corresponding to the probabil-
ity that a randomly selected observation from the x-axis distribution will have
a higher value than a randomly selected observation from the y-axis distri-
bution. Binned effect size plots are also available, in which the distributions
are split into bins (set by the user) and separate effect sizes (Cohen’s d) are
produced for each bin - again providing a means to evaluate the consistency
(or lack thereof) of the difference between two or more distributions at dif-
ferent points on the scale. Evaluation of empirical CDFs is also provided,
with built-in arguments for providing annotations to help evaluate distribu-
tional differences at specific points (e.g., semi-transparent shading). All func-
tion take a consistent argument structure. Calculation of specific effect sizes
is also possible. The following effect sizes are estimable: (a) Cohen’s d, (b)
Hedges’ g, (c) percentage above a cut, (d) transformed (normalized) percent-
age above a cut, (e) area under the PP curve, and (f) the V statistic (see Ho,
2009; <doi:10.3102/1076998609332755>), which essentially transforms the
area under the curve to standard deviation units. By default, effect sizes are
calculated for all possible pairwise comparisons, but a reference group (distri-
bution) can be specified. / MIT


Name Version
r-etc 1.3 The package allows selecting those treatments of a one-way layout being noarch
equivalent to a control. Bonferroni adjusted two one-sided t-tests (TOST) and
related simultaneous confidence intervals are given for both differences or ra-
tios of means of normally distributed data. For the case of equal variances
and balanced sample sizes for the treatment groups, the single-step procedure
of Bofinger and Bofinger (1995) can be chosen. For non-normal data, the
Wilcoxon test is applied. / GPL-3
r-etm 1.0.5 The etm (empirical transition matrix) package permits to estimate the ma- linux-
trix of transition probabilities for any time-inhomogeneous multistate model 64,
with finite state space using the Aalen-Johansen estimator. Functions for osx-
data preparation and for displaying are also included (Allignol et al., 2011 64,
<doi:10.18637/jss.v038.i04>). Functionals of the Aalen-Johansen estimator, win-
e.g., excess length-of-stay in an intermediate state, can also be computed (Al- 64
lignol et al. 2011 <doi:10.1007/s00180-010-0200-x>). / MIT
r-etma 1.1_1 Traditional meta-regression based method has been developed for using meta- noarch
analysis data, but it faced the challenge of inconsistent estimates. This package
purpose a new statistical method to detect epistasis using incomplete informa-
tion summary, and have proven it not only successfully let consistency of evi-
dence, but also increase the power compared with traditional method (Detailed
tutorial is shown in website). / GPL-3
r-etrunct 0.1 Computes moments of univariate truncated t distribution. There is only one noarch
exported function, e_trunct(), which should be seen for details. / MIT
r-etseed 0.1.0 Client to interact with the ‘etcd’ ‘key-value’ data store <https://github.com/ noarch
coreos/etcd>. Functions included for managing directories, keys, nodes, and
getting statistics. / MIT
r-europop 0.3.1 This dataset contains population estimates of all European cities with at least noarch
10,000 inhabitants during the period 1500-1800. These data are adapted from
Jan De Vries, European Urbanization, 1500-1800 (1984). / CC0
r-eurosarcbayes 1.1 Bayesian sample size calculation software and examples for EuroSARC clin- noarch
ical trials which utilise Bayesian methodology. These trials rely on binomial
based endpoints so the majority of programs found here relate to this sort of
endpoint. Developed as part of the EuroSARC FP7 grant. / GPL-2
r-evaluate 0.13 Parsing and evaluation tools that make it easy to recreate the command line linux-
behaviour of R. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r- 1.1.0 Provides Some of the most important evaluation measures for evaluating a noarch
evaluationmeasures model. Just by giving the real and predicted class, measures such as accuracy,
sensitivity, specificity, ppv, npv, fmeasure, mcc and . . . will be returned. /
GPL-3
r- 1.14 Uses data and constants to calculate potential evapotranspiration (PET) and noarch
evapotranspiration actual evapotranspiration (AET) from 21 different formulations including Pen-
man, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations. /
GPL-2


Name Version
r-evcombr 0.1_2 Package for combining pieces of evidence / MIT noarch
r-evd 2.3_3 Extends simulation, distribution, quantile and density functions to univariate linux-
and multivariate parametric extreme value distributions, and provides fitting 64,
functions which calculate maximum likelihood estimates for univariate and osx-64
bivariate maxima models, and for univariate and bivariate threshold models. /
GPL-3
r-evdbayes 1.1_1 Provides functions for the bayesian analysis of extreme value models, using linux-
MCMC methods. / GPL-2 64,
osx-64
r-eventdatar 0.2.0 Event dataset repository including both real-life and artificial event logs. They noarch
can be used in combination with functionalities provided by the ‘bupaR’ pack-
ages ‘edeaR’, ‘processmapR’, etc. / MIT
r-eventinterval 1.3 Functions for analysis of rate changes in sequential events. / GPL-2 noarch
r-events 0.5 Stores, manipulates, aggregates and otherwise messes with event data from noarch
KEDS/TABARI or any other extraction tool with similar output / GPL-3
r-evir 1.7_4 Functions for extreme value theory, which may be divided into the following noarch
groups; exploratory data analysis, block maxima, peaks over thresholds (uni-
variate and bivariate), point processes, gev/gpd distributions. / GPL-2
r-evmix 2.12 The usual distribution functions, maximum likelihood inference and model di- noarch
agnostics for univariate stationary extreme value mixture models are provided.
Kernel density estimation including various boundary corrected kernel den-
sity estimation methods and a wide choice of kernels, with cross-validation
likelihood based bandwidth estimator. Reasonable consistency with the base
functions in the ‘evd’ package is provided, so that users can safely interchange
most code. / GPL-3
r-evolvability 1.1.0 An implementation of the evolvability parameters defined in Hansen and noarch
Houle (2008). / GPL-2
r-evorag 2.0 Uses maximum likelihood to estimate rates of trait evolution across environ- noarch
mental gradients. / GPL-2
r-ew 1.1 Edgeworth Expansion calculation. / GPL-3 noarch
r-ewgof 2.2.2 Contains a large number of the goodness-of-fit tests for the Exponential and linux-
Weibull distributions classified into families: the tests based on the empirical 64,
distribution function, the tests based on the probability plot, the tests based osx-
on the normalized spacings, the tests based on the Laplace transform and the 64,
likelihood based tests. / GPL (>= 2.0) win-
64
r-exact 1.7 Performs unconditional exact tests and power calculations for 2x2 contingency noarch
tables. Unconditional exact tests are often more powerful than conditional
exact tests and asymptotic tests. / GPL-2
r-exactcidiff 1.3 This is a package for exact Confidence Intervals for the difference between noarch
two independent or dependent proportions. / GPL-2
r-exactloglintest 1.4.2 Monte Carlo and MCMC goodness of fit tests for log-linear models / GPL-3 linux-
64,
osx-
64,
win-
64
r-exactmeta 1.0_2 Perform exact fixed effect meta analysis for rare events data without the need noarch
of artificial continuity correction. / GPL-2


Name Version
r-exactranktests 0.8_30Computes exact conditional p-values and quantiles using an implementation linux-
of the Shift-Algorithm by Streitberg & Roehmel. / GPL-2 64,
osx-
64,
win-
64
r-excel.link 0.9.8_1
Allows access to data in running instance of Microsoft Excel (e. g. ‘xl[a1] win-
= xl[b2]*3’ and so on). Graphics can be transferred with ‘xl[a1] = cur- 64
rent.graphics()’. Additionally there are function for reading/writing ‘Excel’
files - ‘xl.read.file’/’xl.save.file’. They are not fast but able to read/write
‘*.xlsb’-files and password-protected files. There is an Excel workbook with
examples of calling R from Excel in the ‘doc’ folder. It tries to keep things as
simple as possible - there are no needs in any additional installations besides
R, only ‘VBA’ code in the Excel workbook. Microsoft Excel is required for
this package. / GPL-2
r-excelr 0.3.0 An R interface to ‘jExcel’ library to create web-based interactive tables and noarch
spreadsheets compatible with ‘Excel’ or any other spreadsheet software. / MIT
r-excerptr 2.0.0 This is an R interface to the python package ‘excerpts’ (<https://pypi.python. noarch
org/pypi/excerpts>). / BSD_2_clause
r-excessmass 1.0 Implementation of a function which calculates the empirical excess mass for noarch
given eqn{lambda} and given maximal number of modes (excessm()). Of-
fering powerful plot features to visualize empirical excess mass (exmplot()).
This includes the possibility of drawing several plots (with different maximal
number of modes / cut off values) in a single graph. / LGPL-3
r-excon 0.2.5 Interactive tools to explore topographic-like data sets. Such data sets take the noarch
form of a matrix in which the rows and columns provide location/frequency
information, and the matrix elements contain altitude/response information.
Such data is found in cartography, 2D spectroscopy and chemometrics. The
functions in this package create interactive web pages showing the contoured
data, possibly with slices from the original matrix parallel to each dimension.
The interactive behavior is created using the ‘D3.js’ ‘JavaScript’ library by
Mike Bostock. / GPL-3
r-excursions 2.4.4 Functions that compute probabilistic excursion sets, contour credibility re- linux-
gions, contour avoiding regions, and simultaneous confidence bands for 64,
latent Gaussian random processes and fields. The package also con- osx-64
tains functions that calculate these quantities for models estimated with
the INLA package. The main references for excursions are Bolin and
Lindgren (2015) <doi:10.1111/rssb.12055>, Bolin and Lindgren (2017)
<doi:10.1080/10618600.2016.1228537>, and Bolin and Lindgren (2018)
<doi:10.18637/jss.v086.i05>. These can be generated by the citation function
in R. / GPL-3


Name Version
r-exdex 1.0.1 Performs frequentist inference for the extremal index of a stationary time se- linux-
ries. Two types of methodology are used. One type is based on a model that 64,
relates the distribution of block maxima to the marginal distribution of se- osx-64
ries and leads to the semiparametric maxima estimators described in Northrop
(2015) <doi:10.1007/s10687-015-0221-5> and Berghaus and Bucher (2018)
<doi:10.1214/17-AOS1621>. Sliding block maxima are used to increase pre-
cision of estimation. The other type of methodology uses a model for the
distribution of threshold inter-exceedance times (Ferro and Segers (2003)
<doi:10.1111/1467-9868.00401>). Two versions of this type of approach are
provided, following Suveges (2007) <doi:10.1007/s10687-007-0034-2> and
Suveges and Davison (2010) <doi:10.1214/09-AOAS292>. / GPL-2
r-exif 0.1.0 Extracts Exchangeable Image File Format (EXIF) metadata, such as camera linux-
make and model, ISO speed and the date-time the picture was taken on, from 64,
JPEG images. Incorporates the ‘easyexif’ (https://github.com/mayanklahiri/ osx-64
easyexif) library. / BSD_2_clause
r-exiftoolr 0.1.2 Reads, writes, and edits EXIF and other file metadata using ExifTool <http: noarch
//www.sno.phy.queensu.ca/~phil/exiftool/>, returning read results as a data
frame. ExifTool supports many different metadata formats including EXIF,
GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix,
AFCP and ID3, as well as the maker notes of many digital cameras by
Canon, Casio, DJI, FLIR, FujiFilm, GE, GoPro, HP, JVC/Victor, Kodak, Leaf,
Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson, Pana-
sonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung, Sanyo,
Sigma/Foveon and Sony. / GPL-2
r-expde 0.1.4 Modular implementation of the Differential Evolution algorithm for experi- noarch
menting with different types of operators. / GPL-2
r-experiment 1.2.0 Provides various statistical methods for designing and analyzing random- linux-
ized experiments. One functionality of the package is the implementation of 64,
randomized-block and matched-pair designs based on possibly multivariate osx-64
pre-treatment covariates. The package also provides the tools to analyze vari-
ous randomized experiments including cluster randomized experiments, two-
stage randomized experiments, randomized experiments with noncompliance,
and randomized experiments with missing data. / GPL-2
r-expert 1.0_0 Expert opinion (or judgment) is a body of techniques to estimate the distri- noarch
bution of a random variable when data is scarce or unavailable. Opinions on
the quantiles of the distribution are sought from experts in the field and aggre-
gated into a final estimate. The package supports aggregation by means of the
Cooke, Mendel-Sheridan and predefined weights models. / GPL-2
r-expint 0.1_5 The exponential integrals E_1(x), E_2(x), E_n(x) and Ei(x), and the incom- linux-
plete gamma function G(a, x) defined for negative values of its first argument. 64,
The package also gives easy access to the underlying C routines through an osx-64
API; see the package vignette for details. A test package included in sub-
directory example_API provides an implementation. C routines derived from
the GNU Scientific Library <https://www.gnu.org/software/gsl/>. / GPL-2
r-expm 0.999_4
Computation of the matrix exponential, logarithm, sqrt, and related quantities. linux-
/ GPL-2 64,
osx-64
r-exporkit 0.9.4 An R-interface to the Fortran package Expokit. / GPL-2 linux-
64,
osx-64


Name Version
r-expperm 1.6 A set of functions for computing expected permutation matrices given a matrix linux-
of likelihoods for each individual assignment. It has been written to accom- 64,
pany the forthcoming paper ‘Computing expectations and marginal likelihoods osx-
for permutations’. Publication details will be updated as soon as they are fi- 64,
nalized. / GPL-3 win-
64
r-exprep 1.0 Allows to calculate the probabilities of occurrences of an event in a great num- noarch
ber of repetitions of Bernoulli experiment, through the application of the local
and the integral theorem of De Moivre Laplace, and the theorem of Poisson.
Gives the possibility to show the results graphically and analytically, and to
compare the results obtained by the application of the above theorems with
those calculated by the direct application of the Binomial formula. Is basically
useful for educational purposes. / Unlimited
r-expss 0.9.1 Package computes and displays tables with support for ‘SPSS’-style labels, noarch
multiple and nested banners, weights, multiple-response variables and signifi-
cance testing. There are facilities for nice output of tables in ‘knitr’, ‘Shiny’,
‘*.xlsx’ files, R and ‘Jupyter’ notebooks. Methods for labelled variables add
value labels support to base R functions and to some functions from other
packages. Additionally, the package brings popular data transformation func-
tions from ‘SPSS’ Statistics and ‘Excel’: ‘RECODE’, ‘COUNT’, ‘COM-
PUTE’, ‘DO IF’, ‘COUNTIF’, ‘VLOOKUP’ and etc. These functions are very
useful for data processing in marketing research surveys. Package intended to
help people to move data processing from ‘Excel’ and ‘SPSS’ to R. / GPL-2
r-exptest 1.2 Tests for the composite hypothesis of exponentiality / GPL-3 noarch
r-exrq 1.0 Estimation for high conditional quantiles based on quantile regression. / GPL- noarch
3
r-exsic 1.1.1 The package provides tools for botanists, plant taxonomists, curators of plant noarch
genebanks and perhaps other biological collections. / MIT
r-exteriormatch 1.0.0 If one treated group is matched to one control reservoir in two different ways to noarch
produce two sets of treated-control matched pairs, then the two control groups
may be entwined, in the sense that some control individuals are in both control
groups. The exterior match is used to compare the two control groups. / GPL-2
r-extlasso 0.2 The package estimates coefficients of extended LASSO penalized linear re- noarch
gression and generalized linear models. Currently lasso and elastic net pe-
nalized linear regression and generalized linear models are considered. The
package currently utilizes an accurate approximation of L1 penalty and then
a modified Jacobi algorithm to estimate the coefficients. There is provision
for plotting of the solutions and predictions of coefficients at given values of
lambda. The package also contains functions for cross validation to select a
suitable lambda value given the data. The package also provides a function for
estimation in fused lasso penalized linear regression. / GPL-2
r-extmallows 0.1.0 For multiple full/partial ranking lists, R package ‘ExtMallows’ can (1) detect noarch
whether the input ranking lists are over-correlated, and (2) use the Mallows
model or extended Mallows model to integrate the ranking lists, and (3) use
hierarchical extended Mallows model for rank integration if there are groups
of over-correlated ranking lists. / GPL-2
r-extrabinomial 2.1 This package tests for differences in minor allele frequency between groups noarch
and is based on an extra-binomial variation model for pooled sequencing data.
/ GPL-3


Name Version
r-extradistr 1.8.11Density, distribution function, quantile function and random generation for linux-
a number of univariate and multivariate distributions. This package imple- 64,
ments the following distributions: Bernoulli, beta-binomial, beta-negative osx-
binomial, beta prime, Bhattacharjee, Birnbaum-Saunders, bivariate nor- 64,
mal, bivariate Poisson, categorical, Dirichlet, Dirichlet-multinomial, discrete win-
gamma, discrete Laplace, discrete normal, discrete uniform, discrete Weibull, 64
Frechet, gamma-Poisson, generalized extreme value, Gompertz, generalized
Pareto, Gumbel, half-Cauchy, half-normal, half-t, Huber density, inverse chi-
squared, inverse-gamma, Kumaraswamy, Laplace, location-scale t, logarith-
mic, Lomax, multivariate hypergeometric, multinomial, negative hypergeo-
metric, non-standard beta, normal mixture, Poisson mixture, Pareto, power,
reparametrized beta, Rayleigh, shifted Gompertz, Skellam, slash, triangular,
truncated binomial, truncated normal, truncated Poisson, Tukey lambda, Wald,
zero-inflated binomial, zero-inflated negative binomial, zero-inflated Poisson.
/ GPL-2
r-extrafontdb 1.0 Package for holding the database for the extrafont package / GPL-2 noarch
r-extratrees 1.0.5 Classification and regression based on an ensemble of decision trees. The noarch
package also provides extensions of ExtraTrees to multi-task learning and
quantile regression. Uses Java implementation of the method. / Apache Li-
cense 2.0
r-extremebounds 0.1.6 An implementation of Extreme Bounds Analysis (EBA), a global sensitivity noarch
analysis that examines the robustness of determinants in regression models.
The package supports both Leamer’s and Sala-i-Martin’s versions of EBA,
and allows users to customize all aspects of the analysis. / GPL-2
r-extremefit 1.0.2 Extreme value theory, nonparametric kernel estimation, tail conditional proba- noarch
bilities, extreme conditional quantile, adaptive estimation, quantile regression,
survival probabilities. / GPL-2
r-extremis 0.90 Conducts inference in statistical models for extreme values (de Car- linux-
valho et al (2012), <doi:10.1080/03610926.2012.709905>; de Carvalho and 64,
Davison (2014), <10.1080/01621459.2013.872651>; Einmahl et al (2016), osx-
<doi:10.1111/rssb.12099>). / GPL-3 64,
win-
64
r-extremogram 1.0.2 Estimation of the sample univariate, cross and return time extremograms. The noarch
package can also adds empirical confidence bands to each of the extremogram
plots via a permutation procedure under the assumption that the data are in-
dependent. Finally, the stationary bootstrap allows us to construct credible
confidence bands for the extremograms. / GPL-3
r-extweibquant 1.1 It implements the subjectively censored Weibull MLE and censored Weibull linux-
mixture methods for the lower quantile estimation. Quantile estimates from 64,
these two methods are robust to model misspecification in the lower tail. It osx-
also includes functions to evaluation the standard error of the resulting quantile
64,
estimates. Also, the methods here can be used to fit the Weibull or Weibull win-
mixture for the Type-I or Type-II right censored data. / GPL-2 64
r-eyetracking 1.1 Misc function for working with eyetracking data / GPL-3 noarch
r-ezglm 1.0 This package implements a simplified version of least squares, and logistic linux-
regression for efficiently selecting the significant non-additive interactions be-
64,
tween two variables. / GPL-2 osx-
64,
win-
64


Name Version
r-ezknitr 0.6 An extension of ‘knitr’ that adds flexibility in several ways. One common noarch
source of frustration with ‘knitr’ is that it assumes the directory where the
source file lives should be the working directory, which is often not true.
‘ezknitr’ addresses this problem by giving you complete control over where
all the inputs and outputs are, and adds several other convenient features to
make rendering markdown/HTML documents easier. / MIT
r-fabci 0.1 Frequentist assisted by Bayes (FAB) confidence interval construction. See noarch
‘Adaptive multigroup confidence intervals with constant coverage’ by Yu and
Hoff <https://arxiv.org/abs/1612.08287>. / GPL-3
r-fabricatr 0.10.0Helps you imagine your data before you collect it. Hierarchical data structures noarch
and correlated data can be easily simulated, either from random number gener-
ators or by resampling from existing data sources. This package is faster with
‘data.table’ and ‘mvnfast’ installed. / MIT
r-facebook.s4 1.1.0 Provides an interface to the Facebook API and builds collections of elements noarch
that reflects the graph architecture of Facebook. See <https://developers.
facebook.com/docs/graph-api> for more information. / MIT
r- 1.0 The package estimates Factor Mixture Analysis via the EM algorithm / GPL-2 noarch
factmixtanalysis
r-factorial2x2 0.1.0 Used for the design and analysis of a 2x2 factorial trial for a noarch
time-to-event endpoint. Performs power calculations and signifi-
cance testing. Important reference papers include Slud EV. (1994)
<https://www.ncbi.nlm.nih.gov/pubmed/8086609> Lin DY, Gong J,
Gallo P, Bunn PH, Couper D. (2016) <DOI:10.1111/biom.12507>
Leifer ES, Troendle JF, Kolecki A, Follmann DA. (2019)
<https://github.com/EricSLeifer/factorial2x2/blob/master/Leifer%20et%20al%20Factorial.pdf>.
/ GPL-2
r-factorplot 1.1_2 Methods to calculate, print, summarize and plot pairwise differences from noarch
GLMs, GLHT or Multinomial Logit models. / GPL-2
r-factorqr 0.1_4 Package to fit Bayesian quantile regression models that assume a factor struc- linux-
ture for at least part of the design matrix. / GPL-2 64,
osx-
64,
win-
64
r-factorsr 1.4 It identifies the factors significantly related to species richness, and their rela- noarch
tive contribution, using multiple regressions and support vector machine mod-
els. It uses an output file of ‘ModestR’ (<http://www.ipez.es/ModestR>) with
data of richness of the species and environmental variables in a cell size defined
by the user. The residuals of the support vector machine model are shown on a
map. Negative residuals may be potential areas with undiscovered and/or un-
registered species, or areas with decreased species richness due to the negative
effect of anthropogenic factors. / GPL-2
r-factualr 0.5 Per the Factual.com website, Factual is a platform where anyone can share and noarch
mash open, living data on any subject. The data is in the form of tables and is
accessible via REST API. The factualR package is a thin wrapper around the
Factual.com API, to make it even easier for people working with R to explore
Factual.com data sets. / Apache License 2.0
r-fadist 2.2 Probability distributions that are sometimes useful in hydrology. / GPL-2 noarch
r-fahrmeir 2016.5.31
Data and functions for the book Multivariate Statistical Modelling Based on noarch
Generalized Linear Models, first edition, by Ludwig Fahrmeir and Gerhard
Tutz. Useful when using the book. / GPL-2


Name Version
r-fail 1.3 More comfortable interface to work with R data or source files in a key-value noarch
fashion. / BSD_3_clause
r-faisalconjoint 1.15 It is used for systematic analysis of decisions based on attributes and its levels. noarch
/ GPL-3
r-falcon 0.2 This is a method for Allele-specific DNA Copy Number Profiling using Next- linux-
Generation Sequencing. Given the allele-specific coverage at the variant loci, 64,
this program segments the genome into regions of homogeneous allele-specific osx-
copy number. It requires, as input, the read counts for each variant allele in 64,
a pair of case and control samples. For detection of somatic mutations, the win-
case and control samples can be the tumor and normal sample from the same 64
individual. / GPL-2
r-falconx 0.2 This is a method for Allele-specific DNA Copy Number profiling for whole- linux-
Exome sequencing data. Given the allele-specific coverage and site biases at 64,
the variant loci, this program segments the genome into regions of homoge- osx-
neous allele-specific copy number. It requires, as input, the read counts for 64,
each variant allele in a pair of case and control samples, as well as the site win-
biases. For detection of somatic mutations, the case and control samples can 64
be the tumor and normal sample from the same individual. The implemented
method is based on the paper: Chen, H., Jiang, Y., Maxwell, K., Nathanson,
K. and Zhang, N. (under review). Allele-specific copy number estimation by
whole Exome sequencing. / GPL-2
r-fam.recrisk 0.1 Given vectors of family sizes and number of affecteds per family, calculates noarch
the risk of disease recurrence in an unaffected person, conditional on a family
having at least k affected members. Methods also model heterogeneity of dis-
ease risk across families by fitting a mixture model, allowing for high and low
risk families. / GPL-2
r-famle 1.3.5 Estimate parameters of univariate probability distributions with maximum linux-
likelihood and Bayesian methods. / GPL-2 64,
osx-
64,
win-
64
r-fanc 2.2 Computes the penalized maximum likelihood estimates of factor loadings and linux-
unique variances for various tuning parameters. The pathwise coordinate de- 64,
scent along with EM algorithm is used. This package also includes a new osx-
graphical tool which outputs path diagram, goodness-of-fit indices and model 64,
selection criteria for each regularization parameter. The user can change the win-
regularization parameter by manipulating scrollbars, which is helpful to find a 64
suitable value of regularization parameter. / GPL-2
r-fancova 0.5_1 This package contains a collection of R functions to perform nonparametric noarch
analysis of covariance for regression curves or surfaces. Testing the equality
or parallelism of nonparametric curves or surfaces is equivalent to analysis
of variance (ANOVA) or analysis of covariance (ANCOVA) for one-sample
functional data. Three different testing methods are available in the package,
including one based on L-2 distance, one based on an ANOVA statistic, and
one based on variance estimators. / GPL-3
r-fancycut 0.1.2 Provides the function fancycut() which is like cut() except you can mix left noarch
open and right open intervals with point values, intervals that are closed on
both ends and intervals that are open on both ends. / CC0


Name Version
r-fanplot 3.4.1 Visualise sequential distributions using a range of plotting styles. Sequential noarch
distribution data can be input as either simulations or values corresponding to
percentiles over time. Plots are added to existing graphic devices using the fan
function. Users can choose from four different styles, including fan chart type
plots, where a set of coloured polygon, with shadings corresponding to the
percentile values are layered to represent different uncertainty levels. / GPL-2
r-fansi 0.4.0 Counterparts to R string manipulation functions that account for the effects of linux-
ANSI text formatting control sequences. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64
r-far 0.6_5 Modelizations and previsions functions for Functional AutoRegressive pro- linux-
cesses using nonparametric methods: functional kernel, estimation of the co- 64,
variance operator in a subspace, . . . / LGPL-2.1 osx-
64,
win-
64
r-faraway 1.0.7 Books are Practical Regression and ANOVA in R on CRAN, Linear Models noarch
with R published 1st Ed. August 2004, 2nd Ed. July 2014 by CRC press,
ISBN 9781439887332, and Extending the Linear Model with R published
by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN
9781584884248. / GPL-3
r-farmtest 1.0.3 Performs robust multiple testing for means in the presence of known and un- linux-
known latent factors. It implements a robust procedure to estimate distribu- 64,
tion parameters using the Huber’s loss function and accounts for strong de- osx-
pendence among coordinates via an approximate factor model. This method 64,
is particularly suitable for high dimensional data when there are many vari- win-
ables but only a small number of observations available. Moreover, the 64
method is tailored to cases when the underlying distribution deviates from
Gaussian, which is commonly assumed in the literature. Besides the re-
sults of hypotheses testing, the estimated underlying factors and diagnostic
plots are also output. Multiple comparison correction is done after estimat-
ing the proportion of true null hypotheses using the method in Storey (2015)
<https://github.com/jdstorey/qvalue>. For detailed description of methods and
further references, see the papers on the ‘FarmTest’ method: Fan et al. (2017)
<arXiv:1711.05386> and Zhou et al. (2017) <arXiv:1711.05381>. / GPL-2
r-farver 1.1.0 The encoding of colour can be handled in many different ways, using different linux-
colour spaces. As different colour spaces have different uses, efficient conver- 64,
sion between these representations are important. The ‘farver’ package pro- osx-
vides a set of functions that gives access to very fast colour space conversion 64,
and comparisons implemented in C, and offers 100-fold speed improvements win-
over the ‘convertColor’ function in the ‘grDevices’ package. / MIT 64
r-faseg 0.1.9 It contains a function designed to the joint segmentation in the mean of sev- noarch
eral correlated series. The method is described in the paper X. Collilieux, E.
Lebarbier and S. Robin. A factor model approach for the joint segmentation
with between-series correlation (2015) <arXiv:1505.05660>. / GPL-2


Name Version
r-fasjem 1.1.2 This is an R implementation of A Fast and Scalable Joint Estimator for Learn- noarch
ing Multiple Related Sparse Gaussian Graphical Models (FASJEM). The FAS-
JEM algorithm can be used to estimate multiple related precision matrices.
For instance, it can identify context-specific gene networks from multi-context
gene expression datasets. By performing data-driven network inference from
high-dimensional and heterogonous data sets, this tool can help users effec-
tively translate aggregated data into knowledge that take the form of graphs
among entities. Please run demo(fasjem) to learn the basic functions provided
by this package. For more details, please see <http://proceedings.mlr.press/
v54/wang17e/wang17e.pdf>. / GPL-2
r-fast 0.64 The Fourier Amplitude Sensitivity Test (FAST) is a method to determine noarch
global sensitivities of a model on parameter changes with relatively few model
runs. This package implements this sensitivity analysis method. / GPL-2
r-fasta 0.1.0 A collection of acceleration schemes for proximal gradient methods for es- noarch
timating penalized regression parameters described in Goldstein, Studer, and
Baraniuk (2016) <arXiv:1411.3406>. Schemes such as Fast Iterative Shrink-
age and Thresholding Algorithm (FISTA) by Beck and Teboulle (2009)
<doi:10.1137/080716542> and the adaptive stepsize rule introduced in Wright,
Nowak, and Figueiredo (2009) <doi:10.1109/TSP.2009.2016892> are in-
cluded. You provide the objective function and proximal mappings, and it
takes care of the issues like stepsize selection, acceleration, and stopping con-
ditions for you. / MIT
r-fastadaboost 1.0.0 Implements Adaboost based on C backend code. This is blazingly fast and linux-
especially useful for large, in memory data sets. The package uses decision 64,
trees as weak classifiers. Once the classifiers have been trained, they can osx-
be used to predict new data. Currently, we support only binary classifica- 64,
tion tasks. The package implements the Adaboost.M1 algorithm and the real win-
Adaboost(SAMME.R) algorithm. / MIT 64
r-fastbandchol 0.1.1 Fast and numerically stable estimation of a covariance matrix by banding the linux-
Cholesky factor using a modified Gram-Schmidt algorithm implemented in 64,
RcppArmadilo. See <http://stat.umn.edu/~molst029> for details on the algo- osx-
rithm. / GPL-2 64,
win-
64
r-fastclime 1.4.1 Provides a method of recovering the precision matrix efficiently and solving linux-
for the dantzig selector by applying the parametric simplex method. The com- 64,
putation is based on a linear optimization solver. It also contains a generic osx-
LP solver and a parameterized LP solver using parametric simplex method. / 64,
GPL-2 win-
64
r-fastcluster 1.1.25This is a two-in-one package which provides interfaces to both R and ‘Python’. linux-
It implements fast hierarchical, agglomerative clustering routines. Part of the 64,
functionality is designed as drop-in replacement for existing routines: link- osx-
age() in the ‘SciPy’ package ‘scipy.cluster.hierarchy’, hclust() in R’s ‘stats’ 64,
package, and the ‘flashClust’ package. It provides the same functionality with win-
the benefit of a much faster implementation. Moreover, there are memory- 64
saving routines for clustering of vector data, which go beyond what the ex-
isting packages provide. For information on how to install the ‘Python’
files, see the file INSTALL in the source distribution. Based on the present
package, Christoph Dalitz also wrote a pure ‘C’ interface to ‘fastcluster’:
<http://informatik.hsnr.de/~dalitz/data/hclust>. / GPL-2


Name Version
r-fastcmh 0.2.7 A method which uses the Cochran-Mantel-Haenszel test with significant pat- linux-
tern mining to detect intervals in binary genotype data which are significantly 64,
associated with a particular phenotype, while accounting for categorical co- osx-
variates. / GPL-2 | GPL-3 64,
win-
64
r-fastcmprsk 1.1.1 In competing risks regression, the proportional subdistribution hazards (PSH) linux-
model is popular for its direct assessment of covariate effects on the cumu- 64,
lative incidence function. This package allows for both penalized and unpe- osx-
nalized PSH regression in linear time using a novel forward-backward scan. 64,
Penalties include Ridge, Lease Absolute Shrinkage and Selection Operator win-
(LASSO), Smoothly Clipped Absolute Deviation (SCAD), Minimax Concave 64
Plus (MCP), and elastic net. / GPL-3
r-fastcox 1.1.3 We implement a cocktail algorithm, a good mixture of coordinate decent, the linux-
majorization-minimization principle and the strong rule, for computing the so- 64,
lution paths of the elastic net penalized Cox’s proportional hazards model. osx-
The package is an implementation of Yang, Y. and Zou, H. (2013) DOI: 64,
<doi:10.4310/SII.2013.v6.n2.a1>. / GPL-2 win-
64
r-fastdigest 0.6_3 Provides an R interface to Bob Jenkin’s streaming, non-cryptographic linux-
‘SpookyHash’ hash algorithm for use in digest-based comparisons of R ob- 64,
jects. ‘fastdigest’ plugs directly into R’s internal serialization machinery, al- osx-
lowing digests of all R objects the serialize() function supports, including 64,
reference-style objects via custom hooks. Speed is high and scales linearly win-
by object size; memory usage is constant and negligible. / Artistic-2.0 64
r-fasteraster 1.1.1 If there is a need to recognise edges on a raster image or a bitmap or any kind linux-
of a matrix, one can find packages that does only 90 degrees vectorization. 64,
Typically the nature of artefact images is linear and can be vectorized in much osx-
more efficient way than draw a series of 90 degrees lines. The fasteraster pack- 64,
age does recognition of lines using only one pass. It also allows to calculate win-
mass and the mass centers for the recognized zones or polygons. / GPL-2 64
r-fasterelasticnet 1.1.2 Fit Elastic Net, Lasso, and Ridge regression and do cross-validation linux-
in a fast way. We build the algorithm based on Least An- 64,
gle Regression by Bradley Efron, Trevor Hastie, Iain Johnstone, etc. osx-
(2004)(<doi:10.1214/009053604000000067 >) and some algorithms like 64,
Givens rotation and Forward/Back Substitution. In this way, many matrices win-
to be computed are retained as triangular matrices which can eventually speed 64
up the computation. The fitting algorithm for Elastic Net is written in C using
Armadillo linear algebra library. / GPL-2
r-fasterize 1.0.0 Provides a drop-in replacement for rasterize() from the ‘raster’ package linux-
that takes ‘sf’-type objects, and is much faster. There is support for the 64,
main options provided by the rasterize() function, including setting the osx-
field used and background value, and options for aggregating multi-layer 64,
rasters. Uses the scan line algorithm attributed to Wylie et al. (1967) win-
<doi:10.1145/1465611.1465619>. / MIT 64
r-fastghquad 1.0 Fast, numerically-stable Gauss-Hermite quadrature rules and utility func- linux-
tions for adaptive GH quadrature. See Liu, Q. and Pierce, D. A. (1994) 64,
<doi:10.2307/2337136> for a reference on these methods. / MIT osx-
64,
win-
64


Name Version
r-fastglm 0.0.1 Fits generalized linear models efficiently using ‘RcppEigen’. The iteratively linux-
reweighted least squares implementation utilizes the step-halving approach 64,
of Marschner (2011) <doi:10.32614/RJ-2011-012> to help safeguard against osx-
convergence issues. / GPL-2 64,
win-
64
r-fastgraph 2.1 Provides functionality to produce graphs of probability density functions and noarch
cumulative distribution functions with few keystrokes, allows shading under
the curve of the probability density function to illustrate concepts such as p-
values and critical values, and fits a simple linear regression line on a scatter
plot with the equation as the main title. / GPL-3
r-fasthcs 0.0.6 The FastHCS algorithm of Schmitt and Vakili (2014) <doi:10.1007/s11222- linux-
015-9602-5> for high-dimensional, robust PCA modelling and associated out- 64,
lier detection and diagnostic tools. / GPL-2 osx-
64,
win-
64
r-fasthica 1.0.2 It implements HICA (Hierarchical Independent Component Analysis) algo- noarch
rithm. This approach, obtained through the integration between treelets
and Independent Component Analysis, is able to provide a multi-scale non-
orthogonal data-driven basis, whose elements have a phenomenological inter-
pretation according to the problem under study. / GPL-2
r-fastica 1.2_1 Implementation of FastICA algorithm to perform Independent Component linux-
Analysis (ICA) and Projection Pursuit. / GPL-2 | GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-fastimputation 2.0 TrainFastImputation() uses training data to describe a multivariate normal noarch
distribution that the data approximates or can be transformed into approx-
imating and stores this information as an object of class ‘FastImputation-
Patterns’. FastImputation() function uses this ‘FastImputationPatterns’ ob-
ject to impute (make a good guess at) missing data in a single line or a
whole data frame of data. This approximates the process used by ‘Amelia’
<http://gking.harvard.edu/amelia/> but is much faster when filling in values
for a single line of data. / GPL-2
r-fastjt 1.0.5 This ‘Rcpp’-based package implements highly efficient functions for the cal- linux-
culation of the Jonckheere-Terpstra statistic. It can be used for a variety of 64,
applications, including feature selection in machine learning problems, or to osx-
conduct genome-wide association studies (GWAS) with multiple quantitative 64,
phenotypes. The code leverages ‘OpenMP’ directives for multi-core comput- win-
ing to reduce overall processing time. / GPL-2 64


Name Version
r- 2018.12.10
Estimate spike times from calcium imaging data using an L0 penalty. / GPL-3 linux-
fastlzerospikeinference 64,
osx-
64,
win-
64
r-fastm 0.0_4 Implements the new algorithm for fast computation of M-scatter matrices linux-
using a partial Newton-Raphson procedure for several estimators. The al- 64,
gorithm is described in Duembgen, Nordhausen and Schuhmacher (2016) osx-
<doi:10.1016/j.jmva.2015.11.009>. / GPL-2 64,
win-
64
r-fastmap 1.0.0 Fast implementation of a key-value store. Environments are commonly used linux-
as key-value stores, but every time a new key is used, it is added to R’s global 64,
symbol table, causing a small amount of memory leakage. This can be prob- osx-
lematic in cases where many different keys are used. Fastmap avoids this 64,
memory leak issue by implementing the map using data structures in C. / MIT win-
64
r-fastmatch 1.1_0 Package providing a fast match() replacement for cases that require repeated linux-
look-ups. It is slightly faster that R’s built-in match() function on first match 64,
against a table, but extremely fast on any subsequent lookup as it keeps the osx-
hash table in memory. / GPL-2 64,
win-
64
r-fastnaivebayes 2.1.0 This is an extremely fast implementation of a Naive Bayes classifier. This noarch
package is currently the only package that supports a Bernoulli distribu-
tion, a Multinomial distribution, and a Gaussian distribution, making it
suitable for both binary features, frequency counts, and numerical fea-
tures. Another feature is the support of a mix of different event mod-
els. Only numerical variables are allowed, however, categorical variables
can be transformed into dummies and used with the Bernoulli distribu-
tion. The implementation is largely based on the paper A comparison of
event models for Naive Bayes anti-spam e-mail filtering written by K.M.
Schneider (2003) <doi:10.3115/1067807>. Any issues can be submitted to:
<https://github.com/mskogholt/fastNaiveBayes/issues>. / GPL-3
r-fastpcs 0.1.3 The FastPCS algorithm of Vakili and Schmitt (2014) linux-
<doi:10.1016/j.csda.2013.07.021> for robust estimation of multivariate 64,
location and scatter and multivariate outliers detection. / GPL-2 osx-
64,
win-
64
r-fastpseudo 0.1 Computes pseudo-observations for survival analysis on right-censored data noarch
based on restricted mean survival time. / GPL-2
r-fastrcs 0.0.8 The FastRCS algorithm of Vakili and Schmitt (2014) for robust fit of the mul- linux-
tivariable linear regression model and outliers detection. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-fastrweb 1.1_1.1
Infrastrcture for creating rich, dynamic web content using R scripts while linux-
maintaining very fast response time. / GPL-2 64,
osx-64
r-fastsom 1.0.0 Functions for computing spillover measures, especially spillover tables and linux-
spillover indices, as well as their average, minimal, and maximal values. / 64,
GPL-2 osx-
64,
win-
64
r-fasttextr 1.0 An interface to the ‘fastText’ library <https://github.com/facebookresearch/ linux-
fastText>. The package can be used for text classification and to learn word 64,
vectors. The install folder contains the ‘PATENTS’ file. An example how to osx-
use ‘fastTextR’ can be found in the ‘README’ file. / BSD_3_clause 64,
win-
64
r-fasttime 1.0_2 Fast functions for timestamp manipulation that avoid system calls and take linux-
shortcuts to facilitate operations on very large data. / GPL-2 64,
osx-
64,
win-
64
r-favnums 1.0.0 A dataset of favourite numbers, selected from an online poll of over 30,000 noarch
people by Alex Bellos (http://pages.bloomsbury.com/favouritenumber). / CC0
r-fbasics 3042.89
Provides a collection of functions to explore and to investigate basic prop- linux-
erties of financial returns and related quantities. The covered fields include 32,
techniques of explorative data analysis and the investigation of distributional linux-
properties, including parameter estimation and hypothesis testing. Even more 64,
there are several utility functions for data handling and management. / GPL osx-
(>= 2) 64,
win-
32,
win-
64
r-fbfsearch 1.1 We propose an objective Bayesian algorithm for searching the space of Gaus- linux-
sian directed acyclic graph (DAG) models. The algorithm proposed makes use 64,
of moment fractional Bayes factors (MFBF) and thus it is suitable for learning osx-
sparse graph. The algorithm is implemented by using Armadillo: an open- 64,
source C linear algebra library. / GPL-2 win-
64
r-fbn 1.5.1 Normalizes the data from a file containing the raw values of the SNP probes noarch
of microarrray data by using the FISH probes and their corresponding CNs. /
GPL-2
r-fbonds 3042.78
It implements the Nelson-Siegel and the Nelson-Siegel-Svensson term struc- noarch
tures. / GPL-2


Name Version
r-fbranks 2.0 This package uses time dependent Poisson regression and a record of goals noarch
scored in matches to rank teams via estimated attack and defense strengths.
The statistical model is based on Dixon and Coles (1997) Modeling Associa-
tion Football Scores and Inefficiencies in the Football Betting Market, Applied
Statistics, Volume 46, Issue 2, 265-280. The package has a some webscrapers
to assist in the development and updating of a match database. If the match
database contains unconnected clusters (i.e. sets of teams that have only played
each other and not played teams from other sets), each cluster is ranked sep-
arately relative to the median team strength in the cluster. The package con-
tains functions for predicting and simulating tournaments and leagues from
estimated models. The package allows fitting via the glm(), speedglm(), and
glmnet() functions. The latter allows fast and efficient fitting of very large
numbers of teams. The fitting algorithm will analyze the match data and de-
termine which teams form a cluster (a set of teams where there is a path of
matches connecting every team) and fit each cluster separately. / GPL-2
r-fc 0.1.0 Provides a streamlined, standard evaluation-based approach to multivariate noarch
function composition. Allows for chaining commands via a forward-pipe op-
erator, %>%. / GPL-2
r-fcd 0.1 Efficient procedures for community detection in network studies, especially noarch
for sparse networks with not very obvious community structure. The algo-
rithms impose penalties on the differences of the coordinates which represent
the community labels of the nodes. / GPL (>= 2.0)
r-fclust 2.1 Algorithms for fuzzy clustering, cluster validity indices and plots for cluster linux-
validity and visualizing fuzzy clustering results. / GPL-2 64,
osx-
64,
win-
64
r-fcmapper 1.1 Provides several functions to create and manipulate fuzzy cognitive noarch
maps. It is based on ‘FCMapper’ for Excel, distributed at <http://
www.fcmappers.net/joomla/>, developed by Michael Bachhofer and Martin
Wildenberg. Maps are inputted as adjacency matrices. Attributes of the maps
and the equilibrium values of the concepts (including with user-defined con-
strained values) can be calculated. The maps can be graphed with a function
that calls ‘igraph’. Multiple maps with shared concepts can be aggregated. /
GPL-2
r-fcros 1.6.1 A fold change rank based method is presented to search for genes with chang- linux-
ing expression and to detect recurrent chromosomal copy number aberrations. 64,
This method may be useful for high-throughput biological data (micro-array, osx-
sequencing, . . . ). Probabilities are associated with genes or probes in the data 64,
set and there is no problem of multiple tests when using this method. For win-
array-based comparative genomic hybridization data, segmentation results are 64
obtained by merging the significant probes detected. / GPL-2


Name Version
r-fda 2.4.8 These functions were developed to support functional data analysis as de- noarch
scribed in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Anal-
ysis. New York: Springer. They were ported from earlier versions in Mat-
lab and S-PLUS. An introduction appears in Ramsay, J. O., Hooker, Giles,
and Graves, Spencer (2009) Functional Data Analysis with R and Matlab
(Springer). The package includes data sets and script files working many
examples including all but one of the 76 figures in this latter book. Matlab
versions of the code and sample analyses are no longer distributed through
CRAN, as they were when the book was published. For those, ftp from
<http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/> There you find
a set of .zip files containing the functions and sample analyses, as well as two
.txt files giving instructions for installation and some additional information.
The changes from Version 2.4.1 are fixes of bugs in density.fd and removal of
functions create.polynomial.basis, polynompen, and polynomial. These were
deleted because the monomial basis does the same thing and because there
were errors in the code. / GPL-2
r-fdakma 1.2.1 It performs simultaneously clustering and alignment of a multidimensional or noarch
unidimensional functional dataset by means of k-mean alignment. / GPL-3
r-fdamixed 0.6 Likelihood based analysis of 1-dimension functional data in a mixed-effects linux-
model framework. Matrix computation are approximated by semi-explicit op- 64,
erator equivalents with linear computational complexity. Markussen (2013) osx-
<doi:10.3150/11-BEJ389>. / GPL-2 64,
win-
64
r-fdrci 2.1 FDR functions for permutation-based estimators, including pi0 as well as FDR noarch
confidence intervals. The confidence intervals account for dependencies be-
tween tests by the incorporation of an overdispersion parameter, which is esti-
mated from the permuted data. / Artistic-2.0
r-fdrsampsize 1.0 Defines a collection of functions to compute average power and sample size noarch
for studies that use the false discovery rate as the final measure of statistical
significance. / GPL-2
r-fdrtool 1.2.15Estimates both tail area-based false discovery rates (Fdr) as well as local false linux-
discovery rates (fdr) for a variety of null models (p-values, z-scores, correla- 64,
tion coefficients, t-scores). The proportion of null values and the parameters osx-
of the null distribution are adaptively estimated from the data. In addition, the 64,
package contains functions for non-parametric density estimation (Grenander win-
estimator), for monotone regression (isotonic regression and antitonic regres- 64
sion with weights), for computing the greatest convex minorant (GCM) and
the least concave majorant (LCM), for the half-normal and correlation dis-
tributions, and for computing empirical higher criticism (HC) scores and the
corresponding decision threshold. / GPL-3
r-fdth 1.2_1 Perform frequency distribution tables, associated histograms and polygons noarch
from vector, data.frame and matrix objects for numerical and categorical vari-
ables. / GPL-2


Name Version
r-feather 0.3.3 Read and write feather files, a lightweight binary columnar data store designed linux-
for maximum speed. / Apache License 2.0 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-featurehashing 0.9.1.3Feature hashing, also called as the hashing trick, is a method to transform linux-
features of a instance to a vector. Thus, it is a method to transform a real 64,
dataset to a matrix. Without looking up the indices in an associative array, osx-
it applies a hash function to the features and uses their hash values as in- 64,
dices directly. The method of feature hashing in this package was proposed win-
in Weinberger et al. (2009) <arXiv:0902.2206>. The hashing algorithm is 64
the murmurhash3 from the ‘digest’ package. Please see the README in
<https://github.com/wush978/FeatureHashing> for more information. / GPL-
3
r-featurizer 0.2 A collection of functions that would help one to build features based on exter- noarch
nal data. Very useful for Data Scientists in data to day work. Many functions
create features using parallel computation. Since the nitty gritty of parallel
computation is hidden under the hood, the user need not worry about creating
clusters and shutting them down. / GPL-2
r-fechner 1.0_3 Functions and example datasets for Fechnerian scaling of discrete object sets. linux-
User can compute Fechnerian distances among objects representing subjec- 64,
tive dissimilarities, and other related information. See package?fechner for an osx-
overview. / GPL-2 64,
win-
64
r-federalregister 0.2.0 Access data from the Federal Register API <https://www.federalregister.gov/ noarch
developers/api/v1>. / GPL-2
r-fedreporter 0.2.1 Downloads data from Federal ‘RePORTER’ <https://api.federalreporter.nih. noarch
gov/> using the Federal ‘RePORTER’ API. Allows the user to search job
projects from different government agencies. / GPL-3
r-fenmlm 2.4.2 Efficient estimation of maximum likelihood models with multiple fixed- linux-
effects. Standard-errors can easily and flexibly be clustered and estimations 64,
exported. / GPL-2 osx-
64,
win-
64
r-fermicatsr 1.4 Data from various catalogs of astrophysical gamma-ray sources detected by noarch
NASA’s Large Area Telescope (The Astrophysical Journal, 697, 1071, 2009
June 1), on board the Fermi gamma-ray satellite. More information on Fermi
and its data products is available from the Fermi Science Support Center (http:
//fermi.gsfc.nasa.gov/ssc/). / CC0
r-fextremes 3042.82
Provides functions for analysing and modelling extreme events in financial noarch
time Series. The topics include: (i) data pre-processing, (ii) explorative data
analysis, (iii) peak over threshold modelling, (iv) block maxima modelling, (v)
estimation of VaR and CVaR, and (vi) the computation of the extreme index. /
GPL-2


Name Version
r-ff 2.2_14The ff package provides data structures that are stored on disk but behave (al- linux-
most) as if they were in RAM by transparently mapping only a section (page- 64,
size) in main memory - the effective virtual memory consumption per ff object. osx-
ff supports R’s standard atomic data types ‘double’, ‘logical’, ‘raw’ and ‘inte- 64,
ger’ and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nib- win-
ble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), 64
short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float
with NAs). For example ‘quad’ allows efficient storage of genomic data as an
‘A’,’T’,’G’,’C’ factor. The unsigned types support ‘circular’ arithmetic. There
is also support for close-to-atomic types ‘factor’, ‘ordered’, ‘POSIXct’, ‘Date’
and custom close-to-atomic types. ff not only has native C-support for vec-
tors, matrices and arrays with flexible dimorder (major column-order, major
row-order and generalizations for arrays). There is also a ffdf class not un-
like data.frames and import/export filters for csv files. ff objects store raw
data in binary flat files in native encoding, and complement this with metadata
stored in R as physical and virtual attributes. ff objects have well-defined hy-
brid copying semantics, which gives rise to certain performance improvements
through virtualization. ff objects can be stored and reopened across R sessions.
ff files can be shared by multiple ff R objects (using different data en/de-coding
schemes) in the same process or from multiple R processes to exploit paral-
lelism. A wide choice of finalizer options allows to work with ‘permanent’
files as well as creating/removing ‘temporary’ ff files completely transparent
to the user. On certain OS/Filesystem combinations, creating the ff files works
without notable delay thanks to using sparse file allocation. Several access
optimization techniques such as Hybrid Index Preprocessing and Virtualiza-
tion are implemented to achieve good performance even with large datasets,
for example virtual matrix transpose without touching a single byte on disk.
Further, to reduce disk I/O, ‘logicals’ and non-standard data types get stored
native and compact on binary flat files i.e. logicals take up exactly 2 bits to
represent TRUE, FALSE and NA. Beyond basic access functions, the ff pack-
age also provides compatibility functions that facilitate writing code for ff and
ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff,
ffapply). ff interfaces closely with functionality from package ‘bit’: chun-
ked looping, fast bit operations and coercions between different objects that
can store subscript information (‘bit’, ‘bitwhich’, ff ‘boolean’, ri range index,
hi hybrid index). This allows to work interactively with selections of large
datasets and quickly modify selection criteria. Further high-performance en-
hancements can be made available upon request. / GPL-2
r-ffield 0.1.0 Force field simulation of interaction of set of points. Very useful for placing noarch
text labels on graphs, such as scatterplots. / GPL-3


Name Version
r-ffmanova 1.1.0 General linear modeling with multiple responses (MANCOVA). An over- noarch
all p-value for each model term is calculated by the 50-50 MANOVA
method by Langsrud (2002) <doi:10.1111/1467-9884.00320>, which han-
dles collinear responses. Rotation testing, described by Langsrud (2005)
<doi:10.1007/s11222-005-4789-5>, is used to compute adjusted single re-
sponse p-values according to familywise error rates and false discovery
rates (FDR). The approach to FDR is described in the appendix of Moen
et al. (2005) <doi:10.1128/AEM.71.4.2086-2094.2005>. Unbalanced de-
signs are handled by Type II sums of squares as argued in Langsrud (2003)
<doi:10.1023/A:1023260610025>. Furthermore, the Type II philosophy is ex-
tended to continuous design variables as described in Langsrud et al. (2007)
<doi:10.1080/02664760701594246>. This means that the method is invariant
to scale changes and that common pitfalls are avoided. / GPL-2
r-ffmetadata 1.0.0 A collection of functions that allows users to retrieve metadata for the Frag- noarch
ile Families challenge via a Web API (<http://api.metadata.fragilefamilies.
princeton.edu>). Users can select and search metadata for relevant variables
by filtering on different attribute names. / MIT
r-ffstream 0.1.6 An implementation of the adaptive forgetting factor scheme described in Bo- linux-
denham and Adams (2016) <doi:10.1007/s11222-016-9684-8> which adap- 64,
tively estimates the mean and variance of a stream in order to detect multiple osx-
changepoints in streaming data. The implementation is in C and uses Rcpp. 64,
Additionally, implementations of the fixed forgetting factor scheme from the win-
same paper, as well as the classic CUSUM and EWMA methods, are included. 64
/ GPL-2 | GPL-3
r-fftw 1.0_5 Provides a simple and efficient wrapper around the fastest Fourier transform linux-
in the west (FFTW) <http://www.fftw.org/> library. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-fftwtools 0.9_8 Provides a wrapper for several ‘FFTW’ functions. This package provides linux-
access to the two-dimensional ‘FFT’, the multivariate ‘FFT’, and the one- 64,
dimensional real to complex ‘FFT’ using the ‘FFTW3’ library. The package osx-
includes the functions fftw() and mvfftw() which are designed to mimic the 64,
functionality of the R functions fft() and mvfft(). The ‘FFT’ functions have win-
a parameter that allows them to not return the redundant complex conjugate 64
when the input is real data. / GPL-2
r-fgac 0.6_1 Bi-variate data fitting is done by two stochastic components: the marginal dis- noarch
tributions and the dependency structure. The dependency structure is modeled
through a copula. An algorithm was implemented considering seven fami-
lies of copulas (Generalized Archimedean Copulas), the best fitting can be
obtained looking all copula’s options (totally positive of order 2 and stochasti-
cally increasing models). / GPL-3
r-fgalgorithm 1.0 This is a package for implementation of Flury-Gautschi algorithms. / GPL-2 noarch


Name Version
r-fgarch 3042.83.1
Provides a collection of functions to analyze and model heteroskedastic be- linux-
havior in financial time series models. / GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-fgeo.x 1.1.4 Access small example datasets from Luquillo, a ForestGEO site in Puerto Rico noarch
(<https://forestgeo.si.edu/sites/north-america/luquillo>). / GPL-3
r-fgof 0.2_1 Goodness-of-fit test with multiplier or parametric bootstrap. / GPL-3 noarch
r-fgpt 2.3 A permutation technique to explore and control for spatial autocorrelation. noarch
This package contains low level functions for performing permutations and
calculating statistics as well as higher level functions. Higher level functions
are an easy to use function for performing spatially restricted permutation tests
and summarize and plot results. / GPL-3
r-fgsg 1.0.2 Implement algorithms for feature grouping and selection over an undirected linux-
graph, solves problems like graph fused lasso, graph OSCAR and so on. / 64,
GPL-2 osx-
64,
win-
64
r-fgui 1.0_8 Rapidly create a GUI interface for a function you created by automatically cre- noarch
ating widgets for arguments of the function. Automatically parses help rou-
tines for context-sensitive help to these arguments. The interface essentially
a wrapper to some Tcl/Tk routines to both simplify and facilitate GUI cre-
ation. More advanced Tcl/Tk routines/GUI objects can be incorporated into
the interface for greater customization for the more experienced. / GPL-3
r-fhdi 1.3.2 Impute general multivariate missing data with the fractional hot deck imputa- linux-
tion based on Jaekwang Kim (2011) <doi:10.1093/biomet/asq073>. / GPL-2 64,
osx-
64,
win-
64
r-fhidata 2019.8.27
Provides structural data for Norway. Datasets relating to maps, pop- noarch
ulation in municipalities, vaccination coverage for childhood vaccines,
municipality/county matching, and how different municipalities have
merged/redistricted over time from 2006 to 2019. / GPL-3
r-fi 1.0 Provide functions for forest inventory calculations. Common volumetric equa- noarch
tions (Smalian, Newton and Huber) as well stacking factor and form / GPL-3


Name Version
r-fiberld 0.1_6 Routines for estimating tree fiber (tracheid) length distributions in the stand- noarch
ing tree based on increment core samples. Two types of data can be used with
the package, increment core data measured by means of an optical fiber ana-
lyzer (OFA), e.g. such as the Kajaani Fiber Lab, or measured by microscopy.
Increment core data analyzed by OFAs consist of the cell lengths of both cut
and uncut fibres (tracheids) and fines (such as ray parenchyma cells) without
being able to identify which cells are cut or if they are fines or fibres. The
microscopy measured data consist of the observed lengths of the uncut fibres
in the increment core. A censored version of a mixture of the fine and fiber
length distributions is proposed to fit the OFA data, under distributional as-
sumptions (Svensson et al., 2006) <doi:10.1111/j.1467-9469.2006.00501.x>.
The package offers two choices for the assumptions of the underlying density
functions of the true fiber (fine) lenghts of those fibers (fines) that at least par-
tially appear in the increment core, being the generalized gamma and the log
normal densities. / GPL-2
r-filehash 2.4_2 Implements a simple key-value style database where character string keys are linux-
associated with data values that are stored on the disk. A simple interface is 64,
provided for inserting, retrieving, and deleting data from the database. Utilities osx-
are provided that allow ‘filehash’ databases to be treated much like environ- 64,
ments and lists are already used in R. These utilities are provided to encourage win-
interactive and exploratory analysis on large datasets. Three different file for- 64
mats for representing the database are currently available and new formats can
easily be incorporated by third parties for use in the ‘filehash’ framework. /
GPL-2
r-filelock 1.0.2 Place an exclusive or shared lock on a file. It uses ‘LockFile’ on Windows and linux-
‘fcntl’ locks on Unix-like systems. / MIT 64,
osx-
64,
win-
64
r-filematrix 1.3 Interface for working with large matrices stored in files, not in computer mem- noarch
ory. Supports multiple non-character data types (double, integer, logical and
raw) of various sizes (e.g. 8 and 4 byte real values). Access to parts of the
matrix is done by indexing, exactly as with usual R matrices. Supports very
large matrices. Tested on multi-terabyte matrices. Allows for more than 2^32
rows or columns. Allows for quick addition of extra columns to a filematrix.
Cross-platform as the package has R code only. / LGPL-3
r-filenamer 0.2.3 Create descriptive file names with ease. New file names are automatically (but noarch
optionally) time stamped and placed in date stamped directories. Streamline
your analysis pipeline with input and output file names that have informative
tags and proper file extensions. / GPL-3
r-files 0.0.1 Functions for printing the contents of a folder as columns in a ragged-bottom noarch
data.frame and for viewing the details (size, time created, time modified, etc.)
of a folder’s top level contents. / GPL-3
r-fillr 0.1.1 Edit vectors to fill missing values, based on the vector itself. / MIT noarch
r-fimport 3042.85
Provides a collection of utility functions to download and manage data sets noarch
from the Internet or from other sources. / GPL-2
r-finana 0.1.2 Functions for financial analysis and financial modeling, including batch graphs noarch
generation, beta calculation, descriptive statistics, annuity calculation, bond
pricing and financial data download. / GPL-2


Name Version
r- 1.3.1 Infrastructure for defining meta-data and relationships for financial instru- noarch
financialinstrument ments. / GPL-3
r-financialmath 0.1.1 Contains financial math functions and introductory derivative functions in- noarch
cluded in the Society of Actuaries and Casualty Actuarial Society ‘Financial
Mathematics’ exam, and some topics in the ‘Models for Financial Economics’
exam. / GPL-2
r-finasym 1.0 This package accomplishes two tasks: a) it classifies implicit trading activity noarch
from quotes in OTC markets using the algorithm of Lee and Ready (1991); b)
based on information for trade initiation, the package computes the probability
of informed trading of Easley and O’Hara (1987). / GPL-3
r- 1.1.0 Estimation and regularization for covariance matrix of asset returns. For co- noarch
fincovregularization variance matrix estimation, three major types of factor models are included:
macroeconomic factor model, fundamental factor model and statistical fac-
tor model. For covariance matrix regularization, four regularized estimators
are included: banding, tapering, hard-thresholding and soft- thresholding.
The tuning parameters of these regularized estimators are selected via cross-
validation. / GPL-2
r-findallroots 1.0 Find all root(s) of the equation,including complex roots;Find root(s) of the noarch
equation by dichotomy.Besides,in dichotomy, more than one interval can be
given at a time. / GPL-2
r-findpython 1.0.5 Package designed to find an acceptable python binary. / MIT file LICENSE linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-findr 0.2.1 Scans all directories and subdirectories of a path for code snippets, R scripts, noarch
R Markdown, PDF or text files containing a specific pattern. Files found can
be copied to a new folder. / GPL-3
r-finepop 1.5.1 Statistical tool set for population genetics. The package provides following noarch
functions: 1) empirical Bayes estimator of Fst and other measures of ge-
netic differentiation, 2) regression analysis of environmental effects on genetic
differentiation using bootstrap method, 3) interfaces to read and manipulate
‘GENEPOP’ format data files and allele/haplotype frequency format files. /
GPL (>= 2.0)
r-fingerprint 3.5.7 Functions to manipulate binary fingerprints of arbitrary length. A fingerprint linux-
is represented by an object of S4 class ‘fingerprint’ which is internally repre- 64,
sented a vector of integers, such that each element represents the position in osx-
the fingerprint that is set to 1. The bitwise logical functions in R are over- 64,
ridden so that they can be used directly with ‘fingerprint’ objects. A number win-
of distance metrics are also available (many contributed by Michael Fadock). 64
Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hy-
persphere) and can also be folded using OR. Arbitrary fingerprint formats can
be handled via line handlers. Currently handlers are provided for CDK, MOE
and BCI fingerprint data. / GPL-3


Name Version
r-fints 0.4_6 R companion to Tsay (2005) Analysis of Financial Time Series, second edition noarch
(Wiley). Includes data sets, functions and script files required to work some
of the examples. Version 0.3-x includes R objects for all data files used in the
text and script files to recreate most of the analyses in chapters 1-3 and 9 plus
parts of chapters 4 and 11. / GPL-2
r-fire 1.0 The algorithm assigns rareness/ outlierness score to every sample in volumi- linux-
nous datasets. The algorithm makes multiple estimations of the proximity 64,
between a pair of samples, in low-dimensional spaces. To compute proximity, osx-
FiRE uses Sketching, a variant of locality sensitive hashing. For more details: 64,
Jindal, A., Gupta, P., Jayadeva and Sengupta, D., 2018. Discovery of rare cells win-
from voluminous single cell expression data. Nature Communications, 9(1), 64
p.4719. <doi:10.1038/s41467-018-07234-6>. / GPL-3
r-fishdata 0.1.3 A collection of four datasets based around the population dynamics of mi- noarch
gratory fish. Datasets contain both basic size information on a per fish basis,
as well as otolith data that contains a per day record of fish growth history.
All data in this package was collected by the author, from 2015-2016, in the
Wellington region of New Zealand. / GPL-3
r-fisherem 1.5.1 The FisherEM algorithm, proposed by Bouveyron & Brunet (201) noarch
<doi:10.1007/s11222-011-9249-9>, is an efficient method for the clustering of
high-dimensional data. FisherEM models and clusters the data in a discrimina-
tive and low-dimensional latent subspace. It also provides a low-dimensional
representation of the clustered data. A sparse version of Fisher-EM algorithm
is also provided. / GPL-2
r-fisheyer 0.9 fisheyeR provides tools for creating Interactive Data Visualizations by imple- noarch
menting ideas from Furnas, Munzner, Costa and Venturini. / GPL-2
r-fishical 1.1 FisHiCal integrates Hi-C and FISH data, offering a modular and easy-to-use linux-
tool for chromosomal spatial analysis. / GPL-3 64,
osx-
64,
win-
64
r-fishkirkko2015 1.0.0 Dataset of 302 measurements of 11 fish species to accompany the manuscript noarch
Length-weight relationships of six freshwater fish species from lake Kirkko-
jarvi, Finland. / GPL-3
r-fishmethods 1.11_0Functions for applying a wide range of fisheries stock assessment methods. / noarch
GPL-2
r-fishmod 0.29 Fits models to catch and effort data. Single-species models are 1) delta log- linux-
normal, 2) Tweedie, or 3) Poisson-gamma (G)LMs. / GPL-3 64,
osx-
64,
win-
64
r-fishtree 0.3.1 An interface to the Fish Tree of Life API to download taxonomies, phylo- noarch
genies, fossil calibrations, and diversification rate information for ray-finned
fishes. / BSD_2_clause
r-fit.models 0.5_14The fit.models function and its associated methods (coefficients, print, sum- noarch
mary, plot, etc.) were originally provided in the robust package to compare
robustly and classically fitted model objects. The aim of the fit.models pack-
age is to separate this fitted model object comparison functionality from the
robust package and to extend it to support fitting methods (e.g., classical, ro-
bust, Bayesian, regularized, etc.) more generally. / GPL-3


Name Version
r-fitbitscraper 0.1.8 Scrapes data from Fitbit <http://www.fitbit.com>. This does not use the official noarch
API, but instead uses the API that the web dashboard uses to generate the
graphs displayed on the dashboard after login at <http://www.fitbit.com>. /
MIT
r-fitdc 0.0.1 A pure R package for decoding activity files written in the FIT (Flexible and noarch
Interoperable Data Transfer) format. A format that is fast becoming the stan-
dard for recording running and cycling data. Details of the FIT protocol can
be found at <https://www.thisisant.com/resources/fit>. / MIT
r-fitdrc 1.1.1 Fits Density Ratio Classes to elicited probability-quantile points or intervals. / noarch
GPL-2
r-fitpoly 3.0.0 Genotyping assays for bi-allelic markers (e.g. SNPs) produce signal intensities noarch
for the two alleles. ‘fitPoly’ assigns genotypes (allele dosages) to a collection
of polyploid samples based on these signal intensities. ‘fitPoly’ replaces the
older package ‘fitTetra’ that was limited (a.o.) to only tetraploid populations
whereas ‘fitPoly’ accepts any ploidy level. Reference: Voorrips RE, Gort G,
Vosman B (2011) <doi:10.1186/1471-2105-12-172>. / GPL-2
r-fitsio 2.1_0 Utilities to read and write files in the FITS (Flexible Image Transport Sys- noarch
tem) format, a standard format in astronomy (see e.g. <https://en.wikipedia.
org/wiki/FITS> for more information). Present low-level routines allow:
reading, parsing, and modifying FITS headers; reading FITS images (multi-
dimensional arrays); reading FITS binary and ASCII tables; and writing FITS
images (multi-dimensional arrays). Higher-level functions allow: reading files
composed of one or more headers and a single (perhaps multidimensional)
image or single table; reading tables into data frames; generating vectors for
image array axes; scaling and writing images as 16-bit integers. Known in-
completenesses are reading random group extensions, as well as bit, complex,
and array descriptor data types in binary tables. / GPL-2
r-fittetra 1.0 Package fitTetra contains three functions that can be used to assign genotypes noarch
to a collection of tetraploid samples based on bialleleic marker assays. Func-
tions fitTetra (to fit several models for one marker from the data and select
the best fitting) or saveMarkerModels (calls fitTetra for multiple markers and
saves the results to files) will probably be the most convenient to use. Func-
tion CodomMarker offers more control and fits one specified model for a given
marker. / GPL (>= 2.2)
r-fivethirtyeight 0.5.0 Datasets and code published by the data journalism website ‘FiveThirtyEight’ noarch
available at <https://github.com/fivethirtyeight/data>. Note that while we re-
ceived guidance from editors at ‘FiveThirtyEight’, this package is not officially
published by ‘FiveThirtyEight’. / MIT
r-fixedpoint 0.6.1 For functions that take and return vectors (or scalars), this package provides noarch
8 algorithms for finding fixed point vectors (vectors for which the inputs and
outputs to the function are the same vector). These algorithms include An-
derson (1965) acceleration <doi:10.1145/321296.321305>, epsilon extrapola-
tion methods (Wynn 1962 <doi:10.2307/2004051>) and minimal polynomial
methods (Cabay and Jackson 1976 <doi:10.1137/0713060>). / MIT
r- 1.0 Distribution functions and test for over-representation of short distances in the noarch
fixedtimeevents Liland distribution. Simulation functions are included for comparison. / GPL-
2


Name Version
r-fixest 0.1.0 Fast and user-friendly estimation of econometric models with multiple fixed- linux-
effects. Includes ordinary least squares (OLS), generalized linear models 64,
(GLM) and the negative binomial. The core of the package is based on osx-
optimized parallel C code, scaling especially well for large data sets. The 64,
method to obtain the fixed-effects coefficients is based on Berge (2018) <https: win-
//wwwen.uni.lu/content/download/110162/1299525/file/2018_13>. Further 64
provides tools to export and view the results of several estimations with in-
tuitive design to cluster the standard-errors. / GPL-3
r-fixseqmtp 0.1.2 Several generalized / directional Fixed Sequence Multiple Testing Procedures noarch
(FSMTPs) are developed for testing a sequence of pre-ordered hypotheses
while controlling the FWER, FDR and Directional Error (mdFWER). All three
FWER controlling generalized FSMTPs are designed under arbitrary depen-
dence, which allow any number of acceptances. Two FDR controlling gen-
eralized FSMTPs are respectively designed under arbitrary dependence and
independence, which allow more but a given number of acceptances. Two md-
FWER controlling directional FSMTPs are respectively designed under arbi-
trary dependence and independence, which can also make directional decisions
based on the signs of the test statistics. The main functions for each proposed
generalized / directional FSMTPs are designed to calculate adjusted p-values
and critical values, respectively. For users’ convenience, the functions also
provide the output option for printing decision rules. / GPL-2
r-fizzbuzzr 0.1.1 An implementation of the Fizz Buzz algorithm, as defined e.g. in <https: noarch
//en.wikipedia.org/wiki/Fizz_buzz>. It provides the standard algorithm with
3 replaced by Fizz and 5 replaced by Buzz, with the option of specifying start
and end numbers, step size and the numbers being replaced by fizz and buzz,
respectively. This package gives interviewers the optional answer of I use
fizzbuzzR::fizzbuzz() when interviewing rather than having to write an algo-
rithm themselves. / GPL-3
r-flagr 0.3.2 Three methods are implemented in R to facilitate the aggregations of flags noarch
in official statistics. From the underlying flags the highest in the hierar-
chy, the most frequent, or with the highest total weight is propagated to the
flag(s) for EU or other aggregates. Below there are some reference documents
for the topic: <https://sdmx.org/wp-content/uploads/CL_OBS_STATUS_v2_
1.docx>, <https://sdmx.org/wp-content/uploads/CL_CONF_STATUS_1_2_
2018.docx>, <http://ec.europa.eu/eurostat/data/database/information>, <http:
//www.oecd.org/sdd/33869551.pdf>, <https://sdmx.org/wp-content/uploads/
CL_OBS_STATUS_implementation_20-10-2014.pdf>. / EUPL-1.1
r-flam 3.2 Implements the fused lasso additive model as proposed in Petersen, A., Witten, linux-
D., and Simon, N. (2016). Fused Lasso Additive Model. Journal of Computa- 64,
tional and Graphical Statistics, 25(4): 1005-1025. / GPL-2 osx-
64,
win-
64


r-flamingos 0.1.0 Provides a variety of original and flexible user-friendly statistical la- linux-
tent variable models for the simultaneous clustering and segmentation 64,
of heterogeneous functional data (i.e time series, or more generally osx-
longitudinal data, fitted by unsupervised algorithms, including EM 64,
algorithms. Functional Latent Data Models for Clustering hetero- win-
geneous curves (‘FLaMingos’) are originally introduced and written 64
in ‘Matlab’ by Faicel Chamroukhi <https://github.com/fchamroukhi?
utf8=?&tab=repositories&q=mix&type=public&language=matlab>. The
references are mainly the following ones. Chamroukhi F. (2010)
<https://chamroukhi.com/FChamroukhi-PhD.pdf>. Chamroukhi F., Same A.,
Govaert, G. and Aknin P. (2010) <doi:10.1016/j.neucom.2009.12.023>.
Chamroukhi F., Same A., Aknin P. and Govaert G. (2011).
<doi:10.1109/IJCNN.2011.6033590>. Same A., Chamroukhi F., Gov-
aert G. and Aknin, P. (2011) <doi:10.1007/s11634-011-0096-5>. Chamroukhi
F., and Glotin H. (2012) <doi:10.1109/IJCNN.2012.6252818>. Chamroukhi
F., Glotin H. and Same A. (2013) <doi:10.1016/j.neucom.2012.10.030>.
Chamroukhi F. (2015) <https://chamroukhi.com/FChamroukhi-HDR.pdf>.
Chamroukhi F. and Nguyen H-D. (2019) <doi:10.1002/widm.1298>. / GPL-3
r-flare 1.6.0.2Provide the implementation of a family of Lasso variants including Dantzig linux-
Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional 64,
sparse linear model. We adopt the alternating direction method of multipliers osx-
and convert the original optimization problem into a sequential L1 penalized 64,
least square minimization problem, which can be efficiently solved by lin- win-
earization algorithm. A multi-stage screening approach is adopted for further 64
acceleration. Besides the sparse linear model estimation, we also provide the
extension of these Lasso variants to sparse Gaussian graphical model estima-
tion including TIGER and CLIME using either L1 or adaptive penalty. Missing
values can be tolerated for Dantzig selector and CLIME. The computation is
memory-optimized using the sparse matrix output. / GPL-2
r-flashclust 1.01_2Fast implementation of hierarchical clustering / GPL-2 linux-
64,
osx-
64,
win-
64
r-flatxml 0.0.2 On import, the XML information is converted to a dataframe that reflects noarch
the hierarchical XML structure. Intuitive functions allow to navigate within
this transparent XML data structure (without any knowledge of ‘XPath’).
‘flatXML’ also provides tools to extract data from the XML into a flat
dataframe that can be used to perform statistical operations. / GPL-3
r-flexclust 1.4_0 The main function kcca implements a general framework for k-centroids clus- linux-
ter analysis supporting arbitrary distance measures and centroid computation. 64,
Further cluster methods include hard competitive learning, neural gas, and osx-
QT clustering. There are numerous visualization methods for cluster results 64,
(neighborhood graphs, convex cluster hulls, barcharts of centroids, . . . ), and win-
bootstrap methods for the analysis of cluster stability. / GPL-2 64
r-flexdashboard 0.5.1.1Format for converting an R Markdown document to a grid oriented dashboard. noarch
The dashboard flexibly adapts the size of it’s components to the containing
web page. / MIT


r-flexdir 1.0 Provides tools to work with the Flexible Dirichlet distribution. The main fea- noarch
tures are an E-M algorithm for computing the maximum likelihood estimate of
the parameter vector and a function based on conditional bootstrap to estimate
its asymptotic variance-covariance matrix. It contains also functions to plot
graphs, to generate random observations and to handle compositional data. /
GPL-2
r-flexmet 1.0.0.0Application of the filtered monotonic polynomial (FMP) item response model noarch
to flexibly fit item response models. The package includes tools that allow the
item response model to be build on any monotonic transformation of the latent
trait metric, as described by Feuerstahler (2016) <http://hdl.handle.net/11299/
182267>. / GPL-3
r-flexmix 2.3_15A general framework for finite mixtures of regression models using the EM al- noarch
gorithm is implemented. The E-step and all data handling are provided, while
the M-step can be supplied by the user to easily define new models. Exist-
ing drivers implement mixtures of standard linear models, generalized linear
models and model-based clustering. / GPL-2
r-flexparamcurve 1.5_5 Model selection tools and ‘selfStart’ functions to fit parametric curves in ‘nls’, noarch
‘nlsList’ and ‘nlme’ frameworks. / GPL-2
r-flexpm 2.0 Estimation of flexible parametric models for survival data. / GPL-2 noarch
r-flickrapi 0.1.0.0Provides an interface to the Flickr API <https://www.flickr.com/services/api/> noarch
and allows R users to download data on Flickr. / GPL-2
r-flipscores 0.2 Provides robust tests for testing in GLMs, by sign-flipping score contributions. noarch
The tests are often robust against overdispersion, heteroscedasticity and, in
some cases, ignored nuisance variables. See Hemerik and Goeman (2017)
<doi:10.1007/s11749-017-0571-1>. / GPL-3
r-fllat 1.2_1 Fits the Fused Lasso Latent Feature model, which is used for modeling multi- linux-
sample aCGH data to identify regions of copy number variation (CNV). Pro- 64,
duces a set of features that describe the patterns of CNV and a set of weights osx-
that describe the composition of each sample. Also provides functions for 64,
choosing the optimal tuning parameters and the appropriate number of fea- win-
tures, and for estimating the false discovery rate. / GPL-2 64
r-float 0.2_3 R comes with a suite of utilities for linear algebra with numeric (double preci- linux-
sion) vectors/matrices. However, sometimes single precision (or less!) is more 64,
than enough for a particular task. This package extends R’s linear algebra fa- osx-
cilities to include 32-bit float (single precision) data. Float vectors/matrices 64,
have half the precision of their numeric-type counterparts but are generally win-
faster to numerically operate on, for a performance vs accuracy trade-off. The 64
internal representation is an S4 class, which allows us to keep the syntax iden-
tical to that of base R’s. Interaction between floats and base types for binary
operators is generally possible; in these cases, type promotion always defaults
to the higher precision. The package ships with copies of the single precision
‘BLAS’ and ‘LAPACK’, which are automatically built in the event they are
not available on the system. / BSD_2_clause
r-flock 0.7 Implements synchronization between R processes (spawned by using the par- linux-
allel package for instance) using file locks. Supports both exclusive and shared
64,
locking. / Apache License 2.0 osx-
64,
win-
64


Name Version
r-flower 1.0 Flowering is an important life history trait of flowering plants. It has been noarch
mainly analyzed with respect to flowering onset and duration of flowering.
This tools provide some functions to compute the temporal distribution of an
flowering individual related to other population members. fCV() measures the
temporal variation in flowering. RIind() measures the rank order of flowering
for individual plants within a population. SI(), SI2(), SI3(), and SI4() calculate
flowering synchrony with different methods. / GPL (>= 1.0)
r-flowfield 1.0 Flow field forecasting draws information from an interpolated flow field of the noarch
observed time series to incrementally build a forecast. / GPL-3
r-flowregenvcost 0.1.1 An application to calculate the daily environmental costs of river flow regula- noarch
tion by dams based on GarcÃa de Jalon et al. 2017 <doi:10.1007/s11269-017-
1663-0>. / MIT
r-flows 1.1.1 Selections on flow matrices, statistics on selected flows, map and graph visu- noarch
alisations. / GPL-3
r-flr 1.0 FLR algorithm for classification / GPL-2 noarch
r-flsa 1.5.1 Implements a path algorithm for the Fused Lasso Signal Approximator. linux-
For more details see the help files or the article by Hoefling (2009) 64,
<arXiv:0910.0526>. / GPL-2 osx-
64,
win-
64
r-fluosurv 1.0.0 Use spectrophotometry measurements performed on insects as a way to in- noarch
fer pathogens virulence. Insect movements cause fluctuations in fluorescence
signal, and functions are provided to estimate when the insect has died as the
moment when variance in autofluorescence signal drops to zero. The pack-
age provides functions to obtain this estimate together with functions to im-
port spectrophotometry data from a Biotek microplate reader. Details of the
method are given in Parthuisot et al. (2018) <doi:10.1101/297929>. / GPL-3
r-flury 0.1_3 Contains data sets from Bernard Flury (1997) A First Course in Multivariate noarch
Statistics, Springer NY / GPL-2
r-flux 0.3_0 Functions for the calculation of greenhouse gas flux rates from closed chamber noarch
concentration measurements. The package follows a modular concept: Fluxes
can be calculated in just two simple steps or in several steps if more control
in details is wanted. Additionally plot and preparation functions as well as
functions for modelling gpp and reco are provided. / GPL-2
r-fluxweb 0.2.0 Compute energy fluxes in trophic networks, from resources to their consumers, noarch
and can be applied to systems ranging from simple two-species interactions to
highly complex food webs. It implements the approach described in Gauzens
et al. (2017) <doi:10.1101/229450> to calculate energy fluxes, which are also
used to calculate equilibrium stability. / GPL (>= 2.0)
r-fmcmc 0.2_0 Provides a friendly (flexible) Markov Chain Monte Carlo (MCMC) framework noarch
for implementing Metropolis-Hastings algorithm in a modular way allowing
users to specify automatic convergence checker, personalized transition ker-
nels, and out-of-the-box multiple MCMC chains using parallel computing.
Most of the methods implemented in this package can be found in Brooks
et al. (2011, ISBN 9781420079425). / MIT


Name Version
r-fmdates 0.1.4 Implements common date calculations relevant for specifying the economic noarch
nature of financial market contracts that are typically defined by International
Swap Dealer Association (ISDA, <http://www2.isda.org>) legal documenta-
tion. This includes methods to check whether dates are business days in cer-
tain locales, functions to adjust and shift dates and time length (or day counter)
calculations. / GPL-2
r-fmp 1.4 Estimates Filtered Monotonic Polynomial IRT Models as described by Liang noarch
and Browne (2015) <DOI:10.3102/1076998614556816>. / GPL-2
r-fmrs 1.0_9 Provides parameter estimation as well as variable selection in Finite Mixture of linux-
Accelerated Failure Time Regression and Finite Mixture of Regression Mod- 64,
els. Furthermore, this package provides Ridge Regression and Elastic Net. / osx-
GPL-3 64,
win-
64
r-fmsb 0.6.3 Several utility functions for the book entitled Practices of Medical and Health noarch
Data Analysis using R (Pearson Education Japan, 2007) with Japanese demo-
graphic data and some demographic analysis related functions. / GPL-2
r-fmsmsnreg 1.0 Fit linear regression models where the random errors follow a finite mixture of noarch
of Skew Heavy-Tailed Errors. / GPL-2
r-fmstable 0.1_2 This package implements some basic procedures for dealing with log maxi- linux-
mally skew stable distributions, which are also called finite moment log stable 64,
distributions. / GPL-3 osx-
64,
win-
64
r-fnn 1.1.3 Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related linux-
applications including KNN classification, regression and information mea- 64,
sures are implemented. / GPL-2 osx-
64,
win-
64
r-fnonlinear 3042.79
Provides a collection of functions for testing various aspects of univariate time linux-
series including independence and neglected nonlinearities. Further provides 64,
functions to investigate the chaotic behavior of time series processes and to osx-
simulate different types of chaotic time series maps. / GPL-2 64,
win-
64
r-foba 0.1 foba is a package that implements forward, backward, and foba sparse learn- noarch
ing algorithms for ridge regression, described in the paper Adaptive Forward-
Backward Greedy Algorithm for Learning Sparse Representations. / GPL-2
r-focusedmds 1.3.3 Takes a distance matrix and plots it as an interactive graph. One point is fo- noarch
cused at the center of the graph, around which all other points are plotted in
their exact distances as given in the distance matrix. All other non-focus points
are plotted as best as possible in relation to one another. Double click on any
point to choose a new focus point, and hover over points to see their ID labels.
If color label categories are given, hover over colors in the legend to high-
light only those points and click on colors to highlight multiple groups. For
more information on the rationale and mathematical background, as well as an
interactive introduction, see <https://lea-urpa.github.io/focusedMDS.html>. /
GPL-3


Name Version
r-folderfun 0.1.2 If you find yourself working on multiple different projects in R, you’ll want a noarch
series of folders pointing to raw data, processed data, plot results, intermediate
table outputs, etc. This package makes it easier to do that by providing a
quick and easy way to create and use functions for project-level directories. /
BSD_2_clause
r- 0.1.1 Provides fonts licensed under the ‘Bitstream Vera Fonts’ license for the noarch
fontbitstreamvera ‘fontquiver’ package. / file LICENCE (FOSS)
r-fontcm 1.1 Computer Modern font for use with extrafont package / GPL-2 noarch
r-fontliberation 0.1.0 A placeholder for the Liberation fontset intended for the fontquiver package. noarch
This fontset covers the 12 combinations of families (sans, serif, mono) and
faces (plain, bold, italic, bold italic) supported in R graphics devices. / file
LICENSE (FOSS)
r-foolbox 0.1.1 Provides functionality for manipulating functions and translating them in noarch
metaprogramming. / GPL-3
r-foptions 3042.86
Provides a collection of functions to valuate basic options. This includes the linux-
generalized Black-Scholes option, options on futures and options on commod- 64,
ity futures. / GPL-2 osx-
64,
win-
64
r-forcats 0.4.0 Helpers for reordering factor levels (including moving specified levels to front, linux-
ordering by first appearance, reversing, and randomly shuffling), and tools for 32,
modifying factor levels (including collapsing rare levels into other, ‘anonymis- linux-
ing’, and manually ‘recoding’). / GPL-3 64,
noarch,
osx-
64,
win-
32,
win-
64
r-foreach 1.4.4 Support for the foreach looping construct. Foreach is an idiom that allows linux-
for iterating over elements in a collection, without the use of an explicit loop 32,
counter. This package in particular is intended to be used for its return value, linux-
rather than for its side effects. In that sense, it is similar to the standard lapply 64,
function, but doesn’t require the evaluation of a function. Using foreach with- noarch,
out side effects also facilitates executing the loop in parallel. / Apache License osx-
(== 2.0) 64,
win-
32,
win-
64


Name Version
r-forecast 8.6 Methods and tools for displaying and analysing univariate time series fore- linux-
casts including exponential smoothing via state space models and automatic 32,
ARIMA modelling. / GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64
r- 1.1 Aim: Supports the most frequently used methods to combine forecasts. noarch
forecastcombinations Among others: Simple average, Ordinary Least Squares, Least Absolute De-
viation, Constrained Least Squares, Variance-based, Best Individual model,
Complete subset regressions and Information-theoretic (information criteria
based). / GPL-2
r-forecastsnsts 1.3_0 Methods to compute linear h-step ahead prediction coefficients based on lo- linux-
calised and iterated Yule-Walker estimates and empirical mean squared and 64,
absolute prediction errors for the resulting predictors. Also, functions to com-
osx-
pute autocovariances for AR(p) processes, to simulate tvARMA(p,q) time se- 64,
ries, and to verify an assumption from Kley et al. (2019), Electronic of Statis-
win-
tics, forthcoming. Preprint <arXiv:1611.04460>. / GPL-2 64
r-foreign 0.8_71Reading and writing data stored by some versions of ‘Epi Info’, ‘Minitab’, ‘S’,linux-
‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, and for reading and writing some 32,
‘dBase’ files. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
r-forestfit 0.4 Developed for the following tasks. I) Computing the probability density func- noarch
tion, cumulative distribution function, random generation, and estimating the
parameters of the eleven mixture models including mixture of Birnbaum-
Saunders, BurrXII, Chen, F, Frechet, gamma, Gompertz, log-logistic, log-
normal, Lomax, and Weibull. II) Point estimation of the parameters of two-
and three-parameter Weibull distributions. In the case of two-parameter,
twelve methods consist of generalized least square type 1, generalized least
square type 2, L-moment, maximum likelihood, logarithmic moment, mo-
ment, percentile, rank correlation, least square, weighted maximum likeli-
hood, U-statistic, weighted least square are used and investigated methods for
the three-parameter case are: maximum likelihood, modified moment type
1, modified moment type 2, modified moment type 3, modified maximum
likelihood type 1, modified maximum likelihood type 2, modified maximum
likelihood type 3, modified maximum likelihood type 4, moment, maximum
product spacing, T-L moment, and weighted maximum likelihood. III) The
Bayesian estimators of the three-parameter Weibull distribution. IV) Estimat-
ing parameters of the three-parameter Weibull distribution fitted to grouped
data using three methods including approximated maximum likelihood, expec-
tation maximization, and maximum likelihood. V) Estimating the parameters
of the gamma, log-normal, and Weibull mixture models fitted to the grouped
data through the EM algorithm. VI) Estimating parameters of the non-linear
growth curve fitted to the height-diameter observations. / GPL-2
r-foresthes 1.0_1 Assessing forest ecosystem health is an effective way for forest resource man- noarch
agement.The national forest health evaluation system at the forest stand level
using analytic hierarchy process, has a high application value and practical sig-
nificance. The package can effectively and easily realize the total assessment
process, and help foresters to further assess and management forest resources.
/ GPL-2
r-forestplot 1.9 A forest plot that allows for multiple confidence intervals per row, custom noarch
fonts for each text element, custom confidence intervals, text mixed with ex-
pressions, and more. The aim is to extend the use of forest plots beyond meta-
analyses. This is a more general version of the original ‘rmeta’ package’s
forestplot() function and relies heavily on the ‘grid’ package. / GPL-2
r-foretell 0.2.0 Project Customer Retention based on Beta Geometric, Beta Discrete Weibull noarch
and Latent Class Discrete Weibull Models.This package is based on Fader and
Hardie (2007) <doi:10.1002/dir.20074> and Fader and Hardie et al. (2018)
<doi:10.1016/j.intmar.2018.01.002>. / GPL-3
r-forge 0.2.0 Helper functions with a consistent interface to coerce and verify the types and noarch
shapes of values for input checking. / Apache License (>= 2.0)
r-forit 1.0 This package provides estimates of tree volume and biomass from Italian NFI noarch
models / GPL-3
r-formalseries 1.0 Implemented, addition, subtracking, multiplication, division in formal series noarch
rings of any number of variables (except division is only to 3 variables). Also
are available [ [<- operators. / GPL-2


Name Version
r-formatr 1.6 Provides a function tidy_source() to format R source code. Spaces and indent linux-
will be added to the code automatically, and comments will be preserved under 32,
certain conditions, so that R code will be more human-readable and tidy. There linux-
is also a Shiny app as a user interface in this package (see tidy_app()). / GPL 64,
noarch,
osx-
64,
win-
32,
win-
64
r-formattable 0.2.0.1Provides functions to create formattable vectors and data frames. ‘Format- linux-
table’ vectors are printed with text formatting, and formattable data frames are 32,
printed with multiple types of formatting in HTML to improve the readability linux-
of data presented in tabular form rendered in web pages. / MIT file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-formula 1.2_3 Infrastructure for extended formulas with multiple parts on the linux-
right-hand side and/or multiple responses on the left-hand side (see 32,
<DOI:10.18637/jss.v034.i01>). / GPL-2 | GPL-3 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-fortunes 1.5_4 A collection of fortunes from the R community. / GPL-2 | GPL-3 noarch
r-forward 1.0.4 Robust analysis using forward search in linear and generalized linear regres- noarch
sion models, as described in Atkinson, A.C. and Riani, M. (2000), Robust
Diagnostic Regression Analysis, First Edition. New York: Springer. / GPL-2
r-forwards 0.1.3 Anonymized data from surveys conducted by Forwards <https://forwards. noarch
github.io/>, the R Foundation task force on women and other under-
represented groups. Currently, a single data set of responses to a survey of
attendees at useR! 2016 <https://www.r-project.org/useR-2016/>, the R user
conference held at Stanford University, Stanford, California, USA, June 27 -
June 30 2016. / CC0
r-forwardsearch 1.0 Forward Search analysis of time series regressions. Implements the asymptotic noarch
theory developed in Johansen and Nielsen (2013, 2014). / GPL-3
r-foto 1.0.0 The Fourier Transform Textural Ordination method uses a principal compo- noarch
nent analysis on radially averaged two dimensional Fourier spectra to charac-
terize image texture. / AGPL-3


Name Version
r-fourgametep 0.1.0 The four-gamete test is based on the infinite-sites model which assumes that noarch
the probability of the same mutation occurring twice (recurrent or parallel mu-
tations) and the probability of a mutation back to the original state (reverse
mutations) are close to zero. Without these types of mutations, the only expla-
nation for observing the four dilocus genotypes (example below) is recombi-
nation (Hudson and Kaplan 1985, Genetics 111:147-164). Thus, the presence
of all four gametes is also called phylogenetic incompatibility. / GPL-2
r-fourierin 0.2.4 Computes Fourier integrals of functions of one and two variables using the linux-
Fast Fourier transform. The Fourier transforms must be evaluated on a regular 64,
grid for fast evaluation. / MIT osx-
64,
win-
64
r-fourpno 1.0.5 Estimate Barton & Lord’s (1981) <doi:10.1002/j.2333-8504.1981.tb01255.x> linux-
four parameter IRT model with lower and upper asymptotes using Bayesian 64,
formulation described by Culpepper (2016) <doi:10.1007/s11336-015-9477- osx-
6>. / GPL-2 64,
win-
64
r-fourscores 1.5.1 A game for two players: Who gets first four in a row (horizontal, vertical or noarch
diagonal) wins. As board game published by Milton Bradley, designed by
Howard Wexler and Ned Strongin. / GPL-3
r-fpca2d 1.0 Compute the two dimension functional principal component scores for a series noarch
of two dimension images. / GPL-3
r-fpca3d 1.0 Run three dimensional functional principal component analysis noarch
and return the three dimensional functional principal component
scores. The details of the method are explained in Lin et al.(2015)
<doi:10.1371/journal.pone.0132945>. / GPL-2 | GPL-3
r-fpcompare 0.2.3 Comparisons of floating point numbers are problematic due to errors associ- noarch
ated with the binary representation of decimal numbers. Despite being aware
of these problems, people still use numerical methods that fail to account for
these and other rounding errors (this pitfall is the first to be highlighted in
Circle 1 of Burns (2012) ‘The R Inferno’ <http://www.burns-stat.com/pages/
Tutor/R_inferno.pdf>). This package provides new relational operators use-
ful for performing floating point number comparisons with a set tolerance. /
GPL-3
r-fpeek 0.1.1 Tools to help text files importation. It can return the number of lines; print the linux-
first and last lines; convert encoding. Operations are made without reading the 64,
entire file before starting, resulting in good performances with large files. This osx-
package provides an alternative to a simple use of the ‘head’, ‘tail’, ‘wc’ and 64,
‘iconv’ programs that are not always available on machine where R is installed. win-
/ MIT 64
r-fpest 0.1.1 Given the values of sampled units and selection probabilities the desraj func- noarch
tion in the package computes the estimated value of the total as well as esti-
mated variance. / GPL-3


Name Version
r-fpop 2019.08.26
A dynamic programming algorithm for the fast segmentation of univariate sig- linux-
nals into piecewise constant profiles. The ‘fpop’ package is a wrapper to a 64,
C implementation of the fpop (Functional Pruning Optimal Partioning) algo- osx-
rithm described in Maidstone et al. 2017 <doi:10.1007/s11222-016-9636-3>. 64,
The problem of detecting changepoints in an univariate sequence is formulated win-
in terms of minimising the mean squared error over segmentations. The fpop 64
algorithm exactly minimizes the mean squared error for a penalty linear in the
number of changepoints. / LGPL-2.1
r-fpow 0.0_2 Returns the noncentrality parameter of the noncentral F distribution if prob- linux-
ability of type I and type II error, degrees of freedom of the numerator and 64,
the denominator are given. It may be useful for computing minimal detectable osx-
differences for general ANOVA models. This program is documented in the 64,
paper of A. Baharev, S. Kemeny, On the computation of the noncentral F and win-
noncentral beta distribution; Statistics and Computing, 2008, 18 (3), 333-340. 64
/ CC0
r-fptdapprox 2.1 Efficient approximation of first-passage-time densities for diffusion processes noarch
based on the First-Passage-Time Location (FPTL) function. / GPL-2
r-fracdiff 1.4_2 Maximum likelihood estimation of the parameters of a fractionally differenced linux-
ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989). / GPL (>= 32,
2) linux-
64,
osx-
64,
win-
32,
win-
64
r-fracprolif 1.0.7 Functions for fitting data to a quiescent growth model, i.e. a growth process noarch
that involves members of the population who stop dividing or propagating. /
GPL-2
r-fractaldim 0.8_4 Implements various methods for estimating fractal dimension of time series noarch
and 2-dimensional data. / GPL-2
r- 1.1.2 The parameters p and q are estimated with the aid of a randomized Sierpin- noarch
fractalparameterestimationski Carpet which is built on a [p-p-p-q]-model. Thereby, for three times a
simulation with a p-value and once with a q-value is assumed. Hence, these
parameters are estimated and displayed. Moreover, functions for simulating
random Sierpinski-Carpets with constant and variable probabilities are in-
cluded. For more details on the method please see Hermann et al. (2015)
<doi:10.1002/sim.6497>. / GPL-2
r-fraction 1.0 This is the package which can help you turn numeric,dataframe,matrix into noarch
fraction form. / GPL-2
r-fractional 0.1.3 The main function of this package allows numerical vector objects to be dis- linux-
played with their values in vulgar fractional form. This is convenient if pat- 64,
terns can then be more easily detected. In some cases replacing the compo- osx-
nents of a numeric vector by a rational approximation can also be expected to 64,
remove some component of round-off error. The main functions form a re- win-
implementation of the functions ‘fractions’ and ‘rational’ of the MASS pack- 64
age, but using a radically improved programming strategy. / GPL-2


Name Version
r-fragman 1.0.9 Performs fragment analysis using genetic data coming from capillary elec- noarch
trophoresis machines. These are files with FSA extension which stands for
FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain
DNA fragment intensities read by machinery. In addition to visualization, it
performs automatic scoring of SSRs (Sample Sequence Repeats; a type of ge-
netic marker very common across the genome) and other type of PCR markers
(standing for Polymerase Chain Reaction) in biparental populations such as
F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
/ GPL-3
r-frailtyhl 2.2 Implements the h-likelihood estimation procedures for general frailty models noarch
including competing-risk models and joint models. / Unlimited
r-frambgrowth 0.1.0 Generation of theoretical size distributions of framboidal or sunflower pyrite. noarch
The growth mechanisms used are surface and supply controlled and dependent
or independent of size. The algorithms are fully described in the published
work in Mineralogy and Petrology journal: Theoretical growth of framboidal
and sunflower pyrite using the R-package frambgrowth The authors Merinero,
R., and Cardenes, V. (2018). <DOI:10.1007/s00710-017-0535-x>. / GPL-2
r-franc 1.1.2 With no external dependencies and support for 335 languages; all languages noarch
spoken by more than one million speakers. ‘Franc’ is a port of the ‘JavaScript’
project of the same name, see <https://github.com/wooorm/franc>. / MIT
r-frapplot 0.1.3 Automatically process Fluorescence Recovery After Photobleaching (FRAP) noarch
data and generate consistent, publishable figures. Note: this pack-
age does not replace ‘ImageJ’ (or its equivalence) in raw image
quantification. Some references about the methods: Sprague, Brian
L. (2004) <doi:10.1529/biophysj.103.026765>; Day, Charles A. (2012)
<doi:10.1002/0471142956.cy0219s62>. / MIT
r-frbs 3.1_0 An implementation of various learning algorithms based on fuzzy rule-based noarch
systems (FRBSs) for dealing with classification and regression tasks. More-
over, it allows to construct an FRBS model defined by human experts. FRBSs
are based on the concept of fuzzy sets, proposed by Zadeh in 1965, which aims
at representing the reasoning of human experts in a set of IF-THEN rules, to
handle real-life problems in, e.g., control, prediction and inference, data min-
ing, bioinformatics data processing, and robotics. FRBSs are also known as
fuzzy inference systems and fuzzy models. During the modeling of an FRBS,
there are two important steps that need to be conducted: structure identifica-
tion and parameter estimation. Nowadays, there exists a wide variety of algo-
rithms to generate fuzzy IF-THEN rules automatically from numerical data,
covering both steps. Approaches that have been used in the past are, e.g.,
heuristic procedures, neuro-fuzzy techniques, clustering methods, genetic al-
gorithms, squares methods, etc. Furthermore, in this version we provide a uni-
versal framework named ‘frbsPMML’, which is adopted from the Predictive
Model Markup Language (PMML), for representing FRBS models. PMML is
an XML-based language to provide a standard for describing models produced
by data mining and machine learning algorithms. Therefore, we are allowed to
export and import an FRBS model to/from ‘frbsPMML’. Finally, this package
aims to implement the most widely used standard procedures, thus offering a
standard package for FRBS modeling to the R community. / GPL-2
r-frcc 1.0 This package implements the functions associated with Fast Regularized noarch
Canonical Correlation Analysis. / GPL-2


Name Version
r-freegroup 1.1_0 Provides functionality for manipulating elements of the free group (juxtaposi- noarch
tion is represented by a plus) including inversion, multiplication by a scalar,
group-theoretic power operation, and Tietze forms. The package is fully vec-
torized. / GPL-2
r-freeknotsplines 1.0.1 Algorithms for fitting free-knot splines for data with one independent variable linux-
and one dependent variable. Four free-knot spline algorithms are provided 64,
for the case where the number of knots is known in advance. A knot-search osx-
algorithm is provided for the case where the number of knots is not known in 64,
advance. In addition, methods are available to compute the fitted values, the win-
residuals, and the coefficients of the splines, and to plot the results, along with 64
a method to summarize the results. / GPL-2
r-freestats 0.0.3 A collections of useful statistical functions used in Columbia course noarch
W4240/W4400. / BSD_3_clause
r- 0.1.0 Provides functions to read data from neuroimaging files in ‘FreeSurfer’ <http: noarch
freesurferformats //freesurfer.net/> binary formats. This includes the following file formats: 1)
MGH/MGZ format files, which can contain multi-dimensional images or other
data. Typically they contain time-series of three-dimensional brain scans ac-
quired by magnetic resonance imaging (MRI). They can also contain vertex-
wise measures of surface morphometry data. The MGH format is named after
the Massachusetts General Hospital, and the MGZ format is a compressed
version of the same format. 2) ‘FreeSurfer’ morphometry data files in binary
‘curv’ format. These contain vertex-wise surface measures, i.e., one scalar
value for each vertex of a brain surface mesh. These are typically values like
the cortical thickness or brain surface area at each vertex. / MIT
r-fregression 3042.82
A collection of functions for linear and non-linear regression modelling. It noarch
implements a wrapper for several regression models available in the base and
contributed packages of R. / GPL-2
r-freq 1.0 Real capture frequencies will be fitted to various distributions which provide noarch
the basis of estimating population sizes, their standard error, and symmetric as
well as asymmetric confidence intervalls. / GPL-2
r-freqdist 0.1 Generates a frequency distribution. The frequency distribution includes raw noarch
frequencies, percentages in each category, and cumulative frequencies. The
frequency distribution can be stored as a data frame. / GPL-2
r-frlr 1.1 When fitting a set of linear regressions which have some same variables, linux-
we can separate the matrix and reduce the computation cost. This package 64,
aims to fit a set of repeated linear regressions faster. More details can be osx-
found in this blog Lijun Wang (2017) <https://stats.hohoweiya.xyz/2017/09/ 64,
26/An-R-Package-Fit-Repeated-Linear-Regressions/>. / GPL-2 win-
64
r-frm 1.2.2 Estimation and specification analysis of one- and two-part fractional regression noarch
models and calculation of partial effects. / GPL-2
r-frmhet 1.1.3 Estimation and specification analysis of fractional regression models with ne- noarch
glected heterogeneity and/or endogenous covariates. / GPL-2
r-frmpd 1.1.0 Estimation of panel data regression models for fractional responses. / GPL-2 noarch
r-fromo 0.2.1 Fast, numerically robust computation of weighted moments via ‘Rcpp’. Sup- linux-
ports computation on vectors and matrices, and Monoidal append of mo- 64,
ments. Moments and cumulants over running fixed length windows can be osx-
computed, as well as over time-based windows. Moment computations are 64,
via a generalization of Welford’s method, as described by Bennett et. (2009) win-
<doi:10.1109/CLUSTR.2009.5289161>. / LGPL-3 64


Name Version
r-frost 0.0.4 A compilation of empirical methods used by farmers and agronomic engineers noarch
to predict the minimum temperature to detect a frost night. These functions
use variables such as environmental temperature, relative humidity, and dew
point. See <http://sedici.unlp.edu.ar/handle/10915/72102> <http://www.fao.
org/docrep/008/y7223e/y7223e0b.htm#bm11.8> for details. / MIT
r-frt 0.1 Perform full randomization tests. / GPL-2 noarch
r-fs 1.2.7 A cross-platform interface to file system operations, built on top of the ‘libuv’ linux-
C library. / GPL-3 64,
osx-
64,
win-
32,
win-
64
r-fsadata 0.3.8 The datasets to support the Fish Stock Assessment (‘FSA’) package. / GPL-2 noarch
r-fselectorrcpp 0.3.1 ‘Rcpp’ (free of ‘Java’/’Weka’) implementation of ‘FSelector’ entropy-based linux-
feature selection algorithms based on an MDL discretization (Fayyad U. 64,
M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued At- osx-
tributes for Classification Learning. In 13’th International Joint Confer- 64,
ence on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, win-
Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/ 64
022.pdf> with a sparse matrix support. It is also equipped with a parallel
backend. / GPL-2
r-fsia 1.1.1 Import data of tests and questionnaires from FormScanner. FormScanner is noarch
an open source software that converts scanned images to data using optical
mark recognition (OMR) and it can be downloaded from <http://sourceforge.
net/projects/formscanner/>. The spreadsheet file created by FormScanner is
imported in a convenient format to perform the analyses provided by the pack-
age. These analyses include the conversion of multiple responses to binary
(correct/incorrect) data, the computation of the number of corrected responses
for each subject or item, scoring using weights,the computation and the graph-
ical representation of the frequencies of the responses to each item and the
report of the responses of a few subjects. / GPL-3
r-fsinteract 0.1.2 Performs fast detection of interactions in large-scale data using the method linux-
of random intersection trees introduced in Shah, R. D. and Meinshausen, N. 64,
(2014) <http://www.jmlr.org/papers/v15/shah14a.html>. The algorithm finds osx-
potentially high-order interactions in high-dimensional binary two-class clas- 64,
sification data, without requiring lower order interactions to be informative. win-
The search is particularly fast when the matrices of predictors are sparse. It 64
can also be used to perform market basket analysis when supplied with a sin-
gle binary data matrix. Here it will find collections of columns which for many
rows contain all 1’s. / GPL-2
r-fst 0.9.0 Multithreaded serialization of compressed data frames using the ‘fst’ format. linux-
The ‘fst’ format allows for random access of stored data and compression with 64,
the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD compres- osx-
sion library is owned by Facebook Inc. / AGPL-3 64,
win-
64


r-fstability 0.1.2 Has two functions to help with calculating feature selection stability. ‘Lump’ noarch
is a function that groups subset vectors into a dataframe, and adds NA
to shorter vectors so they all have the same length. ‘ASM’ is a function
that takes a dataframe of subset vectors and the original vector of features
as inputs, and calculates the Stability of the feature selection. The calcu-
lation for ‘asm’ uses the Adjusted Stability Measure proposed in: ‘Lust-
garten’, ‘Gopalakrishnan’, & ‘Visweswaran’ (2009)<https://www.ncbi.nlm.
nih.gov/pmc/articles/PMC2815476/>. / GPL-3
r-fsthet 1.0.1 A program to generate smoothed quantiles for the Fst-heterozygosity dis- noarch
tribution. Designed for use with large numbers of loci (e.g., genome-wide
SNPs). The best case for analyzing the Fst-heterozygosity distribution is when
many populations (>10) have been sampled. See Flanagan & Jones (2017)
<doi:10.1093/jhered/esx048>. / GPL-2
r-fticrms 0.8 This package was developed partially with funding from the NIH Training noarch
Program in Biomolecular Technology (2-T32-GM08799). / GPL-2
r-ftnonpar 0.1_88The package contains R-functions to perform the methods in nonparametric linux-
regression and density estimation, described in Davies, P. L. and Kovac, A. 64,
(2001) Local Extremes, Runs, Strings and Multiresolution (with discussion) osx-
Annals of Statistics. 29. p1-65 Davies, P. L. and Kovac, A. (2004) Densi- 64,
ties, Spectral Densities and Modality Annals of Statistics. Annals of Statistics. win-
32. p1093-1136 Kovac, A. (2006) Smooth functions and local extreme values. 64
Computational Statistics and Data Analysis (to appear) Dumbgen, L. and Ko-
vac, A. (2006) Extensions of smoothing via taut strings Davies, P. L. (1995)
Data features. Statistica Neerlandica 49,185-245. / GPL-2
r-ftrading 3042.79A collection of functions for trading and rebalancing financial instruments. It noarch
implements various technical indicators to analyse time series such as moving
averages or stochastic oscillators. / GPL-2
r-fts 0.9.9.2Fast operations for time series objects. / GPL-3 linux-
64,
osx-
64,
win-
64
r-fueleconomy 0.1 Fuel economy data from the EPA, 1985-2015, conveniently packaged for con- noarch
sumption by R users. / CC0
r-fugue 0.1.7 As in music, a fugue statistic repeats a theme in small variations. Here, noarch
the psi-function that defines an m-statistic is slightly altered to maintain the
same design sensitivity in matched sets of different sizes. The main func-
tions in the package are sen() and senCI(). For sensitivity analyses for m-
statistics, see Rosenbaum (2007) Biometrics 63 456-464 <doi:10.1111/j.1541-
0420.2006.00717.x>. / GPL-2
r-fun 0.2 This is a collection of R games and other funny stuff, such as the classic Mine noarch
sweeper and sliding puzzles. / GPL-3
r-funchir 0.1.4 A set of functions, some subset of which I use in every .R file I write. Exam- noarch
ples are table2(), which adds useful functionalities to base table (sorting, built-
in proportion argument, etc.); lyx.xtable(), which converts xtable() output to
a format more easily copy-pasted into LyX; pdf2(), which writes a plot to file
while also displaying it in the RStudio plot window; and abbr_to_colClass(),
which is a much more concise way of feeding many types to a colClass argu-
ment in a data reader. / GPL-2


Name Version
r-funchisq 2.4.8_1
Statistical hypothesis testing methods for inferring model-free functional linux-
dependency using asymptotic chi-squared or exact distributions. Func- 64,
tional test statistics are asymmetric and functionally optimal, unique osx-
from other related statistics. Tests in this package reveal evidence for 64,
causality based on the causality-by-functionality principle. They in- win-
clude asymptotic functional chi-squared tests (‘Zhang & Song’ 2013) 64
<arXiv:1311.2707> and an exact functional test (‘Zhong & Song’ 2019)
<doi:10.1109/TCBB.2018.2809743>. The normalized functional chi-squared
test was used by Best Performer ‘NMSUSongLab’ in HPN-DREAM
(DREAM8) Breast Cancer Network Inference Challenges (‘Hill et al’ 2016)
<doi:10.1038/nmeth.3773>. A function index (‘Zhong & Song’ in press) (‘Ku-
mar et al’ 2018) <doi:10.1109/BIBM.2018.8621502> derived from the func-
tional test statistic offers a new effect size measure for the strength of func-
tional dependency, a better alternative to conditional entropy in many aspects.
For continuous data, these tests offer an advantage over regression analysis
when a parametric functional form cannot be assumed; for categorical data,
they provide a novel means to assess directional dependency not possible with
symmetrical Pearson’s chi-squared or Fisher’s exact tests. / LGPL-3
r-functional 0.6 Curry, Compose, and other higher-order functions / GPL (>= 2) linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-functools 0.2.0 Extends functional programming in R by providing support to the usual higher noarch
order functional suspects (Map, Reduce, Filter, etc.). / MIT
r-funique 0.0.1 Similar to base’s unique function, only optimized for working with data noarch
frames, especially those that contain date-time columns. / MIT
r-funitroots 3042.79
Provides four addons for analyzing trends and unit roots in financial time se- linux-
ries: (i) functions for the density and probability of the augmented Dickey- 64,
Fuller Test, (ii) functions for the density and probability of MacKinnon’s unit osx-
root test statistics, (iii) reimplementations for the ADF and MacKinnon Test, 64,
and (iv) an ‘urca’ Unit Root Test Interface for Pfaff’s unit root test suite. / win-
GPL-2 64
r-funr 0.3.2 A small utility which wraps Rscript and provides access to all R functions from noarch
the shell. / MIT


Name Version
r-funreg 1.2 Performs functional regression, and some related approaches, for inten- noarch
sive longitudinal data (see the book by Walls & Schafer, 2006, Models
for Intensive Longitudinal Data, Oxford) when such data is not necessar-
ily observed on an equally spaced grid of times. The approach gener-
ally follows the ideas of Goldsmith, Bobb, Crainiceanu, Caffo, and Reich
(2011)<DOI:10.1198/jcgs.2010.10007> and the approach taken in their sam-
ple code, but with some modifications to make it more feasible to use with
long rather than wide, non-rectangular longitudinal datasets with unequal and
potentially random measurement times. It also allows easy plotting of the cor-
relation between the smoothed covariate and the outcome as a function of time,
which can add additional insights on how to interpret a functional regression.
Additionally, it also provides several permutation tests for the significance of
the functional predictor. The heuristic interpretation of ‘‘time” is used to de-
scribe the index of the functional predictor, but the same methods can equally
be used for another unidimensional continuous index, such as space along a
north-south axis. The development of this package was part of a research
project supported by Award R03 CA171809-01 from the National Cancer In-
stitute and Award P50 DA010075 from the National Institute on Drug Abuse.
The content is solely the responsibility of the authors and does not necessar-
ily represent the official views of the National Institute on Drug Abuse, the
National Cancer Institute, or the National Institutes of Health. / GPL-2
r-funta 0.1.0 Computes the functional tangential angle pseudo-depth and its robustified ver- noarch
sion from the paper by Kuhnt and Rehage (2016). See Kuhnt, S.; Rehage, A.
(2016): An angle-based multivariate functional pseudo-depth for shape outlier
detection, JMVA 146, 325-340, <doi:10.1016/j.jmva.2015.10.016> for details.
/ GPL-3
r-fusionclust 1.0.0 Provides the Big Merge Tracker and COSCI algorithms for convex cluster- noarch
ing and feature screening using L1 fusion penalty. See Radchenko, P. and
Mukherjee, G. (2017) <doi:10.1111/rssb.12226> and T.Banerjee et al. (2017)
<doi:10.1016/j.jmva.2017.08.001> for more details. / GPL-2
r-fusionlearn 0.1.1 The fusion learning method uses a model selection algorithm to learn from noarch
multiple data sets across different experimental platforms through group penal-
ization. The responses of interest may include a mix of discrete and continuous
variables. The responses may share the same set of predictors, however, the
models and parameters differ across different platforms. Integrating informa-
tion from different data sets can enhance the power of model selection. Pack-
age is based on Xin Gao, Raymond J. Carroll (2017) <arXiv:1610.00667v1>.
/ GPL-2
r-futile.options 1.0.1 A scoped options management framework. Used in other packages. / LGPL-3 noarch


Name Version
r-futility 0.4 Randomized clinical trials commonly follow participants for a time-to-event noarch
efficacy endpoint for a fixed period of time. Consequently, at the time when
the last enrolled participant completes their follow-up, the number of observed
endpoints is a random variable. Assuming data collected through an interim
timepoint, simulation-based estimation and inferential procedures in the stan-
dard right-censored failure time analysis framework are conducted for the dis-
tribution of the number of endpoints–in total as well as by treatment arm–at
the end of the follow-up period. The future (i.e., yet unobserved) enrollment,
endpoint, and dropout times are generated according to mechanisms specified
in the simTrial() function in the ‘seqDesign’ package. A Bayesian model for
the endpoint rate, offering the option to specify a robust mixture prior distribu-
tion, is used for generating future data (see the vignette for details). Inference
can be restricted to participants who received treatment according to the pro-
tocol and are observed to be at risk for the endpoint at a specified timepoint.
Plotting functions are provided for graphical display of results. / GPL-2
r-fuzzyahp 0.9.1 Calculation of AHP (Analytic Hierarchy Process - <http://en.wikipedia.org/ noarch
wiki/Analytic_hierarchy_process>) with classic and fuzzy weights based on
Saaty’s pairwise comparison method for determination of weights. / LGPL-3
r-fuzzyfdr 1.0 Exact calculation of fuzzy decision rules for multiple testing. Choose to con- noarch
trol FDR (false discovery rate) using the Benjamini and Hochberg method, or
FWER (family wise error rate) using the Bonferroni method. Kulinsakaya and
Lewin (2007). / GPL-3
r-fuzzynumbers 0.4_6 S4 classes and methods to deal with fuzzy numbers. They allow for computing noarch
any arithmetic operations (e.g., by using the Zadeh extension principle), per-
forming approximation of arbitrary fuzzy numbers by trapezoidal and piece-
wise linear ones, preparing plots for publications, computing possibility and
necessity values for comparisons, etc. / LGPL-3
r-fuzzyr 2.1 Design and simulate fuzzy logic systems using Type 1 Fuzzy Logic. This noarch
toolkit includes with graphical user interface (GUI) and an adaptive neuro-
fuzzy inference system (ANFIS). This toolkit is a continuation from the pre-
vious package (‘FuzzyToolkitUoN’). Produced by the Intelligent Modelling &
Analysis Group, University of Nottingham. / GPL-2
r-fuzzyranktests 0.3_10Does fuzzy tests and confidence intervals (following Geyer and Meeden, Sta- linux-
tistical Science, 2005, <doi:10.1214/088342305000000340>) for sign test and 64,
Wilcoxon signed rank and rank sum tests. / MIT osx-
64,
win-
64
r-fuzzysim 2.0 Functions to calculate fuzzy versions of species’ occurrence patterns based noarch
on presence-absence data (including inverse distance interpolation, trend sur-
face analysis and prevalence-independent favourability GLM), and pair-wise
fuzzy similarity (based on fuzzy versions of commonly used similarity indices)
among those occurrence patterns. Includes also functions for model compari-
son (overlap and fuzzy similarity, loss or gain), and for data preparation, such
as obtaining unique abbreviations of species names, converting species lists
(long format) to presence-absence tables (wide format), transposing part of a
data frame, assessing the false discovery rate, or analysing and dealing with
multicollinearity among variables. Includes also sample datasets for providing
practical examples. / GPL-3


Name Version
r-fuzzystattra 1.0 The aim of the package is to provide some basic functions for doing statistics noarch
with trapezoidal fuzzy numbers. In particular, the package contains several
functions for simulating trapezoidal fuzzy numbers, as well as for calculating
some central tendency measures (mean and two types of median), some scale
measures (variance, ADD, MDD, Sn, Qn, Tn and some M-estimators) and one
diversity index and one inequality index. Moreover, functions for calculating
the 1-norm distance, the mid/spr distance and the (phi,theta)-wabl/ldev/rdev
distance between fuzzy numbers are included, and a function to calculate the
value phi-wabl given a sample of trapezoidal fuzzy numbers. / GPL-2
r- 1.0 A custom framework for working with Type 1 Fuzzy Logic, produced by the noarch
fuzzytoolkituon University of Nottingham IMA Group. / GPL-2
r-fuzzywuzzyr 1.0.3 Fuzzy string matching implementation of the ‘fuzzywuzzy’ <https://github. noarch
com/seatgeek/fuzzywuzzy> ‘python’ package. It uses the Levenshtein Dis-
tance <https://en.wikipedia.org/wiki/Levenshtein_distance> to calculate the
differences between sequences. / GPL-2
r-fwdselect 2.1.0 A simple method to select the best model or best subset of variables using linux-
different types of data (binary, Gaussian or Poisson) and applying it in different 32,
contexts (parametric or non-parametric). / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-fwi.fbp 1.7 Provides three functions to calculate the outputs of the two main compo- noarch
nents of the Canadian Forest Fire Danger Rating System (CFFDRS): the Fire
Weather Index (FWI) System and the Fire Behaviour Prediction (FBP) System.
/ GPL-2
r-fwsim 0.3.4 Simulates a population under the Fisher-Wright model (fixed or stochastic linux-
population size) with a one-step neutral mutation process (stepwise mutation 64,
model, logistic mutation model and exponential mutation model supported). osx-
The stochastic population sizes are random Poisson distributed and different 64,
kinds of population growth are supported. For the stepwise mutation model, it win-
is possible to specify locus and direction specific mutation rate (in terms of up- 64
wards and downwards mutation rate). Intermediate generations can be saved
in order to study e.g. drift. / GPL-2
r-g.data 2.4 Create and maintain delayed-data packages (ddp’s). Data stored in a ddp are noarch
available on demand, but do not take up memory until requested. You attach a
ddp with g.data.attach(), then read from it and assign to it in a manner similar
to S-PLUS, except that you must run g.data.save() to actually commit to disk.
/ GPL-3
r-g1dbn 3.1.1 G1DBN performs DBN inference using 1st order conditional dependencies. / noarch
GPL-2
r-g3viz 1.1.2 R interface for ‘g3-lollipop’ JavaScript library. Visualize genetic mutation data noarch
using an interactive lollipop diagram in RStudio or your browser. / MIT


Name Version
r-ga 3.2 Flexible general-purpose toolbox implementing genetic algorithms (GAs) for linux-
stochastic optimisation. Binary, real-valued, and permutation representations 64,
are available to optimize a fitness function, i.e. a function provided by users de- osx-
pending on their objective function. Several genetic operators are available and 64,
can be combined to explore the best settings for the current task. Furthermore, win-
users can define new genetic operators and easily evaluate their performances. 64
Local search using general-purpose optimisation algorithms can be applied
stochastically to exploit interesting regions. GAs can be run sequentially or in
parallel, using an explicit master-slave parallelisation or a coarse-grain islands
approach. / GPL-2
r-gad 1.1.1 This package analyses complex ANOVA models with any combination of or- noarch
thogonal/nested and fixed/random factors, as described by Underwood (1997).
There are two restrictions: (i) data must be balanced; (ii) fixed nested fac-
tors are not allowed. Homogeneity of variances is checked using Cochran’s C
test and ‘a posteriori’ comparisons of means are done using Student-Newman-
Keuls (SNK) procedure. / GPL (>= 2.0)
r-gadag 0.99.0Sparse large Directed Acyclic Graphs learning with a combination of a convex linux-
program and a tailored genetic algorithm (see Champion et al. (2017) <https: 64,
//hal.archives-ouvertes.fr/hal-01172745v2/document>). / GPL-2 osx-
64,
win-
64
r-gadifpt 1.0 In this package we consider Gaussian Diffusion processes and smooth thresh- noarch
olds. After evaluating the mean of the process to check the subthreshold reg-
imen hypothesis, the FPT density function is reconstructed via the numerical
quadrature of the integral equation in (Buonocore 1987); first passage times are
also generated by the method in (Buonocore 2014) and results are compared.
The timestep of the simulations can iteratively be refined. User should provide
the functional form for the drift and the infinitesimal variance in the script
‘userfunc.R’ and for the threshold in the script ‘userthresh.R’. All the param-
eters required by the implementation are to be set in the script ‘userparam.R’.
Example scripts for common drifts and thresholds are given. / GPL-2
r-gafit 0.5.1 A group of sample points are evaluated against a user-defined expression, linux-
the sample points are lists of parameters with values that may be substituted 64,
into that expression. The genetic algorithm attempts to make the result of osx-
the expression as low as possible (usually this would be the sum of residuals 64,
squared). / GPL-2 win-
64
r-gains 1.2 Constructs gains tables and lift charts for prediction algorithms. Gains ta- noarch
bles and lift charts are commonly used in direct marketing applications. The
method is described in Drozdenko and Drake (2002), Optimal Database Mar-
keting, Chapter 11. / GPL-3
r-gaipe 1.0 GAIPE implements graphical representation of accuracy in parameter estima- noarch
tion (AIPE) on RMSEA for sample size planning in structural equation mod-
eling. Sample sizes suggested by RMSEA with AIPE method and power anal-
ysis approach can also be obtained separately using the provided functions. /
GPL-2


Name Version
r-galgo 1.4 Build multivariate predictive models from large datasets having far larger num- linux-
ber of features than samples such as in functional genomics datasets. Trevino 64,
and Falciani (2006) <doi:10.1093/bioinformatics/btl074>. / GPL-2 osx-
64,
win-
64
r-gam 1.16.1Functions for fitting and working with generalized additive models, as de- linux-
scribed in chapter 7 of Statistical Models in S (Chambers and Hastie (eds), 64,
1991), and Generalized Additive Models (Hastie and Tibshirani, 1990). / GPL- osx-
2 64,
win-
64
r-gamair 1.0_2 Data sets and scripts used in the book ‘Generalized Additive Models: An In- noarch
troduction with R’, Wood (2006,2017) CRC. / GPL-2
r-gambin 2.4.1 Fits unimodal and multimodal gambin distributions to species-abundance noarch
distributions from ecological data, as in in Matthews et al. (2014)
<DOI:10.1111/ecog.00861>. ‘gambin’ is short for ‘gamma-binomial’. The
main function is fit_abundances(), which estimates the ‘alpha’ parameter(s) of
the gambin distribution using maximum likelihood. Functions are also pro-
vided to generate the gambin distribution and for calculating likelihood statis-
tics. / GPL-3
r-gamboost 1.2_3 This package provides routines for fitting generalized linear and and general- linux-
ized additive models by likelihood based boosting, using penalized B-splines 64,
/ GPL-2 osx-
64,
win-
64
r-games 1.1.2 Provides estimation and analysis functions for strategic statistical models. / noarch
GPL-2
r-gamesga 1.1.3.6Finds adaptive strategies for sequential symmetric games using a genetic al- linux-
gorithm. Currently, any symmetric two by two matrix is allowed, and strate- 64,
gies can remember the history of an opponent’s play from the previous three osx-
rounds of moves in iterated interactions between players. The genetic algo- 64,
rithm returns a list of adaptive strategies given payoffs, and the mean fitness of win-
strategies in each generation. / MIT 64
r-gamlr 1.13_5The gamma lasso algorithm provides regularization paths corresponding to a linux-
range of non-convex cost functions between L0 and L1 norms. As much as 64,
possible, usage for this package is analogous to that for the glmnet package osx-
(which does the same thing for penalization between L1 and L2 norms). For 64,
details see: Taddy (2017 JCGS), One-Step Estimator Paths for Concave Reg- win-
ularization, <arXiv:1308.5623>. / GPL-3 64
r-gamlss.data 5.1_4 Data used as examples to demonstrate GAMLSS models. / GPL-2 | GPL-3 noarch
r-gamlss.dist 5.1_4 A set of distributions which can be used for modelling the response variables linux-
in Generalized Additive Models for Location Scale and Shape, Rigby and 64,
Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distri- osx-
butions can be continuous, discrete or mixed distributions. Extra distributions 64,
can be created, by transforming, any continuous distribution defined on the win-
real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a 64
‘’log” or a ‘’logit’ transformation respectively. / GPL-2 | GPL-3
r-gamm4 0.2_5 Estimate generalized additive mixed models via a version of function gamm() noarch
from ‘mgcv’, using ‘lme4’ for estimation. / GPL-2


Name Version
r-gammslice 2.0_2 Uses a slice sampling-based Markov chain Monte Carlo to conduct Bayesian linux-
fitting and inference for generalized additive mixed models. Generalized lin- 64,
ear mixed models and generalized additive models are also handled as special osx-
cases of generalized additive mixed models. The methodology and software is 64,
described in Pham, T.H. and Wand, M.P. (2018). Australian and New Zealand win-
Journal of Statistics, 60, 279-330 <DOI:10.1111/ANZS.12241>. / GPL-2 64
r-gamrr 0.6.0 To calculate the relative risk (RR) for the generalized additive model. / GPL-3 noarch
r-ganpadata 1.0 This is a dataset package for GANPA, which implements a network-based gene noarch
weighting approach to pathway analysis. This package includes data useful for
GANPA, such as a functional association network, pathways, an expression
dataset and multi-subunit proteins. / GPL-2
r-gap 1.2.1 It is designed as an integrated package for genetic data analysis of both pop- linux-
ulation and family data. Currently, it contains functions for sample size cal- 64,
culations of both population-based and family-based designs, probability of osx-
familial disease aggregation, kinship calculation, statistics in linkage analysis, 64,
and association analysis involving genetic markers including haplotype analy- win-
sis with or without environmental covariates. / GPL-2 64
r-gap.datasets 0.0.4 Datasets associated with the ‘gap’ package. Currently, it includes an example noarch
data for regional association plot (CDKN), an example data for a genomewide
association meta-analysis (OPG), Manhattan plots with (hr1420, mhtdata) and
without (w4) gene annotations. / GPL-2
r-gaparsimony 0.9.2 Methodology that combines feature selection, model tuning, and parsimonious noarch
model selection with Genetic Algorithms (GA) proposed in {Martinez-de-
Pison} (2015) <DOI:10.1016/j.asoc.2015.06.012>. To this objective, a novel
GA selection procedure is introduced based on separate cost and complexity
evaluations. / GPL-2
r-gar 1.1 The functions included are used to obtain initial authentication with Google noarch
Analytics as well as simple and organized data retrieval from the API. Allows
for retrieval from multiple profiles at once. / GPL-2
r-garray 1.1.2 Organize a so-called ragged array as generalized arrays, which is simply an ar- noarch
ray with sub-dimensions denoting the subdivision of dimensions (grouping of
members within dimensions). By the margins (names of dimensions and sub-
dimensions) in generalized arrays, operators and utility functions provided in
this package automatically match the margins, doing map-reduce style paral-
lel computation along margins. Generalized arrays are also cooperative to R’s
native functions that work on simple arrays. / GPL-3
r-gaselect 1.0.7 Provides a genetic algorithm for finding variable subsets in high dimensional linux-
data with high prediction performance. The genetic algorithm can use ordinary 64,
least squares (OLS) regression models or partial least squares (PLS) regression osx-
models to evaluate the prediction power of variable subsets. By supporting 64,
different cross-validation schemes, the user can fine-tune the tradeoff between win-
speed and quality of the solution. / GPL-2 64
r-gatepoints 0.1.3 Allows user to choose/gate a region on the plot and returns points within it. / noarch
GPL-2


Name Version
r-gausscov 0.0.2 Given the standard linear model the traditional way of deciding whether to linux-
include the jth covariate is to apply the F-test to decide whether the corre- 64,
sponding beta coefficient is zero. The Gaussian covariate method is completely osx-
different. The question as to whether the beta coefficient is or is not zero is re- 64,
placed by the question as to whether the covariate is better or worse than i.i.d. win-
Gaussian noise. The P-value for the covariate is the probability that Gaus- 64
sian noise is better. Surprisingly this can be given exactly and it is the same
a the P-value for the classical model based on the F-distribution. The Gaus-
sian covariate P-value is model free, it is the same for any data set. Using the
idea it is possible to do covariate selection for a small number of covariates
25 by considering all subsets. Post selection inference causes no problems as
the P-values hold whatever the data. The idea extends to stepwise regression
again with exact probabilities. In the simplest version the only parameter is a
specified cut-off P-value which can be interpreted as the probability of a false
positive being included in the final selection. For more information see the
website below and the accompanying papers: L. Davies and L. Duembgen, A
Model-free Approach to Linear Least Squares Regression with Exact Proba-
bilities and Applications to Covariate Selection, 2019, <arXiv:1906.01990>.
L. Davies, Lasso, Knockoff and Gaussian covariates: A comparison, 2018,
<arXiv:1807.09633v4>. / GPL-3
r-gaussdiff 1.1 A collection difference measures for multivariate Gaussian probability density noarch
functions, such as the Euclidea mean, the Mahalanobis distance, the Kullback-
Leibler divergence, the J-Coefficient, the Minkowski L2-distance, the Chi-
square divergence and the Hellinger Coefficient. / GPL-2
r-gaussfacts 0.0.2 Display a random fact about Carl Friedrich Gauss based the on collection cu- noarch
rated by Mike Cavers via the <http://gaussfacts.com> site. / GPL-2
r- 1.0.1 Inference, goodness-of-fit test, and prediction densities and intervals for uni- noarch
gaussianhmm1d variate Gaussian Hidden Markov Models (HMM). The goodness-of-fit is based
on a Cramer-von Mises statistic and uses parametric bootstrap to estimate the
p-value. The description of the methodology is taken from Chapter 10.2 of
Remillard (2013) <doi:10.1201/b14285>. / GPL-2
r-gb 2.3.3 A collection of algorithms and functions for fitting data to a generalized linux-
lambda distribution via moment matching methods, and generalized bootstrap- 64,
ping. / Unlimited osx-
64,
win-
64
r-gbm 2.1.5 An implementation of extensions to Freund and Schapire’s AdaBoost algo- linux-
rithm and Friedman’s gradient boosting machine. Includes regression methods 64,
for least squares, absolute loss, t-distribution loss, quantile regression, logis- osx-
tic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, 64,
AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank mea- win-
sures (LambdaMart). Originally developed by Greg Ridgeway. / GPL-2 64
r-gbrd 0.4_11Provides utilities for processing Rd objects and files. Extract argument de- noarch
scriptions and other parts of the help pages of functions. / GPL-2
r-gcai.bias 1.0 Many inherited biases and effects exists in RNA-seq due to both biological noarch
and technical effects. We observed the biological variance of testing target
transcripts can influence the yield of sequencing reads, which might indicate
a resource competition existing in RNA-seq. We developed this package to
capture the bias depending on local sequence and perform the correction of this
type of bias by borrowing information from spike-in measurement. / GPL-2


Name Version
r-gcat 0.1 These are two-sample tests for categorical data utilizing similarity information linux-
among the categories. They are useful when there is underlying structure on 64,
the categories. / GPL-2 osx-
64,
win-
64
r-gcd 4.0.4 Contains the Global Charcoal database data. Data include charcoal series (age, noarch
depth, charcoal quantity, associated units and methods) and information on
sedimentary sites (localisation, depositional environment, biome, etc.) as well
as publications informations. Since 4.0.0 the GCD mirrors the online SQL
database at <http://paleofire.org>. / GPL-2
r-gcdnet 1.0.5 A generalized coordinate descent (GCD) algorithm for computing the solu- linux-
tion path of the hybrid Huberized support vector machine (HHSVM) and its 64,
generalization, including the LASSO and elastic net (adaptive) penalized least osx-
squares, logistic regression, HHSVM, squared hinge loss SVM and expectile 64,
regression. / GPL-2 win-
64
r-gckrig 1.1.3 Provides a variety of functions to analyze and model geostatistical count data linux-
with Gaussian copulas, including 1) data simulation and visualization; 2) cor- 64,
relation structure assessment (here also known as the Normal To Anything); 3) osx-
calculate multivariate normal rectangle probabilities; 4) likelihood inference 64,
and parallel prediction at predictive locations. / GPL-2 win-
64
r-gclus 1.3.2 Orders panels in scatterplot matrices and parallel coordinate displays by some noarch
merit index. Package contains various indices of merit, ordering functions, and
enhanced versions of pairs and parcoord which color panels according to their
merit level. / GPL-2
r-gconcord 0.41 Estimates a sparse inverse covariance matrix from a convex pseudo-likelihood linux-
function with L1 penalty / GPL-2 64,
osx-
64,
win-
64
r-gcookbook 2.0 Data sets used in the book R Graphics Cookbook by Winston Chang, published noarch
by O’Reilly Media. / GPL-2
r-gcpm 1.2.2 Analyze the default risk of credit portfolios. Commonly known models, like linux-
CreditRisk or the CreditMetrics model are implemented in their very basic set- 64,
tings. The portfolio loss distribution can be achieved either by simulation or osx-
analytically in case of the classic CreditRisk model. Models are only imple- 64,
mented to respect losses caused by defaults, i.e. migration risk is not included. win-
The package structure is kept flexible especially with respect to distributional 64
assumptions in order to quantify the sensitivity of risk figures with respect to
several assumptions. Therefore the package can be used to determine the credit
risk of a given portfolio as well as to quantify model sensitivities. / GPL-2
r-gd 1.7 Geographical detectors for measuring spatial stratified heterogeneity, as de- noarch
scribed in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and Jin-
feng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the optimal
discretization of continuous data, four primary functions of geographical de-
tectors, comparison of size effects of spatial unit and the visualizations of re-
sults. The descriptions of the package, methods and case datasets refer to the
citation information below. / GPL-2


Name Version
r-gdadata 0.93 Datasets used in the book ‘Graphical Data Analysis with R’ (Antony Unwin, noarch
CRC Press 2015). / GPL-2
r-gdata 2.18.0Various R programming tools for data manipulation, including: - medical unit linux-
conversions (‘ConvertMedUnits’, ‘MedUnits’), - combining objects (‘bind- 32,
Data’, ‘cbindX’, ‘combine’, ‘interleave’), - character vector operations (‘cen- linux-
terText’, ‘startsWith’, ‘trim’), - factor manipulation (‘levels’, ‘reorder.factor’, 64,
‘mapLevels’), - obtaining information about R objects (‘object.size’, ‘elem’, noarch,
‘env’, ‘humanReadable’, ‘is.what’, ‘ll’, ‘keep’, ‘ls.funs’, ‘Args’,’nPairs’, osx-
‘nobs’), - manipulating MS-Excel formatted files (‘read.xls’, ‘installXLSX- 64,
support’, ‘sheetCount’, ‘xlsFormats’), - generating fixed-width format files win-
(‘write.fwf’), - extricating components of date & time objects (‘getYear’, ‘get- 32,
Month’, ‘getDay’, ‘getHour’, ‘getMin’, ‘getSec’), - operations on columns win-
of data frames (‘matchcols’, ‘rename.vars’), - matrix operations (‘unmatrix’, 64
‘upperTriangle’, ‘lowerTriangle’), - operations on vectors (‘case’, ‘unknown-
ToNA’, ‘duplicated2’, ‘trimSum’), - operations on data frames (‘frameApply’,
‘wideByFactor’), - value of last evaluated expression (‘ans’), and - wrapper for
‘sample’ that ensures consistent behavior for both scalar and vector arguments
(‘resample’). / GPL-2
r-gdistance 1.2_2 Calculate distances and routes on geographic grids. / GPL-2 noarch
r-gdmp 0.2.0 Manage and analyze high-dimensional SNP data from chips with multiple den- linux-
sities. / GPL-2 64,
osx-
64,
win-
64
r-gdns 0.3.1 To address the problem of insecurity of ‘UDP’-based ‘DNS’ requests, ‘Google noarch
Public DNS’ offers ‘DNS’ resolution over an encrypted ‘HTTPS’ connection.
‘DNS-over-HTTPS’ greatly enhances privacy and security between a client
and a recursive resolver, and complements ‘DNSSEC’ to provide end-to-end
authenticated ‘DNS’ lookups. Functions that enable querying individual re-
quests that bulk requests that return detailed responses and bulk requests are
both provided. Support for reverse lookups is also provided. See <https:
//developers.google.com/speed/public-dns/docs/dns-over-https> for more in-
formation. / AGPL-3
r-gdpc 1.1.0 Functions to compute the Generalized Dynamic Principal Components intro- linux-
duced in Peña and Yohai (2016) <DOI:10.1080/01621459.2015.1072542>. / 64,
GPL-2 osx-
64,
win-
64
r-gds 0.1.0 Contains a function called gds() which accepts three input parameters like noarch
lower limits, upper limits and the frequencies of the corresponding classes.
The gds() function calculate and return the values of mean (‘gmean’), median
(‘gmedian’), mode (‘gmode’), variance (‘gvar’), standard deviation (‘gstdev’),
coefficient of variance (‘gcv’), quartiles (‘gq1’, ‘gq2’, ‘gq3’), inter-quartile
range (‘gIQR’), skewness (‘g1’), and kurtosis (‘g2’) which facilitate effective
data analysis. For skewness and kurtosis calculations we use moments. / GPL-
2


Name Version
r-gee 4.13_19
Generalized Estimation Equation solver. / GPL-2 linux-
64,
osx-
64,
win-
64
r-gee4 0.1.0.0Fit joint mean-covariance models for longitudinal data within the framework linux-
of (weighted) generalised estimating equations (GEE/WGEE). The models 64,
and their components are represented using S4 classes and methods. The core osx-
computational algorithms are implemented using the ‘Armadillo’ C library for 64,
numerical linear algebra and ‘RcppArmadillo’ glue. / GPL-2 win-
64
r-geem 0.10.1GEE estimation of the parameters in mean structures with possible correlation noarch
between the outcomes. User-specified mean link and variance functions are
allowed, along with observation weighting. The ‘M’ in the name ‘geeM’ is
meant to emphasize the use of the Matrix package, which allows for an imple-
mentation based fully in R. / GPL-3
r-geepack 1.2_1 Generalized estimating equations solver for parameters in mean, scale, and linux-
correlation structures, through mean link, scale link, and correlation link. Can 64,
also handle clustered categorical responses. / GPL-3 osx-
64,
win-
64
r-geigen 2.3 Functions to compute generalized eigenvalues and eigenvectors, the general- linux-
ized Schur decomposition and the generalized Singular Value Decomposition 64,
of a matrix pair, using Lapack routines. / GPL-2 osx-
64,
win-
64
r-gelnet 1.2.1 Implements several extensions of the elastic net regularization scheme. These linux-
extensions include individual feature penalties for the L1 term, feature-feature 64,
penalties for the L2 term, as well as translation coefficients for the latter. / osx-
GPL-3 64,
win-
64
r-gen2stage 1.0 One can find single-stage and two-stage designs for a phase II single-arm study noarch
with either efficacy or safety/toxicity endpoints as described in Kim and Wong
(2019) <doi:10.29220/CSAM.2019.26.2.163>. / GPL-2
r-genalg 0.2.0 R based genetic algorithm for binary and floating point chromosomes. / GPL-2 noarch
r-genbinomapps 1.0_2 Density, distribution function, quantile function and random generation for noarch
the Generalized Binomial Distribution. Functions to compute the Clopper-
Pearson Confidence Interval and the required sample size. Enhanced model
for burn-in studies, where failures are tackled by countermeasures. / GPL-3
r-gendata 1.1 Set of functions to create datasets using a correlation matrix. / GPL-3 noarch
r-genderizer 2.1.1 Utilizes the ‘genderize.io’ Application Programming Interface to predict gen- noarch
der from first names extracted from a text vector. The accuracy of prediction
could be controlled by two parameters: counts of a first name in the database
and probability of prediction. / MIT


Name Version
r-gendist 2.0 Computes the probability density function (pdf), cumulative distribution func- noarch
tion (cdf), quantile function (qf) and generates random values (rg) for the fol-
lowing general models : mixture models, composite models, folded models,
skewed symmetric models and arc tan models. / GPL-2
r-genef 1.0 This package implements several generalized F-statistics. The current version noarch
includes a generalized F-statistic based on the flexible isotonic/monotonic re-
gression or order restricted hypothesis testing. / GPL-2
r-genelistpie 1.0 geneListPie package is for mapping a gene list to function categories defined noarch
in GOSlim or Kegg. The results can be plotted as a pie chart to provide a quick
view of the genes distribution of the gene list among the function categories.
The gene list must contain a list of gene symbols. The package contains a set of
pre-processed gene sets obtained from Gene Ontology and MSigDB including
human, mouse, rat and yeast. To provide a high level concise view, only GO
slim and kegg are provided. The gene sets are regulared updated. User can
also use customized gene sets. User can use the R Pie() or Pie3D() function
for plotting the pie chart. Users can also choose to output the gene function
mapping results and use external software such as Excel(R) for ploting. / GPL-
3
r-genemodel 1.1.0 Using simple input, this package creates plots of gene models. Users can create noarch
plots of alternatively spliced gene variants and the positions of mutations and
other gene features. / GPL-2
r-genepi 1.0.1 Functions for Genetic Epi Methods Developed at MSKCC / GPL-2 linux-
64,
osx-
64,
win-
64
r-genepop 1.1.3 Makes the Genepop software available in R. This software implements a mix- linux-
ture of traditional population genetic methods and some more focused devel- 64,
opments: it computes exact tests for Hardy-Weinberg equilibrium, for popu- osx-
lation differentiation and for genotypic disequilibrium among pairs of loci; it 64,
computes estimates of F-statistics, null allele frequencies, allele size-based win-
statistics for microsatellites, etc.; and it performs analyses of isolation by 64
distance from pairwise comparisons of individuals or population samples. /
CeCILL-2
r-generalhoslem 1.3.4 Functions to assess the goodness of fit of binary, multinomial and ordinal lo- noarch
gistic models. Included are the Hosmer-Lemeshow tests (binary, multinomial
and ordinal) and the Lipsitz and Pulkstenis-Robinson tests (ordinal). / GPL-2
r- 0.8_4 Functions for the hyperbolic and related distributions. Density, distribution noarch
generalizedhyperbolic and quantile functions and random number generation are provided for the hy-
perbolic distribution, the generalized hyperbolic distribution, the generalized
inverse Gaussian distribution and the skew-Laplace distribution. Additional
functionality is provided for the hyperbolic distribution, normal inverse Gaus-
sian distribution and generalized inverse Gaussian distribution, including fit-
ting of these distributions to data. Linear models with hyperbolic errors may
be fitted using hyperblmFit. / GPL-2
r-generaloaxaca 1.0 Perform the Blinder-Oaxaca decomposition for generalized linear model with noarch
bootstrapped standard errors. The twofold and threefold decomposition are
given, even the generalized linear model output in each group. / GPL-2
r-generator 0.1.0 Allows users to quickly and easily generate fake data containing Personally noarch
Identifiable Information (PII) through convenience functions. / MIT


Name Version
r-generics 0.0.2 In order to reduce potential package dependencies and conflicts, generics pro- linux-
vides a number of commonly used S3 generics. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
64
r- 2014.02.17
A tool for finding an ensemble gene-signature by a steepest ascending algo- noarch
genesignaturefinder rithm partially supervised by survival time data. / GPL-2
r-genesysr 0.9.2 Access data on plant genetic resources from genebanks around the world noarch
published on Genesys (<https://www.genesys-pgr.org>). Your use of data is
subject to terms and conditions available at <https://www.genesys-pgr.org/
content/legal/terms>. / Apache License 2.0
r-genetics 1.3.8.1.2
Classes and methods for handling genetic data. Includes classes to rep- noarch
resent genotypes and haplotypes at single markers up to multiple mark-
ers on multiple chromosomes. Function include allele frequencies, flagging
homo/heterozygotes, flagging carriers of certain alleles, estimating and testing
for Hardy-Weinberg disequilibrium, estimating and testing for linkage dise-
quilibrium, . . . / GPL-3
r- 0.8 Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of noarch
geneticsubsetter Transformed Kinships (MTK), measures that can indicate a subset would be
beneficial for rare-trait discovery and genome-wide association scanning, re-
spectively. / GPL-2
r-genie 1.0.4 A new hierarchical clustering linkage criterion: the Genie algorithm links two linux-
clusters in such a way that a chosen economic inequity measure (e.g., the 64,
Gini index) of the cluster sizes does not increase drastically above a given osx-
threshold. Benchmarks indicate a high practical usefulness of the introduced 64,
method: it most often outperforms the Ward or average linkage in terms of the win-
clustering quality while retaining the single linkage speed, see (Gagolewski 64
et al. 2016a <DOI:10.1016/j.ins.2016.05.003>, 2016b <DOI:10.1007/978-3-
319-45656-0_16>) for more details. / GPL-3
r-genkern 1.2_60Computes generalised KDEs / GPL-2 linux-
64,
osx-
64,
win-
64
r-genlasso 1.4 Provides fast algorithms for computing the solution path for generalized lasso linux-
problems. Important use cases are the fused lasso over an arbitrary graph, and 64,
trend fitting of any given polynomial order. Specialized implementations for osx-
the latter two problems are given to improve stability and speed. / GPL (>= 64,
2.0) win-
64


Name Version
r-genmeta 0.1 Generalized meta-analysis is a technique for estimating parameters associated noarch
with a multiple regression model through meta-analysis of studies which may
have information only on partial sets of the regressors. It estimates the effects
of each variable while fully adjusting for all other variables that are measured
in at least one of the studies. Using algebraic relationships between regres-
sion parameters in different dimensions, a set of moment equations is spec-
ified for estimating the parameters of a maximal model through information
available on sets of parameter estimates from a series of reduced models avail-
able from the different studies. The specification of the equations requires
a reference dataset to estimate the joint distribution of the covariates. These
equations are solved using the generalized method of moments approach, with
the optimal weighting of the equations taking into account uncertainty asso-
ciated with estimates of the parameters of the reduced models. The proposed
framework is implemented using iterated reweighted least squares algorithm
for fitting generalized linear regression models. For more details about the
method, please see pre-print version of the manuscript on generalized meta-
analysis by Prosenjit Kundu, Runlong Tang and Nilanjan Chatterjee (2018)
<arXiv:1708.03818>. / GPL-3
r-genodds 1.0.0 Calculates Agresti’s (1980) <https://www.jstor.org/stable/2530495> general- linux-
ized odds ratios. For a randomly selected pair of observations from two groups, 64,
calculates the odds that the second group will have a higher scoring outcome osx-
than that of the first group. Package provides hypothesis testing for if this odds 64,
ratio is significantly different to 1 (equal chance). / GPL-2 win-
64
r- 1.0_1 Local structure in genomic data often induces dependence between observa- noarch
genomic.autocorr tions taken at different genomic locations. Ignoring this dependence leads to
underestimation of the standard error of parameter estimates. This package
uses block bootstrapping to estimate asymptotically correct standard errors of
parameters from any standard generalised linear model that may be fit by the
glm() function. / GPL-2
r-genomicper 1.6 Circular genomic permutation approach uses GWAS results to establish the noarch
significance of pathway/gene-set associations whilst accounting for genomic
structure. All SNPs in the GWAS are placed in a ‘circular genome’ according
to their location. Then the complete set of SNP association p-values are per-
muted by rotation with respect to the SNPs’ genomic locations. Two testing
frameworks are available: permutations at the gene level, and permutations at
the SNP level. The permutation at the gene level uses fisher’s combination
test to calculate a single gene p-value, followed by the hypergeometric test.
The SNP count methodology maps each SNP to pathways/gene-sets and cal-
culates the proportion of SNPs for the real and the permutated datasets above
a pre-defined threshold. Genomicper requires a matrix of GWAS association
p-values. The SNPs annotation and pathways annotations can be performed
within the package or provided by the user. / GPL-2
r-genoplotr 0.8.9 Draws gene or genome maps and comparisons between these, in a publication- noarch
grade manner. Starting from simple, common files, it will draw postscript or
PDF files that can be sent as such to journals. / GPL-2
r-genord 1.4.0 A gaussian copula based procedure for generating samples from discrete ran- noarch
dom variables with prescribed correlation matrix and marginal distributions. /
GPL-3


Name Version
r-gensa 1.1.7 Performs search for global minimum of a very complex non-linear objective linux-
function with a very large number of optima. / GPL-2 64,
osx-
64,
win-
64
r-gensemble 1.0.1 Generalized ensemble methods allowing arbitrary underlying models to be noarch
used. Currently only bagging is supported. / GPL-2
r-gensurv 1.0.3 Generation of survival data with one (binary) time-dependent covariate. Gen- linux-
eration of survival data arising from a progressive illness-death model. / GPL-2 64,
osx-
64,
win-
64
r-gensvm 0.1.1 The GenSVM classifier is a generalized multiclass support vector machine linux-
(SVM). This classifier aims to find decision boundaries that separate the 64,
classes with as wide a margin as possible. In GenSVM, the loss function is win-
very flexible in the way that misclassifications are penalized. This allows the 64
user to tune the classifier to the dataset at hand and potentially obtain higher
classification accuracy than alternative multiclass SVMs. Moreover, this flex-
ibility means that GenSVM has a number of other multiclass SVMs as special
cases. One of the other advantages of GenSVM is that it is trained in the primal
space, allowing the use of warm starts during optimization. This means that
for common tasks such as cross validation or repeated model fitting, GenSVM
can be trained very quickly. Based on: G.J.J. van den Burg and P.J.F. Groenen
(2018) <http://www.jmlr.org/papers/v17/14-526.html>. / GPL-2
r-gentag 1.0 Implement a coherent and flexible protocol for animal color tagging. ‘GenTag’ noarch
provides a simple computational routine with low CPU usage to create color
sequences for animal tag. First, a single-color tag sequence is created from
an algorithm selected by the user, followed by verification of the combina-
tion uniqueness. Three methods to produce color tag sequences are provided.
Users can modify the main function core to allow a wide range of applications.
/ GPL-2
r-genwin 0.1 Defines window or bin boundaries for the analysis of genomic data. Bound- noarch
aries are based on the inflection points of a cubic smoothing spline fitted to
the raw data. Along with defining boundaries, a technique to evaluate results
obtained from unequally-sized windows is provided. Applications are partic-
ularly pertinent for, though not limited to, genome scans for selection based
on variability between populations (e.g. using Wright’s fixations index, Fst,
which measures variability in subpopulations relative to the total population).
/ MIT
r-geoboxplot 1.0 Make geographic box plot as detailed in Willmott et al. (2007). / GPL-2 noarch
r-geocount 1.150120
This package provides a variety of functions to analyze and model geostatis- linux-
tical count data with generalized linear spatial models, including 1) simulate 64,
and visualize the data; 2) posterior sampling with robust MCMC algorithms (in osx-
serial or parallel way); 3) perform prediction for unsampled locations; 4) con- 64,
duct Bayesian model checking procedure to evaluate the goodness of fitting; 5) win-
conduct transformed residual checking procedure. In the package, seamlessly 64
embedded C programs and parallel computing techniques are implemented to
speed up the computing processes. / GPL-2


Name Version
r-geode 1.0 Given expression data this package calculate a multivariate geometrical char- noarch
acterization of the differential expression and can also perform gene-set en-
richment. / GPL-2
r-geodist 0.0.3 Dependency-free, ultra fast calculation of geodesic distances. Includes linux-
the reference nanometre-accuracy geodesic distances of Karney (2013) 64,
<doi:10.1007/s00190-012-0578-z>, as used by the ‘sf’ package, as well as osx-
Haversine and Vincenty distances. Default distance measure is the Mapbox 64,
cheap ruler which is generally more accurate than Haversine or Vincenty for win-
distances out to a few hundred kilometres, and is considerably faster. The main 64
function accepts one or two inputs in almost any generic rectangular form, and
returns either matrices of pairwise distances, or vectors of sequential distances.
/ MIT
r-geohashtools 0.2.4 Tools for working with Gustavo Niemeyer’s geohash coordinate system, linux-
ported to R from Hiroaki Kawai’s ‘Python’ implementation and embellished 64,
to sit naturally in the R ecosystem. / MIT osx-
64,
win-
64
r-geojsonr 1.0.7 Includes functions for processing GeoJson objects <https://en.wikipedia.org/ linux-
wiki/GeoJSON> relying on ‘RFC 7946’ <https://tools.ietf.org/pdf/rfc7946. 64,
pdf>. The geojson encoding is based on ‘json11’, a tiny JSON library for osx-
‘C11’ <https://github.com/dropbox/json11>. Furthermore, the source code is 64,
exported in R through the ‘Rcpp’ and ‘RcppArmadillo’ packages. / MIT win-
64
r-geomapdata 1.0_4 Set of data for use in package GEOmap. Includes world map, USA map, Coso noarch
map, Japan Map, ETOPO5 / GPL-3
r-geomedb 2.0.0 The Genomic Observatory Metadatabase (GeOMe Database) is an open access noarch
repository for geographic and ecological metadata associated with sequenced
samples. This package is used to retrieve GeOMe data for analysis. See <http:
//www.geome-db.org> for more information regarding GeOMe. / GPL-3
r-geometa 0.5_0 Provides facilities to handle reading and writing of geographic metadata de- noarch
fined with OGC/ISO 19115, 11119 and 19110 geographic information meta-
data standards, and encoded using the ISO 19139 (XML) standard. It includes
also a facility to check the validity of ISO 19139 XML encoded metadata. /
MIT
r-geometry 0.4.1 Makes the qhull library (www.qhull.org) available in R, in a similar manner linux-
as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangu- 32,
lations, halfspace intersections about a point, Voronoi diagrams, furthest-site linux-
Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 64,
3-d, 4-d, and higher dimensions. It implements the Quickhull algorithm for osx-
computing the convex hull. Qhull does not support constrained Delaunay tri- 64,
angulations, or mesh generation of non-convex objects, but the package does win-
include some R functions that allow for this. Currently the package only gives 32,
access to Delaunay triangulation and convex hull computation. / GPL (>= 3) win-
64
r-geonames 0.999 The web service at <https://www.geonames.org/> provides a number of spatial noarch
data queries, including administrative area hierarchies, city locations and some
country postal code queries. A (free) username is required and rate limits exist.
/ GPL-3


Name Version
r-geoops 0.2.0 Tools for doing calculations and manipulations on ‘GeoJSON’, a ‘geospatial’ linux-
data interchange format (<https://tools.ietf.org/html/rfc7946>). ‘GeoJSON’ is 64,
also valid ‘JSON’. / MIT osx-
64,
win-
64
r-geosapi 0.4_0 Provides an R interface to the GeoServer REST API, allowing to up- noarch
load and publish data in a GeoServer web-application and expose data
to OGC Web-Services. The package currently supports all CRUD (Cre-
ate,Read,Update,Delete) operations on GeoServer workspaces, namespaces,
datastores (stores of vector data), featuretypes, layers, styles, as well as vector
data upload operations. For more information about the GeoServer REST API,
see <http://docs.geoserver.org/stable/en/user/rest/>. / MIT
r-geoscale 2.0 Function for adding the geological timescale to bivariate plots. / GPL-2 noarch
r-geosed 0.1.1 Find the smallest circle that contains all longitude and latitude input points. noarch
From the generated center and radius, variable side polygons can be created,
navigation based on bearing and distance can be applied, and more. Based on
a modified version of Welzl’s algorithm for smallest circle. Distance calcula-
tions are based on the haversine formula. Calculations for distance, midpoint,
bearing and more are derived from <https://www.movable-type.co.uk>. / MIT
r-geosphere 1.5_10Spherical trigonometry for geographic applications. That is, compute dis- linux-
tances and related measures for angular (longitude/latitude) locations. / GPL-3 64,
osx-
64,
win-
64
r-geostatsp 1.7.8 Geostatistical modelling facilities using Raster and SpatialPoints objects are linux-
provided. Non-Gaussian models are fit using INLA, and Gaussian geosta- 64,
tistical models use Maximum Likelihood Estimation. For details see Brown osx-
(2015) <doi:10.18637/jss.v063.i12>. / GPL-3 64,
win-
64
r-geotech 1.0 A compilation of functions for performing calculations and creating plots that noarch
commonly arise in geotechnical engineering and soil mechanics. The types
of calculations that are currently included are: (1) phase diagrams and index
parameters, (2) grain-size distributions, (3) plasticity, (4) soil classification,
(5) compaction, (6) groundwater, (7) subsurface stresses (geostatic and in-
duced), (8) Mohr circle analyses, (9) consolidation settlement and rate, (10)
shear strength, (11) bearing capacity, (12) lateral earth pressures, (13) slope
stability, and (14) subsurface explorations. Geotechnical engineering students,
educators, researchers, and practitioners will find this package useful. / GPL-3
r-geotools 0.1 Tools / GPL-3 noarch
r-geozoo 0.5.1 Geometric objects defined in ‘geozoo’ can be simulated or displayed in the R noarch
package ‘tourr’. / GPL-2
r-gepaf 0.1.1 Encode and decode the Google Encoded Polyline Algorithm Format (<https: noarch
//developers.google.com/maps/documentation/utilities/polylinealgorithm>). /
GPL-3
r-gesca 1.0.4 Fit a variety of component-based structural equation models. / GPL-2 noarch


Name Version
r-gestalt 0.1.8 Provides a suite of function-building tools centered around a (forward) compo- noarch
sition operator, %>>>%, which extends the semantics of the ‘magrittr’ %>%
operator and supports ‘tidyverse’ quasiquotation. It enables you to construct
composite functions that can be inspected and transformed as list-like objects.
In conjunction with %>>>%, a compact function constructor, fn(), and a func-
tion that performs partial application, partial(), are also provided. Both support
quasiquotation. / MIT
r-gethr 0.1.0 Full access to the Geth command line interface for running full Ethereum noarch
nodes. With gethr it is possible to carry out different tasks such as mine ether,
transfer funds, create contacts, explore block history, etc. The package also
provides access to all the available APIs. The officially exposed by Ethereum
blockchains (eth, shh, web3, net) and some provided directly by Geth (admin,
debug, miner, personal, txpool). For more details on Ethereum, access the
project website <https://www.ethereum.org/>. For more details on the Geth
client, access the project website <https://github.com/ethereum/go-ethereum/
wiki/geth/>. / MIT
r-getopt 1.20.3Package designed to be used with Rscript to write ‘‘#!” shebang scripts that linux-
accept short and long flags/options. Many users will prefer using instead the 32,
packages optparse or argparse which add extra features like automatically gen- linux-
erated help option and usage, support for default values, positional argument 64,
support, etc. / GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64
r-getpass 0.2_2 A micro-package for reading passwords, i.e. reading user input with masking, linux-
so that the input is not displayed as it is typed. Currently we have support 64,
for ‘RStudio’, the command line (every OS), and any platform where ‘tcltk’ is osx-
present. / BSD_2_clause 64,
win-
64
r-gets 0.19 Automated General-to-Specific (GETS) modelling of the mean and variance noarch
of a regression, and indicator saturation methods for detecting and testing for
structural breaks in the mean. / GPL-2
r-gettz 0.0.3 A function to retrieve the system timezone on Unix systems which has been linux-
found to find an answer when ‘Sys.timezone()’ has failed. It is based on an an- 64,
swer by Duane McCully posted on ‘StackOverflow’, and adapted to be callable osx-
from R. The package also builds on Windows, but just returns NULL. / GPL-2 64,
win-
64
r-gevcdn 1.1.6 Implements a flexible nonlinear modelling framework for nonstationary gen- noarch
eralized extreme value analysis in hydroclimatology following Cannon (2010)
<doi:10.1002/hyp.7506>. / GPL-2
r-gexp 1.0_0 Generates experiments - simulating structured or experimental data as: com- noarch
pletely randomized design, randomized block design, latin square design, fac-
torial and split-plot experiments (Ferreira, 2008, ISBN:8587692526; Naes et
al., 2007 <doi:10.1002/qre.841>; Rencher et al., 2007, ISBN:9780471754985;
Montgomery, 2001, ISBN:0471316490). / GPL-2


Name Version
r-gfa 1.0.3 Factor analysis implementation for multiple data sources, i.e., for groups noarch
of variables. The whole data analysis pipeline is provided, including func-
tions and recommendations for data normalization and model definition, as
well as missing value prediction and model visualization. The model group
factor analysis (GFA) is inferred with Gibbs sampling, and it has been
presented originally by Virtanen et al. (2012), and extended in Klami et
al. (2015) <DOI:10.1109/TNNLS.2014.2376974> and Bunte et al. (2016)
<DOI:10.1093/bioinformatics/btw207>; for details, see the citation info. /
MIT
r-gforce 0.1.4 A complete suite of computationally efficient methods for high dimensional linux-
clustering and inference problems in G-Latent Models (a type of Latent Vari- 64,
able Gaussian graphical model). The main feature is the FORCE (First-Order, win-
Certifiable, Efficient) clustering algorithm which is a fast solver for a semi- 64
definite programming (SDP) relaxation of the K-means problem. For certain
types of graphical models (G-Latent Models), with high probability the al-
gorithm not only finds the optimal clustering, but produces a certificate of
having done so. This certificate, however, is model independent and so can
also be used to certify data clustering problems. The ‘GFORCE’ package
also contains implementations of inferential procedures for G-Latent graphi-
cal models using n-fold cross validation. Also included are native code im-
plementations of other popular clustering methods such as Lloyd’s algorithm
with kmeans initialization and complete linkage hierarchical clustering. The
FORCE method is due to Eisenach and Liu (2019) <arxiv:1806.00530>. /
GPL-2
r-gglasso 1.4 A unified algorithm, blockwise-majorization-descent (BMD), for efficiently linux-
computing the solution paths of the group-lasso penalized least squares, lo- 64,
gistic regression, Huberized SVM and squared SVM. The package is an im- osx-
plementation of Yang, Y. and Zou, H. (2015) DOI: <doi:10.1007/s11222-014- 64,
9498-5>. / GPL-2 win-
64
r-ggm 2.3 Functions and datasets for maximum likelihood fitting of some classes of noarch
graphical Markov models. / GPL-2
r-ggmridge 1.1 Estimation of partial correlation matrix using ridge penalty followed by thresh- noarch
olding and reestimation. Under multivariate Gaussian assumption, the matrix
constitutes an Gaussian graphical model (GGM). / GPL-2
r-ggmselect 0.1_12.2
Graph estimation in Gaussian Graphical Models. The main functions return linux-
the adjacency matrix of an undirected graph estimated from a data matrix. / 64,
GPL-3 osx-
64,
win-
64


Name Version
r-ggplot2 3.1.1 A system for ‘declaratively’ creating graphics, based on The Grammar of linux-
Graphics. You provide the data, tell ‘ggplot2’ how to map variables to aes- 32,
thetics, what graphical primitives to use, and it takes care of the details. / linux-
GPL-2 | file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-ggplot2movies 0.0.1 A dataset about movies. This was previously contained in ggplot2, but has noarch
been moved its own package to reduce the download size of ggplot2. / GPL-3
r-ggroups 1.2.1 Calculates additive and dominance genetic relationship matrices and their in- noarch
verses, in matrix and tabular-sparse formats. It includes functions for checking
and processing pedigree, as well as functions to calculate the matrix of genetic
group contributions (Q), and adding those contributions to the genetic merit of
animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>). Calcula-
tion of Q is computationally extensive. There are computationally optimized
functions to calculate Q. / GPL-3
r-ggversa 0.0.1 A collection of datasets for the upcoming book Graficas versatiles con ggplot: noarch
Analisis visuales de datos, by Raymond L. Tremblay and Julian Hernandez-
Serano. / GPL-2
r-ggvis 0.4.4 An implementation of an interactive grammar of graphics, taking the best parts linux-
of ‘ggplot2’, combining them with the reactive framework of ‘shiny’ and draw- 32,
ing web graphics using ‘vega’. / GPL-2 | file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-gh 1.0.1 Minimal client to access the ‘GitHub’ ‘API’. / MIT file LICENSE noarch
r-ghibli 0.3.0 Colour palettes inspired by Studio Ghibli <https://en.wikipedia.org/wiki/ noarch
Studio_Ghibli> films, ported to R for your enjoyment. / MIT
r-ghs 0.1 Draw posterior samples to estimate the precision matrix for multivariate Gaus- noarch
sian data. Posterior means of the samples is the graphical horseshoe es-
timate by Li, Bhadra and Craig(2017) <arXiv:1707.06661>. The function
uses matrix decomposition and variable change from the Bayesian graphical
lasso by Wang(2012) <doi:10.1214/12-BA729>, and the variable augmenta-
tion for sampling under the horseshoe prior by Makalic and Schmidt(2016)
<arXiv:1508.03884>. Structure of the graphical horseshoe function was in-
spired by the Bayesian graphical lasso function using blocked sampling, au-
thored by Wang(2012) <doi:10.1214/12-BA729>. / GPL-2


Name Version
r-ghyp 1.5.7 Detailed functionality for working with the univariate and multivariate Gen- linux-
eralized Hyperbolic distribution and its special cases (Hyperbolic (hyp), Nor- 64,
mal Inverse Gaussian (NIG), Variance Gamma (VG), skewed Student-t and osx-
Gaussian distribution). Especially, it contains fitting procedures, an AIC-based 64,
model selection routine, and functions for the computation of density, quantile, win-
probability, random variates, expected shortfall and some portfolio optimiza- 64
tion and plotting routines as well as the likelihood ratio test. In addition, it
contains the Generalized Inverse Gaussian distribution. / GPL-2
r-gibbs.met 1.1_3 This package provides two generic functions for performing Markov chain noarch
sampling in a naive way for a user-defined target distribution, which involves
only continuous variables. The function gibbs_met performs Gibbs sampling
with each 1-dimensional distribution sampled with Metropolis update using
Gaussian proposal distribution centered at the previous state. The function
met_gaussian updates the whole state with Metropolis method using inde-
pendent Gaussian proposal distribution centered at the previous state. The
sampling is carried out without considering any special tricks for improving
efficiency. This package is aimed at only routine applications of MCMC in
moderate-dimensional problems. / GPL-2
r-gibbsacov 1.1 Gibbs sampler for one-way linear mixed-effects models (ANOVA, ANCOVA) noarch
with homoscedasticity of errors and uniform priors. / GPL-2
r-gifi 0.3_9 Implements categorical principal component analysis (‘PRINCALS’), mul- linux-
tiple correspondence analysis (‘HOMALS’), monotone regression analysis 64,
(‘MORALS’). It replaces the ‘homals’ package. / GPL-3 osx-
64,
win-
64
r-gifski 0.8.6 Multi-threaded GIF encoder written in Rust: <https://gif.ski/>. Converts im- osx-
ages to GIF animations using pngquant’s efficient cross-frame palettes and 64,
temporal dithering with thousands of colors per frame. / MIT win-
64
r-gifti 0.7.5 Functions to read in the geometry format under the ‘Neuroimaging’ ‘Informat- noarch
ics’ Technology Initiative (‘NIfTI’), called ‘GIFTI’ <https://www.nitrc.org/
projects/gifti/>. These files contain surfaces of brain imaging data. / GPL-
2
r-gigrvg 0.5 Generator and density function for the Generalized Inverse Gaussian (GIG) linux-
distribution. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-gillespiessa 0.6.1 Provides a simple to use, intuitive, and extensible interface to several stochastic noarch
simulation algorithms for generating simulated trajectories of finite population
continuous-time model. Currently it implements Gillespie’s exact stochas-
tic simulation algorithm (Direct method) and several approximate methods
(Explicit tau-leap, Binomial tau-leap, and Optimized tau-leap). The package
also contains a library of template models that can be run as demo models
and can easily be customized and extended. Currently the following mod-
els are included, ‘Decaying-Dimerization’ reaction set, linear chain system,
logistic growth model, ‘Lotka’ predator-prey model, Rosenzweig-MacArthur
predator-prey model, ‘Kermack-McKendrick’ SIR model, and a ‘metapopula-
tion’ SIRS model. Pineda-Krch et al. (2008) <doi:10.18637/jss.v025.i12>. /
GPL-3
r-gim 0.11.0Implements the generalized integration model, which integrates individual- noarch
level data and summary statistics under a generalized linear model framework.
It supports continuous and binary outcomes to be modeled by the linear and
logistic regression models. / MIT
r-giniwegneg 1.0.1 Gini-based coefficients and plot of the ordinary and generalized curve of max- noarch
imum inequality in the presence of weighted and negative attributes. / GPL-3
r-gipfrm 3.1 Maximum likelihood estimation under relational models, with or without the noarch
overall effect. / GPL-2
r-giraf 1.0 Allows calculation on, and sampling from Gibbs Random Fields, and more linux-
precisely general homogeneous Potts model. The primary tool is the exact 64,
computation of the intractable normalising constant for small rectangular lat- osx-
tices. Beside the latter function, it contains method that give exact sample 64,
from the likelihood for small enough rectangular lattices or approximate sam- win-
ple from the likelihood using MCMC samplers for large lattices. / GPL-2 64
r-gistr 0.4.2 Work with ‘GitHub’ ‘gists’ from ‘R’ (e.g., <http://en.wikipedia.org/wiki/ linux-
GitHub#Gist>, <https://help.github.com/articles/about-gists/>). A ‘gist’ is 32,
simply one or more files with code/text/images/etc. This package allows the linux-
user to create new ‘gists’, update ‘gists’ with new files, rename files, delete 64,
files, get and delete ‘gists’, star and ‘un-star’ ‘gists’, fork ‘gists’, open a ‘gist’ noarch,
in your default browser, get embed code for a ‘gist’, list ‘gist’ ‘commits’, and osx-
get rate limit information when ‘authenticated’. Some requests require authen- 64,
tication and some do not. ‘Gists’ website: <https://gist.github.com/>. / MIT win-
file LICENSE 32,
win-
64
r-git2r 0.25.2Interface to the ‘libgit2’ library, which is a pure C implementation of the ‘Git’ linux-
core methods. Provides access to ‘Git’ repositories to extract data and running 32,
some basic ‘Git’ commands. / GPL-2 linux-
64,
osx-
64,
win-
32,
win-
64
r-git2rdata 0.1 Make versioning of data.frame easy and efficient using git repositories. / GPL- noarch
3


Name Version
r-gitlink 0.1.3 Provides helpers to add ‘Git’ links to ‘shiny’ applications, ‘rmarkdown’ doc- noarch
uments, and other ‘HTML’ based resources. This is most commonly used for
‘GitHub’ ribbons. / MIT
r-gk2011 0.1.3 Implementations of the treatment effect estimators for hybrid (self-selection) noarch
experiments, as developed by Brian J. Gaines and James H. Kuklinski, (2011),
Experimental Estimation of Heterogeneous Treatment Effects Related to Self-
Selection, American Journal of Political Science 55(3): 724-736. / GPL-2
r-glaciersmbm 0.1 A fully distributed glacier surface mass balance model developed for the simu- noarch
lation of accumulation and ablation processes on debris-free as well as debris-
covered glaciers. / GPL-3
r-glamlasso 3.0 Functions capable of performing efficient design matrix free penalized estima- linux-
tion in large scale 2 and 3-dimensional generalized linear array model frame- 64,
work. The generic glamlasso() function solves the penalized maximum like- osx-
lihood estimation (PMLE) problem in a pure generalized linear array model 64,
(GLAM) as well as in a GLAM containing a non-tensor component. Currently win-
Lasso or Smoothly Clipped Absolute Deviation (SCAD) penalized estimation 64
is possible for the followings models: The Gaussian model with identity link,
the Binomial model with logit link, the Poisson model with log link and the
Gamma model with log link. Furthermore this package also contains two func-
tions that can be used to fit special cases of GLAMs, see glamlassoRR() and
glamlassoS(). The procedure underlying these functions is based on the gdpg
algorithm from Lund et al. (2017) <doi:10.1080/10618600.2017.1279548>. /
GPL-3
r-glarma 1.6_0 Functions are provided for estimation, testing, diagnostic checking and fore- noarch
casting of generalized linear autoregressive moving average (GLARMA) mod-
els for discrete valued time series with regression variables. These are a class
of observation driven non-linear non-Gaussian state space models. The state
vector consists of a linear regression component plus an observation driven
component consisting of an autoregressive-moving average (ARMA) filter of
past predictive residuals. Currently three distributions (Poisson, negative bi-
nomial and binomial) can be used for the response series. Three options (Pear-
son, score-type and unscaled) for the residuals in the observation driven com-
ponent are available. Estimation is via maximum likelihood (conditional on
initializing values for the ARMA process) optimized using Fisher scoring or
Newton Raphson iterative methods. Likelihood ratio and Wald tests for the ob-
servation driven component allow testing for serial dependence in generalized
linear model settings. Graphical diagnostics including model fits, autocorrela-
tion functions and probability integral transform residuals are included in the
package. Several standard data sets are included in the package. / GPL-2
r-glassdoor 0.8.1 Interacts with the ‘Glassdoor’ API <https://www.glassdoor.com/developer/ noarch
index.htm>. Allows the user to search job statistics, employer statistics, and
job progression, where ‘Glassdoor’ provides a breakdown of other jobs a per-
son did after their current one. / GPL-2
r-glasso 1.10 Estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. linux-
Facilities are provided for estimates along a path of values for the regulariza-
64,
tion parameter. / GPL-2 osx-
64,
win-
64


Name Version
r-glassofast 1.0 A fast and improved implementation of the graphical LASSO. / GPL-3 linux-
64,
osx-
64,
win-
64
r-glba 0.2 Analyses response times and accuracies from psychological experiments with noarch
the linear ballistic accumulator (LBA) model from Brown and Heathcote
(2008). The LBA model is optionally fitted with explanatory variables on the
parameters such as the drift rate, the boundary and the starting point param-
eters. A log-link function on the linear predictors can be used to ensure that
parameters remain positive when needed. / GPL-3
r-glcm 1.6.4 Enables calculation of image textures (Haralick 1973) linux-
<doi:10.1109/TSMC.1973.4309314> from grey-level co-occurrence ma- 64,
trices (GLCMs). Supports processing images that cannot fit in memory. / osx-
GPL-3 64,
win-
64
r-gldex 2.0.0.6The fitting algorithms considered in this package have two major objectives. linux-
One is to provide a smoothing device to fit distributions to data using the 64,
weight and unweighted discretised approach based on the bin width of the osx-
histogram. The other is to provide a definitive fit to the data set using the 64,
maximum likelihood and quantile matching estimation. Other methods such win-
as moment matching, starship method, L moment matching are also provided. 64
Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and
comparing mean, variance, skewness and kurtosis of the data with the fitted
distribution. / GPL-3
r-gldrm 1.5 Fits a generalized linear density ratio model (GLDRM). A GLDRM is a noarch
semiparametric generalized linear model. In contrast to a GLM, which
assumes a particular exponential family distribution, the GLDRM uses a
semiparametric likelihood to estimate the reference distribution. The ref-
erence distribution may be any discrete, continuous, or mixed exponen-
tial family distribution. The model parameters, which include both the
regression coefficients and the cdf of the unspecified reference distribu-
tion, are estimated by maximizing a semiparametric likelihood. Regres-
sion coefficients are estimated with no loss of efficiency, i.e. the asymp-
totic variance is the same as if the true exponential family distribution were
known. Huang (2014) <doi:10.1080/01621459.2013.824892>. Huang and
Rathouz (2012) <doi:10.1093/biomet/asr075>. Rathouz and Gao (2008)
<doi:10.1093/biostatistics/kxn030>. / MIT
r-glide 1.0.2 Functions evaluate global and individual tests for direct effects in Mendelianlinux-
randomization studies. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-glinternet 1.0.10Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that linux-
satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, 64,
then its two associated main effects also have nonzero estimated coefficients. osx-
Accommodates categorical variables (factors) with arbitrary numbers of lev- 64,
els, continuous variables, and combinations thereof. Implements the machin- win-
ery described in the paper Learning interactions via hierarchical group-lasso 64
regularization (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie
(2015) <DOI:10.1080/10618600.2014.938812>. / GPL-2
r-gllm 0.37 Routines for log-linear models of incomplete contingency tables, including linux-
some latent class models, via EM and Fisher scoring approaches. Allows boot- 64,
strapping. See Espeland and Hui (1987) <doi:10.2307/2531553> for general osx-
approach. / GPL-2 | GPL-3 64,
win-
64
r-glm.deploy 1.0.4 Provides two functions that generate source code implementing the predict linux-
function of fitted glm objects. In this version, code can be generated for ei- 64,
ther ‘C’ or ‘Java’. The idea is to provide a tool for the easy and fast deploy- osx-
ment of glm predictive models into production. The source code generated by 64,
this package implements two function/methods. One of such functions imple- win-
ments the equivalent to predict(type=response), while the second implements 64
predict(type=link). Source code is written to disk as a .c or .java file in the
specified path. In the case of c, an .h file is also generated. / GPL-3
r-glm.predict 3.1_0 Functions to calculate predicted values and the difference between the two noarch
cases with confidence interval for lm() [linear model], glm() [general linear
model], glm.nb() [negative binomial model], polr() [ordinal logistic model]
and multinom() [multinomial model] using Monte Carlo simulations. Refer-
ence: Bennet A. Zelner (2009) <doi:10.1002/smj.783>. / GPL-2
r-glm2 1.2.1 Fits generalized linear models using the same model specification as glm in the noarch
stats package, but with a modified default fitting method that provides greater
stability for models that may fail to converge using glm. / GPL-2
r-glmaspu 1.0 Several tests for high dimensional generalized linear models have been pro- linux-
posed recently. In this package, we implemented a new test called adaptive 64,
sum of powered score (aSPU) for high dimensional generalized linear mod- osx-
els, which is often more powerful than the existing methods in a wide sce- 64,
narios. We also implemented permutation based version of several existing win-
methods for research purpose. We recommend users use the aSPU test for 64
their real testing problem. You can learn more about the tests implemented
in the package via the following papers: 1. Pan, W., Kim, J., Zhang, Y.,
Shen, X. and Wei, P. (2014) <DOI:10.1534/genetics.114.165035> A power-
ful and adaptive association test for rare variants, Genetics, 197(4). 2. Guo,
B., and Chen, S. X. (2016) <DOI:10.1111/rssb.12152>. Tests for high di-
mensional generalized linear models. Journal of the Royal Statistical Society:
Series B. 3. Goeman, J. J., Van Houwelingen, H. C., and Finos, L. (2011)
<DOI:10.1093/biomet/asr016>. Testing against a high-dimensional alternative
in the generalized linear model: asymptotic type I error control. Biometrika,
98(2). / GPL-2
r-glmbb 0.3 Find all hierarchical models of specified generalized linear model with in- noarch
formation criterion (AIC, BIC, or AICc) within specified cutoff of minimum
value. Alternatively, find all such graphical models. Use branch and bound
algorithm so we do not have to fit all models. / MIT


Name Version
r-glmc 0.3_1 Fits generalized linear models where the parameters are subject to linear con- noarch
straints. The model is specified by giving a symbolic description of the linear
predictor, a description of the error distribution, and a matrix of constraints on
the parameters. / GPL-2
r-glmdm 2.60 This package contains functions to perform generalized linear mixed Dirichlet noarch
models using posterior simulation. / GPL-3
r-glmgraph 1.0.3 We propose to use sparse regression model to achieve variable selection while linux-
accounting for graph-constraints among coefficients. Different linear com- 64,
bination of a sparsity penalty(L1) and a smoothness(MCP) penalty has been osx-
used, which induces both sparsity of the solution and certain smoothness on 64,
the linear coefficients. / GPL-2 win-
64
r-glmlep 0.2 Efficient algorithms for fitting regularization paths for linear or logistic regres- linux-
sion models penalized by LEP. / GPL-2 64,
osx-
64,
win-
64
r-glmmadaptive 0.6_0 Fits generalized linear mixed models for a single grouping factor under max- noarch
imum likelihood approximating the integrals over the random effects with an
adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates
(1995) <doi:10.1080/10618600.1995.10474663>. / GPL-3
r-glmmboot 0.4.0 Performs bootstrap resampling for most models that update() works for. There noarch
are two primary functions: bootstrap_model() performs block resampling if
random effects are present, and case resampling if not; bootstrap_ci() con-
verts output from bootstrap model runs into confidence intervals and p-values.
By default, bootstrap_model() calls bootstrap_ci(). Package motivated by
Humphrey and Swingley (2018) <arXiv:1805.08670>. / AGPL-3
r-glmmlasso 1.5.1 A variable selection approach for generalized linear mixed models by L1- noarch
penalized estimation is provided. / GPL-2
r-glmmml 1.1.0 Binomial and Poisson regression for clustered data, fixed and random effects linux-
with bootstrapping. / GPL-3 64,
osx-
64,
win-
64
r-glmmrr 0.2.0 Generalized Linear Mixed Model (GLMM) for Binary Randomized Response noarch
Data. Includes Cauchit, Compl. Log-Log, Logistic, and Probit link functions
for Bernoulli Distributed RR data. RR Designs: Warner, Forced Response,
Unrelated Question, Kuk, Crosswise, and Triangular. / GPL-2 | GPL-3
r-glmmsr 0.2.3 Conduct inference about generalized linear mixed models, with a choice about linux-
which method to use to approximate the likelihood. In addition to the Laplace 64,
and adaptive Gaussian quadrature approximations, which are borrowed from osx-
‘lme4’, the likelihood may be approximated by the sequential reduction ap- 64,
proximation, or an importance sampling approximation. These methods pro- win-
vide an accurate approximation to the likelihood in some situations where it is 64
not possible to use adaptive Gaussian quadrature. / GPL-2


Name Version
r-glmnet 2.0_16Extremely efficient procedures for fitting the entire lasso or elastic-net regular- linux-
ization path for linear regression, logistic and multinomial regression models, 32,
Poisson regression and the Cox model. Two recent additions are the multiple- linux-
response Gaussian, and the grouped multinomial regression. The algorithm 64,
uses cyclical coordinate descent in a path-wise fashion, as described in the osx-
paper linked to via the URL below. / GPL-2 64,
win-
32,
win-
64
r-glmnetcr 1.0.4 Penalized methods are useful for fitting over-parameterized models. This noarch
package includes functions for restructuring an ordinal response dataset for
fitting continuation ratio models for datasets where the number of covariates
exceeds the sample size or when there is collinearity among the covariates.
The glmnet fitting algorithm is used to fit the continuation ratio model after
data restructuring. / GPL-2
r-glmnetutils 1.1.2 Provides a formula interface for the ‘glmnet’ package for elasticnet regression, noarch
a method for cross-validating the alpha parameter, and other quality-of-life
tools. / GPL-2
r-glmpath 0.98 A path-following algorithm for L1 regularized generalized linear models and linux-
Cox proportional hazards model. / GPL-2 64,
osx-
64,
win-
64
r-glmsdata 1.0.0 Data sets from the book Generalized Linear Models with Examples in R by noarch
Dunn and Smyth. / GPL-2
r-glmtlp 1.1 It provides an extremely efficient procedure for fitting the entire truncated lasso noarch
regularization path for linear regression, logistic and multinomial regression
models, Poisson regression and the Cox model. The algorithm uses the dif-
ference of convex technique. The detail of the algorithm is described in Shen,
Pan and Zhu (2012) <doi:10.1080/01621459.2011.645783>. The package is
inherited from a popular R package ‘glmnet’ and many functions in ‘glmnet’
can be directly used in ‘glmtlp’. You can learn more details by the online
manual (<http://wuchong.org/glmtlp.html>). / GPL-2
r-glmulti 1.0.7.1Automated model selection and model-averaging. Provides a wrapper for glm noarch
and other functions, automatically generating all possible models (under con-
straints set by the user) with the specified response and explanatory variables,
and finding the best models in terms of some Information Criterion (AIC, AICc
or BIC). Can handle very large numbers of candidate models. Features a Ge-
netic Algorithm to find the best models when an exhaustive screening of the
candidates is not feasible. / GPL-2
r-glmx 0.1_1 Extended techniques for generalized linear models (GLMs), especially for bi- noarch
nary responses, including parametric links and heteroskedastic latent variables.
/ GPL-2 | GPL-3
r-globalgsa 1.0 Implementation of three different Gene set analysis (GSA) algorithms for com- noarch
bining the individual pvalues of a set of genetic variats (SNPs) in a gene level
pvalue. The implementation includes the selection of the best inheritance
model for each SNP. / GPL-2
r-globaloptions 0.1.0 It provides more configurations on the option values such as validation and noarch
filtering on the values, making options invisible or private. / MIT


Name Version
r-globals 0.12.4Identifies global (unknown or free) objects in R expressions by code inspection noarch
using various strategies, e.g. conservative or liberal. The objective of this
package is to make it as simple as possible to identify global objects for the
purpose of exporting them in distributed compute environments. / LGPL-2.1
r-globe 1.2_0 Basic functions for plotting 2D and 3D views of a sphere, by default the Earth noarch
with its major coastline, and additional lines and points. / GPL (>= 2.0)
r-glogis 1.0_1 Tools for the generalized logistic distribution (Type I, also known as skew- noarch
logistic distribution), encompassing basic distribution functions (p, q, d, r,
score), maximum likelihood estimation, and structural change methods. /
GPL-2 | GPL-3
r-glrt 2.0 Functions to conduct four generalized logrank tests and a score test under a noarch
proportional hazards model / GPL-2
r-glrth 0.2.0 Likelihood ratio tests for genome-wide association and genome-wide linkage noarch
analysis under heterogeneity. / GPL-3
r-glsme 1.0.4 Performs linear regression with correlated predictors, responses and correlated noarch
measurement errors in predictors and responses, correcting for biased caused
by these. / GPL-2
r-glue 1.3.1 An implementation of interpreted string literals, inspired by Python’s Lit- linux-
eral String Interpolation <https://www.python.org/dev/peps/pep-0498/> and 32,
Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia’s Triple- linux-
Quoted String Literals <https://docs.julialang.org/en/stable/manual/strings/ 64,
#triple-quoted-string-literals>. / MIT file LICENSE osx-
64,
win-
32,
win-
64
r-gmac 3.0 Performs genomic mediation analysis with adaptive confounding adjustment noarch
(GMAC) proposed by Yang et al. (2017) <doi:10.1101/078683>. It imple-
ments large scale mediation analysis and adaptively selects potential con-
founding variables to adjust for each mediation test from a pool of candidate
confounders. The package is tailored for but not limited to genomic media-
tion analysis (e.g., cis-gene mediating trans-gene regulation pattern where an
eQTL, its cis-linking gene transcript, and its trans-gene transcript play the roles
as treatment, mediator and the outcome, respectively), restricting to scenarios
with the presence of cis-association (i.e., treatment-mediator association) and
random eQTL (i.e., treatment). / GPL-3
r-gmapsdistance 3.4 Get distance and travel time between two points from Google Maps. Four noarch
possible modes of transportation (bicycling, walking, driving and public trans-
portation). / GPL-2
r-gmdatabase 0.5.0 A template for a geometallurgical database and a fast and easy interface for noarch
accessing it is provided in this package. / GPL-2 | LGPL-2
r-gmdh 1.6 Group method of data handling (GMDH) - type neural network algorithm noarch
is the heuristic self-organization method for modelling the complex systems.
In this package, GMDH-type neural network algorithms are applied to make
short term forecasting for a univariate time series. / GPL-2


Name Version
r-gmdhreg 0.2.0 Regression using GMDH algorithms from Prof. Alexey G. Ivakhnenko. Group noarch
Method of Data Handling (GMDH), or polynomial neural networks, is a fam-
ily of inductive algorithms that performs gradually complicated polynomial
models and selecting the best solution by an external criterion. In other words,
inductive GMDH algorithms give possibility finding automatically interrela-
tions in data, and selecting an optimal structure of model or network. The
package includes GMDH Combinatorial, GMDH MIA (Multilayered Iterative
Algorithm), GMDH GIA (Generalized Iterative Algorithm) and GMDH Com-
binatorial with Active Neurons. An introduction of GMDH algorithms: Far-
low, S.J. (1981): The GMDH algorithm of Ivakhnenko, The American Statis-
tician, 35(4), pp. 210-215. <doi:10.2307/2683292> Ivakhnenko A.G. (1968):
The Group Method of Data Handling - A Rival of the Method of Stochastic
Approximation, Soviet Automatic Control, 13(3), pp. 43-55. / GPL-3
r-gmediation 0.1.1 Current version of this R package conducts mediation path analysis for multi- noarch
ple mediators in two stages. / GPL-2 | GPL-3
r-gmfd 1.0.1 Some methods for the inference and clustering of univariate and multivari- noarch
ate functional data, using a generalization of Mahalanobis distance, along
with some functions useful for the analysis of functional data. For further
details, see Martino A., Ghiglietti, A., Ieva, F. and Paganoni A. M. (2017)
<arXiv:1708.00386>. / GPL-3
r-gmm 1.6_2 It is a complete suite to estimate models based on moment conditions. noarch
It includes the two step Generalized method of moments (Hansen 1982;
<doi:10.2307/1912775>), the iterated GMM and continuous updated es-
timator (Hansen, Eaton and Yaron 1996; <doi:10.2307/1392442>) and
several methods that belong to the Generalized Empirical Likelihood fam-
ily of estimators (Smith 1997; <doi:10.1111/j.0013-0133.1997.174.x>,
Kitamura 1997; <doi:10.1214/aos/1069362388>, Newey and Smith
2004; <doi:10.1111/j.1468-0262.2004.00482.x>, and Anatolyev 2005
<doi:10.1111/j.1468-0262.2005.00601.x>). / GPL-2
r-gmmboost 1.1.2 Likelihood-based Boosting for Generalized mixed models / GPL-2 noarch
r-gmodels 2.18.1Various R programming tools for model fitting. / GPL-2 noarch
r-gmp 0.5_13.5
Multiple Precision Arithmetic (big integers and rationals, prime number tests, linux-
matrix computation), arithmetic without limitations using the C library GMP 32,
(GNU Multiple Precision Arithmetic). / GPL linux-
64,
osx-
64,
win-
32,
win-
64
r-gmt 2.0_1 Interface between the GMT map-making software and R, enabling the user to noarch
manipulate geographic data within R and call GMT commands to draw and
annotate maps in postscript format. The gmt package is about interactive data
analysis, rapidly visualizing subsets and summaries of geographic data, while
performing statistical analysis in the R console. / GPL-2
r-gnorm 1.0.0 Functions for obtaining generalized normal/exponential power distribution noarch
probabilities, quantiles, densities and random deviates. The generalized nor-
mal/exponential power distribution was introduced by Subbotin (1923) and
rediscovered by Nadarajah (2005). The parametrization given by Nadarajah
(2005) <doi:10.1080/02664760500079464> is used. / GPL-2


Name Version
r-gnumeric 0.7_8 Read data files readable by ‘gnumeric’ into ‘R’. Can read whole sheet or a noarch
range, from several file formats, including the native format of ‘gnumeric’.
Reading is done by using ‘ssconvert’ (a file converter utility included in the
‘gnumeric’ distribution <http://projects.gnome.org/gnumeric/>) to convert the
requested part to CSV. From ‘gnumeric’ files (but not other formats) can list
sheet names and sheet sizes or read all sheets. / GPL-2
r-gofkernel 2.1_1 Tests of goodness-of-fit based on a kernel smoothing of the data. / GPL-3 noarch
r-gogarch 0.7_2 Implementation of the GO-GARCH model class / GPL-2 noarch
r-gomms 1.0 A zero-inflated quasi-Poisson factor model to display similarity between sam- noarch
ples visually in a low (2 or 3) dimensional space. / GPL-2
r- 0.0.2 Association analysis between categorical variables using the Goodman and noarch
goodmankruskal Kruskal tau measure. This asymmetric association measure allows the detec-
tion of asymmetric relations between categorical variables (e.g., one variable
obtained by re-grouping another). / MIT
r-googleformr 0.0.3 GET and POST data to Google Forms; an API to Google Forms, allowing noarch
users to POST data securely to Google Forms without needing authentication
or permissioning. / GPL-2
r- 0.1.0 Allows you to retrieve information from the ‘Google Knowledge Graph’ API noarch
googleknowledgegraphr <https://www.google.com/intl/bn/insidesearch/features/search/knowledge.
html> and process it in R in various forms. The ‘Knowledge Graph Search’
API lets you find entities in the ‘Google Knowledge Graph’. The API
uses standard ‘schema.org’ types and is compliant with the ‘JSON-LD’
specification. / MIT
r-googlevis 0.6.4 R interface to Google’s chart tools, allowing users to create interactive charts noarch
based on data frames. Charts are displayed locally via the R HTTP help server.
A modern browser with an Internet connection is required and for some charts
a Flash player. The data remains local and is not uploaded to Google. / GPL-2
r-goric 1.1_0 Generalized Order-Restricted Information Criterion (GORIC) value for a set noarch
of hypotheses in multivariate linear models and generalised linear models. /
GPL-2
r-govstatjpn 0.1 This package purposes to deal with public survey data of Japanese government noarch
via their Application Programming Interface (http://statdb.nstac.go.jp/) / GPL-
3
r-gower 0.2.0 Compute Gower’s distance (or similarity) coefficient between records. Com- linux-
pute the top-n matches between records. Core algorithms are executed in par- 32,
allel on systems supporting OpenMP. / GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64
r-gparotation 2014.11_1
Gradient Projection Algorithm Rotation for Factor Analysis. See ?GPArota- noarch
tion.Intro for more details. / GPL-2
r-gpca 1.0 This package implements guided principal components analysis for the detec- noarch
tion of batch effects in high-throughput data. / GPL-2


r-gpdtest 0.4 This package computes the bootstrap goodness-of-fit test for the generalized noarch
Pareto distribution by Villasenor-Alva and Gonzalez-Estrada (2009). The null
hypothesis includes heavy and non-heavy tailed gPd’s. A function for fitting
the gPd to data using the parameter estimation methods proposed in the same
article is also provided. / GPL-2
r-gpk 1.0 Collection of datasets as prepared by Profs. A.P. Gore, S.A. Paranjape, and noarch
M.B. Kulkarni of Department of Statistics, Poona University, India. With their
permission, first letter of their names forms the name of this package, the pack-
age has been built by me and made available for the benefit of R users. This
collection requires a rich class of models and can be a very useful building
block for a beginner. / GPL-2
r-gplots 3.0.1.1Various R programming tools for plotting data, including: - calculating linux-
and plotting locally smoothed summary function as (‘bandplot’, ‘wapply’), 32,
- enhanced versions of standard plots (‘barplot2’, ‘boxplot2’, ‘heatmap.2’, linux-
‘smartlegend’), - manipulating colors (‘col2hex’, ‘colorpanel’, ‘redgreen’, 64,
‘greenred’, ‘bluered’, ‘redblue’, ‘rich.colors’), - calculating and plotting two- noarch,
dimensional data summaries (‘ci2d’, ‘hist2d’), - enhanced regression diagnos- osx-
tic plots (‘lmplot2’, ‘residplot’), - formula-enabled interface to ‘stats::lowess’ 64,
function (‘lowess’), - displaying textual data in plots (‘textplot’, ‘sinkplot’), - win-
plotting a matrix where each cell contains a dot whose size reflects the relative 32,
magnitude of the elements (‘balloonplot’), - plotting Venn diagrams (‘venn’), - win-
displaying Open-Office style plots (‘ooplot’), - plotting multiple data on same 64
region, with separate axes (‘overplot’), - plotting means and confidence in-
tervals (‘plotCI’, ‘plotmeans’), - spacing points in an x-y plot so they don’t
overlap (‘space’). / GPL-2
r-gpltr 1.2 Combining a generalized linear model with an additional tree part on the same noarch
scale. A four-step procedure is proposed to fit the model and test the joint
effect of the selected tree part while adjusting on confounding factors. We also
proposed an ensemble procedure based on the bagging to improve prediction
accuracy and computed several scores of importance for variable selection. /
GPL (>= 2.0)
r-gpr 1.1 This package provides a minimalistic functionality necessary to apply Gaus- noarch
sian Process in R. They provide a selection of functionalities of GPML Matlab
library. / GPL-3
r-gprofiler 0.6.8 This package has been deprecated and will not be updated. New noarch
users should use the package ‘gprofiler2’ (<https://CRAN.R-project.org/
package=gprofiler2>) for up-to-date data and improved functionality. Func-
tional enrichment analysis, gene identifier conversion and mapping ho-
mologous genes across related organisms via the ‘g:Profiler’ toolkit
(<https://biit.cs.ut.ee/gprofiler/>). / GPL-2


r-graddescent 3.0 An implementation of various learning algorithms based on Gradient Descent noarch
for dealing with regression tasks. The variants of gradient descent algorithm
are : Mini-Batch Gradient Descent (MBGD), which is an optimization to use
training data partially to reduce the computation load. Stochastic Gradient
Descent (SGD), which is an optimization to use a random data in learning to
reduce the computation load drastically. Stochastic Average Gradient (SAG),
which is a SGD-based algorithm to minimize stochastic step to average. Mo-
mentum Gradient Descent (MGD), which is an optimization to speed-up gra-
dient descent learning. Accelerated Gradient Descent (AGD), which is an
optimization to accelerate gradient descent learning. Adagrad, which is a
gradient-descent-based algorithm that accumulate previous cost to do adap-
tive learning. Adadelta, which is a gradient-descent-based algorithm that use
hessian approximation to do adaptive learning. RMSprop, which is a gradient-
descent-based algorithm that combine Adagrad and Adadelta adaptive learn-
ing ability. Adam, which is a gradient-descent-based algorithm that mean and
variance moment to do adaptive learning. Stochastic Variance Reduce Gradi-
ent (SVRG), which is an optimization SGD-based algorithm to accelerates the
process toward converging by reducing the gradient. Semi Stochastic Gradi-
ent Descent (SSGD),which is a SGD-based algorithm that combine GD and
SGD to accelerates the process toward converging by choosing one of the gra-
dients at a time. Stochastic Recursive Gradient Algorithm (SARAH), which is
an optimization algorithm similarly SVRG to accelerates the process toward
converging by accumulated stochastic information. Stochastic Recursive Gra-
dient Algorithm (SARAHPlus), which is a SARAH practical variant algorithm
to accelerates the process toward converging provides a possibility of earlier
termination. / GPL-2
r-grade 0.2_1 Provides functions for matching student-answers to teacher answers for a va- noarch
riety of data types. / GPL-2
r-grader 1.0.1 After being given the location of your students’ submissions and a test file, the noarch
function runs each .R file, and evaluates the results from all the given tests.
Results are neatly returned in a data frame that has a row for each student, and
a column for each test. / MIT
r- 0.1.0.0Widget for an interactive selection and modification of a color gradient. ‘gra- noarch
gradientpickerd3 dientPickerD3’ allows addition, removement and replacement of color ticks.
List of numeric values will automatically translate in their corresponding tick
position within the numeric range. App returns a data.frame containing tick
values, colors and the positions in percent (0.0 to 1.0) for each color tick in the
gradient. The original JS ‘jquery-gradient-picker’ was implemented by Matt
Crinklaw-Vogt (nick: tantaman) <https://github.com/tantaman/>. Widget and
JS modifications were done by CD. Peikert. / GPL-3
r-gramevol 2.1_3 A native R implementation of grammatical evolution (GE). GE facilitates the noarch
discovery of programs that can achieve a desired goal. This is done by per-
forming an evolutionary optimisation over a population of R expressions gen-
erated via a user-defined context-free grammar (CFG) and cost function. /
GPL-2
r-grangers 0.1.0 Contains five functions performing the calculation of unconditional and con- noarch
ditional Granger-causality spectra, bootstrap inference on both, and inference
on the difference between them via the bootstrap approach of Farne’ and Mon-
tanari, 2018 <arXiv:1803.00374>. / GPL-2


Name Version
r-grape 0.1.1 Gene-Ranking Analysis of Pathway Expression (GRAPE) is a tool for sum- noarch
marizing the consensus behavior of biological pathways in the form of a tem-
plate, and for quantifying the extent to which individual samples deviate from
the template. GRAPE templates are based only on the relative rankings of the
genes within the pathway and can be used for classification of tissue types or
disease subtypes. GRAPE can be used to represent gene-expression samples as
vectors of pathway scores, where each pathway score indicates the departure
from a given collection of reference samples. The resulting pathway- space
representation can be used as the feature set for various applications, includ-
ing survival analysis and drug-response prediction. Users of GRAPE should
use the following citation: Klein MI, Stern DF, and Zhao H. GRAPE: A path-
way template method to characterize tissue-specific functionality from gene
expression profiles. BMC Bioinformatics, 18:317 (June 2017). / GPL-2
r-grapes 1.0.0 Turn arbitrary functions into binary operators. / GPL-3 noarch
r-grapfa 1.0 gRapfa is for modelling discrete longitudinal data using acyclic probabilis- noarch
tic finite automata (APFA). The package contains functions for constructing
APFA models from a given data using penalized likelihood methods. For
graphical display of APFA models, gRapfa depends on ‘igraph package’.
gRapfa also contains an interface function to Beagle software that implements
an efficient model selection algorithm. / GPL-2
r-grapher 1.9_86A multi-platform user interface for drawing highly customizable graphs in R. noarch
It aims to be a valuable help to quickly draw publishable graphs without any
knowledge of R commands. Six kinds of graph are available: histogram, box-
and-whisker plot, bar plot, pie chart, curve and scatter plot. / GPL-2
r-graphfactor 1.1 A Network Implementation of Fuzzy Sets: Build Network Objects from Mul- noarch
tivariate Flat Files. For more information on fuzzy sets, refer to: Zadeh, L.A.
(1964) <DOI:10.1016/S0019-9958(65)90241-X>. / GPL-2
r-graphicsqc 1.0_8 Functions to generate graphics files, compare them with model files, and report noarch
the results, including visual and textual diffs of any differences. / GPL-2
r- 2.0 Optimizing a function F(U), where U is a semi-orthogonal matrix and F is noarch
grassmannoptim invariant under an orthogonal transformation of U / GPL-2
r-graticule 0.1.2 Create graticule lines and labels for maps. Control the creation of lines by noarch
setting their placement (at particular meridians and parallels) and extent (along
parallels and meridians). Labels are created independently of lines. / GPL-3
r-grcdata 1.0 We implement two main functions. The first function uses a given grouped noarch
and/or right-censored grouping scheme and empirical data to infer parameters,
and implements chi-square goodness-of-fit tests. The second function searches
for the global optimal grouping scheme of grouped and/or right-censored count
responses in surveys. / GPL-3
r- 1.0 These are GreedyExperimentalDesign Java dependency libraries. Note: this noarch
greedyexperimentaldesignjars
package has no functionality of its own and should not be installed as a stan-
dalone package without GreedyExperimentalDesign. / GPL-3
r-greenclust 1.0.0 Implements a method of iteratively collapsing the rows of a contingency table, noarch
two at a time, by selecting the pair of categories whose combination yields
a new table with the smallest loss of chi-squared, as described by Greenacre,
M.J. (1988) <doi:10.1007/BF01901670>. The result is compatible with the
class of object returned by the ‘stats’ package’s hclust() function and can be
used similarly (plotted as a dendrogram, cut, etc.). Additional functions are
provided for automatic cutting and diagnostic plotting. / MIT


r-gremlin 0.1.0.1Fit linear mixed-effects models using restricted (or residual) maximum like- noarch
lihood (REML) and with generalized inverse matrices to specify covariance
structures for random effects. In particular, the package is suited to fit quan-
titative genetic mixed models, often referred to as ‘animal models’ (Kruuk.
2004 <DOI: 10.1098/rstb.2003.1437>). Implements the average information
algorithm as the main tool to maximize the restricted likelihood, but with other
algorithms available (Meyer. 1997. Genet Sel Evol 29:97; Meyer and Smith.
1998. Genet Sel Evol 28:23.). / GPL-3
r-grex 1.9 Convert ‘Ensembl’ gene identifiers from Genotype-Tissue Expression (GTEx) noarch
data to identifiers in other annotation systems, including ‘Entrez’, ‘HGNC’,
and ‘UniProt’. / GPL-3
r-gridbase 0.4_7 Integration of base and grid graphics / GPL linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-gridbezier 1.1_1 Functions for rendering Bezier curves (Pomax, 2018) <https://pomax.github. noarch
io/bezierinfo/> in ‘grid’. There is support for both quadratic and cubic Bezier
curves. There are also functions for calculating points on curves, tangents to
curves, and normals to curves. / GPL-2
r-gridextra 2.3 Provides a number of user-level functions to work with grid graphics, notably linux-
to arrange multiple grid-based plots on a page, and draw tables. / GPL (>= 2) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-gridgraphics 0.4_1 Functions to convert a page of plots drawn with the ‘graphics’ package into noarch
identical output drawn with the ‘grid’ package. The result looks like the orig-
inal ‘graphics’-based plot, but consists of ‘grid’ grobs and viewports that can
then be manipulated with ‘grid’ functions (e.g., edit grobs and revisit view-
ports). / GPL-2
r-gridsvg 1.7_0 Functions to export graphics drawn with package grid to SVG format. Addi- noarch
tional functions provide access to SVG features that are not available in stan-
dard R graphics, such as hyperlinks, animation, filters, masks, clipping paths,
and gradient and pattern fills. / GPL-3
r-grimport 0.9_2 Functions for converting, importing, and drawing PostScript pictures in R noarch
plots. / GPL-2


Name Version
r-grimport2 0.1_5 Functions for importing external vector images and drawing them as part of ‘R’ noarch
plots. This package is different from the ‘grImport’ package because, where
that package imports ‘PostScript’ format images, this package imports ‘SVG’
format images. Furthermore, this package imports a specific subset of ‘SVG’,
so external images must be preprocessed using a package like ‘rsvg’ to produce
‘SVG’ that this package can import. ‘SVG’ features that are not supported by
‘R’ graphics, e.g., gradient fills, can be imported and then exported via the
‘gridSVG’ package. / GPL-2
r-grnn 0.1.0 The program GRNN implements the algorithm proposed by Specht (1991). / noarch
AGPL-3
r-grouped 0.6_0 Regression models for grouped and coarse data, under the Coarsened At Ran- noarch
dom assumption. / GPL-2
r-groupica 0.1.1 Contains an implementation of an independent component analysis (ICA) for noarch
grouped data. The main function groupICA() performs a blind source sep-
aration, by maximizing an independence across sources and allows to ad-
just for varying confounding for user-specified groups. Additionally, the
package contains the function uwedge() which can be used to approximately
jointly diagonalize a list of matrices. For more details see the project website
<https://sweichwald.de/groupICA/>. / AGPL-3
r-grouptest 1.0.1 Contains functions for a two-stage multiple testing procedure for grouped hy- noarch
pothesis, aiming at controlling both the total posterior false discovery rate and
within-group false discovery rate. / GPL-3
r-growthmodels 1.2.0 A compilation of nonlinear growth models used in many areas / GPL-3 noarch
r-growthrate 1.3 A nonparametric empirical Bayes method for recovering gradients (or growth noarch
velocities) from observations of smooth functions (e.g., growth curves) at iso-
lated time points. / GPL-3
r-grplasso 0.4_6 Fits user-specified (GLM-) models with group lasso penalty. / GPL-3 noarch
r-grpreg 3.2_1 Efficient algorithms for fitting the regularization path of linear or logistic re- linux-
gression models with grouped penalties. This includes group selection meth- 32,
ods such as group lasso, group MCP, and group SCAD as well as bi-level linux-
selection methods such as the group exponential lasso, the composite MCP, 64,
and the group bridge. / GPL-3 osx-
64,
win-
32,
win-
64
r-grpregoverlap 2.2_0 Fit the regularization path of linear, logistic or Cox models with overlapping noarch
grouped covariates based on the latent group lasso approach. Latent group
MCP/SCAD as well as bi-level selection methods, namely the group expo-
nential lasso and the composite MCP are also available. This package serves
as an extension of R package ‘grpreg’ (by Dr. Patrick Breheny <patrick-
breheny@uiowa.edu>) for grouped variable selection involving overlaps be-
tween groups. / GPL-3
r-grpss 3.0.1 Contains the tools to screen grouped variables, and select screened grouped noarch
variables afterwards. The main function grpss() can perform the grouped vari-
ables screening as well as selection for ultra-high dimensional data with group
structure. The screening step is primarily used to reduce the dimensions of
data so that the selection procedure can easily handle the moderate or low di-
mensions instead of ultra-high dimensions. / GPL-2 | GPL-3


Name Version
r-grpstring 0.3.2 Methods include converting series of event names to strings, finding common noarch
patterns in a group of strings, discovering featured patterns when comparing
two groups of strings as well as the number and starting position of each pat-
tern in each string, obtaining transition matrix, computing transition entropy,
statistically comparing the difference between two groups of strings, and clus-
tering string groups. Event names can be any action names or labels such as
events in log files or areas of interest (AOIs) in eye tracking research. / GPL-2
r-grs.test 1.1 Computational resources for test proposed by Gibbons, Ross, Shanken noarch
(1989)<DOI:10.2307/1913625>. It also has the functions for the power anal-
ysis and the choice of the optimal level of significance. The optimal level is
determined by minimizing the expected loss from hypothesis testing. / GPL-2
r-grt 0.2.1 Functions to generate and analyze data for psychology experiments based on noarch
the General Recognition Theory. / GPL-2
r-grto 1.3 Offers functions for the comparison of Gutenberg-Richter b-values. Several noarch
functions in GRTo are helpful for the assessment of the quality of seismicity
catalogs. / GPL-3
r-gsa 1.03.1Gene Set Analysis. / LGPL-3 noarch
r- 1.0 Provides the p-value for a joint test of association between a phenotype and a noarch
gsafishercombined set of genetic variants (SNPs) by combining marginal p-values using the Fisher
method. See Fisher, R.A. (1925,ISBN:0-05-002170-2) Statistical Methods for
Research Workers. / GPL-2
r-gsalib 2.1 This package contains utility functions used by the Genome Analysis Toolkit noarch
(GATK) to load tables and plot data. The GATK is a toolkit for variant discov-
ery in high-throughput sequencing data. / MIT
r-gsaq 1.0 Computation of Quantitative Trait Loci hits in the selected gene set. Perform- noarch
ing gene set validation with Quantitative Trait Loci information. Performing
gene set enrichment analysis with available Quantitative Trait Loci data and
computation of statistical significance value from gene set analysis. Obtain-
ing the list of Quantitative Trait Loci hit genes along with their overlapped
Quantitative Trait Loci names. / GPL-2
r-gsarima 0.1_4 Write SARIMA models in (finite) AR representation and simulate generalized noarch
multiplicative seasonal autoregressive moving average (time) series with Nor-
mal / Gaussian, Poisson or negative binomial distribution. / GPL-2
r-gseg 0.6 Using an approach based on similarity graph to estimate change-point(s) noarch
and the corresponding p-values. Can be applied to any type of data (high-
dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure
is available. / GPL-2
r-gsg 2.0 gsg (gam selection gradients) provides a unified approach to the regression noarch
analysis of selection from longitudinal data collected from natural populations.
/ GPL-2
r-gsheet 0.4.2 Simple package to download Google Sheets using just the sharing link. noarch
Spreadsheets can be downloaded as a data frame, or as plain text to parse
manually. Google Sheets is the new name for Google Docs Spreadsheets. /
GPL-3


Name Version
r-gsl 2.1_6 An R wrapper for the special functions and quasi random number genera- linux-
tors of the Gnu Scientific Library (http://www.gnu.org/software/gsl/). See gsl- 32,
package.Rd for details of overall package organization, and Misc.Rd for some linux-
functions that are widely used in the package, and some tips on installation. / 64,
GPL-3 osx-
64,
win-
32,
win-
64
r-gsloid 0.1.0 Contains published data sets for global benthic d18O data for 0-5.3 Myr noarch
<doi:10.1029/2004PA001071> and global sea levels based on marine sediment
core data for 0-800 ka <doi:10.5194/cp-12-1-2016>. / MIT
r-gsm 1.3.2 Implementation of a Bayesian approach for estimating a mixture of gamma noarch
distributions in which the mixing occurs over the shape parameter. This fam-
ily provides a flexible and novel approach for modeling heavy-tailed distri-
butions, it is computationally efficient, and it only requires to specify a prior
distribution for a single parameter. / GPL-2
r-gsmx 1.3 Estimating trait heritability and handling overfitting. This package includes a noarch
collection of functions for (1) estimating genetic variance-covariances and cal-
culate trait heritability; and (2) handling overfitting by calculating the variance
components and the heritability through cross validation. / GPL-2
r-gss 2.1_9 A comprehensive package for structural multivariate function estimation using linux-
smoothing splines. / GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-gstream 0.2.0 Uses an approach based on k-nearest neighbor information to sequentially de- noarch
tect change-points. Offers analytic approximations for false discovery con-
trol given user-specified average run length. Can be applied to any type of
data (high-dimensional, non-Euclidean, etc.) as long as a reasonable simi-
larity measure is available. See references (1) Chen, H. (2019) Sequential
change-point detection based on nearest neighbors. The Annals of Statistics,
47(3):1381-1407. (2) Chu, L. and Chen, H. (2018) Sequential change-point
detection for high-dimensional and non-Euclidean data <arXiv:1810.05973>.
/ GPL-2


Name Version
r-gsubfn 0.7 The gsubfn function is like gsub but can take a replacement function or cer- noarch
tain other objects instead of the replacement string. Matches and back refer-
ences are input to the replacement function and replaced by the function out-
put. gsubfn can be used to split strings based on content rather than delimiters
and for quasi-perl-style string interpolation. The package also has facilities for
translating formulas to functions and allowing such formulas in function calls
instead of functions. This can be used with R functions such as apply, sapply,
lapply, optim, integrate, xyplot, Filter and any other function that expects an-
other function as an input argument or functions like cat or sql calls that may
involve strings where substitution is desirable. There is also a facility for re-
turning multiple objects from functions and a version of transform that allows
the RHS to refer to LHS used in the same transform. / GPL-2
r-gsw 1.0_5 Provides an interface to the Gibbs ‘SeaWater’ (‘TEOS-10’) C library, version linux-
3.05-4 (commit ‘5b4d959e54031f9e972f3e863f63e67fa4f5bfec’, dated 2017- 32,
08-07, available at <https://github.com/TEOS-10/GSW-C>, which stems from linux-
‘Matlab’ and other code written by members of Working Group 127 of 64,
‘SCOR’/’IAPSO’ (Scientific Committee on Oceanic Research / International osx-
Association for the Physical Sciences of the Oceans). / GPL (>= 2) | file LI- 64,
CENSE win-
32,
win-
64
r-gt4ireval 2.0 Provides tools to measure the reliability of an Information Retrieval test col- noarch
lection. It allows users to estimate reliability using Generalizability Theory
and map those estimates onto well-known indicators such as Kendall tau cor-
relation or sensitivity. / MIT
r-gtable 0.3.0 Tools to make it easier to work with tables of ‘grobs’. The ‘gtable’ package linux-
defines a ‘gtable’ grob class that specifies a grid along with a list of grobs and 32,
their placement in the grid. Further the package makes it easy to manipulate linux-
and combine ‘gtable’ objects so that complex compositions can be build up 64,
sequentially. / GPL-2 noarch,
osx-
64,
win-
32,
win-
64
r-gtcorr 0.2_1 This package provides functions to calculate the efficiencies (expected tests per noarch
unit) of hierarchical and matrix group testing procedures. Efficiencies can be
calculated in the presense of correlated responses under multiple arrangements
of clustesrs. Efficiencies can also be evaluated in the presense of test error. /
GPL-3
r-gtests 0.2 Four graph-based tests are provided for testing whether two samples are from noarch
the same distribution. It works for both continuous data and discrete data. /
GPL-2
r-gtheory 0.1.2 Estimates variance components, generalizability coefficients, universe scores, noarch
and standard errors when observed scores contain variation from one or more
measurement facets (e.g., items and raters). / GPL-3


Name Version
r-gtools 3.8.1 Functions to assist in R programming, including: - assist in developing, up- linux-
dating, and maintaining R and R packages (‘ask’, ‘checkRVersion’, ‘getDe- 32,
pendencies’, ‘keywords’, ‘scat’), - calculate the logit and inverse logit trans- linux-
formations (‘logit’, ‘inv.logit’), - test if a value is missing, empty or contains 64,
only NA and NULL values (‘invalid’), - manipulate R’s .Last function (‘add- osx-
Last’), - define macros (‘defmacro’), - detect odd and even integers (‘odd’, 64,
‘even’), - convert strings containing non-ASCII characters (like single quotes) win-
to plain ASCII (‘ASCIIfy’), - perform a binary search (‘binsearch’), - sort 32,
strings containing both numeric and character components (‘mixedsort’), - cre- win-
ate a factor variable from the quantiles of a continuous variable (‘quantcut’), 64
- enumerate permutations and combinations (‘combinations’, ‘permutation’),
- calculate and convert between fold-change and log-ratio (‘foldchange’, ‘lo-
gratio2foldchange’, ‘foldchange2logratio’), - calculate probabilities and gen-
erate random numbers from Dirichlet distributions (‘rdirichlet’, ‘ddirichlet’),
- apply a function over adjacent subsets of a vector (‘running’), - modify the
TCP_NODELAY (‘de-Nagle’) flag for socket objects, - efficient ‘rbind’ of data
frames, even if the column names don’t match (‘smartbind’), - generate sig-
nificance stars from p-values (‘stars.pval’), - convert characters to/from ASCII
codes. / GPL-2
r-gtwas 1.1.0 Quantitative trait loci mapping and genome wide association analysis are used noarch
to find candidate molecular marker or region associated with phenotype based
on linkage analysis and linkage disequilibrium. Gene expression quantita-
tive trait loci mapping is used to find candidate molecular marker or region
associated with gene expression. In this package, we applied the method
in Liu W. (2011) <doi:10.1007/s00122-011-1631-7> and Gusev A. (2016)
<doi:10.1038/ng.3506> to genome and transcriptome wide association study,
which is aimed at revealing the association relationship between phenotype
and molecular markers, expression levels, molecular markers nested within
different related expression effect and expression effect nested within different
related molecular marker effect. F test based on full and reduced model are
performed to obtain p value or likelihood ratio statistic. The best linear model
can be obtained by stepwise regression analysis. / GPL-2
r-gtx 0.0.8 Assorted tools for genetic association analyses. The current focus is on im- noarch
plementing (either exactly or approximately) regression analyses using sum-
mary statistics instead of using subject-specific data. So far, functions exist
to support multi-SNP risk score analyses, multi-SNP conditional regression
analyses, and multi-phenotype analyses, using summary statistics. There are
helper functions for reading and manipulating subject-specific genotype data,
which provide a platform for calculating the summary statistics, or for using
R to conduct other analyses not supported by specific GWAS analysis tools. /
GPL-2
r-guardianr 0.9 Provides an interface to the Open Platform’s Content API of the Guardian Me- noarch
dia Group. It retrieves content from news outlets The Observer, The Guardian,
and guardian.co.uk from 1999 to current day. / GPL-2
r-guerry 1.6_1 This package comprises maps of France in 1830, multivariate data from A.- noarch
M. Guerry and others, and statistical and graphic methods related to Guerry’s
Moral Statistics of France. The goal is to facilitate the exploration and devel-
opment of statistical and graphic methods for multivariate data in a geo-spatial
context of historical interest. / GPL-3


Name Version
r-guide 1.2.7 A nice GUI for financial DErivatives in R. / GPL-2 linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-gumbel 1.10_2Provides probability functions (cumulative distribution and density functions), noarch
simulation function (Gumbel copula multivariate simulation) and estimation
functions (Maximum Likelihood Estimation, Inference For Margins, Moment
Based Estimation and Canonical Maximum Likelihood). / GPL-2
r-gustave 0.4.0 Provides a toolkit for analytical variance estimation in survey sampling. Apart noarch
from the implementation of standard variance estimators, its main feature is
to help the sampling expert produce easy-to-use variance estimation wrappers,
where systematic operations (linearization, domain estimation) are handled in
a consistent and transparent way. / GPL-3
r-gvarx 1.1 Perform the estimation and inference of stationary Global Vector Au- noarch
toregression model (GVAR) of Pesaran, Schuermann and Weiner (2004)
<DOI:10.1198/073500104000000019> and Dees, di Mauro, Pesaran and
Smith (2007) <DOI:10.1002/jae.932>. / GPL-2
r-gvc 0.5.2 Several tools for Global Value Chain (‘GVC’) analysis are implemented. / noarch
GPL-3
r-gvcm.cat 1.9 Generalized structured regression models with regularized categorical effects, noarch
categorical effect modifiers, continuous effects and smooth effects. / GPL-2
r-gvlma 1.0.0.3Methods from the paper: Pena, EA and Slate, EH, Global Validation of Linear noarch
Model Assumptions, J. American Statistical Association, 101(473):341-354,
2006. / GPL-3
r-gweram 1.0 This package provides functions to calculate the significance threshold for con- noarch
trolling the type I error rate in mixed-model association mapping analyses. /
GPL-2
r-gwg 1.0 Based on calculations of 758 women this package calculates positive predic- noarch
tive values (PPV) and negative predictive values (NPV) for inadequate and
excessive gestational weight gain (GWG) for different prevalences for differ-
ent BMI categories. / GPL-2
r-gwidgets 0.0_54.1
Provides a toolkit-independent API for building interactive GUIs. At least one noarch
of the ‘gWidgetsXXX packages’, such as gWidgetstcltk, needs to be installed.
Some icons are on loan from the scigraphica project <http://scigraphica.
sourceforge.net>. / GPL-2
r-gwidgets2 1.0_8 Re-implementation of the ‘gWidgets’ API. The API is defined in this pack- noarch
age. A second, toolkit-specific package is required to use it. There are three
in development: ‘gWidgets2RGtk2’, ‘gWidgets2Qt’, and ‘gWidgets2tcltk’. /
GPL-3
r-gwrm 2.1.0.3Statistical functions to fit, validate and describe a Generalized Waring Regres- noarch
sion Model (GWRM). / GPL-2 | GPL-3


Name Version
r-gwrpvr 1.0 Computes the sample probability value (p-value) for the estimated coefficient noarch
from a standard genome-wide univariate regression. It computes the exact
finite-sample p-value under the assumption that the measured phenotype (the
dependent variable in the regression) has a known Bernoulli-normal mixture
distribution. Finite-sample genome-wide regression p-values (Gwrpv) with a
non-normally distributed phenotype (Gregory Connor and Michael O’Neill,
bioRxiv 204727 <doi:10.1101/204727>). / GPL-3
r-gwsignif 1.2 The correlations and linkage disequilibrium between tests can vary as a func- noarch
tion of minor allele frequency thresholds used to filter variants, and also varies
with different choices of test statistic for region-based tests. Appropriate
genome-wide significance thresholds can be estimated empirically through
permutation on only a small proportion of the whole genome. / GPL-2
r-gxm 1.1 Quantifying and testing gene-by-measured-environment interaction in behav- noarch
ior genetic designs. / GPL-2
r-gym 0.1.0 OpenAI Gym is a open-source Python toolkit for developing and comparing noarch
reinforcement learning algorithms. This is a wrapper for the OpenAI Gym
API, and enables access to an ever-growing variety of environments. For more
details on OpenAI Gym, please see here: <https://github.com/openai/gym>.
For more details on the OpenAI Gym API specification, please see here:
<https://github.com/openai/gym-http-api>. / MIT
r-h2o 3.26.0.2
R interface for ‘H2O’, the scalable open source machine learning platform that noarch
offers parallelized implementations of many supervised and unsupervised ma-
chine learning algorithms such as Generalized Linear Models, Gradient Boost-
ing Machines (including XGBoost), Random Forests, Deep Neural Networks
(Deep Learning), Stacked Ensembles, Naive Bayes, Cox Proportional Haz-
ards, K-Means, PCA, Word2Vec, as well as a fully automatic machine learning
algorithm (AutoML). / Apache License (== 2.0)
r-h2o4gpu 0.2.0 Interface to ‘H2O4GPU’ <https://github.com/h2oai/h2o4gpu>, a collection of noarch
‘GPU’ solvers for machine learning algorithms. / Apache License 2.0
r-hac 1.0_5 Package provides the estimation of the structure and the parameters, sampling noarch
methods and structural plots of Hierarchical Archimedean Copulae (HAC). /
GPL-3
r- 0.2 Provides a framework for writing map/reduce scripts for use in Hadoop noarch
hadoopstreaming Streaming. Also facilitates operating on data in a streaming fashion, without
Hadoop. / GPL-3
r-hail 0.1.1 Read data from the City of Portland’s ‘HYDRA’ <http://or.water.usgs.gov/ noarch
precip/> rainfall datasets within R. / MIT
r-halfcircle 0.1.0 There are growing concerns on flow data in diverse fields including trade, mi- noarch
gration, knowledge diffusion, disease spread, and transportation. The package
is an effective visual support to learn the pattern of flow which is called halfcir-
cle diagram. The flow between two nodes placed on the center line of a circle
is represented using a half circle drawn from the origin to the destination in a
clockwise direction. Through changing the order of nodes, the halfcircle dia-
gram enables users to examine the complex relationship between bidirectional
flow and each potential determinants. Furthermore, the halfmeancenter func-
tion, which calculates (un) weighted mean center of half circles, makes the
comparison easier. / MIT


Name Version
r-hamlet 0.9.6 Various functions and algorithms are provided here for solving optimal match- noarch
ing tasks in the context of preclinical cancer studies. Further, various helper
and plotting functions are provided for unsupervised and supervised machine
learning as well as longitudinal mixed-effects modeling of tumor growth re-
sponse patterns. / GPL-2
r-handtill2001 0.2_12An S4 implementation of Eq. (3) and Eq. (7) by David J. Hand and Robert J. noarch
Till (2001) <DOI:10.1023/A:1010920819831>. / GPL-2
r-handyplots 1.1.3 Several handy plots for quickly looking at the relationship between two nu- noarch
meric vectors of equal length. Quickly visualize scatter plots, residual plots,
qq-plots, box plots, confidence intervals, and prediction intervals. / GPL-2
r-hapim 1.3 The package provides a set of functions whose aim is to propose 4 methods of noarch
QTL detection. HAPimLD is an interval-mapping method designed for unre-
lated individuals with no family information that makes use of linkage dise-
quilibrium. HAPimLDL is an interval-mapping method for design of half-sib
families. It combines linkage analysis and linkage disequilibrium. HaploMax
is based on an analysis of variance with a dose haplotype effect. HaploMaxHS
is based on an analysis of variance with a sire effect and a dose haplotype
effect in half-sib family design. Fundings for the package development were
provided to the LDLmapQTL project by the ANR GENANIMAL program and
APIS-GENE. / GPL-3
r- 0.1.2 Reconstruction of founder haplotype blocks from time series data. / GPL-3 noarch
haploreconstruct
r-haplosim 1.8.4 Simulate haplotypes through meioses. Allows specification of population pa- noarch
rameters. / GPL-2
r-haplotyper 0.1 Function to identify haplotypes within QTL (Quantitative Trait Loci). One noarch
haplotype is a combination of SNP (Single Nucleotide Polymorphisms) within
the QTL. This function groups together all individuals of a population with the
same haplotype. Each group contains individual with the same allele in each
SNP, whether or not missing data. Thus, haplotyper groups individuals, that
to be imputed, have a non-zero probability of having the same alleles in the
entire sequence of SNP’s. Moreover, haplotyper calculates such probability
from relative frequencies. / GPL-3
r-happytime 0.1.0 There are two interesting games in this package, one is 2048 games(for win- noarch
dows), using up and down to control the direction until there is a 2048 figure.
And the other is ‘what to eat today’,preparing for people who choose difficul-
ties, including most of the delicious Cantonese cuisine. / GPL-2
r- 1.0 Fits the first harmonics in a Fourier expansion to one or more time series. noarch
harmonicregression Trend elimination can be performed. Computed values include estimates of
amplitudes and phases, as well as confidence intervals and p-values for the
null hypothesis of Gaussian noise. / MIT
r-hartools 0.0.5 The goal of ‘HARtools’ is to provide a simple set of functions to read/parse, noarch
write and visualise HTTP Archive (‘HAR’) files in R. / GPL-3


r-harvest.tree 1.1 Aimed at applying the Harvest classification tree algorithm, modified algo- noarch
rithm of classic classification tree.The harvested tree has advantage of deleting
redundant rules in trees, leading to a simplify and more efficient tree model.It
was firstly used in drug discovery field, but it also performs well in other
kinds of data, especially when the region of a class is disconnected. This
package also improves the basic harvest classification tree algorithm by ex-
tending the field of data of algorithm to both continuous and categorical vari-
ables. To learn more about the harvest classification tree algorithm, you can go
to http://www.stat.ubc.ca/Research/TechReports/techreports/220.pdf for more
information. / GPL-2
r-hash 2.2.6.1Implements a data structure similar to hashes in Perl and dictionaries in Python noarch
but with a purposefully R flavor. For objects of appreciable size, access using
hashes outperforms native named lists and vectors. / GPL-2
r-hashids 0.9.0 An R port of the hashids library. hashids generates YouTube-like hashes from noarch
integers or vector of integers. Hashes generated from integers are relatively
short, unique and non-seqential. hashids can be used to generate unique ids
for URLs and hide database row numbers from the user. By default hashids
will avoid generating common English cursewords by preventing certain let-
ters being next to each other. hashids are not one-way: it is easy to encode an
integer to a hashid and decode a hashid back into an integer. / MIT
r-haven 2.1.0 Import foreign statistical formats into R via the embedded ‘ReadStat’ C library, linux-
<https://github.com/WizardMac/ReadStat>. / MIT file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-hazer 1.1.1 Provides a set of functions to estimate haziness of an image based on RGB noarch
bands. It returns a haze factor, varying from 0 to 1, a metric for fogginess
and cloudiness. The package also presents additional functions to estimate
brightness, darkness and contrast rasters of the RGB image. This package can
be used for several applications such as inference of weather quality data and
performing environmental studies from interpreting digital images. / AGPL-3
r-hazus 0.1 Damage Functions (DFs), also known as Vulnerability Functions, associate noarch
the physical damage to a building or a structure (and also its contents and
inventory) from natural disasters to financial damage. The Federal Emergency
Management Agency (FEMA) in USA developed several thousand DFs and
these serve as a benchmark in natural catastrophe modeling, both in academia
and industry. However, these DFs and their documentation are buried within
the HAZUS software are not easily accessible for analysis and visualization.
This package provides more than 1300 raw DFs used by FEMA’s HAZUS
software and also functionality to extract and visualize DFs specific to the
flood hazard. The vignette included with this package demonstrates its use. /
GPL-2
r-hbim 1.0.3 Calculate expected relative risk and proportion protected assuming normally noarch
distributed log10 transformed antibody dose for several component vaccine.
Uses Hill models for each component which are combined under Bliss inde-
pendence. / GPL-2


Name Version
r-hbm 1.0 A package for building hierarchical block matrices from association matrices noarch
and for performing multi-scale analysis. It specifically targets chromatin con-
tact maps, generated from high-throughput chromosome conformation capture
data, such as 5C and Hi-C, and provides methods for detecting movements
and for computing chain hierarchy and region communicability across scales.
/ GPL-2
r-hbsae 1.0 Functions to compute small area estimates based on a basic area or unit-level noarch
model. The model is fit using restricted maximum likelihood, or in a hierar-
chical Bayesian way. In the latter case numerical integration is used to average
over the posterior density for the between-area variance. The output includes
the model fit, small area estimates and corresponding MSEs, as well as some
model selection measures. Additional functions provide means to compute ag-
gregate estimates and MSEs, to minimally adjust the small area estimates to
benchmarks at a higher aggregation level, and to graphically compare different
sets of small area estimates. / GPL-3
r-hbstm 1.0.1 This package fits Hierarchical Bayesian space-Time models for Gaussian data. noarch
Furthermore, its functions have been implemented for analysing the fitting
qualities of those models. / GPL (>= 2.0)
r-hcandersenr 0.2.0 Texts for H.C. Andersens fairy tales, ready for text analysis. Fairy tales in noarch
German, Danish, English, Spanish and French. / MIT
r-hcc 0.54 A new diagnostic check for model adequacy in regression and generalized noarch
linear models is implemented. / GPL-2
r-hcci 1.0.0 This package calculates the interval estimates for the parameters of linear mod- noarch
els heteroscedastic regression using bootstrap - (Wild Bootstrap) and double
bootstrap-t (Wild Bootstrap). It is also possible to calculate confidence inter-
vals using the percentile bootstrap and percentile bootstrap double. It is possi-
ble to calculate consistent estimates of the covariance matrix of the parameters
of linear regression models with heteroskedasticity of unknown form. The
package also provides function to calculate consistently the covariance matrix
of the parameters of linear models with heteroskedasticity of unknown form. /
GPL-2
r-hchinamap 0.1.0 By binding R functions and the ‘Highmaps’ <https://www.highcharts.com.cn/ noarch
products/highmaps> chart library, ‘hchinamap’ package provides a simple way
to map China and its provinces. The map of China drawn by this package con-
tains complete Chinese territory, especially the Nine-dotted line, South Tibet,
Hong Kong, Macao and Taiwan. / MIT
r-hcp 0.1 Estimation of parameters in 3-segment (i.e. 2 change-point) regression models noarch
with heteroscedastic variances is provided based on both likelihood and hybrid
Bayesian approaches, with and without continuity constraints at the change
points. / GPL-2 | GPL-3
r-hcr 0.1.1 This code provides a method to fit the hidden compact representation model noarch
as well as to identify the causal direction on discrete data. We implement an
effective solution to recover the above hidden compact representation under
the likelihood framework. Please see the Causal Discovery from Discrete Data
using Hidden Compact Representation from NIPS 2018 by Ruichu Cai, Jie
Qiao, Kun Zhang, Zhenjie Zhang and Zhifeng Hao (2018) <https://nips.cc/
Conferences/2018/Schedule?showEvent=11274> for a description of some of
our methods. / GPL-2
r-hda 0.2_14Functions to perform dimensionality reduction for classification if the covari- noarch
ance matrices of the classes are unequal. / GPL-2


Name Version
r-hdci 1.0_2 Fits regression models on high dimensional data to estimate coefficients and noarch
use bootstrap method to obtain confidence intervals. Choices for regression
models are Lasso, LassoOLS, Lasso partial ridge, LassoOLS partial ridge. /
GNU General Public License version 2
r-hdfqlr 0.6_1 Provides an interface to ‘HDFql’ <http://www.hdfql.com/> and helper func- noarch
tions for reading data from and writing data to ‘HDF5’ files. ‘HDFql’ pro-
vides a high-level language for managing ‘HDF5’ data that is platform inde-
pendent. For more information, see the reference manual <http://www.hdfql.
com/resources/HDFqlReferenceManual.pdf>. / GPL-3
r-hdinterval 0.2.0 A generic function and a set of methods to calculate highest density inter- noarch
vals for a variety of classes of objects which can specify a probability density
distribution, including MCMC output, fitted density objects, and functions. /
GPL-3
r-hdmd 1.2 High Dimensional Molecular Data (HDMD) typically have many more vari- noarch
ables or dimensions than observations or replicates (D>>N). This can cause
many statistical procedures to fail, become intractable, or produce mislead-
ing results. This package provides several tools to reduce dimensionality and
analyze biological data for meaningful interpretation of results. Factor Anal-
ysis (FA), Principal Components Analysis (PCA) and Discriminant Analysis
(DA) are frequently used multivariate techniques. However, PCA methods
prcomp and princomp do not reflect the proportion of total variation of each
principal component. Loadings.variation displays the relative and cumulative
contribution of variation for each component by accounting for all variability
in data. When D>>N, the maximum likelihood method cannot be applied in
FA and the the principal axes method must be used instead, as in factor.pa
of the psych package. The factor.pa.ginv function in this package further al-
lows for a singular covariance matrix by applying a general inverse method
to estimate factor scores. Moreover, factor.pa.ginv removes and warns of any
variables that are constant, which would otherwise create an invalid covari-
ance matrix. Promax.only further allows users to define rotation parameters
during factor estimation. Similar to the Euclidean distance, the Mahalanobis
distance estimates the relationship among groups. pairwise.mahalanobis com-
putes all such pairwise Mahalanobis distances among groups and is useful for
quantifying the separation of groups in DA. Genetic sequences are composed
of discrete alphabetic characters, which makes estimates of variability diffi-
cult. MolecularEntropy and MolecularMI calculate the entropy and mutual
information to estimate variability and covariability, respectively, of DNA or
Amino Acid sequences. Functional grouping of amino acids (Atchley et al
1999) is also available for entropy and mutual information estimation. Mu-
tual information values can be normalized by NMI to account for the back-
ground distribution arising from the stochastic pairing of independent, random
sites. Alternatively, discrete alphabetic sequences can be transformed into bi-
ologically informative metrics to be used in various multivariate procedures.
FactorTransform converts amino acid sequences using the amino acid indices
determined by Atchley et al 2005. / GPL-2
r-hdpca 1.0.0 In high-dimensional settings: Estimate the number of distant spikes based noarch
on the Generalized Spiked Population (GSP) model. Estimate the population
eigenvalues, angles between the sample and population eigenvectors, correla-
tions between the sample and population PC scores, and the asymptotic shrink-
age factors. Adjust the shrinkage bias in the predicted PC scores. / GPL-2


Name Version
r-heatex 1.0 The heatex package calculates heat storage in the body and the components of noarch
heat exchange (conductive, convective, radiative, and evaporative) between the
body and the environment during physical activity based on the principles of
partitional calorimetry. The program enables heat exchange calculations for a
range of environmental conditions when wearing various clothing ensembles.
/ GPL-3
r-heatmap.plus 1.3 Allows heatmap matrix to have non-identical X- and Y-dimensions. Allows noarch
multiple tracks of annotation for RowSideColors and ColSideColors. / GPL-3
r-heatmapfit 2.0.4 Generates a fit plot for diagnosing misspecification in models of binary de- noarch
pendent variables, and calculates the related heatmap fit statistic described in
Esarey and Pierce (2012) <DOI:10.1093/pan/mps026>. / GPL-2
r-hedgehog 0.1 Hedgehog will eat all your bugs. ‘Hedgehog’ is a property-based testing pack- noarch
age in the spirit of ‘QuickCheck’. With ‘Hedgehog’, one can test properties of
their programs against randomly generated input, providing far superior test
coverage compared to unit testing. One of the key benefits of ‘Hedgehog’ is
integrated shrinking of counterexamples, which allows one to quickly find the
cause of bugs, given salient examples when incorrect behaviour occurs. / MIT
r-hellno 0.0.1 Base R’s default setting for ‘stringsAsFactors’ within ‘data.frame()’ and noarch
‘as.data.frame()’ is supposedly the most often complained about piece of
code in the R infrastructure. The ‘hellno’ package provides an explicit so-
lution without changing R itself or having to mess around with options.
It tries to solve this problem by providing alternative ‘data.frame()’ and
‘as.data.frame()’ functions that are in fact simple wrappers around base
R’s ‘data.frame()’ and ‘as.data.frame()’ with ‘stringsAsFactors’ option set to
‘HELLNO’ ( which in turn equals FALSE ) by default. / MIT
r-hellojavaworld 0.0_9 A dummy package to demonstrate how to interface to a jar file that resides noarch
inside an R package. / GPL-3
r-helminthr 1.0.7 Access to large host-parasite data is often hampered by the availability of data noarch
and difficulty in obtaining it in a programmatic way to encourage analyses.
‘helminthR’ provides a programmatic interface to the London Natural
History Museum’s host-parasite database, one of the largest host-parasite
databases existing currently <http://www.nhm.ac.uk/research-curation/
scientific-resources/taxonomy-systematics/host-parasites/>. The package
allows the user to query by host species, parasite species, and geographic
location. / GPL-3
r-helpersmg 3.7 Contains many functions useful for managing ‘NetCDF’ files (see <http://en. noarch
wikipedia.org/wiki/NetCDF>), get tide levels on any point of the globe, get
moon phase and time for sun rise and fall, analyse and reconstruct periodic
time series of temperature with irregular sinusoidal pattern, show scales and
wind rose in plot with change of color of text, Metropolis-Hastings algorithm
for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search
files in disk by there names or their content, read the contents of all files from
a folder at one time. / GPL-2
r-helsinki 0.9.29Tools for accessing various open data sources in the Helsinki region in Fin- noarch
land. Current data sources include the Real Estate Department (<http://ptp.hel.
fi/avoindata/>), Service Map API (<http://api.hel.fi/servicemap/v1/>), Linked
Events API (<http://api.hel.fi/linkedevents/v0.1/>), Helsinki Region Infoshare
statistics API (<https://dev.hel.fi/stats/>). / BSD_2_clause


Name Version
r-here 0.1 Constructs paths to your project’s files. The ‘here()’ function uses a reasonable noarch
heuristics to find your project’s files, based on the current working directory
at the time when the package is loaded. Use it as a drop-in replacement for
‘file.path()’, it will always locate the files relative to your project root. / GPL-
3
r-heritability 1.2 Implements marker-based estimation of heritability when observations on ge- noarch
netically identical replicates are available. These can be either observations
on individual plants or plot-level data in a field trial. Heritability can then
be estimated using a mixed model for the individual plant or plot data. For
comparison, also mixed-model based estimation using genotypic means and
estimation of repeatability with ANOVA are implemented. For illustration the
package contains several datasets for the model species Arabidopsis thaliana.
/ GPL-3
r-hermite 1.1.2 Probability functions and other utilities for the generalized Hermite distribu- noarch
tion. / GPL-2
r-hero 0.0.3 Data and data-generating functions related to the paper Fast Bivariate Penal- noarch
ized Splines by Xiao et al. (2012) <doi:10.1111/rssb.12007>. A hero is a spe-
cific type of sandwich. Dictionary.com (2018) <https://www.dictionary.com>
describes a hero as: a large sandwich, usually consisting of a small loaf of
bread or long roll cut in half lengthwise and containing a variety of ingredi-
ents, as meat, cheese, lettuce, and tomatoes. / GPL-2
r-het.test 0.1 An implementation of White’s Test for Heteroskedasticity as outlined in noarch
Doornik (1996). / GPL-2
r-hett 0.3_2 Functions for the fitting and summarizing of heteroscedastic t-regression. / noarch
GPL-2
r-hexbin 1.27.2Binning and plotting functions for hexagonal bins. / GPL-2 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-hexview 0.3_4 Functions to view files in raw binary form like in a hex editor. Additional noarch
functions to specify and read arbitrary binary formats. / GPL-2
r-hflights 0.1 A data only package containing commercial domestic flights that departed noarch
Houston (IAH and HOU) in 2011. / CC0
r-hglm.data 1.0_1 This data-only package was created for distributing data used in the examples noarch
of the ‘hglm’ package. / GPL-2
r-hgnchelper 0.7.1 Contains functions for identifying and correcting HGNC human gene symbols noarch
and MGI mouse gene symbols which have been converted to date format by
Excel, withdrawn, or aliased. Also contains functions for reversibly converting
between HGNC symbols and valid R names. / GPL (>= 2.0)
r-hgsl 1.0.0 Estimation of high-dimensional multi-response regression with heterogeneous noarch
noises under Heterogeneous group square-root Lasso penalty. For details see:
Ren, Z., Kang, Y., Fan, Y. and Lv, J. (2018)<arXiv:1606.03803>. / GPL-2


Name Version
r-hiddenf 2.0 Computes the ACMIF test and Bonferroni-adjusted p-value of interaction in noarch
two-factor studies. Produces corresponding interaction plot and analysis of
variance tables and p-values from several other tests of non-additivity. / GPL-
2
r-hierdiversity 0.1 Hierarchical group-wise partitioning of phenotypic diversity into within-group noarch
(alpha), among-group (beta), and pooled-total (gamma) components using Hill
numbers. Turnover and overlap are also calculated as standardized alternatives
to beta diversity. Hierarchical bootstrapping is used to approximate uncertainty
around each diversity component. / GPL-2
r-hiertest 1.1 Implementation of the convex hierarchical testing (CHT) procedure introduced noarch
in Bien, Simon, and Tibshirani (2015) Convex Hierarchical Testing of Interac-
tions. Annals of Applied Statistics. Vol. 9, No. 1, 27-42. / GPL-3
r-hiest 2.0 Uses likelihood to estimate ancestry and heterozygosity. Evaluates simple hy- noarch
brid classifications (parentals, F1, F2, backcrosses). Estimates genomic clines.
/ GPL-3
r-highcharter 0.7.0 A wrapper for the ‘Highcharts’ library including shortcut functions to plot linux-
R objects. ‘Highcharts’ <http://www.highcharts.com/> is a charting library 32,
offering numerous chart types with a simple configuration syntax. / MIT file linux-
LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-highlight 0.5.0 Syntax highlighter for R code based on the results of the R parser. Render- linux-
ing in HTML and latex markup. Custom Sweave driver performing syntax 64,
highlighting of R code chunks. / GPL-3 osx-
64,
win-
64
r-highlighthtml 0.2.1 A tool to format R markdown with CSS ids for HTML output. The tool may be noarch
most helpful for those using markdown to create reproducible documents. The
biggest limitations in formatting is the knowledge of CSS by the document
authors. / MIT
r-highmean 3.0 Provides various tests for comparing high-dimensional mean vectors in two noarch
sample populations. / GPL-2
r-highr 0.8 Provides syntax highlighting for R source code. Currently it supports LaTeX linux-
and HTML output. Source code of other languages is supported via Andre 32,
Simon’s highlight package (<http://www.andre-simon.de>). / GPL linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-highscreen 0.3 Can be used to carry out extraction, normalization, quality control (QC), can- noarch
didate hits identification and visualization for plate based assays, in drug dis-
covery. This project was funded by the Division of Allergy, Immunology,
and Transplantation, National Institute of Allergy and Infectious Diseases, Na-
tional Institutes of Health, Department of Health and Human Services, under
contract No. HHSN272201400054C entitled Adjuvant Discovery For Vac-
cines Against West Nile Virus and Influenza, awarded to Duke University and
lead by Drs. Herman Staats and Soman Abraham. / GPL-3
r-highttest 1.1 Implements the method developed by Cao and Kosorok (2011) for the signifi- noarch
cance analysis of thousands of features in high-dimensional biological studies.
It is an asymptotically valid data-driven procedure to find critical values for
rejection regions controlling the k-familywise error rate, false discovery rate,
and the tail probability of false discovery proportion. / GPL-2
r-higrad 0.1.0 Implements the Hierarchical Incremental GRAdient Descent (HiGrad) algo- noarch
rithm, a first-order algorithm for finding the minimizer of a function in online
learning just like stochastic gradient descent (SGD). In addition, this method
attaches a confidence interval to assess the uncertainty of its predictions. See
Su and Zhu (2018) <arXiv:1802.04876> for details. / GPL-3
r-hilmm 1.1 Estimation of heritability with confidence intervals in linear mixed models. / noarch
GPL-2
r- 1.0.0 H(x) is the h-index for the past x years. Here, the h(x) of a scien- noarch
hindexcalculator tist/department/etc. can be calculated using the exported excel file from a Web
of Science citation report of a search. Also calculated is the year of first pub-
lication, total number of publications, and sum of times cited for the specified
period. Therefore, for h-10: the date of first publication, total number of pub-
lications, and sum of times cited in the past 10 years are calculated. Note: the
excel file has to first be saved in a .csv format. / AGPL-3
r-histdata 0.8_4 The ‘HistData’ package provides a collection of small data sets that are inter- noarch
esting and important in the history of statistics and data visualization. The goal
of the package is to make these available, both for instructional use and for his-
torical research. Some of these present interesting challenges for graphics or
analysis in R. / GPL-3
r-histogram 0.0_25Automatic construction of regular and irregular histograms as described in noarch
Rozenholc/Mildenberger/Gather (2010). / GPL-2
r-historydata 0.1 These sample data sets are intended for historians learning R. They include noarch
population, institutional, religious, military, and prosopographical data suit-
able for mapping, quantitative analysis, and network analysis. / MIT
r-hiv.lifetables 0.1 The functions in this package produce a complete set of mortality rates as a noarch
function of a combination of HIV prevalence and either life expectancy at birth
(e0), child mortality (5q0), or child mortality with adult mortality (45q15) /
Unlimited
r-hive 0.2_0 Hadoop InteractiVE facilitates distributed computing via the MapReduce noarch
paradigm through R and Hadoop. An easy to use interface to Hadoop, the
Hadoop Distributed File System (HDFS), and Hadoop Streaming is provided.
/ GPL-3
r-hk80 0.0.2 This is a collection of functions for converting coordinates between noarch
WGS84UTM, WGS84GEO, HK80UTM, HK80GEO and HK1980GRID Co-
ordinate Systems used in Hong Kong SAR, based on the algorithms described
in Explanatory Notes on Geodetic Datums in Hong Kong by Survey and Map-
ping Office Lands Department, Hong Kong Government (1995). / GPL-2


Name Version
r-hkclustering 1.0.1 Implements an ensemble algorithm for clustering combining a k-means and a noarch
hierarchical clustering approach. / GPL-2
r-hkex.api 0.1 A set of functions helps to retrieve data from HKEX (Hong Kong Stock Ex- noarch
change), see <https://www.hkex.com.hk/> for more information. In addition,
a function generates insert SQL statements from a dataframe. / GPL-3
r-hmdhfdplus 1.9.1 Utilities for reading data from the Human Mortality Database (<https://www. noarch
mortality.org>), Human Fertility Database (<https://www.humanfertility.
org>), and similar databases from the web or locally into an R session as
data.frame objects. These are the two most widely used sources of demo-
graphic data to study basic demographic change, trends, and develop new de-
mographic methods. Other supported databases at this time include the Human
Fertility Collection (<http://www.fertilitydata.org/>), The Japanese Mortality
Database (<http://www.ipss.go.jp/p-toukei/JMD>), and the Canadian Human
Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and
data are standardized. / GPL-2
r-hmeasure 1.0_2 Classification performance metrics that are derived from the ROC curve of noarch
a classifier. The package includes the H-measure performance metric as
described in <http://link.springer.com/article/10.1007/s10994-009-5119-5>,
which computes the minimum total misclassification cost, integrating over
any uncertainty about the relative misclassification costs, as per a user-defined
prior. It also offers a one-stop-shop for other scalar metrics of performance,
including sensitivity, specificity and many others, and also offers plotting tools
for ROC curves and related statistics. / MIT
r-hmisc 4.2_0 Contains many functions useful for data analysis, high-level graphics, utility linux-
operations, functions for computing sample size and power, importing and 32,
annotating datasets, imputing missing values, advanced table making, variable linux-
clustering, character string manipulation, conversion of R objects to LaTeX 64,
and html code, and recoding variables. / GPL (>= 2) osx-
64,
win-
32,
win-
64
r-hmm 1.0 Easy to use library to setup, apply and make inference with discrete time and noarch
discrete space Hidden Markov Models / GPL-2
r-hmmcont 1.0 The package includes the functions designed to analyse continuous observa- noarch
tions processes with the Hidden Markov Model approach. They include Baum-
Welch and Viterbi algorithms and additional visualisation functions. The ob-
servations are assumed to have Gaussian distribution and to be weakly station-
ary processes. The package was created for analyses of financial time series,
but can also be applied to any continuous observations processes. / GPL-3
r-hmmpa 1.0.1 Analysing time-series accelerometer data to quantify length and intensity of noarch
physical activity using hidden Markov models. It also contains the traditional
cut-off point method. Witowski V, Foraita R, Pitsiladis Y, Pigeot I, Wirsik N
(2014)<doi:10.1371/journal.pone.0114089>. / GPL-3
r-hmr 0.4.2 Statistical analysis of static chamber concentration data for trace gas flux esti- noarch
mation. / GPL-2


Name Version
r-hms 0.4.2 Implements an S3 class for storing and formatting time-of-day values, based linux-
on the ‘difftime’ class. / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-hmstimer 0.0.2 Tracks elapsed clock time using a ‘hms()’ scalar (inherits from ‘difftime()’ noarch
with seconds as the unit). / MIT
r-hmvd 1.0 Perform association test between a group of variable and the outcome. / GPL-3 noarch
r-hnp 1.2_6 Generates (half-)normal plots with simulation envelopes using different diag- noarch
nostics from a range of different fitted models. A few example datasets are
included. / GPL-2
r-hoardr 0.5.2 Suite of tools for managing cached files, targeting use in other R packages. noarch
Uses ‘rappdirs’ for cross-platform paths. Provides utilities to manage cache
directories, including targeting files by path or by key; cached directories can
be compressed and uncompressed easily to save disk space. / MIT
r-holdem 1.2 Simulates hands and tournaments of Texas Holdem, the most popular form of noarch
poker. For examples of probability problems involving Texas Holdem and a
brief explanation of the game see Schoenberg, F. (2011). An Introduction to
Probability with Texas Hold’em Examples. Taylor and Francis, New York,
ISBN-13: 978-1439827680. / GPL-2
r-homer 0.3.0 A collection of functions useful for the analysis of building physics experi- noarch
ments. / GPL-2
r-homeric 0.1_3 A simple implementation of doughnut plots - pie charts with a blank center. noarch
The package is named after Homer Simpson - arguably the best-known lover
of doughnuts. / GPL-2
r-homtest 1.0_5 A collection of homogeneity tests described in: Viglione A., Laio F., Claps P. noarch
(2007) ‘‘A comparison of homogeneity tests for regional frequency analysis”,
Water Resources Research, 43, W03428, doi:10.1029/2006WR005095. More
on Regional Frequency Analysis can be found in package nsRFA. / GPL-2
r-horizon 1.2 Calculates horizon elevation angle and sky view factor from a digital terrain noarch
model (Dozier and Frew, 1990). / GPL-2
r-hornpa 1.0 A stand-alone function that generates a user specified number of random noarch
datasets and computes eigenvalues using the random datasets (i.e., implements
Horn’s parallel analysis). Users then compare the resulting eigenvalues (the
mean or the specified percentile) from the random datasets (i.e., eigenvalues
resulting from noise) to the eigenvalues generated with the user’s data. Can be
used for both principal components analysis (PCA) and common/exploratory
factor analysis (EFA). The output table shows how large eigenvalues can be as
a result of merely using randomly generated datasets. If the user’s own dataset
has actual eigenvalues greater than the corresponding eigenvalues, that lends
support to retain that factor/component. In other words, if the i(th) eigenvalue
from the actual data was larger than the percentile of the (i)th eigenvalue gen-
erated using randomly generated data, empirical support is provided to retain
that factor/component. Horn, J. (1965). A rationale and test for the number of
factors in factor analysis. Psychometrika, 32, 179-185. / GPL-3


Name Version
r-horseshoe 0.2.0 Contains functions for applying the horseshoe prior to high- dimensional linear noarch
regression, yielding the posterior mean and credible intervals, amongst other
things. The key parameter tau can be equipped with a prior or estimated via
maximum marginal likelihood estimation (MMLE). The main function, horse-
shoe, is for linear regression. In addition, there are functions specifically for
the sparse normal means problem, allowing for faster computation of for ex-
ample the posterior mean and posterior variance. Finally, there is a function
available to perform variable selection, using either a form of thresholding, or
credible intervals. / GPL-3
r-hotelling 1.0_5 A set of R functions which implements Hotelling’s T^2 test and some variants noarch
of it. Functions are also included for Aitchison’s additive log ratio and centred
log ratio transformations. / GPL-2
r-hotspot 1.0 Contains data for software hotspot analysis, along with a function performing noarch
the analysis itself. / GPL-2
r-housingdata 0.3.0 Monthly median home listing, sale price per square foot, and number of units noarch
sold for 2984 counties in the contiguous United States From 2008 to January
2016. Additional data sets containing geographical information and links to
Wikipedia are also included. / CC0
r-howmany 0.3_1 When testing multiple hypotheses simultaneously, this package provides func- noarch
tionality to calculate a lower bound for the number of correct rejections (as a
function of the number of rejected hypotheses), which holds simultaneously
-with high probability- for all possible number of rejections. As a special case,
a lower bound for the total number of false null hypotheses can be inferred.
Dependent test statistics can be handled for multiple tests of associations. For
independent test statistics, it is sufficient to provide a list of p-values. / GPL-3
r-hpackedbubble 0.1.0 By binding R functions and the ‘Highcharts’ <http://www.highcharts.com/> noarch
charting library, ‘hpackedbubble’ package provides a simple way to draw split
packed bubble charts. / MIT
r-hpbayes 0.1 This package provides all the functions necessary to estimate the 8 parameters noarch
of the Heligman Pollard mortality model using a Bayesian Melding procedure
with IMIS as well as to convert those parameters into age-specifc probabilities
of death and a corresponding life table / Unlimited
r-hqmisc 0.1_1 This package contains some miscellaneous convenience functions, to create noarch
a matrix of dummy columns from a factor, to determine whether x lies in
range [a,b], to add a rectangular bracket to an existing plot, and to convert
frequencies between Hz, semitones, mel and Bark. This package also contains
an example data set of a stratified sample of 80 talkers of Dutch. / GPL-2
r-hripw 0.1.2 Estimates the log hazard ratio associated with a binary exposure using a Cox noarch
PH model weighted by the propensity score. Propensity model is estimated
using a simple logistic regression. Variance estimation takes into account the
propensity score estimation step with the method proposed by Hajage et al.
(2018) <doi:10.1002/bimj.201700330>. Both the average treatment effect on
the overall (ATE) or the treated (ATT) population can be estimated. For the
ATE estimation, both unstabilized and stabilized weights can be used. / GPL-2
r-hrw 1.0_3 The book Semiparametric Regression with R by J. Harezlak, D. Ruppert & noarch
M.P. Wand (2018, Springer; ISBN: 978-1-4939-8851-8) makes use of datasets
and scripts to explain semiparametric regression concepts. Each of the book’s
scripts are contained in this package as well as datasets that are not within
other R packages. Functions that aid semiparametric regression analysis are
also included. / GPL-2


Name Version
r-hsaur 1.3_9 Functions, data sets, analyses and examples from the book ‘’A Handbook of noarch
Statistical Analyses Using R” (Brian S. Everitt and Torsten Hothorn, Chapman
& Hall/CRC, 2006). The first chapter of the book, which is entitled ‘’An In-
troduction to R”, is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. / GPL-3
r-hsaur2 1.1_17Functions, data sets, analyses and examples from the second edition of the noarch
book ‘’A Handbook of Statistical Analyses Using R” (Brian S. Everitt and
Torsten Hothorn, Chapman & Hall/CRC, 2008). The first chapter of the book,
which is entitled ‘’An Introduction to R”, is completely included in this pack-
age, for all other chapters, a vignette containing all data analyses is available.
In addition, the package contains Sweave code for producing slides for se-
lected chapters (see HSAUR2/inst/slides). / GPL-2
r-hsaur3 1.0_9 Functions, data sets, analyses and examples from the third edition of the book noarch
‘’A Handbook of Statistical Analyses Using R” (Torsten Hothorn and Brian
S. Everitt, Chapman & Hall/CRC, 2014). The first chapter of the book, which
is entitled ‘’An Introduction to R”, is completely included in this package,
for all other chapters, a vignette containing all data analyses is available. In
addition, Sweave source code for slides of selected chapters is included in
this package (see HSAUR3/inst/slides). The publishers web page is ‘<http:
//www.crcpress.com/product/isbn/9781482204582>’. / GPL-2
r-hsiccca 1.0 Canonical correlation analysis that extracts nonlinear correlation through the noarch
use of Hilbert Schmidt Independence Criterion and Centered Kernel Target
Alignment. / GPL-2
r-hssvd 1.2 A data mining tool for discovering subgroups of patients and genes that simul- noarch
taneously display unusual levels of variability compared to other genes and
patients. Based on sparse singular value decomposition (SSVD), the method
can detect both mean and variance biclusters in the presence of heterogeneous
residual variance. / GPL-2
r-htm2txt 2.1.1 Convert a html document to simple plain texts by removing all html tags. This noarch
package utilizes regular expressions to strip off html tags. It also offers gettxt()
and browse() function, which enables you to get or browse texts at a certain
web page. / GPL-2
r-htmltab 0.7.1 HTML tables are a valuable data source but extracting and recasting these data noarch
into a useful format can be tedious. This package allows to collect structured
information from HTML tables. It is similar to readHTMLTable() of the XML
package but provides three major advantages. First, the function automati-
cally expands row and column spans in the header and body cells. Second,
users are given more control over the identification of header and body rows
which will end up in the R table, including semantic header information that
appear throughout the body. Third, the function preprocesses table code, cor-
rects common types of malformations, removes unneeded parts and so helps
to alleviate the need for tedious post-processing. / MIT


Name Version
r-htmltable 1.13.1Tables with state-of-the-art layout elements such as row spanners, column linux-
spanners, table spanners, zebra striping, and more. While allowing advanced 32,
layout, the underlying css-structure is simple in order to maximize compati- linux-
bility with word processors such as ‘MS Word’ or ‘LibreOffice’. The package 64,
also contains a few text formatting functions that help outputting text compat- noarch,
ible with HTML/LaTeX. / GPL (>= 3) osx-
64,
win-
32,
win-
64
r-htmltools 0.3.6 Tools for HTML generation and output. / GPL (>= 2) linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-htmlwidgets 1.3 A framework for creating HTML widgets that render in various contexts in- linux-
cluding the R console, ‘R Markdown’ documents, and ‘Shiny’ web applica- 32,
tions. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-httpcache 1.1.0 In order to improve performance for HTTP API clients, ‘httpcache’ provides noarch
simple tools for caching and invalidating cache. It includes the HTTP verb
functions GET, PUT, PATCH, POST, and DELETE, which are drop-in re-
placements for those in the ‘httr’ package. These functions are cache-aware
and provide default settings for cache invalidation suitable for RESTful APIs;
the package also enables custom cache-management strategies. Finally, ‘http-
cache’ includes a basic logging framework to facilitate the measurement of
HTTP request time and cache performance. / MIT
r-httpcode 0.2.0 Find and explain the meaning of ‘HTTP’ status codes. Functions included for noarch
searching for codes by full or partial number, by message, and get appropriate
dog and cat images for many status codes. / MIT
r-httprequest 0.0.10HTTP Request protocols. Implements the GET, POST and multipart POST noarch
request. / GPL-2


Name Version
r-httptest 3.2.2 Testing and documenting code that communicates with remote servers can be noarch
painful. Dealing with authentication, server state, and other complications can
make testing seem too costly to bother with. But it doesn’t need to be that
hard. This package enables one to test all of the logic on the R sides of the
API in your package without requiring access to the remote service. Impor-
tantly, it provides three contexts that mock the network connection in different
ways, as well as testing functions to assert that HTTP requests were—or were
not—made. It also allows one to safely record real API responses to use as
test fixtures. The ability to save responses and load them offline also enables
one to write vignettes and other dynamic documents that can be distributed
without access to a live server. / MIT
r-httpuv 1.5.1 Provides low-level socket and protocol support for handling HTTP and Web- linux-
Socket requests directly from within R. It is primarily intended as a building 32,
block for other packages, rather than making it particularly easy to create com- linux-
plete web applications using httpuv alone. httpuv is built on top of the libuv 64,
and http-parser C libraries, both of which were developed by Joyent, Inc. (See osx-
LICENSE file for libuv and http-parser license information.) / GPL (>= 2) | 64,
file LICENSE win-
32,
win-
64
r-httr 1.4.0 Useful tools for working with HTTP organised by HTTP verbs (GET(), linux-
POST(), etc). Configuration functions make it easy to control additional re- 32,
quest components (authenticate(), add_headers() and so on). / MIT file LI- linux-
CENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-hues 0.1 Creating effective colour palettes for figures is challenging. This package noarch
generates and plot palettes of optimally distinct colours in perceptually uni-
form colour space, based on ‘iwanthue’ <http://tools.medialab.sciences-po.fr/
iwanthue/>. This is done through k-means clustering of CIE Lab colour space,
according to user-selected constraints on hue, chroma, and lightness. / LGPL-3
r-humanformat 1.0 Format quantities of time or bytes into human-friendly strings. / MIT noarch
r-humanize 0.2.0 An almost direct port of the ‘python’ ‘humanize’ package <https://github.com/ noarch
jmoiron/humanize>. This package contains utilities to convert values into hu-
man readable forms. / MIT
r-humidity 0.1.4 Vapor pressure, relative humidity, absolute humidity, specific humidity, and noarch
mixing ratio are commonly used water vapor measures in meteorology. This
R package provides functions for calculating saturation vapor pressure (hPa),
partial water vapor pressure (Pa), relative humidity (%), absolute humidity
(kg/m^3), specific humidity (kg/kg), and mixing ratio (kg/kg) from tempera-
ture (K) and dew point (K). Conversion functions between humidity measures
are also provided. / GPL-3


Name Version
r-hunspell 3.0 Low level spell checker and morphological analyzer based on the famous ‘hun- linux-
spell’ library <https://hunspell.github.io>. The package can analyze or check 32,
individual words as well as parse text, latex, html or xml documents. For linux-
a more user-friendly interface use the ‘spelling’ package which builds on this 64,
package to automate checking of files, documentation and vignettes in all com- osx-
mon formats. / GPL-2 | LGPL-2.1 | MPL-1.1 64,
win-
32,
win-
64
r-hurdlr 0.1 When considering count data, it is often the case that many more zero counts noarch
than would be expected of some given distribution are observed. It is well es-
tablished that data such as this can be reliably modelled using zero-inflated or
hurdle distributions, both of which may be applied using the functions in this
package. Bayesian analysis methods are used to best model problematic count
data that cannot be fit to any typical distribution. The package functions are
flexible and versatile, and can be applied to varying count distributions, pa-
rameter estimation with or without explanatory variable information, and are
able to allow for multiple hurdles as it is also not uncommon that count data
have an abundance of large-number observations which would be considered
outliers of the typical distribution. In lieu of throwing out data or misspeci-
fying the typical distribution, these extreme observations can be applied to a
second, extreme distribution. With the given functions of this package, such a
two-hurdle model may be easily specified in order to best manage data that is
both zero-inflated and over-dispersed. / GPL-2
r-hw.pval 1.0 HW.pval calculates plain and fully conditional root-mean-square, chi-square, noarch
and log likelihood-ratio P-values for the user-provided genotypic counts to
be consistent with the Hardy-Weinberg equilibrium model. For further infor-
mation on the Hardy-Weinberg equilibrium model and the pseudocode, refer
to the paper Testing Hardy-Weinberg equilibrium with a simple root-mean-
square statistic by Rachel Ward. / GPL-3
r-hwde 0.67 Fits models for genotypic disequilibria, as described in Huttley and Wilson noarch
(2000), Weir (1996) and Weir and Wilson (1986). Contrast terms are available
that account for first order interactions between loci. Also implements, for a
single locus in a single population, a conditional exact test for Hardy-Weinberg
equilibrium. / GPL-2
r-hweintrinsic 1.2.2 General (multi-allelic) Hardy-Weinberg equilibrium problem from an objec- noarch
tive Bayesian testing standpoint. This aim is achieved through the identifica-
tion of a class of priors specifically designed for this testing problem. A class
of intrinsic priors under the full model is considered. This class is indexed by
a tuning quantity, the training sample size, as discussed in Consonni, Moreno
and Venturini (2010). These priors are objective, satisfy Savage’s continuity
condition and have proved to behave extremely well for many statistical testing
problems. / GPL-2
r-hwriter 1.3.2 Easy-to-use and versatile functions to output R objects in HTML format / noarch
LGPL-2.1
r-hybridhclust 1.0_5 Hybrid hierarchical clustering via mutual clusters. A mutual cluster is a set of noarch
points closer to each other than to all other points. Mutual clusters are used to
enrich top-down hierarchical clustering. / GPL-2


Name Version
r-hydra 0.1.0 Calculate an optimal embedding of a set of data points into low-dimensional noarch
hyperbolic space. This uses the strain-minimizing hyperbolic embedding of
Keller-Ressel and Nargang (2019), see <arXiv:1903.08977>. / GPL-2
r-hydrogeo 0.6_1 Contains one function for drawing Piper diagrams (also called Piper-Hill dia- noarch
grams) of water analyses for major ions. / BSD_2_clause
r-hydrostats 0.2.7 Calculates a suite of hydrologic indices for daily time series data that are noarch
widely used in hydrology and stream ecology. / GPL-2
r-hyperbolicdist 0.6_2 This package provides functions for the hyperbolic and related distributions. noarch
Density, distribution and quantile functions and random number generation are
provided for the hyperbolic distribution, the generalized hyperbolic distribu-
tion, the generalized inverse Gaussian distribution and the skew-Laplace dis-
tribution. Additional functionality is provided for the hyperbolic distribution,
including fitting of the hyperbolic to data. / GPL-2
r-hypercube 0.1.0 Provides methods for organizing data in a hypercube (i.e. a multi- noarch
dimensional cube). Cubes are generated from molten data frames. Each
cube can be manipulated with five operations: rotation (changeDimen-
sionOrder()), dicing and slicing (add.selection(), remove.selection()), drilling
down (add.aggregation()), and rolling up (remove.aggregation()). / GPL-3
r-hypergate 0.8.1 Given a high-dimensional dataset that typically represents a cytometry dataset, noarch
and a subset of the datapoints, this algorithm outputs an hyperrectangle so that
datapoints within the hyperrectangle best correspond to the specified subset. In
essence, this allows the conversion of clustering algorithms’ outputs to gating
strategies outputs. / GPL-3
r-hypergeo 1.2_13The Gaussian hypergeometric function for complex numbers. / GPL-2 noarch
r- 0.1.1 Implements an algorithm for efficient and exact calculation of hypergeometric noarch
hypersampleplan and binomial probabilities using Chebyshev polynomials, while other algo-
rithm use an approximation when N is large. A useful applications is also
considered in this package for the construction of attribute sampling plans
which is an important field of statistical quality control. The quantile, and
the confidence limit for the attribute sampling plan are also implemented in
this package. The hypergeometric distribution can be represented in terms of
Chebyshev polynomials. This representation is particularly useful in the cal-
culation of exact values of hypergeometric variables. / GPL-2
r-hyphy 1.0 A Bay Area high level phylogenetic analysis package mostly using the birth- noarch
death process. Analysis of species tree branching times and simulation of
species trees under a number of different time variable birth-death processes.
Analysis of gene tree species tree reconciliations and simulations of gene trees
in species trees. / GPL-2
r-hypothesestest 1.0 Compute the confidence interval of the population mean with one sample or noarch
of the difference of population means of two samples from normal distribu-
tions or t-distributions.Compute the confidence interval of population variance
with one sample or of the difference of population variances of two samples
by chi-square tests.Test for population mean or the differences of two normal
samples under normality with the given null hypothesis H0,which depends on
the user,so that he can know if he can reject H0 or not at the significance level
alpha.Do the chi-square tests with one or two samples which have multinomial
distributions by using an approximate chi-square distribution when n is large
enough. / GPL-2


Name Version
r-iabin 1.0 In randomized-controlled trials, interim analyses are often planned for possible noarch
early trial termination to claim superiority or futility of a new therapy. Blinded
data also have information about the potential treatment difference between the
groups. We developed a blinded data monitoring tool that enables investigators
to predict whether they observe such an unblinded interim analysis results that
supports early termination of the trial. Investigators may skip some of the
planned interim analyses if an early termination is unlikely. This tool will
provide reference information about N: Sample size at interim analysis, and T:
Total number of responders at interim analysis for decision on performing an
interim analysis. / GPL-2
r-iadapt 0.1.0 Simulate and implement early phase two-stage adaptive dose-finding design noarch
developed by Chiuzan et al. (2018) <DOI:10.1080/19466315.2018.1462727>.
/ LGPL-3
r-ialsasynthesis 0.1.6 Synthesizes information across collaborating research. Created specifically for noarch
Integrative Analysis of Longitudinal Studies of Aging (IALSA). / GPL-2
r-iasd 1.1 Calculate AIC’s and AICc’s of unimodal model (one normal distribution) and noarch
bimodal model(a mixture of two normal distributions) which fit the distribution
of indices of asymmetry (IAS), and plot their density, to help determine IAS
distribution is unimodal or bimodal. / GPL-2
r-iatanalytics 0.1.1 Quickly score raw data outputted from an Implicit Association Test noarch
(IAT; Greenwald, McGhee, & Schwartz, 1998) <doi:10.1037/0022-
3514.74.6.1464>. IAT scores are calculated as specified by Greenwald, Nosek,
and Banaji (2003) <doi:10.1037/0022-3514.85.2.197>. The output of this
function is a data frame that consists of four rows containing the following
information: (1) the overall IAT effect size for the participant’s dataset, (2) the
effect size calculated for odd trials only, (3) the effect size calculated for even
trials only, and (4) the proportion of trials with reaction times under 300ms
(which is important for exclusion purposes). Items (2) and (3) allow for a
measure of the internal consistency of the IAT. Specifically, you can use the
subsetted IAT effect sizes for odd and even trials to calculate Cronbach’s alpha
across participants in the sample. The input function consists of three argu-
ments. First, indicate the name of the dataset to be analyzed. This is the only
required input. Second, indicate the number of trials in your entire IAT (the
default is set to 220, which is typical for most IATs). Last, indicate whether
congruent trials (e.g., flowers and pleasant) or incongruent trials (e.g., guns
and pleasant) were presented first for this participant (the default is set to con-
gruent). Data files should consist of six columns organized in order as follows:
Block (0-6), trial (0-19 for training blocks, 0-39 for test blocks), category (de-
pendent on your IAT), the type of item within that category (dependent on
your IAT), a dummy variable indicating whether the participant was correct or
incorrect on that trial (0=correct, 1=incorrect), and the participantâ C™s reac-
tion time (in milliseconds). A sample dataset (titled ‘sampledata’) is included
in this package to practice with. / MIT


Name Version
r-iatscore 0.1.1 This minimalist package is designed to quickly score raw data outputted from noarch
an Implicit Association Test (IAT; Greenwald, McGhee, & Schwartz, 1998)
<doi:10.1037/0022-3514.74.6.1464>. IAT scores are calculated as specified
by Greenwald, Nosek, and Banaji (2003) <doi:10.1037/0022-3514.85.2.197>.
Outputted values can be interpreted as effect sizes. The input function consists
of three arguments. First, indicate the name of the dataset to be analyzed.
This is the only required input. Second, indicate the number of trials in your
entire IAT (the default is set to 219, which is typical for most IATs). Last,
indicate whether congruent trials (e.g., flowers and pleasant) or incongruent
trials (e.g., guns and pleasant) were presented first for this participant (the
default is set to congruent). The script will tell you how long it took to run
the code, the effect size for the participant, and whether that participant should
be excluded based on the criteria outlined by Greenwald et al. (2003). Data
files should consist of six columns organized in order as follows: Block (0-
6), trial (0-19 for training blocks, 0-39 for test blocks), category (dependent
on your IAT), the type of item within that category (dependent on your IAT),
a dummy variable indicating whether the participant was correct or incorrect
on that trial (0=correct, 1=incorrect), and the participantâ C™s reaction time
(in milliseconds). Three sample datasets are included in this package (labeled
‘IAT’, ‘TooFastIAT’, and ‘BriefIAT’) to practice with. / MIT
r-ibdhaplortools 1.8 Functions to analyze, plot, and store the output of running IBD_Haplo soft- noarch
ware package. More information regarding IBD_Haplo can be found at
http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml. / GPL-3
r-ibdlabels 1.1 Convert label, lexicographic, jacquard and vec, full state description vector. noarch
All conversions are done to and from label, as used in IBD_Haplo. More in-
formation regarding IBD_Haplo can be found at http://www.stat.washington.
edu/thompson/Genepi/pangaea.shtml. / GPL-3
r-ibelief 1.2 Some basic functions to implement belief functions including: transfor- noarch
mation between belief functions using the method introduced by Philippe
Smets (arXiv:1304.1122 [cs.AI]), evidence combination, evidence discount-
ing, decision-making, and constructing masses. Currently, thirteen combina-
tion rules and five decision rules are supported. It can also be used to generate
different types of random masses when working on belief combination and
conflict management. / GPL-2
r-ibmsunburst 0.1.1 Generates Personality Insights sunburst diagrams based on ‘IBM Watson’ Per- noarch
sonality Insights service output. / MIT
r-ibrokers 0.9_12Provides native R access to Interactive Brokers Trader Workstation API. / noarch
GPL-3
r- 1.3.1 Training datasets for iC10; which implements the classifier described in the noarch
ic10trainingdata paper ‘Genome-driven integrated classification of breast cancer validated in
over 7,500 samples’ (Ali HR et al., Genome Biology 2014). It uses copy num-
ber and/or expression form breast cancer data, trains a pamr classifier (Tibshi-
rani et al.) with the features available and predicts the iC10 group. Genomic
annotation for the training dataset has been obtained from Mark Dunning’s
lluminaHumanv3.db package. / GPL-3
r-ic2 1.0_1 Lorenz and concentration curves; Atkinson, Generalized entropy and SGini noarch
indices (with decomposition) / GPL-2
r-ic50 1.4.2 Calculation of IC50 values, automatic drawing of dose-response curves and noarch
validation of compound screens on 96- and 384-well plates. / GPL-3


Name Version
r-ica 1.0_2 Independent Component Analysis (ICA) using various algorithms: FastICA, noarch
Information-Maximization (Infomax), and Joint Approximate Diagonalization
of Eigenmatrices (JADE). / GPL-2
r-icaff 1.0.1 Imperialist Competitive Algorithm (ICA) <http://en.wikipedia.org/wiki/ noarch
Imperialist_competitive_algorithm> is a computational method that is used to
solve optimization problems of different types and it is the mathematical model
and the computer simulation of human social evolution. The package provides
a minimum value for the cost function and the best value for the optimiza-
tion variables by Imperialist Competitive Algorithm. Users can easily define
their own objective function depending on the problem at hand. This version
has been successfully applied to solve optimization problems, for continuous
functions. / GPL-2
r-icarus 0.3.1 Provides user-friendly tools for calibration in survey sampling. The package is noarch
production-oriented, and its interface is inspired by the famous popular macro
‘Calmar’ for SAS, so that ‘Calmar’ users can quickly get used to ‘icarus’. In
addition to calibration (with linear, raking and logit methods), ‘icarus’ features
functions for calibration on tight bounds and penalized calibration. / GPL-3
r-icc 2.3.0 Assist in the estimation of the Intraclass Correlation Coefficient (ICC) from noarch
variance components of a one-way analysis of variance and also estimate the
number of individuals or groups necessary to obtain an ICC estimate with a
desired confidence interval width. / GPL-2
r-icc.sample.size 1.0 Provides functions to calculate the requisite sample size for studies where ICC noarch
is the primary outcome. Can also be used for calculation of power. In both
cases it allows the user to test the impact of changing input variables by cal-
culating the outcome for several different values of input variables. Based off
the work of Zou. Zou, G. Y. (2012). Sample size formulas for estimating
intraclass correlation coefficients with precision and assurance. Statistics in
medicine, 31(29), 3972-3981. / GPL-3
r-iccbin 1.1.1 Assists in generating binary clustered data, estimates of Intracluster Corre- noarch
lation coefficient (ICC) for binary response in 16 different methods, and 5
different types of confidence intervals. / GPL-2
r-icd.data 1.0 Data from the United States Center for Medicare and Medicaid Services noarch
(CMS) is included in this package. There are ICD-9 and ICD-10 diagnos-
tic and procedure codes, and lists of the chapter and sub-chapter headings and
the ranges of ICD codes they encompass. There are also two sample datasets.
These data are used by the ‘icd’ package for finding comorbidities. / GPL-3
r-icdglm 1.0.0 Provides an estimator for generalized linear models with incomplete data for noarch
discrete covariates. The estimation is based on the EM algorithm by the
method of weights by Ibrahim (1990) <DOI:10.2307/2290013>. / GPL-2
r-icebox 1.1.2 Implements Individual Conditional Expectation (ICE) plots, a tool for visu- noarch
alizing the model estimated by any supervised learning algorithm. ICE plots
refine Friedman’s partial dependence plot by graphing the functional relation-
ship between the predicted response and a covariate of interest for individual
observations. Specifically, ICE plots highlight the variation in the fitted values
across the range of a covariate of interest, suggesting where and to what extent
they may exist. / GPL-2 | GPL-3


Name Version
r-iceinfer 1.1 Given two unbiased samples of patient level data on cost and effectiveness for a noarch
pair of treatments, make head-to-head treatment comparisons by (i) generating
the bivariate bootstrap resampling distribution of ICE uncertainty for a speci-
fied value of the shadow price of health, lambda, (ii) form the wedge-shaped
ICE confidence region with specified confidence fraction within [0.50, 0.99]
that is equivariant with respect to changes in lambda, (iii) color the bootstrap
outcomes within the above confidence wedge with economic preferences from
an ICE map with specified values of lambda, beta and gamma parameters,
(iv) display VAGR and ALICE acceptability curves, and (v) illustrate varia-
tion in ICE preferences by displaying potentially non-linear indifference(iso-
preference) curves from an ICE map with specified values of lambda, beta and
either gamma or eta parameters. / GPL-3
r-icemelt 1.0 Estimates the parameters of the semiparametric linear transformation model linux-
using imputation method, naive method and regression calibration method 64,
when time-to-event is interval-censored and a covariate is measured with er- osx-
ror. A right censoring indicator must be available. The methods implemented 64,
in this package can be found in Mandal, S., Wang, S. and Sinha, S. (2019). win-
Analysis of Linear Transformation Models with Covariate Measurement Error 64
and Interval Censoring. (accepted, Statistics In Medicine). / GPL-2
r-icensmis 1.3.1 We consider studies in which information from error-prone diagnostic tests or linux-
self-reports are gathered sequentially to determine the occurrence of a silent 64,
event. Using a likelihood-based approach incorporating the proportional haz- osx-
ards assumption, we provide functions to estimate the survival distribution and 64,
covariate effects. We also provide functions for power and sample size calcu- win-
lations for this setting. / GPL-2 64
r-icesadvice 2.0_0 A collection of functions that facilitate computational steps related to advice noarch
for fisheries management, according to ICES guidelines. These include meth-
ods for calculating reference points and model diagnostics. / GPL-2
r-icesdatras 1.3_0 R interface to access the web services of the ICES (International Council for noarch
the Exploration of the Sea) DATRAS trawl survey database <https://datras.
ices.dk/WebServices/Webservices.aspx>. / GPL-2
r-icestaf 3.1_1 Functions to support the ICES Transparent Assessment Framework <http: noarch
//taf.ices.dk> to organize data, methods, and results used in ICES assessments.
ICES is an organization facilitating international collaboration in marine sci-
ence. / GPL-2
r-icesvocab 1.1_4 R interface to access the RECO POX web services of the ICES (International noarch
Council for the Exploration of the Sea) Vocabularies database <https://vocab.
ices.dk/services/POX.aspx>. / GPL-2
r-icge 0.3 ICGE is a package that helps to estimate the number of real clusters in data noarch
as well as to identify atypical units. The underlying methods are based on
distances rather than on unit x variables. / GPL-2
r-iciter 0.1.0 A minimal wrapper around the NIH’s ‘iCite’ API (<https://icite.od.nih.gov/ noarch
api>). Given a vector of pubmed IDs, this package returns a dataframe of the
information yielded by the ‘iCite’ API. The primary metric yielded by ‘iCite’
is the paper’s relative citation ratio, but the API also returns other meta-data
from the paper, including author names, publication journal, publication year,
paper title, doi, and a number of other citation metrics. / MIT
r-icluster 2.1.0 Integrative clustering of multiple genomic data types using a joint latent vari- noarch
able model. / GPL-2


Name Version
r-icods 1.0 Sieve semiparametric likelihood methods for analyzing interval-censored noarch
failure time data from an outcome-dependent sampling (ODS) design and
from a case-cohort design. Zhou, Q., Cai, J., and Zhou, H. (2018)
<doi:10.1111/biom.12744>; Zhou, Q., Zhou, H., and Cai, J. (2017)
<doi:10.1093/biomet/asw067>. / GPL-2
r-icpsrdata 0.4.0 Reproducible, programmatic retrieval of datasets from the Inter-university noarch
Consortium for Political and Social Research archive. / MIT
r-icr 0.6.0 Provides functions to compute and plot Krippendorff’s inter-coder reliability linux-
coefficient alpha and bootstrapped uncertainty estimates (Krippendorff 2004, 64,
ISBN:0761915443). The bootstrap routines are set up to make use of parallel osx-
threads where supported. / GPL-2 64,
win-
64
r-icranks 3.1 Algorithms to construct simultaneous confidence intervals for the ranks of linux-
means mu_1,. . . ,mu_n based on an independent Gaussian sample using multi- 64,
ple testing techniques. / GPL-2 osx-
64,
win-
64
r-icsw 1.0.0 Provides the necessary tools to estimate average treatment effects with an in- noarch
strumental variable by re-weighting observations using a model of compliance.
/ MIT
r-icv 1.0 Functions for computing the global and local Gaussian density estimates noarch
based on the ICV bandwidth. See the article of Savchuk, O.Y., Hart,
J.D., Sheather, S.J. (2010). Indirect cross-validation for density estima-
tion. Journal of the American Statistical Association, 105(489), 415-423
<doi:10.1198/jasa.2010.tm08532>. / GPL-2
r-idbg 1.0 An interactive R debugger / GPL-2 noarch
r-idcard 0.3.0 The digits of the old version (before 2000 year) of ‘Chinese ID Card Number’ noarch
is 15, this package aims to update to the current version of 18 digits. Besides,
this package can help check whether the given ‘ID’ is right or not. / GPL-3
r-idendr0 1.5.3 Interactive dendrogram that enables the user to select and color clusters, to noarch
zoom and pan the dendrogram, and to visualize the clustered data not only
in a built-in heat map, but also in ‘GGobi’ interactive plots and user-supplied
plots. This is a backport of Qt-based ‘idendro’ (<https://github.com/tsieger/
idendro>) to base R graphics and Tcl/Tk GUI. / GPL-2
r-identity 0.2_1 Calculate identity coefficients, based on Mark Abney’s C code. / GPL-2 linux-
64,
osx-
64,
win-
64


Name Version
r-idetect 0.1.0 Provides efficient implementation of the Isolate-Detect methodology for noarch
the consistent estimation of the number and location of multiple change-
points in one-dimensional data sequences from the deterministic noise
model. For details on the Isolate-Detect methodology, please see
Anastasiou and Fryzlewicz (2018) <https://docs.wixstatic.com/ugd/24cdcc_
6a0866c574654163b8255e272bc0001b.pdf>. Currently implemented scenar-
ios are: piecewise-constant signal with Gaussian noise, piecewise-constant
signal with heavy-tailed noise, continuous piecewise-linear signal with Gaus-
sian noise, continuous piecewise-linear signal with heavy-tailed noise. / GPL-
3
r-idiogramfish 1.0.0 Plot idiograms of several karyotypes having a set of dataframes for chromo- noarch
some data and optionally mark data. Includes also a function to plot holo-
centrics and its marks supporting micrometers and Mb. Marks can have
square or dot form, its legend (label) can be drawn inline or to the right
of karyotypes. It is possible to calculate chromosome indices by Levan et
al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x> , karyotype indices of
Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986)
<doi:10.2307/1221906> and classify chromosomes by morphology Guerra
(1986) and Levan et al. (1964). / GPL-2
r-idmining 1.0.6 Contains techniques for mining large and high-dimensional data sets by using noarch
the concept of Intrinsic Dimension (ID). Here the ID is not necessarily an
integer. It is extended to fractal dimensions. And the Morisita estimator is
used for the ID estimation, but other tools are included as well. / CC BY-NC-
SA 4.0
r-idmtpreg 1.1 Modeling of regression effects for transition probabilities in a progres- linux-
sive illness-death model. Azarang, Scheike, and de Una-Alvarez (2017) 64,
<doi:10.1002/sim.7245>. / GPL-2 osx-
64,
win-
64
r-idpmisc 1.1.19Different high-level graphics functions for displaying large datasets, display- linux-
ing circular data in a very flexible way, finding local maxima, brewing color 64,
ramps, drawing nice arrows, zooming 2D-plots, creating figures with differ- osx-
ently colored margin and plot region. In addition, the package contains auxil- 64,
iary functions for data manipulation like omitting observations with irregular win-
values or selecting data by logical vectors, which include NAs. Other functions 64
are especially useful in spectroscopy and analyses of environmental data: ro-
bust baseline fitting, finding peaks in spectra, converting humidity measures. /
GPL-3
r-idr 1.2 This is a package for estimating the copula mixture model and plotting cor- noarch
respondence curves in Measuring reproducibility of high-throughput experi-
ments (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li,
Brown, Huang, and Bickel / GPL (>= 2.0)
r-ids 1.0.1 Generate random or human readable and pronounceable identifiers. / MIT noarch
r-idx2r 1.0.0 Convert files to and from IDX format to vectors, matrices and arrays. IDX noarch
is a very simple file format designed for storing vectors and multidimensional
matrices in binary format. The format is described on the website from Yann
LeCun <http://yann.lecun.com/exdb/mnist/>. / MIT
r-ieeeround 0.2_0 A pair of functions for getting and setting the IEEE rounding mode for floatinglinux-
point computations. / GPL-2 64,
osx-64


Name Version
r-iemiscdata 0.6.1 Miscellaneous data sets [Engineering Economics, Environmental/ Water Re- noarch
sources Engineering, US Presidential Elections]. / GPL-3
r-iemisctext 0.9.99The eclectic collection includes the following written pieces: The War Prayer noarch
by Mark Twain, War Is A Racket by Major General Smedley Butler, The Mask
of Anarchy: Written on the Occasion of the Massacre at Manchester by Percy
Bysshe Shelley, Connect the D.O.T.S. by Obiora Embry, Untitled: Climate
Strange by Irucka Ajani Embry, and Untitled: Us versus Them or People
Screwing over Other People (as we all live on one Earth and there is no us
versus them in the actual Ultimate Reality} by Irucka Ajani Embry. / GPL-3
r-ifa 7.0 The package performes Independent Factor Analysis / GPL-2 linux-
64,
osx-
64,
win-
64
r-ifctools 0.3.2 Provides utility functions to deal with Italian fiscal code (‘codice fiscale’). / linux-
GPL-3 64,
osx-
64,
win-
64
r-ifs 0.1.5 Iterated Function Systems Estimator. / GPL-2 linux-
64,
osx-
64,
win-
64
r- 0.1.2.0A dataset of the top colours of photos from Instagram taken in 2014 in the noarch
ig.vancouver.2014.topcolour
city of Vancouver, British Columbia, Canada. It consists of: top colour and
counts data. This data was obtained using the Instagram API. Instagram is a
web photo sharing service. It can be found at: <https://instagram.com>. The
Instagram API is documented at: <https://instagram.com/developer/>. / CC0
r-igasso 1.4 A collection of statistical tests for genetic association studies. / GPL-2 noarch
r-igorr 0.8.1 Provides function to read data from the ‘Igor Pro’ data analysis program by noarch
Wavemetrics. The data formats supported are ‘Igor’ packed experiment for-
mat (pxp) and ‘Igor’ binary wave (ibw). See: http://www.wavemetrics.com/
for details. Also includes functions to load special pxp files produced by the
‘Igor Pro’ ‘Neuromatic’ and ‘Nclamp’ packages for recording and analysing
neuronal data. See http://www.neuromatic.thinkrandom.com/ for details. /
GPL-2
r-igraph 1.2.4.1Routines for simple graphs and network analysis. It can handle large graphs linux-
very well and provides functions for generating random and regular graphs, 32,
graph visualization, centrality methods and much more. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
r-igraphdata 1.0.1 A small collection of various network data sets, to use with the ‘igraph’ pack- noarch
age: the Enron email network, various food webs, interactions in the im-
munoglobulin protein, the karate club network, Koenigsberg’s bridges, visuo-
tactile brain areas of the macaque monkey, UK faculty friendship network,
domestic US flights network, etc. / CC BY-SA 4.0 file LICENSE
r-igraphinshiny 0.1 Using ‘shiny’ to demo ‘igraph’ package makes learning graph theory easy and noarch
fun. / GPL-2
r-igraphtosonia 1.0 This program facilitates exporting igraph graphs to the SoNIA file format / noarch
GPL-2
r-igsea 1.2 To integrate multiple GSEA studies, we propose a hybrid strategy, iGSEA- noarch
AT, for choosing random effects (RE) versus fixed effect (FE) models, with an
attempt to achieve the potential maximum statistical efficiency as well as sta-
bility in performance in various practical situations. In addition to iGSEA-AT,
this package also provides options to perform integrative GSEA with testing
based on a FE model (iGSEA-FE) and testing based on a RE model (iGSEA-
RE). The approaches account for different set sizes when testing a database of
gene sets. The function is easy to use, and the three approaches can be applied
to both binary and continuous phenotypes. / GPL-2
r-ihs 1.0 Density, distribution function, quantile function and random generation for the noarch
inverse hyperbolic sine distribution. This package also provides a function
that can fit data to the inverse hyperbolic sine distribution using maximum
likelihood estimation. / GPL-3
r-iilasso 0.0.2 Efficient algorithms for fitting linear / logistic regression model with Indepen- linux-
dently Interpretable Lasso. Takada, M., Suzuki, T., & Fujisawa, H. (2018). 64,
Independently Interpretable Lasso: A New Regularizer for Sparse Regres- osx-
sion with Uncorrelated Variables. AISTATS. <http://proceedings.mlr.press/ 64,
v84/takada18a/takada18a.pdf>. / MIT win-
64
r-im 1.0 Compute moments of images and perform reconstruction from moments. / linux-
GPL-2 64,
osx-
64,
win-
64
r-image 1.0 Performs mQTL (methylation quantitative-trait locus) mapping in bisulfite linux-
sequencing studies by fitting a binomial mixed model and then incorporat- 64,
ing the allelic-specific methylation pattern. Based on Fan, Yue; Vilgalys, osx-
Tauras P.; Sun, Shiquan; Peng, Qinke; Tung, Jenny; Zhou, Xiang (2019) 64,
<doi:10.1101/615039>. / GPL-2 win-
64
r-imageviewer 0.1.0 Display a 2D-matrix data as a interactive zoomable gray-scale image viewer, noarch
providing tools for manual data inspection. The viewer window shows cur-
sor guiding lines and a corresponding data slices for both axes at the current
cursor position. A tool-bar allows adjusting image display brightness/contrast
through WebGL filters and performing basic high-pass/low-pass filtering. /
MIT


Name Version
r-imagine 1.5.2 Provides fast application of image filters to data matrices, using R and C algo- linux-
rithms. / GPL-2 64,
osx-
64,
win-
64
r-imak 1.2.2 This is an Automatic Item Generator for Psychological Assessment. Items noarch
created with the ‘IMak’ package should not be used in applied settings
as part of the working protocol without ensuring first that the items meet
the required psychometric quality standards (see Blum & Holling, 2018)
<DOI:10.3389/fpsyg.2018.01286>. / GPL-3
r-imap 1.32 Zoom in and out of maps or any supplied lines or points, with control for color, noarch
poly fill, and aspect. / GPL-2
r-imfdata 0.2.0 Search, extract and formulate IMF’s datasets. / MIT noarch
r-imgur 1.0.3 A complete API client for the image hosting service Imgur.com, including the noarch
an imgur graphics device, enabling the easy upload and sharing of plots. /
GPL-3
r-imgw 0.2.0 Download Polish meteorological and hydrological data from the Institute of noarch
Meteorology and Water Management - National Research Institute (<https:
//dane.imgw.pl/>). This package also allows for adding geographical coordi-
nates for each observation. / MIT
r-imis 0.1 IMIS algorithm draws samples from the posterior distribution. The user has to noarch
define the following R functions in advance: prior(x) calculates prior density
of x, likelihood(x) calculates the likelihood of x, and sample.prior(n) draws n
samples from the prior distribution. / GPL-2
r-immailgun 0.1.2 Send emails using the ‘mailgun’ api. To use this package you will need an noarch
account from <https://www.mailgun.com> . / GPL-3
r-immigrate 0.0.2 Based on large margin principle, this package performs feature selection linux-
methods: IM4E(Iterative Margin-Maximization under Max-Min Entropy Al- 64,
gorithm); imIM4E(imbalance Iterative Margin-Maximization under Max- osx-
Min Entropy Algorithm); Immigrate(Iterative Max-Min Entropy Margin- 64,
Maximization with Interaction Terms Algorithm); BIM(Boosted version of win-
IMMIGRATE algorithm); Simba(Iterative Search Margin Based Algorithm); 64
LFE(Local Feature Extraction Algorithm). This package also performs pre-
diction for the above feature selection methods. See Zhao et al. (2018)
<arXiv:1810.02658> for more details. / GPL-2
r-impact 0.1.1 Implement a multivariate analysis of the impact of items to identify a bias in noarch
the questionnaire validation of Likert-type scale variables. The items requires
considering a null value (category doesn’t have tendency). Offering frequency,
importance and impact of the items. / GPL-2
r-impactiv 1.0 In this package, you can find two functions proposed in Ding, Geng and Zhou noarch
(2011) to estimate direct and indirect causal effects with randomization and
multiple-component intervention using instrumental variable method. / GPL-
2


Name Version
r-impimp 0.3.1 Imputing blockwise missing data by imprecise imputation, featuring a domain- noarch
based, variable-wise, and case-wise strategy. Furthermore, the estimation of
lower and upper bounds for unconditional and conditional probabilities based
on the obtained imprecise data is implemented. Additionally, two utility func-
tions are supplied: one to check whether variables in a data set contain set-
valued observations; and another to merge two already imprecisely imputed
data. The method is described in a technical report by Endres, Fink and Au-
gustin (2018, <doi:10.5282/ubm/epub.42423>). / GPL-2 | GPL-3
r-implyr 0.2.4 ‘SQL’ back-end to ‘dplyr’ for Apache Impala, the massively parallel process- linux-
ing query engine for Apache ‘Hadoop’. Impala enables low-latency ‘SQL’ 32,
queries on data stored in the ‘Hadoop’ Distributed File System ‘(HDFS)’, linux-
Apache ‘HBase’, Apache ‘Kudu’, Amazon Simple Storage Service ‘(S3)’, 64,
Microsoft Azure Data Lake Store ‘(ADLS)’, and Dell ‘EMC’ ‘Isilon’. See noarch,
<https://impala.apache.org> for more information about Impala. / Apache Li- osx-
cense 2.0 | file LICENSE 64,
win-
32,
win-
64
r-import 1.1.0 This is an alternative mechanism for importing objects from packages. The noarch
syntax allows for importing multiple objects from a package with a single
command in an expressive way. The import package bridges some of the gap
between using library (or require) and direct (single-object) imports. Further-
more the imported objects are not placed in the current environment. It is also
possible to import objects from stand-alone .R files. For more information,
refer to the package vignette. / MIT
r-importar 0.1.1 Enables ‘Python’-like importing/loading of packages or functions with alias- noarch
ing to prevent namespace conflicts. / GPL-3
r-imprprobest 1.0.1 A minimum distance estimator is calculated for an imprecise probability noarch
model. The imprecise probability model consists of upper coherent previsions
whose credal sets are given by a finite number of constraints on the expecta-
tions. The parameter set is finite. The estimator chooses that parameter such
that the empirical measure lies next to the corresponding credal set with re-
spect to the total variation norm. / LGPL-3
r-imptree 0.5.1 Creation of imprecise classification trees. They rely on probability estima- linux-
tion within each node by means of either the imprecise Dirichlet model or the 64,
nonparametric predictive inference approach. The splitting variable is selected osx-
by the strategy presented in Fink and Crossman (2013) <http://www.sipta.org/ 64,
isipta13/index.php?id=paper&paper=014.html>, but also the original impre- win-
cise information gain of Abellan and Moral (2003) <doi:10.1002/int.10143> 64
is covered. / GPL-2
r-imputemdr 1.1.2 This package provides various approaches to handling missing values for the linux-
MDR analysis to identify gene-gene interactions using biallelic marker data in 64,
genetic association studies / GPL-2 osx-
64,
win-
64
r- 0.0.3 Compute missing values on a training data set and impute them on a new data noarch
imputemissings set. Current available options are median/mode and random forest. / GPL-2


Name Version
r-imputer 2.1 Multivariate Expectation-Maximization (EM) based imputation framework noarch
that offers several different algorithms. These include regularisation meth-
ods like Lasso and Ridge regression, tree-based models and dimensionality
reduction methods like PCA and PLS. / GPL-3
r-imputeyn 1.3 Method brings less bias and more efficient estimates for AFT models. / GPL-2 noarch
r-imrmc 1.2.0 Do Multi-Reader, Multi-Case (MRMC) analyses of data from imaging stud- noarch
ies where clinicians (readers) evaluate patient images (cases). What does this
mean? . . . Many imaging studies are designed so that every reader reads
every case in all modalities, a fully-crossed study. In this case, the data is
cross-correlated, and we consider the readers and cases to be cross-correlated
random effects. An MRMC analysis accounts for the variability and corre-
lations from the readers and cases when estimating variances, confidence in-
tervals, and p-values. The functions in this package can treat arbitrary study
designs and studies with missing data, not just fully-crossed study designs.
The initial package analyzes the reader-average area under the receiver operat-
ing characteristic (ROC) curve with U-statistics according to Gallas, Bandos,
Samuelson, and Wagner 2009 <doi:10.1080/03610920802610084>. Addi-
tional functions analyze other endpoints with U-statistics (binary performance
and score differences) following the work by Gallas, Pennello, and Myers 2007
<doi:10.1364/JOSAA.24.000B70>. Package development and documentation
is at <https://github.com/DIDSR/iMRMC/tree/master>. / CC0
r-inarmix 0.4 Fits mixtures models for longitudinal data. Appropriate when the data are linux-
counts and when the correlation structure is assumed to be AR(1). / GPL-2 64,
osx-
64,
win-
64
r-inbreedr 0.3.2 A framework for analysing inbreeding and heterozygosity-fitness correlations noarch
(HFCs) based on microsatellite and SNP markers. / GPL-2
r-inca 0.0.3 Specific functions are provided for rounding real weights to integers and per- linux-
forming an integer programming algorithm for calibration problems. They 64,
are useful for census-weights adjustments, or for performing linear regression osx-
with integer parameters. / GPL-2 64,
win-
64
r- 0.2 Functions for testing mutual independence between many numerical random linux-
independencetests vectors or serial independence of a multivariate stationary sequence. The pro- 64,
posed test works when some or all of the marginal distributions are singular osx-
with respect to Lebesgue measure. / GPL-2 64,
win-
64
r-indexnumr 0.1.2 Computes bilateral and multilateral index numbers. It has support noarch
for several standard bilateral indices as well as the GEKS multi-
lateral index number methods (see Ivancic, Diewert and Fox (2011)
<doi:10.1016/j.jeconom.2010.09.003>) . It also supports updating of GEKS
indexes using several splicing methods. / GPL-2
r-indiantaxcalc 1.0.2 Calculate Indian Income Tax liability for Financial years of Individual resident noarch
aged below 60 years,Senior Citizen,Super Senior Citizen, Firm, Local Author-
ity, Any Non Resident Individual / Hindu Undivided Family / Association of
Persons /Body of Individuals / Artificial Judicial Person, Co-operative Society.
/ GPL-2


Name Version
r-indirect 0.2.0 Functions are provided to facilitate prior elicitation for Bayesian generalised noarch
linear models using independent conditional means priors. The package sup-
ports the elicitation of multivariate normal priors for generalised linear mod-
els. The approach can be applied to indirect elicitation for a generalised linear
model that is linear in the parameters. The package is designed such that the
facilitator executes functions within the R console during the elicitation ses-
sion to provide graphical and numerical feedback at each design point. Vari-
ous methodologies for eliciting fractiles (equivalently, percentiles or quantiles)
are supported, including versions of the approach of Hosack et al. (2017)
<doi:10.1016/j.ress.2017.06.011>. For example, experts may be asked to pro-
vide central credible intervals that correspond to a certain probability. Or ex-
perts may be allowed to vary the probability allocated to the central credible
interval for each design point. Additionally, a median may or may not be
elicited. / GPL-3
r-indtestpp 1.0 Several parametric and non-parametric tests and measures to check indepen- noarch
dence between two or more (homogeneous or nonhomogeneous) point pro-
cesses in time are provided. Tools for simulating point processes in one di-
mension with different types of dependence are also implemented. / GPL-3
r-ineq 0.2_13Inequality, concentration, and poverty measures. Lorenz curves (empirical and noarch
theoretical). / GPL-2 | GPL-3
r-infdim 1.0 This package contains functions to perform calculations of the infine- noarch
dimensional model (IDM) and to produce 95% confidence intervals around
the model elements through bootstrapping. / GPL-2
r-inference 0.1.0 Collection of functions to extract inferential values (point estimates, confi- noarch
dence intervals, p-values, etc) of a fitted model object into a matrix-like object
that can be used for table/report generation; transform point estimates via the
delta method. / GPL-2
r-inferencesmr 1.0 The InferenceSMR package provides functions to make inference about the noarch
standardized mortality ratio (SMR) when evaluating the effect of a screening
program. The package is based on methods described in Sasieni (2003) and
Talbot et al. (2011). / GPL-2
r-inferference 1.0.0 Provides methods for estimating causal effects in the presence of interference noarch
described in B. Saul and M. Hugdens (2017) <doi:10.18637/jss.v082.i02>.
Currently it implements the inverse-probability weighted (IPW) estima-
tors proposed by E.J. Tchetgen Tchetgen and T.J. Vanderweele (2012)
<doi:10.1177/0962280210386779>. / GPL-2
r-infiniumpurify 1.3.1 The proportion of cancer cells in solid tumor sample, known as the tumor pu- noarch
rity, has adverse impact on a variety of data analyses if not properly accounted
for. We develop ‘InfiniumPurify’, which is a comprehensive R package for es-
timating and accounting for tumor purity based on DNA methylation Infinium
450k array data. ‘InfiniumPurify’ provides functionalities for tumor purity es-
timation. In addition, it can perform differential methylation detection and
tumor sample clustering with the consideration of tumor purities. / GPL-2
r-infix 0.1.0 Contains a number of infix binary operators that may be useful in day to day noarch
practices. / GPL-3
r-inflection 1.3.5 Implementation of methods Extremum Surface Estimator (ESE) and Ex- noarch
tremum Distance Estimator (EDE) to identify the inflection point of a curve
. Christopoulos, DT (2014) <arXiv:1206.5478v2 [math.NA]> . Christopou-
los, DT (2016) <https://veltech.edu.in/wp-content/uploads/2016/04/Paper-04-
2016.pdf> . Christopoulos, DT (2016) <doi:10.2139/ssrn.3043076> . / GPL-2


Name Version
r-influence.me 0.9_9 Provides a collection of tools for detecting influential cases in generalized noarch
mixed effects models. It analyses models that were estimated using ‘lme4’.
The basic rationale behind identifying influential data is that when single units
are omitted from the data, models based on these data should not produce sub-
stantially different estimates. To standardize the assessment of how influential
a (single group of) observation(s) is, several measures of influence are com-
mon practice, such as Cook’s Distance. In addition, we provide a measure
of percentage change of the fixed point estimates and a simple procedure to
detect changing levels of significance. / GPL-3
r-influence.sem 2.2 A set of tools for evaluating several measures of case influence for structural noarch
equation models. / GPL-2
r-influencer 0.1.0 Provides functionality to compute various node centrality measures on net- linux-
works. Included are functions to compute betweenness centrality (by utilizing 32,
Madduri and Bader’s SNAP library), implementations of Burt’s constraint and linux-
effective network size (ENS) metrics, Borgatti’s algorithm to identify key play- 64,
ers, and Valente’s bridging metric. On Unix systems, the betweenness, Key osx-
Players, and bridging implementations are parallelized with OpenMP, which 64,
may run faster on systems which have OpenMP configured. / GPL-2 win-
32,
win-
64
r-infodecompute 0.6.1 The main purpose of this package is to generate the structure of the analysis of noarch
variance (ANOVA) table of the two-phase experiments. The user only need to
input the design and the relationships of the random and fixed factors using the
Wilkinson-Rogers’ syntax, this package can then quickly generate the struc-
ture of the ANOVA table with the coefficients of the variance components for
the expected mean squares. Thus, the balanced incomplete block design and
provides the efficiency factors of the fixed effects can also be studied and com-
pared much easily. / GPL-3
r-infotheo 1.2.0 This package implements various measures of information theory based on linux-
several entropy estimators. / GPL-3 64,
osx-
64,
win-
64
r-infotrad 1.2 Estimates the probability of informed trading (PIN) initially introduced noarch
by Easley et. al. (1996) <doi:10.1111/j.1540-6261.1996.tb04074.x>
. Contribution of the package is that it uses likelihood factorizations
of Easley et. al. (2010) <doi:10.1017/S0022109010000074> (EHO
factorization) and Lin and Ke (2011) <doi:10.1016/j.finmar.2011.03.001>
(LK factorization). Moreover, the package uses different estimation
algorithms. Specifically, the grid-search algorithm proposed by Yan
and Zhang (2012) <doi:10.1016/j.jbankfin.2011.08.003> , hierarchical ag-
glomerative clustering approach proposed by Gan et. al. (2015)
<doi:10.1080/14697688.2015.1023336> and later extended by Ersan and Alici
(2016) <doi:10.1016/j.intfin.2016.04.001> . / GPL-3
r-infra 0.1.2 Takes a data frame containing latitude and longitude coordinates and down- noarch
loads images from map servers to determine their file size as a proxy of infras-
tructure / GPL-2


Name Version
r-ini 0.3.1 Parse simple ‘.ini’ configuration files to an structured list. Users can manipu- noarch
late this resulting list with lapply() functions. This same structured list can be
used to write back to file after modifications. / GPL-3
r-injector 0.2.4 R dependency injection framework. Dependency injection allows a program noarch
design to follow the dependency inversion principle. The user delegates to
external code (the injector) the responsibility of providing its dependencies.
This separates the responsibilities of use and construction. / LGPL-3
r-inline 0.3.15Functionality to dynamically define R functions and S4 methods with ‘inlined’ linux-
C, C or Fortran code supporting the .C and .Call calling conventions. / LGPL 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-inplace 0.1.0 It provides in-place operators for R that are equivalent to ‘=’, ‘-=’, ‘*=’, ‘/=’ linux-
in C. Those can be applied on integer|double vectors|matrices. You have also 64,
access to sweep operations (in-place). / GPL-3 osx-
64,
win-
64
r-insiderode 2.0 insideRODE package includes buildin functions from deSolve, compiled noarch
functions from compiler, and C/FORTRAN code interfaces to nlme. It
includes nlmLSODA, nlmODE, nlmVODE,nlmLSODE for general pur-
pose; cfLSODA,cfLSODE, cfODE, cfVODE call C/FORTRAN compiled dll
functions.ver2.0 add sink()function into example it helps to directly com-
bine c/fortran source code in R files. Finally, with new compiler pack-
age, we generated compiled functions: nlmODEcp, nlmVODEcp, nlmL-
SODEcp,nlmLSODAcp and cpODE, cpLSODA, cpLSODE, cpVODE. They
will help to increase speed. / LGPL (> 2.0)
r-insight 0.5.0 A tool to provide an easy, intuitive and consistent access to information con- noarch
tained in various R models, like model formulas, model terms, information
about random effects, data that was used to fit the model or data from response
variables. ‘insight’ mainly revolves around two types of functions: Functions
that find (the names of) information, starting with ‘find_’, and functions that
get the underlying data, starting with ‘get_’. The package has a consistent syn-
tax and works with many different model objects, where otherwise functions
to access these information are missing. / GPL-3
r- 1.0.1 Provides a data-driven projection-based method for estimating changepoints noarch
inspectchangepoint in high-dimensional time series. Multiple changepoints are estimated using a
(wild) binary segmentation scheme. / GPL-3
r-inspectr 1.0.0 Check one column or multiple columns of a dataframe using the preset basic noarch
checks or your own functions. Enables checks without knowledge of lapply()
or sapply(). / CC BY-SA 4.0


Name Version
r-install.load 1.2.1 The function install_load checks the local R library(ies) to see if the required noarch
package(s) is/are installed or not. If the package(s) is/are not installed, then
the package(s) will be installed along with the required dependency(ies). This
function pulls source or binary packages from the Rstudio-sponsored CRAN
mirror and/or the USGS GRAN Repository. Lastly, the chosen package(s)
is/are loaded. The function load_package simply loads the provided packages.
/ CC BY-SA 4.0
r-instar 0.2.4 Provides an interface to the Instagram API <https://instagram.com/ devel- noarch
oper/>, which allows R users to download public pictures filtered by hashtag,
popularity, user or location, and to access public users’ profile data. / GPL-2
r-insurancedata 1.0 Insurance datasets, which are often used in claims severity and claims fre- noarch
quency modelling. It helps testing new regression models in those problems,
such as GLM, GLMM, HGLM, non-linear mixed models etc. Most of the data
sets are applied in the project Mixed models in ratemaking supported by grant
NN 111461540 from Polish National Science Center. / GPL-2
r-intccr 1.1.4 Semiparametric regression models on the cumulative incidence function with noarch
interval-censored competing risks data as described in Bakoyannis, Yu, &
Yiannoutsos (2017) <doi:10.1002/sim.7350>. The main function fits the pro-
portional subdistribution hazards model (Fine-Gray model), the proportional
odds model, and other models that belong to the class of semiparametric gen-
eralized odds rate transformation models. / GPL-2
r-integratebs 0.1.0 Integrated B-spline function. / GPL-2 noarch
r-interact 1.1 This package searches for marginal interactions in a binary response model. linux-
Interact uses permutation methods to estimate false discovery rates for these 64,
marginal interactions and has some, limited visualization capabilities / GPL-3 osx-
64,
win-
64
r-interactiontest 1.2 Implements the procedures suggested in Esarey and Sumner (2017) <http:// noarch
justinesarey.com/interaction-overconfidence.pdf> for controlling the false dis-
covery rate when constructing marginal effects plots for models with interac-
tion terms. / GPL-3
r- 1.0.6.1An extension of the package ‘igraph’. This package create possibly to work noarch
interactiveigraph with ‘igraph’ objects interactively. / GPL-2
r-interatrix 1.1.1 Chi-square tests are computed with corrections. / GPL-2 noarch
r-intercure 0.1.0 Implementations of semiparametric cure rate estimators for interval censored noarch
data in R. The algorithms are based on the promotion time and frailty models,
all for interval censoring. For the frailty model, there is also a implementation
contemplating clustered data. / GPL-2 | GPL-3
r-interep 0.3.0 Extensive penalized variable selection methods have been developed in the linux-
past two decades for analyzing high dimensional omics data, such as gene ex- 64,
pressions, single nucleotide polymorphisms (SNPs), copy number variations osx-
(CNVs) and others. However, lipidomics data have been rarely investigated 64,
by using high dimensional variable selection methods. This package incor- win-
porates our recently developed penalization procedures to conduct interaction 64
analysis for high dimensional lipidomics data with repeated measurements.
The core module of this package is developed in C. The development of this
software package and the associated statistical methods have been partially
supported by an Innovative Research Award from Johnson Cancer Research
Center, Kansas State University. / GPL-2


Name Version
r-interfaceqpcr 1.0 Graphical User Interface allowing to determine the concentration in the sample noarch
in CFU per mL or in number of copies per mL provided to qPCR results after
with or without PMA treatment. This package is simply to use because no
knowledge in R commands is necessary. A graphic represents the standard
curve, and a table containing the result for each sample is created. / GPL-2
r-interferenceci 1.1 Computes large sample confidence intervals of Liu and Hudgens (2014), exact noarch
confidence intervals of Tchetgen Tchetgen and VanderWeele (2012), and exact
confidence intervals of Rigdon and Hudgens (2014) for treatment effects on
a binary outcome in two-stage randomized experiments with interference. /
GPL-3
r-interim 0.8.0 Allows the simulation of the recruitment and both the event and treatment noarch
phase of a clinical trial. Based on these simulations, the timing of interim
analyses can be assessed. / GPL-3
r-interlinear 1.0 Interlinearized glossed texts (IGT) are used in descriptive linguistics for repre- noarch
senting a morphological analysis of a text through a morpheme-by-morpheme
gloss. ‘InterlineaR’ provide a set of functions that targets several popular for-
mats of IGT (‘SIL Toolbox’, ‘EMELD XML’) and that turns an IGT into a
set of data frames following a relational model (the tables represent the dif-
ferent linguistic units: texts, sentences, word, morphems). The same pieces
of software (‘SIL FLEX’, ‘SIL Toolbox’) typically produce dictionaries of the
morphemes used in the glosses. ‘InterlineaR’ provide a function for turning
the LIFT XML dictionary format into a set of data frames following a rela-
tional model in order to represent the dictionary entries, the sense(s) attached
to the entries, the example(s) attached to senses, etc. / BSD_3_clause
r-interp 1.0_32Bivariate data interpolation on regular and irregular grids, either linear or linux-
using splines are the main part of this package. It is intended to provide 64,
FOSS replacement functions for the ACM licensed akima::interp and tri- osx-
pack::tri.mesh functions. Currently the piecewise linear interpolation part of 64,
akima::interp (and also akima::interpp) is implemented in interp::interp, this win-
corresponds to the call akima::interp(. . . , linear=TRUE) which is the default 64
setting and covers most of akima::interp use cases in depending packages.
A re-implementation of Akimas spline interpolation (akima::interp(. . . , lin-
ear=FALSE)) is currently under development and will complete this package
in a later version. Estimators for partial derivatives are already available, these
are a prerequisite for the spline interpolation. The basic part is currently a
GPLed triangulation algorithm (sweep hull algorithm by David Sinclair) pro-
viding the starting point for the piecewise linear interpolator. As side effect this
algorithm is also used to provide replacements for the basic functions of the
tripack package which also suffer from the ACM restrictions. All functions are
designed to be backward compatible with their akima / tripack counterparts. /
GPL-2
r-interpol 1.3.1 A package for numerical encoding as well as for linear and non-linear interpo- noarch
lation of amino acid sequences. / GPL-2
r-interpol.t 2.1.1 Hourly interpolation of daily minimum and maximum temperature series. Car- noarch
ries out interpolation on multiple series ad once. Requires some hourly series
for calibration (alternatively can use default calibration table). / GPL-2
r-interpretr 0.2.4 Compute permutation- based performance measures and create partial depen- noarch
dence plots for (cross-validated) ‘randomForest’ and ‘ada’ models. / GPL-2
r-interva4 1.7.5 Provides an R version of the ‘InterVA4’ software (<http://www.interva.net>) noarch
for coding cause of death from verbal autopsies. It also provides simple graph-
ical representation of individual and population level statistics. / GPL-3


Name Version
r-interva5 1.0.2 Provides an R version of the ‘InterVA5’ software (<http://www.interva.net>) noarch
for coding cause of death from verbal autopsies. It also provides simple graph-
ical representation of individual and population level statistics. / GPL-3
r-intervals 0.15.1Tools for working with and comparing sets of points and intervals. / Artistic- linux-
2.0 64,
osx-
64,
win-
64
r-intervalsurgeon 1.0 Functions for manipulating integer-bounded intervals including finding over- linux-
laps, piling and merging. / GPL-2 64,
osx-
64,
win-
64
r-intervcomp 0.1.2 Performs hypothesis testing using the interval estimates (e.g., confidence in- noarch
tervals). The non-overlapping interval estimates indicates the statistical sig-
nificance. References to these procedures can be found at Noguchi and
Marmolejo-Ramos (2016) <doi:10.1080/00031305.2016.1200487>, Bonett
and Seier (2003) <doi:10.1198/0003130032323>, and Lemm (2006)
<doi:10.1300/J082v51n02_05>. / GPL-3
r- 1.2.2 This package allows a dynamic Bayesian network to be inferred from microar- noarch
interventionaldbn ray timecourse data with interventions (inhibitors). / GPL-2
r-intlik 1.0 This package calculates the integrated likelihood numerically. Given the Like- noarch
lihood function and the prior function, this package integrates out the nuisance
parameters by Metropolis-Hastings (MCMC) Algorithm. / GPL-2
r-intoo 0.3.1 Contains attribute operators (%$% and %$%<-), convenience functions and noarch
functions for printing objects compactly but informatively. And partly sup-
ports nested matrices. / GPL-2
r-intreggof 0.85_5Performs Goodness of Fit for regression models using Integrated Regression linux-
method. Works for several different fitting techniques. / GPL-2 64,
osx-
64,
win-
64
r- 0.0.1 Download financial data from the free ‘Intrinio Stock API’ (<https://intrinio. noarch
intriniostockapi com/>). ‘Intrinio’ offers a REST API which provides financial markets data
including intra-day stock prices, historical stock prices, technical indicators,
company fundamentals, and more. Complete documentation for the ‘Intrinio
Stock API’ is available here: <https://intrinio.com/documentation/api/>. To
access the ‘Intrinio Stock API’, simply create a free account <https://intrinio.
com/>. / MIT
r-intrval 0.1_1 Evaluating if values of vectors are within different open/closed intervals (x noarch
%[]% c(a, b)), or if two closed intervals overlap (c(a1, b1) %[]o[]% c(a2,
b2)). Operators for negation and directional relations also implemented. /
GPL-2
r-intrvals 1.0.0 Calculates event rates and compares means and variances of groups of interval noarch
data corrected for missed arrival observations. / GPL-3


Name Version
r-intsurv 0.2.1 Contains implementations of integrative survival analysis routines, in- linux-
cluding regular Cox cure rate model proposed by Kuk and Chen 64,
(1992) <doi:10.1093/biomet/79.3.531> via an EM algorithm proposed by osx-
Sy and Taylor (2000) <doi:10.1111/j.0006-341X.2000.00227.x>, regular- 64,
ized Cox cure rate model with elastic net penalty following Masud win-
et al. (2018) <doi:10.1177/0962280216677748>, and Zou and Hastie 64
(2005) <doi:10.1111/j.1467-9868.2005.00503.x>, and weighted concor-
dance index for cure models proposed by Asano and Hirakawa (2017)
<doi:10.1080/10543406.2017.1293082>. / GPL-3
r-intubate 1.0.0 Interface to popular R functions with formulas and data, such as ‘lm’, so they noarch
can be included painlessly in data science pipelines implemented by ‘magrittr’
with the operator %>%. / GPL-2
r-inum 1.0_1 Enum-type representation of vectors and representation of intervals, including noarch
a method of coercing variables in data frames. / GPL-2
r- 0.1 The correction is achieved under the assumption that non-migrating cells of noarch
invasioncorrection the essay approximately form a quadratic flow profile due to frictional effects,
compare law of Hagen-Poiseuille for flow in a tube. The script fits a conical
plane to give xyz-coordinates of the cells. It outputs the number of migrated
cells and the new corrected coordinates. / GPL-3
r-invctr 0.1.0 Vector operations between grapes: An infix-only package! The ‘invctr’ func- noarch
tions perform common and less common operations on vectors, data frames
matrices and list objects: - Extracting a value (range), or, finding the indices of
a value (range). - Trimming, or padding a vector with a value of your choice.
- Simple polynomial regression. - Set and membership operations. - General
check & replace function for NAs, Inf and other values. / GPL-3
r-investr 1.4.0 Functions to facilitate inverse estimation (e.g., calibration) in linear, general- noarch
ized linear, nonlinear, and (linear) mixed-effects models. A generic function
is also provided for plotting fitted regression models with or without confi-
dence/prediction bands that may be of use to the general user. / GPL-2
r-invgamma 1.1 Light weight implementation of the standard distribution functions for the in- noarch
verse gamma distribution, wrapping those for the gamma distribution in the
stats package. / GPL-2
r-invlt 0.2.1 Provides two functions for the numerical inversion of Laplace-Transformed noarch
functions, returning the value of the standard (time) domain function at a speci-
fied value. The first algorithm is the first optimum contour algorithm described
by Evans and Chung (2000)[1]. The second algorithm uses the Bromwich con-
tour as per the definition of the inverse Laplace Transform. The latter is un-
stable for numerical inversion and mainly included for comparison or interest.
There are also some additional functions provided for utility, including plot-
ting and some simple Laplace Transform examples, for which there are known
analytical solutions. Polar-cartesian conversion functions are included in this
package and are used by the inversion functions. [1] Evans & Chung, 2000:
Laplace transform inversions using optimal contours in the complex plane;
International Journal of Computer Mathematics v73 pp531-543. / MIT
r-ioncopy 2.1.1 Method for the calculation of copy numbers and calling of copy number alter- noarch
ations. The algorithm uses coverage data from amplicon sequencing of a sam-
ple cohort as input. The method includes significance assessment, correction
for multiple testing and does not depend on normal DNA controls. Budczies
(2016 Mar 15) <doi:10.18632/oncotarget.7451>. / GPL-3


Name Version
r-ionr 0.3.0 Provides item exclusion procedure, which is a formal method to test ‘Indiffer- noarch
ence Of iNdicator’ (ION). When a latent personality trait-outcome association
is assumed, then the association strength should not depend on which subset
of indicators (i.e. items) has been chosen to reflect the trait. Personality traits
are often measured (reflected) by a sum-score of a certain set of indicators.
Item exclusion procedure randomly excludes items from a sum-score and tests,
whether the sum-score - outcome correlation changes. ION has been achieved,
when any item can be excluded from the sum-score without the sum-score -
outcome correlation substantially changing . For more details, see Vainik,
Mottus et. al, (2015) Are Trait-Outcome Associations Caused by Scales or
Particular Items? Example Analysis of Personality Facets and BMI,European
Journal of Personality DOI: <10.1002/per.2009> . / GPL-2
r-iosmooth 0.94 Density, spectral density, and regression estimation using infinite order flat-top noarch
kernels. / GPL-3
r-iotools 0.2_5 Basic I/O tools for streaming and data parsing. / GPL-2 | GPL-3 linux-
64,
osx-64
r-ipcwswitch 1.0.3 Contains functions for formatting clinical trials data and implementing inverse noarch
probability of censoring weights to handle treatment switches when estimating
causal treatment effect in randomized clinical trials. / GPL-3
r-ipdmeta 2.4 This package provides functions to estimate an IPD linear mixed effects model noarch
for a continuous outcome and any categorical covariate from study summary
statistics. There are also functions for estimating the power of a treatment-
covariate interaction test in an individual patient data meta-analysis from ag-
gregate data. / GPL-2
r-ipec 0.1.2 Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear noarch
regression model. / GPL-2
r-ipflasso 0.2 The core of the package is cvr2.ipflasso(), an extension of glmnet to be used noarch
when the (large) set of available predictors is partitioned into several modali-
ties which potentially differ with respect to their information content in terms
of prediction. For example, in biomedical applications patient outcome such
as survival time or response to therapy may have to be predicted based on,
say, mRNA data, miRNA data, methylation data, CNV data, clinical data, etc.
The clinical predictors are on average often much more important for outcome
prediction than the mRNA data. The ipflasso method takes this problem into
account by using different penalty parameters for predictors from different
modalities. The ratio between the different penalty parameters can be chosen
by cross-validation. / GPL-3
r-ipfp 1.0.1 A fast (C) implementation of the iterative proportional fitting procedure. Based linux-
on corresponding code from the networkTomography package. / Apache Li- 64,
cense (== 2.0) osx-64
r-ipmpack 2.1 IPMpack takes demographic vital rates and (optionally) environmental data to noarch
build integral projection models. A number of functional forms for growth and
survival can be incorporated, as well as a range of reproductive strategies. The
package also includes a suite of diagnostic routines, provides classic matrix
model output (e.g., lambda, elasticities, sensitivities), and produces post-hoc
metrics (e.g., passage time and life expectancy). / GPL-3


Name Version
r-ippp 1.1 Generates random numbers corresponding to the events on a Poisson point noarch
process with changing event rates. This includes the possibility to incorporate
additional information such as the number of events occurring or the location
of an already known event. It can also generate the probability density func-
tions of specific events in the cases where additional information is available.
Based on Hohmann (2019) <arXiv:1901.10754>. / CC BY 4.0
r-ipred 0.9_8 Improved predictive models by indirect classification and bagging for classifi- linux-
cation, regression and survival problems as well as resampling based estima- 32,
tors of prediction error. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
r-iptmnetr 0.1.5 Provides an R interface to the ‘iPTMnet’ database REST API, which can be noarch
used to retrieve Post Translational Modification (PTM) data in systems biology
context. This package handles all the aspects of communicating with the API,
which involve sending the request, checking the error codes and parsing the
response in a format that is ready to integrate into existing workflows. / MIT
r-ipwsurvival 0.5 In observational studies, the presence of confounding factors is common and noarch
the comparison of different groups of subjects requires adjustment. In this
package, we propose simple functions to estimate adjusted survival curves and
log-rank test based on inverse probability weighting (IPW). / GPL-2
r-iqlearn 1.5 Estimate an optimal dynamic treatment regime using Interactive Q-learning. / noarch
GPL-2
r-irace 3.3 Iterated race is an extension of the Iterated F-race method for the automatic noarch
configuration of optimization algorithms, that is, (offline) tuning their param-
eters by finding the most appropriate settings given a set of instances of an
optimization problem. / GPL-2
r-irafnet 1.1_1 Provides a flexible integrative algorithm that allows information from prior linux-
data, such as protein protein interactions and gene knock-down, to be jointly 64,
considered for gene regulatory network inference. / GPL-2 osx-64
r-ircor 1.0 Provides implementation of various correlation coefficients of common noarch
use in Information Retrieval. In particular, it includes Kendall (1970,
isbn:0852641990) tau coefficient as well as tau_a and tau_b for the treatment
of ties. It also includes Yilmaz et al. (2008) <doi:10.1145/1390334.1390435>
tauAP correlation coefficient, and versions tauAP_a and tauAP_b developed
by Urbano and Marrero (2017) <doi:10.1145/3121050.3121106> to cope with
ties. / MIT


Name Version
r-irdisplay 0.7.0 An interface to the rich display capabilities of ‘Jupyter’ front-ends (e.g. linux-
‘Jupyter Notebook’) <https://jupyter.org>. Designed to be used from a run- 32,
ning ‘IRkernel’ session <https://irkernel.github.io>. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-iregression 1.2.1 Contains some important regression methods for interval-valued variables. For noarch
each method, it is available the fitted values, residuals and some goodness-of-
fit measures. / GPL-2
r-irepro 1.1 Calculates intraclass correlation coefficient (ICC) for assessing reproducibil- noarch
ity of interval-censored data with two repeated measurements (Kovacic and
Varnai (2014) <doi:10.1097/EDE.0000000000000139>). ICC is estimated by
maximum likelihood from model with one fixed and one random effect (both
intercepts). Help in model checking (normality of subjects’ means and residu-
als) is provided. / GPL-3
r-irg 0.1.1 Fits a double logistic function to NDVI time series and calculates instanta- noarch
neous rate of green (IRG) according to methods described in Bischoff et al.
(2012) <doi:10.1086/667590>. / GPL-3
r- 1.4 Provides the dataset and an implementation of the method illus- linux-
irishdirectorates trated in Friel, N., Rastelli, R., Wyse, J. and Raftery, A.E. (2016) 64,
<DOI:10.1073/pnas.1606295113>. / GPL-3 osx-64
r-irkernel 0.8.15The R kernel for the ‘Jupyter’ environment executes R code which the front- linux-
end (‘Jupyter Notebook’ or other front-ends) submits to the kernel via the net- 32,
work. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-irlba 2.3.3 Fast and memory efficient methods for truncated singular value decomposition linux-
and principal components analysis of large sparse and dense matrices. / GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-irr 0.84.1Coefficients of Interrater Reliability and Agreement for quantitative, ordinal noarch
and nominal data: ICC, Finn-Coefficient, Robinson’s A, Kendall’s W, Cohen’s
Kappa, . . . / GPL-2


Name Version
r-irregular1 1.0.0 Simulation and density evaluation of irregularly sampled stationary AR(1) pro- linux-
cesses with Gaussian errors using the algorithms described in Allévius (2018) 64,
<arXiv:1801.03791>. / GPL-3 osx-64
r-irtdemo 0.1.4 Includes a collection of shiny applications to demonstrate or to explore funda- noarch
mental item response theory (IRT) concepts such as estimation, scoring, and
multidimensional IRT models. / GPL-2
r-irtrees 0.1.0 Helper functions and example data sets accompanying De Boeck, P. and noarch
Partchev, I. (2012) IRTrees: Tree-Based Item Response Models of the GLMM
Family, Journal of Statistical Software - Code Snippets, 48(1), 1-28. / GPL-2
r-isa2 0.3.5 The ISA is a biclustering algorithm that finds modules in an input matrix. A linux-
module or bicluster is a block of the reordered input matrix. / CC BY-NC-SA 64,
4.0 osx-64
r-isat 1.0.5 Reads the output of the ‘PerkinElmer InForm’ software <http://www. noarch
perkinelmer.com/product/inform-cell-analysis-one-seat-cls135781>. In addi-
tion to cell-density count, it can derive statistics of intercellular spatial distance
for each cell-type. / GPL-2
r-isbf 0.2.1 Selection of features for sparse regression estimation (like the LASSO). Selec- linux-
tion of blocks of features when the regression parameter is sparse and constant 64,
by blocks (like the Fused-LASSO). Application to cgh arrays. / GPL-3 osx-64
r- 0.1.0 Implementation of functions to assign corresponding common job prestige noarch
isco08conversions scores (SIOPS, ISEI), the official job or group title and the ISCO-88 code
to given ISCO-08 codes. ISCO-08 is the latest version of the International
Standard Classification of Occupations which is used to organise information
on labour and jobs. / GPL-2
r-isdals 2.0_4 Provides datasets for Introduction to Statistical Data Analysis for the Life Sci- noarch
ences / GPL-2
r-isinglenzmc 0.2.5 Classical Ising Model is a land mark system in statistical physics.The model linux-
explains the physics of spin glasses and magnetic materials, and coopera- 64,
tive phenomenon in general, for example phase transitions and neural net- osx-64
works.This package provides utilities to simulate one dimensional Ising Model
with Metropolis and Glauber Monte Carlo with single flip dynamics in peri-
odic boundary conditions. Utility functions for exact solutions are provided. /
GPL-3
r-isingsampler 0.2 Sample states from the Ising model and compute the probability of states. linux-
Sampling can be done for any number of nodes, but due to the intractibility 64,
of the Ising model the distribution can only be computed up to ~10 nodes. / osx-64
GPL-2
r-island 0.2.4 Tools to develop stochastic models based on the Theory of Is- linux-
land Biogeography (TIB) of MacArthur and Wilson (1967) 64,
<DOI:10.1023/A:1016393430551> and extensions. The package imple- osx-64
ments methods to estimate colonization and extinction rates (including
environmental variables) given presence-absence data, simulate community
assembly, and perform model selection. / GPL-3


Name Version
r-islasso 1.1.0 An implementation of the induced smoothing (IS) idea to lasso regulariza- linux-
tion models to allow estimation and inference on the model coefficients (cur- 64,
rently hypothesis testing only). Linear, logistic, Poisson and gamma regres- win-
sions with several link functions are implemented. The algorithm is described 64
in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V.
(2019) The Induced Smoothed lasso: A practical framework for hypothesis
testing in high dimensional regression. <doi:10.1177/0962280219842890>,
and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019)
The R package islasso: estimation and hypothesis testing in lasso regression.
<doi:10.13140/RG.2.2.16360.11521>. / GPL-2
r-islr 1.2 We provide the collection of data-sets used in the book ‘An Introduction to noarch
Statistical Learning with Applications in R’. / GPL-2
r-ism 0.1.0 The development of ISM was made by Warfield in 1974. ISM is noarch
the process of collaborating distinct or related essentials into a sim-
plified and an organized format. Hence, ISM is a methodology that
seeks the interrelationships among the various elements considered and
endows with a hierarchical and multilevel structure. To run this pack-
age user needs to provide a matrix (VAXO) converted into 0’s and
1’s. Warfield,J.N. (1974) <doi:10.1109/TSMC.1974.5408524> Warfield,J.N.
(1974, E-ISSN:2168-2909). / GPL-3
r-ismev 1.42 Functions to support the computations carried out in ‘An Introduction to Sta- noarch
tistical Modeling of Extreme Values’ by Stuart Coles. The functions may be
divided into the following groups; maxima/minima, order statistics, peaks over
thresholds and point processes. / GPL-2
r-isnullptr 1.0.1 Check if an ‘externalptr’ is a null pointer. R does currently not have a native linux-
function for that purpose. This package contains a C function that returns 64,
TRUE in case of a null pointer. / GPL-3 win-
64
r-iso 0.0_18Linear order and unimodal order (univariate) isotonic regression; bivariate iso- linux-
tonic regression with linear order on both variables. / GPL-2 64,
win-
64
r-isoband 0.2.0 A fast C implementation to generate contour lines (isolines) and contour poly- linux-
gons (isobands) from regularly spaced grids containing elevation data. / MIT 64,
win-
64
r-isoci 1.1 Some functions for confidence intervals for current status data based on trans- noarch
formations and bootstrap. / GPL-2
r-isocodes 2019.04.22
ISO language, territory, currency, script and character codes. Provides ISO linux-
639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 32,
15924 script codes, and the ISO 8859 character codes as well as the UN M.49 linux-
area codes. / GPL-2 64,
noarch,
osx-
64,
win-
32,
win-
64
r-isopat 1.0 The function calculates the isotopic pattern (fine structures) for a given chem- noarch
ical formula. / GPL-2


Name Version
r-isoplotr 3.0 Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Cal- noarch
culates concordia and discordia ages. Performs linear regression of mea-
surements with correlated errors using ‘York’, ‘Titterington’ and ‘Ludwig’
approaches. Generates Kernel Density Estimates (KDEs) and Cumula-
tive Age Distributions (CADs). Produces Multidimensional Scaling (MDS)
configurations and Shepard plots of multi-sample detrital datasets using
the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates
40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means ac-
counting for overdispersion. Calculates U-Th-He (single grain and central)
ages, logratio plots and ternary diagrams. Processes fission track data using
the external detector method and LA-ICP-MS, calculates central ages and plots
fission track and other data on radial (a.k.a. ‘Galbraith’) plots. Constructs total
Pb-U, Pb-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as
well as 230Th-U evolution plots. / GPL-3
r-isospecr 2.0.1 IsoSpec is a fine structure calculator used for obtaining the most probable linux-
masses of a chemical compound given the frequencies of the composing iso- 64
topes and their masses. It finds the smallest set of isotopologues with a given
probability. The probability is assumed to be that of the product of multinomial
distributions, each corresponding to one particular element and parametrized
by the frequencies of finding these elements in nature. These numbers are sup-
plied by IUPAC - the International Union of Pure and Applied Chemistry. /
BSD_2_clause
r-isotonic.pen 1.0 Given a response y and a one- or two-dimensional predictor, the isotonic re- noarch
gression estimator is calculated with the usual orderings. / GPL-2 | GPL-3
r-isoweek 0.6_2 This is an substitute for the %V and %u formats which are not implemented on noarch
Windows. In addition, the package offers functions to convert from standard
calender format yyyy-mm-dd to and from ISO 8601 week format yyyy-Www-
d. / GPL-2
r-isqg 1.2 Accomplish high performance simulations in quantitative genetics. The linux-
molecular genetic components are represented by R6/C classes and meth- 64,
ods. Mimic the meiosis recombination and de novo genetic vari- win-
ability by means a count-location process (Karlin & Liberman, 1978) 64
<doi:10.1073/pnas.75.12.6332>. The core computational algorithm is im-
plemented using ‘Boost’ dynamic bitsets (Schaling, 2014) [ISBN:978-
1937434366]. A mix between low and high level interfaces provides great
flexibility and allows user defined extensions and a wide range of applications.
/ GPL-2
r-isr3 0.98 Performs multivariate normal imputation through iterative sequential regres- linux-
sion. Conditional dependency structure between imputed variables can be 64,
specified a priori to accelerate imputation. / Unlimited win-
64
r-istacr 0.1.0 You can access to open data published in Instituto Canario De Estadistica (IS- noarch
TAC) APIs at <https://www.gobiernodecanarias.org/istac/api/>. / GPL-3
r-iswr 2.0_7 Data sets and scripts for text examples and exercises in P. Dalgaard (2008), noarch
‘Introductory Statistics with R’, 2nd ed., Springer Verlag, ISBN 978-
0387790534. / GPL-2


Name Version
r-italy 0.1.0 Provides two record linkage data sets on the Italian Survey on Household and noarch
Wealth, 2008 and 2010, a sample survey conducted by the Bank of Italy every
two years. The 2010 survey covered 13,702 individuals, while the 2008 survey
covered 13,734 individuals. The following categorical variables are included
in this data set: year of birth, working status, employment status, branch of
activity, town size, geographical area of birth, sex, whether or not Italian na-
tional, and highest educational level obtained. Unique identifiers are avail-
able to assess the accuracy of oneâC™s method. Please see Steorts (2015)
<DOI:10.1214/15-BA965SI> to find more details about the data set. / CC0
r-iterators 1.0.10Support for iterators, which allow a programmer to traverse through all the linux-
elements of a vector, list, or other collection of data. / Apache License (== 32,
2.0) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-iterpc 0.4.1 Iterator for generating permutations and combinations. They can be either noarch
drawn with or without replacement, or with distinct/ non-distinct items (multi-
set). The generated sequences are in lexicographical order (dictionary order).
The algorithms to generate permutations and combinations are memory effi-
cient. These iterative algorithms enable users to process all sequences without
putting all results in the memory at the same time. The algorithms are written
in C/C for faster performance. Note: ‘iterpc’ is no longer being maintained.
Users are recommended to switch to ‘arrangements’. / GPL-2
r-itertools 0.1_3 Various tools for creating iterators, many patterned after functions in the noarch
Python itertools module, and others patterned after functions in the ‘snow’
package. / GPL-2
r-itertools2 0.1.1 A port of Python’s excellent itertools module to R for efficient looping. / MIT noarch
r-itop 1.0.2 Infers a topology of relationships between different datasets, such as noarch
multi-omics and phenotypic data recorded on the same samples. We
based this methodology on the RV coefficient (Robert & Escoufier, 1976,
<doi:10.2307/2347233>), a measure of matrix correlation, which we have
extended for partial matrix correlations and binary data (Aben et al., 2018,
<doi:10.1101/293993>). / GPL-2
r-itree 0.1 This package is based on the code of the rpart package. It extends rpart by linux-
adding additional splitting methods emphasizing interpretable/parsimonious 64,
trees. Unless indicated otherwise, it is safe to assume that all functions herein win-
are extensions of or copied directly from similar or nearly identical rpart meth- 64
ods. As such, the authors of rpart are authors of this package as well. However,
please direct any error reports or other questions about itree to the maintainer
of this package; they are welcome and appreciated. / GPL-2 | GPL-3


Name Version
r-itrlearn 1.0_1 Maximin-projection learning (MPL, Shi, et al., 2018) is implemented for rec- linux-
ommending a meaningful and reliable individualized treatment regime for 64,
future groups of patients based on the observed data from different popula- win-
tions with heterogeneity in individualized decision making. Q-learning and A- 64
learning are implemented for estimating the groupwise contrast function that
shares the same marginal treatment effects. The packages contains classical
Q-learning and A-learning algorithms for a single stage study as a byproduct.
More functions will be added at later versions. / GPL-2
r-itsmr 1.9 Provides functions for modeling and forecasting time series data. Forecast- noarch
ing is based on the innovations algorithm. A description of the innovations
algorithm can be found in the textbook Introduction to Time Series and Fore-
casting by Peter J. Brockwell and Richard A. Davis. <http://www.springer.
com/us/book/9781475777505>. / FreeBSD
r-itunesr 0.1.3 To enable ‘iOS’ App Developers to access iTunes App Store Ratings and Re- noarch
views using R to extract Basic App Information and Reviews submitted by
their App users, Since Apple Store does not provide this straightforward. /
CC0
r-ivfixed 1.0 Fit an Instrumental least square dummy variable model / Artistic-2.0 noarch
r-ivpanel 1.0 Fit the instrumental panel data models: the fixed effects, random effects and noarch
between models. / GPL-3
r-ivprobit 1.1 Compute the instrumental variables probit model using the Amemiya’s noarch
Generalized Least Squares estimators (Amemiya, Takeshi, (1978) <doi:
10.2307/1911443>). / GPL-3
r-jaatha 3.2.1 An estimation method that can use computer simulations to approximate noarch
maximum-likelihood estimates even when the likelihood function can not
be evaluated directly. It can be applied whenever it is feasible to conduct
many simulations, but works best when the data is approximately Poisson dis-
tributed. It was originally designed for demographic inference in evolutionary
biology. It has optional support for conducting coalescent simulation using the
‘coala’ package. / GPL-3
r-jacobieigen 0.3_3 Implements the classical Jacobi algorithm for the eigenvalues and eigenvectors linux-
of a real symmetric matrix, both in pure ‘R’ and in ‘C’ using ‘Rcpp’. Mainly 64,
as a programming example for teaching purposes. / GPL-2 win-
64
r-jacpop 0.6 Uses the Jaccard similarity index to account for population structure in se- noarch
quencing studies. This method was specifically designed to detect population
stratification based on rare variants, hence it will be especially useful in rare
variant analysis. / GPL-3
r-jade 2.0_2 Cardoso’s JADE algorithm as well as his functions for joint diagonalization linux-
are ported to R. Also several other blind source separation (BSS) methods, 64,
like AMUSE and SOBI, and some criteria for performance evaluation of BSS osx-
algorithms, are given. The package is described in Miettinen, Nordhausen and 64,
Taskinen (2017) <doi:10.18637/jss.v076.i02>. / GPL-2 win-
64


Name Version
r-jaggr 0.1.1 All the data and functions used to produce the book. We do not expect most noarch
people to use the package for any other reason than to get simple access to the
‘JAGS’ model files, the data, and perhaps run some of the simple examples.
The authors of the book are David Lucy (now sadly deceased) and James Cur-
ran. It is anticipated that a manuscript will be provided to Taylor and Francis
around February 2020, with bibliographic details to follow at that point. Until
such time, further information can be obtained by emailing James Curran. /
GPL-2
r-jaguar 3.0.1 Implements a novel score test that measures 1) the overall shift in the gene linux-
expression due to genotype (additive genetic effect), and 2) group-specific 64,
changes in gene expression due to genotype (interaction effect) in a mixed- osx-
effects model framework. / GPL-2 64,
win-
64
r-janeaustenr 0.1.5 Full texts for Jane Austen’s 6 completed novels, ready for text analysis. These linux-
novels are Sense and Sensibility, Pride and Prejudice, Mansfield Park, Emma, 32,
Northanger Abbey, and Persuasion. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-jaspar 0.0.1 R modules for JASPAR data processing and visualization / GPL-2 linux-
64,
osx-
64,
win-
64
r-jcp 1.0 Procedures for joint detection of changes in both expectation and variance in noarch
univariate sequences. Performs a statistical test of the null hypothesis of the ab-
sence of change points. In case of rejection performs an algorithm for change
point detection. References - Bivariate change point detection (2019), Michael
Messer. / GPL-3
r-jdmbs 1.3 Black-Scholes model [Black (1973) <doi:10.1086/260062>] is important noarch
to calculate option prices in the stock market and a variety of improved
models are studied. In this package, I propose methods in order to cal-
culate both Black-Scholes model and Jump diffusion model [Kou (2002)
<doi:10.1287/mnsc.48.8.1086.166>] by Monte Carlo methods. This package
can be used for computational finance. / GPL-2
r-jdx 0.1.3 Simplifies and extends data exchange between ‘R’ and ‘Java’. / GPL-2 | noarch
BSD_3_clause


Name Version
r-jeek 1.1.1 Provides a fast and scalable joint estimator for integrating additional knowl- noarch
edge in learning multiple related sparse Gaussian Graphical Models (JEEK).
The JEEK algorithm can be used to fast estimate multiple related precision ma-
trices in a large-scale. For instance, it can identify multiple gene networks from
multi-context gene expression datasets. By performing data-driven network in-
ference from high-dimensional and heterogeneous data sets, this tool can help
users effectively translate aggregated data into knowledge that take the form
of graphs among entities. Please run demo(jeek) to learn the basic functions
provided by this package. For further details, please read the original paper:
Beilun Wang, Arshdeep Sekhon, Yanjun Qi A Fast and Scalable Joint Estima-
tor for Integrating Additional Knowledge in Learning Multiple Related Sparse
Gaussian Graphical Models (ICML 2018) <arXiv:1806.00548>. / GPL-2
r-jenkins 1.0 Manage jobs and builds on your Jenkins CI server <https://jenkins.io/>. Create noarch
and edit projects, schedule builds, manage the queue, download build logs, and
much more. / MIT
r-jetpack 0.4.3 Manage project dependencies from your DESCRIPTION file. Create a repro- noarch
ducible virtual environment with minimal additional files in your project. Pro-
vides tools to add, remove, and update dependencies as well as install existing
dependencies with a single function. / MIT
r-jgl 2.3.1 The Joint Graphical Lasso is a generalized method for estimating Gaussian noarch
graphical models/ sparse inverse covariance matrices/ biological networks on
multiple classes of data. We solve JGL under two penalty functions: The
Fused Graphical Lasso (FGL), which employs a fused penalty to encourage
inverse covariance matrices to be similar across classes, and the Group Graphi-
cal Lasso (GGL), which encourages similar network structure between classes.
FGL is recommended over GGL for most applications. Reference: Danaher P,
Wang P, Witten DM. (2013) <doi:10.1111/rssb.12033>. / GPL-2
r-jiebard 0.1 jiebaR is a package for Chinese text segmentation, keyword extraction and noarch
speech tagging. This package provides the data files required by jiebaR. / MIT
r-jjb 0.1.0 Set of common functions used for manipulating colors, detecting and interact- noarch
ing with ‘RStudio’, modeling, formatting, determining users’ operating sys-
tem, feature scaling, and more! / GPL-2
r-jlctree 0.0.1 Implements the tree-based approach to joint modeling of time-to-event and noarch
longitudinal data. This approach looks for a tree-based partitioning such that
within each estimated latent class defined by a terminal node, the time-to-
event and longitudinal responses display a lack of association. See Zhang and
Simonoff (2018) <arXiv:1812.01774>. / GPL-3
r-jm 1.4_8 Shared parameter models for the joint modeling of longitudinal and time-to- noarch
event data. / GPL-2
r-jmdesign 1.1 Performs power calculations for joint modeling of longitudinal and sur- noarch
vival data with k-th order trajectories when the variance-covariance matrix,
Sigma_theta, is unknown. / GPL-2
r-jmdl 0.3.0 Fit joint mean-correlation models for discrete longitudinal data (Tang linux-
CY,Zhang W, Leng C, 2017 <doi:10.5705/ss.202016.0435>). / GPL-2 64,
osx-
64,
win-
64


Name Version
r-jmetrik 1.1 The main purpose of this package is to make it easy for userR’s to interact with noarch
‘jMetrik’ an open source application for psychometric analysis. For example
it allows useR’s to write data frames to file in a format that can be used by
‘jMetrik’. It also allows useR’s to read *.jmetrik files (e.g. output from an
analysis) for follow-up analysis in R. The *.jmetrik format is a flat file that in-
cludes a multiline header and the data as comma separated values. The header
includes metadata about the file and one row per variable with the following
information in each row: variable name, data type, item scoring, special data
codes, and variable label. / GPL-3
r-jmi 0.1.0 Computes the Jackknife Mutual Information (JMI) between two random vec- linux-
tors and provides the p-value for dependence tests. See Zeng, X., Xia, Y. and 64,
Tong, H. (2018) <doi:10.1073/pnas.1715593115>. / GPL-2 osx-
64,
win-
64
r-jmisc 0.3.1 Some handy function in R / GPL-2 noarch
r-jmotif 1.0.3 Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, linux-
RePair, and RRA algorithms facilitating time series motif (i.e., recurrent pat- 64,
tern), discord (i.e., anomaly), and characteristic pattern discovery along with osx-
interpretable time series classification. / GPL-2 64,
win-
64
r-jmuoutlier 2.2 Performs a permutation test on the difference between two location parame- noarch
ters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test,
a ratio mean deviance test. Also performs some graphing techniques, such as
for confidence intervals, vector addition, and Fourier analysis; and includes
functions related to the Laplace (double exponential) and triangular distribu-
tions. Performs power calculations for the binomial test. / GPL-3
r-jmvcore 1.0.0 A framework for creating rich interactive analyses for the jamovi platform (see noarch
<https://www.jamovi.org> for more information). / GPL-2
r-johnson 1.4 RE.Johnson performs the Johnson Transformation to increase the normality. / noarch
GPL-2
r-joint.cox 3.5 Perform likelihood estimation and dynamic prediction under joint frailty- noarch
copula models for tumour progression and death in meta-analysis. A penal-
ized likelihood method is employed for estimating model parameters, where
the baseline hazard functions are modeled by smoothing splines. The methods
are applicable for meta-analytic data combining several studies. The methods
can analyze data having information on both terminal event time (e.g., time-
to-death) and non-terminal event time (e.g., time-to-tumour progression). See
Emura et al. (2017) <doi:10.1177/0962280215604510> for likelihood estima-
tion, and Emura et al. (2018) <doi:10.1177/0962280216688032> for dynamic
prediction. More details on these methods can also be found in a book of
Emura et al. (2019) <10.1007/978-981-13-3516-7>. Survival data from ovar-
ian cancer patients are also available. / GPL-2
r-jointdiag 0.3 Different algorithms to perform approximate joint diagonalization of a fi- linux-
nite set of square matrices. Depending on the algorithm, orthogonal or non- 64,
orthogonal diagonalizer is found. These algorithms are particularly useful in osx-
the context of blind source separation. / GPL-2 64,
win-
64


Name Version
r-jointnmix 1.0 Fits univariate and joint N-mixture models for data on two unmarked site- noarch
associated species. Includes functions to estimate latent abundances through
empirical Bayes methods. / GPL-2
r-jointpm 2.3.1 A bivariate integration method to estimate risk caused by two extreme and noarch
dependent forcing variables. / GPL-2
r-josae 0.3.0 Implementation of some unit and area level EBLUP estimators as well noarch
as the estimators of their MSE also under heteroscedasticity. The
package further documents the publications Breidenbach and Astrup
(2012) <DOI:10.1007/s10342-012-0596-7>, Breidenbach et al. (2016)
<DOI:10.1016/j.rse.2015.07.026> and Breidenbach et al. (2018 in press). The
vignette further explains the use of the implemented functions. / GPL-2
r-josaplay 0.1.3 Josa in Korean is often determined by judging the previous word. When writ- noarch
ing reports using Rmd, a function that prints the appropriate investigation for
each case is helpful. The ‘josaplay’ package then evaluates the previous word
to determine which josa is appropriate. / MIT
r-jose 1.0 Read and write JSON Web Keys (JWK, rfc7517), generate and verify JSON noarch
Web Signatures (JWS, rfc7515) and encode/decode JSON Web Tokens (JWT,
rfc7519). These standards provide modern signing and encryption formats
that are the basis for services like OAuth 2.0 or LetsEncrypt and are natively
supported by browsers via the JavaScript WebCryptoAPI. / MIT
r-jousboost 2.1.0 Implements under/oversampling for probability estimation. To be used with linux-
machine learning methods such as AdaBoost, random forests, etc. / MIT 64,
osx-
64,
win-
64
r-jpeg 0.1_8 This package provides an easy and simple way to read, write and display linux-
bitmap images stored in the JPEG format. It can read and write both files 32,
and in-memory raw vectors. / GPL-2 | GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64
r-jpen 1.0 A Joint PENalty Estimation of Covariance and Inverse Covariance Matrices. / noarch
GPL-2
r-jqr 1.1.0 Client for ‘jq’, a ‘JSON’ processor (<https://stedolan.github.io/jq/>), written win-
in C. ‘jq’ allows the following with ‘JSON’ data: index into, parse, do calcu- 64
lations, cut up and filter, change key names and values, perform conditionals
and comparisons, and more. / MIT
r-jrc 0.1.1 An ‘httpuv’ based bridge between R and ‘JavaScript’. Provides an easy way noarch
to exchange commands and data between a web page and a currently running
R session. / GPL-3
r-jrf 0.1_4 Simultaneous estimation of multiple related networks. / GPL-2 linux-
64,
osx-
64,
win-
64


Name Version
r-jrich 0.60_35
These functions calculate the taxonomic measures presented in Miranda- noarch
Esquivel (2016). The package introduces Jack-knife resampling in evolution-
ary distinctiveness prioritization analysis, as a way to evaluate the support of
the ranking in area prioritization, and the persistence of a given area in a con-
servation analysis. The algorithm is described in: Miranda-Esquivel, D (2016)
<DOI:10.1007/978-3-319-22461-9_11>. / GPL-3
r-jrvfinance 1.4.1 Implements the basic financial analysis functions similar to (but not identical noarch
to) what is available in most spreadsheet software. This includes finding the
IRR and NPV of regularly spaced cash flows and annuities. Bond pricing and
YTM calculations are included. In addition, Black Scholes option pricing and
Greeks are also provided. / GPL-2
r-json64 0.1.3 Encode/Decode ‘base64’, with support for JSON format, using two functions: noarch
j_encode() and j_decode(). ‘Base64’ is a group of similar binary-to-text encod-
ing schemes that represent binary data in an ASCII string format by translating
it into a radix-64 representation, used when there is a need to encode binary
data that needs to be stored and transferred over media that are designed to deal
with textual data, ensuring that the data will remain intact and without modifi-
cation during transport. <https://developer.mozilla.org/en-US/docs/Web/API/
WindowBase64/Base64_encoding_and_decoding> On the other side, JSON
(JavaScript Object Notation) is a lightweight data-interchange format. Easy
to read, write, parse and generate. It is based on a subset of the JavaScript
Programming Language. JSON is a text format that is completely language
independent but uses conventions that are familiar to programmers of the C-
family of languages, including C, C, C#, Java, JavaScript, Perl, Python, and
many others. JSON structure is built around name:value pairs and ordered list
of values. <https://www.json.org> The first function, j_encode(), let you trans-
form a data.frame or list to a ‘base64’ encoded JSON (or JSON string). The
j_decode() function takes a ‘base64’ string (could be an encoded JSON) and
transform it to a data.frame (or list, depending of the JSON structure). / MIT
r-jsonarr 1.1.1 This package enables users to access MongoDB by running queries and return- noarch
ing their results in R data frames. Usually, data in MongoDB is only available
in the form of a JSON document. jSonarR uses data processing and conversion
capabilities in the jSonar Analytics Platform and the JSON Studio Gateway
(http://www.jsonstudio.com), to convert it to a tabular format which is easy to
use with existing R packages. / AGPL-3
r-jsonlite 1.6 A fast JSON parser and generator optimized for statistical data and the web. linux-
Started out as a fork of ‘RJSONIO’, but has been completely rewritten in re- 32,
cent versions. The package offers flexible, robust, high performance tools for linux-
working with JSON in R and is particularly powerful for building pipelines 64,
and interacting with a web API. The implementation is based on the mapping osx-
described in the vignette (Ooms, 2014). In addition to converting JSON data 64,
from/to R objects, ‘jsonlite’ contains functions to stream, validate, and prettify win-
JSON data. The unit tests included with the package verify that all edge cases 32,
are encoded and decoded consistently for use with dynamic data in systems win-
and applications. / MIT file LICENSE 64
r-jstree 1.0.1 Create and customize interactive trees using the ‘jQuery’ ‘jsTree’ <https: noarch
//www.jstree.com/> plugin library and the ‘htmlwidgets’ package. These trees
can be used directly from the R console, from ‘RStudio’, in Shiny apps and R
Markdown documents. / GPL-2 | GPL-3


Name Version
r-jtgwas 1.5.1 The core of this ‘Rcpp’ based package is a function to compute standardized linux-
Jonckheere-Terpstra test statistics for large numbers of dependent and inde- 64,
pendent variables, e.g., genome-wide analysis. It implements ‘OpenMP’, al- osx-
lowing the option of computing on multiple threads. Supporting functions are 64,
also provided to calculate p-values and summarize results. / GPL-2 win-
64
r-jtrans 0.2.1 Transforming univariate non-normal data to normality using Johnson families noarch
of distributions. Johnson family is a comprehensive distribution family that
accommodates many kinds of non-normal distributions. A bunch of distribu-
tions with various parameters will be fit and the corresponding p-values under
a user-specified normality test will be given. The final transformation will be
the one with the largest p-value under the given normality test. / GPL-2
r-julia 1.1 Generates image data for fractals (Julia and Mandelbrot sets) on the complex noarch
plane in the given region and resolution. / GPL-3
r-juliacall 0.16.6Provides an R interface to ‘Julia’, which is a high-level, high-performance dy- linux-
namic programming language for numerical computing, see <https://julialang. 64,
org/> for more information. It provides a high-level interface as well as a osx-
low-level interface. Using the high level interface, you could call any ‘Julia’ 64,
function just like any R function with automatic type conversion. Using the win-
low level interface, you could deal with C-level SEXP directly while enjoying 64
the convenience of using a high-level programming language like ‘Julia’. /
MIT
r-jumptest 1.1 A fast simulation on stochastic volatility model, with jump tests, p-values pool- linux-
ing, and FDR adjustments. / MIT 64,
osx-
64,
win-
64
r-junctions 1.1 Individual based simulations of hybridizing populations, where the accumula- linux-
tion of junctions is tracked. Furthermore, mathematical equations are provided 64,
to verify simulation outcomes. Both simulations and mathematical equations osx-
are based on Janzen (2018) <doi:10.1101/058107>. / GPL-2 64,
win-
64
r-junr 0.1.3 The ‘Junar’ API is a commercial platform to organize and publish data <http: noarch
//www.junar.com>. It has been used in a number of national and local govern-
ment Open Data initiatives in Latin America and the USA. This package is a
wrapper to make it easier to access data made public through the ‘Junar’ API.
/ MIT
r-jvcoords 1.0.2 Provides functions to standardize and whiten data, and to perform Principal noarch
Component Analysis (PCA). The main advantage of this package over alter-
natives like prcomp() is, that jvcoords makes it easy to convert (additional)
data between the original and the transformed coordinates. The package also
provides a class coords, which can represent affine coordinate transformations.
This class forms the basis of the transformations provided by the package, but
can also be used independently. The implementation has been optimized to be
of comparable speed (and sometimes even faster) than existing alternatives. /
GPL-3
r-jvnvar 1.0 Many method to compute, predict and back-test VaR. For more detail, see the noarch
report: Value at Risk <researchgate.net>. / GPL-3


r-jwutil 1.2.3 This is a set of simple utilities for various data manipulation and testing tasks. linux-
The goal is to use core R tools well, without bringing in many dependen- 64,
cies. Main areas of interest are semi-automated data frame manipulation, such osx-
as converting factors in multiple binary indicator columns. There are testing 64,
functions which provide ‘testthat’ expectations to permute arguments to func- win-
tion calls. There are functions and data to test extreme numbers, dates, and 64
bad input of various kinds which should allow testing failure and corner cases,
which can be used for fuzzing your functions. The test suite has many exam-
ples of usage. / GPL-3
r-kader 0.0.8 Implementation of various kernel adaptive methods in nonparamet- noarch
ric curve estimation like density estimation as introduced in Stute
and Srihera (2011) <doi:10.1016/j.spl.2011.01.013> and Eichner and
Stute (2013) <doi:10.1016/j.jspi.2012.03.011> for pointwise estima-
tion, and like regression as described in Eichner and Stute (2012)
<doi:10.1080/10485252.2012.760737>. / GPL-3
r-kamila 0.1.1.3Implements methods for clustering mixed-type data, specifically combina- linux-
tions of continuous and nominal data. Special attention is paid to the often- 64,
overlooked problem of equitably balancing the contribution of the continuous osx-
and categorical variables. This package implements KAMILA clustering, a 64,
novel method for clustering mixed-type data in the spirit of k-means cluster- win-
ing. It does not require dummy coding of variables, and is efficient enough 64
to scale to rather large data sets. Also implemented is Modha-Spangler clus-
tering, which uses a brute-force strategy to maximize the cluster separation
simultaneously in the continuous and categorical variables. For more informa-
tion, see Foss, Markatou, Ray, & Heching (2016) <doi:10.1007/s10994-016-
5575-7> and Foss & Markatou (2018) <doi:10.18637/jss.v083.i13>. / GPL-3
r-kaphom 0.3 Tests the homogeneity of intraclass kappa statistics obtained from indepen- noarch
dent studies or a stratified study with binary results. It is desired to com-
pare the kappa statistics obtained in multi-center studies or in a single strati-
fied study to give a common or summary kappa using all available informa-
tion. If the homogeneity test of these kappa statistics is not rejected, then
it is possible to make inferences over a single kappa statistic that summa-
rizes all the studies. Muammer Albayrak, Kemal Turhan, Yasemin Yavuz,
Zeliha Aydin Kasap (2019) <doi:10.1080/03610918.2018.1538457> Jun-mo
Nam (2003) <doi:10.1111/j.0006-341X.2003.00118.x> Jun-mo Nam (2005)
<doi:10.1002/sim.2321>Mousumi Banerjee, Michelle Capozzoli, Laura Mc-
Sweeney,Debajyoti Sinha (1999) <doi:10.2307/3315487> Allan Donner,
Michael Eliasziw, Neil Klar (1996) <doi:10.2307/2533154>. / GPL-3


Name Version
r-kappalab 0.4_7 S4 tool box for capacity (or non-additive measure, fuzzy measure) and inte- linux-
gral manipulation in a finite setting. It contains routines for handling various 64,
types of set functions such as games or capacities. It can be used to compute osx-
several non-additive integrals: the Choquet integral, the Sugeno integral, and 64,
the symmetric and asymmetric Choquet integrals. An analysis of capacities in win-
terms of decision behavior can be performed through the computation of vari- 64
ous indices such as the Shapley value, the interaction index, the orness degree,
etc. The well-known Möbius transform, as well as other equivalent repre-
sentations of set functions can also be computed. Kappalab further contains
seven capacity identification routines: three least squares based approaches, a
method based on linear programming, a maximum entropy like method based
on variance minimization, a minimum distance approach and an unsupervised
approach based on parametric entropies. The functions contained in Kappalab
can for instance be used in the framework of multicriteria decision making or
cooperative game theory. / CeCILL
r-kappasize 1.2 Contains basic tools for sample size estimation in studies of interob- noarch
server/interrater agreement (reliability). Includes functions for both the power-
based and confidence interval-based methods, with binary or multinomial out-
comes and two through six raters. / GPL-2
r-kaps 1.0.2 This package provides some routines to conduct the K-adaptive parititioning linux-
(kaps) algorithm for survival data. A function kaps is an implementation ver- 64,
sion of our algorithm. / GPL-3 osx-
64,
win-
64
r-kdensity 1.0.1 Handles univariate non-parametric density estimation with parametric starts noarch
and asymmetric kernels in a simple and flexible way. Kernel density es-
timation with parametric starts involves fitting a parametric density to the
data before making a correction with kernel density estimation, see Hjort
& Glad (1995) <doi:10.1214/aos/1176324627>. Asymmetric kernels make
kernel density estimation more efficient on bounded intervals such as (0, 1)
and the positive half-line. Supported asymmetric kernels are the gamma
kernel of Chen (2000) <doi:10.1023/A:1004165218295>, the beta kernel of
Chen (1999) <doi:10.1016/S0167-9473(99)00010-9>, and the copula kernel
of Jones & Henderson (2007) <doi:10.1093/biomet/asm068>. User-supplied
kernels, parametric starts, and bandwidths are supported. / MIT
r-kdist 0.2 Density, distribution function, quantile function and random generation for the noarch
K-distribution. A plotting function that plots data on Weibull paper and an-
other function to draw additional lines. See results from package in T Lamont-
Smith (2018), submitted J. R. Stat. Soc. / GPL-3
r-kedd 1.0.3 Smoothing techniques and computing bandwidth selectors of the nth derivative noarch
of a probability density for one-dimensional data. / GPL-2
r-keep 1.0 Provides arrays with flexible control over dimension dropping when subscript- noarch
ing. / GPL-3
r-kendall 2.2 Computes the Kendall rank correlation and Mann-Kendall trend test. See doc- linux-
umentation for use of block bootstrap when there is autocorrelation. / GPL-2 64,
osx-
64,
win-
64


r-kendl 1.1 Calculate the kernel-smoothed nonparametric estimator for the exposure dis- noarch
tribution in presence of detection limits. / GPL-2
r-keras 2.2.4.1Interface to ‘Keras’ <https://keras.io>, a high-level neural networks ‘API’. linux-
‘Keras’ was developed with a focus on enabling fast experimentation, supports 32,
both convolution based networks and recurrent networks (as well as combina- linux-
tions of the two), and runs seamlessly on both ‘CPU’ and ‘GPU’ devices. / 64,
MIT file LICENSE noarch,
osx-
64,
win-
64
r-kerasr 0.6.1 Provides a consistent interface to the ‘Keras’ Deep Learning Library directly noarch
from within R. ‘Keras’ provides specifications for describing dense neural
networks, convolution neural networks (CNN) and recurrent neural networks
(RNN) running on top of either ‘TensorFlow’ or ‘Theano’. Type conversions
between Python and R are automatically handled correctly, even when the de-
fault choices would otherwise lead to errors. Includes complete R documenta-
tion and many working examples. / LGPL-2
r-kere 1.0.0 An efficient algorithm inspired by majorization-minimization principle for linux-
solving the entire solution path of a flexible nonparametric expectile regres- 64,
sion estimator constructed in a reproducing kernel Hilbert space. / GPL-2 osx-
64,
win-
64
r-kerndwd 2.0.2 A novel implementation that solves the linear distance weighted discrimination linux-
and the kernel distance weighted discrimination. / GPL-2 64,
osx-
64,
win-
64
r-kernelknn 1.1.0 Extends the simple k-nearest neighbors algorithm by incorporating numerous linux-
kernel functions and a variety of distance metrics. The package takes advan- 64,
tage of ‘RcppArmadillo’ to speed up the calculation of distances between ob- osx-
servations. / MIT 64,
win-
64
r-kernlab 0.9_27Kernel-based machine learning methods for classification, regression, clus- linux-
tering, novelty detection, quantile regression and dimensionality reduction. 32,
Among other methods ‘kernlab’ includes Support Vector Machines, Spectral linux-
Clustering, Kernel PCA, Gaussian Processes and a QP solver. / GPL-2 64,
osx-
64,
win-
32,
win-
64
r-kernscr 1.0.5 Kernel Machine Score Test for Pathway Analysis in the Presence of Semi- noarch
Competing Risks. Method is detailed in: Neykov, Hejblum & Sinnott (2018)
<doi: 10.1177/0962280216653427>. / GPL-2


Name Version
r-kernsmooth 2.23_15
Functions for kernel smoothing (and density estimation) corresponding to the linux-
book: Wand, M.P. and Jones, M.C. (1995) Kernel Smoothing. / Unlimited 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-kexpmv 0.0.3 Implements functions from ‘EXPOKIT’ (<https://www.maths.uq.edu. linux-
au/expokit/>) to calculate matrix exponentials, Sidje RB, (1998) 64,
<doi:10.1145/285861.285868>. Includes functions for small dense ma- osx-
trices along with functions for large sparse matrices. The functions for large 64,
sparse matrices implement Krylov subspace methods which help minimise the win-
computational complexity for matrix exponentials. ‘Kexpmv’ can be utilised 64
to calculate both the matrix exponential in isolation along with the product of
the matrix exponential and a vector. / GPL-2
r- 2.1.0 Control your keyboard and mouse with R code by simulating key presses and win-
keyboardsimulator mouse clicks. The input simulation is implemented with the Windows API. / 64
GPL-2
r-keypress 1.1.1 Wait for a single key press at the ‘R’ prompt. This works in terminals, but linux-
does not currently work in the ‘Windows’ ‘GUI’, the ‘OS X’ ‘GUI’ (‘R.app’), 64,
in ‘Emacs’ ‘ESS’, in an ‘Emacs’ shell buffer or in ‘R Studio’. In these cases osx-
‘keypress’ stops with an error message. / MIT 64,
win-
64
r-keyringr 0.4.0 Decrypts passwords stored in the Gnome Keyring, macOS Keychain and noarch
strings encrypted with the Windows Data Protection API. / MIT
r-kfas 1.3.7 State space modelling is an efficient and flexible framework for statistical in- linux-
ference of a broad class of time series and other data. KFAS includes com- 64,
putationally efficient functions for Kalman filtering, smoothing, forecasting, osx-
and simulation of multivariate exponential family state space models, with ob- 64,
servations from Gaussian, Poisson, binomial, negative binomial, and gamma win-
distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for 64
details. / GPL-2
r-kfda 1.0.0 Kernel Fisher Discriminant Analysis (KFDA) is performed using Kernel Prin- noarch
cipal Component Analysis (KPCA) and Fisher Discriminant Analysis (FDA).
There are some similar packages. First, ‘lfda’ is a package that performs
Local Fisher Discriminant Analysis (LFDA) and performs other functions.
In particular, ‘lfda’ seems to be impossible to test because it needs the la-
bel information of the data in the function argument. Also, the ‘ks’ pack-
age has a limited dimension, which makes it difficult to analyze properly.
This package is a simple and practical package for KFDA based on the pa-
per of Yang, J., Jin, Z., Yang, J. Y., Zhang, D., and Frangi, A. F. (2004)
<DOI:10.1016/j.patcog.2003.10.015>. / GPL-3
r-kfigr 1.2 A streamlined cross-referencing system for R Markdown documents generated noarch
with ‘knitr’. R Markdown is an authoring format for generating dynamic con-
tent from R. ‘kfigr’ provides a hook for anchoring code chunks and a function
to cross-reference document elements generated from said chunks, e.g. figures
and tables. / GPL-3


Name Version
r-kfksds 1.6 Naive implementation of the Kalman filter, smoother and disturbance linux-
smoother for state space models. / GPL-2 64,
osx-
64,
win-
64
r-kgc 1.0.0.2Aids in identifying the Koeppen-Geiger (KG) climatic zone for a given lo- noarch
cation. The Koeppen-Geiger climate zones were first published in 1884, as
a system to classify regions of the earth by their relative heat and humidity
through the year, for the benefit of human health, plant and agriculture and
other human activity [1]. This climate zone classification system, applicable
to all of the earths surface, has continued to be developed by scientists up
to the present day. Recently one of use (FZ) has published updated, higher
accuracy KG climate zone definitions [2]. In this package we use these up-
dated high-resolution maps as the data source [3]. We provide functions that
return the KG climate zone for a given longitude and lattitude, or for a given
United States zip code. In addition the CZUncertainty() function will check
climate zones nearby to check if the given location is near a climate zone
boundary. In addition an interactive shiny app is provided to define the KG
climate zone for a given longitude and lattitude, or United States zip code.
Digital data, as well as animated maps, showing the shift of the climate zones
are provided on the following website <http://koeppen-geiger.vu-wien.ac.at>.
This work was supported by the DOE-EERE SunShot award DE-EE-0007140.
[1] W. Koeppen, (2011) <doi:10.1127/0941-2948/2011/105>. [2] F. Rubel
and M. Kottek, (2010) <doi:10.1127/0941-2948/2010/0430>. [3] F. Rubel, K.
Brugger, K. Haslinger, and I. Auer, (2016) <doi:10.1127/metz/2016/0816>. /
BSD_2_clause
r-kidney.epi 1.1.0 Contains kidney care oriented functions. Current version contains only noarch
function for calculation of Kidney Donor Risk Index and Kidney Donor
Profile Index for kidney transplant donors by Rao et al. (2009)
<doi:10.1097/TP.0b013e3181ac620b>. Citation: Bikbov B. R open source
programming code for calculation of the Kidney Donor Profile Index and Kid-
ney Donor Risk Index. Kidney Diseases (2018) <doi:10.1159/000492427>. /
LGPL-2
r-kimisc 0.4 A collection of useful functions not found anywhere else, mainly for program- noarch
ming: Pretty intervals, generalized lagged differences, checking containment
in an interval, and an alternative interface to assign(). / GPL-3
r-kin.cohort 0.7 Analysis of kin-cohort studies. kin.cohort provides estimates of age-specific noarch
cumulative risk of a disease for carriers and noncarriers of a mutation. The co-
horts are retrospectively built from relatives of probands for whom the geno-
type is known. Currently the method of moments and marginal maximum
likelihood are implemented. Confidence intervals are calculated from boot-
strap samples. Most of the code is a translation from previous ‘MATLAB’
code by N. Chatterjee. / GPL-2


Name Version
r-kinship2 1.8.4 Routines to handle family data with a pedigree object (2014, <doi: noarch
10.1159/000363105>). The initial purpose was to create correlation structures
that describe family relationships such as kinship and identity-by-descent,
which can be used to model family data in mixed effects models, such as in the
coxme function. Also includes a tool for pedigree drawing which is focused
on producing compact layouts without intervention. Recent additions include
utilities to trim the pedigree object with various criteria, and kinship for the X
chromosome. / GPL-2
r-kirby21.base 1.7.0 Multi-modal magnetic resonance imaging (‘MRI’) data from the ‘Kirby21’ noarch
‘reproducibility’ study <https://www.nitrc.org/projects/multimodal/>, includ-
ing functional and structural imaging. / GPL-2
r-kissmig 1.0_3 Simulating species migration and range dynamics under stable or changing linux-
environmental conditions based on a simple, raster-based, stochastic migra- 64,
tion model. Providing accessibility for considering species migration in niche- osx-
based species distribution models. / GPL-3 64,
win-
64
r-kknn 1.3.1 Weighted k-Nearest Neighbors for Classification, Regression and Clustering. linux-
/ GPL-2 64,
osx-
64,
win-
64
r-klin 2007_02_05
The package implements efficient ways to evaluate and solve equations of the noarch
form Ax=b, where A is a kronecker product of matrices. Functions to solve
least squares problems of this type are also included. / GPL-2
r-klustr 0.1.0 Used to create dynamic, interactive ‘D3.js’ based parallel coordinates and prin- noarch
cipal component plots in ‘R’. The plots make visualizing k-means or other
clusters simple and informative. / GPL-3
r-km.ci 0.5_2 Computes various confidence intervals for the Kaplan-Meier estimator, noarch
namely: Petos CI, Rothman CI, CI’s based on Greenwoods variance, Thomas
and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall
and Wellner. / GPL-2
r-kmconfband 0.1 Computes and plots an exact nonparametric band for any user-specified level noarch
of confidence from a single-sample survfit object / GPL-2
r-kmda 1.0 Compute p-values of metabolite differential expression analysis using the noarch
kernel-based approach. / GPL-3
r-kmlcov 1.0.1 ‘kmlcov’ Cluster longitudinal data using the likelihood as a metric of distance. noarch
The generalised linear model allow the user to introduce covariates with dif-
ferent level effects (2 levels). / GPL-2
r-kmodr 0.1.0 An implementation of the ‘k-means–’ algorithm proposed by Chawla and Gio- noarch
nis, 2013 in their paper, k-means– : A unified approach to clustering and
outlier detection. SIAM International Conference on Data Mining (SDM13),
and using ‘ordering’ described by Howe, 2013 in the thesis, Clustering and
anomaly detection in tropical cyclones. Useful for creating (potentially) tighter
clusters than standard k-means and simultaneously finding outliers inexpen-
sively in multidimensional space. / GPL-3
r-kmsurv 0.1_5 Data sets and functions for Klein and Moeschberger (1997), Survival Analysis, noarch
Techniques for Censored and Truncated Data, Springer. / GPL-3


Name Version
r- 0.1.0 The sampl.mcmc() function creates samples of the feasible region of a knap- noarch
knapsacksampling sack problem with both equalities and inequalities constraints. / GPL-2
r-knitlatex 0.9.0 Provides several helper functions for working with ‘knitr’ and ‘LaTeX’. It noarch
includes ‘xTab’ for creating traditional ‘LaTeX’ tables, ‘lTab’ for generat-
ing ‘longtable’ environments, and ‘sTab’ for generating a ‘supertabular’ en-
vironment. Additionally, this package contains a knitr_setup() function which
fixes a well-known bug in ‘knitr’, which distorts the ‘results=asis’ command
when used in conjunction with user-defined commands; and a com command
(<<com=TRUE>>=) which renders the output from ‘knitr’ as a ‘LaTeX’ com-
mand. / GPL-3
r-knitr 1.22 Provides a general-purpose tool for dynamic report generation in R using Lit- linux-
erate Programming techniques. / GPL 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-knitrbootstrap 1.0.2 A framework to create Bootstrap <http://getbootstrap.com/> HTML reports noarch
from ‘knitr’ ‘rmarkdown’. / MIT
r- 1.1.0 Provides a progress bar similar to ‘dplyr’ that can write progress out to a vari- noarch
knitrprogressbar ety of locations, including stdout(), stderr(), or from file(). Useful when using
‘knitr’ or ‘rmarkdown’, and you still want to see progress of calculations in
the terminal. / MIT
r-knncat 1.2.2 Scale categorical variables in such a way as to make NN classification as ac- linux-
curate as possible. The code also handles continuous variables and prior prob- 64,
abilities, and does intelligent variable selection and estimation of both error osx-
rates and the right number of NN’s. / GPL-2 64,
win-
64
r-knngarden 1.0.1 Multi-distance based k-Nearest Neighbors Classification with K Threshold noarch
Value Check and Same K_i Problem Dealing, Missing Observations Filling
/ GPL-2
r-knnindep 2.0 This package provides the implementation of an exact formula of the ith near- noarch
est neighbour distance distribution and implementations of tests of indepen-
dence based on that formula. Furthermore the package provides a general
framework to benchmark tests of independence. / GPL-3
r-knoema 0.1.16Using this package, users can access to the largest collection of public data noarch
and statistics on the Internet featuring about 2.5 billion time series from thou-
sands of sources collected in ‘Knoema’ repository and use rich R calcula-
tions in order to analyze the data. Because data in ‘Knoema’ is time se-
ries data, ‘Knoema’ function offers data in a number of formats usable in R
such as ‘ts’, ‘xts’ or ‘zoo’. For more information about ‘Knoema’ API go to
<https://knoema.com/dev/docs>. / MIT


Name Version
r-knor 0.0_6 The k-means ‘NUMA’ Optimized Routine library or ‘knor’ is a highly opti- linux-
mized and fast library for computing k-means in parallel with accelerations 64,
for Non-Uniform Memory Access (‘NUMA’) architectures. / Apache License osx-
2.0 64,
win-
64
r-knotr 1.0_2 Makes nice pictures of knots using Bezier curves and numerical optimization. noarch
/ GPL-2
r-kodama 1.5 KODAMA algorithm is an unsupervised and semi-supervised learning algo- linux-
rithm that performs feature extraction from noisy and high-dimensional data. 64,
It facilitates identification of patterns representing underlying groups on all osx-
samples in a data set. The algorithm was published by Cacciatore et al. 64,
2014 <DOI:10.1073/pnas.1220873111>. Addition functions was introduced win-
by Cacciatore et al. 2017 <DOI:10.1093/bioinformatics/btw705> to facilitate 64
the identification of key features associated with the generated output and are
easily interpretable for the user. Cross-validated techniques are also included
in this package. / GPL-2
r-kofdata 0.1.3.3Read Swiss time series data from the ‘KOF Datenservice’ API, <https:// noarch
datenservice.kof.ethz.ch>. The API provides macroeconomic survey data,
business cycle and further macro economic time series about Switzerland. The
package itself is a set of wrappers around the ‘KOF Datenservice’ API. The
‘kofdata’ package is able to consume public information as well as data that
requires an API token. / GPL-2
r-kofnga 1.3 Provides a function that uses a genetic algorithm to search for a subset of noarch
size k from the integers 1:n, such that a user-supplied objective function is
minimized at that subset. The selection step is done by tournament selection
based on ranks, and elitism may be used to retain a portion of the best solutions
from one generation to the next. Population objective function values may
optionally be evaluated in parallel. / GPL-2
r-kohonen 3.0.8 Functions to train self-organising maps (SOMs). Also interrogation of the linux-
maps and prediction using trained maps are supported. The name of the pack- 32,
age refers to Teuvo Kohonen, the inventor of the SOM. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
r-kolmim 1.0 Provides an alternative, more efficient evaluation of extreme probabilities of linux-
Kolmogorov’s goodness-of-fit measure, Dn, when compared to the original 64,
implementation of Wang, Marsaglia, and Tsang. These probabilities are used osx-
in Kolmogorov-Smirnov tests when comparing two samples. / GPL-2 64,
win-
64
r-komadown 0.2.0 R Markdown templates based on the ‘KOMA-Script’ classes for LaTeX, addi- noarch
tionally offering cross-referencing via the ‘bookdown’ package. / GPL-3
r-komaletter 0.3.1 An R Markdown template for writing beautiful yet versatile letters, using the noarch
‘KOMA-Script’ letter class ‘scrlttr2’ and an adaptation of the ‘pandoc-letter’
template. ‘scrlttr2’ provides layouts for many different window envelope types
and the possibility to define your own. / GPL-3


Name Version
r-konpsurv 1.0.1 The K-sample omnibus non-proportional hazards (KONP) tests are powerful linux-
non-parametric tests for comparing K (>=2) hazard functions based on right- 64,
censored data (Gorfine, Schlesinger and Hsu, 2019, <arXiv:1901.05739v1>). osx-
These tests are consistent against any differences between the hazard functions 64,
of the groups. The KONP tests are often more powerful than other existing win-
tests, especially under non-proportional hazard functions. / GPL-2 64
r-kpart 1.2.2 Cubic spline fitting along with knot selection, includes support for additional noarch
variables. / GPL-2
r-kpeaks 0.1.0 The input argument k which is the number of clusters is needed to start all of noarch
the partitioning clustering algorithms. In unsupervised learning applications,
an optimal value of this argument is widely determined by using the internal
validity indexes. Since these indexes suggest a k value which is computed on
the clustering results after several runs of a clustering algorithm they are com-
putationally expensive. On the contrary, ‘kpeaks’ enables to estimate k before
running any clustering algorithm. It is based on a simple novel technique using
the descriptive statistics of peak counts of the features in a data set. / GPL-2
r-kpmt 0.1.0 Functions that implement the known population median test. / MIT noarch
r-kpodclustr 1.0 The kpodclustr package implements the k-POD method for clustering partially noarch
observed data. / MIT
r-kriens 0.1 Provides basic functions for Continuation-Passing Style development. / noarch
BSD_3_clause
r-krige 0.2_1 Estimates kriging models for geographical point-referenced data. Method is noarch
described in Monogan and Gill (2016) <doi:10.1017/psrm.2015.5>. / GPL-2
r-kriging 1.1 Simple and highly optimized ordinary kriging algorithm to plot geographical linux-
data / GPL-2 64,
osx-
64,
win-
64
r-krls 1.0_0 Package implements Kernel-based Regularized Least Squares (KRLS), a ma- noarch
chine learning method to fit multidimensional functions y=f(x) for regression
and classification problems without relying on linearity or additivity assump-
tions. KRLS finds the best fitting function by minimizing the squared loss
of a Tikhonov regularization problem, using Gaussian kernels as radial basis
functions. For further details see Hainmueller and Hazlett (2014). / GPL-2
r-krmm 1.0 Solves kernel ridge regression, within the the mixed model framework, for the noarch
linear, polynomial, Gaussian, Laplacian and ANOVA kernels. The model com-
ponents (i.e. fixed and random effects) and variance parameters are estimated
using the expectation-maximization (EM) algorithm. All the estimated com-
ponents and parameters, e.g. BLUP of dual variables and BLUP of random
predictor effects for the linear kernel (also known as RR-BLUP), are avail-
able. The kernel ridge mixed model (KRMM) is described in Jacquin L, Cao
T-V and Ahmadi N (2016) A Unified and Comprehensible View of Parametric
and Kernel Methods for Genomic Prediction with Application to Rice. Front.
Genet. 7:145. <doi:10.3389/fgene.2016.00145>. / GPL-2 | GPL-3


Name Version
r-ksamples 1.2_9 Compares k samples using the Anderson-Darling test, Kruskal-Wallis type linux-
tests with different rank score criteria, Steel’s multiple comparison test, and 64,
the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (lim- osx-
ited) exact P-values, all valid under randomization, with or without ties, or 64,
conditionally under random sampling from populations, given the observed win-
tie pattern. Except for Steel’s test and the JT test it also combines these tests 64
across several blocks of samples. Also analyzed are 2 x t contingency tables
and their blocked combinations using the Kruskal-Wallis criterion. Steel’s test
is inverted to provide simultaneous confidence bounds for shift parameters.
A plotting function compares tail probabilities obtained under asymptotic ap-
proximation with those obtained via simulation or exact calculations. / GPL-2
r-ksd 1.0.0 An adaptation of Kernelized Stein Discrepancy, this package provides a noarch
goodness-of-fit test of whether a given i.i.d. sample is drawn from a given dis-
tribution. It works for any distribution once its score function (the derivative
of log-density) can be provided. This method is based on A Kernelized Stein
Discrepancy for Goodness-of-fit Tests and Model Evaluation by Liu, Lee, and
Jordan, available at <http://arxiv.org/abs/1602.03253>. / MIT
r-kseaapp 0.99.0Infers relative kinase activity from phosphoproteomics data using the method noarch
described by Casado et al. (2013) <doi:10.1126/scisignal.2003573>. / MIT
r-kselection 0.2.0 Selection of k in k-means clustering based on Pham et al. paper ‘‘Selection of noarch
k in k-means clustering”. / GPL-3
r-ksgeneral 0.1.1 Computes a p-value of the one-sample two-sided (or one-sided, as a special linux-
case) Kolmogorov-Smirnov (KS) statistic, for any fixed critical level, and an 64,
arbitrary, possibly large sample size for a pre-specified purely discrete, mixed osx-64
or continuous cumulative distribution function (cdf) under the null hypothesis.
If a data sample is supplied, ‘KSgeneral’ computes the p-value corresponding
to the value of the KS test statistic computed based on the user provided data
sample. The package ‘KSgeneral’ implements a novel, accurate and efficient
method named Exact-KS-FFT, expressing the p-value as a double-boundary
non-crossing probability for a homogeneous Poisson process, which is then
efficiently computed using Fast Fourier Transform (FFT). The package can
also be used to compute and plot the complementary cdf of the KS statistic
which is known to depend on the hypothesized distribution when the latter is
discontinuous (i.e. purely discrete or mixed). / GPL (>= 2.0)
r-ksnn 0.1.2 Prediction with k* nearest neighbor algorithm based on a publication by Anava linux-
and Levy (2016) <arXiv:1701.07266>. / GPL-2 64,
osx-
64,
win-
64
r-kstatistics 1.0 Methods and tools for estimate (joint) cumulants of a given population distri- noarch
bution using (multivariate) k-statistics and (multivariate) polykays,symmetric
unbiased estimators with minimum variance. For more details see Di Nardo
E., Guarino G., Senato D. (2009) <arXiv:0807.5008>. / GPL-3


Name Version
r-kstmatrix 0.1_2 Knowledge space theory by Doignon and Falmagne (1999) <doi:10.1007/978- noarch
3-642-58625-5> is a set- and order-theoretical framework, which proposes
mathematical formalisms to operationalize knowledge structures in a partic-
ular domain. The ‘kstMatrix’ package provides basic functionalities to gener-
ate, handle, and manipulate knowledge structures and knowledge spaces. Op-
posed to the ‘kst’ package, ‘kstMatrix’ uses matrix representations for knowl-
edge structures. Furthermore, ‘kstMatrix’ contains several knowledge spaces
developed by the research group around Cornelia Dowling through querying
experts. / GPL-3
r-kuiper.2samp 1.0 This function performs the two-sample Kuiper test to assess the anomaly noarch
of continuous, one-dimensional probability distributions. References used
for this method are (1). Kuiper, N. H. (1960). <DOI:10.1016/S1385-
7258(60)50006-0> and (2). Paltani, S. (2004). <DOI:10.1051/0004-
6361:20034220>. / AGPL-3
r-kulife 0.1_14Provides various functions and data sets from experiments at the Faculty of noarch
Life Sciences, University of Copenhagen. This package will be discontinued
and archived, and the functions and datasets will be maintained and updated in
the MESS package / GPL-2
r-kvh 1.4.1 The format KVH is a lightweight format that can be read/written both by hu- linux-
mans and machines. It can be useful in situations where XML or alike formats 64,
seem to be an overkill. We provide an ability to parse KVH files in R pretty osx-
fast due to ‘Rcpp’ use. / GPL-2 64,
win-
64
r-kyotil 2018.10_17
Helper functions for creating formatted summary of regression models, writing linux-
publication-ready tables to latex files, and running Monte Carlo experiments. 64,
/ GPL-2 osx-
64,
win-
64
r-kza 4.1.0 Time Series Analysis including break detection, spectral analysis, KZ Fourier linux-
Transforms. / GPL-3 64,
osx-
64,
win-
64
r-kzs 1.4 A spatial smoothing algorithm based on convolutions of finite rectangular ker- noarch
nels that provides sharp resolution in the presence of high levels of noise. /
GPL-2
r-l0ara 0.1.5 An efficient procedure for feature selection for generalized linear models with
linux-
L0 penalty, including linear, logistic, Poisson, gamma, inverse Gaussian re-
64,
gression. Adaptive ridge algorithms are used to fit the models. / GPL-2 osx-
64,
win-
64
r-l1pack 0.38.19
L1 estimation for linear regression, density, distribution function, quan- linux-
tile function and random number generation for univariate and multivariate 64,
Laplace distribution. / GPL (>= 2.0) osx-
64,
win-
64


Name Version
r-l2boost 1.0.1 Efficient implementation of Friedman’s boosting algorithm with l2-loss func- noarch
tion and coordinate direction (design matrix columns) basis functions. / GPL-2
r-label.switching 1.8 The Bayesian estimation of mixture models (and more general hidden Markov noarch
models) suffers from the label switching phenomenon, making the MCMC
output non-identifiable. This package can be used in order to deal with this
problem using various relabelling algorithms. / GPL-2
r-labeledloop 0.1 Support labeled loop and escape from nested loop / MIT noarch
r-labeling 0.3 Provides a range of axis labeling algorithms / MIT file LICENSE | Unlimited linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-labelvector 0.1.0 Labels are a common construct in statistical software providing a human read- noarch
able description of a variable. While variable names are succinct, quick to
type, and follow a language’s naming conventions, labels may be more illus-
trative and may use plain text and spaces. R does not provide native support
for labels. Some packages, however, have made this feature available. Most
notably, the ‘Hmisc’ package provides labelling methods for a number of dif-
ferent object. Due to design decisions, these methods are not all exported, and
so are unavailable for use in package development. The ‘labelVector’ package
supports labels for atomic vectors in a light-weight design that is suitable for
use in other packages. / MIT
r-labrs 0.1.0 Dati, scripts e funzioni per il libro Ricerca sociale con R. Concetti e funzioni noarch
base per la ricerca sociale (Datasets, scripts and functions to support the book
Ricerca sociale con R. Concetti e funzioni base per la ricerca sociale). / GPL-3
r-labstatr 1.0.9 Insieme di funzioni di supporto al volume Laboratorio di Statistica con R, noarch
Iacus-Masarotto, MacGraw-Hill Italia, 2006. This package contains sets
of functions defined in Laboratorio di Statistica con R, Iacus-Masarotto,
MacGraw-Hill Italia, 2006. Function names and docs are in italian as well.
/ GPL-2
r-labstats 1.0.1 Contains data sets to accompany the book: Lazic SE (2016). Experimen- noarch
tal Design for Laboratory Biologists: Maximising Information and Improving
Reproducibility. Cambridge University Press. / GPL-3
r-laeken 0.5.0 Estimation of indicators on social exclusion and poverty, as well as Pareto tail noarch
modeling for empirical income distributions. / GPL-2
r-laercio 1.0_1 The package contains functions to compare and group means. / GPL-3 noarch
r-laf 0.8.0 Methods for fast access to large ASCII files. Currently the following file forlinux-
mats are supported: comma separated format (CSV) and fixed width format. It 64,
is assumed that the files are too large to fit into memory, although the package osx-
can also be used to efficiently access files that do fit into memory. Methods are 64,
provided to access and process files blockwise. Furthermore, an opened file win-
can be accessed as one would an ordinary data.frame. The LaF vignette gives 64
an overview of the functionality provided. / GPL-3
r-lagged 0.3_0 Provides classes and methods for lagged objects. / GPL-2 noarch


Name Version
r-lagsequential 0.1.1 Lag-sequential analysis is a method of assessing of patterns (what tends to noarch
follow what?) in sequences of codes. The codes are typically for dis-
crete behaviors or states. The functions in this package read a stream of
codes, or a frequency transition matrix, and produce a variety of lag se-
quential statistics, including transitional frequencies, expected transitional fre-
quencies, transitional probabilities, z values, adjusted residuals, Yule’s Q val-
ues, likelihood ratio tests of stationarity across time and homogeneity across
groups or segments, transformed kappas for unidirectional dependence, bidi-
rectional dependence, parallel and nonparallel dominance, and significance
levels based on both parametric and randomization tests. The methods are
described in Bakeman & Quera (2011) <doi:10.1017/CBO9781139017343>,
O’Connor (1999) <doi:10.3758/BF03200753>, Wampold & Margolin (1982)
<doi:10.1037/0033-2909.92.3.755>, and Wampold (1995, ISBN:0-89391-
919-5). / GPL-2
r-lahman 6.0_0 Provides the tables from the ‘Sean Lahman Baseball Database’ as a set of R linux-
data.frames. It uses the data on pitching, hitting and fielding performance and 32,
other tables from 1871 through 2015, as recorded in the 2016 version of the linux-
database. / GPL 64,
noarch,
osx-
64,
win-
32,
win-
64
r-lambda.r 1.2.3 A language extension to efficiently write functional programs in R. Syntax ex- noarch
tensions include multi-part function definitions, pattern matching, guard state-
ments, built-in (optional) type safety. / LGPL-3
r-lambda4 3.0 Currently the package includes 14 methods for calculating internal consistency noarch
reliability but is still growing. The package allows users access to whichever
reliability estimator is deemed most appropriate for their situation. / GPL-2
r-lamme 0.0.1 Log-analytic methods intended for testing multiplicative effects. / GPL-3 noarch
r-landest 1.0 Provides functions to estimate survival and a treatment effect using a landmark noarch
estimation approach. / GPL-3
r-landpred 1.0 This package includes functions for landmark prediction of a survival outcome noarch
incorporating covariate and short-term event information. For more informa-
tion about landmark prediction please see: Parast, Layla, Su-Chun Cheng, and
Tianxi Cai. Incorporating short-term outcome information to predict long-term
survival with discrete markers. Biometrical Journal 53.2 (2011): 294-307. /
GPL-3
r-landscaper 1.2 Simulates categorical maps on actual geographical realms, starting from either linux-
empty landscapes or landscapes provided by the user (e.g. land use maps). 64,
Allows to tweak or create landscapes while retaining a high degree of control osx-
on its features, without the hassle of specifying each location attribute. In 64,
this it differs from other tools which generate null or neutral landscapes in a win-
theoretical space. The basic algorithm currently implemented uses a simple 64
agent style/cellular automata growth model, with no rules (apart from areas
of exclusion) and von Neumann neighbourhood (four cells, aka Rook case).
Outputs are raster dataset exportable to any common GIS format. / GPL-3


Name Version
r-langevin 1.2.1 Estimate drift and diffusion functions from time series and generate synthetic linux-
time series from given drift and diffusion coefficients. / GPL-2 64,
osx-
64,
win-
64
r-languagelayer 1.2.4 Improve your text analysis with languagelayer <https://languagelayer.com>, a noarch
powerful language detection API. / MIT
r-languager 1.5.0 Data sets exemplifying statistical methods, and some facilitatory utility func- noarch
tions used in ‘‘Analyzing Linguistic Data: A practical introduction to statistics
using R”, Cambridge University Press, 2008. / GPL-2
r-laplacesdemon 16.1.1Provides a complete environment for Bayesian inference using a variety of noarch
different samplers (see ?LaplacesDemon for an overview). The README
describes the history of the package development process. / MIT
r-larf 1.4 Provides instrumental variable estimation of treatment effects when both the noarch
endogenous treatment and its instrument are binary. Applicable to both binary
and continuous outcomes. / GPL-3
r-largelist 0.3.1 Functions to write or append a R list to a file, as well as read, remove, modify linux-
elements from it without restoring the whole list. / GPL-2 64,
osx-
64,
win-
64
r-lars 1.2 Efficient procedures for fitting an entire lasso sequence with the cost of a single linux-
least squares fit. Least angle regression and infinitesimal forward stagewise 32,
regression are related to the lasso, as described in the paper below. / GPL-2 linux-
64,
osx-
64,
win-
32,
win-
64
r-lasso2 1.2_20Routines and documentation for solving regression problems while imposing linux-
an L1 constraint on the estimates, based on the algorithm of Osborne et al. 64,
(1998). / GPL-2 osx-
64,
win-
64
r-lassopv 0.2.0 Estimate the p-values for predictors x against target variable y in lasso regres- noarch
sion, using the regularization strength when each predictor enters the active
set of regularization path for the first time as the statistic. This is based on
the assumption that predictors (of the same variance) that (first) become ac-
tive earlier tend to be more significant. Three null distributions are supported:
normal and spherical, which are computed separately for each predictor and
analytically under approximation, which aims at efficiency and accuracy for
small p-values. / GPL-3


Name Version
r-lassosir 0.1.1 Estimate the sufficient dimension reduction space using sparsed sliced inverse noarch
regression via Lasso (Lasso-SIR) introduced in Lin, Zhao, and Liu (2017)
<arxiv:1611.06655>. The Lasso-SIR is consistent and achieve the optimal
convergence rate under certain sparsity conditions for the multiple index mod-
els. / GPL-3
r-latdiag 0.2_4 A graph proposed by Rosenbaum is useful for checking some properties of noarch
various sorts of latent scale, this program generates commands to obtain the
graph using ‘dot’ from ‘graphviz’. / GPL-2
r-later 0.8.0 Executes arbitrary R or C functions some time after the current time, after the linux-
R execution stack has emptied. / GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-laterality 0.9.3 Calculates and plots Handedness index (HI), absolute HI, mean HI and z-score noarch
which are commonly used indexes for the study of hand preference (laterality)
in non-human primates. / GPL (>= 2.0)
r-latex2exp 0.4.0 Parses and converts LaTeX math formulas to R’s plotmath expressions, used noarch
to enter mathematical formulas and symbols to be rendered as text, axis labels,
etc. throughout R’s plotting system. / MIT
r-latexpdf 0.1.6 Converts table-like objects to stand-alone PDF or PNG. Can be used to embed noarch
tables and arbitrary content in PDF or Word documents. Provides a low-level R
interface for creating ‘LaTeX’ code, e.g. command() and a high-level interface
for creating PDF documents, e.g. as.pdf.data.frame(). Extensive customiza-
tion is available via mid-level functions, e.g. as.tabular(). See also ‘pack-
age?latexpdf’. Support for PNG is experimental; see ‘as.png.data.frame’.
Adapted from ‘metrumrg’ <http://r-forge.r-project.org/R/?group_id=1215>.
Requires a compatible installation of ‘pdflatex’, e.g. <https://miktex.org/>.
/ GPL-3
r-lattice 0.20_38
A powerful and elegant high-level data visualization system inspired by Trel- linux-
lis graphics, with an emphasis on multivariate data. Lattice is sufficient for32,
typical graphics needs, and is also flexible enough to handle most nonstandardlinux-
requirements. See ?Lattice for an introduction. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64


Name Version
r-latticeextra 0.6_28Building on the infrastructure provided by the lattice package, this package linux-
provides several new high-level functions and methods, as well as additional 32,
utilities such as panel and axis annotation functions. / GPL (>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-lava 1.6.5 A general implementation of Structural Equation Models with latent vari- linux-
ables (MLE, 2SLS, and composite likelihood estimators) with both con- 32,
tinuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen linux-
(2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models 64,
and non-linear latent variable models (Holst and Budtz-Joergensen (2019) noarch,
<doi:10.1093/biostatistics/kxy082>). The package also provides methods for osx-
graph exploration (d-separation, back-door criterion), simulation of general 64,
non-linear latent variable models, and estimation of influence functions for a win-
broad range of statistical models. / GPL-3 32,
win-
64
r-lavaan 0.6_3 Fit a variety of latent variable models, including confirmatory factor analysis, linux-
structural equation modeling and latent growth curve models. / GPL (>= 2) 64,
noarch,
osx-
64,
win-
32,
win-
64
r-lazydata 1.1.0 Supplies a LazyData facility for packages which have data sets but do not pro- noarch
vide LazyData: true. A single function is is included, requireData, which is a
drop-in replacement for base::require, but carrying the additional functional-
ity. By default, it suppresses package startup messages as well. See argument
‘reallyQuitely’. / GPL-2
r-lazyeval 0.2.2 An alternative approach to non-standard evaluation using formulas. Provides linux-
a full implementation of LISP style ‘quasiquotation’, making it easier to gen- 32,
erate code with other code. / GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64
r-lazyrmd 0.2.0.1An R Markdown html document format that provides the ability to lazily load noarch
plot outputs as the user scrolls over them. This is useful for large R Markdown
documents with many plots, as it allows for a fast initial page load and defers
loading of individual graphics to the time that the user navigates near them. /
MIT


Name Version
r-lazysql 0.1.3 Helper functions to build SQL statements for dbGetQuery or dbSendQuery noarch
under program control. They are intended to increase speed of coding and
to reduce coding errors. Arguments are carefully checked, in particular SQL
identifiers such as names of tables or columns. More patterns will be added as
required. / MIT
r-lbreg 1.2 Maximum likelihood estimation of log-binomial regression with special func- noarch
tionality when the MLE is on the boundary of the parameter space. / GPL-2
r-lca 0.1.1 Performs model fitting and significance estimation for Localised Co- noarch
Dependency between pairs of features of a numeric dataset. / GPL-2
r-lcf 1.7.0 Baseline correction, normalization and linear combination fitting (LCF) of X- noarch
ray absorption near edge structure (XANES) spectra. The package includes
data loading of .xmu files exported from ‘ATHENA’ (Ravel and Newville,
2005) <doi:10.1107/S0909049505012719>. Loaded spectra can be back-
ground corrected and all standards can be fitted at once. Two linear combina-
tion fitting functions can be used: (1) fit_athena(): Simply fitting combinations
of standards as in ATHENA, (2) fit_float(): Fitting all standards with changing
baseline correction and edge-step normalization parameters. / GPL-3
r-lcfdata 2.0 This package contains (1) event-related brain potential data recorded from 10 noarch
participants at electrodes Fz, Cz, Pz, and Oz (0–300 ms) in the context of
Antoine Tremblay’s PhD thesis (Tremblay, 2009); (2) ERP amplitudes at elec-
trode Fz restricted to the 100 to 175 millisecond time window; and (3) plotting
data generated from a linear mixed-effects model. / GPL-2
r-lcpm 0.1.0 An implementation of the Log Cumulative Probability Model (LCPM) and noarch
Proportional Probability Model (PPM) for which the Maximum Likelihood
Estimates are determined using constrained optimization. This implementa-
tion accounts for the implicit constraints on the parameter space. Other fea-
tures such as standard errors, z tests and p-values use standard methods adapted
from the results based on constrained optimization. / GPL-3
r-lcyanalysis 1.0.3 Analysis of stock data ups and downs trend, the stock technical analysis indi- noarch
cators function have trend line, reversal pattern and market trend. / GPL-3
r-ldbounds 1.1_1.1
Computations related to group sequential boundaries. Includes calculation of noarch
bounds using the Lan-DeMets alpha spending function approach. / GPL-2
r-ldcorsv 1.3.2 Four measures of linkage disequilibrium are provided: the usual r^2 measure, noarch
the r^2_S measure (r^2 corrected by the structure sample), the r^2_V (r^2 cor-
rected by the relatedness of genotyped individuals), the r^2_VS measure (r^2
corrected by both the relatedness of genotyped individuals and the structure of
the sample). / GPL-2
r-ldlinkr 1.0.0 Provides access to the LDlink API (<https://ldlink.nci.nih.gov/?tab= noarch
apiaccess>) using the R console. This programmatic access facilitates re-
searchers who are interested in performing batch queries in 1000 Genomes
Project data using LDlink. / GPL-2
r-ldrtools 0.2_1 Linear dimension reduction subspaces can be uniquely defined using orthog- noarch
onal projection matrices. This package provides tools to compute distances
between such subspaces and to compute the average subspace. For details see
Liski, E.Nordhausen K., Oja H., Ruiz-Gazen A. (2016) Combining Linear Di-
mension Reduction Subspaces <doi:10.1007/978-81-322-3643-6_7>. / GPL-2


Name Version
r-ldtests 1.0 Exact tests for Linkage Disequilibrium (LD) and Hardy-Weinberg Equilibrium noarch
(HWE). - 2-sided LD tests based on different measures of LD (Kulinskaya and
Lewin 2008) - 1-sided Fisher’s exact test for LD - 2-sided Haldane test for
HWE (Wiggington 2005) - 1-sided test for inbreeding - conditional p-values
proposed in Kulinskaya (2008) to overcome the problems of asymetric distri-
butions (for both LD and HWE) / GPL-3
r-leabra 0.1.0 The algorithm Leabra (local error driven and associative biologically realistic noarch
algorithm) allows for the construction of artificial neural networks that are bi-
ologically realistic and balance supervised and unsupervised learning within a
single framework. This package is based on the ‘MATLAB’ version by Ser-
gio Verduzco-Flores, which in turn was based on the description of the algo-
rithm by Randall O’Reilly (1996) <ftp://grey.colorado.edu/pub/oreilly/thesis/
oreilly_thesis.all.pdf>. For more general (not ‘R’ specific) information on the
algorithm Leabra see <https://grey.colorado.edu/emergent/index.php/Leabra>.
/ GPL-2
r-leafarea 0.1.8 An interface for the image processing program ‘ImageJ’, which allows a rapid noarch
digital image analysis for particle sizes. This package includes function to
write an ‘ImageJ’ macro which is optimized for a leaf area analysis by default.
/ GPL-2
r-leaflet 2.0.2 Create and customize interactive maps using the ‘Leaflet’ JavaScript library linux-
and the ‘htmlwidgets’ package. These maps can be used directly from the R 32,
console, from ‘RStudio’, in Shiny applications and R Markdown documents. / linux-
GPL-3 64,
noarch,
osx-
64,
win-
32,
win-
64
r-leaflet.opacity 0.1.0 Extends the ‘leaflet’ R package with the ‘Leaflet.OpacityControls’ JavaScript noarch
plugin. Adds controls to the leaflet map for adjusting the opacity of a layer. /
GPL-3
r- 1.8.0 Contains third-party map tile provider information from ‘Leaflet.js’, <https: noarch
leaflet.providers //github.com/leaflet-extras/leaflet-providers>, to be used with the ‘leaflet’ R
package. Additionally, ‘leaflet.providers’ enables users to retrieve up-to-date
provider information between package updates. / BSD_2_clause
r-leafletr 0.4_0 Display your spatial data on interactive web-maps using the open-source noarch
JavaScript library Leaflet. ‘leafletR’ provides basic web-mapping function-
ality to combine vector data and online map tiles from different sources. See
<http://leafletjs.com> for more information on Leaflet. / GPL-2


Name Version
r-leafstar 1.0 Implementation of trigonometric functions to calculate the exposure of flat, noarch
tilted surfaces, such as leaves and slopes, to direct solar radiation. It im-
plements the equations in A.G. Escribano-Rocafort, A. Ventre-Lespiaucq, C.
Granado-Yela, et al. (2014) <doi:10.1111/2041-210X.12141> in a few user-
friendly R functions. All functions handle data obtained with ‘Ahmes’ 1.0 for
Android, as well as more traditional data sources (compass, protractor, incli-
nometer). The main function (star()) calculates the potential exposure of flat,
tilted surfaces to direct solar radiation (silhouette to area ratio, STAR). It is
equivalent to the ratio of the leaf projected area to total leaf area, but instead
of using area data it uses spatial position angles, such as pitch, roll and course,
and information on the geographical coordinates, hour, and date. The package
includes additional functions to recalculate STAR with custom settings of lo-
cation and time, to calculate the tilt angle of a surface, and the minimum angle
between two non-orthogonal planes. / AGPL-3
r-leanpubr 0.3.1 Provides access to the ‘Leanpub’ API <https://leanpub.com/help/api> for gath- noarch
ering information about publications and submissions to the ‘Leanpub’ plat-
form. / GPL-3
r-leanr 1.4.9 Implements the method described in Network-based analysis noarch
of omics data: The LEAN method [Gwinner Boulday (2016)
<DOI:10.1093/bioinformatics/btw676>] Given a protein interaction net-
work and a list of p-values describing a measure of interest (as e.g. differential
gene expression) this method computes an enrichment p-value for the protein
neighborhood of each gene and compares it to a background distribution of
randomly drawn p-values. The resulting scores are corrected for multiple
testing and significant hits are returned in tabular format. / GPL-3
r-leap 0.2 Advances in sequencing technology now allow researchers to capture the ex- noarch
pression profiles of individual cells. Several algorithms have been developed
to attempt to account for these effects by determining a cell’s so-called ‘pseu-
dotime’, or relative biological state of transition. By applying these algorithms
to single-cell sequencing data, we can sort cells into their pseudotemporal or-
dering based on gene expression. LEAP (Lag-based Expression Association
for Pseudotime-series) then applies a time-series inspired lag-based correlation
analysis to reveal linearly dependent genetic associations. / GPL-2
r-leapfrog 1.0.7 Contains LEAPFrOG Gradient Optimisation and Expectation Maximisation noarch
functions for inferring parental admixture proportions from an offspring with
SNP genotypes. / GPL-3
r-leaps 3.0 Regression subset selection, including exhaustive search. / GPL (>= 2) linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64


r-learnbayes 2.15.1A collection of functions helpful in learning the basic tenets of Bayesian sta- noarch
tistical inference. It contains functions for summarizing basic one and two pa-
rameter posterior distributions and predictive distributions. It contains MCMC
algorithms for summarizing posterior distributions defined by the user. It also
contains functions for regression models, hierarchical models, Bayesian tests,
and illustrations of Gibbs sampling. / GPL-2
r-learngeom 1.4 Contains some functions to learn and teach basic plane Geometry at under- noarch
graduate level with the aim of being helpful to young students with little pro-
gramming skills. / GPL-2
r-learningr 0.29 Crabs in the English channel, deer skulls, English monarchs, half-caste Manga noarch
characters, Jamaican cities, Shakespeare’s The Tempest, drugged up cyclists
and sexually transmitted diseases. / Unlimited
r-learnn 0.2.0 Implementations of several basic neural network concepts in R, as based on noarch
posts on url{http://qua.st/}. / GPL-3
r-learnr 0.9.2.1Create interactive tutorials using R Markdown. Use a combination of narrative, noarch
figures, videos, exercises, and quizzes to create self-paced tutorials for learning
about R and R packages. / Apache License 2.0 | file LICENSE
r-learnrbook 0.0.2 Datasets used in the book Learn R . . . as you learnt your mother tongue by noarch
Pedro J. Aphalo (2017) <https://leanpub.com/learnr>. / GPL-2
r-leersiecyl 1.0.2 Functions to download data from the SIE, which is the Statistical Information noarch
System (Sistema de Información Estadística) in the Statistical Portal of the
Government of Castilla y León (Spain) <https://estadistica.jcyl.es>. / GPL-2
r-legocolors 0.2.0 Provides a dataset containing several color naming conventions established noarch
by multiple sources, along with associated color metadata. The package
also provides related helper functions for mapping among the different Lego
color naming conventions and between Lego colors, hex colors, and ‘R’ color
names, making it easy to convert any color palette to one based on exist-
ing Lego colors while keeping as close to the original color palette as pos-
sible. The functions use nearest color matching based on Euclidean dis-
tance in RGB space. Naming conventions for color mapping include those
from ‘BrickLink’ (<https://www.bricklink.com>), ‘The Lego Group’ (<https:
//www.lego.com>), ‘LDraw’ (<https://www.ldraw.org/>), and ‘Peeron’ (<http:
//www.peeron.com/>). / MIT
r-leiden 0.3.1 Implements the ‘Python leidenalg’ module to be called in R. Enables cluster- noarch
ing using the leiden algorithm for partition a graph into communities. See the
‘Python’ repository for more details: <https://github.com/vtraag/leidenalg>
Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected com-
munities. <arXiv:1810.08473>. / GPL-3
r-leiv 2.0_7 Estimate the slope and intercept of a bivariate linear relationship by calcu- noarch
lating a posterior density that is invariant to interchange and scaling of the
coordinates. / GPL-2
r-lenses 0.0.3 Provides tools for creating and using lenses to simplify data manipulation. noarch
Lenses are composable getter/setter pairs for working with data in a purely
functional way. Inspired by the ‘Haskell’ library ‘lens’ (Kmett, 2012) <https:
//hackage.haskell.org/package/lens>. For a fairly comprehensive (and highly
technical) history of lenses please see the ‘lens’ wiki <https://github.com/
ekmett/lens/wiki/History-of-Lenses>. / MIT
r-lero.lero 0.2 Generates quotes from ‘Lero Lero’, a database for meaningless sentences filled noarch
with corporate buzzwords, intended to be used as corporate lorem ipsum (see
<http://www.lerolero.com/> for more information). Unfortunately, quotes are
currently portuguese-only. / GPL-3


Name Version
r-lest 1.0.0 Functions for vectorised conditional recoding of variables. case_when() en- noarch
ables you to vectorise multiple if and else statements (like ‘CASE WHEN’ in
‘SQL’). if_else() is a stricter and more predictable version of ifelse() in ‘base’
that preserves attributes. These functions are forked from ‘dplyr’ with all pack-
age dependencies removed and behave identically to the originals. / MIT
r-lestat 1.9 Some simple objects and functions to do statistics using linear models and a noarch
Bayesian framework. / GPL-2
r-lettercase 0.13.1Utilities for formatting strings and character vectors to for capitalization, word noarch
break and white space. Supported formats are: snake_case, spine-case, camel-
Case, PascalCase, Title Case, UPPERCASE, lowercase, Sentence case or com-
binations thereof. ‘lettercase’ strives to provide a simple, consistent, intuitive
and high performing interface. / GPL-2
r-lexiconpt 0.1.0 Provides easy access for sentiment lexicons for those who want to do text noarch
analysis in Portuguese texts. As of now, two Portuguese lexicons are available:
‘SentiLex-PT02’ and ‘OpLexicon’ (v2.1 and v3.0). / GPL-2
r-lfactors 1.0.4 Provides an extension to factors called ‘lfactor’ that are similar to factors but noarch
allows users to refer to ‘lfactor’ levels by either the level or the label. / GPL-2
r-lfdr.mle 1.0 Suite of R functions for the estimation of the local false discovery rate (LFDR) noarch
using Type II maximum likelihood estimation (MLE). / GPL-3
r- 1.0 New empirical Bayes methods aiming at analyzing the association of single noarch
lfdrempiricalbayes nucleotide polymorphisms (SNPs) to some particular disease are implemented
in this package. The package uses local false discovery rate (LFDR) estimates
of SNPs within a sample population defined as a reference class and discovers
if SNPs are associated with the corresponding disease. Although SNPs are
used throughout this document, other biological data such as protein data and
other gene data can be used. Karimnezhad, Ali and Bickel, D. R. (2016) <http:
//hdl.handle.net/10393/34889>. / GPL-3
r-lga 1.1_1 Tools for linear grouping analysis. Three user-level functions: gap, rlga and noarch
lga. / GPL-3
r-lgr 0.3.2 A flexible, feature-rich yet light-weight logging framework based on ‘R6’ noarch
classes. It supports hierarchical loggers, custom log levels, arbitrary data fields
in log events, logging to plaintext, ‘JSON’, (rotating) files, memory buffers,
and databases, as well as email and push notifications. For a full list of fea-
tures with examples please refer to the package vignette. / MIT
r-lgrdata 0.1.1 A largish collection of example datasets, including several classics. Many of noarch
these datasets are well suited for regression, classification, and visualization. /
CC0
r-lgtdl 1.1.5 A very simple implementation of a class for longitudinal data. / GPL-2 noarch
r-lhmixr 0.1.0 Fits sex-specific life-history models for fish and other taxa where some of the noarch
individuals have unknown sex. / GPL-3
r-libcoin 1.0_4 Basic infrastructure for linear test statistics and permutation inference in the linux-
framework of Strasser and Weber (1999) <http://epub.wu.ac.at/102/>. This 64,
package must not be used by end-users. CRAN package ‘coin’ implements all osx-
user interfaces and is ready to be used by anyone. / GPL-2 64,
win-
32,
win-
64


Name Version
r-librarian 1.7.0 Automatically install, update, and load ‘CRAN’, ‘GitHub’, and ‘Bioconduc- noarch
tor’ packages in a single function call. By accepting bare unquoted names for
packages, it’s easy to add or remove packages from the list. / GPL-3
r-librarysnapshot 0.1.2 Generate a local library copy with relevant packages. All packages currently noarch
found within the search path - except base packages - will be copied to the
directory provided and can be used later on with the .libPaths() function. /
MIT
r-lift 0.0.2 Compute the top decile lift and plot the lift curve. Cumulative lift curves are noarch
also supported. / GPL-2
r-liftr 0.9.2 Persistent reproducible reporting by containerization of R Markdown docu- noarch
ments. / GPL-3
r-lightningr 1.0.2 The purpose of this package is to enable usage of lightningviz server to be noarch
accessible from R. The server itself can be found at http://lightning-viz.org/
and is required to work with this package. Package by itself cannot and will
not create any visualizations. / MIT
r-lightsout 0.3 Lights Out is a puzzle game consisting of a grid of lights that are either on noarch
or off. Pressing any light will toggle it and its adjacent lights. The goal of
the game is to switch all the lights off. This package provides an interface to
play the game on different board sizes, both through the command line or with
a visual application. Puzzles can also be solved using the automatic solver
included. View a demo online at http://daattali.com/shiny/lightsout/. / MIT
r-likelihood 1.7 Tools for maximum likelihood estimation of parameters of scientific models. / noarch
GPL-2
r- 0.1.0 Provides likelihood functions as defined by Fisher (1922) noarch
likelihoodexplore <doi:10.1098/rsta.1922.0009> and a function that creates likelihood functions
from density functions. The functions are meant to aid in education of
likelihood based methods. / GPL-2
r-limitplot 1.2 Values below a specified limit of detection are stacked in rows in order to noarch
reduce overplotting and create a clear graphical representation of your data. /
GPL-2
r-linbin 0.1.2 Short for ‘linear binning’, the linbin package provides functions for manipu- noarch
lating, binning, and plotting linearly referenced data. Although developed for
data collected on river networks, it can be used with any interval or point data
referenced to a 1-dimensional coordinate system. Flexible bin generation and
batch processing makes it easy to compute and visualize variables at multiple
scales, useful for identifying patterns within and between variables and inves-
tigating the influence of scale of observation on data interpretation. / AGPL-3
r-lincal 1.0 Estimate and confidence/credible intervals for an unknown regressor x0 given noarch
an observed y0. / GPL-2
r-lindenmayer 0.1.13L-systems or Lindenmayer systems are parallel rewriting systems which can noarch
be used to simulate biological forms and certain kinds of fractals. Briefly, in
an L-system a series of symbols in a string are replaced iteratively according
to rules to give a more complex string. Eventually, the symbols are trans-
lated into turtle graphics for plotting. Wikipedia has a very good introduction:
en.wikipedia.org/wiki/L-system This package provides basic functions for ex-
ploring L-systems. / GPL-3
r- 1.0 Consider linear regression model Y = Xb error where the distribution function noarch
linearregressionmde of errors is unknown, but errors are independent and symmetrically distributed.
The package contains a function named LRMDE which takes Y and X as input
and returns minimum distance estimator of parameter b in the model. / GPL-2


Name Version
r-linkedmatrix 1.3.1 A class that links matrix-like objects (nodes) by rows or by columns while noarch
behaving similarly to a base R matrix. Very large matrices are supported if the
nodes are memory-mapped objects. / MIT
r-linkim 0.1 A linkage information based method for imputing missing diploid genotypes / noarch
GPL-2
r-linl 0.0.3 A ‘LaTeX’ Letter class for ‘rmarkdown’, using the ‘pandoc-letter’ template noarch
adapted for use with ‘markdown’. / GPL-3
r-linlir 1.1 This package implements the methodology of Likelihood-based Imprecise Re- noarch
gression (LIR) for the case of linear regression with interval data. / GPL-2
r-linpk 1.0 Generate concentration-time profiles from linear pharmacokinetic (PK) sys- noarch
tems, possibly with first-order absorption or zero-order infusion, possibly with
one or more peripheral compartments, and possibly under steady-state con-
ditions. Single or multiple doses may be specified. Secondary (derived) PK
parameters (e.g. Cmax, Ctrough, AUC, Tmax, half-life, etc.) are computed. /
GPL-3
r-linprog 0.9_2 This package can be used to solve Linear Programming / Linear Optimization noarch
problems by using the simplex algorithm. / GPL-2
r- 0.3_1 Interactive visualization of effects, response functions and marginal effects for noarch
linreginteractive different kinds of regression models. In this version linear regression mod-
els, generalized linear models, generalized additive models and linear mixed-
effects models are supported. Major features are the interactive approach and
the handling of the effects of categorical covariates: if two or more factors
are used as covariates every combination of the levels of each factor is treated
separately. The automatic calculation of marginal effects and a number of pos-
sibilities to customize the graphical output are useful features as well. / GPL-2
r-linselect 1.1.1 Estimate the mean of a Gaussian vector, by choosing among a large collec- noarch
tion of estimators. In particular it solves the problem of variable selection by
choosing the best predictor among predictors emanating from different meth-
ods as lasso, elastic-net, adaptive lasso, pls, randomForest. Moreover, it can
be applied for choosing the tuning parameter in a Gauss-lasso procedure. /
GPL-3
r-lintr 1.0.3 Checks adherence to a given style, syntax errors and possible semantic issues. linux-
Supports on the fly checking of R code edited with ‘RStudio IDE’, ‘Emacs’, 32,
‘Vim’, ‘Sublime Text’ and ‘Atom’. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-lisa 0.1.0 Contains 128 palettes from Color Lisa. All palettes are based on masterpieces noarch
from the worlds greatest artists. For more information, see <http://colorlisa.
com/>. / MIT
r-lisp 0.1 Though SRFI-1 scopes both list-processing and higher-order programming, noarch
we’ll save some list-orthogonal functions for the ‘functional’ package; this is
freely a mixture of implementation and API. / GPL-2
r-lisreltor 0.1.4 This is an unofficial package aimed at automating the import of LISREL out- noarch
put in R. This package or its maintainer is not in any way affiliated with the
creators of LISREL and SSI, Inc. / GPL-2


Name Version
r-listarrays 0.2.0 A toolbox for R arrays. Flexibly split, bind, reshape, modify, subset and name noarch
arrays. / GPL-3
r-listenv 0.7.0 List environments are environments that have list-like properties. For instance, noarch
the elements of a list environment are ordered and can be accessed and iter-
ated over using index subsetting, e.g. ‘x <- listenv(a = 1, b = 2); for (i in
seq_along(x)) x[[i]] <- x[[i]] ^ 2; y <- as.list(x)’. / LGPL-2.1
r-listest 2.1 Tests for independence between X and Y computed from a paired sam- noarch
ple (x1,y1),. . . (xn,yn) of (X,Y), using one of the following statistics (a) the
Longest Increasing Subsequence (Ln), (b) JLn, a Jackknife version of Ln or
(c) JLMn, a Jackknife version of the longest monotonic subsequence. This
family of tests can be applied under the assumption of continuity of X and Y.
/ GPL-2
r-listviewer 2.1.0 R lists, especially nested lists, can be very difficult to visualize or represent. noarch
Sometimes ‘str()’ is not enough, so this suite of htmlwidgets is designed to
help see, understand, and maybe even modify your R lists. The function ‘re-
actjson()’ requires a package ‘reactR’ that can be installed from CRAN or
<https://github.com/timelyportfolio/reactR>. / MIT
r-listwithdefaults 1.2.0 Provides a function that, as an alternative to base::list, allows default values to noarch
be inherited from another list. / GPL-2
r-liureg 1.1.2 Linear Liu regression coefficient’s estimation and testing with different Liu re- noarch
lated measures such as MSE, R-squared etc. REFERENCES i. Akdeniz and
Kaciranlar (1995) <doi:10.1080/03610929508831585> ii. Druilhet and Mom
(2008) <doi:10.1016/j.jmva.2006.06.011> iii. Imdadullah, Aslam, and Saima
(2017) iv. Liu (1993) <doi:10.1080/03610929308831027> v. Liu (2001)
<doi:10.1016/j.jspi.2010.05.030>. / GPL-2 | GPL-3
r-lllcrc 1.2 Applies local log-linear capture-recapture models (LLLMs) for closed popu- noarch
lations, as described in the doctoral thesis of Zachary Kurtz. The method is
relevant when there are 3-5 capture occasions, with auxiliary covariates avail-
able for all capture occasions. As part of estimating the number of missing
population units, the method estimates the rate of missingness as it varies over
the covariate space. In addition, user-friendly functions are provided to recre-
ate (approximately) the method of Zwane and van der Heijden (2004), which
applied the VGAM package in a way that is closely related to LLLMs. / GPL-2
r-llogistic 1.0.3 Density, distribution function, quantile function and random generation for the noarch
L-Logistic distribution with parameters m and phi. The parameter m is the
median of the distribution. / GPL-3
r-lm.beta 1.5_1 Adds standardized regression coefficients to objects created by lm. Also ex- noarch
tends the S3 methods print, summary and coef with additional boolean argu-
ment standardized. / GPL-2
r-lme4 1.1_21Fit linear and generalized linear mixed-effects models. The models and their linux-
components are represented using S4 classes and methods. The core compu- 32,
tational algorithms are implemented using the ‘Eigen’ C library for numerical linux-
linear algebra and ‘RcppEigen’ glue. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64


Name Version
r-lmec 1.0 This package includes a function to fit a linear mixed-effects model in the for- noarch
mulation described in Laird and Ware (1982) but allowing for censored normal
responses. In this version, the with-in group errors are assumed independent
and identically distributed. / GPL-2
r-lmertest 3.1_0 Provides p-values in type I, II or III anova and summary tables for lmer model linux-
fits (cf. lme4) via Satterthwaite’s degrees of freedom method. A Kenward- 32,
Roger method is also available via the pbkrtest package. Model selection linux-
methods include step, drop1 and anova-like tables for random effects (ranova). 64,
Methods for Least-Square means (LS-means) and tests of linear contrasts of noarch,
fixed effects are also available. / GPL (>= 2) osx-
64,
win-
32,
win-
64
r-lmesplines 1.1_10Add smoothing spline modelling capability to nlme. Fit smoothing spline noarch
terms in Gaussian linear and nonlinear mixed-effects models / GPL-2
r-lmf 1.2 This R package provide methods for estimation and statistical inference on noarch
directional and fluctuating selection in age-structured populations. / GPL-2
r-lmfilter 0.1.2 We present a method based on filtering algorithms to estimate the parameters noarch
of linear regressions, i.e. the coefficients and the variance of the error term.
The proposed algorithms make use of Particle Filters following Ristic, B., Aru-
lampalam, S., Gordon, N. (2004, ISBN: 158053631X) resampling methods. /
GPL-2
r-lmmot 0.1.4 Fit right censored Multiple Ordinal Tobit (MOT) model. / GPL-3 noarch
r-lmodel2 1.7_3 Computes model II simple linear regression using ordinary least squares noarch
(OLS), major axis (MA), standard major axis (SMA), and ranged major axis
(RMA). / GPL-2
r-lmreg 1.2 Data files and a few functions used in the book ‘Linear Models and Regres- noarch
sion with R: An Integrated Approach’ by Debasis Sengupta and Sreenivas Rao
Jammalamadaka (2019). / GPL-2
r-lmridge 1.2 Linear ridge regression coefficient’s estimation and testing with different ridge noarch
related measures such as MSE, R-squared etc. REFERENCES i. Hoerl
and Kennard (1970) <doi:10.2307/1267351> ii. Halawa and El-Bassiouni
(2000) <doi:10.1080/00949650008812006> iii. Imdadullah, Aslam, and
Saima (2017) iv. Marquardt (1970) <doi:10.2307/1267205>. / GPL (>= 2.0)
r-lmtest 0.9_36A collection of tests, data sets, and examples for diagnostic checking in linear linux-
regression models. Furthermore, some generic tools for inference in paramet- 32,
ric models are provided. / GPL-2 | GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64
r-lmviz 0.1.2 Contains three shiny applications. Two are meant to explore linear model in- noarch
ference feature through simulation. The third is a game to learn interpreting
diagnostic plots. / GPL-3


Name Version
r-ln0scis 0.1.5 Construct the simultaneous confidence intervals for ratios of means of Log- noarch
normal populations with zeros. It also has a Python module that do the same
thing, and can be applied to multiple comparisons of parameters of any k mix-
ture distributions. And we provide four methods, the method based on gener-
alized pivotal quantity with order statistics and the quantity based on Wilson
by Li et al. (2009) <doi:10.1016/j.spl.2009.03.004> (GPQW), and the meth-
ods based on generalized pivotal quantity with order statistics and the quan-
tity based on Hannig (2009) <doi:10.1093/biomet/asp050> (GPQH). The other
two methods are based on two-step MOVER intervals by Amany H, Abdel K
(2015) <doi:10.1080/03610918.2013.767911>. We deduce Fiducial general-
ized pivotal two-step MOVER intervals based on Wilson quantity (FMW) and
based on Hannig’s quantity (FMWH). All these approach you can find in the
paper of us which it has been submitted. / GPL-2
r-lncpath 1.1 Identifies pathways synergisticly regulated by the interested lncRNA(long noarch
non-coding RNA) sets based on a lncRNA-mRNA(messenger RNA) interac-
tion network. 1) The lncRNA-mRNA interaction network was built from the
protein-protein interactions and the lncRNA-mRNA co-expression relation-
ships in 28 RNA-Seq data sets. 2) The interested lncRNAs can be mapped into
networks as seed nodes and a random walk strategy will be performed to evalu-
ate the rate of each coding genes influenced by the seed lncRNAs. 3) Pathways
regulated by the lncRNA set will be evaluated by a weighted Kolmogorov-
Smirnov statistic as an ES Score. 4) The p value and false discovery rate value
will also be calculated through a permutation analysis. 5) The running score
of each pathway can be plotted and the heat map of each pathway can also be
plotted if an expression profile is provided. 6) The rank and scores of the gene
list of each pathway can be printed. / GPL-2
r-lnirt 0.4.0 Allows the simultaneous analysis of responses and response times in an Item noarch
Response Theory (IRT) modelling framework. Supports variable person speed
functions (intercept, trend, quadratic), and covariates for item and person
(random) parameters. Data missing-by-design can be specified. Parameter
estimation is done with a MCMC algorithm. LNIRT replaces the package
CIRT, which was written by Rinke Klein Entink. For reference, see the pa-
per by Fox, Klein Entink and Van der Linden (2007), Modeling of Responses
and Response Times with the Package cirt, Journal of Statistical Software,
<doi:10.18637/jss.v020.i07>. / GPL-3
r-loadr 0.1.2 Provides intuitive functions for loading objects into environments, encourag- noarch
ing less cluttered workspaces and sharing variables with large or reusable data
across users and sessions. The user provides named variables which are loaded
into the variable environment for later retrieval. / BSD_2_clause


Name Version
r- 1.3.3 Especially when cross-sectional data are observational, effects of treatment noarch
localcontrolstrategy selection bias and confounding are revealed by using the Nonparametric and
Unsupervised preprocessing methods central to Local Control (LC) Strategy.
The LC objective is to estimate the effect-size distribution that best quan-
tifies a potentially causal relationship between a numeric y-Outcome vari-
able and a t-Treatment variable. This t-variable may be either binary {1 =
new vs 0 = control} or a numeric measure of Exposure level. LC Strategy
starts by CLUSTERING experimental units (patients) on their pre-exposure X-
Covariates, forming mutually exclusive and exhaustive BLOCKS of relatively
well-matched units. The implicit statistical model for LC is thus simple one-
way ANOVA. The Within-Block measures of effect-size are Local Rank Cor-
relations (LRCs) when Exposure is numeric with more than two levels. Oth-
erwise, Treatment choice is Nested within BLOCKS, and effect-sizes are LO-
CAL Treatment Differences (LTDs) between within-cluster y-Outcome Means
[new minus control]. An Instrumental Variable (IV) method is also provided
so that Local Average y-Outcomes (LAOs) within BLOCKS may also con-
tribute information for effect-size inferences . . . assuming that X-Covariates in-
fluence only Treatment choice or Exposure level and otherwise have no direct
effects on y-Outcome. Finally, a Most-Like-Me function provides histograms
of effect-size distributions to aid Doctor-Patient communications about Per-
sonalized Medicine. / GPL-2
r-localsolver 2.3 The package converts R data onto input and data for LocalSolver, exe- noarch
cutes optimization and exposes optimization results as R data. LocalSolver
(http://www.localsolver.com/) is an optimization engine developed by Innova-
tion24 (http://www.innovation24.fr/). It is designed to solve large-scale mixed-
variable non-convex optimization problems. The localsolver package is de-
veloped and maintained by WLOG Solutions (http://www.wlogsolutions.com/
en/) in collaboration with Decision Support and Analysis Division at Warsaw
School of Economics (http://www.sgh.waw.pl/en/). / LGPL-2.1
r-locfdr 1.1_8 Computation of local false discovery rates. / GPL-2 noarch
r-lock5data 2.8 Datasets for Statistics: Unlocking the Power of Data by Lock^5 Datasets for noarch
the first and second editions of the book. Older editions of revised data often
have an extra 1e in the name. / GPL-2
r-lock5withr 1.2.2 Data sets and other utilities for ‘Statistics: Unlocking the Power of Data’ noarch
by Lock, Lock, Lock, Lock and Lock (ISBN : 978-0-470-60187-7, http:
//lock5stat.com/). / GPL-2
r-lodi 0.9.1 Impute observed values below the limit of detection (LOD) via censored like- noarch
lihood multiple imputation (CLMI) in single-pollutant models, developed by
Boss et al (2019) <doi:10.1097/EDE.0000000000001052>. CLMI handles ex-
posure detection limits that may change throughout the course of exposure as-
sessment. ‘lodi’ provides functions for imputing and pooling for this method.
/ GPL-3
r-logcondiscr 1.0.6 Given independent and identically distributed observations X(1), . . . , X(n), al- noarch
lows to compute the maximum likelihood estimator (MLE) of probability mass
function (pmf) under the assumption that it is log-concave, see Weyermann
(2007) and Balabdaoui, Jankowski, Rufibach, and Pavlides (2012). The main
functions of the package are ‘logConDiscrMLE’ that allows computation of
the log-concave MLE, ‘logConDiscrCI’ that computes pointwise confidence
bands for the MLE, and ‘kInflatedLogConDiscr’ that computes a mixture of a
log-concave PMF and a point mass at k. / GPL-2


Name Version
r-logger 0.1 Inspired by the the ‘futile.logger’ R package and ‘logging’ Python module, noarch
this utility provides a flexible and extensible way of formatting and delivering
log messages with low overhead. / AGPL-3
r-logging 0.9_107
Pure R implementation of the ubiquitous log4j package. It offers hierarchic linux-
loggers, multiple handlers per logger, level based filtering, space handling in 32,
messages and custom formatting. / GPL-3 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-logicoil 0.99.0This package contains the functions necessary to run the LOGICOIL algo- noarch
rithm. LOGICOIL can be used to differentiate between antiparallel dimers,
parallel dimers, trimers and higher-order coiled-coil sequence. By covering
>90 percent of the known coiled-coil structures, LOGICOIL is a net improve-
ment compared with other existing methods, which achieve a predictive cov-
erage of around 31 percent of this population. As such, LOGICOIL is particu-
larly useful for researchers looking to characterize novel coiled-coil sequences
or studying coiled-coil containing protein assemblies. It may also be used to
assist in the structural characterization of synthetic coiled-coil sequences. /
GPL-2
r-logistic4p 1.5 Error in a binary dependent variable, also known as misclassification, has not noarch
drawn much attention in psychology. Ignoring misclassification in logistic
regression can result in misleading parameter estimates and statistical infer-
ence. This package conducts logistic regression analysis with misspecification
in outcome variables. / GPL-3
r-logisticrr 0.2.0 Adjusted odds ratio conditional on potential confounders can be directly ob- noarch
tained from logistic regression. However, those adjusted odds ratios have been
widely incorrectly interpreted as a relative risk. As relative risk is often of
interest in public health, we provide a simple code to return adjusted relative
risks from logistic regression model under potential confounders. / GPL-3
r-logitnorm 0.8.37Density, distribution, quantile and random generation function for the logit- noarch
normal distribution. Estimation of the mode and the first two moments. Esti-
mation of distribution parameters. / GPL-2
r-lognorm 0.1.6 The lognormal distribution (Limpert et al. (2001) <doi:10.1641/0006- noarch
3568(2001)051%5B0341:lndats%5D2.0.co;2>) can characterize uncertainty
that is bounded by zero. This package provides estimation of distribution
parameters, computation of moments and other basic statistics, and an ap-
proximation of the distribution of the sum of several correlated lognormally
distributed variables (Lo 2013 <doi:10.12988/ams.2013.39511>). / GPL-2
r-lognormreg 0.2_0 Functions to fits simple linear regression models with log normal errors and noarch
identity link (taking the responses on the original scale). See Muggeo (2018)
<doi:10.13140/RG.2.2.18118.16965>. / GPL-3
r-logofgamma 0.0.1 Uses approximations to compute the natural logarithm of the Gamma function noarch
for large values. / GPL-3
r-logranka 1.0 LogrankA provides a logrank test across unlimited groups with the possibility noarch
to input aggregated survival data. / GPL-2


r-lomb 1.1 Computes the Lomb-Scargle Periodogram for unevenly sampled time series. noarch
Includes a randomization procedure to obtain reliable p-values. / GPL-2
r-longcateda 0.31 Methods for plotting categorical longitudinal and time-series data by mapping noarch
individuals to the vertical space (each horizontal line represents a participant),
time (or repeated measures) to the horizontal space, categorical (or discrete)
states as facets using color or shade, and events to points using plotting char-
acters. Sorting individuals in the vertical space and (or) stratifying them by
groups can reveal patterns in the changes over time. / GPL-3
r-longitudinal 1.1.12Contains general data structures and functions for longitudinal data with multi- noarch
ple variables, repeated measurements, and irregularly spaced time points. Also
implements a shrinkage estimator of dynamical correlation and dynamical co-
variance. / GPL-3
r-longmemo 1.1_1 Datasets and Functionality from ‘Jan Beran’ (1994). Statistics for Long- noarch
Memory Processes; Chapman & Hall. Estimation of Hurst (and more) param-
eters for fractional Gaussian noise, ‘fARIMA’ and ‘FEXP’ models. / GPL-2
r-longpower 1.0_19Compute power and sample size for linear models of longitudinal data. noarch
Supported models include mixed-effects models and models fit by gener-
alized least squares and generalized estimating equations. Relevant for-
mulas are derived by Liu and Liang (1997) <DOI:10.2307/2533554>, Dig-
gle et al (2002) <ISBN:9780199676750>, and Lu, Luo, and Chen (2008)
<DOI:10.2202/1557-4679.1098>. / GPL-2
r-longroc 1.0 Time-dependent Receiver Operating Characteristic curves, Area Under the noarch
Curve, and Net Reclassification Indexes for repeated measures. It is based on
methods in Barbati and Farcomeni (2017) <doi:10.1007/s10260-017-0410-2>.
/ GPL-2
r-loo 2.1.0 Efficient approximate leave-one-out cross-validation (LOO) for Bayesian noarch
models fit using Markov chain Monte Carlo. The approximation uses Pareto
smoothed importance sampling (PSIS), a new procedure for regularizing im-
portance weights. As a byproduct of the calculations, we also obtain approx-
imate standard errors for estimated predictive errors and for the comparison
of predictive errors between models. The package also provides methods for
using stacking and other model weighting techniques to average Bayesian pre-
dictive distributions. / GPL (>= 3)
r-loon.data 0.0.5 Data used as examples in the ‘loon’ package. / GPL-2 noarch
r-loop 1.1 The program can perform loop analysis and plot network structure (espe- noarch
cially for food webs),including minimum spanning tree, loop decomposition
of weighted directed graphs, and other network properties which may be re-
lated to food chain properties in ecology. / GPL-2
r-loopanalyst 1.2_6 Loop analysis makes qualitative predictions of variable change in a system noarch
of causally interdependent variables, where qualitative means sign only (i.e.
increases, decreases, non change, and ambiguous). This implementation in-
cludes output support for graphs in .dot file format for use with visualization
software such as ‘graphviz’ (<http://graphviz.org>). ‘LoopAnalyst’ provides
tools for the construction and output of community matrices, computation and
output of community effect matrices, tables of correlations, adjoint, absolute
feedback, weighted feedback and weighted prediction matrices, change in life
expectancy matrices, and feedback, path and loop enumeration tools. / GPL-2
r-lotkaslaw 0.0.1.0Running Lotka’s Law following Pao (1985)(DOI: 10.1016/0306- noarch
4573(85)90055-X). The Law is based around the proof that the number
of authors making n contributions is about 1/n^{a} of those making one
contribution. / GPL-3


r-lotri 0.1.1 Provides a simple mechanism to specify a symmetric block diagonal matrices noarch
(often used for covariance matrices). This is based on the domain specific lan-
guage implemented in ‘nlmixr’ but expanded to create matrices in R generally
instead of specifying parts of matrices to estimate. / GPL-2
r-lpbrim 1.0.0 Optimization of bipartite modularity using LP-BRIM (Label propagation fol- noarch
lowed by Bipartite Recursively Induced Modularity). / BSD_2_clause
r-lpc 1.0.2.1Implements the LPC method of Witten&Tibshirani(Annals of Applied Statis- noarch
tics 2008) for identification of significant genes in a microarray experiment. /
GPL-2
r-lpcm 0.46_3Fitting multivariate data patterns with local principal curves, including tools noarch
for data compression (projection) and measuring goodness-of-fit; with some
additional functions for mean shift clustering. / GPL-2
r-lpint 2.0 Estimates the intensity function, or its derivative of a given order, of a multi- noarch
plicative counting process using the local polynomial method / GPL (>= 2.0)
r-lpm 2.7 Apply Univariate Long Memory Models, Apply Multivariate Short Memory noarch
Models To Hydrological Dataset, Estimate Intensity Duration Frequency curve
to rainfall series. / GPL-2
r-lpmodeler 0.2_1 lpmodeler is a set of user-friendly functions to simplify the modelling of lin- noarch
ear programs (LP) and mixed integer programs (MIP). It provides a unified
interface compatible with optimization packages: Rsymphony. / GPL-2 |
BSD_2_clause
r-lpower 0.1.0 Computes power, or sample size or the detectable difference for a repeated noarch
measures model with attrition. It requires the variance covariance matrix
of the observations but can compute this matrix for several common ran-
dom effects models. See Diggle, P, Liang, KY and Zeger, SL (1994,
ISBN:9780198522843). / Unlimited
r-lps 1.0.10An implementation of the Linear Predictor Score approach, as initiated by noarch
Radmacher et al. (J Comput Biol 2001) and enhanced by Wright et al. (PNAS
2003) for gene expression signatures. Several tools for unsupervised clustering
of gene expression data are also provided. / GPL-3
r-lpsolve 5.6.13Lp_solve is freely available (under LGPL 2) software for solving linear, integer linux-
and mixed integer programs. In this implementation we supply a wrapper 64,
function in C and some R functions that solve general linear/integer problems, osx-
assignment problems, and transportation problems. This version calls lp_solve 64,
version 5.5. / LGPL-2 win-
32,
win-
64
r-lpwc 0.99.5Computes a time series distance measure for clustering based on weighted noarch
correlation and introduction of lags. The lags capture delayed responses in
a time series dataset. The timepoints must be specified. T. Chandereng, A.
Gitter (2018) <doi:10.1101/292615>. / MIT
r-lrequire 0.1.3 In the fashion of ‘node.js’ <https://nodejs.org/>, requires a file, sourcing into noarch
the current environment only the variables explicitly specified in the mod-
ule.exports or exports list variable. If the file was already sourced, the result
of the earlier sourcing is returned to the caller. / MIT


Name Version
r-lrgs 0.5.3 Implements a Gibbs sampler to do linear regression with multiple covariates, noarch
multiple responses, Gaussian measurement errors on covariates and responses,
Gaussian intrinsic scatter, and a covariate prior distribution which is given
by either a Gaussian mixture of specified size or a Dirichlet process with a
Gaussian base distribution. / MIT
r-lrmest 3.0 When multicollinearity exists among predictor variables of the linear model, noarch
least square estimators does not provide a better solution for estimating pa-
rameters. To deal with multicollinearity several estimators are proposed
in the literature. Some of these estimators are Ordinary Least Square
Estimator (OLSE), Ordinary Generalized Ordinary Least Square Estimator
(OGOLSE), Ordinary Ridge Regression Estimator (ORRE), Ordinary Gen-
eralized Ridge Regression Estimator (OGRRE), Restricted Least Square Es-
timator (RLSE), Ordinary Generalized Restricted Least Square Estimator
(OGRLSE), Ordinary Mixed Regression Estimator (OMRE), Ordinary Gen-
eralized Mixed Regression Estimator (OGMRE), Liu Estimator (LE), Ordi-
nary Generalized Liu Estimator (OGLE), Restricted Liu Estimator (RLE), Or-
dinary Generalized Restricted Liu Estimator (OGRLE), Stochastic Restricted
Liu Estimator (SRLE), Ordinary Generalized Stochastic Restricted Liu Es-
timator (OGSRLE), Type (1),(2),(3) Liu Estimator (Type-1,2,3 LTE), Ordi-
nary Generalized Type (1),(2),(3) Liu Estimator (Type-1,2,3 OGLTE), Type
(1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 ALTE), Ordinary General-
ized Type (1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 OGALTE), Almost
Unbiased Ridge Estimator (AURE), Ordinary Generalized Almost Unbiased
Ridge Estimator (OGAURE), Almost Unbiased Liu Estimator (AULE), Ordi-
nary Generalized Almost Unbiased Liu Estimator (OGAULE), Stochastic Re-
stricted Ridge Estimator (SRRE), Ordinary Generalized Stochastic Restricted
Ridge Estimator (OGSRRE), Restricted Ridge Regression Estimator (RRRE)
and Ordinary Generalized Restricted Ridge Regression Estimator (OGRRRE).
To select the best estimator in a practical situation the Mean Square Error
(MSE) is used. Using this package scalar MSE value of all the above estima-
tors and Prediction Sum of Square (PRESS) values of some of the estimators
can be obtained, and the variation of the MSE and PRESS values for the rele-
vant estimators can be shown graphically. / GPL-2 | GPL-3
r-lrth 1.3 R code of a likelihood ratio test for genome-wide association under genetic noarch
heterogeneity. / GPL-3
r-lsa 0.73.1The basic idea of latent semantic analysis (LSA) is, that text do have a higher noarch
order (=latent semantic) structure which, however, is obscured by word usage
(e.g. through the use of synonyms or polysemy). By using conceptual indices
that are derived statistically via a truncated singular value decomposition (a
two-mode factor analysis) over a given document-term matrix, this variability
problem can be overcome. / GPL-2
r-lsasim 1.0.1 Provides functions to simulate data from large-scale educational assessments, noarch
including background questionnaire data and cognitive item responses that ad-
here to a multiple-matrix sampled design. / GPL-3
r-lsd 4.0_0 Create lots of colorful plots in a plethora of variations. Try the LSD demo- noarch
tour(). / Unlimited


Name Version
r-lsdinterface 0.4.0 Interfaces R with LSD. Reads object-oriented data in results files (.res) pro- noarch
duced by LSD and creates appropriate multi-dimensional arrays in R. Sup-
ports multiple core parallelization of multi-file data reading for increased per-
formance. Also provides functions to extract basic information and statistics
from data files. LSD (Laboratory for Simulation Development) is free soft-
ware developed by Marco Valente (documentation and downloads available at
<http://labsimdev.org>). / GPL-3
r-lsdv 1.1 Fit a least square dummy variable regression / Artistic-2.0 noarch
r-lshorth 0.1_6 Calculates the (localised) length of the shorth and supplies corresponding di- noarch
agnostic plots. / LGPL-3
r-lsm 0.1.8 When the values of the outcome variable Y are either 0 or 1, the function noarch
lsm() calculates the estimation of the log likelihood in the saturated model.
This model is characterized by Llinas (2006, ISSN:2389-8976) in section 2.3
through the assumptions 1 and 2. The function LogLik() works (almost per-
fectly) when the number of independent variables K is high, but for small K
it calculates wrong values in some cases. For this reason, when Y is dichoto-
mous and the data are grouped in J populations, it is recommended to use the
function lsm() because it works very well for all K. / MIT
r-lsmeans 2.30_0Obtain least-squares means for linear, generalized linear, and mixed mod- linux-
els. Compute contrasts or linear functions of least-squares means, and 32,
comparisons of slopes. Plots and compact letter displays. Least-squares linux-
means were proposed in Harvey, W (1960) Least-squares analysis of data 64,
with unequal subclass numbers, Tech Report ARS-20-8, USDA National noarch,
Agricultural Library, and discussed further in Searle, Speed, and Mil- osx-
liken (1980) Population marginal means in the linear model: An alter- 64,
native to least squares means, The American Statistician 34(4), 216-221 win-
<doi:10.1080/00031305.1980.10483031>. NOTE: lsmeans now relies primar- 32,
ily on code in the ‘emmeans’ package. ‘lsmeans’ will be archived in the near win-
future. / GPL-2 | GPL-3 64
r-lsmontecarlo 1.0 The package compiles functions for calculating prices of American put options noarch
with Least Squares Monte Carlo method. The option types are plain vanilla
American put, Asian American put, and Quanto American put. The pricing
algorithms include variance reduction techniques such as Antithetic Variates
and Control Variates. Additional functions are given to derive price surfaces
at different volatilities and strikes, create 3-D plots, quickly generate Geomet-
ric Brownian motion, and calculate prices of European options with Black &
Scholes analytical solution. / GPL-3
r-lspline 1.0_0 Linear splines with convenient parametrisations such that (1) coefficients are noarch
slopes of consecutive segments or (2) coefficients are slope changes at consec-
utive knots. Knots can be set manually or at break points of equal-frequency or
equal-width intervals covering the range of ‘x’. The implementation follows
Greene (2003), chapter 7.2.5. / MIT
r-lspls 0.2_2 Implements the LS-PLS (least squares - partial least squares) method de- noarch
scribed in for instance Jørgensen, K., Segtnan, V. H., Thyholt, K., Næs, T.
(2004) A Comparison of Methods for Analysing Regression Models with Both
Spectral and Designed Variables Journal of Chemometrics, 18(10), 451–464,
<doi:10.1002/cem.890>. / GPL-2


Name Version
r-lsplsglm 1.0 Fit logistic regression models using LS-PLS approaches to analyse both clin- noarch
ical and genomic data. (C. Bazzoli and S. Lambert-Lacroix. (2017) Classifi-
cation using LS-PLS with logistic regression based on both clinical and gene
expression variables <https://hal.archives-ouvertes.fr/hal-01405101>). / GPL-
2
r-lsr 0.5 A collection of tools intended to make introductory statistics easier to teach, in- noarch
cluding wrappers for common hypothesis tests and basic data manipulation. It
accompanies Navarro, D. J. (2015). Learning Statistics with R: A Tutorial for
Psychology Students and Other Beginners, Version 0.5. [Lecture notes] School
of Psychology, University of Adelaide, Adelaide, Australia. ISBN: 978-1-326-
18972-3. URL: http://health.adelaide.edu.au/psychology/ccs/teaching/lsr/. /
GPL-3
r-lsrs 0.2.0 Rapid satellite data streams in operational applications have clear benefits for noarch
monitoring land cover, especially when information can be delivered as fast
as changing surface conditions. Over the past decade, remote sensing has
become a key tool for monitoring and predicting environmental variables by
using satellite data. This package presents the main applications in remote
sensing for land surface monitoring and land cover mapping (soil, vegeta-
tion, water. . . ). Tomlinson, C.J., Chapman, L., Thornes, E., Baker, C (2011)
<doi:10.1002/met.287>. / GPL-3
r-ltable 1.0 Constructs tables of counts and proportions out of data sets. It has simplified noarch
syntax appealing for novice and even for advanced user under time pressure.
It is particularly suitable for exploratory data analysis or presentation to single
out most appropriate pieces of tabulated information. The other important
feature is possibility to insert tables to Excel and Word documents. / GPL-2
r-ltpdvar 1.2 Calculation of rectifying LTPD and AOQL plans for sampling inspection by noarch
variables which minimize mean inspection cost per lot of process average qual-
ity. / GPL-2
r-ltr 1.0.0 A set of functions to execute the linear-transformation of replicate (LTR) al- noarch
gorithm for preprocessing of microarray data / GPL-2
r-ltsbase 1.0.1 This is a new tool to estimate Ridge and Liu estimators based on LTS method noarch
in multiple linear regression analysis. / GPL-3
r-ltxsparklines 1.1.2 Sparklines are small plots (about one line of text high), made popular by noarch
Edward Tufte. This package is the interface from R to the LaTeX package
sparklines by Andreas Loeffer and Dan Luecking (<http://www.ctan.org/pkg/
sparklines>). It can work with Sweave or knitr or other engines that produce
TeX. The package can be used to plot vectors, matrices, data frames, time
series (in ts or zoo format). / GPL-2 | GPL-3
r-lubridate 1.7.4 Functions to work with date-times and time-spans: fast and user friendly pars- linux-
ing of date-time data, extraction and updating of components of a date-time 32,
(years, months, days, hours, minutes, and seconds), algebraic manipulation on linux-
date-time and time-span objects. The ‘lubridate’ package has a consistent and 64,
memorable syntax that makes working with dates easy and fun. Parts of the osx-
‘CCTZ’ source code, released under the Apache 2.0 License, are included in 64,
this package. See <https://github.com/google/cctz> for more details. / GPL win-
(>= 2) 32,
win-
64


Name Version
r-lucid 1.7 Print vectors (and data frames) of floating point numbers using a non-scientific noarch
format optimized for human readers. Vectors of numbers are rounded using
significant digits, aligned at the decimal point, and all zeros trailing the deci-
mal point are dropped. See: Wright (2016). Lucid: An R Package for Pretty-
Printing Floating Point Numbers. In JSM Proceedings, Statistical Computing
Section. Alexandria, VA: American Statistical Association. 2270-2279. /
GPL-3
r-lumberjack 1.0.3 A framework that allows for easy logging of changes in data. Main features: noarch
start tracking changes by adding a single line of code to an existing script.
Track changes in multiple datasets, using multiple loggers. Add custom-built
loggers or use loggers offered by other packages. / GPL-3
r-lunar 0.1_04Provides functions to calculate lunar and other environmental covariates. / noarch
MIT
r-luzlogr 0.2.0 Provides flexible but lightweight logging facilities for R scripts. Supports pri- noarch
ority levels for logs and messages, flagging messages, capturing script output,
switching logs, and logging to files or connections. / MIT
r- 1.0.3 An implementation of algorithms described in Jewell and Witten (2017) noarch
lzerospikeinference <arXiv:1703.08644>. / GPL-3
r-mac 1.1.1 This is an integrated meta-analysis package for conducting a correlational re- noarch
search synthesis. One of the unique features of this package is in its integra-
tion of user-friendly functions to facilitate statistical analyses at each stage in a
meta-analysis with correlations. It uses recommended procedures as described
in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges,
& Valentine, 2009). / GPL-2
r-mad 0.8_2.1
A collection of functions for conducting a meta-analysis with mean differences noarch
data. It uses recommended procedures as described in The Handbook of Re-
search Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009). /
GPL-2
r-maddison 0.1 Contains the Maddison Project database, which provides estimates of GDP noarch
per capita for all countries in the world between AD 1 and 2010. See http:
//www.ggdc.net/maddison for more information. / CC0
r-maditr 0.6.2 Package provides pipe-style interface for ‘data.table’. It preserves all noarch
‘data.table’ features without significant impact on performance. ‘let’ and
‘take’ functions are simplified interfaces for most common data manipula-
tion tasks. For example, you can write ‘mtcars %>% take(mean(mpg), by
= am)’ for aggregation or ‘mtcars %>% let(hp_wt = hp/wt, hp_wt_mpg =
hp_wt/mpg)’ for modification. Use ‘take_if/let_if’ for conditional aggrega-
tion/modification. ‘query_if’ function translates its arguments one-to-one to
‘[.data.table’ method. Additionally there are some conveniences such as auto-
matic ‘data.frame’ conversion to ‘data.table’. / GPL-2
r-madr 1.0.0 Estimates average treatment effects using model average double robust (MA- noarch
DR) estimation. The MA-DR estimator is defined as weighted average of dou-
ble robust estimators, where each double robust estimator corresponds to a
specific choice of the outcome model and the propensity score model. The
MA-DR estimator extend the desirable double robustness property by achiev-
ing consistency under the much weaker assumption that either the true propen-
sity score model or the true outcome model be within a specified, possibly
large, class of models. / GPL-3


Name Version
r-madsim 1.2.1 This function allows to generate two biological conditions synthetic microar- noarch
ray dataset which has similar behavior to those currently observed with com-
mon platforms. User provides a subset of parameters. Available default pa-
rameters settings can be modified. / GPL (>= 2.0)
r-magclass 4.107.0
Data class for increased interoperability working with spatial- temporal data noarch
together with corresponding functions and methods (conversions, basic calcu-
lations and basic data manipulation). The class distinguishes between spatial,
temporal and other dimensions to facilitate the development and interoperabil-
ity of tools build for it. Additional features are name-based addressing of data
and internal consistency checks (e.g. checking for the right data order in cal-
culations). / LGPL-3
r-magic 1.5_9 A collection of efficient, vectorized algorithms for the creation and investiga- linux-
tion of magic squares and hypercubes, including a variety of functions for the 32,
manipulation and analysis of arbitrarily dimensioned arrays. The package in- linux-
cludes methods for creating normal magic squares of any order greater than 64,
2. The ultimate intention is for the package to be a computerized embodiment noarch,
all magic square knowledge, including direct numerical verification of proper- osx-
ties of magic squares (such as recent results on the determinant of odd-ordered 64,
semimagic squares). Some antimagic functionality is included. The package win-
also serves as a rebuttal to the often-heard comment I thought R was just for 32,
statistics. / GPL-2 win-
64
r-magicfor 0.1.0 Magic functions to obtain results from for loops. / MIT noarch
r-magrittr 1.5 Provides a mechanism for chaining commands with a new forward-pipe oper- linux-
ator, %>%. This operator will forward a value, or the result of an expression, 32,
into the next function call/expression. There is flexible support for the type of linux-
right-hand side expressions. For more information, see package vignette. To 64,
quote Rene Magritte, Ceci n’est pas un pipe. / MIT file LICENSE noarch,
osx-
64,
win-
32,
win-
64
r-mail 1.0 Easy to use package for sending email notifications with status information noarch
from R / GPL-2
r-mailr 0.4.1 Interface to Apache Commons Email to send emails from R. / GPL-3 noarch
r-makefiler 1.0 A user-friendly interface for the construction of ‘Makefiles’. / GPL-3 noarch
r-makeproject 1.0 This package creates an empty framework of files and directories for the Load, noarch
Clean, Func, Do structure described by Josh Reich. / GPL-3
r-malani 1.0 Find dark genes. These genes are often disregarded due to no detected muta- noarch
tion or differential expression, but are important in coordinating the function-
ality in cancer networks. / GPL-3
r-mallet 1.0 This package allows you to train topic models in mallet and load results di- noarch
rectly into R. / MIT
r-mams 1.3 Designing multi-arm multi-stage studies with (asymptotically) normal end- noarch
points and known variance. / GPL-2
r- 0.1.5 This will allow easier management of a CRAN-style repository on local net- noarch
managelocalrepo works (i.e. not on CRAN). This might be necessary where hosted packages
contain intellectual property owned by a corporation. / GPL-2


Name Version
r-mancie 1.4 High-dimensional data integration is a critical but difficult problem in ge- noarch
nomics research because of potential biases from high-throughput experi-
ments. We present MANCIE, a computational method for integrating two
genomic data sets with homogenous dimensions from different sources based
on a PCA procedure as an approximation to a Bayesian approach. / GPL-2
r-mangotraining 1.0_7 Datasets designed to be used in conjunction with Mango Solutions training noarch
materials and the book SAMS Teach Yourself R in 24 Hours (ISBN: 978-0-
672-33848-9). / GPL-2
r-mangrove 1.21 Methods for performing genetic risk prediction from genotype data. You can noarch
use it to perform risk prediction for individuals, or for families with missing
data. / GPL-2
r-manipulate 1.0.1 Interactive plotting functions for use within RStudio. The manipulate func- linux-
tion accepts a plotting expression and a set of controls (e.g. slider, picker, 32,
checkbox, or button) which are used to dynamically change values within the linux-
expression. When a value is changed using its corresponding control the ex- 64,
pression is automatically re-executed and the plot is redrawn. / GPL-2 noarch,
osx-
64,
win-
32,
win-
64
r- 0.10.0Like package ‘manipulate’ does for static graphics, this package helps to easily linux-
manipulatewidget add controls like sliders, pickers, checkboxes, etc. that can be used to modify 32,
the input data or the parameters of an interactive chart created with package linux-
‘htmlwidgets’. / GPL (>= 2) | file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-manytests 1.2 Performs the multiple testing procedures of Cox (2011) <doi:10.5170/CERN- noarch
2011-006> and Wong and Cox (2007) <doi:10.1080/02664760701240014>. /
GPL-2
r-maples 1.0 MAPLES is a general method for the estimation of age profiles that uses stan- noarch
dard micro-level demographic survey data. The aim is to estimate smoothed
age profiles and relative risks for time-fixed and time-varying covariates. /
GPL-2
r-mapmisc 1.7.2 A minimal, light-weight set of tools for producing nice looking maps in R, noarch
with support for map projections. / GPL-3
r-mapplots 1.5.1 Create simple maps; add sub-plots like pie plots to a map or any other plot; noarch
format, plot and export gridded data. The package was developed for dis-
playing fisheries data but most functions can be used for more generic data
visualisation. / GPL-2


Name Version
r-mapproj 1.2.6 Converts latitude/longitude into projected coordinates. / Lucent Public License linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-maps 3.3.0 Display of maps. Projection code and larger maps are in separate packages linux-
(‘mapproj’ and ‘mapdata’). / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-maptools 0.9_5 Set of tools for manipulating and reading geographic data, in particular linux-
‘ESRI Shapefiles’; C code used from ‘shapelib’. It includes binary access 32,
to ‘GSHHG’ shoreline files. The package also provides interface wrappers linux-
for exchanging spatial objects with packages such as ‘PBSmapping’, ‘spat- 64,
stat’, ‘maps’, ‘RArcInfo’, ‘Stata tmap’, ‘WinBUGS’, ‘Mondrian’, and others. osx-
/ GPL (>= 2) 64,
win-
32,
win-
64
r-maptree 1.4_7 Functions with example data for graphing, pruning, and mapping models from noarch
hierarchical clustering, and classification and regression trees. / Unlimited
r-mar 1.1_2 R functions for multivariate autoregressive analysis / GPL-2 noarch
r-march 3.1 Computation of various Markovian models for categorical data including ho- noarch
mogeneous Markov chains of any order, MTD models, Hidden Markov mod-
els, and Double Chain Markov Models. / GPL-2
r-mareymap 1.3.4 Local recombination rates are graphically estimated across a genome using noarch
Marey maps. / GPL-2
r-marima 2.2 Multivariate ARIMA and ARIMA-X estimation using Spliid’s algorithm noarch
(marima()) and simulation (marima.sim()). / GPL-2
r-markdown 0.9 Provides R bindings to the ‘Sundown’ ‘Markdown’ rendering library (https:// linux-
github.com/vmg/sundown). ‘Markdown’ is a plain-text formatting syntax that 32,
can be converted to ‘XHTML’ or other formats. See http://en.wikipedia.org/ linux-
wiki/Markdown for more information about ‘Markdown’. / GPL-2 64,
osx-
64,
win-
32,
win-
64


Name Version
r- 0.8.2 Automatic marking of R assignments for students and teachers based on ‘test- noarch
markmyassignment that’ test suites. / BSD_2_clause
r-marl 1.0 Functions provided allow data simulation; construction of weighted relative noarch
likelihood functions; clustering and principal component analysis based on
weighted relative likelihood functions. / GPL-2
r-masae 0.1_5 An S4 implementation of the unbiased extension of the model- as- noarch
sisted synthetic-regression estimator proposed by Mandallaz (2013)
<DOI:10.1139/cjfr-2012-0381>, Mandallaz et al. (2013) <DOI:10.1139/cjfr-
2013-0181> and Mandallaz (2014) <DOI:10.1139/cjfr-2013-0449>. It yields
smaller variances than the standard bias correction, the generalised regression
estimator. / GPL-2
r-mass 7.3_51.3
Functions and datasets to support Venables and Ripley, Modern Applied Statis- linux-
tics with S (4th edition, 2002). / GPL-2 | GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-massign 1.1.0 Constructing matrices for quick prototyping can be a nuisance, requiring the noarch
user to think about how to fill the matrix with values using the matrix() func-
tion. The %<-% operator solves that issue by allowing the user to construct
matrices using code that shows the actual matrices. / MIT
r-masstimate 1.3 Estimation equations are from a variety of sources but are, in general, based noarch
on regressions between skeletal measurements (e.g., femoral circumference)
and body mass in living taxa. / GPL-2
r-mata 0.4 Calculates Model-Averaged Tail Area Wald (MATA-Wald) confidence inter- noarch
vals, which are constructed using single-model estimators and model weights.
See Turek and Fletcher (2012) <doi:10.1016/j.csda.2012.03.002> for details. /
GPL-2
r-matchbook 1.0.7 Provides a wrapper for the some basic functionality around the ‘Matchbook’ noarch
<http://www.matchbook.com> REST API. It features calls to get events, mar-
kets and runners in data frame format. It features functions for bet placement
and position management and also allows reporting of settled bet transactions.
Note: this package uses the back-lay format. The default for odds type, cur-
rency and language are set according to those of the registered user account. /
MIT
r-matconv 0.4.0 Transferring over a code base from Matlab to R is often a repetitive and ineffi- noarch
cient use of time. This package provides a translator for Matlab / Octave code
into R code. It does some syntax changes, but most of the heavy lifting is in the
function changes since the languages are so similar. Options for different data
structures and the functions that can be changed are given. The Matlab code
should be mostly in adherence to the standard style guide but some effort has
been made to accommodate different number of spaces and other small syntax
issues. This will not make the code more R friendly and may not even run
afterwards. However, the rudimentary syntax, base function and data structure
conversion is done quickly so that the maintainer can focus on changes to the
design structure. / GPL-2


Name Version
r-mathgraph 0.9_14Simple tools for constructing and manipulating objects of class mathgraph noarch
from the book S Poetry, available at <http://www.burns-stat.com/pages/
spoetry.html>. / GPL-2
r-matlab 1.0.2 Emulate MATLAB code using R / Artistic-2.0 noarch
r-matlabr 1.5.2 Provides users to call MATLAB from using the system command. Allows noarch
users to submit lines of code or MATLAB m files. This is in comparison to
‘R.matlab’, which creates a MATLAB server. / GPL-2
r-matpow 0.1.1 A general framework for computing powers of matrices. A key feature is noarch
the capability for users to write callback functions, called after each iteration,
thus enabling customization for specific applications. Diverse types of matrix
classes/matrix multiplication are accommodated. If the multiplication type
computes in parallel, then the package computation is also parallel. / GPL-2
r-matrix 1.2_17A rich hierarchy of matrix classes, including triangular, symmetric, and di- linux-
agonal matrices, both dense and sparse and with pattern, logical and numeric 32,
entries. Numerous methods for and operations on these matrices, using ‘LA- linux-
PACK’ and ‘SuiteSparse’ libraries. / GPL (>= 2) | file LICENCE 64,
osx-
64,
win-
32,
win-
64
r-matrixcalc 1.0_3 A collection of functions to support matrix calculations for probability, econo- linux-
metric and numerical analysis. There are additional functions that are compa- 64,
rable to APL functions which are useful for actuarial models such as pension noarch,
mathematics. This package is used for teaching and research purposes at the win-
Department of Finance and Risk Engineering, New York University, Polytech- 64
nic Institute, Brooklyn, NY 11201. / GPL (>= 2)
r-matrixeqtl 2.2 Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix noarch
eQTL can test for association between genotype and gene expression using
linear regression with either additive or ANOVA genotype effects. The mod-
els can include covariates to account for factors as population stratification,
gender, and clinical variables. It also supports models with heteroscedastic
and/or correlated errors, false discovery rate estimation and separate treatment
of local (cis) and distant (trans) eQTLs. / LGPL-3
r-matrixmodels 0.4_1 Modelling with sparse and dense ‘Matrix’ matrices, using modular prediction linux-
and response module classes. / GPL (>= 2) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-matrixnormal 0.0.1 Computes densities, probabilities, and random deviates of the Matrix Normal noarch
(Iranmanesh et al. (2010) <doi:10.7508/ijmsi.2010.02.004>). Also includes
simple but useful matrix functions. See the vignette for more information. /
GPL-3


Name Version
r-matrixstats 0.54.0High-performing functions operating on rows and columns of matrices, e.g. linux-
col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized 64,
per data type and for subsetted calculations such that both memory usage and osx-
processing time is minimized. There are also optimized vector-based methods, 64,
e.g. binMeans(), madDiff() and weightedMedian(). / Artistic-2.0 win-
32,
win-
64
r-matrixstructest 1.0.0 Tests for block-diagonal structure in symmetric matrices (e.g. correlation ma- noarch
trices) under the null hypothesis of exchangeable off-diagonal elements. As
described in Segal et al. (2019), these tests can be useful for construct valida-
tion either by themselves or as a complement to confirmatory factor analysis.
Monte Carlo methods are used to approximate the permutation p-value with
Hubert’s Gamma (Hubert, 1976) and a t-statistic. This package also imple-
ments the chi-squared statistic described by Steiger (1980). Please see Segal,
et al. (2019) <doi:10.1007/s11336-018-9647-4> for more information. / GPL-
3
r-matrixtests 0.1.5 Functions to perform fast statistical hypothesis tests on rows/columns of ma- noarch
trices. The main goals are: 1) speed via vectorization, 2) output that is detailed
and easy to use, 3) compatibility with tests implemented in R (like those avail-
able in the ‘stats’ package). / GPL-2
r-matskew 0.1.5 Performs matrix skew-t parameter estimation, Gallaugher and McNicholas noarch
(2017) <doi: 10.1002/sta4.143>. / GPL-2
r-mattools 1.1 This package in includes functions for receiver operating characteristic (ROC) noarch
analyses as well as Monte Carlo simulation. It includes specific graphical
functions for interpreting the output of these techniques. / GPL-2
r-mavtgsa 1.3 This package is a gene set analysis function for one-sided test (OLS), two- noarch
sided test (multivariate analysis of variance). If the experimental conditions are
equal to 2, the p-value for Hotelling’s t^2 test is calculated. If the experimental
conditions are great than 2, the p-value for Wilks’ Lambda is determined and
post-hoc test is reported too. Three multiple comparison procedures, Dunnett,
Tukey, and sequential pairwise comparison, are implemented. The program
computes the p-values and FDR (false discovery rate) q-values for all gene
sets. The p-values for individual genes in a significant gene set are also listed.
MAVTgsa generates two visualization output: a p-value plot of gene sets (GSA
plot) and a GST-plot of the empirical distribution function of the ranked test
statistics of a given gene set. A Random Forests-based procedure is to iden-
tify gene sets that can accurately predict samples from different experimental
conditions or are associated with the continuous phenotypes. / GPL-2
r-maxlik 1.3_4 Functions for Maximum Likelihood (ML) estimation and non-linear optimiza- linux-
tion, and related tools. It includes a unified way to call different optimizers, 32,
and classes and methods to handle the results from the ML viewpoint. It also linux-
includes a number of convenience tools for testing and developing your own 64,
models. / GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-maxlike 0.1_7 Provides a likelihood-based approach to modeling species distributions using noarch
presence-only data. In contrast to the popular software program MAXENT,
this approach yields estimates of the probability of occurrence, which is a
natural descriptor of a species’ distribution. / GPL-3
r-maxmatching 0.1.0 Computes the maximum matching for unweighted graph and maximum noarch
matching for (un)weighted bipartite graph efficiently. / CC0
r-maxnet 0.1.2 Procedures to fit species distributions models from occurrence records and noarch
environmental variables, using ‘glmnet’ for model fitting. Model structure
is the same as for the ‘Maxent’ Java package, version 3.4.0, with the same
feature types and regularization options. See the ‘Maxent’ website <http:
//biodiversityinformatics.amnh.org/open_source/maxent> for more details. /
MIT
r-maxskew 1.1 It finds Orthogonal Data Projections with Maximal Skewness. The first data noarch
projection in the output is the most skewed among all linear data projections.
The second data projection in the output is the most skewed among all data
projections orthogonal to the first one, and so on. / GPL-2
r-mazegen 0.1.3 A maze generator that creates the Elithorn Maze (HTML file) and the functions noarch
to calculate the associated maze parameters (i.e. Difficulty and Ability). /
GPL-3
r-mazeinda 0.0.1 Methods for calculating and testing the significance of pairwise mono- noarch
tonic association from and based on the work of Pimentel (2009)
<doi:10.4135/9781412985291.n2>. Computation of association of vectors
from one or multiple sets can be performed in parallel thanks to the packages
‘foreach’ and ‘doMC’. / GPL-3
r-mbc 0.10_4Calibrate and apply multivariate bias correction algorithms for climate noarch
model simulations of multiple climate variables. Three methods described
by Cannon (2016) <doi:10.1175/JCLI-D-15-0679.1> and Cannon (2018)
<doi:10.1007/s00382-017-3580-6> are implemented: (i) MBC Pearson cor-
relation (MBCp), (ii) MBC rank correlation (MBCr), and (iii) MBC N-
dimensional PDF transform (MBCn). / GPL-2
r-mbcluster.seq 1.0 Cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or noarch
other digital gene expression (DGE) data / GPL-3
r-mbi 1.0 Over 20 multiple-site diversity indices can be calculated. Later versions will noarch
include phylogenetic diversity / GPL-2
r-mbir 1.3.5 Allows practitioners and researchers a wholesale approach for deriving noarch
magnitude-based inferences from raw data. A major goal of ‘mbir’ is to pro-
grammatically detect appropriate statistical tests to run in lieu of relying on
practitioners to determine correct stepwise procedures independently. / GPL-2
r-mblm 0.12.1Provides linear models based on Theil-Sen single median and Siegel repeated noarch
medians. They are very robust (29 or 50 percent breakdown point, respec-
tively), and if no outliers are present, the estimators are very similar to OLS. /
GPL-2
r-mc2d 0.1_18A complete framework to build and study Two-Dimensional Monte-Carlo sim- noarch
ulations, aka Second-Order Monte-Carlo simulations. Also includes various
distributions (pert, triangular, Bernoulli, empirical discrete and continuous). /
GPL-2
r-mcbftest 0.1.0 Monte Carol based tests for the Behrens Fisher Problem enhance the statisti- noarch
cal power and performs better than Welch’s t-approximation, see Ullah et al.
(2019). / GPL (>= 2.0)


Name Version
r-mcbiopi 1.1.6 Computes the prime implicants or a minimal disjunctive normal form for a noarch
logic expression presented by a truth table or a logic tree. Has been particularly
developed for logic expressions resulting from a logic regression analysis, i.e.
logic expressions typically consisting of up to 16 literals, where the prime
implicants are typically composed of a maximum of 4 or 5 literals. / LGPL-2
r-mcc 1.0 A number of biomedical problems involve performing many hypothesis tests, noarch
with an attendant need to apply stringent thresholds. Often the data take the
form of a series of predictor vectors, each of which must be compared with a
single response vector, perhaps with nuisance covariates. Parametric tests of
association are often used, but can result in inaccurate type I error at the ex-
treme thresholds, even for large sample sizes. Furthermore, standard two-sided
testing can reduce power compared to the doubled p-value, due to asymmetry
in the null distribution. Exact (permutation) testing approaches are attractive,
but can be computationally intensive and cumbersome. MCC is an approxima-
tion to exact association testing of two vectors that is accurate and fast enough
for standard use in high-throughput settings, and can easily provide standard
two-sided or doubled p-values. / GPL-2
r-mccmeiv 2.1 Applying the methodology from Manuel et al. to estimate parameters using noarch
a matched case control data with a mismeasured exposure variable that is ac-
companied by instrumental variables (Submitted). / GPL-2
r-mccr 0.4.4 The Matthews correlation coefficient (MCC) score is calculated (Matthews noarch
BW (1975) <DOI:10.1016/0005-2795(75)90109-9>). / MIT
r-mcgibbsit 1.1.0 ‘mcgibbsit’ provides an implementation of Warnes & Raftery’s MCGibbsit noarch
run-length diagnostic for a set of (not-necessarily independent) MCMC sam-
plers. It combines the estimate error-bounding approach of the Raftery and
Lewis MCMC run length diagnostic with the between verses within chain ap-
proach of the Gelman and Rubin MCMC convergence diagnostic. / GPL-3
r-mcheatmaps 1.0.0 mcheatmaps serves to visualize multiple different symmetric matrices and ma- noarch
trix clusters in a single figure using a dendogram, two half matrices and various
color labels. / GPL-3
r-mchtest 1.0_3 Performs Monte Carlo hypothesis tests, allowing a couple of differ- noarch
ent sequential stopping boundaries. For example, a truncated se-
quential probability ratio test boundary (Fay, Kim and Hachey, 2007
<DOI:10.1198/106186007X257025>) and a boundary proposed by Besag and
Clifford, 1991 <DOI:10.1093/biomet/78.2.301>. Gives valid p-values and
confidence intervals on p-values. / GPL-3
r-mci 1.3.3 Market area models are used to analyze and predict store choices and mar- noarch
ket areas concerning retail and service locations. This package implements
two market area models (Huff Model, Multiplicative Competitive Interaction
Model) into R, while the emphases lie on 1.) fitting these models based on em-
pirical data via OLS regression and nonlinear techniques and 2.) data prepa-
ration and processing (esp. interaction matrices and data preparation for the
MCI Model). / GPL-2
r-mcmcplots 0.4.3 Functions for convenient plotting and viewing of MCMC output. / GPL-2 noarch
r-mconjoint 0.1 The package aids in creating a Conjoint Analysis design with extra cards. Un- noarch
like traditional holdout cards these cards are used to create a set of good (bal-
anced and low correlation) designs. Each of these designs is analyzed and the
average calculated. / GPL-3


Name Version
r-mcparalleldo 1.1.0 Provides a function that wraps mcparallel() and mccollect() from ‘parallel’ noarch
with temporary variables and a task handler. Wrapped in this way the results of
an mcparallel() call can be returned to the R session when the fork is complete
without explicitly issuing a specific mccollect() to retrieve the value. Outside
of top-level tasks, multiple mcparallel() jobs can be retrieved with a single call
to mcparallelDoCheck(). / GPL-2
r-mcpmod 1.0_10Implements a methodology for the design and analysis of dose-response stud- noarch
ies that combines aspects of multiple comparison procedures and modeling ap-
proaches (Bretz, Pinheiro and Branson, 2005, Biometrics 61, 738-748, <doi:
10.1111/j.1541-0420.2005.00344.x>). The package provides tools for the
analysis of dose finding trials as well as a variety of tools necessary to plan
a trial to be conducted with the MCP-Mod methodology. Please note: The
‘MCPMod’ package will not be further developed, all future development of
the MCP-Mod methodology will be done in the ‘DoseFinding’ R-package. /
GPL-3
r- 0.1_0 Analyzes non-normal data via the Multiple Comparison Procedures and Mod- noarch
mcpmodgeneral eling approach (MCP-Mod). Many functions rely on the ‘DoseFinding’ pack-
age. This package makes it so the user does not need to provide or calculate
the mu vector and S matrix. Instead, the user typically supplies the data in
its raw form, and this package will calculate the needed objects and passes
them into the ‘DoseFinding’ functions. If the user wishes to primarily use
the functions provided in the ‘DoseFinding’ package, a singular function (pre-
pareGen()) will provide mu and S. The package currently handles power anal-
ysis and the MCP-Mod procedure for negative binomial, Poisson, and bino-
mial data. The MCP-Mod procedure can also be applied to survival data, but
power analysis is not available. Bretz, F., Pinheiro, J. C., and Branson, M.
(2005) <doi:10.1111/j.1541-0420.2005.00344.x>. Buckland, S. T., Burnham,
K. P. and Augustin, N. H. (1997) <doi:10.2307/2533961>. Pinheiro, J. C.,
Bornkamp, B., Glimm, E. and Bretz, F. (2014) <doi:10.1002/sim.6052>. /
GPL-3
r-mcs 0.1.3 Perform the model confidence set procedure of Hansen et al (2011) noarch
<doi:10.3982/ECTA5771>. / GPL-2
r-mcsim 1.0 Identifies the optimal number of clusters by calculating the similarity between noarch
two clustering methods at the same number of clusters using the corrected
indices of Rand and Jaccard as described in Albatineh and Niewiadomska-
Bugaj (2011). The number of clusters at which the index attain its maximum
more frequently is a candidate for being the optimal number of clusters. /
GPL-2
r-mcsm 1.0 mcsm contains a collection of functions that allows the reenactment of the noarch
R programs used in the book EnteR Monte Carlo Methods without further
programming. Programs being available as well, they can be modified by the
user to conduct one’s own simulations. / GPL-2
r-mctest 1.2 Package computes popular and widely used multicollinearity diagnostic mea- noarch
sures. Package also indicates which regressors may be the reason of collinear-
ity among regressors. / GPL-2
r-mctm 1.0 Transition matrices (probabilities or counts) estimation for discrete Markov noarch
Chains of order n (1 <= n <= 5). / GPL-2


Name Version
r-md 1.0.4 Selects bandwidth for the kernel density estimator with minimum distance noarch
method as proposed by Devroye and Lugosi (1996). The minimum distance
method directly selects the optimal kernel density estimator from countably
infinite kernel density estimators and indirectly selects the optimal bandwidth.
This package selects the optimal bandwidth from finite kernel density estima-
tors. / GPL-2 | GPL-3
r-mdatools 0.9.4 Package implements projection based methods for preprocessing, exploring noarch
and analysis of multivariate data used in chemometrics. / MIT
r-mded 0.1_2 Provides a function for measuring the difference between two independent or noarch
non-independent empirical distributions and returning a significance level of
the difference. / CC0
r-mdendro 1.0.1 A collection of methods for agglomerative hierarchical clustering strategies noarch
on a matrix of distances, implemented using the variable-group approach in-
troduced in Fernandez and Gomez (2008) <doi:10.1007/s00357-008-9004-x>.
Descriptive measures to analyze the resulting hierarchical trees are also pro-
vided. In addition to the usual clustering methods, two parameterized methods
are provided to explore an infinite family of hierarchical clustering strategies.
When there are ties in proximity values, the hierarchical trees obtained are
unique and independent of the order of the elements in the input matrix. /
LGPL-2.1
r-mdhglm 1.8 Allows various models for multivariate response variables where each re- noarch
sponse is assumed to follow double hierarchical generalized linear models.
In double hierarchical generalized linear models, the mean, dispersion param-
eters for variance of random effects, and residual variance can be further mod-
eled as random-effect models. / Unlimited
r-mdimnormn 0.8.0 Normalize data to minimize the difference between sample plates (batch ef- noarch
fects). For given data in a matrix and grouping variable (or plate), the function
‘normn_MA’ normalizes the data on MA coordinates. More details are in the
citation. The primary method is ‘Multi-MA’. Other fitting functions on MA
coordinates can also be employed e.g. loess. / GPL-3
r-mdir.logrank 0.0.4 Implemented are the one-sided and two-sided multiple-direction logrank noarch
test for two-sample right censored data. In addition to the statistics p-
values are calculated: 1. For the one-sided testing problem one p-value
based on a wild bootstrap approach is determined. 2. In the two-sided
case one p-value based on a chi-squared approximation and a second p-
values based on a permutation approach are calculated. Ditzhaus, M. and
Friedrich, S. (2018) <arXiv:1807.05504>. Ditzhaus, M. and Pauly, M. (2018)
<arXiv:1808.05627>. / GPL-2 | GPL-3
r-mdplot 1.0.1 Provides automatization for plot generation succeeding common molecular noarch
dynamics analyses. This includes straightforward plots, such as RMSD (Root-
Mean-Square-Deviation) and RMSF (Root-Mean-Square-Fluctuation) but also
more sophisticated ones such as dihedral angle maps, hydrogen bonds, cluster
bar plots and DSSP (Definition of Secondary Structure of Proteins) analysis.
Currently able to load GROMOS, GROMACS and AMBER formats, respec-
tively. / GPL-3
r-mdscore 0.1_3 A set of functions to obtain modified score test for generalized linear models. noarch
/ GPL-2
r-mdw 2017.12_03
Dimension-reduction methods aim at defining a score that maximizes signal noarch
diversity. Two approaches, namely maximum entropy weights and maximum
variance weights, are provided. / GPL-2


Name Version
r-measurements 1.4.0 Collection of tools to make working with physical measurements easier. Con- noarch
vert between metric and imperial units, or calculate a dimension’s unknown
value from other dimensions’ measurements. / GPL-3
r-measures 0.2 Provides the biggest amount of statistical measures in the whole R world. In- noarch
cludes measures of regression, (multiclass) classification and multilabel clas-
sification. The measures come mainly from the ‘mlr’ package and were pro-
gramed by several ‘mlr’ developers. / GPL-3
r-med 0.1.0 Nonparametric estimation and inference for natural direct and indirect effects noarch
by Chan, Imai, Yam and Zhang (2016) <arXiv:1601.03501>. / GPL-2
r-meddietcalc 0.1.1 Multi Calculator of different scores to measure adherence to Mediterranean noarch
Diet, to compute them in nutriepidemiological data. Additionally, a sample
dataset of this kind of data is provided, and some other minor tools useful in
epidemiological studies. / GPL-3
r-mederrrank 0.0.8 Two distinct but related statistical approaches to the problem of identifying the noarch
combinations of medication error characteristics that are more likely to result
in harm are implemented in this package: 1) a Bayesian hierarchical model
with optimal Bayesian ranking on the log odds of harm, and 2) an empirical
Bayes model that estimates the ratio of the observed count of harm to the count
that would be expected if error characteristics and harm were independent. In
addition, for the Bayesian hierarchical model, the package provides functions
to assess the sensitivity of results to different specifications of the random
effects distributions. / GPL-2
r-medextractr 0.1 Function and support for medication and dosing information extraction from noarch
free-text clinical notes. Medication entities that can be extracted include drug
name, strength, dose amount, dose, frequency, intake time, and time of last
dose. / GPL-2
r-mediacloudr 0.1.0 API wrapper to gather news stories, media information and tags from the ‘me- noarch
diacloud.org’ API, based on a multilevel query <https://mediacloud.org/>. A
personal API key is required. / MIT
r-mediak 1.0 Calculates MeDiA_K (means Mean Distance Association by K-nearest neigh- linux-
bor) in order to detect nonlinear associations. / GPL-3 64,
osx-
64,
win-
64
r-mediana 1.0.8 Provides a general framework for clinical trial simulations based on the Clini- noarch
cal Scenario Evaluation (CSE) approach. The package supports a broad class
of data models (including clinical trials with continuous, binary, survival-type
and count-type endpoints as well as multivariate outcomes that are based on
combinations of different endpoints), analysis strategies and commonly used
evaluation criteria. / GPL-2
r-medicare 0.2.1 Publicly available data from Medicare frequently requires extensive ini- noarch
tial effort to extract desired variables and merge them; this package for-
malizes the techniques I’ve found work best. More information on the
Medicare program, as well as guidance for the publicly available data this
package targets, can be found on CMS’s website covering publicly avail-
able data. See <https://www.cms.gov/Research-Statistics-Data-and-Systems/
Research-Statistics-Data-and-Systems.html>. / MIT
r-meditations 1.0.1 Prints a random quote from Marcus Aurelius’ book Meditations. / GPL-3 noarch
r-medor 0.1 This package contains the functions used to perform some confidence statistics noarch
based in population median. / GPL-3


Name Version
r-mefa 3.2_7 A framework package aimed to provide standardized computational environ- noarch
ment for specialist work via object classes to represent the data coded by sam-
ples, taxa and segments (i.e. subpopulations, repeated measures). It supports
easy processing of the data along with cross tabulation and relational data ta-
bles for samples and taxa. An object of class ‘mefa’ is a project specific com-
pendium of the data and can be easily used in further analyses. Methods are
provided for extraction, aggregation, conversion, plotting, summary and re-
porting of ‘mefa’ objects. Reports can be generated in plain text or LaTeX
format. Vignette contains worked examples. / GPL-2
r-mefa4 0.3_6 An S4 update of the ‘mefa’ package using sparse matrices for enhanced effi- noarch
ciency. Sparse array-like objects are supported via lists of sparse matrices. /
GPL-2
r-meifly 0.3 Exploratory model analysis. Fit and graphical explore ensembles of linear noarch
models. / MIT
r-memnet 0.1.0 Efficient implementations of network science tools to facilitate research into linux-
human (semantic) memory. In its current version, the package contains several 64,
methods to infer networks from verbal fluency data, various network growth osx-
models, diverse (switcher-) random walk processes, and tools to analyze and 64,
visualize networks. To deliver maximum performance the majority of the code win-
is written in C. For an application see: Wulff, D. U., Hills, T., & Mata, R. 64
(2018) <doi:10.31234/osf.io/s73dp>. / GPL-3
r-memo 1.0.1 A simple in-memory, LRU cache that can be wrapped around any function to linux-
memoize it. The cache can be keyed on a hash of the input data (using ‘digest’) 64,
or on pointer equivalence. / MIT osx-
64,
win-
64
r-memoise 1.1.0 Cache the results of a function so that when you call it again with the same linux-
arguments it returns the pre-computed value. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-memor 0.2 A ‘rmarkdown’ template that supports company logo, contact info, watermarks noarch
and more. Currently restricted to ‘Latex’/’Markdown’; a similar ‘HTML’
theme will be added in the future. / GPL-3
r-memss 0.9_3 Data sets and sample analyses from Pinheiro and Bates, Mixed-effects Models noarch
in S and S-PLUS (Springer, 2000). / GPL-2
r-memuse 4.0_0 How much ram do you need to store a 100,000 by 100,000 matrix? How linux-
much ram is your current R session using? How much ram do you even have? 64,
Learn the scintillating answer to these and many more such questions with the osx-
‘memuse’ package. / BSD_2_clause 64,
win-
64


Name Version
r-mergetrees 0.1.3 Aggregates a set of trees with the same leaves to create a consensus tree. The linux-
trees are typically obtained via hierarchical clustering, hence the hclust format 64,
is used to encode both the aggregated trees and the final consensus tree. The osx-
method is exact and proven to be O(nqlog(n)), n being the individuals and q 64,
being the number of trees to aggregate. / GPL-2 win-
64
r-merror 2.0.2 N>=3 methods are used to measure each of n items. The data are used to es- noarch
timate simultaneously systematic error (bias) and random error (imprecision).
Observed measurements for each method or device are assumed to be linear
functions of the unknown true values and the errors are assumed normally dis-
tributed. Maximum likelihood estimation is used for the imprecision standard
deviation estimates. Pairwise calibration curves and plots can be easily gener-
ated. / GPL-2
r-meta4diag 2.0.8 Bayesian inference analysis for bivariate meta-analysis of diagnostic test stud- noarch
ies using integrated nested Laplace approximation with INLA. A purpose built
graphic user interface is available. The installation of R package INLA is
compulsory for successful usage. The INLA package can be obtained from
<http://www.r-inla.org>. We recommend the testing version, which can be
downloaded by running: install.packages(INLA, repos=c(getOption(repos),
INLA=https://inla.r-inla-download.org/R/testing), dep=TRUE). / GPL-3
r-metabel 0.2_0 A package for meta-analysis of genome-wide association scans between quan- noarch
titative or binary traits and SNPs / GPL-2
r-metablue 1.0.0 The sample mean and standard deviation are two commonly used statistics noarch
in meta-analyses, but some trials use other summary statistics such as the
median and quartiles to report the results. Therefore, researchers need to
transform those information back to the sample mean and standard devia-
tion. This package implemented sample mean estimators by Luo et al. (2016)
<arXiv:1505.05687>, sample standard deviation estimators by Wan et al.
(2014) <arXiv:1407.8038>, and the best linear unbiased estimators (BLUEs)
of location and scale parameters by Yang et al. (2018, submitted) based on
sample quantiles derived summaries in a meta-analysis. / GPL-2
r-metabolouise 1.0.0 Simulating dynamic (longitudinal, time-resolved) metabolomics data based on noarch
an underlying biological network. The network is initiating with certain con-
centrations and evolves over a simulated time period. Optionally external in-
fluxes (concentration drivers) can be added. / GPL-3
r-metaboqc 1.0 Takes QC signal for each day and normalize metabolomic data that has been noarch
acquired in a certain period of time. At least three QC per day are required. /
GPL-2
r-metadynminer 0.1.6 Metadynamics is a state of the art biomolecular simulation technique. linux-
‘Plumed’ Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> pro- 64,
gram makes it possible to perform metadynamics using various simulation osx-
codes. The results of metadynamics done in ‘Plumed’ can be analyzed by 64,
‘metadynminer’. The package ‘metadynminer’ reads 1D and 2D metadynam- win-
ics hills files from ‘Plumed’ package. It uses a fast algorithm by Hosek, P. and 64
Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037> to calculate a free energy
surface from hills. Minima can be located and plotted on the free energy sur-
face. Transition states can be analyzed by Nudged Elastic Band method by
Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free en-
ergy surfaces, minima and transition paths can be plotted to produce publica-
tion quality images. / GPL-3


Name Version
r-metafolio 0.1.0 The metafolio R package is a tool to simulate salmon metapopulations and linux-
apply financial portfolio optimization concepts. The package accompanies the 64,
paper ‘Portfolio conservation of metapopulations under climate change’. See osx-
citation(metafolio). / GPL-2 64,
win-
64
r-metafor 2.1_0 A comprehensive collection of functions for conducting meta-analyses in R. noarch
The package includes functions to calculate various effect sizes or outcome
measures, fit fixed-, random-, and mixed-effects models to such data, carry
out moderator and meta-regression analyses, and create various types of meta-
analytical plots (e.g., forest, funnel, radial, L’Abbe, Baujat, GOSH plots). For
meta-analyses of binomial and person-time data, the package also provides
functions that implement specialized methods, including the Mantel-Haenszel
method, Peto’s method, and a variety of suitable generalized linear (mixed-
effects) models (i.e., mixed-effects logistic and Poisson regression models).
Finally, the package provides functionality for fitting meta-analytic multivari-
ate/multilevel models that account for non-independent sampling errors and/or
true effects (e.g., due to the inclusion of multiple treatment studies, multiple
endpoints, or other forms of clustering). Network meta-analyses and meta-
analyses accounting for known correlation structures (e.g., due to phylogenetic
relatedness) can also be conducted. / GPL-2
r- 1.0 A nature-inspired metaheuristics algorithm based on the pollination process linux-
metaheuristicfpa of flowers. This R package makes it easy to implement the standard flower 64,
pollination algorithm for every user. The algorithm was first developed by osx-
Xin-She Yang in 2012 (<DOI:10.1007/978-3-642-32894-7_27>). / GPL-2 64,
win-
64
r- 2.0.0 An implementation of metaheuristic algorithms for continuous noarch
metaheuristicopt optimization. Currently, the package contains the implementa-
tions of 21 algorithms, as follows: particle swarm optimization
(Kennedy and Eberhart, 1995), ant lion optimizer (Mirjalili, 2015
<doi:10.1016/j.advengsoft.2015.01.010>), grey wolf optimizer (Mirjalili
et al., 2014 <doi:10.1016/j.advengsoft.2013.12.007>), dragonfly algorithm
(Mirjalili, 2015 <doi:10.1007/s00521-015-1920-1>), firefly algorithm (Yang,
2009 <doi:10.1007/978-3-642-04944-6_14>), genetic algorithm (Holland,
1992, ISBN:978-0262581110), grasshopper optimisation algorithm (Saremi
et al., 2017 <doi:10.1016/j.advengsoft.2017.01.004>), harmony search
algorithm (Mahdavi et al., 2007 <doi:10.1016/j.amc.2006.11.033>), moth
flame optimizer (Mirjalili, 2015 <doi:10.1016/j.knosys.2015.07.006>, sine
cosine algorithm (Mirjalili, 2016 <doi:10.1016/j.knosys.2015.12.022>),
whale optimization algorithm (Mirjalili and Lewis, 2016
<doi:10.1016/j.advengsoft.2016.01.008>), clonal selection algorithm (Castro,
2002 <doi:10.1109/TEVC.2002.1011539>), differential evolution (Das &
Suganthan, 2011), shuffled frog leaping (Eusuff, Landsey & Pasha, 2006),
cat swarm optimization (Chu et al., 2006), artificial bee colony algorithm
(Karaboga & Akay, 2009), krill-herd algorithm (Gandomi & Alavi, 2012),
cuckoo search (Yang & Deb, 2009), bat algorithm (Yang, 2012), gravitational
based search (Rashedi et al., 2009) and black hole optimization (Hatamlou,
2013). / GPL-2
r-metalik 0.43.0First- and higher-order likelihood inference in meta-analysis and meta- noarch
regression models. / GPL-2


Name Version
r-metansue 2.3 Novel method to unbiasedly include studies with Non- noarch
statistically Significant Unreported Effects (NSUEs) in a
meta-analysis <doi:10.1001/jamapsychiatry.2015.2196> and
<doi:10.1177/0962280218811349>. Briefly, the method first calculates
the interval where the unreported effects (e.g. t-values) should be according to
the threshold of statistical significance used in each study. Afterwards, maxi-
mum likelihood techniques are used to impute the expected effect size of each
study with NSUEs, accounting for between-study heterogeneity and potential
covariates. Multiple imputations of the NSUEs are then randomly created
based on the expected value, variance and statistical significance bounds.
Finally, a restricted-maximum likelihood random-effects meta-analysis is
separately conducted for each set of imputations, and estimations from these
meta-analyses are pooled. Please read the reference in ‘metansue’ for details
of the procedure. / GPL-3
r-metapca 0.1.4 MetaPCA implements simultaneous dimension reduction using PCA when noarch
multiple studies are combined. We propose two basic ideas to find a common
PC subspace by eigenvalue maximization approach and angle minimization
approach, and we extend the concept to incorporate Robust PCA and Sparse
PCA in the meta-analysis realm. / GPL-2
r-metarnaseq 1.0.2 Implementation of two p-value combination techniques (inverse normal and noarch
Fisher methods). A vignette is provided to explain how to perform a meta-
analysis from two independent RNA-seq experiments. / GPL-3
r-metasubtract 1.50 If results from a meta-GWAS are used for validation in one of the cohorts noarch
that was included in the meta-analysis, this will yield biased (i.e. too opti-
mistic) results. The validation cohort needs to be independent from the meta-
Genome-Wide-Association-Study (meta-GWAS) results. ‘MetaSubtract’ will
subtract the results of the respective cohort from the meta-GWAS results ana-
lytically without having to redo the meta-GWAS analysis using the leave-one-
out methodology. It can handle different meta-analyses methods and takes
into account if single or double genomic control correction was applied to the
original meta-analysis. It can also handle different meta-analysis methods. It
can be used for whole GWAS, but also for a limited set of genetic markers. /
GPL-3
r-metatest 1.0_5 Fits and tests meta regression models and generates a number of useful test noarch
statistics: next to t- and z-tests, the likelihood ratio, bartlett corrected likeli-
hood ratio and permutation tests are performed on the model coefficients. /
GPL-3
r-metavcov 1.1 Compute variance-covariance matrix for multivariate meta-analysis. Effect noarch
sizes include correlation (r), mean difference (MD), standardized mean differ-
ence (SMD), log odds ratio (logOR), log risk ratio (logRR), and risk difference
(RD). / GPL-2
r-meteor 0.3_4 A set of functions for weather and climate data manipulation, and other helper linux-
functions, to support dynamic ecological modelling, particularly crop and crop 64,
disease modeling. / GPL-3 osx-
64,
win-
64


Name Version
r-meth27qc 1.1 Meth27QC is a tool for analyzing Illumina Infinium HumanMethylation27 noarch
BeadChip Data and generating QC reports. This package allows users quickly
assess data quality of the Assay. Users can evaluate the data quality in the way
that Illumina GenomeStudio/BeadStudio recommended based on the control
probes. The package reads files exported from GenomeStudio/BeadStudio
software, generating intensity and standard deviation plots grouped by the
types of the control probes. Meth27 carries 40 control probes for staining,
hybridization, target removal, extension, bisulfite conversion, specificity, neg-
ative and non-polymorphic controls. Details of those control probes can be
found in the Infinium Assay for Methylation Protocol Guide from Illumina.We
also used the other non-control probes to plot intensity of detected genes, sig-
nal average for green and red. Outliers can be identified. / GPL-2
r- 0.1.0 Implementation of the methodology from the paper titled Effective noarch
methodcompare plots to assess bias and precision in method comparison studies pub-
lished in Statistical Methods in Medical Research, P. Taffe (2016)
<doi:10.1177/0962280216666667>. / GPL-3
r-metnorm 0.1 Metabolomics data are inevitably subject to a component of unwanted varia- noarch
tion, due to factors such as batch effects, matrix effects, and confounding bio-
logical variation. This package contains a collection of R functions which can
be used to remove unwanted variation and obtain normalized metabolomics
data. / GPL-2 | GPL-3
r-meto 0.1.0 Meteorological Tools following the FAO56 irrigation paper of Allen et al. noarch
(1998) [1]. Functions for calculating: reference evapotranspiration (ETref),
extraterrestrial radiation (Ra), net radiation (Rn), saturation vapor pressure
(satVP), global radiation (Rs), soil heat flux (G), daylight hours, and more.
[1] Allen, R. G., Pereira, L. S., Raes, D., & Smith, M. (1998). Crop
evapotranspiration-Guidelines for computing crop water requirements-FAO Ir-
rigation and drainage paper 56. FAO, Rome, 300(9). / GPL-2
r-metrics 0.1.4 An implementation of evaluation metrics in R that are commonly used in noarch
supervised machine learning. It implements metrics for regression, time se-
ries, binary classification, classification, and information retrieval problems. It
has zero dependencies and a consistent, simple interface for all functions. /
BSD_3_clause
r- 0.9.0 Provides an ‘htmlwidgets’ interface to the ‘MetricsGraphics.js’ (‘D3’-based) noarch
metricsgraphics charting library which is geared towards displaying time-series data. Chart
types include line charts, scatterplots, histograms and rudimentary bar charts.
Support for laying out multiple charts into a grid layout is also provided. All
charts are interactive and many have an option for line, label and region anno-
tations. / MIT
r- 0.2.0 Provides weighted versions of several metrics, scoring functions and perfor- noarch
metricsweighted mance measures used in machine learning, including average unit deviances
of the Bernoulli, Tweedie, Poisson, and Gamma distributions, see Jorgensen
B. (1997, ISBN: 978-0412997112). The package also contains a weighted
version of generalized R-squared, see e.g. Cohen, J. et al. (2002, ISBN: 978-
0805822236). Furthermore, ‘dplyr’ chains are supported. / GPL-2
r-metrology 0.9_28_1
Provides classes and calculation and plotting functions for metrology appli- noarch
cations, including measurement uncertainty estimation and inter-laboratory
metrology comparison studies. / GPL-2
r-metstat 1.0 A diverse collection of metabolomics related statistical tools. / Apache License noarch
(== 2.0)


Name Version
r-mewavg 0.3.0 Computes the average of a sequence of random vectors in a moving expanding linux-
window using a fixed amount of storage / GPL (>= 2.0) 64,
osx-
64,
win-
64
r-mf 4.3.2 Calculate MF (mitigated fraction) with clustering and bootstrap options. See noarch
http://goo.gl/pcXYVr for definition of MF. / MIT
r-mfag 1.5 Performs Multiple Factor Analysis method for quantitative, categorical, fre- noarch
quency and mixed data, in addition to generating a lot of graphics, also has
other useful functions. / GPL-2
r-mfgarch 0.1.8 Estimating GARCH-MIDAS (MIxed-DAta-Sampling) models (Engle, Ghy- linux-
sels, Sohn, 2013, <doi:10.1162/REST_a_00300>) and related statistical infer- 64,
ence, accompanying the paper Two are better than one: volatility forecasting osx-
using multiplicative component GARCH models by Conrad and Kleen (2018, 64,
<doi:10.2139/ssrn.2752354>). The GARCH-MIDAS model decomposes the win-
conditional variance of (daily) stock returns into a short- and long-term com- 64
ponent, where the latter may depend on an exogenous covariate sampled at a
lower frequency. / MIT
r-mfilter 0.1_5 The mFilter package implements several time series filters useful for smooth- noarch
ing and extracting trend and cyclical components of a time series. The routines
are commonly used in economics and finance, however they should also be in-
terest to other areas. Currently, Christiano-Fitzgerald, Baxter-King, Hodrick-
Prescott, Butterworth, and trigonometric regression filters are included in the
package. / GPL-2
r-mfp 1.5.2 Fractional polynomials are used to represent curvature in regression models. noarch
A key reference is Royston and Altman, 1994. / GPL-2
r-mft 2.0 Provides statistical tests and algorithms for the detection of change points noarch
in time series and point processes - particularly for changes in the mean
in time series and for changes in the rate and in the variance in point pro-
cesses. References - Michael Messer, Marietta Kirchner, Julia Schiemann,
Jochen Roeper, Ralph Neininger and Gaby Schneider (2014), A multiple fil-
ter test for the detection of rate changes in renewal processes with varying
variance <doi:10.1214/14-AOAS782>. Stefan Albert, Michael Messer, Ju-
lia Schiemann, Jochen Roeper, Gaby Schneider (2017), Multi-scale detec-
tion of variance changes in renewal processes in the presence of rate change
points <doi:10.1111/jtsa.12254>. Michael Messer, Kaue M. Costa, Jochen
Roeper and Gaby Schneider (2017), Multi-scale detection of rate changes
in spike trains with weak dependencies <doi:10.1007/s10827-016-0635-3>.
Michael Messer, Stefan Albert and Gaby Schneider (2018), The multiple filter
test for change point detection in time series <doi:10.1007/s00184-018-0672-
1>. Michael Messer, Hendrik Backhaus, Albrecht Stroh and Gaby Schneider
(2019) Peak detection in time series. / GPL-3
r-mgarchbekk 0.0.2 Procedures to simulate, estimate and diagnose MGARCH processes of BEKK linux-
and multivariate GJR (bivariate asymmetric GARCH model) specification. / 64,
GPL-3 osx-
64,
win-
64


Name Version
r-mgcv 1.8_28Generalized additive (mixed) models, some of their extensions and other gen- linux-
eralized ridge regression with multiple smoothing parameter estimation by 32,
(Restricted) Marginal Likelihood, Generalized Cross Validation and similar. linux-
Includes a gam() function, a wide variety of smoothers, JAGS support and 64,
distributions beyond the exponential family. / GPL (>= 2) osx-
64,
win-
32,
win-
64
r-mgl 1.1 An aggressive dimensionality reduction and network estimation technique for linux-
a high-dimensional Gaussian graphical model (GGM). Please refer to: Effi- 64,
cient Dimensionality Reduction for High-Dimensional Network Estimation, osx-
Safiye Celik, Benjamin A. Logsdon, Su-In Lee, Proceedings of The 31st Inter- 64,
national Conference on Machine Learning, 2014, p. 1953–1961. / GPL-2 win-
64
r-mglm 0.2.0 Provides functions that (1) fit multivariate discrete distributions, (2) generate noarch
random numbers from multivariate discrete distributions, and (3) run regres-
sion and penalized regression on the multivariate categorical response data.
Implemented models include: multinomial logit model, Dirichlet multinomial
model, generalized Dirichlet multinomial model, and negative multinomial
model. Making the best of the minorization-maximization (MM) algorithm
and Newton-Raphson method, we derive and implement stable and efficient
algorithms to find the maximum likelihood estimates. On a multi-core ma-
chine, multi-threading is supported. / GPL-2
r-mgraster 0.9 Convenience Functions for R Language Access to the v.1 API of the MG- noarch
RAST Metagenome Annotation Server, part of the US Department of Energy
(DOE) Systems Biology Knowledge Base (KBase). / BSD_2_clause
r-mgsda 1.4 Implements Multi-Group Sparse Discriminant Analysis proposal of linux-
I.Gaynanova, J.Booth and M.Wells (2015), Simultaneous sparse es- 64,
timation of canonical vectors in the p>>N setting, JASA, to ap- osx-
pear,[DOI:10.1080/01621459.2015.1034318]. / GPL-2 64,
win-
64
r-mgsub 1.7.1 Designed to enable simultaneous substitution in strings in a safe fashion. Safe noarch
means it does not rely on placeholders (which can cause errors in same length
matches). / MIT
r-mhadaptive 1.1_8 Performs general Metropolis-Hastings Markov Chain Monte Carlo sampling noarch
of a user defined function which returns the un-normalized value (likelihood
times prior) of a Bayesian model. The proposal variance-covariance structure
is updated adaptively for efficient mixing when the structure of the target dis-
tribution is unknown. The package also provides some functions for Bayesian
inference including Bayesian Credible Intervals (BCI) and Deviance Informa-
tion Criterion (DIC) calculation. / GPL-3


Name Version
r-mhctools 1.2.1 Ten tools for analysis of major histocompatibility complex (MHC) data in noarch
non- model species. The functions are tailored for amplicon data sets that
have been filtered using the ‘dada2’ method (for more information visit <https:
//benjjneb.github.io/dada2>), but even other data sets can be analyzed, if the
data tables are formatted according to the description in each function. The Re-
plMatch() function matches replicates in data sets in order to evaluate genotyp-
ing success. The GetReplTable() and GetReplStats() functions perform such
an evaluation. The HpltFind() function infers putative haplotypes from fami-
lies in the data set. The GetHpltTable() and GetHpltStats() functions evaluate
the accuracy of the haplotype inference. The PapaDiv() function compares
parent pairs in the data set and calculate their joint MHC diversity, taking into
account sequence variants that occur in both parents. The CalcPdist() function
calculates the p-distances from pairwise comparisons of all sequences in a data
set, and mean p-distances of all pairwise comparisons within each sample in
a data set. The function includes the options to specify which codons to com-
pare and to calculate amino acid p-distances. The CreateFas() function creates
a fasta file with all the sequences in the data set. The CreateSamplesFas()
function creates a fasta file for each sample in the data set. / MIT
r-mhg 1.1 Runs a minimum-hypergeometric (mHG) test as described in: Eden, E. (2007). noarch
Discovering Motifs in Ranked Lists of DNA Sequences. Haifa. / GPL-2
r-mhsmm 0.4.16Parameter estimation and prediction for hidden Markov and semi-Markov linux-
models for data with multiple observation sequences. Suitable for equidistant 64,
time series data, with multivariate and/or missing data. Allows user defined osx-
emission distributions. / GPL-2 64,
win-
64
r-mht 3.1.2 Multiple Hypothesis Testing For Variable Selection in high dimensional linear linux-
models. This package performs variable selection with multiple hypothesis 64,
testing, either for ordered variable selection or non-ordered variable selection. osx-
In both cases, a sequential procedure is performed. It starts to test the null hy- 64,
pothesis no variable is relevant; if this hypothesis is rejected, it then tests onlywin-
the first variable is relevant, and so on until the null hypothesis is accepted. / 64
GPL-3
r-mhtdiscrete 1.0.1 A comprehensive tool for almost all existing multiple testing methods for dis- noarch
crete data. The package also provides some novel multiple testing procedures
controlling FWER/FDR for discrete data. Given discrete p-values and their
domains, the [method].p.adjust function returns adjusted p-values, which can
be used to compare with the nominal significant level alpha and make deci-
sions. For users’ convenience, the functions also provide the output option for
printing decision rules. / GPL-2
r-mhtmult 0.1.0 A Comprehensive tool for almost all existing multiple testing methods for linux-
multiple families. The package summarizes the existing methods for multi- 64,
ple families multiple testing procedures (MTPs) such as double FDR, group osx-
Benjamini-Hochberg (GBH) procedure and average FDR controlling proce- 64,
dure. The package also provides some novel multiple testing procedures using win-
selective inference idea. / GPL-2 64


Name Version
r-mhtrajectoryr 1.0.1 Spontaneous adverse event reports have a high potential for detecting ad- noarch
verse drug reactions. However, due to their dimension, the analysis of such
databases requires statistical methods. We propose to use a logistic regres-
sion whose sparsity is viewed as a model selection challenge. Since the model
space is huge, a Metropolis-Hastings algorithm carries out the model selection
by maximizing the BIC criterion. / GPL-2
r-mi 1.0 The mi package provides functions for data manipulation, imputing missing noarch
values in an approximate Bayesian framework, diagnostics of the models used
to generate the imputations, confidence-building mechanisms to validate some
of the assumptions of the imputation algorithm, and functions to analyze mul-
tiply imputed data sets with the appropriate degree of sampling uncertainty. /
GPL-2
r-micar 1.1.1 ‘Mica’ is a server application used to create data web portals for large-scale noarch
epidemiological studies or multiple-study consortia. ‘Mica’ helps studies to
provide scientifically robust data visibility and web presence without signifi-
cant information technology effort. ‘Mica’ provides a structured description of
consortia, studies, annotated and searchable data dictionaries, and data access
request management. This ‘Mica’ client allows to perform data extraction for
reporting purposes. / GPL-3
r-miceconindex 0.1_6 Tools for calculating Laspeyres, Paasche, and Fisher price and quantity in- noarch
dices. / GPL-2
r-micefast 0.5.1 Fast imputations under the object-oriented programming paradigm. There was linux-
used quantitative models with a closed-form solution. Thus package is based 64,
on linear algebra operations. The biggest improvement in time performance osx-
could be achieve for a calculation where a grouping variable have to be used. 64,
A single evaluation of a quantitative model for the multiple imputations is win-
another major enhancement. Moreover there are offered a few functions built 64
to work with popular R packages such as ‘data.table’ or ‘dplyr’. / GPL-2
r-michelrodange 1.0.0 Michel Rodange was a Luxembourguish writer and poet who lived noarch
in the 19th century. His most notable work is Rodange (1872,
ISBN:1166177424), (Renert oder de Fuuß am Frack an a Ma’nsgrëßt),
but he also wrote many more works, including Rodange, Tockert (1928)
<https://www.autorenlexikon.lu/page/document/361/3614/1/FRE/index.html>
(D’Léierchen - Dem Léiweckerche säi Lidd) and Rodange, Welter (1929)
<https://www.autorenlexikon.lu/page/document/361/3615/1/FRE/index.html>
(Dem Grow Sigfrid seng Goldkuommer). This package contains three
datasets, each made from the plain text versions of his works available on
<https://data.public.lu/fr/datasets/the-works-in-luxembourguish-of-michel-
rodange/>. / CC0
r-micompr 1.1.0 A procedure for comparing multivariate samples associated with different noarch
groups. It uses principal component analysis to convert multivariate obser-
vations into a set of linearly uncorrelated statistical measures, which are then
compared using a number of statistical methods. The procedure is independent
of the distributional properties of samples and automatically selects features
that best explain their differences, avoiding manual selection of specific points
or summary statistics. It is appropriate for comparing samples of time series,
images, spectrometric measures or similar multivariate observations. / MIT


Name Version
r-microbats 0.1_1 A nature-inspired metaheuristic algorithm based on the echolocation behavior noarch
of microbats that uses frequency tuning to optimize problems in both continu-
ous and discrete dimensions. This R package makes it easy to implement the
standard bat algorithm on any user-supplied function. The algorithm was first
developed by Xin-She Yang in 2010 (<DOI:10.1007/978-3-642-12538-6_6>,
<DOI:10.1109/CINTI.2014.7028669>). / GPL-2
r- 1.4_6 Provides infrastructure to accurately measure and compare the execution time linux-
microbenchmark of R expressions. / BSD_2_clause file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r- 0.4.0 Most multilevel methodologies can only model macro-micro multilevel situ- noarch
micromacromultilevel ations in an unbiased way, wherein group-level predictors (e.g., city temper-
ature) are used to predict an individual-level outcome variable (e.g., citizen
personality). In contrast, this R package enables researchers to model micro-
macro situations, wherein individual-level (micro) predictors (and other group-
level predictors) are used to predict a group-level (macro) outcome variable in
an unbiased way. / GPL-2
r-micromapst 1.1.1 Provides the users with the ability to quickly create Linked Micromap plots noarch
for a collection of geographic areas. Linked Micromaps are visualizations of
georeferenced data that link statistical graphics to an organized series of small
maps or graphic images. The Help description contains examples of how to use
the micromapST function. Contained in this package are border group datasets
to support creating micromaps for the 50 U.S. states and District of Columbia
(51 areas), the U. S. 20 Seer Registries, the 105 counties in the state of Kansas,
the 62 counties of New York, the 24 counties of Maryland, the 29 counties
of Utah, the 32 administrative areas in China, the 218 administrative areas
in the UK and Ireland (for testing only), the 25 districts in the city of Seoul
South Korea, and the 52 counties on the Africa continent. A border group
dataset contains the boundaries related to the data level areas, a second layer
boundaries, a top or third layer boundary, a parameter list of run options, and a
cross indexing table between area names, abbreviations, numeric identification
and alias matching strings for the specific geographic area. By specifying a
border group, the package create micromaps for any geographic region. The
user can create and provide their own border group dataset for any area beyond
the areas contained within the package. Copyrighted 2013, 2014, 2015 and
2016 by Carr, Pearson and Pickle. / GPL-2
r-micropop 1.5 Modelling interacting microbial populations - example applications include noarch
human gut microbiota, rumen microbiota and phytoplankton. Solves a system
of ordinary differential equations to simulate microbial growth and resource
uptake over time. / GPL-3


Name Version
r-microseq 1.2.3 Basic functions for microbial sequence data analysis. The idea is to use the linux-
basic R data structures as much as possible, without building complex data 64,
types. / GPL-2 osx-
64,
win-
64
r-microsoftr 3.5.0.108
Umbrella package with licenses and notices for all Microsoft R packages / file linux-
LICENSE 64,
osx-
64,
win-
64
r-midas 1.0.1 Contains functions for converting existing HTML/JavaScript source into noarch
equivalent ‘shiny’ functions. Bootstraps the process of making new ‘shiny’
functions by allowing us to turn HTML snippets directly into R functions. /
GPL-3
r-midastouch 1.3 Contains the function mice.impute.midastouch(). Technically this function is noarch
to be run from within the ‘mice’ package (van Buuren et al. 2011), type
??mice. It substitutes the method ‘pmm’ within mice by ‘midastouch’. The
authors have shown that ‘midastouch’ is superior to default ‘pmm’. Many
ideas are based on Siddique / Belin 2008’s MIDAS. / GPL-2 | GPL-3
r-midn 1.0 Implementation of the mid-n algorithms presented in Wellek S (2015) noarch
<DOI:10.1111/stan.12063> Statistica Neerlandica 69, 358-373 for exact sam-
ple size calculation for superiority trials with binary outcome. / CC0
r-migest 1.8.0 Indirect methods for estimating bilateral migration flows in the presence noarch
of partial or missing data, including the estimation of bilateral migration
flows from changes in bilateral migrant stock tables (e.g. Abel (2013)
<doi:10.4054/DemRes.2013.28.18>). / GPL-3
r- 0.3.0 This package provides various indices, like Crude Migration Rate, differ- noarch
migration.indices ent Gini indices or the Coefficient of Variation among others, to show the
(un)equality of migration. / AGPL-3
r-milc 1.0 The MILC package is designed to predict individual trajectories using the con- noarch
tinuous time microsimulation model MILC, that describes the natural history
of lung cancer. / GPL-2
r-mime 0.6 Guesses the MIME type from a filename extension using the data derived from linux-
/etc/mime.types in UNIX-type systems. / GPL 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-mimix 1.0 Tools to combine results for multiply-imputed data using mixture approxima- noarch
tions / GPL-2
r-mindonstats 0.11 66 data sets that were imported using read.table() where appropriate but more noarch
commonly after converting to a csv file for importing via read.csv(). / GPL-3


Name Version
r-mined 1.0_2 This is a method (MinED) for mining probability distributions using determin- linux-
istic sampling which is proposed by Joseph, Wang, Gu, Lv, and Tuo (2018). 64,
The MinED samples can be used for approximating the target distribution. osx-
They can be generated from a density function that is known only up to a 64,
proportionality constant and thus, it might find applications in Bayesian com- win-
putation. Moreover, the MinED samples are generated with much fewer eval- 64
uations of the density function compared to random sampling-based methods
such as MCMC and therefore, this method will be especially useful when the
unnormalized posterior is expensive or time consuming to evaluate. / LGPL-
2.1
r-minerva 1.5.8 Wrapper for ‘minepy’ implementation of Maximal Information-based Non- linux-
parametric Exploration statistics (MIC and MINE family). Detailed infor- 64,
mation of the ANSI C implementation of ‘minepy’ can be found at <http: osx-
//minepy.readthedocs.io/en/latest>. / GPL-3 64,
win-
64
r-miney 0.1 This package implements the core idea of games known as ‘Minesweeper’ on noarch
Microsoft Windows or ‘KMines’ for KDE on Unix-like operating systems. /
GPL-2
r-minicran 0.2.12Makes it possible to create an internally consistent repository consisting of noarch
selected packages from CRAN-like repositories. The user specifies a set of
desired packages, and ‘miniCRAN’ recursively reads the dependency tree for
these packages, then downloads only this subset. The user can then install
packages from this repository directly, rather than from CRAN. This is useful
in production settings, e.g. server behind a firewall, or remote locations with
slow (or zero) Internet access. / GPL-2
r-minigui 0.8_1 Quick and simple Tcl/Tk Graphical User Interface to call functions. Also com- noarch
prises a very simple experimental GUI framework. / GPL (<= 2.0)
r-minimalrsd 1.0.0 Generate central composite designs (CCD)with full as well as fractional fac- noarch
torial points (half replicate) and Box Behnken designs (BBD) with minimally
changed run sequence. / GPL-2
r-minimap 0.1.0 Create tile grid maps, which are like choropleth maps except each region is noarch
represented with equal visual space. / MIT
r-minimax 1.0 The minimax family of distributions is a two-parameter family like the beta noarch
family, but computationally a lot more tractible. / GPL-2 | GPL-3
r-minirand 0.1.0 Randomization schedules are generated in the schemes with k (k>=2) treat- noarch
ment groups and any allocation ratios by minimization algorithms. / GPL-2
r-miniui 0.1.1.1Provides UI widget and layout functions for writing Shiny apps that work well linux-
on small screens. / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-minpack.lm 1.2_1 The nls.lm function provides an R interface to lmder and lmdif from the MIN- linux-
PACK library, for solving nonlinear least-squares problems by a modification 64,
of the Levenberg-Marquardt algorithm, with support for lower and upper pa- osx-
rameter bounds. The implementation can be used via nls-like calls using the 64,
nlsLM function. / GPL-3 win-
64
r-minqa 1.2.4 Derivative-free optimization by quadratic approximation based on an interface linux-
to Fortran implementations by M. J. D. Powell. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-minval 0.8_1 For a given set of stoichiometric reactions, this package evaluates the mass and noarch
charge balance, extracts all reactants, products, orphan metabolites, metabolite
names and compartments. Also are included some options to characterize and
write models in TSV and SBML formats. / GPL-2
r-minxent 0.01 This package implements entropy optimization distribution under specified noarch
constraints. It also offers an R interface to the MinxEnt and MaxEnt distri-
butions. / GPL-2
r-mirada 1.13.8_8
This package collects algorithms/functions developed for microRNA profiling linux-
data analyses. Analytical platforms include traditional hybridization microar- 64,
ray, CGH, beads-based microarray, and qRT-PCR array. / GPL-2 osx-
64,
win-
64
r-mirsea 1.1 The tools for ‘MicroRNA Set Enrichment Analysis’ can identify risk path- noarch
ways(or prior gene sets) regulated by microRNA set in the context of mi-
croRNA expression data. (1) This package constructs a correlation profile
of microRNA and pathways by the hypergeometric statistic test. The gene
sets of pathways derived from the three public databases (Kyoto Encyclope-
dia of Genes and Genomes (‘KEGG’); ‘Reactome’; ‘Biocarta’) and the tar-
get gene sets of microRNA are provided by four databases(‘TarBaseV6.0’;
‘mir2Disease’; ‘miRecords’; ‘miRTarBase’;). (2) This package can quantify
the change of correlation between microRNA for each pathway(or prior gene
set) based on a microRNA expression data with cases and controls. (3) This
package uses the weighted Kolmogorov-Smirnov statistic to calculate an en-
richment score (ES) of a microRNA set that co-regulate to a pathway , which
reflects the degree to which a given pathway is associated with the specific
phenotype. (4) This package can provide the visualization of the results. /
GPL-2
r-misaem 0.9.1 Estimate parameters of logistic regression with missing data and perform noarch
model selection, using algorithm Stochastic Approximation EM. / GPL-3
r-misc3d 0.8_4 A collection of miscellaneous 3d plots, including isosurfaces. / GPL-3 noarch
r-miscfuncs 1.2_10Implementing various things including functions for LaTeX tables, the Kalman noarch
filter, web scraping, development tools, relative risk and odds ratio. / GPL-3


Name Version
r-miscor 0.1_1 Statistical test for the product-moment correlation coefficient based on H0: rho noarch
= rho0 including sample size computation, statistical test for comparing the
product-moment correlation coefficient in independent ad dependent samples,
sequential triangular test for the product-moment correlation coefficient, par-
tial and semipartial correlation, simulation of bivariate normal and non-normal
distribution with a specified correlation. / GPL-3
r-misctools 0.6_22Miscellaneous small tools and utilities. Many of them facilitate the work linux-
with matrices, e.g. inserting rows or columns, creating symmetric matrices, 32,
or checking for semidefiniteness. Other tools facilitate the work with regres- linux-
sion models, e.g. extracting the standard errors, obtaining the number of (esti- 64,
mated) parameters, or calculating R-squared values. / GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64
r-mise 0.1.0 Clears the workspace. Useful for the beginnings of R scripts, to avoid potential noarch
problems with accidentally using information from variables or functions from
previous script evaluations, too many figure windows open at the same time,
packages that you don’t need any more, or a cluttered console. Uses code
from various StackOverflow users. See help(mise) for pointers to the relevant
StackOverflow pages. / MIT
r-misreport 0.1.1 Enables investigation of the predictors of misreporting on sensitive survey noarch
questions through a multivariate list experiment regression method. The
method permits researchers to model whether a survey respondent’s answer
to the sensitive item in a list experiment is different from his or her answer to
an analogous direct question. / GPL-3
r-missmech 1.0.2 To test whether the missing data mechanism, in a set of incompletely observed noarch
data, is one of missing completely at random (MCAR). For detailed descrip-
tion see Jamshidian, M. Jalal, S., and Jansen, C. (2014). MissMech: An R
Package for Testing Homoscedasticity, Multivariate Normality, and Missing
Completely at Random (MCAR), Journal of Statistical Software, 56(6), 1-31.
URL http://www.jstatsoft.org/v56/i06/. / GPL-2
r-misssbm 0.2.0 When a network is partially observed (here, NAs in the adjacency matrix rather linux-
than 1 or 0 due to missing information between node pairs), it is possible 64,
to account for the underlying process that generates those NAs. ‘missSBM’ osx-
adjusts the popular stochastic block model from network data sampled under 64,
various missing data conditions, as described in Tabouy, Barbillon and Chiquet win-
(2019) <doi:10.1080/01621459.2018.1562934>. / GPL-3 64
r-mist 1.0 Test for association between a set of SNPS/genes and continuous or binary noarch
outcomes by including variant characteristic information and using (weighted)
score statistics. / LGPL (>= 2.0)
r-mistat 1.0_5 Provide all the data sets and statistical analysis applications used in Modern In- noarch
dustrial Statistics: with applications in R, MINITAB and JMP by R.S. Kenett
and S. Zacks with contributions by D. Amberti, John Wiley and Sons, 2013,
which is a second revised and expanded revision of Modern Industrial Statis-
tics: Design and Control of Quality and Reliability, R. Kenett and S. Zacks,
Duxbury/Wadsworth Publishing, 1998. / GPL-2
r-mistr 0.0.2 A flexible computational framework for mixture distributions with the focus noarch
on the composite models. / GPL-3


Name Version
r-mitisem 1.2 Flexible multivariate function approximation using adapted Mixture of Stu- noarch
dent t Distributions. Mixture of t distribution is obtained using Importance
Sampling weighted Expectation Maximization algorithm. / GPL-3
r-mitools 2.4 Tools to perform analyses and combine results from multiple-imputation noarch
datasets. / GPL-2
r-mittagleffler 0.3.0 Implements the Mittag-Leffler function, distribution, random variate genera- noarch
tion, and estimation. Based on the Laplace-Inversion algorithm by Garrappa,
R. (2015) <doi:10.1137/140971191>. / GPL-2
r-mix 1.0_10Estimation/multiple imputation programs for mixed categorical and continu- linux-
ous data. / Unlimited 64,
osx-
64,
win-
64
r-mixdist 0.5_5 Fit finite mixture distribution models to grouped data and conditional data by noarch
maximum likelihood using a combination of a Newton-type algorithm and the
EM algorithm. / GPL-2
r- 0.1 Missing data imputation for continuous and categorical data, using nonpara- linux-
mixeddataimpute metric Bayesian joint models (specifically the hierarchically coupled mix- 64,
ture model with local dependence described in Murray and Reiter (2015); osx-
see ‘citation(MixedDataImpute)’ or http://arxiv.org/abs/1410.0438). See 64,
‘?hcmm_impute’ for example usage. / GPL-3 win-
64
r-mixedmem 1.1.0 Fits mixed membership models with discrete multivariate data (with or without linux-
repeated measures) following the general framework of Erosheva et al (2004). 64,
This package uses a Variational EM approach by approximating the posterior osx-
distribution of latent memberships and selecting hyperparameters through a 64,
pseudo-MLE procedure. Currently supported data types are Bernoulli, multi- win-
nomial and rank (Plackett-Luce). The extended GoM model with fixed stayers 64
from Erosheva et al (2007) is now also supported. See Airoldi et al (2014) for
other examples of mixed membership models. / GPL-2
r-mixedpsy 1.0.0 Tools for the analysis of psychophysical data. This package allows to esti- noarch
mate the Point of Subjective Equivalence (PSE) and the Just Noticeable Dif-
ference (JND), either from a psychometric function or from a Generalized
Linear Mixed Model (GLMM). Additionally, the package allows plotting the
fitted models and the response data, simulating psychometric functions of
different shapes, and simulating data sets. For a description of the use of
GLMMs applied to psychophysical data, refer to Moscatelli et al. (2012),
<doi:10.1167/12.11.26>. / GPL-2
r-mixedts 1.0.4 We provide detailed functions for univariate Mixed Tempered Stable distribu- noarch
tion. / GPL-2
r-mixemm 1.0 Contains functions for estimating a mixed-effects model for clustered data (or noarch
batch-processed data) with cluster-level (or batch- level) missing values in the
outcome, i.e., the outcomes of some clusters are either all observed or miss-
ing altogether. The model is developed for analyzing incomplete data from
labeling-based quantitative proteomics experiments but is not limited to this
type of data. We used an expectation conditional maximization (ECM) algo-
rithm for model estimation. The cluster-level missingness may depend on the
average value of the outcome in the cluster (missing not at random). / GPL-3


Name Version
r-mixmap 1.3.4 A collection of functions to implement the MixMAP algorithm, which per- noarch
forms gene level tests of association using data from a previous GWAS or
data from a meta-analysis of several GWAS. Conceptually, genes are detected
as significant if the collection of p-values within a gene are determined to be
collectively smaller than would be observed by chance. / GPL-3
r-mixmatrix 0.2.4 Provides sampling and density functions for matrix variate normal, t, and in- linux-
verted t distributions; ML estimation for matrix variate normal and t distri- 64,
butions using the EM algorithm, including some restrictions on the parame- osx-
ters; and classification by linear and quadratic discriminant analysis for ma- 64,
trix variate normal and t distributions described in Thompson et al. (2019) win-
<arXiv:1907.09565>. Performs clustering with matrix variate normal and t 64
mixture models. / GPL-3
r-mixmeta 1.0.3 A collection of functions to perform various meta-analytical models through noarch
a unified mixed-effects framework, including standard univariate fixed and
random-effects meta-analysis and meta-regression, and non-standard exten-
sions such as multivariate, multilevel, longitudinal, and dose-response models.
/ GPL-2
r-mixor 1.0.4 Provides the function ‘mixor’ for fitting a mixed-effects ordinal and binary linux-
response models and associated methods for printing, summarizing, extract- 64,
ing estimated coefficients and variance-covariance matrix, and estimating con- osx-
trasts for the fitted models. / GPL-2 64,
win-
64
r-mixphm 0.7_2 Fits multiple variable mixtures of various parametric proportional hazard mod- noarch
els using the EM-Algorithm. Proportionality restrictions can be imposed on
the latent groups and/or on the variables. Several survival distributions can be
specified. Missing values and censored values are allowed. Independence is
assumed over the single variables. / GPL-2
r-mixrasch 1.1 Estimates Rasch models and mixture Rasch models, including the dichoto- noarch
mous Rasch model, the rating scale model, and the partial credit model. /
GPL-2
r-mixraschtools 1.1 Provides supplemental functions for the ‘mixRasch’ package (Willse, noarch
2014), <https://cran.r-project.org/package=mixRasch/mixRasch.pdf> includ-
ing a plotting function to compare item parameters for multiple class models
and a function that provides average theta values for each class in a mixture
model. / GPL-3
r-mixreg 0.0_6 Fits mixtures of (possibly multivariate) regressions (which has been described noarch
as doing ANCOVA when you don’t know the levels). / GPL-2
r-mixrf 1.0 It offers random-forest-based functions to impute clustered incomplete data. noarch
The package is tailored for but not limited to imputing multitissue expression
data, in which a gene’s expression is measured on the collected tissues of an
individual but missing on the uncollected tissues. / GPL-3
r-mixsal 1.0 The current version of the ‘MixSAL’ package allows users to generate data noarch
from a multivariate SAL distribution or a mixture of multivariate SAL distri-
butions, evaluate the probability density function of a multivariate SAL dis-
tribution or a mixture of multivariate SAL distributions, and fit a mixture of
multivariate SAL distributions using the Expectation-Maximization (EM) al-
gorithm (see Franczak et. al, 2014, <doi:10.1109/TPAMI.2013.216>, for de-
tails). / GPL-2


Name Version
r-mixsim 1.1_3 The utility of this package is in simulating mixtures of Gaussian distribu- linux-
tions with different levels of overlap between mixture components. Pairwise 64,
overlap, defined as a sum of two misclassification probabilities, measures the osx-
degree of interaction between components and can be readily employed to 64,
control the clustering complexity of datasets simulated from mixtures. These win-
datasets can then be used for systematic performance investigation of clus- 64
tering and finite mixture modeling algorithms. Among other capabilities of
‘MixSim’, there are computing the exact overlap for Gaussian mixtures, sim-
ulating Gaussian and non-Gaussian data, simulating outliers and noise vari-
ables, calculating various measures of agreement between two partitionings,
and constructing parallel distribution plots for the graphical display of finite
mixture models. / GPL-2
r-mixsmsn 1.1_5 Functions to fit finite mixture of scale mixture of skew-normal (FM-SMSN) noarch
distributions. / GPL (>= 2.0)
r-mixspe 0.1.1 Mixtures of skewed and elliptical distributions are implemented using mix- noarch
tures of multivariate skew power exponential and power exponential distri-
butions, respectively. A generalized expectation-maximization framework is
used for parameter estimation. Methodology for mixtures of power exponen-
tial distributions is from Dang et al. (2015) <doi: 10.1111/biom.12351>. /
GPL-2
r-mixsqp 0.2_2 Provides optimization algorithms based on sequential quadratic programming linux-
(SQP) for maximum likelihood estimation of the mixture proportions in a finite 64,
mixture model where the component densities are known. The algorithms are osx-
expected to obtain solutions that are at least as accurate as the state-of-the-art 64,
MOSEK interior-point solver (called by function KWDual in the ‘REBayes’ win-
package), and they are expected to arrive at solutions more quickly in large 64
data sets. The algorithms are described in Y. Kim, P. Carbonetto, M. Stephens
& M. Anitescu (2018) <arXiv:1806.01412>. / MIT
r-mixtnb 1.0 Differential expression analysis of RNA-Seq data when replicates under two noarch
conditions are available is performed. First, mixtures of Negative Binomial
distributions are fitted on the data in order to estimate the dispersions, then the
Wald test is computed. / GPL-3
r-mixture 1.5 An implementation of all 14 Gaussian parsimonious clustering models linux-
(GPCMs) for model-based clustering and model-based classification. / GPL-2 64,
osx-
64,
win-
64
r-mixtureinf 1.1 Functions for computing the penalized maximum likelihood estimate (PMLE) noarch
or maximum likelihood estimate (MLE), testing the order of a finite mixture
model using EM-test, drawing histogram of observations and the fitted density
or probability mass function of the mixture model. / AGPL-3
r-mixtureregltic 1.0.0 Fit mixture regression models with nonsusceptibility/cure for left- linux-
truncated and interval-censored (LTIC) data (see Chen et al. (2013) 64,
<doi:10.1002/sim.5845>). This package also provides the nonparametric osx-
maximum likelihood estimator (NPMLE) for the survival/event curves with 64,
LTIC data. / GPL-2 | GPL-3 win-
64


Name Version
r-mize 0.2.2 Optimization algorithms implemented in R, including conjugate gradient noarch
(CG), Broyden-Fletcher-Goldfarb-Shanno (BFGS) and the limited memory
BFGS (L-BFGS) methods. Most internal parameters can be set through the
call interface. The solvers hold up quite well for higher-dimensional prob-
lems. / BSD_2_clause
r-mkde 0.1 Provides functions to compute and visualize movement-based kernel density linux-
estimates (MKDEs) for animal utilization distributions in 2 or 3 spatial dimen- 64,
sions. / GPL-3 osx-
64,
win-
64
r-mkin 0.9.49.5
Calculation routines based on the FOCUS Kinetics Report (2006, 2014). In- noarch
cludes a function for conveniently defining differential equation models, model
solution based on eigenvalues if possible or using numerical solvers and a
choice of the optimisation methods made available by the ‘FME’ package. If
a C compiler (on windows: ‘Rtools’) is installed, differential equation models
are solved using compiled C functions. Please note that no warranty is implied
for correctness of results or fitness for a particular purpose. / GPL-3
r-mkle 0.05 Package for fast computation of the maximum kernel likelihood estimator noarch
(mkle) / GPL-3
r-mknapsack 0.1.0 Package solves multiple knapsack optimisation problem. Given a set of items, noarch
each with volume and value, it will allocate them to knapsacks of a given size
in a way that value of top N knapsacks is as large as possible. / GPL-2
r-mkssd 1.1 mkssd is a package that generates efficient balanced non-aliased multi-level k- noarch
circulant supersaturated designs by interchanging the elements of the generator
vector. The package tries to generate a supersaturated design that has chisquare
efficiency more than user specified efficiency level (mef). The package also
displays the progress of generation of an efficient multi-level k-circulant de-
sign through a progress bar. The progress of 100% means that one full round
of interchange is completed. More than one full round (typically 4-5 rounds)
of interchange may be required for larger designs. / GPL-2
r-ml.msbd 1.1.1 Inference of a multi-states birth-death model from a phylogeny, comprising a noarch
number of states N, birth and death rates for each state and on which edges
each state appears. Inference is done using a hybrid approach: states are pro-
gressively added in a greedy approach. For a fixed number of states N the best
model is selected via maximum likelihood. Reference: J. Barido-Sottani and
T. Stadler (2017) <doi:10.1101/215491>. / GPL-3
r-mlapi 0.1.0 Provides ‘R6’ abstract classes for building machine learning models with noarch
‘scikit-learn’ like API. <http://scikit-learn.org/> is a popular module for
‘Python’ programming language which design became de facto a standard in
industry for machine learning tasks. / MIT
r-mlbench 2.1_1 A collection of artificial and real-world machine learning benchmark prob- linux-
lems, including, e.g., several data sets from the UCI repository. / GPL-2 64,
osx-
64,
win-
64
r-mlbstats 0.1.0 Computational functions for player metrics in major league baseball includ- noarch
ing batting, pitching, fielding, base-running, and overall player statistics. This
package is actively maintained with new metrics being added as they are de-
veloped. / MIT


Name Version
r-mlcm 0.4.2 Conjoint measurement is a psychophysical procedure in which stimulus pairs noarch
are presented that vary along 2 or more dimensions and the observer is required
to compare the stimuli along one of them. This package contains functions
to estimate the contribution of the n scales to the judgment by a maximum
likelihood method under several hypotheses of how the perceptual dimensions
interact. Reference: Knoblauch & Maloney (2012) Modeling Psychophysical
Data in R. <doi:10.1007/978-1-4614-4475-6>. / GPL-2
r-mldr.datasets 0.4.2 Large collection of multilabel datasets along with the functions needed to ex- noarch
port them to several formats, to make partitions, and to obtain bibliographic
information. / LGPL-3
r-mlds 0.4.5 Difference scaling is a method for scaling perceived supra-threshold differ- noarch
ences. The package contains functions that allow the user to design and run a
difference scaling experiment, to fit the resulting data by maximum likelihood
and test the internal validity of the estimated scale. / GPL-2
r-mle.tools 1.0.0 Calculates the expected/observed Fisher information and the bias-corrected noarch
maximum likelihood estimate(s) via Cox-Snell Methodology. / GPL-2
r-mlearning 1.0_0 This package provides a unified interface to various machine learning algo- noarch
rithms. Confusion matrices are provided too. / GPL-2
r-mlecens 0.1_4 This package contains functions to compute the nonparametric maximum like- linux-
lihood estimator (MLE) for the bivariate distribution of (X,Y), when realiza- 64,
tions of (X,Y) cannot be observed directly. To be more precise, we consider osx-
the situation where we observe a set of rectangles that are known to contain the 64,
unobservable realizations of (X,Y). We compute the MLE based on such a set win-
of rectangles. The methods can also be used for univariate censored data (see 64
data set ‘cosmesis’), and for censored data with competing risks (see data set
‘menopause’). We also provide functions to visualize the observed data and
the MLE. / GPL-2
r-mlegp 3.1.7 Maximum likelihood Gaussian process modeling for univariate and multi- linux-
dimensional outputs with diagnostic plots following Santner et al (2003) 64,
<doi:10.1007/978-1-4757-3799-8>. Contact the maintainer for a package ver- osx-
sion that includes sensitivity analysis. / GPL-2 64,
win-
64
r-mleur 1.0_6 Provides functions for unit root testing using MLE method / GPL-2 noarch
r-mlf 1.2.1 Offers a gentle introduction to machine learning concepts for practition- noarch
ers with a statistical pedigree: decomposition of model error (bias-variance
trade-off), nonlinear correlations, information theory and functional permuta-
tion/bootstrap simulations. SzÃ©kely GJ, Rizzo ML, Bakirov NK. (2007).
<doi:10.1214/009053607000000505>. Reshef DN, Reshef YA, Finucane HK,
Grossman SR, McVean G, Turnbaugh PJ, Lander ES, Mitzenmacher M, Sabeti
PC. (2011). <doi:10.1126/science.1205438>. / GPL-2
r-mlica2 2.1 An R code implementation of the maximum likelihood (fixed point) algorithm noarch
of Hyvaerinen, Karhuna, and Oja for independent component analysis. / GPL-
2
r-mlid 1.0.1 Tools and functions to fit a multilevel index of dissimilarity. / GPL-3 noarch
r-mlmetrics 1.1.1 A collection of evaluation metrics, including loss, score and utility functions, noarch
that measure regression, classification and ranking performance. / GPL-2


Name Version
r-mlml2r 0.3.2 Maximum likelihood estimates (MLE) of the proportions of 5-mC and 5- noarch
hmC in the DNA using information from BS-conversion, TAB-conversion, and
oxBS-conversion methods. One can use information from all three methods or
any combination of two of them. Estimates are based on Binomial model by
Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and Kiihl et al. (2019)
<doi:10.1515/sagmb-2018-0031>. / MIT
r-mlmmm 0.3_1.2
Computational strategies for multivariate linear mixed-effects models with linux-
missing values, Schafer and Yucel (2002), Journal of Computational and 64,
Graphical Statistics, 11, 421-442. / GPL-2 osx-
64,
win-
64
r-mlmrev 1.0_7 Data and examples from a multilevel modelling software review as well as linux-
other well-known data sets from the multilevel modelling literature. / GPL 32,
(>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-mlphaser 0.01 Phase haplotypes from genotypes based on a list of known haplotypes. Suited noarch
to highly diverse loci such as HLA. / GPL-2
r-mlpugs 0.2.0 An implementation of classifier chains (CC’s) for multi-label prediction. Users noarch
can employ an external package (e.g. ‘randomForest’, ‘C50’), or supply their
own. The package can train a single set of CC’s or train an ensemble of CC’s
– in parallel if running in a multi-core environment. New observations are
classified using a Gibbs sampler since each unobserved label is conditioned
on the others. The package includes methods for evaluating the predictions
for accuracy and aggregating across iterations and models to produce binary
or probabilistic classifications. / MIT
r-mlr3misc 0.1.3 Frequently used helper functions and assertions used in ‘mlr3’ and its com- linux-
panion packages. Comes with helper functions for functional programming, 64,
for printing, to work with ‘data.table’, as well as some generally useful ‘R6’ osx-
classes. This package also supersedes the package ‘BBmisc’. / LGPL-3 64,
win-
64
r-mlsjunkgen 0.1.1 Generate a stream of pseudo-random numbers generated using the MLS Junk noarch
Generator algorithm. Functions exist to generate single pseudo-random num-
bers as well as a vector, data frame, or matrix of pseudo-random numbers. /
MIT
r-mltest 1.0.1 A fast, robust and easy-to-use calculation of multi-class classification evalua- noarch
tion metrics based on confusion matrix. / GPL-2
r-mltools 0.3.5 A collection of machine learning helper functions, particularly assisting in the noarch
Exploratory Data Analysis phase. Makes heavy use of the ‘data.table’ pack-
age for optimal speed and memory efficiency. Highlights include a versatile
bin_data() function, sparsify() for converting a data.table to sparse matrix for-
mat with one-hot encoding, fast evaluation metrics, and empirical_cdf() for
calculating empirical Multivariate Cumulative Distribution Functions. / MIT


Name Version
r-mm4lmm 1.1.5 The main function MMEst() performs (Restricted) Maximum Likelihood in a linux-
variance component mixed models using a Min-Max (MM) algorithm (Hunter, 64,
D. R., & Lange, K. (2004) <doi:10.1198/0003130042836>). / GPL-2 osx-
64,
win-
64
r-mmac 0.1.2 Contains the data sets for the textbook Mathematical Modeling and Applied noarch
Calculus by Joel Kilty and Alex M. McAllister. The book will be published
by Oxford University Press in 2018 with ISBN-13: 978-019882472. / GPL-2
r-mmand 1.5.4 Provides tools for performing mathematical morphology operations, such as linux-
erosion and dilation, on data of arbitrary dimensionality. Can also be used 64,
for finding connected components, resampling, filtering, smoothing and other osx-
image processing-style operations. / GPL-2 64,
win-
64
r-mmap 0.6_17R interface to POSIX mmap and Window’s MapViewOfFile. / GPL-3 linux-
64,
osx-
64,
win-
64
r-mmc 0.0.3 Provides routines for multivariate measurement error correction. Includes pro- noarch
cedures for linear, logistic and Cox regression models. Bootstrapped standard
errors and confidence intervals can be obtained for corrected estimates. / GPL-
3
r-mmds 1.1 This library implements mixture model distance sampling methods. See Miller noarch
and Thomas (in prep.). / GPL-2
r-mme 0.1_6 Fit Gaussian Multinomial mixed-effects models for small area estimation: noarch
Model 1, with one random effect in each category of the response variable
(Lopez-Vizcaino,E. et al., 2013) <doi:10.1177/1471082X13478873>; Model
2, introducing independent time effect; Model 3, introducing correlated time
effect. mme calculates direct and parametric bootstrap MSE estimators
(Lopez-Vizcaino,E et al., 2014) <doi:10.1111/rssa.12085>. / GPL-2
r-mmeln 1.3 Fit multivariate mixture of normal distribution using covariance structure. / noarch
GPL-3
r-mmeta 2.3 A novel multivariate meta-analysis. / GPL-2 linux-
64,
osx-
64,
win-
64
r-mmmgee 1.20 Provides global hypothesis tests, multiple testing procedures and simultaneous noarch
confidence intervals for multiple linear contrasts of regression coefficients in
a single generalized estimating equation (GEE) model or across multiple GEE
models. GEE models are fit by a modified version of the ‘geeM’ package. /
GPL-3
r-mmms 0.1 The package implements a multi-marker molecular signature (MMMS) ap- noarch
proach for treatment-specific subgroup identification. / GPL-3


Name Version
r-mmpa 1.2.0 To determine the number of quantitative assays needed for a sample of data noarch
using pooled testing methods, which include mini-pooling (MP), MP with al-
gorithm (MPA), and marker-assisted MPA (mMPA). To estimate the number of
assays needed, the package also provides a tool to conduct Monte Carlo (MC)
to simulate different orders in which the sample would be collected to form
pools. Using MC avoids the dependence of the estimated number of assays on
any specific ordering of the samples to form pools. / MIT
r-mmpf 0.0.5 Marginalizes prediction functions using Monte-Carlo integration and com- noarch
putes permutation importance. / MIT
r-mmpp 0.6 Compute similarities and distances between marked point processes. / GPL-2 noarch
r-mmsample 0.1 Subset a control group to match an intervention group on a set of features linux-
using multivariate matching and propensity score calipers. Based on methods 64,
in Rosenbaum and Rubin (1985). / GPL-3 osx-
64,
win-
64
r-mmtsne 0.1.0 An implementation of multiple maps t-distributed stochastic neighbor em- noarch
bedding (t-SNE). Multiple maps t-SNE is a method for projecting high-
dimensional data into several low-dimensional maps such that non-metric
space properties are better preserved than they would be by a single map. Mul-
tiple maps t-SNE with only one map is equivalent to standard t-SNE. When
projecting onto more than one map, multiple maps t-SNE estimates a set of la-
tent weights that allow each point to contribute to one or more maps depending
on similarity relationships in the original data. This implementation is a port of
the original ‘Matlab’ library by Laurens van der Maaten. See Van der Maaten
and Hinton (2012) <doi:10.1007/s10994-011-5273-4>. This material is based
upon work supported by the United States Air Force and Defense Advanced
Research Project Agency (DARPA) under Contract No. FA8750-17-C-0020.
Any opinions, findings and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect the views of
the United States Air Force and Defense Advanced Research Projects Agency.
Distribution Statement A: Approved for Public Release; Distribution Unlim-
ited. / FreeBSD | file LICENSE
r-mmwrweek 0.1.1 The first day of any MMWR week is Sunday. MMWR week numbering is noarch
sequential beginning with 1 and incrementing with each week to a maximum
of 52 or 53. MMWR week #1 of an MMWR year is the first week of the
year that has at least four days in the calendar year. This package provides
functionality to convert Dates to MMWR day, week, and year and the reverse.
/ GPL-2
r-mnormpow 0.1.1 Computes integral of f(x)*x_i^k on a product of intervals, where f is the den- linux-
sity of a gaussian law. This a is small alteration of the mnormt code from A. 64,
Genz and A. Azzalini. / GPL-2 osx-
64,
win-
64


Name Version
r-mnormt 1.5_5 Functions are provided for computing the density and the distribution func- linux-
tion of multivariate normal and t random variables, and for generating random 32,
vectors sampled from these distributions. Probabilities are computed via non- linux-
Monte Carlo methods; different routines are used in the case d=1, d=2, d>2, if 64,
d denotes the number of dimensions. / GPL-2 | GPL-3 osx-
64,
win-
32,
win-
64
r-mnp 3.1_0 Fits the Bayesian multinomial probit model via Markov chain Monte Carlo. linux-
The multinomial probit model is often used to analyze the discrete choices 64,
made by individuals recorded in survey data. Examples where the multino- osx-
mial probit model may be useful include the analysis of product choice by 64,
consumers in market research and the analysis of candidate or party choice by win-
voters in electoral studies. The MNP package can also fit the model with dif- 64
ferent choice sets for each individual, and complete or partial individual choice
orderings of the available alternatives from the choice set. The estimation is
based on the efficient marginal data augmentation algorithm that is developed
by Imai and van Dyk (2005). ‘‘A Bayesian Analysis of the Multinomial Probit
Model Using the Data Augmentation,” Journal of Econometrics, Vol. 124, No.
2 (February), pp. 311-334. <DOI:10.1016/j.jeconom.2004.02.002> Detailed
examples are given in Imai and van Dyk (2005). ‘‘MNP: R Package for Fitting
the Multinomial Probit Model.” Journal of Statistical Software, Vol. 14, No. 3
(May), pp. 1-32. <DOI:10.18637/jss.v014.i03>. / GPL-2
r-mns 1.0 An implementation of the mixed neighbourhood selection (MNS) algorithm. noarch
The MNS algorithm can be used to estimate multiple related precision ma-
trices. In particular, the motivation behind this work was driven by the need
to understand functional connectivity networks across multiple subjects. This
package also contains an implementation of a novel algorithm through which
to simulate multiple related precision matrices which exhibit properties fre-
quently reported in neuroimaging analysis. / GPL-2
r-moc 2.0 Fits and vizualize user defined finite mixture models for multivariate obser- linux-
vations using maximum likelihood. (McLachlan, G., Peel, D. (2000) Finite 64,
Mixture Models. Wiley-Interscience.) / GPL-2 osx-
64,
win-
64
r-mocca 1.3 Provides methods to analyze cluster alternatives based on multi-objective op- noarch
timization of cluster validation indices. For details see Kraus et al. (2011)
<doi:10.1007/s00180-011-0244-6>. / Artistic-2.0
r-mockery 0.4.2 The two main functionalities of this package are creating mock objects (func- noarch
tions) and selectively intercepting calls to a given function that originate in
some other function. It can be used with any testing framework available for
R. Mock objects can be injected with either this package’s own stub() function
or a similar with_mock() facility present in the ‘testthat’ package. / MIT
r-mockr 0.1 Provides a means to mock a package function, i.e., temporarily substitute it for noarch
testing. Designed as a drop-in replacement for ‘testthat::with_mock()’, which
may break in R 3.4.0 and later. / GPL-3


Name Version
r-mod 0.1.3 Creates modules inline or from a file. Modules can contain any R object and be noarch
nested. Each module have their own scope and package search path that does
not interfere with one another or the user’s working environment. / GPL-3
r-mod09nrt 0.14 Package for processing downloaded MODIS Surface reflectance Product HDF noarch
files. Specifically, MOD09 surface reflectance product files, and the asso-
ciated MOD03 geolocation files (for MODIS-TERRA). The package will
be most effective if the user installs MRTSwath (MODIS Reprojection Tool
for swath products; <https://lpdaac.usgs.gov/tools/modis_reprojection_tool_
swath>, and adds the directory with the MRTSwath executable to the default
R PATH by editing ~/.Rprofile. / GPL-2
r-modalclust 0.7 Performs Modal Clustering (MAC) including Hierarchical Modal Clustering noarch
(HMAC) along with their parallel implementation (PHMAC) over several pro-
cessors. These model-based non-parametric clustering techniques can extract
clusters in very high dimensions with arbitrary density shapes. By default clus-
tering is performed over several resolutions and the results are summarised as a
hierarchical tree. Associated plot functions are also provided. There is a pack-
age vignette that provides many examples. This version adheres to CRAN
policy of not spanning more than two child processes by default. / GPL-2
r-modcmfitr 0.1.0 Fits a modified version of the Connor-Mosimann distribution (Connor & Mosi- noarch
mann (1969)<doi:10.2307/2283728>), a Connor-Mosimann distribution or
Dirichlet distribution (e.g. Gelman, Carlin, Stern & Rubin Chapter 3.5 (2004,
<ISBN:1-58488-388-X>) to elicited quantiles of a multinomial distribution.
Code is also provided to sample from the distributions, generating inputs suit-
able for a probabilistic sensitivity analysis / Monte Carlo simulation in a deci-
sion model. / GPL-2
r-modehunt 1.0.7 Given independent and identically distributed observations X(1), . . . , X(n) noarch
from a density f, provides five methods to perform a multiscale analysis about f
as well as the necessary critical values. The first method, introduced in Duem-
bgen and Walther (2008), provides simultaneous confidence statements for the
existence and location of local increases (or decreases) of f, based on all inter-
vals I(all) spanned by any two observations X(j), X(k). The second method ap-
proximates the latter approach by using only a subset of I(all) and is therefore
computationally much more efficient, but asymptotically equivalent. Omitting
the additive correction term Gamma in either method offers another two ap-
proaches which are more powerful on small scales and less powerful on large
scales, however, not asymptotically minimax optimal anymore. Finally, the
block procedure is a compromise between adding Gamma or not, having in-
termediate power properties. The latter is again asymptotically equivalent to
the first and was introduced in Rufibach and Walther (2010). / GPL-2
r-modelgood 1.0.9 Bootstrap cross-validation for ROC, AUC and Brier score to assess and com- linux-
pare predictions of binary status responses. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-modelltest 1.0.0 An implementation of the cross-validated difference in means (CVDM) test linux-
by Desmarais and Harden (2014) <doi:10.1007/s11135-013-9884-7> (see also 64,
Harden and Desmarais, 2011 <doi:10.1177/1532440011408929>) and the osx-
cross-validated median fit (CVMF) test by Desmarais and Harden (2012) 64,
<doi:10.1093/pan/mpr042>. These tests use leave-one-out cross-validated win-
log-likelihoods to assist in selecting among model estimations. You can also 64
utilize data from Golder (2010) <doi:10.1177/0010414009341714> and Joshi
& Mason (2008) <doi:10.1177/0022343308096155> that are included to fa-
cilitate examples from real-world analysis. / GPL-3
r-modelmetrics 1.2.2 Collection of metrics for evaluating models written in C using ‘Rcpp’. / GPL linux-
(>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-modelobj 4.0 A utility library to facilitate the generalization of statistical methods built on noarch
a regression framework. Package developers can use ‘modelObj’ methods to
initiate a regression analysis without concern for the details of the regression
model and the method to be used to obtain parameter estimates. The specifics
of the regression step are left to the user to define when calling the function.
The user of a function developed within the ‘modelObj’ framework creates as
input a ‘modelObj’ that contains the model and the R methods to be used to
obtain parameter estimates and to obtain predictions. In this way, a user can
easily go from linear to non-linear models within the same package. / GPL-2
r-modelr 0.1.4 Functions for modelling that help you seamlessly integrate modelling into a linux-
pipeline of data manipulation and visualisation. / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-modeltools 0.2_22A collection of tools to deal with statistical models. The functionality is ex- linux-
perimental and the user interface is likely to change in the future. The docu- 32,
mentation is rather terse, but packages ‘coin’ and ‘party’ have some working linux-
examples. However, if you find the implemented ideas interesting we would 64,
be very interested in a discussion of this proposal. Contributions are more than noarch,
welcome! / GPL-2 osx-
64,
win-
32,
win-
64


Name Version
r- 0.1 Makes a word cloud of text, sized by the frequency of the word, and colored noarch
modelwordcloud either by user-specified colors or colored by the strength of the coefficient of
that text derived from a regression model. / LGPL-2.1
r-modes 0.7.0 Designed with a dual purpose of accurately estimating the mode (or modes) noarch
as well as characterizing the modality of data. The specific application area
includes complex or mixture distributions particularly in a big data environ-
ment. The heterogeneous nature of (big) data may require deep introspec-
tive statistical and machine learning techniques, but these statistical tools of-
ten fail when applied without first understanding the data. In small datasets,
this often isn’t a big issue, but when dealing with large scale data analysis
or big data thoroughly inspecting each dimension typically yields an O(n^n-
1) problem. As such, dealing with big data require an alternative toolkit.
This package not only identifies the mode or modes for various data types,
it also provides a programmatic way of understanding the modality (i.e. uni-
modal, bimodal, etc.) of a dataset (whether it’s big data or not). See
<http://www.sdeevi.com/modes_package> for examples and discussion. / CC
BY-NC-SA 4.0
r-modeva 1.3.2 Analyses species distribution models and evaluates their performance. It in- noarch
cludes functions for performing variation partitioning, calculating several mea-
sures of model discrimination and calibration, optimizing prediction thresh-
olds based on a number of criteria, performing multivariate environmental
similarity surface (MESS) analysis, and displaying various analytical plots.
/ GPL-3
r-modifiedmk 1.4.0 Power of non-parametric Mann-Kendall test and Spearman’s Rho test noarch
is highly influenced by serially correlated data. To address this is-
sue, trend tests may be applied on the modified versions of the
time series data by Block Bootstrapping (BBS), Prewhitening (PW)
, Trend Free Prewhitening (TFPW), Bias Corrected Prewhitening
and Variance Correction Approach by calculating effective sample
size. Mann, H. B. (1945).<doi:10.1017/CBO9781107415324.004>.
Kendall, M. (1975). Multivariate analysis. Charles Griffin&Company
Ltd,. sen, P. K. (1968).<doi:10.2307/2285891>. Önöz, B., &
Bayazit, M. (2012) <doi:10.1002/hyp.8438>. Hamed, K. H.
(2009).<doi:10.1016/j.jhydrol.2009.01.040>. Yue, S., & Wang, C. Y.
(2002) <doi:10.1029/2001WR000861>. Yue, S., Pilon, P., Phinney, B., &
Cavadias, G. (2002) <doi:10.1002/hyp.1095>. Hamed, K. H., & Ramachandra
Rao, A. (1998) <doi:10.1016/S0022-1694(97)00125-X>. Yue, S., & Wang,
C. Y. (2004) <doi:10.1023/B:WARM.0000043140.61082.60>. / AGPL-3
r-modmarg 0.9.2 Calculate predicted levels and marginal effects, using the delta method to cal- noarch
culate standard errors. This is an R-based version of the ‘margins’ command
from Stata. / GPL-3
r-modmax 1.1 The algorithms implemented here are used to detect the community structure noarch
of a network. These algorithms follow different approaches, but are all based
on the concept of modularity maximization. / GPL-2
r-modtempeff 1.5.2 Fits a Constrained Segmented Distributed Lag regression model to epidemio- noarch
logical time series of mortality, temperature, and other confounders. / GPL-3
r-modturpoint 0.1.0 Turning point method is a method proposed by Choi (1990) noarch
<doi:10.2307/2531453> to estimate 50 percent effective dose (ED50) in
the study of drug sensitivity. The method has its own advantages for that it can
provide robust ED50 estimation. This package contains the modified function
of Choi’s turning point method. / GPL-3


Name Version
r-modules 0.8.0 Provides modules as an organizational unit for source code. Modules enforce noarch
to be more rigorous when defining dependencies and have a local search path.
They can be used as a sub unit within packages or in scripts. / MIT
r-modygliani 1.0 RMSD and Internal Energy analysis of NAMD and YASARA Molecular Dy- noarch
namics output files. Allows to comparison of different dynamics per different
complexes. Input files have to be ASCII files tab separated. / MIT
r-mogavs 1.1.0 Functions for exploring the best subsets in regression with a genetic al- noarch
gorithm. The package is much faster than methods relying on com-
plete enumeration, and is suitable for data sets with large number of vari-
ables. For more information, see Sinha, Malo & Kuosmanen (2015)
<doi:10.1080/10618600.2014.899236>. / GPL-2
r-mole 1.0.1 Model for simulating language evolution in terms of cultural evo- noarch
lution (Smith & Kirby (2008) <DOI:10.1098/rstb.2008.0145>; Deacon
1997). The focus is on the emergence of argument-marking sys-
tems (Dowty (1991) <DOI:10.1353/lan.1991.0021>, Van Valin 1999,
Dryer 2002, Lestrade 2015a), i.e. noun marking (Aristar (1997)
<DOI:10.1075/sl.21.2.04ari>, Lestrade (2010) <DOI:10.7282/T3ZG6R4S>),
person indexing (Ariel 1999, Dahl (2000) <DOI:10.1075/fol.7.1.03dah>,
Bhat 2004), and word order (Dryer 2013), but extensions are foreseen.
Agents start out with a protolanguage (a language without grammar; Bicker-
ton (1981) <DOI:10.17169/langsci.b91.109>, Jackendoff 2002, Arbib (2015)
<DOI:10.1002/9781118346136.ch27>) and interact through language games
(Steels 1997). Over time, grammatical constructions emerge that may or
may not become obligatory (for which the tolerance principle is assumed;
Yang 2016). Throughout the simulation, uniformitarianism of principles
is assumed (Hopper (1987) <DOI:10.3765/bls.v13i0.1834>, Givon (1995)
<DOI:10.1075/z.74>, Croft (2000), Saffran (2001) <DOI:10.1111/1467-
8721.01243>, Heine & Kuteva 2007), in which maximal psychological valid-
ity is aimed at (Grice (1975) <DOI:10.1057/9780230005853_5>, Levelt 1989,
Gaerdenfors 2000) and language representation is usage based (Tomasello
2003, Bybee 2010). In Lestrade (2015b) <DOI:10.15496/publikation-
8640>, Lestrade (2015c) <DOI:10.1075/avt.32.08les>, and Lestrade (2016)
<DOI:10.17617/2.2248195>), which reported on the results of preliminary
versions, this package was announced as WDWTW (for who does what to
whom), but for reasons of pronunciation and generalization the title was
changed. / GPL-2
r-momentchi2 0.1.5 A collection of moment-matching methods for computing the cumulative noarch
distribution function of a positively-weighted sum of chi-squared random
variables. Methods include the Satterthwaite-Welch method, Hall-Buckley-
Eagleson method, Wood’s F method, and the Lindsay-Pilla-Basak method. /
GPL-2 | GPL-3
r-moments 0.14 Functions to calculate: moments, Pearson’s kurtosis, Geary’s kurtosis and noarch
skewness; tests related to them (Anscombe-Glynn, D’Agostino, Bonett-Seier).
/ GPL-2


Name Version
r-momtrunc 4.51 It computes the raw moments for the truncated and folded multivariate nor- noarch
mal, Skew-normal (SN), Extended skew normal (ESN) and Student’s t-
distribution. It also offers specific functions to compute the mean and variance-
covariance matrix as well as the cumulative distribution function (cdf) for
the folded normal, SN, ESN, and folded t-distribution. Density and ran-
dom deviates are offered for the ESN (SN as particular case) distribution.
Most algorithms are extensions based on Kan, R., & Robotti, C. (2017)
<doi:10.1080/10618600.2017.1322092>. / GPL-2
r-mondate 0.10.01.02
Keep track of dates in terms of months. Model dates as at close of business. noarch
Perform date arithmetic in units of months and years (multiples of months).
Allow infinite dates to model ultimate time spans. / GPL-2
r-mondrian 1.0_0 The unique function of this package allows representing in a single graph the noarch
relative occurrence and co-occurrence of events measured in a sample. As ex-
amples, the package was applied to describe the occurrence and co-occurrence
of different species of bacterial or viral symbionts infecting arthropods at the
individual level. The graphics allows determining the prevalence of each sym-
biont and the patterns of multiple infections (i.e. how different symbionts
share or not the same individual hosts). We named the package after the fa-
mous painter as the graphical output recalls Mondrian’s paintings. / GPL (>=
2.0)
r-monetdb.r 1.0.1 Allows to pull data from MonetDB into R. Includes a DBI implementation and linux-
a dplyr backend. / MPL (== 2.0) 64,
osx-
64,
win-
64
r-mongolite 2.0.1 High-performance ‘MongoDB’ client based on ‘libmongoc’ and ‘jsonlite’. In- linux-
cludes support for aggregation, indexing, map-reduce, streaming, encryption, 32,
enterprise authentication. The online user manual provides an overview of linux-
the available methods in the package: <https://jeroen.github.io/mongolite/>. / 64,
Apache License 2.0 osx-
64,
win-
32,
win-
64
r-monographar 1.2.0 Contains functions intended to facilitate the production of plant taxonomic noarch
monographs. The package includes functions to convert tables into taxo-
nomic descriptions, lists of collectors, examined specimens, and can generate a
monograph skeleton. Additionally, wrapper functions to batch the production
of phenology charts and distributional and diversity maps are also available. /
GPL-2


Name Version
r-monomvn 1.9_10Estimation of multivariate normal and student-t data of arbitrary dimension linux-
where the pattern of missing data is monotone. Through the use of parsi- 64,
monious/shrinkage regressions (plsr, pcr, lasso, ridge, etc.), where standard osx-
regressions fail, the package can handle a nearly arbitrary amount of missing 64,
data. The current version supports maximum likelihood inference and a full win-
Bayesian approach employing scale-mixtures for Gibbs sampling. Monotone 64
data augmentation extends this Bayesian approach to arbitrary missingness
patterns. A fully functional standalone interface to the Bayesian lasso (from
Park & Casella), Normal-Gamma (from Griffin & Brown), Horseshoe (from
Carvalho, Polson, & Scott), and ridge regression with model selection via Re-
versible Jump, and student-t errors (from Geweke) is also provided. / LGPL-3
r-monopoly 0.3_10Functions for fitting monotone polynomials to data. Detailed discussion of linux-
the methodologies used can be found in Murray, Mueller and Turlach (2013) 64,
<doi:10.1007/s00180-012-0390-5> and Murray, Mueller and Turlach (2016) osx-
<doi:10.1080/00949655.2016.1139582>. / GPL-2 64,
win-
64
r-monotonicity 1.3 Test for monotonicity in financial variables sorted by portfolios. It is conven- noarch
tional practice in empirical research to form portfolios of assets ranked by a
certain sort variable. A t-test is then used to consider the mean return spread
between the portfolios with the highest and lowest values of the sort variable.
Yet comparing only the average returns on the top and bottom portfolios does
not provide a sufficient way to test for a monotonic relation between expected
returns and the sort variable. This package provides nonparametric tests for
the full set of monotonic patterns by Patton, A. and Timmermann, A. (2010)
<doi:10.1016/j.jfineco.2010.06.006> and compares the proposed results with
extant alternatives such as t-tests, Bonferroni bounds, and multivariate inequal-
ity tests through empirical applications and simulations. / BSD_3_clause
r-monreg 0.1.3 Estimates monotone regression and variance functions in a nonparametric linux-
model. / GPL-2 64,
osx-
64,
win-
64
r-monte.carlo.se 0.1.0 Computes Monte Carlo standard errors for summaries of Monte Carlo out- noarch
put. Summaries and their standard errors are based on columns of Monte
Carlo simulation output. Dennis D. Boos and Jason A. Osborne (2015)
<doi:10.1111/insr.12087>. / GPL-3
r-mopsocd 0.5.1 A multi-objective optimization solver based on particle swarm optimization noarch
with crowding distance. / GPL-2
r-morder 0.1 MOrder provide functions to check time homogeneity and order of markov noarch
chain by using chi-squared test, AIC value and BIC value. / GPL-2
r- 1.0 This package is a port of the MATLAB colourmap functions accompanying the noarch
morgenstemning paper M. Geissbuehler and T. Lasser, How to display data by color schemes
compatible with red-green color perception deficiencies, Opt. Express 21,
9862-9874 (2013) to R. / GPL-3


Name Version
r-morsegen 1.2 MorseGen is a program for generating raw data based on user-specified sum- noarch
mary (descriptive) statistics. Samples based on the supplied statistics are
drawn from a normal distribution (or, in some cases, an exponential distri-
bution) and scaled to match the desired descriptive statistics. Intended uses
include creating raw data that fits desired characteristics or to replicate the
results in a published study. / GPL-2
r-mosaicdata 0.17.0Data sets from Project MOSAIC (<http://mosaic-web.org>) used to teach noarch
mathematics, statistics, computation and modeling. Funded by the NSF,
Project MOSAIC is a community of educators working to tie together as-
pects of quantitative work that students in science, technology, engineering
and mathematics will need in their professional lives, but which are usually
taught in isolation, if at all. / GPL-2
r-most 0.1.0 Provides functions similar to the ‘SAS’ macros previously provided to ac- noarch
company Collins, Dziak, and Li (2009) <DOI:10.1037/a0015826> and Dziak,
Nahum-Shani, and Collins (2012) <DOI:10.1037/a0026972>, papers which
outline practical benefits and challenges of factorial and fractional factorial ex-
periments for scientists interested in developing biological and/or behavioral
interventions, especially in the context of the multiphase optimization strat-
egy (see Collins, Kugler & Gwadz 2016) <DOI:10.1007/s10461-015-1145-
4>. The package currently contains three functions. First, RelativeCosts1()
draws a graph of the relative cost of complete and reduced factorial designs
versus other alternatives. Second, RandomAssignmentGenerator() returns a
dataframe which contains a list of random numbers that can be used to con-
veniently assign participants to conditions in an experiment with many condi-
tions. Third, FactorialPowerPlan() estimates the power, detectable effect size,
or required sample size of a factorial or fractional factorial experiment, for
main effects or interactions, given several possible choices of effect size met-
ric, and allowing pretests and clustering. / GPL-2
r-motilitylab 0.2_5 Statistics to quantify tracks of moving things (x-y-z-t data), such as cells, bac- noarch
teria or animals. Available measures include mean square displacement, con-
finement ratio, autocorrelation, straightness, turning angle, and fractal dimen-
sion. / GPL-2
r-moult 2.1.0 Functions to estimate start and duration of moult from moult data, based on noarch
models developed in Underhill and Zucchini (1988, 1990). / GPL-2
r-mountainplot 1.2 Lattice functions for drawing folded empirical cumulative distribution plots, noarch
or mountain plots. A mountain plot is similar to an empirical CDF plot, except
that the curve increases from 0 to 0.5, then decreases from 0.5 to 1 using an
inverted scale at the right side. / GPL-3
r-mozzie 0.1.0 Weekly notified dengue cases in 25 districts of Sri Lanka from 2008/ week-52 noarch
to 2014/ week-21. / CC0
r-mp 0.4.1 Multidimensional projection techniques are used to create two dimensional linux-
representations of multidimensional data sets. / GPL-3 64,
osx-
64,
win-
64


Name Version
r-mpci 1.0.7 It performs the followings Multivariate Process Capability Indices: Shahriari noarch
et al. (1995) Multivariate Capability Vector, Taam et al. (1993) Multivariate
Capability Index (MCpm), Pan and Lee (2010) proposal (NMCpm) and the
followings based on Principal Component Analysis (PCA):Wang and Chen
(1998), Xekalaki and Perakis (2002) and Wang (2005). Two datasets are in-
cluded. / GPL-2
r-mpcmp 0.1.3 A collection of functions for estimation, testing and diagnostic checking for noarch
the mean-parametrized Conway-Maxwell Poisson (COM-Poisson) regression
model of Huang (2017) <doi:10.1177/1471082X17697749>. / GPL-2
r-mpcv 1.1 Multivariate process capability analysis using the multivariate process capa- noarch
bility vector. Allows to analyze a multivariate process with both normally
and non-normally distributed and also with dependent and independent qual-
ity characteristics. / GPL (>= 2.0)
r-mpdir 0.1_16Data sets and scripts for Modeling Psychophysical Data in R (Springer). / noarch
GPL-2
r-mpe 1.0 Functions for calculating sample size and power for clinical trials with multiple noarch
(co-)primary endpoints. / LGPL-3
r-mpinet 1.0 noarch
(1) Our system provides a network-based strategies for metabolite pathway
identification.(2) The MPINet can support the identification of pathways
using Hypergeometric test based on metabolite set. (3)MPINet can sup-
port pathways from multiple databases. / GPL-2
r-mpkn 0.1.0 A matrix discrete model having the form ‘M[i1] = (I Q)*M[i]’. The calcula- noarch
tion of the values of ‘M[i]’ only for pre-selected values of ‘i’. The method
of calculation is presented in the vignette ‘Fundament’ (‘Base’). Maybe it‘s
own idea of the author of the package. A weakness is that the method gives
information only in selected steps of the process. It mainly refers to cases with
matrices that are not Markov chain. If ‘Q’ is Markov transition matrix, then
MUPkL() may be used to calculate the steady-state distribution ‘p’ for ‘p =
Q*p’. Matrix power of non integer (matrix.powerni()) gives the same results
as a mpower() from package ‘matlib’. References: Markov chains, (<https://
en.wikipedia.org/wiki/Markov_chain#Expected_number_of_visits>). Donald
R. Burleson, Ph.D. (2005), ON NON-INTEGER POWERS OF A SQUARE
MATRIX, (<http://www.blackmesapress.com/Eigenvalues.htm>). / GPL-3
r- 1.1 Computing modified profile likelihood estimates for Weibull Shape and Re- noarch
mplikelihoodwb gression Parameters. Modified likelihood estimates are provided. / GPL-2
r-mpm 1.0_22Exploratory graphical analysis of multivariate data, specifically gene expres- noarch
sion data with different projection methods: principal component analysis,
correspondence analysis, spectral map analysis. / GPL-2
r-mpmi 0.43 Uses a kernel smoothing approach to calculate Mutual Information for com- linux-
parisons between all types of variables including continuous vs continuous, 64,
continuous vs discrete and discrete vs discrete. Uses a nonparametric bias osx-
correction giving Bias Corrected Mutual Information (BCMI). Implemented 64,
efficiently in Fortran 95 with OpenMP and suited to large genomic datasets. / win-
GPL-3 64
r-mpn 0.3.0 Calculates the Most Probable Number (MPN) to quantify the concentration noarch
(density) of microbes in serial dilutions of a laboratory sample (described in
Jarvis, 2010 <doi:10.1111/j.1365-2672.2010.04792.x>). Also calculates the
Aerobic Plate Count (APC) for similar microbial enumeration experiments. /
Unlimited


Name Version
r-mppa 1.0 A procedure to test for dependence between point processes on the real line, noarch
e.g. causal dependence, correlation, inhibition or anti-correlation. The pack-
age also provides a number of utilities for plotting simultaneous point pro-
cesses, and combining p-values. / GPL-2
r-mpr 1.0.4 Package for fitting Multi-Parameter Regression (MPR) models to right- noarch
censored survival data. These are flexible parametric regression models which
extend standard models, for example, proportional hazards. / GPL-3
r-mps 2.3.0 Developed for computing the probability density function, computing the cu- noarch
mulative distribution function, computing the quantile function, random gen-
eration, and estimating the parameters of 24 G-family of statistical distri-
butions via the maximum product spacing approach introduced in <https:
//www.jstor.org/stable/2345411>. The set of families contains: beta G distri-
bution, beta exponential G distribution, beta extended G distribution, exponen-
tiated G distribution, exponentiated exponential Poisson G distribution, expo-
nentiated generalized G distribution, exponentiated Kumaraswamy G distribu-
tion, gamma type I G distribution, gamma type II G distribution, gamma uni-
form G distribution, gamma-X generated of log-logistic family of G distribu-
tion, gamma-X family of modified beta exponential G distribution, geometric
exponential Poisson G distribution, generalized beta G distribution, general-
ized transmuted G distribution, Kumaraswamy G distribution, log gamma type
I G distribution, log gamma type II G distribution, Marshall Olkin G distribu-
tion, Marshall Olkin Kumaraswamy G distribution, modified beta G distribu-
tion, odd log-logistic G distribution, truncated-exponential skew-symmetric G
distribution, and Weibull G distribution. / GPL-2
r-mpsem 0.3_6 Computational tools to represent phylogenetic signals using adapted eigenvec- linux-
tor maps. / GPL-2 64,
osx-
64,
win-
64
r-mpsychor 0.10_7Supplementary materials and datasets for the book Modern Psychometrics noarch
With R (Mair, 2018, Springer useR! series). / GPL-2
r-mpt 0.6_0 Fitting and testing multinomial processing tree (MPT) models, a class noarch
of nonlinear models for categorical data. The parameters are the
link probabilities of a tree-like graph and represent the latent cogni-
tive processing steps executed to arrive at observable response cate-
gories (Batchelder & Riefer, 1999 <doi:10.3758/bf03210812>; Erdfelder et
al., 2009 <doi:10.1027/0044-3409.217.3.108>; Riefer & Batchelder, 1988
<doi:10.1037/0033-295x.95.3.318>). / GPL-2


Name Version
r-mptinr 1.11.0Provides a user-friendly way for the analysis of multinomial processing tree linux-
(MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multino- 64,
mial modeling and the measurement of cognitive processes. Psychological osx-
Review, 95, 318-339) for single and multiple datasets. The main functions 64,
perform model fitting and model selection. Model selection can be done using win-
AIC, BIC, or the Fisher Information Approximation (FIA) a measure based 64
on the Minimum Description Length (MDL) framework. The model and re-
strictions can be specified in external files or within an R script in an intuitive
syntax or using the context-free language for MPTs. The ‘classical’ .EQN file
format for model files is also supported. Besides MPTs, this package can fit a
wide variety of other cognitive models such as SDT models (see fit.model). It
also supports multicore fitting and FIA calculation (using the snowfall pack-
age), can generate or bootstrap data for simulations, and plot predicted versus
observed data. / GPL-2
r-mpv 1.55 Most of this package consists of data sets from the textbook Introduction to noarch
Linear Regression Analysis (3rd ed), by Montgomery, Peck and Vining. Some
additional data sets and functions related to visualization of linear and non-
parametric regression results are included. / Unlimited
r-mra 2.16.11
Accomplishes mark-recapture analysis with covariates. Models avail- linux-
able include the Cormack-Jolly-Seber open population (Cormack (1972) 64,
<doi:10.2307/2556151>; Jolly (1965) <doi:10.2307/2333826>; Seber (1965) osx-
<doi:10.2307/2333827>) and Huggin’s (1989) <doi:10.2307/2336377> closed 64,
population. Link functions include logit, sine, and hazard. Model selection, win-
model averaging, plot, and simulation routines included. Open population size 64
by the Horvitz-Thompson (1959) <doi:10.2307/2280784> estimator. / GPL-3
r-mratios 1.4.0 Performs (simultaneous) inferences for ratios of linear combinations of co- noarch
efficients in the general linear model. Multiple comparisons and simulta-
neous confidence interval estimations can be performed for ratios of treat-
ment means in the normal one-way layout with homogeneous and hetero-
geneous treatment variances, according to Dilba et al. (2007) <https://cran.
r-project.org/doc/Rnews/Rnews_2007-1.pdf> and Hasler and Hothorn (2008)
<doi:10.1002/bimj.200710466>. Confidence interval estimations for ratios of
linear combinations of linear model parameters like in (multiple) slope ratio
and parallel line assays can be carried out. Moreover, it is possible to calcu-
late the sample sizes required in comparisons with a control based on relative
margins. For the simple two-sample problem, functions for a t-test for ratio-
formatted hypotheses and the corresponding confidence interval are provided
assuming homogeneous or heterogeneous group variances. / GPL-2
r-mrbayes 0.1.0 Bayesian estimation of inverse variance weighted (IVW), Burgess et al. noarch
(2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden et al. (2015)
<doi:10.1093/ije/dyv080>, summary data models for Mendelian randomiza-
tion analyses. / GPL-3
r-mrclient 3.4.3 A free, community-supported, data science tool for high performance analytics linux-
/ Proprietary 64,
win-
64
r-mrclient-mlm 3.4.3 Pre-trained machine learning models for sentiment analysis and image detec- noarch
tion / Proprietary


Name Version
r-mrclient-mml 3.4.3 Provides state-of-the-art fast, scalable machine learning algorithms and trans- linux-
forms for R / Proprietary 64,
win-
64
r-mreg 1.1 Implements the methods described in Bond S, Farewell V, 2006, Exact Like- noarch
lihood Estimation for a Negative Binomial Regression Model with Missing
Outcomes, Biometrics / GPL-3
r-mrfse 0.1 A Markov random field structure estimator that uses a penalized maximum linux-
conditional likelihood method similar to the Bayesian Information Criterion 64,
(Frondana, 2016) <doi:10.11606/T.45.2018.tde-02022018-151123>. / GPL-3 osx-
64,
win-
64
r-mri 1.0.1 It provides functions to compute the values of different modifications of the noarch
Rand and Wallace indices. The indices are used to measure the stability or
similarity of two partitions obtained on two different sets of units with a non-
empty intercept. Splitting and merging of clusters can (depends on the selected
index) have a different effect on the value of the indices. The indices are pro-
posed in Cugmas and Ferligoj (2018) <http://ibmi.mf.uni-lj.si/mz/2018/no-1/
Cugmas2018.pdf>. / GPL-2
r-mrm 1.1.6 Conditional maximum likelihood estimation via the EM algorithm and linux-
information-criterion-based model selection in binary mixed Rasch models. 64,
/ GPL-2 osx-
64,
win-
64
r-mrmre 2.0.9 Computes mutual information matrices from continuous, categorical and sur- linux-
vival variables, as well as feature selection with minimum redundancy, maxi- 64,
mum relevance (mRMR) and a new ensemble mRMR technique with DOI: N osx-
De Jay et al. (2013) <doi:10.1093/bioinformatics/btt383>. / Artistic-2.0 64,
win-
64
r-mro 0.1.1 Computes multiple correlation coefficient when the data matrix is given and linux-
tests its significance. / GPL-2 64,
win-
64
r-mrpostman 0.2.0 Multiple IMAP (Internet Message Access Protocol) commands based on the noarch
RFC 3501 manual (Crispin, 2003, <doi:10.17487/RFC3501>), its updates, and
other related documents. Besides other features, ‘mRpostman’ provides func-
tions for listing, selecting and renaming mailboxes, as well as moving, fetch-
ing, and searching for messages using several criteria. / GPL-3
r-mrqol 1.0 We can calculate directly used this package the Minimal Clinically Important noarch
Difference by applying the Anchor-based method and the Response shift effect
by applying the Then-Test method. / GPL (>= 2.0)
r-mrs 1.2.4 An implementation of the MRS algorithm for comparison across distributions, linux-
as described in Jacopo Soriano, Li Ma (2016) <doi:10.1111/rssb.12180>. The 64,
model is based on a nonparametric process taking the form of a Markov model osx-
that transitions between a null and an alternative state on a multi-resolution 64,
partition tree of the sample space. MRS effectively detects and characterizes win-
a variety of underlying differences. These differences can be visualized using 64
several plotting functions. / GPL-3


Name Version
r-mrsurv 0.2 This package contains functions, data and examples to compute a noarch
multiplicative-regression model for relative survival. / GPL-2
r-mrtsamplesize 0.1.0 Provide a sample size calculator for micro-randomized trials (MRTs) based on noarch
methodology developed in Sample Size Calculations for Micro-randomized
Trials in mHealth by Liao et al. (2016) <DOI:10.1002/sim.6847>. / GPL-2
r-ms.sev 1.0.4 Calculates ARMSS (age related multiple sclerosis severity), and both local and noarch
global MSSS (multiple sclerosis severity score). / GPL-2
r-msaface 0.1.0 The new methodology moving subset analysis provides functions to inves- noarch
tigate the effect of environmental conditions on the CO2 fertilization effect
within longterm free air carbon enrichment (FACE) experiments. In general,
the functionality is applicable to derive the influence of a third variable (forc-
ing experiment-support variable) on the relation between a dependent and an
independent variable. / GPL-3
r-msap 1.1.8 Statistical Analyses of Methylation-sensitive Amplification Polymorphism noarch
(MSAP) assays. / GPL-2
r-msar 0.3.0 Visualises multiple sequence alignments dynamically within the Shiny web noarch
application framework. / BSL-1.0
r-msbox 1.2.1 Common mass spectrometry tools described in John Roboz (2013) noarch
<doi:10.1201/b15436>. It allows checking element isotopes, calculating (iso-
tope labelled) exact monoisitopic mass, m/z values and mass accuracy, and
inspecting possible contaminant mass peaks, examining possible adducts in
electrospray ionization (ESI) and matrix-assisted laser desorption ionization
(MALDI) ion sources. / GPL-2
r-msbp 1.4 Performs Bayesian nonparametric multiscale density estimation and mul- linux-
tiscale testing of group differences with multiscale Bernstein polynomials 64,
(msBP) mixtures as in Canale and Dunson (2016). / GPL-2 osx-
64,
win-
64
r-mscombine 1.4 Find common entities detected in both positive and negative ionization mode, noarch
delete this entity in the less sensible mode and combine both matrices. / GPL-2
r-msda 1.0.2 Efficient procedures for computing a new Multi-Class Sparse Discriminant linux-
Analysis method that estimates all discriminant directions simultaneously. / 64,
GPL-2 osx-
64,
win-
64
r-msde 1.0.4 Implements an MCMC sampler for the posterior distribution of arbitrary time- linux-
homogeneous multivariate stochastic differential equation (SDE) models with 64,
possibly latent components. The package provides a simple entry point to inte- osx-
grate user-defined models directly with the sampler’s C code, and parallelizes 64,
large portions of the calculations when compiled with ‘OpenMP’. / GPL-3 win-
64
r-mseapca 1.0 This package provides functions for metabolite set enrichment analysis noarch
(MSEA) and principal component analysis (PCA), and converting metabolite
set list from your own csv files or KEGG’s tar.gz files to XML documents.
This package is suitable for computation of MSEA for factor loading in PCA.
/ BSD
r-msg 0.4 A companion to the Chinese book ‘‘Modern Statistical Graphics”. / GPL-3 noarch


Name Version
r-msglasso 2.1 For fitting multivariate response and multiple predictor linear regressions with linux-
an arbitrary group structure assigned on the regression coefficient matrix, us- 64,
ing the multivariate sparse group lasso and the mixed coordinate descent algo- osx-
rithm. / GPL-2 64,
win-
64
r-msgpackr 1.1 This is the library that can serialize or unserialize MessagePack format data. / noarch
BSD_2_clause
r-msgps 1.3.1 Computes the degrees of freedom of the lasso, elastic net, generalized elastic linux-
net and adaptive lasso based on the generalized path seeking algorithm. The 64,
optimal model can be selected by model selection criteria including Mallows’ osx-
Cp, bias-corrected AIC (AICc), generalized cross validation (GCV) and BIC. 64,
/ GPL-2 win-
64
r-msimcc 0.0.1 Micro simulation model to reproduce natural history of cervical can- linux-
cer and cost-effectiveness evaluation of prevention strategies. See 64,
Georgalis L, de Sanjose S, Esnaola M, Bosch F X, Diaz M (2016) osx-
<doi:10.1097/CEJ.0000000000000202> for more details. / GPL-2 64,
win-
64
r-msma 2.0 Several functions can be used to analyze multiblock multivariable data. If the noarch
input is a single matrix, then principal components analysis (PCA) is imple-
mented. If the input is a list of matrices, then multiblock PCA is implemented.
If the input is two matrices, for exploratory and objective variables, then partial
least squares (PLS) analysis is implemented. If the input is two lists of matri-
ces, for exploratory and objective variables, then multiblock PLS analysis is
implemented. Additionally, if an extra outcome variable is specified, then a
supervised version of the methods above is implemented. For each method,
sparse modeling is also incorporated. Functions for selecting the number of
components and regularized parameters are also provided. / GPL-2
r-msme 0.5.3 Functions and datasets from Hilbe, J.M., and Robinson, A.P. 2013. Methods noarch
of Statistical Model Estimation. Chapman & Hall / CRC. / GPL-3
r-msmwra 1.3 Data sets in the book entitled Multivariate Statistical Methods with R Applica- noarch
tions, H.Bulut (2018). The book will be published in Turkish and the original
name of this book will be R Uygulamalari ile Cok Degiskenli Istatistiksel Yon-
temler. / GPL-3
r-mssm 0.1.2 Provides methods to perform parameter estimation and make analysis of mul- linux-
tivariate observed outcomes through time which depends on a latent state vari- 64,
able. All methods scale well in the dimension of the observed outcomes at osx-
each time point. The package contains an implementation of a Laplace ap- 64,
proximation, particle filters like suggested by Lin, Zhang, Cheng, & Chen win-
(2005) <doi:10.1198/016214505000000349>, and the gradient and observed 64
information matrix approximation suggested by Poyiadjis, Doucet, & Singh
(2011) <doi:10.1093/biomet/asq062>. / GPL-2
r-mssqlr 1.0.0 Can be used to query data from data from Microsoft SQL Server (MSSQL, see noarch
<http://www.microsoft.com/sqlserver/> for more information). Based on the
concepts of Entity Framework, the package allows querying data from MSSQL
Database. / GPL-3


Name Version
r-mstate 0.2.11Contains functions for data preparation, descriptives, hazard estimation and linux-
prediction with Aalen-Johansen or simulation in competing risks and multi- 64,
state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>. / osx-
GPL-2 64,
win-
64
r-mstknnclust 0.1.0 Implements the MST-kNN clustering algorithm which was proposed noarch
by Inostroza-Ponta, M. (2008) <https://trove.nla.gov.au/work/28729389?
selectedversion=NBD44634158>. / GPL-2
r-mstr 1.2 Generation of response patterns under dichotomous and polytomous comput- noarch
erized multistage testing (MST) framework. It holds various item response
theory (IRT) and score-based methods to select the next module and estimate
ability levels (Magis, Yan and von Davier (2017, ISBN:978-3-319-69218-0)).
/ GPL-2
r-mstrio 10.11.1
Interface for creating data sets and extracting data through the ‘MicroStrat- noarch
egy’ REST API. Access the demo API at <https://demo.microstrategy.com/
MicroStrategyLibrary/api-docs/index.html>. / Apache License 2.0 | file LI-
CENSE
r-msu 0.0.1 Estimators for multivariate symmetrical uncertainty based on the work of Gus- noarch
tavo Sosa et al. (2016) <arXiv:1709.08730>, total correlation, information
gain and symmetrical uncertainty of categorical variables. / GPL-3
r-mswm 1.4 Estimation, inference and diagnostics for Univariate Autoregressive Markov noarch
Switching Models for Linear and Generalized Models. Distributions for the
series include gaussian, Poisson, binomial and gamma cases. The EM algo-
rithm is used for estimation (see Perlin (2012) <doi:10.2139/ssrn.1714016>).
/ GPL (>= 2.0)
r-mtdrh 0.1.0 The Mass Transportation Distance rank histogram was developed to assess noarch
the reliability of scenarios with equal or different probabilities of occurrence
<doi:10.1002/we.1872>. / GPL-2
r-mthapower 0.1.1 Calculate Sample Size and Power for Association Studies Involving Mitochon- noarch
drial DNA Haplogroups. Based on formulae by Samuels et al. AJHG, 2006.
78(4):713-720. <DOI:10.1086/502682>. / GPL-3
r-mtlr 0.2.1 An implementation of Multi-Task Logistic Regression (MTLR) for R. This linux-
package is based on the method proposed by Yu et al. (2011) which utilized 64,
MTLR for generating individual survival curves by learning feature weights osx-
which vary across time. This model was further extended to account for left 64,
and interval censored data. / GPL-2 win-
64


Name Version
r-mts 1.0 Multivariate Time Series (MTS) is a general package for analyzing multivari- linux-
ate linear time series and estimating multivariate volatility models. It also 64,
handles factor models, constrained factor models, asymptotic principal com- osx-
ponent analysis commonly used in finance and econometrics, and principal 64,
volatility component analysis. (a) For the multivariate linear time series anal- win-
ysis, the package performs model specification, estimation, model checking, 64
and prediction for many widely used models, including vector AR models,
vector MA models, vector ARMA models, seasonal vector ARMA models,
VAR models with exogenous variables, multivariate regression models with
time series errors, augmented VAR models, and Error-correction VAR mod-
els for co-integrated time series. For model specification, the package per-
forms structural specification to overcome the difficulties of identifiability of
VARMA models. The methods used for structural specification include Kro-
necker indices and Scalar Component Models. (b) For multivariate volatility
modeling, the MTS package handles several commonly used models, includ-
ing multivariate exponentially weighted moving-average volatility, Cholesky
decomposition volatility models, dynamic conditional correlation (DCC) mod-
els, copula-based volatility models, and low-dimensional BEKK models. The
package also considers multiple tests for conditional heteroscedasticity, in-
cluding rank-based statistics. (c) Finally, the MTS package also performs
forecasting using diffusion index, transfer function analysis, Bayesian esti-
mation of VAR models, and multivariate time series analysis with missing
values.Users can also use the package to simulate VARMA models, to com-
pute impulse response functions of a fitted VARMA model, and to calculate
theoretical cross-covariance matrices of a given VARMA model. / Artistic-2.0
r-mtsys 1.2.0 Mahalanobis-Taguchi (MT) system is a collection of multivariate analysis noarch
methods developed for the field of quality engineering. MT system consists
of two families depending on their purpose. One is a family of Mahalanobis-
Taguchi (MT) methods (in the broad sense) for diagnosis (see Woodall, W. H.,
Koudelik, R., Tsui, K. L., Kim, S. B., Stoumbos, Z. G., and Carvounis, C.
P. (2003) <doi:10.1198/004017002188618626>) and the other is a family of
Taguchi (T) methods for forecasting (see Kawada, H., and Nagata, Y. (2015)
<doi:10.17929/tqs.1.12>). The MT package contains three basic methods for
the family of MT methods and one basic method for the family of T meth-
ods. The MT method (in the narrow sense), the Mahalanobis-Taguchi Adjoint
(MTA) methods, and the Recognition-Taguchi (RT) method are for the MT
method and the two-sided Taguchi (T1) method is for the family of T meth-
ods. In addition, the Ta and Tb methods, which are the improved versions of
the T1 method, are included. / MIT
r-muchpoint 0.6.1 Nonparametric approach to estimate the location of block boundaries (change- linux-
points) of non-overlapping blocks in a random symmetric matrix which 64,
consists of random variables whose distribution changes from block to osx-
block. BRAULT Vincent, OUADAH Sarah, SANSONNET Laure and LEVY- 64,
LEDUC Celine (2017) <doi:10.1016/j.jmva.2017.12.005>. / GPL-2 win-
64
r-muckrock 0.1.0 A data package containing public domain information on requests made by noarch
the ‘MuckRock’ (https://www.muckrock.com/) project under the United States
Freedom of Information Act. / Unlimited


Name Version
r-mudens 1.3.2 Compute a density estimate from a vector of right-censored survival time using linux-
kernel functions. / GPL-2 64,
osx-
64,
win-
64
r-muerelativerisk 0.1.1 Implements an estimator for relative risk based on the median unbiased esti- noarch
mator. The relative risk estimator is well defined and performs satisfactorily
for a wide range of data configurations. The details of the method are available
in Carter et al (2010) <doi:10.1111/j.1467-9876.2010.00711.x>. / GPL-3
r-muficokriging 1.2 This package builds multi-fidelity cokriging models from responses with dif- noarch
ferent levels of fidelity. Important functions : MuFicokm, predict.MuFicokm,
summary.MuFicokm. / GPL-3
r-muhaz 1.2.6.1Produces a smooth estimate of the hazard function for censored data. / GPL-3 linux-
64,
osx-
64,
win-
64
r-mullerplot 0.1.2 Generates Muller plot from parental/genealogy/phylogeny information and noarch
population/abundance/frequency dynamics data. Muller plots are plots which
combine information about succession of different OTUs (genotypes, pheno-
types, species, . . . ) and information about dynamics of their abundances (pop-
ulations or frequencies) over time. They are powerful and fascinating tools
to visualize evolutionary dynamics. They may be employed also in study of
diversity and its dynamics, i.e. how diversity emerges and how changes over
time. They are called Muller plots in honor of Hermann Joseph Muller which
used them to explain his idea of Muller’s ratchet (Muller, 1932, American Nat-
uralist). A big difference between Muller plots and normal box plots of abun-
dances is that a Muller plot depicts not only the relative abundances but also
succession of OTUs based on their genealogy/phylogeny/parental relation. In
a Muller plot, horizontal axis is time/generations and vertical axis represents
relative abundances of OTUs at the corresponding times/generations. Differ-
ent OTUs are usually shown with polygons with different colors and each OTU
originates somewhere in the middle of its parent area in order to illustrate their
succession in evolutionary process. To generate a Muller plot one needs the ge-
nealogy/phylogeny/parental relation of OTUs and their abundances over time.
MullerPlot package has the tools to generate Muller plots which clearly depict
the origin of successors of OTUs. / GPL-3
r-mulset 1.0.0 Computes efficient data distributions from highly inconsistent datasets with noarch
many missing values using multi-set intersections. Based upon hash func-
tions, ‘mulset’ can quickly identify intersections from very large matrices of
input vectors across columns and rows and thus provides scalable solution for
dealing with missing values. Tomic et al. (2019) <doi:10.1101/545186>. /
EUPL (>= 1.2)


Name Version
r-multcomp 1.4_10Simultaneous tests and confidence intervals for general linear hypotheses in linux-
parametric models, including linear, generalized linear, linear mixed effects, 32,
and survival models. The package includes demos reproducing analyzes pre- linux-
sented in the book Multiple Comparisons Using R (Bretz, Hothorn, Westfall, 64,
2010, CRC Press). / GPL-2 noarch,
osx-
64,
win-
32,
win-
64
r-multcompview 0.1_7 Convert a logical vector or a vector of p-values or a correlation, difference, noarch
or distance matrix into a display identifying the pairs for which the differ-
ences were not significantly different. Designed for use in conjunction with
the output of functions like TukeyHSD, dist{stats}, simint, simtest, csimint,
csimtest{multcomp}, friedmanmc, kruskalmc{pgirmess}. / GPL-3
r-multdm 1.0 Allows to perform the multivariate version of the Diebold-Mariano test for noarch
equal predictive ability of multiple forecast comparison. Main reference: Mar-
iano, R.S., Preve, D. (2012) <doi:10.1016/j.jeconom.2012.01.014>. / GPL-3
r-multeq 2.3 Equivalence tests and related confidence intervals for the comparison of two noarch
treatments, simultaneously for one or many normally distributed, primary re-
sponse variables (endpoints). The step-up procedure of Quan et al. (2001) is
both applied for differences and extended to ratios of means. A related single-
step procedure is also available. / GPL-3
r-multfisher 1.1 Calculates exact hypothesis tests to compare a treatment and a reference noarch
group with respect to multiple binary endpoints. The tested null hypothesis
is an identical multidimensional distribution of successes and failures in both
groups. The alternative hypothesis is a larger success proportion in the treat-
ment group in at least one endpoint. The tests are based on the multivariate
permutation distribution of subjects between the two groups. For this permu-
tation distribution, rejection regions are calculated that satisfy one of different
possible optimization criteria. In particular, regions with maximal exhaustion
of the nominal significance level, maximal power under a specified alterna-
tive or maximal number of elements can be found. Optimization is achieved
by a branch-and-bound algorithm. By application of the closed testing princi-
ple, the global hypothesis tests are extended to multiple testing procedures. /
GPL-3


Name Version
r-multiapply 2.1.1 The base apply function and its variants, as well as the related functions in noarch
the ‘plyr’ package, typically apply user-defined functions to a single argument
(or a list of vectorized arguments in the case of mapply). The ‘multiApply’
package extends this paradigm with its only function, Apply, which efficiently
applies functions taking one or a list of multiple unidimensional or multidi-
mensional arrays (or combinations thereof) as input. The input arrays can
have different numbers of dimensions as well as different dimension lengths,
and the applied function can return one or a list of unidimensional or multidi-
mensional arrays as output. This saves development time by preventing the R
user from writing often error-prone and memory-inefficient loops dealing with
multiple complex arrays. Also, a remarkable feature of Apply is the transpar-
ent use of multi-core through its parameter ‘ncores’. In contrast to the base
apply function, this package suggests the use of ‘target dimensions’ as oppo-
site to the ‘margins’ for specifying the dimensions relevant to the function to
be applied. / LGPL-3
r- 0.1_1 Efficient finite difference method for valuing European and American multi- noarch
multiassetoptions asset options. / GPL-2 | GPL-3
r-multiband 0.1.0 Algorithms for performing joint parameter estimation in astronomical survey noarch
data acquired in multiple bands. / MIT
r-multica 1.1 Implements a generalization of the Cochran-Armitage trend test to multino- noarch
mial data. In addition to an overall test, multiple testing adjusted p-values for
trend in individual outcomes and power calculation is available. / GPL-2
r-multicmp 1.1 A toolkit containing statistical analysis models motivated by multivariate noarch
forms of the Conway-Maxwell-Poisson (COM-Poisson) distribution for flex-
ible modeling of multivariate count data, especially in the presence of
data dispersion. Currently the package only supports bivariate data, via
the bivariate COM-Poisson distribution described in Sellers et al. (2016)
<doi:10.1016/j.jmva.2016.04.007>. Future development will extend the pack-
age to higher-dimensional data. / GPL-3
r-multicnvdetect 0.1_1 This package provides a tool for analysis of multiple CNV. / GPL-2 linux-
64,
osx-
64,
win-
64
r-multicoll 1.0 The detection of worrying approximate collinearity in a multiple linear regres- noarch
sion model is a problem addressed in all existing statistical packages. How-
ever, we have detected deficits regarding to the incorrect treatment of quali-
tative independent variables and the role of the intercept of the model. The
objective of this package is to correct these deficits. In this package will be
available detection and treatment techniques traditionally used as the recently
developed. D.A. Belsley (1982) <doi:10.1016/0304-4076(82)90020-3>. D.
A. Belsley (1991, ISBN: 978-0471528890). C. Garcia, R. Salmeron and C.B.
Garcia (2019) <doi:10.1080/00949655.2018.1543423>. R. Salmeron, C.B.
Garcia and J. Garcia (2018) <doi:10.1080/00949655.2018.1463376>. G.W.
Stewart (1987) <doi:10.1214/ss/1177013444>. / GPL-2


Name Version
r-multicool 0.1_10A set of tools to permute multisets without loops or hash tables and to generate linux-
integer partitions. The permutation functions are based on C code from Aaron 64,
Williams. Cool-lex order is similar to colexicographical order. The algo- osx-
rithm is described in Williams, A. (2009) <DOI:10.1145/1496770.1496877> 64,
Loopless Generation of Multiset Permutations by Prefix Shifts. Sympo- win-
sium on Discrete Algorithms, New York, United States. The permuta- 64
tion code is distributed without restrictions. The code for stable and effi-
cient computation of multinomial coefficients comes from Dave Barber. The
code can be download from <http://tamivox.org/dave/multinomial/code.html>
and is distributed without conditions. The package also generates the
integer partitions of a positive, non-zero integer n. The C code for
this is based on Python code from Jerome Kelleher which can be found
here <http://jeromekelleher.net/tag/integer-partitions.html>. The C code and
Python code are distributed without conditions. / GPL-2
r-multifit 1.0.0 Test for independence of two random vectors, learn and report the de- linux-
pendency structure. For more information, see Gorsky and Ma (2018) 64,
<arXiv:1806.06777>. / CC0 osx-
64,
win-
64
r-multifwf 0.2.2 Read a table of fixed width formatted data of different types into a data.frame noarch
for each type. / GPL-2
r-multigroup 0.4.4 Several functions are presented in order to study data in a group structure, noarch
where the same set of variables are measured on different groups of individu-
als. / GPL-3
r-multijoin 0.1.1 Wrapper around the Unix join facility which is more efficient than the built-in noarch
R routine merge(). The package enables the joining of multiple files on disk at
once. The files can be compressed and various filters can be deployed before
joining. Compiles only under Unix. / GPL-3
r-multilaterals 1.0 Computing transitive (and non-transitive) index numbers (Coelli et al., 2005 noarch
<doi:10.1007/b136381>) for cross-sections and panel data. For the calculation
of transitive indexes, the EKS (Coelli et al., 2005 <doi:10.1007/b136381>;
Rao et al., 2002 <doi:10.1007/978-1-4615-0851-9_4>) and Minimum span-
ning tree (Hill, 2004 <doi:10.1257/0002828043052178>) methods are imple-
mented. Traditional fixed-base and chained indexes, and their growth rates,
can also be derived using the Paasche, Laspeyres, Fisher and Tornqvist formu-
las. / GPL-3
r-multilevel 2.6 The functions in this package are designed to be used in the analysis of mul- noarch
tilevel data by applied psychologists. The package includes functions for esti-
mating common within-group agreement and reliability indices. The package
also contains basic data manipulation functions that facilitate the analysis of
multilevel and longitudinal data. / GPL-2
r-multinbmod 1.0 This is a likelihood approach for the regression analysis of overdispersed cor- noarch
related count data with cluster varying covariates. The approach fits a multi-
variate negative binomial model by maximum likelihood and provides robust
estimates of the regression coefficients. / GPL-2
r-multinet 3.0.3 Functions for the creation/generation and analysis of multilayer social net- linux-
works. / GPL-3 64,
osx-64


Name Version
r-multinomialci 1.1 An implementation of a method for building simultaneous confidence inter- noarch
vals for the probabilities of a multinomial distribution given a set of obser-
vations, proposed by Sison and Glaz in their paper: Sison, C.P and J. Glaz.
Simultaneous confidence intervals and sample size determination for multino-
mial proportions. Journal of the American Statistical Association, 90:366-369
(1995). The method is an R translation of the SAS code implemented by May
and Johnson in their paper: May, W.L. and W.D. Johnson. Constructing two-
sided simultaneous confidence intervals for multinomial proportions for small
counts in a large number of cells. Journal of Statistical Software 5(6) (2000).
Paper and code available at <DOI:10.18637/jss.v005.i06>. / LGPL-3
r-multiord 2.4.1 A method for multivariate ordinal data generation given marginal distribu- noarch
tions and correlation matrix based on the methodology proposed by Demirtas
(2006). / GPL-2
r- 0.2.0 Provides the Augmented Dickey-Fuller test and its variations to check noarch
multiplebubbles the existence of bubbles (explosive behavior) for time series, based on
the article by Peter C. B. Phillips, Shuping Shi and Jun Yu (2015a)
<doi:10.1111/iere.12131>. Some functions may take a while depending on
the size of the data used, or the number of Monte Carlo replications applied. /
GPL-2
r-multiplencc 1.2_1 Fit Cox proportional hazard models with a weighted partial likelihood. It han- noarch
dles one or multiple endpoints, additional matching and makes it possible to
reuse controls for other endpoints. / GPL-2
r-multiplex 2.9 Algebraic procedures for the analysis of multiple social networks are delivered noarch
with this package. Among other things, it makes possible to create and manip-
ulate multivariate network data with different formats, and there are effective
ways available to treat multiple networks with routines that combine algebraic
systems like the partially ordered semigroup or the semiring structure together
with the relational bundles occurring in different types of multivariate net-
work data sets. It also provides an algebraic approach for two-mode networks
through Galois derivations between families of the pairs of subsets in the two
domains. / GPL-3
r-multipol 1.0_7 Various utilities to manipulate multivariate polynomials. / GPL-3 noarch
r-multirdpg 1.0.1 Fits the Multiple Random Dot Product Graph Model and performs a test for noarch
whether two networks come from the same distribution. Both methods are pro-
posed in Nielsen, A.M., Witten, D., (2018) The Multiple Random Dot Product
Graph Model, arXiv preprint <arXiv:1811.12172> (Submitted to Journal of
Computational and Graphical Statistics). / GPL-2
r-multirich 2.1.1 Functions to calculate Unique Trait Combinations (UTC) and scaled Unique noarch
Trait Combinations (sUTC) as measures of multivariate richness. The pack-
age can also calculate beta-diversity for trait richness and can partition this
into nestedness-related and turnover components. The code will also calculate
several measures of overlap. / GPL-2
r-multirng 1.2.2 Pseudo-random number generation for 11 multivariate distributions: noarch
Normal, t, Uniform, Bernoulli, Hypergeometric, Beta (Dirichlet),
Multinomial, Dirichlet-Multinomial, Laplace, Wishart, and Inverted
Wishart. The details of the method are explained in Demirtas (2004)
<DOI:10.22237/jmasm/1099268340>. / GPL-2 | GPL-3


Name Version
r-multirobust 1.0.5 Multiply robust estimation for population mean (Han and noarch
Wang 2013) <doi:10.1093/biomet/ass087>, regression analysis
(Han 2014) <doi:10.1080/01621459.2014.880058> (Han 2016)
<doi:10.1111/sjos.12177> and quantile regression (Han et al. 2019)
<doi:10.1111/rssb.12309>. / GPL-2
r-multiroc 1.1.1 Tools to solve real-world problems with multiple classes classifications noarch
by computing the areas under ROC and PR curve via micro-averaging
and macro-averaging. The vignettes of this package can be found
via <https://github.com/WandeRum/multiROC>. The methodology is de-
scribed in V. Van Asch (2013) <https://www.clips.uantwerpen.be/~vincent/
pdf/microaverage.pdf> and Pedregosa et al. (2011) <http://scikit-learn.org/
stable/auto_examples/model_selection/plot_roc.html>. / GPL-3
r-multirr 1.1 Calculates bias, precision, and power for multi-level random regressions. Ran- noarch
dom regressions are types of hierarchical models in which data are structured
in groups and (regression) coefficients can vary by groups. Tools to estimate
model performance are designed mostly for scenarios where (regression) co-
efficients vary at just one level. ‘MultiRR’ provides simulation and analytical
tools (based on ‘lme4’) to study model performance for random regressions
that vary at more than one level (multi-level random regressions), allowing
researchers to determine optimal sampling designs. / GPL-2
r-multisom 1.3 Implements two versions of the algorithm namely: stochastic and batch. The noarch
package determines also the best number of clusters and offers to the user the
best clustering scheme from different results. / GPL-2
r- 1.0 The multispatial convergent cross mapping algorithm can be used as a test for linux-
multispatialccm causal associations between pairs of processes represented by time series. This 64,
is a combination of convergent cross mapping (CCM), described in Sugihara et osx-
al., 2012, Science, 338, 496-500, and dew-drop regression, described in Hsieh 64,
et al., 2008, American Naturalist, 171, 71â C“80. The algorithm allows CCM win-
to be implemented on data that are not from a single long time series. Instead, 64
data can come from many short time series, which are stitched together using
bootstrapping. / GPL-2
r-multisv 0.0_67MultiSV is an R package for identification of structural variations in multiple noarch
populations based on whole genome resequencing. It fits linear mixed model
and identifies structural variations in multiple populations using whole genome
sequencing data. It could also be manipulated to use on RNA-seq data for dif-
ferential gene expression (implementation in future releases). Main steps for
analysis include generating read depth in bins using ComputeBinCounts. con-
version of bins to MultiSV format using Bin2MultiSV. Finally, identification
of structural variations using CallMultiSV. / LGPL-3
r-multitaper 1.0_14Implements multitaper spectral analysis using discrete prolate spheroidal se- linux-
quences (Slepians) and sine tapers. It includes an adaptive weighted multitaper 64,
spectral estimate, a coherence estimate, Thomson’s Harmonic F-test, and com- osx-
plex demodulation. The Slepians sequences are generated efficiently using a 64,
tridiagonal matrix solution, and jackknifed confidence intervals are available win-
for most estimates. / GPL-2 64


Name Version
r-multivariance 2.2.0 Distance multivariance is a measure of dependence which can be used to de- linux-
tect and quantify dependence. The necessary functions are implemented in 64,
this packages, and examples are given. For the theoretic background we refer osx-
to the papers: B. Böttcher, Dependence and Dependence Structures: Estima- 64,
tion and Visualization Using Distance Multivariance. <arXiv:1712.06532>. B. win-
Böttcher, M. Keller-Ressel, R.L. Schilling, Detecting independence of random 64
vectors: generalized distance covariance and Gaussian covariance. VMSTA,
2018, Vol. 5, No. 3, 353-383. <arXiv:1711.07778>. B. Böttcher, M. Keller-
Ressel, R.L. Schilling, Distance multivariance: New dependence measures for
random vectors. <arXiv:1711.07775>. G. Berschneider, B. Böttcher, On com-
plex Gaussian random fields, Gaussian quadratic forms and sample distance
multivariance. <arXiv:1808.07280>. / GPL-3
r- 1.1.5 Models and predicts multiple output features in single random forest consid- linux-
multivariaterandomforest ering the linear relation among the output features, see details in Rahman et al 64,
(2017)<doi:10.1093/bioinformatics/btw765>. / GPL-2 osx-
64,
win-
64
r-multivarsel 1.1.3 It performs variable selection in a multivariate linear model by estimating the noarch
covariance matrix of the residuals then use it to remove the dependence that
may exist among the responses and eventually performs variable selection by
using the Lasso criterion. The method is described in the paper Perrot-Dockès
et al. (2017) <arXiv:1704.00076>. / GPL-2
r-multivator 1.1_9 A multivariate generalization of the emulator package. / GPL-2 noarch
r-multiwave 1.4 Computation of an estimation of the long-memory parameters and noarch
the long-run covariance matrix using a multivariate model (Lo-
bato (1999) <doi:10.1016/S0304-4076(98)00038-4>; Shimotsu (2007)
<doi:10.1016/j.jeconom.2006.01.003>). Two semi-parametric meth-
ods are implemented: a Fourier based approach (Shimotsu (2007)
<doi:10.1016/j.jeconom.2006.01.003>) and a wavelet based approach
(Achard and Gannaz (2016) <doi:10.1111/jtsa.12170>). / GPL-2
r-multiway 1.0_6 Fits multi-way component models via alternating least squares algorithms with noarch
optional constraints. Fit models include N-way Canonical Polyadic Decompo-
sition, Individual Differences Scaling, Multiway Covariates Regression, Paral-
lel Factor Analysis (1 and 2), Simultaneous Component Analysis, and Tucker
Factor Analysis. / GPL-2
r- 1.2 Functions to predict one multi-way array (i.e., a tensor) from an- noarch
multiwayregression other multi-way array, using a low-rank CANDECOMP/PARAFAC
(CP) factorization and a ridge (L_2) penalty [Lock, EF (2018)
<doi:10.1080/10618600.2017.1401544>]. Also includes functions to
sample from the Bayesian posterior of a tensor-on-tensor model. / GPL-3
r-multiwayvcov 1.2.3 Exports two functions implementing multi-way clustering using the method noarch
suggested by Cameron, Gelbach, & Miller (2011) and cluster (or block) boot-
strapping for estimating variance-covariance matrices. Normal one and two-
way clustering matches the results of other common statistical packages. Miss-
ing values are handled transparently and rudimentary parallelization support is
provided. / BSD_2_clause


Name Version
r-multnonparam 1.2.8 A collection of multivariate nonparametric methods, selected in part to sup- linux-
port an MS level course in nonparametric statistical methods. Methods in- 64,
clude adjustments for multiple comparisons, implementation of multivariate osx-
Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confi- 64,
dence region, some permutation tests for linear models, and some algorithms win-
for calculating exact probabilities associated with one- and two- stage testing 64
involving Mann-Whitney-Wilcoxon statistics. / GPL-2
r-multxpert 0.1 Implementation of commonly used p-value-based and parametric multiple noarch
testing procedures (computation of adjusted p-values and simultaneous con-
fidence intervals) and parallel gatekeeping procedures based on the methodol-
ogy presented in the book Multiple Testing Problems in Pharmaceutical Statis-
tics (edited by Alex Dmitrienko, Ajit C. Tamhane and Frank Bretz) published
by Chapman and Hall/CRC Press 2009. / GPL-2
r-mumin 1.43.6Tools for performing model selection and model averaging. Automated model noarch
selection through subsetting the maximum model, with optional constraints for
model inclusion. Model parameter and prediction averaging based on model
weights derived from information criteria (AICc and alike) or custom model
weighting schemes. / GPL-2
r-munsell 0.5.0 Provides easy access to, and manipulation of, the Munsell colours. Provides linux-
a mapping between Munsell’s original notation (e.g. 5R 5/10) and hexadec- 32,
imal strings suitable for use directly in R graphics. Also provides utilities to linux-
explore slices through the Munsell colour tree, to transform Munsell colours 64,
and display colour palettes. / MIT file LICENSE noarch,
osx-
64,
win-
32,
win-
64
r-murl 0.1_11Provides mailmerge methods for reading spreadsheets of addresses and other noarch
relevant information to create standardized but customizable letters. Provides
a method for mapping US ZIP codes, including those of letter recipients. Pro-
vides a method for parsing and processing html code from online job postings
of the American Political Science Association. / GPL-2
r- 0.11 Data and code for the paper by Ehm, Gneiting, Jordan and Krueger (‘Of Quan- noarch
murphydiagram tiles and Expectiles: Consistent Scoring Functions, Choquet Representations,
and Forecast Rankings’, 2015). / GPL-3
r-murty 0.3.0 Calculates k-best solutions and costs for an assignment problem following the noarch
method outlined in Murty (1968) <doi:10.1287/opre.16.3.682>. / MIT
r-mus 0.1.6 Sampling and evaluation methods to apply Monetary Unit Sampling (or in noarch
older literature Dollar Unit Sampling) during an audit of financial statements.
/ GPL-2
r-music 0.1.1 An aid for learning and using music theory. You can build chords, scales, noarch
and chord progressions using 12-note equal temperament tuning (12-ET) or
user-defined tuning. Includes functions to visualize notes on a piano using
ASCII plots in the console and to plot waveforms using base graphics. It
allows simple playback of notes and chords using the ‘audio’ package. / GPL-
3
r-mustat 1.7.0 Performs Wilcox rank sum test, Kruskal rank sum test, Friedman rank sum test noarch
and McNemar test. / GPL-2


Name Version
r-mvar 2.0.9 Package for multivariate analysis, having functions that perform simple cor- linux-
respondence analysis (CA) and multiple correspondence analysis (MCA), 64,
principal components analysis (PCA), canonical correlation analysis (CCA), osx-
factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and 64,
quadratic discriminant analysis (QDA), hierarchical and non-hierarchical clus- win-
ter analysis, simple and multiple linear regression, multiple factor analysis 64
(MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, pro-
jection pursuit (PP), grant tour method and other useful functions for the mul-
tivariate analysis. / GPL-2
r-mvar.pt 2.0.9 Pacote para analise multivariada, tendo funcoes que executam analise de cor- linux-
respondencia simples (CA) e multipla (MCA), analise de componentes prin- 64,
cipais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), osx-
escalonamento multidimensional (MDS), analise discriminante linear (LDA) 64,
e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regres- win-
sao linear simples e multipla, analise de multiplos fatores (MFA) para dados 64
quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, projection
pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada. /
GPL-2
r-mvb 1.1 Fit log-linear model for multivariate Bernoulli distribution with mixed effect linux-
models and LASSO / GPL (>= 2.0) 64,
osx-
64,
win-
64
r-mvbinary 1.1 Modelling Multivariate Binary Data with Blocks of Specific One-Factor Dis- noarch
tribution. Variables are grouped into independent blocks. Each variable is
described by two continuous parameters (its marginal probability and its de-
pendency strength with the other block variables), and one binary parameter
(positive or negative dependency). Model selection consists in the estimation
of the repartition of the variables into blocks. It is carried out by the maximiza-
tion of the BIC criterion by a deterministic (faster) algorithm or by a stochas-
tic (more time consuming but optimal) algorithm. Tool functions facilitate the
model interpretation. / GPL-2
r-mvbutils 2.8.232
Hierarchical workspace tree, code editing and backup, easy package prep, edit- noarch
ing of packages while loaded, per-object lazy-loading, easy documentation,
macro functions, and miscellaneous utilities. Needed by debug package. /
GPL-2


Name Version
r-mvcluster 1.0 Implementation of multi-view bi-clustering algorithms. When a sample is linux-
characterized by two or more sets of input features, it creates multiple data ma- 64,
trices for the same set of examples, each corresponding to a view. For instance, osx-
individuals who are diagnosed with a disorder can be described by their clini- 64,
cal symptoms (one view) and their genomic markers (another view). Rows of win-
a data matrix correspond to examples and columns correspond to features. A 64
multi-view bi-clustering algorithm groups examples (rows) consistently across
the views and simultaneously identifies the subset of features (columns) in
each view that are associated with the row groups. This mvcluster package
includes three such methods. (1) MVSVDL1: multi-view bi-clustering based
on singular value decomposition where the left singular vectors are used to
identify row clusters and the right singular vectors are used to identify features
(columns) for each row cluster. Each singular vector is regularized by the L1
vector norm. (2) MVLRRL0: multi-view bi-clustering based on sparse low
rank representation (i.e., matrix approximation) where the decomposed com-
ponents are regularized by the so-called L0 vector norm (which is not really
a vector norm). (3) MVLRRL1: multi-view bi-clustering based on sparse low
rank representation (i.e., matrix approximation) where the decomposed com-
ponents are regularized by the L1 vector norm. / GPL-3
r-mvcwt 1.3.1 Computes the continuous wavelet transform of irregularly sampled time series. noarch
/ GPL-3
r-mvglmmrank 1.2_2 Maximum likelihood estimates are obtained via an EM algorithm with either noarch
a first-order or a fully exponential Laplace approximation. / GPL-2
r-mvisage 0.2.1 Pearson and Spearman correlation coefficients are commonly used to quantify noarch
the strength of bivariate associations of genomic variables. For example, cor-
relations of gene-level DNA copy number and gene expression measurements
may be used to assess the impact of DNA copy number changes on gene ex-
pression in tumor tissue. ‘MVisAGe’ enables users to quickly compute and vi-
sualize the correlations in order to assess the effect of regional genomic events
such as changes in DNA copy number or DNA methylation level. Please see
Walter V, Du Y, Danilova L, Hayward MC, Hayes DN, 2018. Cancer Research
<doi:10.1158/0008-5472.CAN-17-3464>. / GPL-3
r-mvlm 0.1.4 Allows a user to conduct multivariate multiple regression using analytic p- noarch
values rather than classic approximate F-tests. / GPL-2
r-mvmeta 0.4.11Collection of functions to perform fixed and random-effects multivariate and noarch
univariate meta-analysis and meta-regression. / GPL-2
r-mvmise 1.0 Offers a general framework of multivariate mixed-effects models for noarch
the joint analysis of multiple correlated outcomes with clustered data
structures and potential missingness proposed by Wang et al. (2018)
<doi:10.1093/biostatistics/kxy022>. The missingness of outcome values may
depend on the values themselves (missing not at random and non-ignorable),
or may depend on only the covariates (missing at random and ignorable), or
both. This package provides functions for two models: 1) mvMISE_b() allows
correlated outcome-specific random intercepts with a factor-analytic structure,
and 2) mvMISE_e() allows the correlated outcome-specific error terms with a
graphical lasso penalty on the error precision matrix. Both functions are mo-
tivated by the multivariate data analysis on data with clustered structures from
labelling-based quantitative proteomic studies. These models and functions
can also be applied to univariate and multivariate analyses of clustered data
with balanced or unbalanced design and no missingness. / GPL-3


Name Version
r-mvna 2.0.1 Computes the Nelson-Aalen estimator of the cumulative transition hazard for linux-
arbitrary Markov multistate models <ISBN:978-0-387-68560-1>. / MIT 64,
osx-
64,
win-
64
r-mvnbayesian 0.0.8_11
Tools of Bayesian analysis framework using the method suggested by Berger noarch
(1985) <doi:10.1007/978-1-4757-4286-2> for multivariate normal (MVN)
distribution and multivariate normal mixture (MixMVN) distribution: a) cal-
culating Bayesian posteriori of (Mix)MVN distribution; b) generating random
vectors of (Mix)MVN distribution; c) Markov chain Monte Carlo (MCMC)
for (Mix)MVN distribution. / GPL-2
r-mvnfast 0.2.5 Provides computationally efficient tools related to the multivariate normal and linux-
Student’s t distributions. The main functionalities are: simulating multivariate 64,
random vectors, evaluating multivariate normal or Student’s t densities and osx-
Mahalanobis distances. These tools are very efficient thanks to the use of C 64,
code and of the OpenMP API. / GPL (>= 2.0) win-
64
r-mvnggrad 0.1.5 Package for moving grid adjustment in plant breeding field trials. / GPL-2 noarch
r-mvnmle 0.1_11.1
Finds the maximum likelihood estimate of the mean vector and variance- linux-
covariance matrix for multivariate normal data with missing values. / GPL-2 64,
osx-
64,
win-
64
r-mvnormtest 0.1_9 Generalization of shapiro-wilk test for multivariate variables. / GPL-3 noarch
r-mvnpermute 1.0.0 Given a vector of multivariate normal data, a matrix of covariates and the data noarch
covariance matrix, generate new multivariate normal samples that have the
same covariance matrix based on permutations of the transformed data resid-
uals. / GPL (>= 3.0)
r-mvntest 1.1_0 Routines for assessing multivariate normality. Implements three Wald’s type noarch
chi-squared tests; non-parametric Anderson-Darling and Cramer-von Mises
tests; Doornik-Hansen test, Royston test and Henze-Zirkler test. / GPL-2
r-mvprobit 0.1_8 Tools for estimating multivariate probit models, calculating conditional and noarch
unconditional expectations, and calculating marginal effects on conditional
and unconditional expectations. / GPL-2
r-mvprpb 1.0.4 Computes orthant probabilities multivariate normal distribution. / noarch
BSD_3_clause
r-mvrtn 1.0 Mean, variance, and random variates for left/right truncated normal distribu- linux-
tions. / LGPL (>= 2.0, < 3) | Mozilla Public License 64,
osx-
64,
win-
64
r-mvshapirotest 1.0 This package implements the generalization of the Shapiro-Wilk test for mul- noarch
tivariate normality proposed by Villasenor-Alva and Gonzalez-Estrada (2009).
/ GPL-3


Name Version
r-mvt 0.3 Routines to perform estimation and inference under the multivariate t- linux-
distribution. Currently, the following methodologies are implemented: mul- 64,
tivariate mean and covariance estimation, hypothesis testing about the mean, osx-
equicorrelation and homogeneity of variances, the Wilson-Hilferty transfor- 64,
mation, QQ-plots with envelopes and random variate generation. Some auxil- win-
iary functions are also provided. / GPL-2 64
r-mvtmeta 1.0 This package contains functions to run fixed effects or random effects multi- noarch
variate meta-analysis. / GPL-2
r-mvtnorm 1.0_10Computes multivariate normal and t probabilities, quantiles, random deviates linux-
and densities. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-mvtsplot 1.0_1 A function for plotting multivariate time series data / GPL-2 noarch
r-mwaved 1.1.7 Computes the Wavelet deconvolution estimate of a common signal present linux-
in multiple channels that have possible different levels of blur and 64,
long memory additive error, see Kulik, Sapatinas and Wishart (2015), osx-
<doi:10.1016/j.acha.2014.04.004>. / GPL-3 64,
win-
64
r-mwlasso 1.3.1 The Moving-Window Lasso (MWLasso) method for genome-wide association noarch
studies. A window scans the design matrix. For predictors in the same window,
their coefficients estimates are smoothed. / GPL-3
r-mwridge 1.0.0 A two stage moving-window Ridge method for coefficients estimation and noarch
model prediction. In the first stage, moving-window penalty and L1 penalty
are applied. In the second stage, ridge regression is applied. / GPL-3
r-mwright 0.3.2 Implements random number generation, plotting, and estimation algorithms noarch
for the two-parameter one-sided and two-sided M-Wright (Mainardi-Wright)
family. The M-Wright distributions naturally generalize the widely used one-
sided (Airy and half-normal or half-Gaussian) and symmetric (Airy and Gaus-
sian or normal) models. These are widely studied in time-fractional differen-
tial equations. References: Cahoy and Minkabo (2017) <doi:10.3233/MAS-
170388>; Cahoy (2012) <doi:10.1007/s00180-011-0269-x>; Cahoy (2012)
<doi:10.1080/03610926.2010.543299>; Cahoy (2011); Mainardi, Mura, and
Pagnini (2010) <doi:10.1155/2010/104505>. / GPL-3
r-mwshiny 2.0.0 A simple function, mwsApp(), that runs a ‘shiny’ app spanning multiple, con- noarch
nected windows. This uses all standard ‘shiny’ conventions, and depends only
on the ‘shiny’ package. / MIT
r-mxkssd 1.1 mxkssd is a package that generates efficient balanced mixed-level k-circulant noarch
supersaturated designs by interchanging the elements of the generator vector.
The package tries to generate a supersaturated design that has EfNOD effi-
ciency more than user specified efficiency level (mef). The package also dis-
plays the progress of generation of an efficient mixed-level k-circulant design
through a progress bar. The progress of 100 per cent means that one full round
of interchange is completed. More than one full round (typically 4-5 rounds)
of interchange may be required for larger designs. / GPL-2


Name Version
r-mycobacrvr 1.0 The mycobacrvR package contains utilities to provide detailed information for noarch
B cell and T cell epitopes for predicted adhesins from various servers such
as ABCpred, Bcepred, Bimas, Propred, NetMHC and IEDB. Please refer the
URL below to download data files (data_mycobacrvR.zip) used in functions
of this package. / GPL-2
r-mycor 0.1.1 Perform correlation and linear regression test among the numeric fields in a noarch
data.frame automatically and make plots using pairs or lattice::parallelplot. /
CC0
r-myepisodes 1.1.1 Useful functions for accessing MyEpisodes feeds and episode information as noarch
well as other tv episode related actions through www.myepisodes.com / GPL-2
r-myrrixjars 1.0_2 External jars required for package ‘Myrrix’. ‘Myrrix’ is a recommendation noarch
engine. / Apache License (== 2.0)
r-n1qn1 6.0.1_3
Provides ‘Scilab’ ‘n1qn1’, or Quasi-Newton BFGS qn without constraints and linux-
‘qnbd’ or Quasi-Newton BFGS with constraints. This takes more memory 64,
than traditional L-BFGS. The n1qn1 routine is useful since it allows prespec- osx-
ification of a Hessian. If the Hessian is near enough the truth in optimiza- 64,
tion it can speed up the optimization problem. Both algorithms are described win-
in the ‘Scilab’ optimization documentation located at <http://www.scilab.org/ 64
content/download/250/1714/file/optimization_in_scilab.pdf>. / CeCILL-2
r-na.tools 0.3.1 This comprehensive toolkit provide a consistent and extensible framework for noarch
working with missing values in vectors. The companion package ‘tidyimpute’
provides similar functionality for list-like and table-like structures). Functions
exist for detection, removal, replacement, imputation, recollection, etc. of
‘NAs’. / GPL-3
r-nabor 0.5.0 An R wrapper for ‘libnabo’, an exact or approximate k nearest neighbour linux-
library which is optimised for low dimensional spaces (e.g. 3D). ‘libnabo’ 64,
has speed and space advantages over the ‘ANN’ library wrapped by package osx-
‘RANN’. ‘nabor’ includes a knn function that is designed as a drop-in replace- 64,
ment for ‘RANN’ function nn2. In addition, objects which include the k-d tree win-
search structure can be returned to speed up repeated queries of the same set 64
of target points. / BSD_3_clause
r-nada 1.6_1 Contains methods described by Dennis Helsel in his book Nondetects And noarch
Data Analysis: Statistics for Censored Environmental Data. / GPL-2
r-nadiv 2.16.0.0
Constructs (non)additive genetic relationship matrices, and their inverses, from linux-
a pedigree to be used in linear mixed effect models (A.K.A. the ‘animal 64,
model’). Also includes other functions to facilitate the use of animal mod- osx-
els. Some functions have been created to be used in conjunction with the R 64,
package ‘asreml’ for the ‘ASReml’ software, which can be obtained upon pur- win-
chase from ‘VSN’ international (<http://www.vsni.co.uk/software/asreml>). / 64
GPL-2
r-naepprimer 1.0.1 Contains a sample of the 2005 Grade 8 Mathematics data from the National noarch
Assessment of Educational Progress (NAEP). This data set is called the NAEP
Primer. / GPL-2
r-naivebayes 0.9.6 In this implementation of the Naive Bayes classifier following class condi- noarch
tional distributions are available: Bernoulli, Categorical, Gaussian, Poisson
and non-parametric representation of the class conditional density estimated
via Kernel Density Estimation. / GPL-2


Name Version
r-nam 1.7.2 Designed for association studies in nested association mapping (NAM) panels, linux-
experimental and random panels. The method is described by Xavier et al. 64,
(2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome- osx-
wide associations of multiple populations, marker quality control, population 64,
genetics analysis, genome-wide prediction, solving mixed models and finding win-
variance components through likelihood and Bayesian methods. / GPL-3 64
r-namedcapture 2019.7.30
User-friendly wrappers for named capture regular expressions. / GPL-3 noarch
r-nameneedle 1.2.4 The Needleman-Wunsch global alignment algorithm can be used to find ap- noarch
proximate matches between sample names in different data sets. See Wang et
al. (2010) <doi:10.4137/CIN.S5613>. / Apache License (== 2.0)
r-namespace 0.9.1 This package provides user-level functions to manage namespaces not linux-
(yet) available in base R: ‘registerNamespace’, ‘unregisterNames- 64,
pace’, ‘makeNamespace’, and ‘getRegisteredNamespace’ . (‘mak- osx-
eNamespaces’ is extracted from the R ‘base’ package source code: 64,
src/library/base/R/namespace.R) / GPL-2 win-
64
r-naptime 1.3.0 Provides a near drop-in replacement for base::Sys.sleep() that allows more noarch
types of input to produce delays in the execution of code and can si-
lence/prevent typical sources of error. / GPL-2
r-nardl 0.1.5 Computes the nonlinear cointegrating autoregressive distributed lag model noarch
with p lags of the dependent variables and q lags of independent variables pro-
posed by (Shin, Yu & Greenwood-Nimmo, 2014 <doi:10.1007/978-1-4899-
8008-3_9>). / GPL-3
r-nasaweather 0.1 This package contains tidied data from the ASA 2006 data expo, as well as a noarch
number of useful other related data sets. / GPL-3
r-nat.utils 0.5.1 Utility functions that may be of general interest but are specifically required noarch
by the ‘NeuroAnatomy Toolbox’ (‘nat’). Includes functions to provide a basic
make style system to update files based on timestamp information, file locking
and ‘touch’ utility. Convenience functions for working with file paths include
‘abs2rel’, ‘split_path’ and ‘common_path’. Finally there are utility functions
for working with ‘zip’ and ‘gzip’ files including integrity tests. / GPL-3
r-natural 0.9.0 Implementation of the two error variance estimation methods in high- linux-
dimensional linear models of Yu, Bien (2017) <arXiv:1712.02412>. / GPL-3 64,
osx-
64,
win-
64
r-naturalsort 0.1.3 Provides functions related to human natural ordering. It handles adjacent digits noarch
in a character sequence as a number so that natural sort function arranges a
character vector by their numbers, not digit characters. It is typically seen
when operating systems lists file names. For example, a sequence a-1.png,
a-2.png, a-10.png looks naturally ordered because 1 < 2 < 10 and natural sort
algorithm arranges so whereas general sort algorithms arrange it into a-1.png,
a-10.png, a-2.png owing to their third and fourth characters. / BSD_3_clause
r-naturesounds 1.0.1 Collection of example animal sounds for bioacoustic analysis. / GPL-2 noarch
r-nb 0.9 Estimate the effective population size of a closed population using genetic data noarch
collected from two or more data points. / GPL-2


Name Version
r-nb.mclust 1.1.1 Model-based clustering of high-dimensional non-negative data that follow noarch
Generalized Negative Binomial distribution. All functions in this package ap-
plies to either continuous or integer data. Correlation between variables are
allowed, while samples are assumed to be independent. / GPL-2
r-nbc4va 1.1 An implementation of the Naive Bayes Classifier (NBC) algorithm used noarch
for Verbal Autopsy (VA) built on code from Miasnikof et al (2015)
<DOI:10.1186/s12916-015-0521-2>. / GPL-3
r-nbclust 3.0 It provides 30 indexes for determining the optimal number of clusters in a data noarch
set and offers the best clustering scheme from different results to the user. /
GPL-2
r-nbconvertr 1.0.2 Calls the ‘Jupyter’/’IPython’ script ‘nbconvert’ to create vignettes from note- noarch
books. Those notebooks (‘.ipynb’ files) are files containing rich text, code,
and its output. Code cells can be edited and evaluated interactively. See
<http://ipython.org/notebook.html> for more information. / GPL-3
r-nbddirichlet 1.3 The Dirichlet (aka NBD-Dirichlet) model describes the purchase incidence noarch
and brand choice of consumer products. We estimate the model and summa-
rize various theoretical quantities of interest to marketing researchers. Also
provides functions for making tables that compare observed and theoretical
statistics. / GPL-3
r-ncbit 2013.03.29
making NCBI taxonomic data locally available and searchable as an R object noarch
/ GPL-2
r-ncdf4 1.16.1Provides a high-level R interface to data files written using Unidata’s netCDF linux-
library (version 4 or earlier), which are binary data files that are portable across 64,
platforms and include metadata information in addition to the data sets. Using osx-64
this package, netCDF files (either version 4 or classic version 3) can be opened
and data sets read in easily. It is also easy to create new netCDF dimensions,
variables, and files, in either version 3 or 4 format, and manipulate existing
netCDF files. This package replaces the former ncdf package, which only
worked with netcdf version 3 files. For various reasons the names of the func-
tions have had to be changed from the names in the ncdf package. The old ncdf
package is still available at the URL given below, if you need to have backward
compatibility. It should be possible to have both the ncdf and ncdf4 packages
installed simultaneously without a problem. However, the ncdf package does
not provide an interface for netcdf version 4 files. / GPL-3
r-ncdunnett 1.1.0 Computes the noncentral Dunnett’s test distribution (pdf, cdf and quantile) and noarch
generates random numbers. / GPL-2
r-ncf 1.2_8 R functions for analyzing spatial (cross-)covariance: the nonparametric (cross- noarch
)covariance function, the spline correlogram, the nonparametric phase coher-
ence function, local indicators of spatial association (LISA), (Mantel) correlo-
gram, (Partial) Mantel test. / GPL-3
r-ncg 0.1.1 Computes the noncentral gamma function: pdf, cdf, quantile function and in- noarch
verse for the noncentrality parameter. / GPL-2
r-ncopula 0.1.1 Construct and manipulate hierarchical Archimedean copulas with multivariate noarch
compound distributions. The model used is the one of Cossette et al. (2017)
<doi:10.1016/j.insmatheco.2017.06.001>. / GPL-2


Name Version
r-ncpen 1.0.0 An efficient unified nonconvex penalized estimation algorithm for Gaussian linux-
(linear), binomial Logit (logistic), Poisson, multinomial Logit, and Cox pro- 64,
portional hazard regression models. The unified algorithm is implemented osx-
based on the convex concave procedure and the algorithm can be applied to 64,
most of the existing nonconvex penalties. The algorithm also supports convex win-
penalty: least absolute shrinkage and selection operator (LASSO). Supported 64
nonconvex penalties include smoothly clipped absolute deviation (SCAD),
minimax concave penalty (MCP), truncated LASSO penalty (TLP), clipped
LASSO (CLASSO), sparse ridge (SRIDGE), modified bridge (MBRIDGE)
and modified log (MLOG). For high-dimensional data (data set with many
variables), the algorithm selects relevant variables producing a parsimonious
regression model. Kim, D., Lee, S. and Kwon, S. (2018) <arXiv:1811.05061>,
Lee, S., Kwon, S. and Kim, Y. (2016) <doi:10.1016/j.csda.2015.08.019>,
Kwon, S., Lee, S. and Kim, Y. (2015) <doi:10.1016/j.csda.2015.07.001>.
(This research is funded by Julian Virtue Professorship from Center for Ap-
plied Research at Pepperdine Graziadio Business School and the National Re-
search Foundation of Korea.) / GPL-3
r-ncvreg 3.11_1Fits regularization paths for linear regression, GLM, and Cox regression mod- linux-
els using lasso or nonconvex penalties, in particular the minimax concave 64,
penalty (MCP) and smoothly clipped absolute deviation (SCAD) penalty, with osx-
options for additional L2 penalties (the elastic net idea). Utilities for carry- 64,
ing out cross-validation as well as post-fitting visualization, summarization, win-
inference, and prediction are also provided. / GPL-3 64
r-ndp 0.1.0 An interactive presentation on the topic of normal distribution using ‘rmark- noarch
down’ and ‘shiny’ packages. It is helpful to those who want to learn normal
distribution quickly and get a hands on experience. The presentation has a
template for solving problems on normal distribution. Runtime examples are
provided in the package function as well as at <https://kartikeyastat.shinyapps.
io/NormalDistribution/>. / GPL-2
r-nearender 1.5 Performs network enrichment analysis against functional gene sets. Bench- noarch
marks networks. Renders raw gene profile matrices of dimensionality N genes
x N samples into the space of gene set (typically pathway) enrichment scores
of dimensionality N pathways x N samples. / GPL-3
r-neariso 1.0.1 Implements a path algorithm for Near-Isotonic Regression. For more details linux-
see the help files. / GPL-2 64,
osx-
64,
win-
64
r-neat 1.1.3 Includes functions and examples to compute NEAT, the Network Enrichment noarch
Analysis Test described in Signorelli et al. (2016, <DOI:10.1186/s12859-016-
1203-6>). / GPL-3
r-neatranges 0.1.0 Collapse, partition, combine, fill gaps in and expand date/time ranges. / MIT noarch
r-needs 0.0.3 A simple function for easier package loading and auto-installation. / MIT noarch
r-needy 0.2 needy is a small utility library designed to make testing function inputs less noarch
difficult. R is a dynamically typed language, but larger projects need input
checking for scalabity. needy offers a single function, require_a( ), which lets
you specify the traits an input object should have, such as class, size, numerical
properties or number of parameters, while reducing boilerplate code and aiding
debugging. / MIT


Name Version
r- 1.0 The Negative Binomial regression with mean and shape modeling and mean noarch
negbinbetabinreg and variance modeling and Beta Binomial regression with mean and dispersion
modeling. / GPL-2
r-negenes 1.0_12Estimating the number of essential genes in a genome on the basis of data linux-
from a random transposon mutagenesis experiment, through the use of a Gibbs 64,
sampler. Lamichhane et al. (2003) <doi:10.1073/pnas.1231432100>. / GPL-3 osx-
64,
win-
64
r-neighbr 1.0.2 Classification, regression, and clustering with k nearest neighbors algorithm. noarch
Implements several distance and similarity measures, covering continuous and
logical features. Outputs ranked neighbors. Most features of this package are
directly based on the PMML specification for KNN. / GPL (>= 2.1)
r-nephro 1.2 Set of functions to estimate renal function and other phenotypes of interest noarch
in nephrology based on different biomechimal traits. MDRD, CKD-EPI, and
Virga equations are compared in Pattaro (2013) <doi:10.1159/000351043>,
where the respective references are given. In addition, the software in-
cludes Stevens (2008) <doi:10.1053/j.ajkd.2007.11.018> and Cockroft (1976)
<doi:10.1159/000180580> formulas. / GPL-3
r-nestedcohort 1.1_3 Estimate hazard ratios, survival curves and attributable risks for cohorts with noarch
missing covariates, using Cox models or Kaplan-Meier estimated for strata.
This handles studies nested within cohorts, such as case-cohort studies with
stratified sampling. See http://www.r-project.org/doc/Rnews/Rnews_2008-1.
pdf / GPL-2
r-nestfs 0.9.2 Implementation of forward selection based on cross-validated linear and logis- noarch
tic regression. / GPL-2
r-netchain 0.1.0 In networks, treatments may spill over from the treated individual to his or her linux-
social contacts and outcomes may be contagious over time. Under this setting, 64,
causal inference on the collective outcome observed over all network is often osx-
of interest. We use chain graph models approximating the projection of the 64,
full longitudinal data onto the observed data to identify the causal effect of win-
the intervention on the whole outcome. Justification of such approximation is 64
demonstrated in Ogburn et al. (2018) <arXiv:1812.04990>. / GPL-3
r-netcoh 0.2 Model fitting procedures for regression with network cohesion effects, when linux-
a network connecting sample individuals is available in a regression problem. 64,
In the future, other commonly used statistical models will be added, such as osx-
gaussian graphical model. / GPL-2 64,
win-
64
r-netcomp 1.6 This package contains functions to carry out high throughput data analysis and linux-
to conduct data set comparisons. Similarity matrices from high throughput 64,
phenotypic data containing uninformative (e.g. wild type) or missing data can osx-
be calculated to report similarity of response. A suite of graph comparisons 64,
using an adjacency or correlation matrix format are included to facilitate quick win-
network analysis. / GPL-3 64
r-netdata 0.3 This package contains all data needed for Dan McFarland’s SNA R labs. / noarch
GPL-2


Name Version
r-netindices 1.4.4 Given a network (e.g. a food web), estimates several network indices. These noarch
include: Ascendency network indices, Direct and indirect dependencies, Ef-
fective measures, Environ network indices, General network indices, Path-
way analysis, Network uncertainty indices and constraint efficiencies and the
trophic level and omnivory indices of food webs. / GPL-2
r-netrankr 0.2.1 Implements methods for centrality related analyses of networks. While the linux-
package includes the possibility to build more than 20 indices, its main fo- 64,
cus lies on index-free assessment of centrality via partial rankings obtained by osx-
neighborhood-inclusion or positional dominance. These partial rankings can 64,
be analyzed with different methods, including probabilistic methods like com- win-
puting expected node ranks and relative rank probabilities (how likely is it that 64
a node is more central than another?). The methodology is described in depth
in the vignettes and in Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>. /
MIT
r-netregr 1.0.1 Regress network responses (both directed and undirected) onto covariates of noarch
interest that may be actor-, relation-, or network-valued. In addition, com-
pute principled variance estimates of the coefficients assuming that the errors
are jointly exchangeable. Missing data is accommodated. Additionally imple-
ments building and inversion of covariance matrices under joint exchangeabil-
ity, and generates random covariance matrices from this class. For more detail
on methods, see Marrs, Fosdick, and McCormick (2017) <arXiv:1701.05530>.
/ MIT
r-nets 0.9 Sparse VAR estimation based on LASSO. / GPL-3 linux-
64,
osx-
64,
win-
64
r-netsimr 0.1.0 Assists actuaries and other insurance modellers in pricing, reserving and capi- noarch
tal modelling for non-life insurance and reinsurance modelling. Provides func-
tions that help model excess levels, capping and pure Incurred but not reported
claims (pure IBNR). Includes capped mean, exposure curves and increased
limit factor curves (ILFs) for LogNormal, Gamma, Pareto, Sliced LogNormal-
Pareto and Sliced Gamma-Pareto distributions. Includes mean, probability
density function (pdf), cumulative probability function (cdf) and inverse cumu-
lative probability function for Sliced LogNormal-Pareto and Sliced Gamma-
Pareto distributions. Includes calculating pure IBNR exposure with LogNor-
mal and Gamma distribution for reporting delay. / GPL-3
r-netswan 0.1 A set of functions for studying network robustness, resilience and vulnerabil- noarch
ity. / GPL-2
r-netweaver 0.0.6 Implements various simple function utilities and flexible pipelines to generate noarch
circular images for visualizing complex genomic and network data analysis
features. / GPL-3


Name Version
r-networkd3 0.4 Creates ‘D3’ ‘JavaScript’ network, tree, dendrogram, and Sankey graphs from linux-
‘R’. / GPL (>= 3) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-networkgen 0.1.1 A network Maze generator that creates different types of network mazes. / noarch
GPL-3
r-neural 1.4.2.2RBF and MLP neural networks with graphical user interface / GPL-2 noarch
r-neuralnet 1.44.2Training of neural networks using backpropagation, resilient backpropaga- noarch
tion with (Riedmiller, 1994) or without weight backtracking (Riedmiller and
Braun, 1993) or the modified globally convergent version by Anastasiadis et al.
(2005). The package allows flexible settings through custom-choice of error
and activation function. Furthermore, the calculation of generalized weights
(Intrator O & Intrator N, 1993) is implemented. / GPL-2
r-neuroblastoma 1.0 Annotated neuroblastoma copy number profiles, a benchmark data set for noarch
change-point detection algorithms. / GPL-3
r-neurohcp 0.8.1 Downloads and reads data from Human ‘Connectome’ Project <https://db. noarch
humanconnectome.org> using Amazon Web Services (‘AWS’) ‘S3’ buckets.
/ GPL-2
r-neurosim 0.2_12The package allows users to generate fMRI time series or 4D data. Some high- linux-
level functions are created for fast data generation with only a few arguments 64,
and a diversity of functions to define activation and noise. For more advanced osx-
users it is possible to use the low-level functions and manipulate the arguments. 64,
/ GPL-2 win-
64
r-neverhpfilter 0.2_0 In the working paper titled Why You Should Never Use the Hodrick-Prescott noarch
Filter, James D. Hamilton proposes an interesting new alternative to economic
time series filtering. The neverhpfilter package provides functions for imple-
menting his solution. Hamilton (2017) <doi:10.3386/w23429>. / GPL-3
r-newdistns 2.1 Computes the probability density function, cumulative distribution function, noarch
quantile function, random numbers and measures of inference for the fol-
lowing general families of distributions (each family defined in terms of an
arbitrary cdf G): Marshall Olkin G distributions, exponentiated G distribu-
tions, beta G distributions, gamma G distributions, Kumaraswamy G distribu-
tions, generalized beta G distributions, beta extended G distributions, gamma
G distributions, gamma uniform G distributions, beta exponential G distribu-
tions, Weibull G distributions, log gamma G I distributions, log gamma G
II distributions, exponentiated generalized G distributions, exponentiated Ku-
maraswamy G distributions, geometric exponential Poisson G distributions,
truncated-exponential skew-symmetric G distributions, modified beta G distri-
butions, and exponentiated exponential Poisson G distributions. / GPL-2


r-newtestsurvrec 1.0.2 Implements the routines to compare the survival curves with recurrent events, noarch
including the estimations of survival curves. The first model is a model for
recurrent event, when the data are correlated or not correlated. It was proposed
by Wang and Chang (1999) <doi:10.2307/2669690>. In the independent case,
the survival function can be estimated by the generalization of the limit product
model of Pena (2001) <doi:10.1198/016214501753381922>. / GPL-2
r-nfactors 2.3.3.1Indices, heuristics and strategies to help determine the number of fac- noarch
tors/components to retain: 1. Acceleration factor (af with or without Paral-
lel Analysis); 2. Optimal Coordinates (noc with or without Parallel Analy-
sis); 3. Parallel analysis (components, factors and bootstrap); 4. lambda >
mean(lambda) (Kaiser, CFA and related); 5. Cattell-Nelson-Gorsuch (CNG);
6. Zoski and Jurs multiple regression (b, t and p); 7. Zoski and Jurs standard
error of the regression coeffcient (sescree); 8. Nelson R2; 9. Bartlett khi-2;
10. Anderson khi-2; 11. Lawley khi-2 and 12. Bentler-Yuan khi-2. / GPL-2
r-nfca 0.3 Numerical Formal Concept Analysis (nFCA) is a modern unsupervised learn- noarch
ing tool for analyzing general numerical data. Given input data, this R package
nFCA outputs two nFCA graphs: a H-graph and an I-graph that reveal system-
atic, hierarchical clustering and inherent structure of the data. / GPL-2
r-nfwdist 0.1.0 Density, distribution function, quantile function and random generation for noarch
the 3D Navarro, Frenk & White (NFW) profile. For details see Robotham &
Howlett (2018) <arXiv:1805.09550>. / GPL-3
r-ngram 3.0.4 An n-gram is a sequence of n words taken, in order, from a body of text. linux-
This is a collection of utilities for creating, displaying, summarizing, and bab- 64,
bling n-grams. The ‘tokenization’ and babbling are handled by very efficient osx-
C code, which can even be built as its own standalone library. The babbler is 64,
a simple Markov chain. The package also offers a vignette with complete ex- win-
ample ‘workflows’ and information about the utilities offered in the package. 64
/ BSD_2_clause
r-ngspatial 1.2_1 Provides tools for analyzing spatial data, especially non- Gaussian linux-
areal data. The current version supports the sparse restricted spa- 64,
tial regression model of Hughes and Haran (2013) <DOI:10.1111/j.1467- osx-
9868.2012.01041.x>, the centered autologistic model of Caragea and Kaiser 64,
(2009) <DOI:10.1198/jabes.2009.07032>, and the Bayesian spatial filtering win-
model of Hughes (2017) <arXiv:1706.04651>. / GPL-2 64
r-nhanes 2.1.0 Body Shape and related measurements from the US National Health and Nu- noarch
trition Examination Survey (NHANES, 1999-2004). See http://www.cdc.gov/
nchs/nhanes.htm for details. / GPL-2
r-nhds 1.0.3 The National Hospital Discharge Survey (2010) summarizes the state of pa- noarch
tients at the end of their hospital admissions. The US CDC publishes the
data in the public domain, and describes it as follows: The National Hospital
Discharge Survey (NHDS) is a continuing nationwide sample survey of short-
stay hospitals in the United States. The scope of NHDS encompasses patients
discharged from noninstitutional hospitals, exclusive of military and Depart-
ment of Veterans Affairs hospitals, located in the 50 States and the District
of Columbia. Only hospitals having six or more beds for in-patient use are
included in the survey. See <https://www.cdc.gov/nchs/nhds> for more infor-
mation. / GPL-3
r-nhldata 1.0.0 Each dataset contains scores for every game during a specific season of the noarch
NHL. / CC0


Name Version
r-nhsrdatasets 0.1.1 Free United Kingdom National Health Service (NHS) and other healthcare, or noarch
population health-related data for education and training purposes. This pack-
age currently contains a single simulated hospital dataset for teaching regres-
sion methods, with the addition of more datasets planned for future releases.
This package exists to support skills development in the NHS-R community:
<https://nhsrcommunity.com/>. / CC0
r-nice 0.4_1 Get or set UNIX priority (niceness) of running R process. / MIT linux-
64,
osx-64
r-nicherover 1.0 This package uses a probabilistic method to calculate niche regions and pair- noarch
wise niche overlap using multidimensional niche indicator data (e.g., stable
isotopes, environmental variables, etc.). The niche region is defined as the
joint probability density function of the multidimensional niche indicators at
a user-defined probability alpha (e.g., 95%). Uncertainty is accounted for in a
Bayesian framework, and the method can be extended to three or more indica-
tor dimensions. It provides directional estimates of niche overlap, accounts for
species-specific distributions in multivariate niche space, and produces unique
and consistent bivariate projections of the multivariate niche region. A forth-
coming article by Swanson et al. (Ecology, 2014) provides a detailed descrip-
tion of the methodology. See the package vignette for a worked example using
fish stable isotope data. / GPL-2
r-nightday 1.0.1.1Computes and plots the boundary between night and day. / GPL-3 noarch
r-nilde 1.1_3 Routines for enumerating all existing nonnegative integer solutions of a linear noarch
Diophantine equation. The package provides routines for solving 0-1, bounded
and unbounded knapsack problems; 0-1, bounded and unbounded subset sum
problems; additive partitioning of natural numbers; and one-dimensional bin-
packing problem. / GPL-2
r-nimble 0.8.0 A system for writing hierarchical statistical models largely compatible with linux-
‘BUGS’ and ‘JAGS’, writing nimbleFunctions to operate models and do basic 64,
R-style math, and compiling both models and nimbleFunctions via custom- osx-
generated C. ‘NIMBLE’ includes default methods for MCMC, particle filter- 64,
ing, Monte Carlo Expectation Maximization, and some other tools. The nim- win-
bleFunction system makes it easy to do things like implement new MCMC 64
samplers from R, customize the assignment of samplers to different parts of a
model from R, and compile the new samplers automatically via C alongside the
samplers ‘NIMBLE’ provides. ‘NIMBLE’ extends the ‘BUGS’/’JAGS’ lan-
guage by making it extensible: New distributions and functions can be added,
including as calls to external compiled code. Although most people think of
MCMC as the main goal of the ‘BUGS’/’JAGS’ language for writing models,
one can use ‘NIMBLE’ for writing arbitrary other kinds of model-generic al-
gorithms as well. A full User Manual is available at <https://r-nimble.org>. /
BSD_3_clause | GPL-2
r-nipals 0.5 Principal Components Analysis of a matrix using Non-linear Itera- noarch
tive Partial Least Squares with Gram-Schmidt orthogonalization of the
scores and loadings. Optimized for speed. See Andrecut (2009)
<doi:10.1089/cmb.2008.0221>. / GPL-3
r-nistnls 0.9_13Datasets for testing nonlinear regression routines. / GPL-2 noarch
r-nistunits 1.0.1 Fundamental physical constants (Quantity, Value, Uncertainty, Unit) for SI noarch
(International System of Units) and non-SI units, plus unit conversions Based
on the data from NIST (National Institute of Standards and Technology, USA)
/ GPL-3


Name Version
r-nlar 0.4.0 Client for programmatic access to the 2007 and 2012 National Lakes Assess- noarch
ment database <https://www.epa.gov/national-aquatic-resource-surveys/nla>
containing data for hundreds of lakes in the lower 48 states of the contigu-
ous US. / GPL-3
r-nlcoptim 0.6 Optimization for nonlinear objective and constraint functions. Linear or non- noarch
linear equality and inequality constraints are allowed. It accepts the input pa-
rameters as a constrained matrix. / GPL-3
r-nleqslv 3.3.2 Solve a system of nonlinear equations using a Broyden or a Newton method linux-
with a choice of global strategies such as line search and trust region. There 64,
are options for using a numerical or user supplied Jacobian, for specifying osx-
a banded numerical Jacobian and for allowing a singular or ill-conditioned 64,
Jacobian. / GPL-2 win-
64
r-nlgeocoder 0.1.3 R interface to the open location server API of ‘Publieke Diensten Op de Kaart’ noarch
(<http://www.pdok.nl>). It offers geocoding, address suggestions and lookup
of geographical objects. Included is an utility function for displaying leaflet
tiles restricted to the Netherlands. / GPL-2
r-nlirms 3.4.4 Design of non-life insurance rate-making system with a frequency and a noarch
severity component based on the a posteriori criteria. The rate-making
system is a general form of bonus-malus system introduced by Lemaire
(1995), <doi:10.1007/978-94-011-0631-3> and Frangos and Vrontos (2001),
<doi:10.2143/AST.31.1.991>. / MIT
r-nlme 3.1_139
Fit and compare Gaussian linear and nonlinear mixed-effects models. / GPL linux-
(>= 2) | file LICENCE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-nlmeode 1.1 This package combines the odesolve and nlme packages for mixed-effects noarch
modelling using differential equations. / LGPL-2.1
r-nlmeu 0.70_3nlmeU: Datasets and utility functions enhancing functionality of nlme pack- noarch
age. Datasets, functions and scripts are described in book titled ‘Linear Mixed-
Effects Models: A Step-by-Step Approach’ by Galecki and Burzykowski
(2013). Package is under development. / GPL-2
r-nlmrt 2016.3.2
Replacement for nls() tools for working with nonlinear least squares prob- noarch
lems. The calling structure is similar to, but much simpler than, that of the
nls() function. Moreover, where nls() specifically does NOT deal with small
or zero residual problems, nlmrt is quite happy to solve them. It also attempts
to be more robust in finding solutions, thereby avoiding ‘singular gradient’
messages that arise in the Gauss-Newton method within nls(). The Marquardt-
Nash approach in nlmrt generally works more reliably to get a solution, though
this may be one of a set of possibilities, and may also be statistically unsatis-
factory. Added print and summary as of August 28, 2012. / GPL-2
r-nlms 1.1 Package to select best model among several linear and nonlinear models. The noarch
main function uses the gnls() function from the ‘nlme’ package to fit the data to
nine regression models, named: linear, quadratic, cubic, logistic, exponential,
power, monod, haldane, logit. / GPL-3


Name Version
r-nloptr 1.2.1 nloptr is an R interface to NLopt. NLopt is a free/open-source library for linux-
nonlinear optimization, providing a common interface for a number of differ- 32,
ent free optimization routines available online as well as original implementa- linux-
tions of various other algorithms. See http://ab-initio.mit.edu/wiki/index.php/ 64,
NLopt_Introduction for more information on the available algorithms. Dur- osx-
ing installation on Unix the NLopt code is downloaded and compiled from the 64,
NLopt website. / LGPL-3 win-
32,
win-
64
r-nlp 0.2_0 Basic classes and methods for Natural Language Processing. / GPL-3 linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-nlroot 1.0 This is a package which can help you search for the root of a equation. / GPL-2 noarch
r-nls2 0.2 Adds brute force and multiple starting values to nls. / GPL-2 noarch
r-nlshrink 1.0.1 Non-linear shrinkage estimation of population eigenvalues and covariance ma- noarch
trices, based on publications by Ledoit and Wolf (2004, 2015, 2016). / GPL-3
r-nlsmsn 0.0_4 Fit univariate non-linear scale mixture of skew-normal(NL-SMSN) regression. noarch
/ GPL (>= 3.0)
r-nlsr 2019.9.7
Provides tools for working with nonlinear least squares problems. It is in- noarch
tended to eventually supersede the ‘nls()’ function in the R distribution. For
example, ‘nls()’ specifically does NOT deal with small or zero residual prob-
lems as its Gauss-Newton method frequently stops with ‘singular gradient’
messages. ‘nlsr’ is based on the now-deprecated package ‘nlmrt’, and has
refactored functions and R-language symbolic derivative features. / GPL-2
r-nlsrk 1.1 Performs univariate or multivariate computation of a single ODE or of a set of noarch
ODE (ordinary differential equations). / GPL-2
r-nlstools 1.0_2 Several tools for assessing the quality of fit of a gaussian nonlinear model are noarch
provided. / GPL-2
r-nlsylinks 2.0.6 Utilities and kinship information for behavior genetics and developmental noarch
research using the National Longitudinal Survey of Youth (NLSY; <http:
//www.bls.gov/nls/>). / GPL-3
r-nltm 1.4.2 Fits a non-linear transformation model (‘nltm’) for analyzing survival data, linux-
see Tsodikov (2003) <doi:10.1111/1467-9868.00414>. The class of ‘nltm’ 64,
includes the following currently supported models: Cox proportional hazard, osx-
proportional hazard cure, proportional odds, proportional hazard - proportional 64,
hazard cure, proportional hazard - proportional odds cure, Gamma frailty, and win-
proportional hazard - proportional odds. / GPL-2 64
r-nltt 1.4.1 Provides functions to calculate the normalised Lineage-Through- Time (nLTT) noarch
statistic, given two phylogenetic trees. The nLTT statistic measures the differ-
ence between two Lineage-Through-Time curves, where each curve is nor-
malised both in time and in number of lineages. / GPL-2


Name Version
r-nlwaldtest 1.1.3 Wald Test for nonlinear restrictions on model parameters and confidence in- noarch
tervals for nonlinear functions of parameters using delta-method. Applicable
after ANY model, provided parameters estimates and their covariance matrix
are available. / GPL-2
r-nmainla 0.1.2 Performs network meta-analysis using integrated nested Laplace approxima- noarch
tions (‘INLA’). Includes methods to assess the heterogeneity and inconsistency
in the network. Contains more than ten different network meta-analysis data.
‘INLA’ package can be obtained from <http://www.r-inla.org>. We recom-
mend the testing version. / GPL-2
r-nmf 0.21.0Provides a framework to perform Non-negative Matrix Factorization (NMF). linux-
The package implements a set of already published algorithms and seeding 32,
methods, and provides a framework to test, develop and plug new/custom al- linux-
gorithms. Most of the built-in algorithms have been optimized in C, and the 64,
main interface function provides an easy way of performing parallel computa- osx-
tions on multicore machines. / GPL (>= 2) 64,
win-
32,
win-
64
r-nmfgpu4r 0.2.5.2Wrapper package for the nmfgpu library, which implements several Non- linux-
negative Matrix Factorization (NMF) algorithms for CUDA platforms. By 64,
using the acceleration of GPGPU computing, the NMF can be used for real- osx-
world problems inside the R environment. All CUDA devices starting with 64,
Kepler architecture are supported by the library. / GPL-3 win-
64
r-nmfn 2.0 Non-negative Matrix Factorization / GPL-3 noarch
r-nmi 2.0 Calculates the normalized mutual information (NMI) of two community struc- noarch
tures in network analysis. / GNU General Public License version 2
r-nmof 1.6_0 Functions, examples and data from the book Numerical Methods and Opti- noarch
mization in Finance by M. Gilli, D. Maringer and E. Schumann (2011), ISBN
978-0123756626. The package provides implementations of several optimisa-
tion heuristics, such as Differential Evolution, Genetic Algorithms and Thresh-
old Accepting. There are also functions for the valuation of financial instru-
ments, such as bonds and options, and functions that help with stochastic sim-
ulations. / GPL-3
r-nmw 0.1.4 This shows how NONMEM(R) <http://www.iconplc.com/innovation/ noarch
nonmem/> software works. NONMEM’s classical estimation methods
like ‘First Order(FO) approximation’, ‘First Order Conditional Estima-
tion(FOCE)’, and ‘Laplacian approximation’ are explained. / GPL-3
r-nna 0.0.2.1Calculates spatial pattern analysis using a T-square sample procedure. This noarch
method is based on two measures x and y. x - Distance from the random point
to the nearest individual. y - Distance from individual to its nearest neighbor.
This is a methodology commonly used in phytosociology or marine benthos
ecology to analyze the species’ distribution (random, uniform or clumped pat-
terns). Ludwig & Reynolds (1988, ISBN:0471832359). / GPL-2


Name Version
r-nnet 7.3_12Software for feed-forward neural networks with a single hidden layer, and for linux-
multinomial log-linear models. / GPL-2 | GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-nnlasso 0.3 Estimates of coefficients of lasso penalized linear regression and generalized noarch
linear models subject to non-negativity constraints on the parameters using
multiplicative iterative algorithm. Entire regularization path for a sequence
of lambda values can be obtained. Functions are available for creating plots
of regularization path, cross validation and estimating coefficients at a given
lambda value. There is also provision for obtaining standard error of coeffi-
cient estimates. / GPL-2
r-nnlm 0.4.3 This is a package for Non-Negative Linear Models (NNLM). It implements linux-
fast sequential coordinate descent algorithms for non-negative linear regres- 64,
sion and non-negative matrix factorization (NMF). It supports mean square osx-
error and Kullback-Leibler divergence loss. Many other features are also im- 64,
plemented, including missing value imputation, domain knowledge integra- win-
tion, designable W and H matrices and multiple forms of regularizations. / 64
BSD_2_clause
r-nnls 1.4 An R interface to the Lawson-Hanson implementation of an algorithm for non- linux-
negative least squares (NNLS). Also allows the combination of non-negative 64,
and non-positive constraints. / GPL-2 osx-
64,
win-
64
r-nnmis 1.0.1 Imputation for both missing covariates and censored observations noarch
(optional) for survival data with missing covariates by the nearest
neighbor based multiple imputation algorithm as described in Hsu et
al. (2006) <doi:10.1002/sim.2452>, and Hsu and Yu (2018) <doi:
10.1177/0962280218772592>. Note that the current version can only
impute for a situation with one missing covariate. / LGPL-2
r-noaaoceans 0.1.0 Provides a small set of tools for collecting data from National Oceanic and noarch
Atmospheric Administration (NOAA) data sources. The functions provided
in the package are wrappers around NOAA’s existing APIs which is found at
<https://tidesandcurrents.noaa.gov/api/>. / MIT
r-nodbi 0.2.0 Simplified document database manipulation and analysis, including sup- noarch
port for many ‘NoSQL’ databases, including document databases (‘Elastic-
search’, ‘CouchDB’, ‘MongoDB’), ‘key-value’ databases (‘Redis’), and other
‘NoSQL’ types (‘etcd’). / MIT


Name Version
r-nodeharvest 0.7_3 Node harvest is a simple interpretable tree-like estimator for high-dimensional noarch
regression and classification. A few nodes are selected from an initially large
ensemble of nodes, each associated with a positive weight. New observations
can fall into one or several nodes and predictions are the weighted average
response across all these groups. The package offers visualization of the esti-
mator. Predictions can return the nodes a new observation fell into, along with
the mean response of training observations in each node, offering a simple
explanation of the prediction. / GPL-3
r-nofrills 0.3.0 Provides a compact variation of the usual syntax of function declaration, in noarch
order to support tidyverse-style quasiquotation of a function’s arguments and
body. / MIT
r-noia 0.97.1The NOIA model, as described extensively in Alvarez-Castro & Carlborg noarch
(2007), is a framework facilitating the estimation of genetic effects and
genotype-to-phenotype maps. This package provides the basic tools to per-
form linear and multilinear regressions from real populations (provided the
phenotype and the genotype of every individuals), estimating the genetic ef-
fects from different reference points, the genotypic values, and the decompo-
sition of genetic variances in a multi-locus, 2 alleles system. This package is
presented in Le Rouzic & Alvarez-Castro (2008). / GPL-2
r-noisyce2 1.0.0 Cross-Entropy optimisation of unconstrained deterministic and noisy func- noarch
tions illustrated in Rubinstein and Kroese (2004, ISBN: 978-1-4419-1940-3)
through a highly flexible and customisable function which allows user to de-
fine custom variable domains, sampling distributions, updating and smoothing
rules, and stopping criteria. Several built-in methods and settings make the
package very easy-to-use under standard optimisation problems. / GPL-2
r-nomclust 1.1.1106
Package for hierarchical clustering of objects characterized by nominal vari- noarch
ables. / GPL-2
r-nomnoml 0.1.0 A tool for drawing sassy ‘UML’ diagrams based on a simple syntax, see noarch
<http://www.nomnoml.com>. Supports styling, R Markdown and exporting
diagrams in the PNG format. / MIT
r-noncensus 0.1 A collection of various regional information determined by the U.S. Census noarch
Bureau along with demographic data. / MIT
r-noncompart 0.4.4 Conduct a noncompartmental analysis as closely as possible to the noarch
most widely used commercial software for pharmacokinetic analy-
sis, i.e. ‘Phoenix(R) WinNonlin(R)’ <https://www.certara.com/software/
pkpd-modeling-and-simulation/phoenix-winnonlin/>. Some features are 1)
Use of CDISC SDTM terms 2) Automatic slope selection with the same crite-
rion of WinNonlin(R) 3) Supporting both ‘linear-up linear-down’ and ‘linear-
up log-down’ method 4) Interval(partial) AUCs with ‘linear’ or ‘log’ inter-
polation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and
Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016.
(ISBN:9198299107). / GPL-3
r-noncompliance 0.2.2 A finite-population significance test of the ‘sharp’ causal null hypothesis thatlinux-
treatment exposure X has no effect on final outcome Y, within the principal 64,
stratum of Compliers. A generalized likelihood ratio test statistic is used, andosx-
the resulting p-value is exact. Currently, it is assumed that there are only Com-
64,
pliers and Never Takers in the population. / GPL-3 win-
64


Name Version
r-nonneg.cg 0.1.6 Minimize a differentiable function subject to all the variables being non- linux-
negative (i.e. >= 0), using a Conjugate-Gradient algorithm based on a mod- 64,
ified Polak-Ribiere-Polyak formula as described in (Li, Can, 2013, <https: osx-
//www.hindawi.com/journals/jam/2013/986317/abs/>). / BSD_2_clause 64,
win-
64
r-nonnest2 0.5_2 Testing non-nested models via theory supplied by Vuong (1989) noarch
<DOI:10.2307/1912557>. Includes tests of model distinguishability and
of model fit that can be applied to both nested and non-nested models. Also
includes functionality to obtain confidence intervals associated with AIC
and BIC. This material is partially based on work supported by the National
Science Foundation under Grant Number SES-1061334. / GPL-2 | GPL-3
r-nonnormvtdist 1.0.1 Implements calculation of probability density function, cumulative distribu- noarch
tion function, equicoordinate quantile function and survival function, and ran-
dom numbers generation for the following multivariate distributions: Lomax
(Pareto Type II), generalized Lomax, Mardia’s Pareto of Type I, Logistic,
Burr, Cook-Johnson’s uniform, F and Inverted Beta. See Tapan Nayak (1987)
<doi:10.2307/3214068>. / GPL-3
r-nonpar 1.0.1 Contains the following 5 nonparametric hypothesis tests: The Sign Test, The 2 noarch
Sample Median Test, Miller’s Jackknife Procedure, Cochran’s Q Test, & The
Stuart-Maxwell Test. / GPL-3
r-nonpareil 3.3.4 Plot, process, and analyze NPO files produced by ‘Nonpareil’ <http:// noarch
enve-omics.ce.gatech.edu/nonpareil>. / Artistic-2.0
r- 3.0 Provides tests of significance for covariates (or groups of covariates) in a fully linux-
nonpmodelcheck nonparametric regression model and a variable (or group) selection procedure 64,
based on False Discovery Rate. In addition, it provides a function for local osx-
polynomial regression for any number of dimensions, using a bandwidth spec- 64,
ified by the user or automatically chosen by cross validation or an adaptive win-
procedure. / GPL-2 64
r-nontargetdata 1.1 Data sets for isotope pattern grouping of LC-HRMS peaks with package non- noarch
target. Based on a vast set of unique PubChem molecular formulas, quantized
(a) m/z, (b) m/z differences, (c) intensity ratios and (d) marker centroids of
simulated centroid pairs are listed for different instrument resolutions. / GPL-
3
r-nopaco 1.0.6 A non-parametric test for multi-observer concordance and differences between linux-
concordances in (un)balanced data. / GPL-3 64,
osx-
64,
win-
64
r-nor1mix 1.3_0 Onedimensional Normal (i.e. Gaussian) Mixture Models Classes, for, e.g., noarch
density estimation or clustering algorithms research and teaching; providing
the widely used Marron-Wand densities. Efficient random number generation
and graphics. Fitting to data by efficient ML (Maximum Likelihood) or tradi-
tional EM estimation. / GPL-2
r-nordklimdata1 1.2 The Nordklim dataset 1.0 is a unique and useful achievement for climate anal- noarch
ysis. It includes observations of twelve different climate elements from more
than 100 stations in the Nordic region, in time span over 100 years. The project
contractors were NORDKLIM/NORDMET on behalf of the National meteo-
rological services in Denmark (DMI), Finland (FMI), Iceland (VI), Norway
(DNMI) and Sweden (SMHI). / GPL-3


Name Version
r-norm 1.0_9.5
Analysis of multivariate normal datasets with missing values / file LICENSE linux-
64,
osx-
64,
win-
64
r-norm2 2.0.2 Functions for parameter estimation, Bayesian posterior simulation and mul- linux-
tiple imputation from incomplete multivariate data under a normal model. / 64,
GPL-3 osx-
64,
win-
64
r-normalp 0.7.0.1Collection of utilities referred to Exponential Power distribution, also known noarch
as General Error Distribution (see Mineo, A.M. and Ruggieri, M. (2005), A
software Tool for the Exponential Power Distribution: The normalp package.
In Journal of Statistical Software, Vol. 12, Issue 4). / GPL-3
r-normalr 1.0.0 The robustness of many of the statistical techniques, such as factor analysis, noarch
applied in the social sciences rests upon the assumption of item-level normal-
ity. However, when dealing with real data, these assumptions are often not
met. The Box-Cox transformation (Box & Cox, 1964) <http://www.jstor.org/
stable/2984418> provides an optimal transformation for non-normal variables.
Yet, for large datasets of continuous variables, its application in current soft-
ware programs is cumbersome with analysts having to take several steps to
normalise each variable. We present an R package ‘normalr’ that enables re-
searchers to make convenient optimal transformations of multiple variables in
datasets. This R package enables users to quickly and accurately: (1) anchor
all of their variables at 1.00, (2) select the desired precision with which the
optimal lambda is estimated, (3) apply each unique exponent to its variable,
(4) rescale resultant values to within their original X1 and X(n) ranges, and (5)
provide original and transformed estimates of skewness, kurtosis, and other
inferential assessments of normality. / GPL-3
r- 0.1.0 It provides a framework and a fast and simple way for researchers to eval- noarch
normexpression uate methods (particularly some data-driven methods or their own methods)
and then select a best one for data normalization in the gene expression anal-
ysis, based on the consistency of metrics and the consistency of datasets.
Zhenfeng Wu, Weixiang Liu, Xiufeng Jin, Deshui Yu, Hua Wang, Gus-
tavo Glusman, Max Robinson, Lin Liu, Jishou Ruan and Shan Gao (2018)
<doi:10.1101/251140>. / Artistic-2.0
r-normt3 1.0_3 Evaluates the probability density function of the sum of the Gaussian and Stu- linux-
dent’s t density on 3 degrees of freedom. Evaluates the p.d.f. of the sphered 64,
Student’s t density function. Also evaluates the erf, and erfc functions on osx-
complex-valued arguments. Thanks to Krishna Myneni the function is calcu- 64,
lates the Faddeeva function also! / GPL-2 win-
64
r-normtest 1.1 Tests for the composite hypothesis of normality / GPL-3 noarch
r-normwhn.test 1.0 Includes Omnibus Univariate and Multivariate Normality Tests (See Doornik noarch
and Hansen (1994)). One variation allows for the possibility of weak depen-
dence rather than independence in the variable(s). Also included is an univari-
ate white noise test where the null hypothesis is white noise rather than strict
white noise. / GPL-3


Name Version
r-nortara 1.0.0 An implementation of a specific method for generating n-dimensional random noarch
vectors with given marginal distributions and correlation matrix. The method
uses the NORTA (NORmal To Anything) approach which generates a stan-
dard normal random vector and then transforms it into a random vector with
specified marginal distributions and the RA (Retrospective Approximation) al-
gorithm which is a generic stochastic root-finding algorithm. The marginals
can be continuous or discrete. See the vignette of package for more details. /
MIT
r-nortest 1.0_4 Five omnibus tests for testing the composite hypothesis of normality. / GPL-2 noarch
r-nortestarma 1.0.2 Tests the goodness-of-fit to the Normal distribution for the errors of an ARMA linux-
model. / GPL (> 2) 64,
osx-
64,
win-
64
r-nose 1.0 The nose package consists of a collection of three functions for classifying noarch
sparseness in typical 2 x 2 data sets with at least one cell should have zero
count. These functions are based on the three widely applied summary mea-
sures for 2 x 2 categorical data viz, Risk Difference (RD), Relative Risk (RR),
Odds Ratio (OR). This package helps to identify suitable continuity correc-
tion for zero cells when a multi centre analysis or a meta analysis is carried
out. Further, it can be considered as a tool for sensitivity analysis for adding
a continuity correction and to identify the presence of Simpson’s paradox. /
GPL-2
r-not 1.2 Provides efficient implementation of the Narrowest-Over-Threshold method- linux-
ology for detecting an unknown number of change-points occurring at 64,
unknown locations in one-dimensional data following deterministic sig- osx-
nal noise model, see R. Baranowski, Y. Chen and P. Fryzlewicz (2019) 64,
<doi:10.1111/rssb.12322>. Currently implemented scenarios are: piecewise- win-
constant signal, piecewise-constant signal with a heavy-tailed noise, 64
piecewise-linear signal, piecewise-quadratic signal, piecewise-constant signal
and with piecewise-constant variance of the noise. / GPL-2
r-notemd 0.1.0 When building a ‘shiny’ app to generate reports (pdf or ‘word’), we can insert noarch
a comment box in front-end side for user to write down them notes and use
this package to document those notes in reports. / MIT
r-notifyr 1.02 This Package provides a connection to the pushover.net API to send push no- noarch
tification to your smartphone directly from R. (ACCOUNT REQUIRED!) /
GPL-2
r-noweb 1.0_4 The noweb system for source code, implemented in R. / LGPL-2 noarch
r-nozzle.r1 1.1_1 The Nozzle package provides an API to generate HTML reports with dynamic noarch
user interface elements based on JavaScript and CSS (Cascading Style Sheets).
Nozzle was designed to facilitate summarization and rapid browsing of com-
plex results in data analysis pipelines where multiple analyses are performed
frequently on big data sets. The package can be applied to any project where
user-friendly reports need to be created. / LGPL-2


Name Version
r-np 0.60_9Nonparametric (and semiparametric) kernel methods that seamlessly handle a linux-
mix of continuous, unordered, and ordered factor data types. We would like 64,
to gratefully acknowledge support from the Natural Sciences and Engineer- osx-
ing Research Council of Canada (NSERC, <http://www.nserc-crsng.gc.ca>), 64,
the Social Sciences and Humanities Research Council of Canada (SSHRC, win-
<http://www.sshrc-crsh.gc.ca>), and the Shared Hierarchical Academic Re- 64
search Computing Network (SHARCNET, <http://www.sharcnet.ca>). / GPL-
3
r-nparcomp 3.0 With this package, it is possible to compute nonparametric simultaneous con- noarch
fidence intervals for relative contrast effects in the unbalanced one way layout.
Moreover, it computes simultaneous p-values. The simultaneous confidence
intervals can be computed using multivariate normal distribution, multivari-
ate t-distribution with a Satterthwaite Approximation of the degree of freedom
or using multivariate range preserving transformations with Logit or Probit
as transformation function. 2 sample comparisons can be performed with the
same methods described above. There is no assumption on the underlying dis-
tribution function, only that the data have to be at least ordinal numbers. See
Konietschke et al. (2015) <doi:10.18637/jss.v064.i09> for details. / GPL-3
r-nparld 2.1 The package nparLD is designed to perform nonparametric analysis of lon- noarch
gitudinal data in factorial experiments. Longitudinal data are those which
are collected from the same subjects over time, and they frequently arise in
biological sciences. Nonparametric methods do not require distributional as-
sumptions, and are applicable to a variety of data types (continuous, discrete,
purely ordinal, and dichotomous). Such methods are also robust with respect
to outliers and for small sample sizes. / GPL-2
r-nparsurv 0.1.0 Nonparametric Tests for Main Effects, Simple Effects and Interaction Effect noarch
with Censored Data and Two Factorial Influencing Variables. / GPL-2
r- 0.1 These routines create multiple imputations of missing at random categorical linux-
npbayesimputecat data, and create multiply imputed synthesis of categorical data, with or with- 64,
out structural zeros. Imputations and syntheses are based on Dirichlet process osx-
mixtures of multinomial distributions, which is a non-parametric Bayesian 64,
modeling approach that allows for flexible joint modeling. / GPL-3 win-
64
r-npcd 1.0_10An array of nonparametric and parametric estimation methods for cognitive di- noarch
agnostic models, including nonparametric classification of examinee attribute
profiles, joint maximum likelihood estimation (JMLE) of examinee attribute
profiles and item parameters, and nonparametric refinement of the Q-matrix, as
well as conditional maximum likelihood estimation (CMLE) of examinee at-
tribute profiles given item parameters and CMLE of item parameters given ex-
aminee attribute profiles. Currently the nonparametric methods in the package
support both conjunctive and disjunctive models, and the parametric methods
in the package support the DINA model, the DINO model, the NIDA model,
the G-NIDA model, and the R-RUM model. / LGPL-2.1
r-npcoptest 1.03 A non parametric test for change points detection in the dependence between linux-
the components of multivariate data, with or without (multiple) changes in the
64,
marginal distributions. The full details, justification and examples are pub-osx-
lished in Rohmer (2016) <doi:10.1016/j.spl.2016.06.026>. / GPL-3 64,
win-
64


Name Version
r-npcp 0.1_11Provides nonparametric CUSUM tests for detecting changes in possibly se- linux-
rially dependent univariate or multivariate observations. Tests sensitive to 64,
changes in the expectation, the variance, the covariance, the autocovariance, osx-
the distribution function, Spearman’s rho, Kendall’s tau, Gini’s mean differ- 64,
ence, and the copula are provided, as well as a test for detecting changes in win-
the distribution of independent block maxima (with environmental studies in 64
mind). The latest additions are a test sensitive to changes in the autocopula and
a combined test of stationarity sensitive to changes in the distribution function
and the autocopula. / GPL-3
r-npexact 0.2 Provides several novel exact hypothesis tests with minimal assumptions on the noarch
errors. The tests are exact, meaning that their p-values are correct for the given
sample sizes (the p-values are not derived from asymptotic analysis). The test
for stochastic inequality is for ordinal comparisons based on two independent
samples and requires no assumptions on the errors. The other tests include
tests for the mean and variance of a single sample and comparing means in
independent samples. All these tests only require that the data has known
bounds (such as percentages that lie in [0,100]. These bounds are part of the
input. / GPL-2
r-nphazardrate 0.1 Provides functions and examples for histogram, kernel (classical, variable noarch
bandwidth and transformations based), discrete and semiparametric hazard
rate estimators. / GPL-2
r-nplplot 4.5 This package provides routines for plotting linkage and association results noarch
along a chromosome, with marker names displayed along the top border.
There are also routines for generating BED and BedGraph custom tracks for
viewing in the UCSC genome browser. The data reformatting program Mega2
uses this package to plot output from a variety of programs. / GPL-3
r-nplr 0.1_7 Performing drug response analyses and IC50 estimations using n-Parameter noarch
logistic regression. Can also be applied to proliferation analyses. / GPL-3
r-npmlda 1.0.0 Support the book: Wu CO and Tian X (2018). Nonparametric Models for Lon- noarch
gitudinal Data. Chapman & Hall/CRC (to appear); and provide fit for using
global and local smoothing methods for the conditional-mean and conditional-
distribution based models with longitudinal Data. / GPL-2
r-npmlecmprsk 3.0 Given a failure type, the function computes covariate-specific probability of noarch
failure over time and covariate-specific conditional hazard rate based on pos-
sibly right-censored competing risk data. Specifically, it computes the non-
parametric maximum-likelihood estimates of these quantities and their asymp-
totic variances in a semi-parametric mixture model for competing-risks data,
as described in Chang et al. (2007a). / Artistic-2.0
r-npmlencc 1.0 To compute the non-parametric maximum likelihood estimates (NPMLEs) and noarch
penalized NPMLEs with SCAD, HARD and LASSO penalties for nested case-
control or case-cohort sampling design with time matching under Cox’s re-
gression model. It also proposes the standard error formula for estimator us-
ing observed profile likelihood. For details about (penalized) NPNLEs see the
original paper Penalized Full Likelihood Approach to Variable Selection for
Cox’s Regression Model under Nested Case-Control Sampling by Wang et al.
(2019) <doi:10.1007/s10985-019-09475-z>. / GPL-2
r-npmr 1.2 Fit multinomial logistic regression with a penalty on the nuclear norm noarch
of the estimated regression coefficient matrix, using proximal gradient
descent. Reference: Powers S, Hastie T and Tibshirani R (2018)
<doi:10.1177/1471082X18777669>. / GPL-2


Name Version
r-npmv 2.4.0 Performs analysis of one-way multivariate data, for small samples using noarch
Nonparametric techniques. Using approximations for ANOVA Type, Wilks’
Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package
compares the multivariate distributions for a single explanatory variable. The
comparison is also performed using a permutation test for each of the four
test statistics. The package also performs an all-subsets algorithm regarding
variables and regarding factor levels. / GPL-2
r-npmvcp 1.1 Nonparametric Multivariate Change Point Model / GPL-2 noarch
r-npordtests 1.1 Performs nonparametric tests for equality of location against ordered alterna- noarch
tives. / GPL-2
r-npp 0.2.0 Posterior sampling in several commonly used distributions using normalized noarch
power prior as described in Duan, Ye and Smith (2006) <doi:10.1002/env.752>
and Ibrahim et.al. (2015) <doi:10.1002/sim.6728>. Sampling of the power
parameter is achieved via either independence Metropolis-Hastings or random
walk Metropolis-Hastings based on transformation. / GPL-2
r-nppbib 1.1_0 Implements a nonparametric statistical test for rank or score data from noarch
partially-balanced incomplete block-design experiments. / GPL-2
r-npreg 1.0_0 Multiple and generalized nonparametric regression using smoothing spline noarch
ANOVA models and generalized additive models. Includes support for Gaus-
sian and non-Gaussian responses, smoothers for multiple types of predictors,
interactions between smoothers of mixed types, and eight different methods
for smoothing parameter selection. / GPL-2
r- 1.0_5 Implements several nonparametric regression approaches for the inclusion of linux-
nprocregression covariate information on the receiver operating characteristic (ROC) frame- 64,
work. / GPL-3 osx-
64,
win-
64
r-nps 1.1 Small functions to make working with survey data in the context of a Net noarch
Promoter programme easier. Specifically, data transformation methods, some
methods for examining the statistical properties of the NPS, such as its vari-
ance and standard errors, and some simple inferential testing procedures. Net
Promoter and NPS are registered trademarks of Bain & Company, Satmetrix
Systems and Fred Reichheld. / GPL-2
r-npsimex 0.2_1 This package contains a collection of functions to to perform nonparametric linux-
deconvolution using simulation extrapolation (SIMEX). We propose an esti- 64,
mator that adopts the SIMEX idea but bypasses the simulation step in the orig- osx-
inal SIMEX algorithm. There is no bandwidth parameter and the estimate is 64,
determined by appropriately selecting design points. See details in: Wang, win-
X.F., Sun, J. and Fan, Z. (2011). Deconvolution density estimation with het- 64
eroscedastic errors using SIMEX. / GPL-3
r-npst 2.0 Package ‘npst’ generalizes Hewitt’s (1971) test for seasonality and Rogerson’s linux-
(1996) extension based on Monte-Carlo simulation. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-nptest 1.0_0 Robust permutation tests for location, correlation, and regression problems, as noarch
described in Helwig (2019) <doi:10.1002/wics.1457>. Univariate and multi-
variate tests are supported. For each problem, exact tests and Monte Carlo
approximations are available. Parallel computing is implemented via the ‘par-
allel’ package. / GPL-2
r-nricens 1.6 Calculating the net reclassification improvement (NRI) for risk prediction noarch
models with time to event and binary data. / GPL-2
r-nscancor 0.6.1_25
Two implementations of canonical correlation analysis (CCA) that are based noarch
on iterated regression. By choosing the appropriate regression algorithm
for each data domain, it is possible to enforce sparsity, non-negativity or
other kinds of constraints on the projection vectors. Multiple canonical
variables are computed sequentially using a generalized deflation scheme,
where the additional correlation not explained by previous variables is max-
imized. ‘nscancor’ is used to analyze paired data from two domains, and
has the same interface as the ‘cancor’ function from the ‘stats’ package
(plus some extra parameters). ‘mcancor’ is appropriate for analyzing data
from three or more domains. See <http://sigg-iten.ch/learningbits/2014/01/
20/canonical-correlation-analysis-under-constraints/> and Sigg et al. (2007)
<doi:10.1109/MLSP.2007.4414315> for more details. / GPL-2
r-nscluster 1.3.1 Simulation and estimation for Neyman-Scott spatial cluster point process mod- linux-
els and their extensions, based on the methodology in Tanaka, Ogata, and 64,
Stoyan (2008) <doi:10.1002/bimj.200610339>. To estimate parameters by the osx-
simplex method, parallel computation using ‘OpenMP’ application program- 64,
ming interface is available. / GPL-2 win-
64
r-nseval 0.4 Facilities to capture, inspect, manipulate, and create lazy values (promises), linux-
. . . lists, and active calls. / GPL (>= 2.0) 64,
osx-
64,
win-
64
r-nsgp 1.0.5 A Gaussian process regression using a Gaussian kernel for both one-sample noarch
and two-sample cases. Includes non-stationary Gaussian kernel (exponential
decay function) and several likelihood ratio tests for differential testing along
target points. / GPL-2
r-nso1212 1.0.0 National Statistical Office of Mongolia (NSO) is the national statistical service noarch
and an organization of Mongolian government. NSO provides open access and
official data via its web site <http://www.1212.mn/> and API <http://opendata.
1212.mn/en/doc>. The package NSO1212 has functions for accessing the API
service. The functions are compatible with the API v2.0 and get data sets and
its detailed informations from the API. / GPL-3


Name Version
r-nsprcomp 0.5.1_2
Two methods for performing a constrained principal component analysis noarch
(PCA), where non-negativity and/or sparsity constraints are enforced on the
principal axes (PAs). The function ‘nsprcomp’ computes one principal com-
ponent (PC) after the other. Each PA is optimized such that the corre-
sponding PC has maximum additional variance not explained by the pre-
vious components. In contrast, the function ‘nscumcomp’ jointly com-
putes all PCs such that the cumulative variance is maximal. Both functions
have the same interface as the ‘prcomp’ function from the ‘stats’ package
(plus some extra parameters), and both return the result of the analysis as
an object of class ‘nsprcomp’, which inherits from ‘prcomp’. See <https:
//sigg-iten.ch/learningbits/2013/05/27/nsprcomp-is-on-cran/> and Sigg et al.
(2008) <doi:10.1145/1390156.1390277> for more details. / GPL-2
r-nsrfa 0.7_14A collection of statistical tools for objective (non-supervised) applications of linux-
the Regional Frequency Analysis methods in hydrology. The package refers to 64,
the index-value method and, more precisely, helps the hydrologist to: (1) re- osx-
gionalize the index-value; (2) form homogeneous regions with similar growth 64,
curves; (3) fit distribution functions to the empirical regional growth curves. win-
Most of the methods are those described in the Flood Estimation Handbook 64
(Centre for Ecology & Hydrology, 1999, ISBN:9781906698003). Homo-
geneity tests from Hosking and Wallis (1993) <doi:10.1029/92WR01980> and
Viglione et al. (2007) <doi:10.1029/2006WR005095> are available. / GPL-2
r-nsrr 0.1.2 Allows users to access data from the National Sleep Research Resource noarch
(‘NSRR’) <https://sleepdata.org/>. / GPL-3
r-numbers 0.7_1 Provides number-theoretic functions for factorization, prime numbers, twin noarch
primes, primitive roots, modular logarithm and inverses, extended GCD, Farey
series and continuous fractions. Includes Legendre and Jacobi symbols, some
divisor functions, Euler’s Phi function, etc. / GPL-3
r-numbersbr 0.0.2 Validate, format and compare identification numbers used in Brazil. These noarch
numbers are used to identify individuals (CPF), vehicles (RENAVAN), compa-
nies (CNPJ) and etc. Functions to format, validate and compare these numbers
have been implemented in a vectorized way in order to speed up validations
and comparisons in big datasets. / MIT
r-numderiv 2016.8_1
Methods for calculating (usually) accurate numerical first and second order linux-
derivatives. Accurate calculations are done using ‘Richardson”s’ extrapolation 32,
or, when applicable, a complex step derivative is available. A simple difference
linux-
method is also provided. Simple difference is (usually) less accurate but is 64,
much quicker than ‘Richardson”s’ extrapolation and provides a useful cross- noarch,
check. Methods are provided for real scalar and vector valued functions. / osx-
GPL-2 64,
win-
32,
win-
64


Name Version
r-numero 1.2.0 High-dimensional datasets that do not exhibit a clear intrinsic clustered struc- linux-
ture pose a challenge to conventional clustering algorithms. For this reason, 64,
we developed an unsupervised framework that helps scientists to better sub- osx-
group their datasets based on visual cues, please see Gao S, Mutter S, Casey A, 64,
Makinen V-P (2018) Numero: a statistical framework to define multivariable win-
subgroups in complex population-based datasets, Int J Epidemiology, dyy113, 64
<doi:10.1093/ije/dyy113>. The framework includes the necessary functions
to construct a self-organizing map of the data, to evaluate the statistical signif-
icance of the observed data patterns, and to visualize the results. / GPL-2
r-numform 0.5.0 Format numbers and plots for publication; includes the removal of leading noarch
zeros, standardization of number of digits, addition of affixes, and a p-value
formatter. These tools combine the functionality of several ‘base’ functions
such as ‘paste()’, ‘format()’, and ‘sprintf()’ into specific use case functions
that are named in a way that is consistent with usage, making their names easy
to remember and easy to deploy. / GPL-2
r-numgen 0.1.1 A number series generator that creates number series items based on cognitive noarch
models. / GPL-3
r-numkm 0.1.0 To add the table of numbers at risk below the Kaplan-Meier plot. / GPL-3 noarch
r-numosl 2.6 Package for optimizing regular numeric problems in optically stimulated lumi- linux-
nescence dating, such as: equivalent dose calculation, dose rate determination, 64,
growth curve fitting, decay curve decomposition, statistical age model opti- osx-
mization, and statistical plot visualization. / GPL-3 64,
win-
64
r- 1.0 This package contains the Audio Scrobbler data set used as an example in the noarch
nutshell.audioscrobbler book R in a Nutshell from O’Reilly Media. For more information about this
book, see http://shop.oreilly.com/product/0636920022008.do / CC BY-NC-SA
3.0
r-nutshell.bbdb 1.0 This package contains the baseball databank data set used as an example in noarch
the book R in a Nutshell from O’Reilly Media. For more information about
this book, see http://shop.oreilly.com/product/0636920022008.do / CC BY-
NC-ND 3.0 US
r-nvennr 0.2.1 Provides an interface for the nVenn algorithm (Perez-Silva et al. 2018) linux-
<DOI:10.1093/bioinformatics/bty109>. This algorithm works for any num- 64,
ber of sets, and usually yields pleasing and informative Venn diagrams with osx-
proportionality information. However, representing more than six sets takes 64,
a long time and is hard to interpret, unless many of the regions are empty. win-
If you cannot make sense of the result, you may want to consider ‘UpSetR’ 64
<https://cran.r-project.org/package=UpSetR/README.html>. / MIT
r-nws 1.7.0.1Provides coordination and parallel execution facilities, as well as limited cross- noarch
language data exchange, using the netWorkSpaces server developed by REvo-
lution Computing / GPL-2


Name Version
r-nycflights13 1.0.0 Airline on-time data for all flights departing NYC in 2013. Also includes linux-
useful ‘metadata’ on airlines, airports, weather, and planes. / CC0 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-nzelect 0.4.0 Convenient access to New Zealand election results by voting place. Voting noarch
places have been matched to Regional Council, Territorial Authority, and Area
Unit, to facilitate matching with additional data. Opinion polls since 2002 and
some convenience analytical function are also supplied. / GPL-3
r-nzilbb.labbcat 0.2_2 ‘LaBB-CAT’ is a web-based language corpus management system devel- noarch
oped by the New Zealand Institute of Language, Brain and Behaviour
(NZILBB) - see <https://labbcat.canterbury.ac.nz>. This package defines
functions for accessing corpus data in a ‘LaBB-CAT’ instance. You must
have at least version 20190425.1121 of ‘LaBB-CAT’ to use this package.
For more information about ‘LaBB-CAT’, see Robert Fromont and Jennifer
Hay (2008) <doi:10.3366/E1749503208000142> or Robert Fromont (2017)
<doi:10.1016/j.csl.2017.01.004>. / GPL-3
r-nzpullover 0.3.0 Datasets of driving offences and fines in New Zealand be- noarch
tween 2009 and 2017. Originally published by the New
Zealand Police at <http://www.police.govt.nz/about-us/publication/
road-policing-driver-offence-data-january-2009-december-2017>. / CC0
r-oacolors 0.0.4 Provides carefully chosen color palettes as used a.o. at OpenAnalytics <http: noarch
//www.openanalytics.eu>. / GPL-3
r-oaiharvester 0.3_0 Harvest metadata using the Open Archives Initiative Protocol for Metadata noarch
Harvesting (OAI-PMH) version 2.0 (for more information, see <http://www.
openarchives.org/OAI/openarchivesprotocol.html>). / GPL-2
r-oak 0.2.3 Functions and classes to create and manipulate trees and nodes. / MIT noarch
r-oaqc 1.0 Implements the efficient algorithm by Ortmann and Brandes (2017) linux-
<doi:10.1007/s41109-017-0027-2> to compute the orbit-aware frequency dis- 64,
tribution of induced and non-induced quads, i.e. subgraphs of size four. Given osx-
an edge matrix, data frame, or a graph object (e.g., ‘igraph’), the orbit-aware 64,
counts are computed respective each of the edges and nodes. / GPL-3 win-
64
r-oarray 1.4_9 Generalise the starting point of the array index. / GPL-3 noarch
r-objectsignals 0.10.2A mutable Signal object can report changes to its state, clients could register noarch
functions so that they are called whenever the signal is emited. The signal
could be emited, disconnected, blocked, unblocked, and buffered. / GPL-2
r-obliclus 0.9 This package conducts factor rotation techniques which intentd to identify a linux-
simple and well-clustered structure in a factor loading matrix. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-obmbpkg 1.0.0 Applies an objective Bayesian method to the Mb capture-recapture model to noarch
estimate the population size N. The Mb model is a class of capture-recapture
methods used to account for variations in capture probability due to animal
behavior. Under the Mb formulation, the initial capture of an animal may
effect the probability of subsequent captures due to their becoming trap happy
or trap shy. / GPL-3
r-obs.agree 1.0 The package includes two functions for measuring agreement. Raw Agree- noarch
ment Indices (RAI) to categorical data and Information-Based Measure of Dis-
agreement (IBMD) to continuous data. It can be used for multiple raters and
multiple readings cases. / GPL-2
r-obsmd 5.0 Implements the objective Bayesian methodology proposed in Consonni and linux-
Deldossi in order to choose the optimal experiment that better discrimi- 64,
nate between competing models. G.Consonni, L. Deldossi (2014) Objec- osx-
tive Bayesian Model Discrimination in Follow-up Experimental Designs, Test. 64,
<DOI:10.1007/s11749-015-0461-3>. / GPL-2 win-
64
r-obssens 1.3 Observational studies are limited in that there could be an unmeasured variable noarch
related to both the response variable and the primary predictor. If this unmea-
sured variable were included in the analysis it would change the relationship
(possibly changing the conclusions). Sensitivity analysis is a way to see how
much of a relationship needs to exist with the unmeasured variable before the
conclusions change. This package provides tools for doing a sensitivity analy-
sis for regression (linear, logistic, and cox) style models. / GPL-2
r-oca 0.1 Computes optimal capital allocations based on some standard principles such noarch
as Haircut, Overbeck type II and the Covariance Allocation Principle. It
also provides some shortcuts for obtaining the Value at Risk and the Ex-
pectation Shortfall, using both the normal and the t-student distribution, see
Urbina and GuillÃ©n (2014)<doi:10.1016/j.eswa.2014.05.017> and Urbina
(2013)<http://hdl.handle.net/2099.1/19443>. / GPL-2
r-occ 1.1 Generic function for estimating positron emission tomography (PET) neurore- noarch
ceptor occupancies from the total volumes of distribution of a set of regions of
interest. Fittings methods include the simple ‘reference region’ and ‘ordinary
least squares’ (sometimes known as occupancy plot) methods, as well as the
more efficient ‘restricted maximum likelihood estimation’. / GPL-3
r-oce 1.0_1 Supports the analysis of Oceanographic data, including ‘ADCP’ measure- linux-
ments, measurements made with ‘argo’ floats, ‘CTD’ measurements, sectional 32,
data, sea-level time series, coastline and topographic data, etc. Provides spe- linux-
cialized functions for calculating seawater properties such as potential tem- 64,
perature in either the ‘UNESCO’ or ‘TEOS-10’ equation of state. Produces osx-
graphical displays that conform to the conventions of the Oceanographic liter- 64,
ature. / GPL (>= 2) win-
32,
win-
64
r-ocedata 0.1.5 Several important and Oceanographic data sets are provided. These are partic- noarch
ularly useful to the ‘oce’ package, but can also be helpful in a general context.
/ GPL-2
r-ocomposition 1.1 Regression model where the response variable is a rank-indexed compositional noarch
vector (non-negative values that sum up to one and are ordered from the largest
to the smallest). Parameters are estimated in the Bayesian framework using
MCMC methods. / GPL-2


Name Version
r-ocp 0.1.1 Implements the Bayesian online changepoint detection method by Adams noarch
and MacKay (2007) <arXiv:0710.3742> for univariate or multivariate data.
Gaussian and Poisson probability models are implemented. Provides post-
processing functions with alternative ways to extract changepoints. / GPL-3
r-odata 0.6 Helper methods for accessing data from web service based on OData Proto- noarch
col. It provides several helper methods to access the service metadata, the
data from datasets and to download some file resources (it only support CSV
for now). For more information about OData go to <http://www.odata.org/
documentation/>. / GPL-2
r-odb 1.1.1 This package provides functions to create, connect, update and query HSQL noarch
databases embedded in Open Document Databases (.odb) files, as OpenOffice
and LibreOffice do. / GPL-3
r-odbc 1.1.5 A DBI-compatible interface to ODBC databases. / MIT file LICENSE linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-odds.converter 1.4.8 Conversion between the most common odds types for sports betting. Hong noarch
Kong odds, US odds, Decimal odds, Indonesian odds, Malaysian odds, and
raw Probability are covered in this package. / GPL-3
r-odds.n.ends 0.1.1 Computes odds ratios and 95% confidence intervals from a generalized lin- noarch
ear model object. It also computes model significance with the chi-squared
statistic and p-value and it computes model fit using a contingency table to
determine the percent of observations for which the model correctly predicts
the value of the outcome. Calculates model sensitivity and specificity. / CC0
r-odeintr 1.7.1 Wraps the Boost odeint library for integration of differential equations. / GPL- linux-
2 64,
osx-
64,
win-
64
r-odenetwork 1.3.1 Simulates a network of ordinary differential equations of order two. The noarch
package provides an easy interface to construct networks. In addition
you are able to define different external triggers to manipulate the trajec-
tory. The method is described by Surmann, Ligges, and Weihs (2014)
<doi:10.1109/ENERGYCON.2014.6850482>. / LGPL-3


Name Version
r-odr 1.0.0 Calculate the optimal sample allocation that minimizes the variance of treat- noarch
ment effect in multilevel randomized trials under fixed budget and cost struc-
ture, perform power analyses with and without accommodating costs and bud-
get. The references for proposed methods are: (1) Shen, Z. (in progress).
Using optimal sample allocation to improve statistical precision and design
efficiency for multilevel randomized trials. (unpublished doctoral disserta-
tion). University of Cincinnati, Cincinnati, OH. (2) Shen, Z., & Kelcey, B.
(revise & resubmit). Optimal sample allocation accounts for the full varia-
tion of sampling costs in cluster-randomized trials. Journal of Educational and
Behavioral Statistics. (3) Shen, Z., & Kelcey, B. (2018, April). Optimal de-
sign of cluster randomized trials under condition- and unit-specific cost struc-
tures. Roundtable discussion presented at American Educational Research
Association (AERA) annual conference. (4) Champely., S. (2018). pwr: Ba-
sic functions for power analysis (Version 1.2-2) [Software]. Available from
<https://CRAN.R-project.org/package=pwr>. / GPL-3
r-ods 0.2.0 Outcome-dependent sampling (ODS) schemes are cost-effective ways to en- noarch
hance study efficiency. In ODS designs, one observes the exposure/covariates
with a probability that depends on the outcome variable. Popular ODS de-
signs include case-control for binary outcome, case-cohort for time-to-event
outcome, and continuous outcome ODS design (Zhou et al. 2002) <doi:
10.1111/j.0006-341X.2002.00413.x>. Because ODS data has biased sam-
pling nature, standard statistical analysis such as linear regression will lead
to biases estimates of the population parameters. This package implements
four statistical methods related to ODS designs: (1) An empirical likelihood
method analyzing the primary continuous outcome with respect to exposure
variables in continuous ODS design (Zhou et al., 2002). (2) A partial lin-
ear model analyzing the primary outcome in continuous ODS design (Zhou,
Qin and Longnecker, 2011) <doi: 10.1111/j.1541-0420.2010.01500.x>. (3)
Analyze a secondary outcome in continuous ODS design (Pan et al. 2018)
<doi: 10.1002/sim.7672>. (4) An estimated likelihood method analyz-
ing a secondary outcome in case-cohort data (Pan et al. 2017) <doi:
10.1111/biom.12838>. / GPL-2
r-oem 2.0.9 Solves penalized least squares problems for big tall data us- linux-
ing the orthogonalizing EM algorithm of Xiong et al. (2016) 64,
<doi:10.1080/00401706.2015.1054436>. The main fitting function is osx-
oem() and the functions cv.oem() and xval.oem() are for cross validation, the 64,
latter being an accelerated cross validation function for linear models. The win-
big.oem() function allows for out of memory fitting. / GPL-2 64
r-officer 0.3.5 Access and manipulate ‘Microsoft Word’ and ‘Microsoft PowerPoint’ docu- linux-
ments from R. The package focuses on tabular and graphical reporting from 64,
R; it also provides two functions that let users get document content into data osx-
objects. A set of functions lets add and remove images, tables and paragraphs 64,
of text in new or existing documents. When working with ‘PowerPoint’ pre- win-
sentations, slides can be added or removed; shapes inside slides can also be 64
added or removed. When working with ‘Word’ documents, a cursor can be
used to help insert or delete content at a specific location in the document. The
package does not require any installation of Microsoft products to be able to
write Microsoft files. / GPL-3


Name Version
r-offlinechange 0.0.2 Detect the number and locations of change points. The locations can be either linux-
exact or in terms of ranges, depending on the available computational resource. 64,
The method is based on Jie Ding, Yu Xiang, Lu Shen, Vahid Tarokh (2016) osx-
<arXiv:1605.00346v2>. / GPL-3 64,
win-
64
r-ogi 1.0.0 Consider a data matrix of n individuals with p variates. The objective general noarch
index (OGI) is a general index that combines the p variates into a univariate
index in order to rank the n individuals. The OGI is always positively cor-
related with each of the variates. More details can be found in Sei (2016)
<doi:10.1016/j.jmva.2016.02.005>. / GPL-3
r-oglmx 3.0.0.0Ordered models such as ordered probit and ordered logit presume that the error noarch
variance is constant across observations. In the case that this assumption does
not hold estimates of marginal effects are typically biased (Weiss (1997)). This
package allows for generalization of ordered probit and ordered logit models
by allowing the user to specify a model for the variance. Furthermore, the
package includes functions to calculate the marginal effects. Wrapper func-
tions to estimate the standard limited dependent variable models are also in-
cluded. / GPL-2
r-ohit 1.0.0 Ing and Lai (2011) <doi:10.5705/ss.2010.081> proposed a high-dimensional noarch
model selection procedure that comprises three steps: orthogonal greedy algo-
rithm (OGA), high-dimensional information criterion (HDIC), and Trim. The
first two steps, OGA and HDIC, are used to sequentially select input variables
and determine stopping rules, respectively. The third step, Trim, is used to
delete irrelevant variables remaining in the second step. This package aims
at fitting a high-dimensional linear regression model via OGAHDICTrim. /
GPL-2
r-ohpl 1.4 Ordered homogeneity pursuit lasso (OHPL) algorithm for group variable se- noarch
lection proposed in Lin et al. (2017) <DOI:10.1016/j.chemolab.2017.07.004>.
The OHPL method exploits the homogeneity structure in high-dimensional
data and enjoys the grouping effect to select groups of important variables
automatically. This feature makes it particularly useful for high-dimensional
datasets with strongly correlated variables, such as spectroscopic data. / GPL-
3
r-ohtadstats 2.1.0 Calculate’s Tomoka Ohta’s partitioning of linkage disequilibrium, noarch
deemed D-statistics, for pairs of loci. Beissinger et al. (2016)
<doi:10.1038/hdy.2015.81>. / MIT
r-oidata 1.0 A collection of data sets from several sources that may be useful for teaching, noarch
practice, or other purposes. Functions have also been included to assist in the
retrieval of table data from websites or in visualizing sample data. / GPL-2 |
GPL-3
r-okcupiddata 0.1.0 Cleaned profile data from OkCupid Profile Data for Introductory Statistics noarch
and Data Science Courses (Journal of Statistics Education 2015 <http://www.
amstat.org/publications/jse/v23n2/kim.pdf>). / CC0
r-okmesonet 0.1.5 okmesonet retrieves and summarizes Oklahoma (USA) Mesonet climatologi- noarch
cal data provided by the Oklahoma Climatological Survey. Measurements are
recorded every five minutes at approximately 120 stations throughout Okla-
homa and are available in near real-time. / GPL-2


Name Version
r-olctools 0.3.0 ‘Open Location Codes’ <http://openlocationcode.com/> are a Google-created linux-
standard for identifying geographic locations. ‘olctools’ provides utilities for 64,
validating, encoding and decoding entries that follow this standard. / MIT osx-
64,
win-
64
r- 1.3 Calculate the theorical specificity of a system of multiple primers used for noarch
oligospecificitysystem PCR, qPCR primers or degenerated primer design / GPL-2
r-olscurve 0.2.0 Provides tools for more easily organizing and plotting individual ordinary least noarch
square (OLS) growth curve trajectories. / GPL-2
r-omd 1.0 This package including two useful function, which can be used for filter the noarch
molecular descriptors matrix for QSAR. / GPL-2
r-omickriging 1.4.0 It provides functions to generate a correlation matrix from a genetic dataset noarch
and to use this matrix to predict the phenotype of an individual by using the
phenotypes of the remaining individuals through kriging. Kriging is a geo-
statistical method for optimal prediction or best unbiased linear prediction. It
consists of predicting the value of a variable at an unobserved location as a
weighted sum of the variable at observed locations. Intuitively, it works as a
reverse linear regression: instead of computing correlation (univariate regres-
sion coefficients are simply scaled correlation) between a dependent variable
Y and independent variables X, it uses known correlation between X and Y to
predict Y. / GPL-3
r-omisc 0.1.2 Primarily devoted to implementing the Univariate Bootstrap (as well as the noarch
Traditional Bootstrap). In addition there are multiple functions for DeFries-
Fulker behavioral genetics models. The univariate bootstrapping functions,
DeFries-Fulker functions, regression and traditional bootstrapping functions
form the original core. Additional features may come online later, how-
ever this software is a work in progress. For more information about uni-
variate bootstrapping see: Lee and Rodgers (1998) and Beasley et al (2007)
<doi.org/10.1037/1082-989X.12.4.414>. / GPL-3
r-onage 1.0.1 Implementation of a likelihood ratio test of differential onset of senescence noarch
between two groups. Given two groups with measures of age and of an in-
dividual trait likely to be subjected to senescence (e.g. body mass), ‘OnAge’
provides an asymptotic p-value for the null hypothesis that senescence starts
at the same age in both groups. The package implements the procedure used
in Douhard et al. (2017) <doi:10.1111/oik.04421>. / GPL-3
r-oncomodel 1.0 Computing probabilistic tree models for oncogenesis based on genetic data noarch
using maximum likelihood. / GPL-2
r-oncotree 0.3.3 Contains functions to construct and evaluate directed tree structures that model noarch
the process of occurrence of genetic alterations during carcinogenesis. / GPL-2
r- 1.0.3 Purpose of this package is it to plan, monitor and evaluate oncological phase linux-
onearmphasetwostudy II studies. In general this kind of studies are single-arm trials with planned 64,
interim analysis and binary endpoint. To meet the resulting requirements, the osx-
package provides functions to calculate and evaluate ‘Simon’s two-stage de- 64,
signs’ and ‘so-called’ ‘subset designs’. If you are unfamiliar with this pack- win-
age a good starting point is to take a closer look at the functions getSolu- 64
tions() and getSolutionsSub1().The web-based tool (<https://imbi.shinyapps.
io/phaseII-app/>) extends the functionality of our R package by means of a
proper dealing with over- and underrunning. The R function binom.test of
the ‘stats’ R package and the package ‘binom’ might be helpful to assess the
performance of the corresponding one-stage design as a reference. / GPL-2


Name Version
r-onehot 0.1.1 Quickly create numeric matrices for machine learning algorithms that require linux-
them. It converts factor columns into onehot vectors. / MIT 64,
osx-
64,
win-
64
r-oner 2.2 Implements the One Rule (OneR) Machine Learning classification algorithm noarch
(Holte, R.C. (1993) <doi:10.1023/A:1022631118932>) with enhancements for
sophisticated handling of numeric data and missing values together with ex-
tensive diagnostic functions. It is useful as a baseline for machine learning
models and the rules are often helpful heuristics. / MIT
r-onetr 1.0.3 Provides a series of functions designed to enable users to easily search and noarch
interact with occupational data from the O*NET API <www.onetonline.org>.
The package produces parsed and listed XML data for custom interactions, or
pre-packaged functions for easy extraction of specific data (e.g., Knowledge,
Skills, Abilities, Work Styles, etc.). / GPL-3
r-onetwosamples 1.0_3 In this package, we introduce an R function one_two_sample() which can deal noarch
with one and two (normal) samples. For one normal sample x, the function
reports descriptive statistics, plot, interval estimation and test of hypothesis of
x. For two normal samples x and y, the function reports descriptive statistics,
plot, interval estimation and test of hypothesis of x and y, respectively. It also
reports interval estimation and test of hypothesis of mu1-mu2 (the difference
of the means of x and y) and sigma1^2 / sigma2^2 (the ratio of the variances
of x and y), tests whether x and y are from the same population, finds the
correlation coefficient of x and y if x and y have the same length. / GPL-2
r-onion 1.2_7 Quaternions and Octonions are four- and eight- dimensional extensions of the linux-
complex numbers. They are normed division algebras over the real numbers 64,
and find applications in spatial rotations (quaternions) and string theory and osx-
relativity (octonions). The quaternions are noncommutative and the octonions 64,
nonassociative. See RKS Hankin 2006, Rnews Volume 6/2: 49-51, and the win-
package vignette, for more details. / GPL-3 64
r-onlinevar 0.1_1 Functions for recursive online fitting of time-adaptive lasso vector auto re- linux-
gression. A recursive coordinate descent algorithm is used to estimate sparse 64,
vector auto regressive models and exponential forgetting is applied to allow osx-
model changes. Details can be found in Jakob W. Messner and Pierre Pinson 64,
(2018). Online adaptive LASSO estimation in Vector Auto Regressive models win-
for wind power forecasting in high dimension. International Journal of Fore- 64
casting, in press. <doi:10.1016/j.ijforecast.2018.02.001>. / GPL-2 | GPL-3
r-onnx 0.0.2 R Interface to ‘ONNX’ - Open Neural Network Exchange <https://onnx.ai/>. noarch
‘ONNX’ provides an open source format for machine learning models. It de-
fines an extensible computation graph model, as well as definitions of built-in
operators and standard data types. / MIT License file LICENSE
r-ontologyindex 2.5 Functions for reading ontologies into R as lists and manipulating sets of onto- noarch
logical terms - ‘ontologyX: A suite of R packages for working with ontological
data’, Greene et al 2017 <doi:10.1093/bioinformatics/btw763>. / GPL-2
r-oomisc 1.2 Includes miscellaneous functions. / GPL-2 noarch


Name Version
r-oompabase 3.2.9 Provides the class unions that must be preloaded in order for the basic tools in noarch
the OOMPA (Object-Oriented Microarray and Proteomics Analysis) project to
be defined and loaded. It also includes vectorized operations for row-by-row
means, variances, and t-tests. Finally, it provides new color schemes. Details
on the packages in the OOMPA project can be found at <http://oompa.r-forge.
r-project.org/>. / Apache License (== 2.0)
r-oompadata 3.1.1 This is a data-only package to provide example data for other packages that noarch
are part of the Object-Oriented Microrray and Proteomics Analysis suite of
packages. These are described in more detail at the package URL. / Apache
License (== 2.0)
r-oor 0.1.2 Implementation of optimistic optimization methods for global optimization of noarch
deterministic or stochastic functions. The algorithms feature guarantees of the
convergence to a global optimum. They require minimal assumptions on the
(only local) smoothness, where the smoothness parameter does not need to be
known. They are expected to be useful for the most difficult functions when
we have no information on smoothness and the gradients are unknown or do
not exist. Due to the weak assumptions, however, they can be mostly effective
only in small dimensions, for example, for hyperparameter tuning. / LGPL-3
r-opalr 1.2.0 Data integration Web application for biobanks by ‘OBiBa’. ‘Opal’ is the core noarch
database application for biobanks. Participant data, once collected from any
data source, must be integrated and stored in a central data repository under
a uniform model. ‘Opal’ is such a central repository. It can import, process,
validate, query, analyze, report, and export data. ‘Opal’ is typically used in
a research center to analyze the data acquired at assessment centres. Its ulti-
mate purpose is to achieve seamless data-sharing among biobanks. This ‘Opal’
client allows to interact with ‘Opal’ web services and to perform operations on
the R server side. ‘DataSHIELD’ administration tools are also provided. /
GPL-3
r-opart 2019.1.0
A reference implementation of standard optimal partitioning algorithm linux-
in C using square-error loss and Poisson loss functions as described 64,
by Robert Maidstone (2016) <doi:10.1007/s11222-016-9636-3>, Toby osx-
Hocking (2016) <doi:10.1007/s11222-016-9636-3>, Guillem Rigaill 64,
(2016) <doi:10.1007/s11222-016-9636-3>, Paul Fearnhead (2016) win-
<doi:10.1007/s11222-016-9636-3>. It scales quadratically with number 64
of data points in terms of time-complexity. / GPL-3
r-opencv 0.1 Experimenting with computer vision and machine learning in R. This package linux-
exposes some of the available ‘OpenCV’ vision algorithms, such as edge, body 64,
or face detection. These can either be applied to analyze static images, or to osx-64
filter live video footage from a camera device. / MIT
r-openintro 1.7.1 Supplemental functions and data for ‘OpenIntro’ resources, which includes noarch
open-source textbooks and resources for introductory statistics at <http://www.
openintro.org>. The package contains data sets used in our open-source text-
books along with custom plotting functions for reproducing book figures. Note
that many functions and examples include color transparency; some plotting
elements may not show up properly (or at all) when run in some versions of
Windows operating system. / GPL-2 | GPL-3


Name Version
r- 0.2_5 The OpenMPController package provides a function omp_set_num_threads() linux-
openmpcontroller to set the number of OpenMP threads to be used. This may be useful, for 64,
example, when linking against a vendor optimised BLAS/LAPACK library osx-
(e.g. the AMD Core Math Library), since the defaults used by those libraries 64,
may not be highly performant. / GPL-2 win-
64
r-opennlpdata 1.5.3_4
Apache OpenNLP jars and basic English language models. / GPL-3 noarch
r-openssl 1.3 Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. linux-
Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic 32,
signatures can either be created and verified manually or via x509 certificates. linux-
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for 64,
asymmetric (public key) encryption or EC for Diffie Hellman. High-level en- osx-
velope functions combine RSA and AES for encrypting arbitrary sized data. 64,
Other utilities include key generators, hash functions (md5, sha1, sha256, etc), win-
base64 encoder, a secure random number generator, and ‘bignum’ math meth- 32,
ods for manually performing crypto calculations on large multibyte integers. / win-
MIT file LICENSE 64
r-openxlsx 4.1.0 Simplifies the creation of Excel .xlsx files by providing a high level interface to linux-
writing, styling and editing worksheets. Through the use of ‘Rcpp’, read/write 32,
times are comparable to the ‘xlsx’ and ‘XLConnect’ packages with the added linux-
benefit of removing the dependency on Java. / MIT file LICENSE 64,
osx-
64,
win-
32,
win-
64
r-opera 1.0 Misc methods to form online predictions, for regression-oriented time-series, noarch
by combining a finite set of forecasts provided by the user. / LGPL-3
r-operator.tools 1.6.3 Provides a collection of utilities that allow programming with R’s operators. noarch
Routines allow classifying operators, translating to and from an operator and
its underlying function, and inverting some operators (e.g. comparison opera-
tors), etc. All methods can be extended to custom infix operators. / GPL-2
r-operators 0.1_8 A set of binary operators for common tasks such as regex manipulation. / MIT noarch
r-opi 2.7 Implementation of the Open Perimetry Interface (OPI) for simulating and con- noarch
trolling visual field machines using R. The OPI is a standard for interfacing
with visual field testing machines (perimeters). It specifies basic functions
that allow many visual field tests to be constructed. As of October 2017 it is
fully implemented on the Octopus 900 and partially on the Heidelberg Edge
Perimeter, the Kowa AP 7000, the CrewT imo and the Centervue Compass. It
also has a cousin: the R package ‘visualFields’, which has tools for analysing
and manipulating visual field data. / GPL-3
r-opportunistic 1.2 Computes the routing distribution, the expectation of the number of broad- noarch
casts, transmissions and receptions considering an Opportunistic transport
model. It provides theoretical results and also estimated values based on Monte
Carlo simulations. / GPL-2
r-ops 1.0 Comparison of data by Pearson product-moment correlation coefficients is noarch
prone to outliers. The problem can be alleviated by normalizing data with
outliers before computing the Pearson correlation coefficient. The sample pro-
vides such normalization by optimal power space transformation. / Apache
License 2.0


Name Version
r-optauc 1.0 Searches for optimal linear combination of multiple diagnostic tests (mark- noarch
ers) that maximizes the area under the receiver operating characteristic curve
(AUC); performs an approximated cross-validation for estimating the AUC
associated with the estimated coefficients. / GPL-2
r-optextras 2016_8.8
Tools to assist in safely applying user generated objective and derivative func- noarch
tion to optimization programs. These are primarily function minimization
methods with at most bounds and masks on the parameters. Provides a way
to check the basic computation of objective functions that the user provides,
along with proposed gradient and Hessian functions, as well as to wrap such
functions to avoid failures when inadmissible parameters are provided. Check
bounds and masks. Check scaling or optimality conditions. Perform an axial
search to seek lower points on the objective function surface. Includes forward,
central and backward gradient approximation codes. / GPL-2
r-optgs 1.1.1 Functions to find near-optimal multi-stage designs for continuous outcomes. / linux-
GPL-2 64,
osx-
64,
win-
64
r-opthedging 1.0 Estimation of value and hedging strategy of call and put options, based on opti- linux-
mal hedging and Monte Carlo method, from Chapter 3 of ‘Statistical Methods 64,
for Financial Engineering’, by Bruno Remillard, CRC Press, (2013). / GPL-2 osx-
64,
win-
64
r-optifunset 1.0 A single function ‘options.ifunset(. . . )’ is contained herewith, which allows noarch
the user to set a global option ONLY if it is not already set. By this token,
for package maintainers this function can be used in preference to the standard
‘options(. . . )’ function, making provision for THEIR end user to place ‘op-
tions(. . . )’ directives within their ‘.Rprofile’ file, which will not be overridden
at the point when a package is loaded. / GPL-2
r-optigrab 0.9.2.1Parse options from the command-line using a simple, clean syntax. It requires noarch
little or no specification and supports short and long options, GNU-, Java- or
Microsoft- style syntaxes, verb commands and more. / GPL-3
r- 1.1_4 Computes optimal cutpoints for diagnostic tests or continuous markers. Vari- noarch
optimalcutpoints ous approaches for selecting optimal cutoffs have been implemented, including
methods based on cost-benefit analysis and diagnostic test accuracy measures
(Sensitivity/Specificity, Predictive Values and Diagnostic Likelihood Ratios).
Numerical and graphical output for all methods is easily obtained. / GPL-3
‘r- 0.2 Algorithms for D-, A- and IV-optimal designs of experiments. Some of noarch
optimaldesign < the functions in this package require the ‘gurobi’ software and its accom-
http://www.iam.fmph.uniba.sk/design/
panying R package. For their installation, please follow the instructions at
>‘_ <www.gurobi.com> and the file gurobi_inst.txt, respectively. / GPL-3
r-optimbase 1.0_9 Provides a set of commands to manage an abstract optimization method. The noarch
goal is to provide a building block for a large class of specialized optimization
methods. This package manages: the number of variables, the minimum and
maximum bounds, the number of non linear inequality constraints, the cost
function, the logging system, various termination criteria, etc. . . / CeCILL-2


Name Version
r-optimization 1.0_7 Flexible optimizer with numerous input specifications for detailed parameter- linux-
isation. Designed for complex loss functions with state and parameter space 64,
constraints. Visualization tools for validation and analysis of the convergence osx-
are included. / GPL-2 64,
win-
64
r-optimparallel 0.8_1 Provides a parallel version of the L-BFGS-B method of optim(). The main noarch
function of the package is optimParallel(), which has the same usage and out-
put as optim(). Using optimParallel() can significantly reduce the optimization
time. / GPL-2
r-optimstrat 2.0 Intended to assist in the choice of the sampling strategy to implement in a noarch
survey. / GPL-2
r-optimx 2018_7.10
Provides a replacement and extension of the optim() function to call to several noarch
function minimization codes in R in a single statement. These methods handle
smooth, possibly box constrained functions of several or many parameters.
Note that function ‘optimr()’ was prepared to simplify the incorporation of
minimization codes going forward. Also implements some utility codes and
some extra solvers, including safeguarded Newton methods. Many methods
previously separate are now included here. / GPL-2
r-optinterim 3.0.1 Optimal two and three stage designs monitoring time-to-event endpoints at a noarch
specified timepoint / GPL-2
r-optional 2.0 Introduces optional types with some() and none, as well as match_with() from noarch
functional languages. / BSL
r-optionpricing 0.1 Efficient Monte Carlo Algorithms for the price and the sensitivities of Asian noarch
and European Options under Geometric Brownian Motion. / GPL-2 | GPL-3
r-optionstrat 1.4.0 Utilizes the Black-Scholes-Merton option pricing model to calculate key op- noarch
tion analytics and perform graphical analysis of various option strategies.
Provides functions to calculate the option premium and option greeks of
European-style options. / GPL-3
r-optiscale 1.1 Tools for performing an optimal scaling transformation on a data vector / GPL- noarch
2
r-optismixture 0.1 Code for optimal mixture weights in importance sampling. Workhorse func- noarch
tions penoptpersp() and penoptpersp.alpha.only() minimize estimated vari-
ances with and without control variates respectively. It can be used in adaptive
mixture importance sampling, for example, function batch.estimation() does
two stages, a pilot estimate of mixing alpha and a following importance sam-
pling. / GPL-2
r-optparse 1.6.2 A command line parser inspired by Python’s ‘optparse’ library to be used with noarch
Rscript to write #! shebang scripts that accept short and long flag/options. /
GPL-2
r-optr 1.2.5 Solves linear systems of form Ax=b via Gauss elimination, LU decomposition, noarch
Gauss-Seidel, Conjugate Gradient Method (CGM) and Cholesky methods. /
GPL-2
r-optrees 1.0 Finds optimal trees in weighted graphs. In particular, this package provides noarch
solving tools for minimum cost spanning tree problems, minimum cost ar-
borescence problems, shortest path tree problems and minimum cut tree prob-
lem. / GPL-3


Name Version
r-opusminer 0.1_0 Provides a simple R interface to the OPUS Miner algorithm (implemented linux-
in C) for finding the top-k productive, non-redundant itemsets from transac- 64,
tion data. The OPUS Miner algorithm uses the OPUS search algorithm to osx-
efficiently discover the key associations in transaction data, in the form of 64,
self-sufficient itemsets, using either leverage or lift. See <http://i.giwebb.com/ win-
index.php/research/association-discovery/> for more information in relation to 64
the OPUS Miner algorithm. / GPL-3
r-orca 1.1_1 Implements orbit counting using a fast combinatorial approach. Counts orbits linux-
of nodes and edges from edge matrix or data frame, or a graph object from the 64,
graph package. / LGPL-3 osx-
64,
win-
64
r-orclus 0.2_6 Functions to perform subspace clustering and classification. / GPL-2 noarch
r-orcutt 2.3 Solve first order autocorrelation problems using an iterative method. This pro- noarch
cedure estimates both autocorrelation and beta coefficients recursively until
we reach the convergence (8th decimal as default). The residuals are com-
puted after estimating Beta using EGLS approach and Rho is estimated using
the previous residuals. / GPL-2
r-orddisp 1.0.1 Estimate location-shift models or rating-scale models accounting for response noarch
styles (RSRS) for the regression analysis of ordinal responses. / GPL-2
r-orddom 3.1 Computes ordinal, statistics and effect sizes as an alternative to mean compar- noarch
ison: Cliff’s delta or success rate difference (SRD), Vargha and Delaney’s A
or the Area Under a Receiver Operating Characteristic Curve (AUC), the dis-
crete type of McGraw & Wong’s Common Language Effect Size (CLES) or
Grissom & Kim’s Probability of Superiority (PS), and the Number needed to
treat (NNT) effect size. Moreover, comparisons to Cohen’s d are offered based
on Huberty & Lowman’s Percentage of Group (Non-)Overlap considerations.
/ GPL-2
r-order2parent 1.0 This package uses B-spline based nonparametric smooth estimators to estimate noarch
parent distributions given observations on multiple order statistics. / GPL-2
r-ordering 0.7.0 Functions to test/check/verify/investigate the ordering of vectors. The noarch
‘is_[strictly_]*’ family of functions test vectors for ‘sorted’, ‘monotonic’, ‘in-
creasing’, ‘decreasing’ order; ‘is_constant’ and ‘is_incremental’ test for the
degree of ordering. ordering provides a numeric indication of ordering -2
(strictly decreasing) to 2 (strictly increasing). / GPL-2
r-orderstats 0.1.0 All the methods in this package generate a vector of uniform order statistics noarch
using a beta distribution and use an inverse cumulative distribution function
for some distribution to give a vector of random order statistic variables for
some distribution. This is much more efficient than using a loop since it is
directly sampling from the order statistic distribution. / GPL-2
r-ordfacreg 1.0.6 In biomedical studies, researchers are often interested in assessing the asso- noarch
ciation between one or more ordinal explanatory variables and an outcome
variable, at the same time adjusting for covariates of any type. The outcome
variable may be continuous, binary, or represent censored survival times. In
the absence of a precise knowledge of the response function, using mono-
tonicity constraints on the ordinal variables improves efficiency in estimating
parameters, especially when sample sizes are small. This package implements
an active set algorithm that efficiently computes such estimators. / GPL-2


Name Version
r-ordinalclust 1.3.4 Ordinal data classification, clustering and co-clustering using model-based ap- linux-
proach with the Bos distribution for ordinal data (Christophe Biernacki and 64,
Julien Jacques (2016) <doi:10.1007/s11222-015-9585-2>). / GPL-2 osx-
64,
win-
64
r-ordinalcont 2.0.1 A regression framework for response variables which are continuous self- noarch
rating scales such as the Visual Analog Scale (VAS) used in pain assessment,
or the Linear Analog Self-Assessment (LASA) scales in quality of life studies.
These scales measure subjects’ perception of an intangible quantity, and can-
not be handled as ratio variables because of their inherent non-linearity. We
treat them as ordinal variables, measured on a continuous scale. A function
(the g function) connects the scale with an underlying continuous latent vari-
able. The link function is the inverse of the CDF of the assumed underlying
distribution of the latent variable. A variety of link functions are currently
implemented. / GPL-2
r-ordinalgmifs 1.0.6 Provides a function for fitting cumulative link, adjacent category, forward and linux-
backward continuation ratio, and stereotype ordinal response models when 64,
the number of parameters exceeds the sample size, using the the generalized osx-
monotone incremental forward stagewise method. / GPL-2 64,
win-
64
r-ordinallbm 1.0 It implements functions for simulation and estimation of the ordinal latent noarch
block model (OLBM), as described in Corneli, Bouveyron and Latouche
(2019). / GPL-2
r-ordinalnet 2.6 Fits ordinal regression models with elastic net penalty. Supported model fam- noarch
ilies include cumulative probability, stopping ratio, continuation ratio, and ad-
jacent category. These families are a subset of vector glm’s which belong to a
model class we call the elementwise link multinomial-ordinal (ELMO) class.
Each family in this class links a vector of covariates to a vector of class prob-
abilities. Each of these families has a parallel form, which is appropriate for
ordinal response data, as well as a nonparallel form that is appropriate for an
unordered categorical response, or as a more flexible model for ordinal data.
The parallel model has a single set of coefficients, whereas the nonparallel
model has a set of coefficients for each response category except the baseline
category. It is also possible to fit a model with both parallel and nonparallel
terms, which we call the semi-parallel model. The semi-parallel model has
the flexibility of the nonparallel model, but the elastic net penalty shrinks it
toward the parallel model. For details, refer to Wurm, Hanlon, and Rathouz
(2017) <arXiv:1706.05003>. / MIT
r-ordmonreg 1.0.3 We consider the problem of estimating two isotonic regression curves g1* and noarch
g2* under the constraint that they are ordered, i.e. g1* <= g2*. Given two
sets of n data points y_1, . . . , y_n and z_1, . . . , z_n that are observed at (the
same) deterministic design points x_1, . . . , x_n, the estimates are obtained by
minimizing the Least Squares criterion L(a, b) = sum_{i=1}^n (y_i - a_i)^2
w1(x_i) sum_{i=1}^n (z_i - b_i)^2 w2(x_i) over the class of pairs of vectors
(a, b) such that a and b are isotonic and a_i <= b_i for all i = 1, . . . , n. We offer
two different approaches to compute the estimates: a projected subgradient
algorithm where the projection is calculated using a PAVA as well as Dykstra’s
cyclical projection algorithm. / GPL-2


Name Version
r-ore 1.6.2 Provides an alternative to R’s built-in functionality for handling regular expres- linux-
sions, based on the Onigmo library. Offers first-class compiled regex objects, 64,
partial matching and function-based substitutions, amongst other features. / osx-
BSD_3_clause 64,
win-
64
r-ores 0.3.1 A connector to ORES (<http://ores.wmflabs.org/>), an AI project to provide noarch
edit scoring for content on Wikipedia and other Wikimedia projects. This lets
a researcher identify if edits are likely to be reverted, damaging, or made in
good faith. / MIT
r-org 2019.4.2
A system to help you organize projects. Most analyses have three (or more) noarch
main sections: code, results, and data, each with different requirements (ver-
sion control/sharing/encryption). You provide folder locations and ‘org’ helps
you take care of the details. / GPL-3
r-orgmassspecr 0.5_3 Organic/biological mass spectrometry data analysis. / BSD_2_clause noarch
r-oriclust 1.0_1 ORIClust is a user-friendly R-based software package for gene clustering. noarch
Clusters are given by genes matched to prespecified profiles across various
ordered treatment groups. It is particularly useful for analyzing data obtained
from short time-course or dose-response microarray experiments. / GPL-2
r-orientlib 0.10.3Representations, conversions and display of orientation SO(3) data. See the noarch
orientlib help topic for details. / GPL-3
r-ormdr 1.3_2 Odds ratio based multifactor-dimensionality reduction method for detecting linux-
gene-gene interactions / GPL-2 64,
osx-
64,
win-
64
r-orsifronts 0.1.1 A data set package with the Orsi fronts as a ‘SpatialLinesDataFrame’ ob- noarch
ject. The Orsi et al. (1995) fronts are published at the Southern Ocean Atlas
Database Page, please see package CITATION for details. / GPL-3
r-orsk 1.0_5 Convert odds ratio to relative risk in cohort studies with partial data informa- linux-
tion (Wang (2013) <doi:10.18637/jss.v055.i05>). / GPL-2 64,
osx-
64,
win-
64
r- 0.1.6 Represents the basis functions for B-splines in a simple matrix formulation noarch
orthogonalsplinebasis that facilitates, taking integrals, derivatives, and making orthogonal the basis
functions. / GPL-2
r-orthopanels 1.1_3 Implements the orthogonal reparameterization approach recommended by noarch
Lancaster (2002) to estimate dynamic panel models with fixed effects (and
optionally: panel specific intercepts). The approach uses a likelihood-based
estimator and produces estimates that are asymptotically unbiased as N goes
to infinity, with a T as low as 2. / GPL-3
r-osc 1.0.4 Allows distance based spatial clustering of georeferenced data by implement- linux-
ing the City Clustering Algorithm - CCA. Multiple versions allow clustering 64,
for matrix, raster and single coordinates on a plain (euclidean distance) or on osx-
a sphere (great-circle or orthodromic distance). / GPL-3 64,
win-
64


Name Version
r- 0.1.0 The supplied code allows for the generation of discrete time series of oscillat- noarch
oscillatorgenerator ing species. General shapes can be selected by means of individual functions,
which are widely customizable by means of function arguments. All code was
developed in the Biological Information Processing Group at the BioQuant
Center at Heidelberg University, Germany. / GPL-3
r-osdesign 1.7 The osDesign serves for planning an observational study. Currently, function- linux-
ality is focused on the two-phase and case-control designs. Functions in this 64,
packages provides Monte Carlo based evaluation of operating characteristics osx-
such as powers for estimators of the components of a logistic regression model. 64,
/ GPL-3 win-
64
r-osdr 1.1.3 Provides routines for finding an Optimal System of Distinct Representatives noarch
(OSDR), as defined by D.Gale (1968) <doi:10.1016/S0021-9800(68)80039-
0>. / GPL-2
r-oshka 0.1.2 Expands quoted language by recursively replacing any symbol that points to noarch
quoted language with the language it points to. The recursive process con-
tinues until only symbols that point to non-language objects remain. The re-
sulting quoted language can then be evaluated normally. This differs from
the traditional ‘quote’/’eval’ pattern because it resolves intermediate language
objects that would interfere with evaluation. / GPL-2
r-osmose 0.1.1 The multispecies and individual-based model (IBM) ‘OSMOSE’ (Shin and noarch
Curry (2001) <doi:10.1016/S0990-7440(01)01106-8> and Shin and Curry
(2004) <doi:10.1139/f03-154>) focuses on fish species. This model assumes
opportunistic predation based on spatial co-occurrence and size adequacy be-
tween a predator and its prey (size-based opportunistic predation). It repre-
sents fish individuals grouped into schools, which are characterized by their
size, weight, age, taxonomy and geographical location (2D model), and which
undergo major processes of fish life cycle (growth, explicit predation, natural
and starvation mortalities, reproduction and migration) and fishing exploita-
tion. The model needs basic biological parameters that are often available for
a wide range of species, and which can be found in ‘FishBase’ for instance
(see <http://www.fishbase.org/search.php>), and fish spatial distribution data.
This package provides tools to build and run simulations using the ‘OSMOSE’
model. / CeCILL
r-osqp 0.6.0.2Provides bindings to the ‘OSQP’ solver. The ‘OSQP’ solver is a numer- linux-
ical optimization package or solving convex quadratic programs written in 64,
‘C’ and based on the alternating direction method of multipliers. See osx-
<arXiv:1711.08013> for details. / Apache License 2.0 | file LICENSE 64,
win-
64
r-osrmr 0.1.35Wrapper around the ‘Open Source Routing Machine (OSRM)’ API <http:// noarch
project-osrm.org/>. ‘osrmr’ works with API versions 4 and 5 and can handle
servers that run locally as well as the ‘OSRM’ webserver. / GPL-3


Name Version
r-ote 1.0 Functions for creating ensembles of optimal trees for regression, classification noarch
and class membership probability estimation are given. A few trees are se-
lected from an initial set of trees grown by random forest for the ensemble on
the basis of their individual and collective performance. Trees are assessed
on out-of-bag data and on an independent training data set for individual and
collective performance respectively. The prediction functions return estimates
of the test responses and their class membership probabilities. Unexplained
variations, error rates, confusion matrix, Brier scores, etc. are also returned for
the test data. / GPL-2
r-otrselect 1.0 A penalized regression framework that can simultaneously estimate the opti- noarch
mal treatment strategy and identify important variables. Appropriate for either
censored or uncensored continuous response. / GPL-2
r-otutable 1.1.2 Analyses of OTU tables produced by 16S rRNA gene amplicon sequencing, as noarch
well as example data. It contains the data and scripts used in the paper Linz,
et al. (2017) Bacterial community composition and dynamics spanning five
years in freshwater bog lakes, <doi: 10.1128/mSphere.00169-17>. / GPL-3
r-outbreaks 1.5.0 Empirical or simulated disease outbreak data, provided either as RData or as noarch
text files. / GPL-2
r-outlierdc 0.3_0 This package provides three algorithms to detect outlying observations for cen- noarch
sored survival data. / GPL-3
r-outliers 0.14 A collection of some tests commonly used for identifying outliers. / GPL-2 noarch
r- 1.0 Functions to process ‘’outranking” ELECTRE methods existing in the litera- noarch
outrankingtools ture. See, e.g., <http://en.wikipedia.org/wiki/ELECTRE> about the outrank-
ing approach and the foundations of ELECTRE methods. / GPL-2
r-overlap 0.3.2 Provides functions to fit kernel density functions to data on temporal activity linux-
patterns of animals; estimate coefficients of overlapping of densities for two 64,
species; and calculate bootstrap estimates of confidence intervals. / GPL-3 osx-
64,
win-
64
r-overture 0.4_0 Simplifies MCMC setup by automatically looping through sampling functions noarch
and saving the results. Reduces the memory footprint of running MCMC and
saves samples to disk as the chain runs. Allows samples from the chain to
be analyzed while the MCMC is still running. Provides functions for com-
monly performed operations such as calculating Metropolis acceptance ratios
and creating adaptive Metropolis samplers. References: Roberts and Rosen-
thal (2009) <doi:10.1198/jcgs.2009.06134>. / LGPL-3
r-owea 0.1.1 An implementation of optimal weight exchange algorithm Yang(2013) noarch
<doi:10.1080/01621459.2013.806268> for three models. They are Crossover
model with subject dropout, crossover model with proportional first order
residual effects and interference model. You can use it to find either A-opt
or D-opt approximate designs. Exact designs can be automatically rounded
from approximate designs and relative efficiency is provided as well. / GPL-3
r-oxcaar 1.0.0 A set of tools that enables using ‘OxCal’ from within R. ‘OxCal’ (<https: noarch
//c14.arch.ox.ac.uk/oxcal.html>) is a standard archaeological tool intended to
provide 14C calibration and analysis of archaeological and environmental
chronological information. ‘OxcAAR’ allows simple calibration with ‘Oxcal’
and plotting of the results as well as the execution of sophisticated (‘OxCal’)
code and the import of the results of bulk analysis and complex Bayesian se-
quential calibration. / GPL-2


Name Version
r-oxybs 1.5 Provides utilities for processing of Oxy-Bisulfite microarray data (e.g. via the noarch
Illumina Infinium platform, <http://www.illumina.com>) with tandem arrays,
one using conventional bisulfite conversion, the other using oxy-bisulfite con-
version. / GPL-2
r-oz 1.0_21Functions for plotting Australia’s coastline and state boundaries. / GPL-2 noarch
r-p2distance 1.0.1 The welfare’s synthetic indicator provides an ideal tool for measuring multi- noarch
dimensional concepts such as welfare, development, living standards, etc. It
enables information from the various indicators to be aggregated into a single
synthetic measure. / GPL-3
r-p3state.msm 1.3 Analyzing survival data from illness-death model / GPL-3 noarch
r-pabonlasso 1.0 Pabon Lasso is a graphical method for monitoring the efficiency of different noarch
wards of a hospital or different hospitals.Pabon Lasso graph is divided into 4
parts which are created after drawing the average of BTR and BOR. The part
in the left-down side is Zone I, left-up side is Zone II, Right-up side part is
Zone III and the last part is Zone IV. / GPL-2
r-pacbo 0.1.0 A function for clustering online datasets. The number of cells is data-driven linux-
which need not to be chosen in advance by the user. The method is introduced 64,
and fully described in Le Li, Benjamin Guedj and Sebastien Loustau (2016), osx-
PAC-Bayesian Online Clustering (arXiv preprint: <https://arxiv.org/abs/1602. 64,
00522>). / GPL-2 win-
64
r-pacbpred 0.92.2This package is intended to perform estimation and prediction in high- noarch
dimensional additive models, using a sparse PAC-Bayesian point of view and a
MCMC algorithm. The method is fully described in Guedj and Alquier (2013),
‘PAC-Bayesian Estimation and Prediction in Sparse Additive Models’, Elec-
tronic Journal of Statistics, 7, 264–291. / GPL-2
r-pack 0.1_1 Functions to easily convert data to binary formats other programs/machines noarch
can understand. / GPL-3
r-packcircles 0.3.3 Simple algorithms for circle packing. / MIT linux-
64,
osx-
64,
win-
64
r-packclassic 0.5.2 This package comes to illustrate the book Petit Manuel de Programmation noarch
Orientee Objet sous R / GPL (>= 2.0)
r-packrat 0.5.0 Manage the R packages your project depends on in an isolated, portable, and linux-
reproducible way. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-packs4 0.9.3 Illustration of the book Petit Manuel de Programmation Orientee Objet sous noarch
R. The english version A (Not so) Short Introduction to S4 is on CRAN, ‘Con-
tributed documentation’. / GPL-2


Name Version
r-pacman 0.5.1 Tools to more conveniently perform tasks associated with add-on packages. noarch
pacman conveniently wraps library and package related functions and names
them in an intuitive and consistent fashion. It seeks to combine functionality
from lower level functions which can speed up workflow. / GPL-2
r-pact 0.5.0 A prediction-based approach to the analysis of data from randomized clinical noarch
trials is implemented. Based on response and covariate data from a randomized
clinical trial comparing a new experimental treatment E versus a control C, the
objective is to develop and internally validate a model that can identify subjects
likely to benefit from E rather than C. Currently, survival and binary response
types are permitted. / GPL-3
r-pade 0.1_4 Given a vector of Taylor series coefficients of sufficient length as input, the noarch
function returns the numerator and denominator coefficients for the Padé ap-
proximant of appropriate order. / GPL-2 | BSD_2_clause
r-paf 1.0 Calculate unadjusted/adjusted attributable fraction function of a set of covari- noarch
ates for a censored survival outcome from a Cox model using the method pro-
posed by Chen, Lin and Zeng (Biometrika 97, 713-726., 2010). / GPL-2
r-pagenum 1.1 A simple way to add page numbers to base/ggplot/lattice graphics. / GPL-3 noarch
r-pageviews 0.3.0 Pageview data from the ‘Wikimedia’ sites, such as ‘Wikipedia’ <https:// noarch
www.wikipedia.org/>, from entire projects to per-article levels of granu-
larity, through the new RESTful API and data source <https:// wikime-
dia.org/api/rest_v1/?doc>. / MIT
r-pagi 1.0 The package can identify the dysregulated KEGG pathways based on global noarch
influence from the internal effect of pathways and crosstalk between pathways.
(1) The PAGI package can prioritize the pathways associated with two biolog-
ical states by statistical significance or FDR. (2) The PAGI package can eval-
uated the global influence factor (GIF) score in the global gene-gene network
constructed based on the relationships of genes extracted from each pathway
in KEGG database and the overlapped genes between pathways. / GPL-2
r-pagwas 2.0 Bayesian hierarchical methods for pathway analysis of genomewide associa- noarch
tion data: Normal/Bayes factors and Sparse Normal/Adaptive lasso. The Fre-
quentist Fisher’s product method is included as well. / GPL-2
r-painter 0.1.0 Functions for creating color palettes, visualizing palettes, modifying colors, noarch
and assigning colors for plotting. / GPL-3
r-paintmap 1.0 Plots matrices of colours as grids of coloured squares - aka heatmaps, guaran- noarch
teeing legible row and column names, without transformation of values, with-
out re-ordering rows or columns, and without dendrograms. / GPL-2
r-pairedci 0.5_4 The package contains two functions: paired.Loc and paired.Scale. A para- noarch
metric and nonparametric confidence interval can be computed for the ratio of
locations (paired.Loc) and the ratio of scales (paired.Scale). The samples must
be paired and expected values must be positive. / GPL-2
r-pairheatmap 1.0.1 A tool to compare two heatmaps and discover patterns within and across noarch
groups. In the context of biology, group can be defined based on gene on-
tology. / GPL-2
r-pairsd3 0.1.0 Creates an interactive scatterplot matrix using the D3 JavaScript library. See noarch
<http://d3js.org/> for more information on D3. / GPL-3
r-pairwise 0.4.4_5.1
Performs the explicit calculation – not estimation! – of the Rasch item pa- noarch
rameters for dichotomous and polytomous item responses, using a pairwise
comparison approach. Person parameters (WLE) are calculated according to
Warm’s weighted likelihood approach. / GPL-3


Name Version
r-pairwised 0.9.62Pairing observations according to a chosen formula and facilitates bilateral noarch
analysis of the panel data. Paring is possible for observations, as well as for
vectors of observations ordered with respect to time. / GPL-2
r- 0.1.0 Provides data set and functions for exploration of Multiple Indicator Cluster noarch
pakpmics2014ch Survey (MICS) 2014 Child questionnaire data for Punjab, Pakistan (<http:
//www.mics.unicef.org/surveys>). / GPL-2
r- 0.1.0 Provides data set and function for exploration of Multiple Indicator Clus- noarch
pakpmics2014hh ter Survey (MICS) 2014 Household questionnaire data for Punjab, Pakistan
(<http://www.mics.unicef.org/surveys>). / GPL-2
r- 0.1.0 Provides data set and function for exploration of Multiple Indicator Cluster noarch
pakpmics2014hl Survey (MICS) 2014 Household Listing questionnaire data for Punjab, Pak-
istan (<http://www.mics.unicef.org/surveys>). / GPL-2
r- 0.1.0 Provides data set and function for exploration of Multiple Indicator Cluster noarch
pakpmics2014wm Survey (MICS) 2014 Women (age 15-49 years) questionnaire data for Punjab,
Pakistan (<http://www.mics.unicef.org/surveys>). / GPL-2
r-palasso 0.0.5 Implements sparse regression with paired covariates (Rauschenberger et noarch
al. 2019). For the optional shrinkage, install ashr (<https://github.com/
stephens999/ashr>) and CorShrink (<https://github.com/kkdey/CorShrink>)
from GitHub (see README). / GPL-3
r-paleobiodb 0.6.0 Includes 19 functions to wrap each endpoint of the PaleobioDB API, plus 8 noarch
functions to visualize and process the fossil data. The API documentation for
the Paleobiology Database can be found in <http://paleobiodb.org/data1.1/>. /
GPL-2
r-paleomorph 0.1.4 Fill missing symmetrical data with mirroring, calculate Procrustes alignments noarch
with or without scaling, and compute standard or vector correlation and covari-
ance matrices (congruence coefficients) of 3D landmarks. Tolerates missing
data for all analyses. / MIT
r-paleots 0.5.2 Facilitates analysis of paleontological sequences of trait values. Functions noarch
are provided to fit, using maximum likelihood, simple evolutionary mod-
els (including unbiased random walks, directional evolution,stasis, Ornstein-
Uhlenbeck, covariate-tracking) and complex models (punctuation, mode
shifts). / GPL-3
r-palettesforr 0.1.2 A set of palettes imported from ‘Gimp’ distributed under GPL3 (<https://www. noarch
gimp.org/about/COPYING>), and ‘Inkscape’ distributed under GPL2 (<https:
//inkscape.org/about/license/>). / GPL-2
r-palettetown 0.1.1 Use Pokemon(R) inspired palettes with additional ‘ggplot2’ scales. Palettes noarch
are the colours in each Pokemon’s sprite, ordered by how common they are in
the image. The first 386 Pokemon are currently provided. / MIT
r-palinsol 0.93 R package to compute Incoming Solar Radiation (insolation) for palaeoclimate noarch
studies. Features three solutions: Berger (1978), Berger and Loutre (1991)
and Laskar et al. (2004). Computes daily-mean, season-averaged and annual
means for all latitudes. / file LICENSE (FOSS)
r-palr 0.0.6 Colour palettes for data, based on some well known public data sets. / GPL-3 noarch


Name Version
r-pameasures 0.1.0 We propose a pair of summary measures for the predictive power of a pre- noarch
diction function based on a regression model. The regression model can be
linear or nonlinear, parametric, semi-parametric, or nonparametric, and cor-
rectly specified or mis-specified. The first measure, R-squared, is an extension
of the classical R-squared statistic for a linear model, quantifying the predic-
tion function’s ability to capture the variability of the response. The second
measure, L-squared, quantifies the prediction function’s bias for predicting the
mean regression function. When used together, they give a complete summary
of the predictive power of a prediction function. Please refer to Gang Li and
Xiaoyan Wang (2016) <arXiv:1611.03063> for more details. / GPL-3
r-pampe 1.1.2 Implements the Panel Data Approach Method for program evaluation as de- noarch
veloped in Hsiao, Ching and Ki Wan (2012). pampe estimates the effect of an
intervention by comparing the evolution of the outcome for a unit affected by
an intervention or treatment to the evolution of the unit had it not been affected
by the intervention. / GPL-2
r-pamr 1.56.1Some functions for sample classification in microarrays. / GPL-2 linux-
64,
osx-
64,
win-
64
r-pan 1.6 It provides functions and examples for maximum likelihood estimation for linux-
generalized linear mixed models and Gibbs sampler for multivariate linear 64,
mixed models with incomplete data, as described in Schafer JL (1997) Imputa- osx-
tion of missing covariates under a multivariate linear mixed model. Technical 64,
report 97-04, Dept. of Statistics, The Pennsylvania State University. / GPL-3 win-
64
r-pander 0.6.3 Contains some functions catching all messages, ‘stdout’ and other useful in- linux-
formation while evaluating R code and other helpers to return user specified 64,
text elements (like: header, paragraph, table, image, lists etc.) in ‘pandoc’ osx-
markdown or several type of R objects similarly automatically transformed to 64,
markdown format. Also capable of exporting/converting (the resulting) com- win-
plex ‘pandoc’ documents to e.g. HTML, ‘PDF’, ‘docx’ or ‘odt’. This latter 64
reporting feature is supported in brew syntax or with a custom reference class
with a smarty caching ‘backend’. / AGPL-3
r-pandocfilters 0.1_3 The document converter ‘pandoc’ <http://pandoc.org/> is widely used in the noarch
R community. One feature of ‘pandoc’ is that it can produce and consume
JSON-formatted abstract syntax trees (AST). This allows to transform a given
source document into JSON-formatted AST, alter it by so called filters and
pass the altered JSON-formatted AST back to ‘pandoc’. This package pro-
vides functions which allow to write such filters in native R code. Although
this package is inspired by the Python package ‘pandocfilters’ <https://github.
com/jgm/pandocfilters/>, it provides additional convenience functions which
make it simple to use the ‘pandocfilters’ package as a report generator. Since
‘pandocfilters’ inherits most of it’s functionality from ‘pandoc’ it can create
documents in many formats (for more information see <http://pandoc.org/>)
but is also bound to the same limitations as ‘pandoc’. / GPL-3


r- 0.1.1 Aggregate Business Tendency Survey Data (and other qualitative surveys) to noarch
panelaggregation time series at various aggregation levels. Run aggregation of survey data in a
speedy, re-traceable and a easily deployable way. Aggregation is substantially
accelerated by use of data.table. This package intends to provide an interface
that is less general and abstract than data.table but rather geared towards survey
researchers. / GPL-2
r-paneldata 1.0 Linear models for panel data: the fixed effect model and the random effect noarch
model / Artistic-2.0
r-panjen 1.6 A central decision in a parametric regression is how to specify the relation noarch
between an dependent variable and each explanatory variable. This package
provides a semi-parametric tool for comparing different transformations of an
explanatory variables in a parametric regression. The functions is relevant in
a situation, where you would use a box-cox or Box-Tidwell transformations.
In contrast to the classic power-transformations, the methods in this package
allows for theoretical driven user input and the possibility to compare with a
non-parametric transformation. / GPL-2
r-paperplanes 0.0.1.9This is a data only package, that provides distances from a paper plane exper- noarch
iment. / GPL-3
r-parade 0.1 Tool for producing Pen’s parade graphs, useful for visualizing inequalities noarch
in income, wages or other variables, as proposed by Pen (1971, ISBN: 978-
0140212594). Income or another economic variable is captured by the vertical
axis, while the population is arranged in ascending order of income along the
horizontal axis. Pen’s income parades provide an easy-to-interpret visualiza-
tion of economic inequalities. / GPL-2
r- 0.9_1 Passing a given function name or a call to the parallelize/parallelize_call func- noarch
parallelize.dynamic tions analyses and executes the code, if possible in parallel. Parallel code
execution can be performed locally or on remote batch queuing systems. /
LGPL-3
r-parallelmap 1.4 Unified parallelization framework for multiple back-end, designed for internal noarch
package and interactive usage. The main operation is parallel mapping over
lists. Supports ‘local’, ‘multicore’, ‘mpi’ and ‘BatchJobs’ mode. Allows tag-
ging of the parallel operation with a level name that can be later selected by the
user to switch on parallel execution for exactly this operation. / BSD_2_clause
r- 1.0 Recent Bayesian Markov chain Monto Carlo (MCMC) methods have been de- noarch
parallelmcmccombine veloped for big data sets that are too large to be analyzed using traditional
statistical methods. These methods partition the data into non-overlapping
subsets, and perform parallel independent Bayesian MCMC analyses on the
data subsets, creating independent subposterior samples for each data subset.
These independent subposterior samples are combined through four functions
in this package, including averaging across subset samples, weighted aver-
aging across subsets samples, and kernel smoothing across subset samples.
The four functions assume the user has previously run the Bayesian anal-
ysis and has produced the independent subposterior samples outside of the
package; the functions use as input the array of subposterior samples. The
methods have been demonstrated to be useful for Bayesian MCMC models in-
cluding Bayesian logistic regression, Bayesian Gaussian mixture models and
Bayesian hierarchical Poisson-Gamma models. The methods are appropriate
for Bayesian hierarchical models with hyperparameters, as long as data values
in a single level of the hierarchy are not split into subsets. / GPL-2


Name Version
r-parallelml 1.2 By sampling your data, running the provided classifier on these samples in noarch
parallel on your own machine and letting your models vote on a prediction,
we return much faster predictions than the regular machine learning algorithm
and possibly even more accurate predictions. / GPL-2
r-parallelpc 1.2 Parallelise constraint based causality discovery and causal inference methods. noarch
The parallelised algorithms in the package will generate the same results as
that of the ‘pcalg’ package but will be much more efficient. / GPL-2
r-parallelsvm 0.1_9 By sampling your data, running the Support-Vector-Machine algorithm on noarch
these samples in parallel on your own machine and letting your models vote
on a prediction, we return much faster predictions than the regular Support-
Vector-Machine and possibly even more accurate predictions. / GPL-2
r-params 0.6.1 An interface to simplify organizing parameters used in a package, using ex- noarch
ternal configuration files. This attempts to provide a cleaner alternative to
options(). / GPL-2
r-paramtest 0.1.0 Run simulations or other functions while easily varying parameters from one noarch
iteration to the next. Some common use cases would be grid search for ma-
chine learning algorithms, running sets of simulations (e.g., estimating statisti-
cal power for complex models), or bootstrapping under various conditions. See
the ‘paramtest’ documentation for more information and examples. / GPL-3
r-paran 1.5.2 An implementation of Horn’s technique for numerically and graphically eval- noarch
uating the components or factors retained in a principle components analysis
(PCA) or common factor analysis (FA). Horn’s method contrasts eigenvalues
produced through a PCA or FA on a number of random data sets of uncor-
related variables with the same number of variables and observations as the
experimental or observational data set to produce eigenvalues for components
or factors that are adjusted for the sample error-induced inflation. Compo-
nents with adjusted eigenvalues greater than one are retained. paran may also
be used to conduct parallel analysis following Glorfeld’s (1995) suggestions
to reduce the likelihood of over-retention. / GPL-2
r-parentoffspring 1.0 Conduct the Parent-Offspring Test Using Monomorphic SNP Markers. The noarch
similarity to the parents is computed for each offspring, and a plot of similarity
for all offspring is produced. One can keep the offspring above some threshold
for the similarity for further studies. / GPL-2
r-parglm 0.1.3 Provides a parallel estimation method for generalized linear models without linux-
compiling with a multithreaded LAPACK or BLAS. / GPL-2 64,
osx-
64,
win-
64
r-parmigene 1.0.2 The package provides a parallel estimation of the mutual information based on linux-
entropy estimates from k-nearest neighbors distances and algorithms for the 64,
reconstruction of gene regulatory networks. / AGPL-3 osx-
64,
win-
64
r-parse 0.1.0 Model-based clustering and identifying informative features based on regular- noarch
ization methods. The package includes three regularization methods - PAir-
wise Reciprocal fuSE (PARSE) penalty proposed by Wang, Zhou and Hoet-
ing (2016), the adaptive L1 penalty (APL1) and the adaptive pairwise fusion
penalty (APFP). Heatmaps are included to shown the identification of infor-
mative features. / CC0


Name Version
r-parsetools 0.1.1 Tools and utilities for dealing with parse data. Parse data represents the parse noarch
tree as data with location and type information. This package provides func-
tions for navigating the parse tree as a data frame. / GPL-2
r-partdsa 0.9.14A novel tool for generating a piecewise constant estimation list of increasingly noarch
complex predictors based on an intensive and comprehensive search over the
entire covariate space. / GPL-2
r- 2.0 Tests for a comparison of two partially overlapping samples. A comparison noarch
partiallyoverlapping of means using the partially overlapping samples t-test: See Derrick, Russ,
Toher and White (2017), Test statistics for the comparison of means for two
samples which include both paired observations and independent observations,
Journal of Modern Applied Statistical Methods, 16(1). A comparison of pro-
portions using the partially overlapping samples z-test: See Derrick, Dobson-
Mckittrick, Toher and White (2015), Test statistics for comparing two pro-
portions with partially overlapping samples. Journal of Applied Quantitative
Methods, 10(3). / GPL-3
r-partialor 0.9 Computes Odds Ratio adjusted for a vector of possibly continuous covariates noarch
/ GPL-2
r-partitionbefsp 1.0 A collection of functions that can be used to estimate selection and comple- noarch
mentarity effects, sensu Loreau & Hector (2001) <doi:10.1038/35083573>,
even in cases where data are only available for a random subset of species (i.e.
incomplete sample-level data). A full derivation and explanation of the statisti-
cal corrections used here is available in Clark et al. (2019) <doi:10.1111/2041-
210X.13285>. / GPL-3
r-partitionmap 0.5 Low-dimensional embedding, using Random Forests for multiclass classifica- noarch
tion / GPL-3
r-partitionmetric 1.1 partitionMetric computes a distance between two partitions of a set. / noarch
BSD_2_clause
r-partsm 1.1_2 This package performs basic functions to fit and predict periodic autoregres- noarch
sive time series models. These models are discussed in the book P.H. Franses
(1996) Periodicity and Stochastic Trends in Economic Time Series, Oxford
University Press. Data set analyzed in that book is also provided. NOTE: the
package was orphaned during several years. It is now only maintained, but
no major enhancement are expected, and the maintainer cannot provide any
support. / GPL-2
r-party 1.3_3 A computational toolbox for recursive partitioning. The core of the pack- linux-
age is ctree(), an implementation of conditional inference trees which em- 64,
bed tree-structured regression models into a well defined theory of condi- osx-
tional inference procedures. This non-parametric class of regression trees is 64,
applicable to all kinds of regression problems, including nominal, ordinal, nu- win-
meric, censored as well as multivariate response variables and arbitrary mea- 64
surement scales of the covariates. Based on conditional inference trees, cfor-
est() provides an implementation of Breiman’s random forests. The function
mob() implements an algorithm for recursive partitioning based on paramet-
ric models (e.g. linear models, GLMs or survival regression) employing pa-
rameter instability tests for split selection. Extensible functionality for visu-
alizing tree-structured regression models is available. The methods are de-
scribed in Hothorn et al. (2006) <doi:10.1198/106186006X133933>, Zeileis
et al. (2008) <doi:10.1198/106186008X319331> and Strobl et al. (2007)
<doi:10.1186/1471-2105-8-25>. / GPL-2
r-pas 1.2.5 An R package for polygenic trait analysis. / GPL-2 noarch


Name Version
r-pass.lme 0.9.0 Power and sample size calculation for testing fixed effect coefficients in mul- noarch
tilevel linear mixed effect models with one or more than one independent pop-
ulations. Laird, Nan M. and Ware, James H. (1982) <doi:10.2307/2529876>.
/ GPL-3
r-passport 0.2.0 Smooths the process of working with country names and codes via powerful noarch
parsing, standardization, and conversion utilities arranged in a simple, con-
sistent API. Country name formats include multiple sources including the
Unicode Common Locale Data Repository (CLDR, <http://cldr.unicode.org/>)
common-sense standardized names in hundreds of languages. / GPL-3
r-password 1.0_0 Create random passwords of letters, numbers and punctuation. / GPL-3 noarch
r-pastecs 1.3.21Regularisation, decomposition and analysis of space-time series. The noarch
pastecs R package is a PNEC-Art4 and IFREMER (Benoit Beliaeff
<Benoit.Beliaeff@ifremer.fr>) initiative to bring PASSTEC 2000 functionali-
ties to R. / GPL-2
r-pastis 0.1_2 A pre-processor for mrBayes that assimilates sequences, taxonomic informa- noarch
tion and tree constraints as per xxx. The main functions of interest for most
users will be pastis_simple, pastis_main and conch. The main analysis is con-
ducted with pastis_simple or pastis_main followed by a manual execution of
mrBayes (>3.2). The placement of taxa not contained in the tree constraint can
be investigated using conch. / GPL-3
r-paswr 1.1 Data and functions for the book PROBABILITY and STATISTICS WITH R. noarch
/ GPL-2
r-patchdvi 1.9.1616
Functions to patch specials in .dvi files, or entries in .synctex files. Works with linux-
concordance=TRUE in Sweave or knitr to link sources to previews. / GPL-2 64,
osx-
64,
win-
64
r-patchplot 0.1.5 Functions to generate scatterplots with images patches instead of usual glyphs, noarch
with associated utilities. / LGPL-3
r-patchsynctex 0.1_4 This utility eases the debugging of literate documents (‘noweb’ files) by patch- noarch
ing the synchronization information (the ‘.synctex(.gz)’ file) produced by
‘pdflatex’ with concordance information produced by ‘Sweave’ or ‘knitr’ and
‘Sweave’ or ‘knitr’ ; this allows for bilateral communication between a text
editor (visualizing the ‘noweb’ source) and a viewer (visualizing the resultant
‘PDF’), thus bypassing the intermediate ‘TeX’ file. / GPL-2
r-patentsview 0.2.2 Provides functions to simplify the ‘PatentsView’ API (<http://www. noarch
patentsview.org/api/doc.html>) query language, send GET and POST requests
to the API’s seven endpoints, and parse the data that comes back. / MIT
r-pathlibr 0.1.0 An OO Interface for path manipulation, emulating pythons pathlib. / MIT noarch
r-pathmapping 1.0.2 Functions to compute and display the area-based deviation between spatial linux-
paths and to compute a mapping based on minimizing area and distance-based 64,
cost. For details, see: Mueller, S. T., Perelman, B. S., & Veinott, E. S. (2016) osx-
<DOI:10.3758/s13428-015-0562-7>. / GPL-2 64,
win-
64


Name Version
r-patternator 0.1.0 Provides a set of functions to efficiently recognize and clean the continuous noarch
dorsal pattern of a female brown anole lizard (Anolis sagrei) traced from ‘Im-
ageJ’, an open platform for scientific image analysis (see <https://imagej.net>
for more information), and extract common features such as the pattern sinu-
osity indices, coefficient of variation, and max-min width. / GPL-2
r-pawacc 1.2.2 This is a collection of functions to process, format and store accelerometer noarch
data. / GPL-2
r-pawls 1.0.0 Efficient algorithms for fitting weighted least squares regression with linux-
eqn{L_{1}}{L1} regularization on both the coefficients and weight vectors, 64,
which is able to perform simultaneous variable selection and outliers detection osx-
efficiently. / GPL-2 64,
win-
64
r-paws.common 0.2.0 Functions for making low-level API requests to Amazon Web Services <https: noarch
//aws.amazon.com>. The functions handle building, signing, and sending
requests, and receiving responses. They are designed to help build higher-
level interfaces to individual services, such as Simple Storage Service (S3). /
Apache License (>= 2.0)
r-pbapply 1.4_2 A lightweight package that adds progress bar to vectorized R functions (’*ap- noarch
ply’). The implementation can easily be added to functions where showing the
progress is useful (e.g. bootstrap). The type and style of the progress bar (with
percentages or remaining time) can be set through options. Supports several
parallel processing backends. / GPL-2
r-pbdncdf4 0.1_4 This package adds collective parallel read and write capability to the R package
linux-
ncdf4 version 1.8. Typical use is as a parallel NetCDF4 file reader in SPMD 64,
style programming. Each R process reads and writes its own data in a synchro- osx-
nized collective mode, resulting in faster parallel performance. Performance 64,
improvement is conditional on a parallel file system. / GPL-3 win-
64
r-pbdprof 0.3_1 MPI profiling tools. / Mozilla Public License 2.0 osx-
64,
win-
64
r-pbdrpc 0.2_1 A very light implementation yet secure for remote procedure calls with uni- linux-
fied interface via ssh (OpenSSH) or plink/plink.exe (PuTTY). / Mozilla Public 64,
License 2.0 osx-
64,
win-
64
r-pbdzmq 0.3_3 ‘ZeroMQ’ is a well-known library for high-performance asynchronous mes- linux-
saging in scalable, distributed applications. This package provides high level 32,
R wrapper functions to easily utilize ‘ZeroMQ’. We mainly focus on inter- linux-
active client/server programming frameworks. For convenience, a minimal 64,
‘ZeroMQ’ library (4.2.2) is shipped with ‘pbdZMQ’, which can be used if no osx-
system installation of ‘ZeroMQ’ is available. A few wrapper functions com- 64,
patible with ‘rzmq’ are also provided. / GPL-3 win-
32,
win-
64


Name Version
r-pbibd 1.3 The PBIB designs are important type of incomplete block designs having wide noarch
area of their applications for example in agricultural experiments, in plant
breeding, in sample surveys etc. This package constructs various series of
PBIB designs and assists in checking all the necessary conditions of PBIB
designs and the association scheme on which these designs are based on. It
also assists in calculating the efficiencies of PBIB designs with any number
of associate classes. The package also constructs Youden-m square designs
which are Row-Column designs for the two-way elimination of heterogeneity.
The incomplete columns of these Youden-m square designs constitute PBIB
designs. With the present functionality, the package will be of immense im-
portance for the researchers as it will help them to construct PBIB designs,
to check if their PBIB designs and association scheme satisfy various neces-
sary conditions for the existence, to calculate the efficiencies of PBIB designs
based on any association scheme and to construct Youden-m square designs for
the two-way elimination of heterogeneity. R. C. Bose and K. R. Nair (1939)
<http://www.jstor.org/stable/40383923>. / GPL-2
r-pbimisc 1.0 A set of datasets and functions used in the book ‘Modele liniowe i mieszane noarch
w R, wraz z przykladami w analizie danych’. Datasets either come from real
studies or are created to be as similar as possible to real studies. / GPL-2
r-pbivnorm 0.6.0 Provides a vectorized R function for calculating probabilities from a standard linux-
bivariate normal CDF. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64
r-pbkrtest 0.4_7 Test in mixed effects models. Attention is on mixed effects models as imple- linux-
mented in the ‘lme4’ package. This package implements a parametric boot- 32,
strap test and a Kenward Roger modification of F-tests for linear mixed effects linux-
models and a parametric bootstrap test for generalized linear mixed models. / 64,
GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64
r-pbm 1.1.0 Binding models which are useful when analysing protein-ligand inter- noarch
actions by techniques such as Biolayer Interferometry (BLI) or Sur-
face Plasmon Resonance (SPR). Naman B. Shah, Thomas M. Dun-
can (2014) <doi:10.3791/51383>. Hoang H. Nguyen et al. (2015)
<doi:10.3390/s150510481>. After initial binding parameters are known, bind-
ing curves can be simulated and parameters can be varied. The models within
this package may also be used to fit a curve to measured binding data using
non-linear regression. / MIT


Name Version
r-pbmcapply 1.5.0 A light-weight package helps you track and visualize the progress of parallel linux-
version of vectorized R functions (mc*apply). Parallelization (mc.core > 1) 64,
works only on *nix (Linux, Unix such as macOS) system due to the lack of osx-
fork() functionality, which is essential for mc*apply, on Windows. / MIT 64,
win-
64
r-pbo 1.3.4 Following the method of Bailey et al., computes for a collection of candidate noarch
models the probability of backtest overfitting, the performance degradation
and probability of loss, and the stochastic dominance. / MIT
r-pbrackets 1.0 Adds different kinds of brackets to a plot, including braces, chevrons, paren- noarch
theses or square brackets. / GPL (>= 2.0)
r-pbrf 1.0.0 Provides three ways to estimate the probability of being in response function linux-
(PBRF) The estimates are presented in Tsai, Luo and Crowley (2017) <doi: 64,
10.1007/978-981-10-0126-0_10>. / GPL-2 osx-
64,
win-
64
r-pbs 1.1 Periodic B Splines Basis / GPL-2 noarch
r-pbsddesolve 1.12.4Routines for solving systems of delay differential equations by interfacing nu- linux-
merical routines written by Simon N. Wood , with contributions by Benjamin 64,
J. Cairns. These numerical routines first appeared in Simon Wood’s ‘solv95’ osx-
program. This package includes a vignette and a complete user’s guide. ‘PB- 64,
Sddesolve’ originally appeared on CRAN under the name ‘ddesolve’. That win-
version is no longer supported. The current name emphasizes a close associa- 64
tion with other PBS packages, particularly ‘PBSmodelling’. / GPL-2
r-pbsmapping 2.72.1This software has evolved from fisheries research conducted at the Pacific Bi- linux-
ological Station (PBS) in ‘Nanaimo’, British Columbia, Canada. It extends the 64,
R language to include two-dimensional plotting features similar to those com- osx-
monly available in a Geographic Information System (GIS). Embedded C code 64,
speeds algorithms from computational geometry, such as finding polygons that win-
contain specified point events or converting between longitude-latitude and 64
Universal Transverse Mercator (UTM) coordinates. Additionally, we include
‘C’ code developed by Angus Johnson for the ‘Clipper’ library, data for a
global shoreline, and other data sets in the public domain. Under the user’s
R library directory ‘.libPaths()’, specifically in ‘./PBSmapping/doc’, a com-
plete user’s guide is offered and should be consulted to use package functions
effectively. / GPL-2
r-pbsmodelling 2.68.8Provides software to facilitate the design, testing, and operation of computer linux-
models. It focuses particularly on tools that make it easy to construct and 64,
edit a customized graphical user interface (‘GUI’). Although our simplified osx-
‘GUI’ language depends heavily on the R interface to the ‘Tcl/Tk’ package, 64,
a user does not need to know ‘Tcl/Tk’. Examples illustrate models built with win-
other R packages, including ‘PBSmapping’, ‘PBSddesolve’, and ‘BRugs’. A 64
complete user’s guide ‘PBSmodelling-UG.pdf’ shows how to use this package
effectively. / GPL-2
r-pbv 0.2_16Computes probabilities of the bivariate normal distribution
linux-
in a vectorized R function (Drezner & Wesolowsky, 1990, 64,
<doi:10.1080/00949659008811236>). / GPL-2 osx-
64,
win-
64


Name Version
r-pca4ts 0.1 To seek for a contemporaneous linear transformation for a multivariate time linux-
series such that the transformed series is segmented into several lower- 64,
dimensional subseries, and those subseries are uncorrelated with each other osx-
both contemporaneously and serially. / GPL-2 64,
win-
64
r-pcamixdata 3.1 Implements principal component analysis, orthogonal rotation and multiple noarch
factor analysis for a mixture of quantitative and qualitative variables. / GPL
(>= 2.0)
r-pcapp 1.9_73Provides functions for robust PCA by projection pursuit. The methods are linux-
described in Croux et al. (2006) <doi:10.2139/ssrn.968376>, Croux et al. 32,
(2013) <doi:10.1080/00401706.2012.727746>, Todorov and Filzmoser (2013) linux-
<doi:10.1007/978-3-642-33042-1_31>. / GPL (>= 3) 64,
osx-
64,
win-
32,
win-
64
r-pcensmix 1.2_1 Functions for generating progressively Type-II censored data in a mixture noarch
structure and fitting models using a constrained EM algorithm. It can also
create a progressive Type-II censored version of a given real dataset to be con-
sidered for model fitting. / GPL-2
r-pcfam 1.0 We provide several algorithms to compute the genotype ancestry scores (such noarch
as eigenvector projections) in the case where highly correlated individuals are
involved. / GPL-2
r-pcg 1.1 The package solves linear system of equations Ax=b by using Preconditioned noarch
Conjugate Gradient Algorithm where A is real symmetric positive definite ma-
trix. A suitable preconditioner matrix may be provided by user. This can also
be used to minimize quadratic function (x’Ax)/2-bx for unknown x. / GPL-2
r-pch 1.3 Using piecewise constant hazards models is a very flexible approach for the noarch
analysis of survival data. The time line is divided into sub-intervals; for each
interval, a different hazard is estimated using Poisson regression. / GPL-2
r-pcict 0.5_4.1
Provides a work-alike to R’s POSIXct class which implements 360- and 365-linux-
day calendars in addition to the gregorian calendar. / GPL-2 64,
osx-
64,
win-
64
r-pcirt 0.2.4 Estimates the multidimensional polytomous Rasch model (Rasch, 1961) with linux-
conditional maximum likelihood estimation. / GPL-3 64,
osx-
64,
win-
64


r-pcit 1.5_3 Apply Partial Correlation coefficient with Information Theory (PCIT) to a linux-
correlation matrix. The PCIT algorithm identifies meaningful correlations to 64,
define edges in a weighted network. The algorithm can be applied to any osx-
correlation-based network including but not limited to gene co-expression net- 64,
works. To reduce compute time by making use of multiple compute cores, win-
simply run PCIT on a computer with has multiple cores and also has the Rmpi 64
package installed. PCIT will then auto-detect the multicore environment and
run in parallel mode without the need to rewrite your scripts. This makes
scripts, using PCIT, portable across single core (or no Rmpi package installed)
computers which will run in serial mode and multicore (with Rmpi package
installed) computers which will run in parallel mode. / GPL-3
r-pco 1.0.1 Computation of the Pedroni (1999) panel cointegration test statistics. Reported noarch
are the empirical and the standardized values. / GPL-2
r-pcse 1.9.1.1A function to estimate panel-corrected standard errors. Data may contain bal- noarch
anced or unbalanced panels. / GPL-3
r-pcsinr 0.1.0 Parallel Constraint Satisfaction (PCS) models are an increasingly common noarch
class of models in Psychology, with applications to reading and word recogni-
tion (McClelland & Rumelhart, 1981), judgment and decision making (Glöck-
ner & Betsch, 2008; Glöckner, Hilbig, & Jekel, 2014), and several other fields
(e.g. Read, Vanman, & Miller, 1997). In each of these fields, they provide
a quantitative model of psychological phenomena, with precise predictions
regarding choice probabilities, decision times, and often the degree of confi-
dence. This package provides the necessary functions to create and simulate
basic Parallel Constraint Satisfaction networks within R. / GPL-3
r-pdc 1.0.3 Permutation Distribution Clustering is a clustering method for time series. Dis- linux-
similarity of time series is formalized as the divergence between their permu- 64,
tation distributions. The permutation distribution was proposed as measure of osx-
the complexity of a time series. / GPL-3 64,
win-
64
r-pder 1.0_1 Data sets for the Panel Data Econometrics with R noarch
<doi:10.1002/9781119504641> book. / GPL-2
r-pdfestimator 0.1_3 Farmer, J., D. Jacobs (2108) <DOI:10.1371/journal.pone.0196937>. A non- linux-
parametric density estimator based on the maximum-entropy method. Accu- 64,
rately predicts a probability density function (PDF) for random data using a osx-
novel iterative scoring function to determine the best fit without overfitting to 64,
the sample. / GPL-2 win-
64
r-pdftables 0.1 Allows the user to convert PDF tables to formats more amenable to analysis noarch
(‘.csv’, ‘.xml’, or ‘.xlsx’) by wrapping the PDFTables API. In order to use the
package, the user needs to sign up for an API account on the PDFTables web-
site (<https://pdftables.com/pdf-to-excel-api>). The package works by taking
a PDF file as input, uploading it to PDFTables, and returning a file with the
extracted data. / CC0


Name Version
r-pdftools 2.2 Utilities based on ‘libpoppler’ for extracting text, fonts, attachments and meta- linux-
data from a PDF file. Also supports high quality rendering of PDF documents 64,
into PNG, JPEG, TIFF format, or into raw bitmap vectors for further process- osx-
ing in R. / MIT file LICENSE 64,
win-
32,
win-
64
r-pdist 1.2 Computes the euclidean distance between rows of a matrix X and rows of an- linux-
other matrix Y. Previously, this could be done by binding the two matrices 64,
together and calling ‘dist’, but this creates unnecessary computation by com- osx-
puting the distances between a row of X and another row of X, and likewise 64,
for Y. pdist strictly computes distances across the two matrices, not within the win-
same matrix, making computations significantly faster for certain use cases. / 64
GPL-3
r-pdm 0.1 Measures real distances in pictures. With PDM() function, you can choose one noarch
‘*.jpg’ file, select the measure in mm of scale, starting and and finishing point
in the graphical scale, the name of the measure, and starting and and finishing
point of the measures. After, ask the user for a new measure. / GPL-3
r-pdsce 1.2 A package to compute and tune some positive definite and sparse covariance linux-
estimators / GPL-2 64,
osx-
64,
win-
64
r-pdshiny 0.1.0 Interactive shiny application for working with Probability Distributions. Cal- noarch
culations and Graphs are provided. / GPL-2
r-peacock.test 1.0 The original definition of the two and three dimensional Kolmogorov-Smirnov noarch
two-sample test statistics given by Peacock (1983) is implemented. Two R-
functions: peacock2 and peacock3, are provided to compute the test statistics
in two and three dimensional spaces, respectively. Note the Peacock test is
different from the Fasano and Franceschini test (1987). The latter is a variant
of the Peacock test. / GPL-2
r-peacots 1.3 Calculates the periodogram of a time series, maximum-likelihood fits an noarch
Ornstein-Uhlenbeck state space (OUSS) null model and evaluates the statisti-
cal significance of periodogram peaks against the OUSS null hypothesis. The
OUSS is a parsimonious model for stochastically fluctuating variables with
linear stabilizing forces, subject to uncorrelated measurement errors. Contrary
to the classical white noise null model for detecting cyclicity, the OUSS model
can account for temporal correlations typically occurring in ecological and ge-
ological time series. / GPL-3
r-peakerror 2017.06.19
Chromatin immunoprecipitation DNA sequencing results in genomic tracks linux-
that show enriched regions or peaks where proteins are bound. This package 64,
implements fast C code that computes the true and false positives with respect osx-
to a database of annotated regions. / GPL-3 64,
win-
64
r-peakpick 0.11 Biologically inspired methods for detecting peaks in one-dimensional data, noarch
such as time series or genomics data. The algorithms were originally designed
by Weber, Ramachandran, and Henikoff, see documentation. / MIT


Name Version
r-peakram 1.0.2 When working with big data sets, RAM conservation is critically important. noarch
However, it is not always enough to just monitor the size of the objects cre-
ated. So-called copy-on-modify behavior, characteristic of R, means that some
expressions or functions may require an unexpectedly large amount of RAM
overhead. For example, replacing a single value in a matrix duplicates that
matrix in the back-end, making this task require twice as much RAM as that
used by the matrix itself. This package makes it easy to monitor the total and
peak RAM used so that developers can quickly identify and eliminate RAM
hungry code. / GPL-2
r-peaksegdisk 2019.9.10
Disk-based implementation of Functional Pruning Optimal Partitioning with linux-
up-down constraints <arXiv:1810.00117> for single-sample peak calling (in- 64,
dependently for each sample and genomic problem), can handle huge data sets osx-
(10^7 or more). / GPL-3 64,
win-
64
r-peaksegdp 2017.08.15
A quadratic time dynamic programming algorithm can be used to compute an linux-
approximate solution to the problem of finding the most likely changepoints 64,
with respect to the Poisson likelihood, subject to a constraint on the number of osx-
segments, and the changes which must alternate: up, down, up, down, etc. For 64,
more info read <http://proceedings.mlr.press/v37/hocking15.html> PeakSeg: win-
constrained optimal segmentation and supervised penalty learning for peak 64
detection in count data by TD Hocking et al, proceedings of ICML2015. /
GPL-3
r-pear 1.2 Package for estimating periodic autoregressive models. Datasets: monthly noarch
ozone and Fraser riverflow. Plots: periodic versions of boxplot, auto/partial
correlations, moving-average expansion. / GPL-2
r-pearson7 1.0_2 Supports maximum likelihood inference for the Pearson VII distribution with noarch
shape parameter 3/2 and free location and scale parameters. This distribution
is relevant when estimating the velocity of processive motor proteins with ran-
dom detachment. / GPL-2
r-pearsonds 1.1 Implementation of the Pearson distribution system, including full support for linux-
the (d,p,q,r)-family of functions for probability distributions and fitting via 64,
method of moments and maximum likelihood method. / GPL-2 osx-
64,
win-
64
r-pearsonica 1.2_4 The Pearson-ICA algorithm is a mutual information-based method for blind noarch
separation of statistically independent source signals. It has been shown that
the minimization of mutual information leads to iterative use of score func-
tions, i.e. derivatives of log densities. The Pearson system allows adaptive
modeling of score functions. The flexibility of the Pearson system makes it
possible to model a wide range of source distributions including asymmetric
distributions. The algorithm is designed especially for problems with asym-
metric sources but it works for symmetric sources as well. / GPL-2
r-pedigreemm 0.3_3 Fit pedigree-based mixed-effects models. / GPL-2 linux-
64,
osx-
64,
win-
64


Name Version
r-pedigreetools 0.1 Tools to sort, edit and prune pedigrees and to extract the inbreeding coefficients linux-
and the relationship matrix (includes code for pedigrees from self-pollinated 64,
species). The use of pedigree data is central to genetics research within the osx-
animal and plant breeding communities to predict breeding values. The rela- 64,
tionship matrix between the individuals can be derived from pedigree struc- win-
ture following the algorithms described for example in Vazquez et al., 2010 64
<doi:10.2527/jas.2009-1952>. / GPL-3
r-pedometrics 0.6_6 Functions to employ many of the tools and techniques used in the field of linux-
pedometrics. / GPL-2 64,
osx-
64,
win-
64
r- 2.2.1 Provides functions to perform the peer performance analysis of funds’ returns noarch
peerperformance as described in Ardia and Boudt (2018) <doi:10.1016/j.jbankfin.2017.10.014>.
/ GPL-2
r-pegrouptesting 1.0 The population proportion using group testing can be estimated by different noarch
methods. Four functions including p.mle(), p.gart(), p.burrow() and p.order()
are provided to implement four estimating methods including the maximum
likelihood estimate, Gart’s estimate, Burrow’s estimate, and order statistic es-
timate. / GPL-2
r-pemm 1.0 This package provides functions to perform multivariate Gaussian parameter noarch
estimation based on data with abundance-dependent missingness. It imple-
ments a penalized Expectation-Maximization (EM) algorithm. The package is
tailored for but not limited to proteomics data applications, in which a large
proportion of the data are often missing-not-at-random with lower values (or
absolute values) more likely to be missing. / GPL-3
r-penalized 0.9_51Fitting possibly high dimensional penalized regression models. The penalty linux-
structure can be any combination of an L1 penalty (lasso and fused lasso), an 64,
L2 penalty (ridge) and a positivity constraint on the regression coefficients. osx-
The supported regression models are linear, logistic and Poisson regression 64,
and the Cox Proportional Hazards model. Cross-validation routines allow op- win-
timization of the tuning parameters. / GPL-2 64
r-pencoxfrail 1.0.1 A regularization approach for Cox Frailty Models by penalization methods is linux-
provided. / GPL-2 64,
osx-
64,
win-
64
r-penmsm 0.99 Structured fusion Lasso penalized estimation of multi-state models with the linux-
penalty applied to absolute effects and absolute effect differences (i.e., effects 64,
on transition-type specific hazard rates). / GPL-2 osx-
64,
win-
64
r-pense 1.2.5 Robust penalized elastic net S and MM estimator for linear regression. The linux-
method is described in detail in Cohen Freue, G. V., Kepplinger, D., Salibian- 64,
Barrera, M., and Smucler, E. (2017) <https://gcohenfr.github.io/pdfs/PENSE_ osx-
manuscript.pdf>. / GPL-2 64,
win-
64


Name Version
r-pepsavims 0.9.1 An implementation of the data processing and data analysis portion of a noarch
pipeline named the PepSAVI-MS which is currently under development by
the Hicks laboratory at the University of North Carolina. The statistical anal-
ysis package presented herein provides a collection of software tools used to
facilitate the prioritization of putative bioactive peptides from a complex bio-
logical matrix. Tools are provided to deconvolute mass spectrometry features
into a single representation for each peptide charge state, filter compounds to
include only those possibly contributing to the observed bioactivity, and pri-
oritize these remaining compounds for those most likely contributing to each
bioactivity data set. / CC BY-NC-SA 4.0
r-peptides 2.4.1 Includes functions to calculate several physicochemical properties and indices linux-
for amino-acid sequences as well as to read and plot ‘XVG’ output files from 64,
the ‘GROMACS’ molecular dynamics package. / GPL-2 osx-
64,
win-
64
r-perc 0.1.3 To find the certainty of dominance interactions with indirect interactions being noarch
considered. / GPL-2
r-perccal 1.0 Contains functions which allow the user to compute confidence intervals linux-
quickly using the double bootstrap-based percentile calibrated (‘perc-cal’) 64,
method for linear regression coefficients. ‘perccal_interval()’ is the primary osx-
user-facing function within this package. / GPL-3 64,
win-
64
r- 1.5.3 Collection of econometric functions for performance and risk analysis. In linux-
performanceanalytics addition to standard risk and performance metrics, this package aims to aid 64,
practitioners and researchers in utilizing the latest research in analysis of non- osx-
normal return streams. In general, it is most tested on return (rather than price) 64,
data on a regular scale, but most functions will work with irregular return data win-
as well, and increasing numbers of functions will work with P&L or price data 64
where possible. / GPL-2 | GPL-3
r-periodictable 0.1.2 Provides a dataset containing properties for chemical elements. Helper func- noarch
tions are also provided to access some atomic properties. / GPL-3
r-perm 1.0_0.0
Perform Exact or Asymptotic permutation tests / GPL linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-permalgo 1.1 This version of the permutational algorithm generates a dataset in which event noarch
and censoring times are conditional on an user-specified list of covariates,
some or all of which are time-dependent. / GPL-2


Name Version
r-permallows 1.13 Includes functions to work with the Mallows and Generalized Mallows Mod- linux-
els. The considered distances are Kendall’s-tau, Cayley, Hamming and Ulam 64,
and it includes functions for making inference, sampling and learning such osx-
distributions, some of which are novel in the literature. As a by-product, 64,
PerMallows also includes operations for permutations, paying special atten- win-
tion to those related with the Kendall’s-tau, Cayley, Ulam and Hamming dis- 64
tances. It is also possible to generate random permutations at a given distance,
or with a given number of inversions, or cycles, or fixed points or even with a
given length on LIS (longest increasing subsequence). / GPL-2
r-permdep 1.0.2 Implementations of permutation approach to hypothesis testing for quasi- linux-
independence of truncation time and failure time. The implemented ap- 64,
proaches are powerful against non-monotone alternatives and thereby offer osx-
protection against erroneous assumptions of quasi-independence. The pro- 64,
posed tests use either a conditional or an unconditional method to eval- win-
uate the permutation p-value. The conditional method was first devel- 64
oped in Tsai (1980) <doi:10.2307/2336059> and Efron and Petrosian (1992)
<doi:10.1086/171931>. The unconditional method provides a valid approxi-
mation to the conditional method, yet computationally simpler and does not
hold fixed the size of each risk sets. Users also have an option to carry out the
proposed permutation tests in a parallel computing fashion. / GPL-3
r-permgs 0.2.5 Permutational group-sequential tests for time-to-event data based on the log- noarch
rank test statistic. Supports exact permutation test when the censoring dis-
tributions are equal in the treatment and the control group and approximate
imputation-permutation methods when the censoring distributions are differ-
ent. / GPL-3
r-permute 0.9_5 A set of restricted permutation designs for freely exchangeable, line transects noarch
(time series), and spatial grid designs plus permutation of blocks (groups of
samples) is provided. ‘permute’ also allows split-plot designs, in which the
whole-plots or split-plots or both can be freely-exchangeable or one of the
restricted designs. The ‘permute’ package is modelled after the permutation
schemes of ‘Canoco 3.1’ (and later) by Cajo ter Braak. / GPL-2
r- 1.0 Translate words from English to Persian (Over 67,000 words) / GPL-2 noarch
persiandictionary
r- 1.0 Allows users to stem Persian texts for text analysis. / GPL-2 noarch
persianstemmer
r-perturb 2.10 Use the perturb() function to evaluates collinearity by adding random noise noarch
to selected variables (Hendrickx & Pelzer 2004). The colldiag function() cal-
culates condition numbers and variance decomposition proportions to test for
collinearity and uncover its sources (Belsley 1980). / GPL-2
r-pesel 0.7.2 Automatic estimation of number of principal components in PCA with noarch
PEnalized SEmi-integrated Likelihood (PESEL). See Piotr Sobczyk,
Malgorzata Bogdan, Julie Josse ‘Bayesian dimensionality reduc-
tion with PCA using penalized semi-integrated likelihood’ (2017)
<doi:10.1080/10618600.2017.1340302>. / GPL-3
r-pet 0.5.1 Implementation of different analytic/direct and iterative reconstruction meth- linux-
ods of radon transformed data such as PET data. It also offer the possibility to64,
simulate PET data. / GPL-2 osx-
64,
win-
64


Name Version
r-petfinder 2.0.0 Wrapper of the ‘Petfinder API’ <https://www.petfinder.com/developers/v2/ noarch
docs/> that implements methods for interacting with and extracting data from
the ‘Petfinder’ database. The ‘Petfinder REST API’ allows access to the
‘Petfinder’ database, one of the largest online databases of adoptable animals
and animal welfare organizations across North America. / MIT
r-petitr 1.0 Calculates the relative growth rate (RGR) of a series of individuals by building noarch
a life table and solving the Lotka-Birch equation. (See Birch, L. C. 1948. The
intrinsic rate of natural increase of an insect population. - Journal of Animal
Ecology 17: 15-26) <doi:10.2307/1605>. / GPL-2
r-pgam 0.4.15This work is an extension of the state space model for Poisson count data, linux-
Poisson-Gamma model, towards a semiparametric specification. Just like 64,
the generalized additive models (GAM), cubic splines are used for covariate osx-
smoothing. The semiparametric models are fitted by an iterative process that 64,
combines maximization of likelihood and backfitting algorithm. / GPL-2 win-
64
r-pgbart 0.6.16The Particle Gibbs sampler and Gibbs/Metropolis-Hastings sampler were im- linux-
plemented to fit Bayesian additive regression tree model. Construction of 64,
the model (training) and prediction for a new data set (testing) can be sep- osx-
arated. Our reference papers are: Lakshminarayanan B, Roy D, Teh Y 64,
W. Particle Gibbs for Bayesian additive regression trees[C], Artificial In- win-
telligence and Statistics. 2015: 553-561, <http://proceedings.mlr.press/v38/ 64
lakshminarayanan15.pdf> and Chipman, H., George, E., and McCulloch R.
(2010) Bayesian Additive Regression Trees. The Annals of Applied Statistics,
4,1, 266-298, <doi:10.1214/09-aoas285>. / GPL-2
r-pgdraw 1.1 Generates random samples from the Polya-Gamma distribution using linux-
an implementation of the algorithm described in J. Windle’s PhD the- 64,
sis (2013) <https://repositories.lib.utexas.edu/bitstream/handle/2152/21842/ osx-
WINDLE-DISSERTATION-2013.pdf>. The underlying implementation is in 64,
C. / GPL-3 win-
64
r-pgee 1.5 Fits penalized generalized estimating equations to longitudinal data with high- noarch
dimensional covariates. / GPL-2
r-pgee.mixed 0.1.0 Perform simultaneous estimation and variable selection for correlated bivariate linux-
mixed outcomes (one continuous outcome and one binary outcome per clus- 64,
ter) using penalized generalized estimating equations. In addition, clustered osx-
Gaussian and binary outcomes can also be modeled. The SCAD, MCP, and 64,
LASSO penalties are supported. Cross-validation can be performed to find the win-
optimal regularization parameter(s). / GPL-2 64
r-pgls 0.0_1 Based on the Generalized Least Square model for comparative Phylogenetics noarch
(ref). / GPL-2
‘r-pgm2 1.0_1 Construction method of nested resolvable designs from a projective geometry noarch
<https://sites.google.com/site/mohamedlaibwebpage/
defined on Galois field of order 2. The obtained Resolvable designs are used
>‘_ to build uniform design. The presented results are based on <https://eudml.
org/doc/219563> and A. Boudraa et al. (See references). / GPL-3
r-pgmm 1.2.3 Carries out model-based clustering or classification using parsimonious Gaus- linux-
sian mixture models. McNicholas and Murphy (2008) <doi:10.1007/s11222- 64,
008-9056-0>, McNicholas (2010) <doi:10.1016/j.jspi.2009.11.006>, McNi- osx-
cholas and Murphy (2010) <doi:10.1093/bioinformatics/btq498>, McNicholas 64,
et al. (2010) <doi:10.1016/j.csda.2009.02.011>. / GPL-2 win-
64


Name Version
r-pgnorm 2.0 Evaluation of the pdf and the cdf of the univariate, noncentral, p-generalized noarch
normal distribution. Sampling from the univariate, noncentral, p-generalized
normal distribution using either the p-generalized polar method, the p-
generalized rejecting polar method, the Monty Python method, the Ziggurat
method or the method of Nardon and Pianca. The package also includes rou-
tines for the simulation of the bivariate, p-generalized uniform distribution and
the simulation of the corresponding angular distribution. / GPL-2
r-pgsc 1.0.0 Computes the generalized synthetic control estimator described in Powell linux-
(2017) <doi:10.7249/WR1142>. Provides both point estimates, and hypoth- 64,
esis testing. / GPL-2 osx-
64,
win-
64
r-ph2bayes 0.0.2 An implementation of Bayesian single-arm phase II design methods for linux-
binary outcome based on posterior probability (Thall and Simon (1994) 64,
<doi:10.2307/2533377>) and predictive probability (Lee and Liu (2008) osx-
<doi:10.1177/1740774508089279>). / GPL-3 64,
win-
64
r-ph2hetero 1.0.2 Implementation of Jones (2007) <doi:10.1016/j.cct.2007.02.008> , linux-
Tournoux-Facon (2011) <doi:10.1002/sim.4148> and Parashar (2016) 64,
<doi:10.1002/pst.1742> designs. / GPL-3 osx-
64,
win-
64
r-ph2mult 0.1.1 Provide multinomial design methods under intersection-union test (IUT) and noarch
union-intersection test (UIT) scheme for Phase II trial. The design types in-
clude : Minimax (minimize the maximum sample size), Optimal (minimize
the expected sample size), Admissible (minimize the Bayesian risk) and Max-
power (maximize the exact power level). / GPL-2
r-phase123 2.1 Contains three simulation functions for implementing the entire Phase 123 linux-
trial and the separate Eff-Tox and Phase 3 portions of the trial, which may 64,
be beneficial for use on clusters. The functions AssignEffTox() and Random- osx-
izeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() 64,
determines the optimal dose to continue with during Phase 3. The functions win-
ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival 64
for the agent doses and control and ReturnOCS() gives the operating charac-
teristics of the design. / GPL-2
r-phd 0.1 Provides permutation methods for testing in high-dimensional linear models. noarch
The tests are often robust against heteroscedasticity and non-normality and
usually perform well under anti-sparsity. See Hemerik and Goeman (2018)
<doi:10.1007/s11749-017-0571-1>. / GPL-3
r-pheatmap 1.0.12Implementation of heatmaps that offers more control over dimensions and ap- noarch
pearance. / GPL-2
r-phenability 2.0 An alternative to carrying out phenotypic adaptability and stability analyses, noarch
taking into account nonparametric statistics. Can be used as a robust approach,
less sensitive to departures from common genotypic, environmental, and GxE
effects data assumptions (e.g., normal distribution of errors). / GPL-3


Name Version
r-phenex 1.4_5 Provides some easy-to-use functions for spatial analyses of (plant-) phenolog- linux-
ical data sets and satellite observations of vegetation. / GPL-2 64,
osx-
64,
win-
64
r-pheno 1.6 Provides some easy-to-use functions for time series analyses of (plant-) pheno- linux-
logical data sets. These functions mainly deal with the estimation of combined 64,
phenological time series and are usually wrappers for functions that are already osx-
implemented in other R packages adapted to the special structure of phenolog- 64,
ical data and the needs of phenologists. Some date conversion functions to win-
handle Julian dates are also provided. / GPL-2 64
r-phenocamapi 0.1.5 A bundle to facilitate working with PhenoCam timeseries and data. The user noarch
would be able to obtain phenological time-series and site metadata from the
PhenoCam network <https://phenocam.sr.unh.edu/webcam/>. / AGPL-3
r-pheval 0.5.4 Provides tools for the evaluation of the goodness of fit and the predictive ca- noarch
pacity of the proportional hazards model. / GPL (>= 2.0)
r-phidelta 1.0.1 Analysis of features by phi delta diagrams. In particular, functions for reading noarch
data and calculating phi and delta as well as the functionality to plot it. More-
over it is possible to do further analysis on the data by generating rankings.
For more information on phi delta diagrams, see also Giuliano Armano (2015)
<doi:10.1016/j.ins.2015.07.028>. / GPL-2
r-phmm 0.7_11Fits proportional hazards model incorporating random effects using an linux-
EM algorithm using Markov Chain Monte Carlo at E-step. Vaida 64,
and Xu (2000) <DOI:10.1002/1097-0258(20001230)19:24%3C3309::AID- osx-
SIM825%3E3.0.CO;2-9>. / GPL-3 64,
win-
64
r-phonenumber 0.2.2 Convert English letters to numbers or numbers to English letters as on a tele- noarch
phone keypad. When converting letters to numbers, a character vector is re-
turned with A, B, or C becoming 2, D, E, or F becoming 3, etc. When convert-
ing numbers to letters, a character vector is returned with multiple elements
(i.e., 2 becomes a vector of A, B, and C). / MIT
r-phonics 1.3.2 Provides a collection of phonetic algorithms including Soundex, Metaphone, linux-
NYSIIS, Caverphone, and others. / BSD_2_clause 64,
osx-
64,
win-
64
r-phontools 0.2_2.1
Contains tools for the organization, display, and analysis of the sorts of data noarch
frequently encountered in phonetics research and experimentation, including
the easy creation of IPA vowel plots, and the creation and manipulation of
WAVE audio files. / BSD_2_clause
r-phreeqc 3.4.10A geochemical modeling program developed by the US Geological Survey that linux-
is designed to perform a wide variety of aqueous geochemical calculations, 64,
including speciation, batch-reaction, one-dimensional reactive-transport, and osx-
inverse geochemical calculations. / GPL-3 64,
win-
64


Name Version
r-phtt 3.1.2 The package provides estimation procedures for panel data with large dimen- noarch
sions n, T, and general forms of unobservable heterogeneous effects. Particu-
larly, the estimation procedures are those of Bai (2009) and Kneip, Sickles, and
Song (2012), which complement one another very well: both models assume
the unobservable heterogeneous effects to have a factor structure. The method
of Bai (2009) assumes that the factors are stationary, whereas the method of
Kneip et al. (2012) allows the factors to be non-stationary. Additionally, the
‘phtt’ package provides a wide range of dimensionality criteria in order to esti-
mate the number of the unobserved factors simultaneously with the remaining
model parameters. / GPL-2
r-phuassess 1.1 Assessment of habitat selection by means of the permutation-based combina- noarch
tion of sign tests (Fattorini et al., 2014 <DOI:10.1007/s10651-013-0250-7>).
To exemplify the application of this procedure, habitat selection is assessed for
a population of European Brown Hares settled in central Italy. / GPL-2
r-phuse 0.1.8 Make it easy to review, download and execute scripts stored in Github ‘phuse- noarch
scripts’ repository <https://github.com/phuse-org/phuse-scripts>. Some ex-
amples included show the web application framework using the script meta-
data. The ‘PhUSE’ is Pharmaceutical Users Software Exchange <http://www.
phuse.eu>. / MIT
r-phyclust 0.1_25Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time linux-
Markov Chain model-based approach to identify population structure from 64,
molecular data without assuming linkage equilibrium. The package phyclust osx-
(Chen 2011) provides a convenient implementation of phyloclustering for 64,
DNA and SNP data, capable of clustering individuals into subpopulations win-
and identifying molecular sequences representative of those subpopulations. 64
It is designed in C for performance, interfaced with R for visualization, and
incorporates other popular open source programs including ms (Hudson
2002) <doi:10.1093/bioinformatics/18.2.337>, seq-gen (Rambaut and Grassly
1997) <doi:10.1093/bioinformatics/13.3.235>, Hap-Clustering (Tzeng
2005) <doi:10.1002/gepi.20063> and PAML baseml (Yang 1997, 2007)
<doi:10.1093/bioinformatics/13.5.555>, <doi:10.1093/molbev/msm088>, for
simulating data, additional analyses, and searching the best tree. See the
phyclust website for more information, documentations and examples. /
GPL-2
r-phylin 2.0 The spatial interpolation of genetic distances between samples is based on a noarch
modified kriging method that accepts a genetic distance matrix and generates
a map of probability of lineage presence. This package also offers tools to
generate a map of potential contact zones between groups with user-defined
thresholds in the tree to account for old and recent divergence. Additionally, it
has functions for IDW interpolation using genetic data and midpoints. / GPL-2
r-phyloclim 0.9.5 Implements some methods in phyloclimatic modeling: estimation of ancestral noarch
climatic niches, age-range-correlation, niche equivalency test and background-
similarity test. / GPL-2
r-phylogr 1.0.10Manipulation and analysis of phylogenetically simulated data sets and phylo- noarch
genetically based analyses using GLS. / GPL-2
r-phylogram 2.1.0 Contains functions for developing phylogenetic trees as deeply- noarch
nested lists (dendrogram objects). Enables bi-directional conversion
between dendrogram and phylo objects (see Paradis et al (2004)
<doi:10.1093/bioinformatics/btg412>), and features several tools for
command-line tree manipulation and import/export via Newick parenthetic
text. / GPL-3


Name Version
r-phyloland 1.3 Phyloland package models a space colonization process mapped onto a phy- linux-
logeny, it aims at estimating limited dispersal and ecological competitive ex- 64,
clusion in a Bayesian MCMC statistical phylogeographic framework (please osx-
refer to phyloland-package help for details.) / GPL-2 64,
win-
64
r-phylomeasures 2.1 Given a phylogenetic tree T and an assemblage S of species represented as linux-
a subset of tips in T, we want to compute a measure of the diversity of the 64,
species in S with respect to T. The current package offers efficient algorithms osx-
that can process large phylogenetic data for several such measures. Most im- 64,
portantly, the package includes algorithms for computing efficiently the stan- win-
dardized versions of phylogenetic measures and their p-values, which are es- 64
sential for null model comparisons. Among other functions, the package pro-
vides efficient computation of richness-standardized versions for indices such
as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic
diversity index (PDI), and the corresponding indices of two-sample measures.
The package also introduces a new single-sample measure, the Core Ances-
tor Cost (CAC); the package provides functions for computing the value and
the standardised index of the CAC and, more than that, there is an extra func-
tion available that can compute exactly any statistical moment of the mea-
sure. The package supports computations under different null models, includ-
ing abundance-weighted models. / GPL-3
r-phylometrics 0.0.1 Provides functions to estimate statistical errors of phylogenetic metrics partic- noarch
ularly to detect binary trait influence on diversification, as well as a function to
simulate trees with fixed number of sampled taxa and trait prevalence. / GPL-2
r-phylotate 1.3 Functions to read and write APE-compatible phylogenetic trees in NEXUS noarch
and Newick formats, while preserving annotations. / MIT
r-phylotools 0.2.2 A collection of tools for building RAxML supermatrix using PHYLIP or noarch
aligned FASTA files. These functions will be useful for building large phy-
logenies using multiple markers. / GPL-2
r-phyreg 1.0.2 Provides general linear model facilities (single y-variable, multiple x-variables noarch
with arbitrary mixture of continuous and categorical and arbitrary interactions)
for cross-species data. The method is, however, based on the nowadays rather
uncommon situation in which uncertainty about a phylogeny is well repre-
sented by adopting a single polytomous tree. The theory is in A. Grafen
(1989, Proc. R. Soc. B 326, 119-157) and aims to cope with both recog-
nised phylogeny (closely related species tend to be similar) and unrecognised
phylogeny (a polytomy usually indicates ignorance about the true sequence of
binary splits). / GPL-2 | GPL-3
r-physactbedrest 1.0 Contains a function to categorize accelerometer readings collected in free- noarch
living (e.g., for 24 hours/day for 7 days), preprocessed and compressed as
counts (unit-less value) in a specified time period termed epoch (e.g., 1 minute)
as either bedrest (sleep) or active. The input is a matrix with a timestamp col-
umn and a column with number of counts per epoch. The output is the same
dataframe with an additional column termed bedrest. In the bedrest column
each line (epoch) contains a function-generated classification ‘br’ or ‘a’ de-
noting bedrest/sleep and activity, respectively. The package is designed to be
used after wear/nonwear marking function in the ‘PhysicalActivity’ package.
/ GPL-3


Name Version
r- 0.2_2 It provides a function wearingMarking for classification of monitor wear and noarch
physicalactivity nonwear time intervals in accelerometer data collected to assess physical ac-
tivity. The package also contains functions for making plot for accelerometer
data and obtaining the summary of various information including daily moni-
tor wear time and the mean monitor wear time during valid days. The revised
package version 0.2-1 improved the functions in the previous version regarding
speed and robustness. In addition, several functions were added: markDeliv-
ery can classify days for ActiGraph delivery by mail; markPAI can categorize
physical activity intensity level based on user-defined cut-points of accelerom-
eter counts. It also supports importing ActiGraph AGD files with readActi-
graph and queryActigraph functions. The package also better supports time
zones and daylight saving. / GPL-3
r-physiology 1.2.1 A variety of formulae are provided for estimation of physiologic characteristics linux-
of infants, children, and adults. Calculations include: body surface area, ideal 64,
weight, airway dead-space, the alveolar gas equation, and GFR. Each formula osx-
is referenced to the original publication. Future functions will cover more 64,
material with a focus on anaesthesia, critical care and peri-operative medicine. win-
/ GPL-3 64
r-picasso 1.3.1 Computationally efficient tools for fitting generalized linear model with con- linux-
vex or non-convex penalty. Users can enjoy the superior statistical property 64,
of non-convex penalty such as SCAD and MCP which has significantly less osx-
estimation error and overfitting compared to convex penalty such as lasso and 64,
ridge. Computation is handled by multi-stage convex relaxation and the Path- win-
wIse CAlibrated Sparse Shooting algOrithm (PICASSO) which exploits warm 64
start initialization, active set updating, and strong rule for coordinate pres-
election to boost computation, and attains a linear convergence to a unique
sparse local optimum with optimal statistical properties. The computation is
memory-optimized using the sparse matrix output. / GPL-3
r- 1.0.4 This function fits a reversible jump Bayesian piecewise exponential model linux-
pieceexpintensity that also includes the intensity of each event considered along with the rate 64,
of events. / GPL-2 osx-
64,
win-
64
r-piggyback 0.0.10Because larger (> 50 MB) data files cannot easily be committed to git, a dif- noarch
ferent approach is required to manage data associated with an analysis in a
GitHub repository. This package provides a simple work-around by allowing
larger (up to 2 GB) data files to piggyback on a repository as assets attached
to individual GitHub releases. These files are not handled by git in any way,
but instead are uploaded, downloaded, or edited directly by calls through the
GitHub API. These data files can be versioned manually by creating different
releases. This approach works equally well with public or private repositories.
Data can be uploaded and downloaded programmatically from scripts. No
authentication is required to download data from public repositories. / GPL-3
r-pigshift 1.0.1 Fits models of gene expression evolution to expression data from coregulated noarch
groups of genes, assuming inverse gamma distributed rate variation. / GPL-3


Name Version
r-pijavski 1.0 Global univariate minimization of Lipschitz functions is performed by using linux-
Pijavski method, which was published in Pijavski (1972) <DOI:10.1016/0041- 64,
5553(72)90115-2>. / LGPL-3 osx-
64,
win-
64
r-pillar 1.3.1 Provides a ‘pillar’ generic designed for formatting columns of data using the linux-
full range of colours provided by modern terminals. / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-pinfsc50 1.1.0 Genomic data for the plant pathogen Phytophthora infestans. It includes a noarch
variant file (‘VCF’), a sequence file (‘FASTA’) and an annotation file (‘GFF’).
This package is intended to be used as example data for packages that work
with genomic data. / GPL-3
r-pingr 1.1.2 Check if a remote computer is up. It can either just call the system ping com- linux-
mand, or check a specified TCP port. / MIT 64,
osx-
64,
win-
64
r-pinnacle.api 2.3.3 An interface to the API by Pinnacle that allows Pinnacle customers to interact noarch
with the sports market data in R.See <https://www.pinnacle.com/en/api> for
more information. The Pinnacle API can be used to place wagers, retrieve line
information, retrieve account information.Please be aware that the TOC of Pin-
nacle apply <https://www.pinnacle.com/en/termsandconditions>. An account
with Pinnacle is necessary to use the Pinnacle API. / GPL-3
r-pinochet 0.1.0 Packages data about the victims of the Pinochet regime as compiled by the noarch
Chilean National Commission for Truth and Reconciliation Report (1991,
ISBN:9780268016463). / MIT
r-pinp 0.0.8 A ‘PNAS’-alike style for ‘rmarkdown’, derived from the ‘Proceedings of the noarch
National Academy of Sciences of the United States of America’ (‘PNAS’, see
<https://www.pnas.org>) ‘LaTeX’ style, and adapted for use with ‘markdown’
and ‘pandoc’. / GPL-3
r-pins 0.1.2 Pin remote resources into a local cache to work offline, improve speed and noarch
avoid recomputing; discover and share resources in local folders, ‘GitHub’,
‘Kaggle’ or ‘RStudio Connect’. Resources can be anything from ‘CSV’,
‘JSON’, or image files to arbitrary R objects. / Apache License 2.0
r-pipefittr 0.1.2 To take nested function calls and convert them to a more readable form using noarch
pipes from package ‘magrittr’. / MIT


r-pipegs 0.4 Code for various permutation p-values estimation methods for gene set test. noarch
The description of corresponding methods can be found in the dissertation
of Yu He(2016) Efficient permutation P-value estimation for gene set tests
<https://searchworks.stanford.edu/view/11849351>. One of the methods also
corresponds to the paper Permutation p-value approximation via generalized
Stolarsky invariance <arXiv:1603.02757>. / GPL-2
r-pipeliner 0.1.1 A framework for defining ‘pipelines’ of functions for applying data transfor- noarch
mations, model estimation and inverse-transformations, resulting in predicted
value generation (or model-scoring) functions that automatically apply the
entire pipeline of functions required to go from input to predicted output. /
Apache License 2.0
r-piper 0.6.1.3Provides various styles of function chaining methods: Pipe operator, Pipe ob- noarch
ject, and pipeline function, each representing a distinct pipeline model yet
sharing almost a common set of features: A value can be piped to the first
unnamed argument of a function and to dot symbol in an enclosed expression.
The syntax is designed to make the pipeline more readable and friendly to a
wide range of operations. / MIT
r-pips 1.0.1 Generate Predicted Interval Plots. Simulate and plot confidence intervals of an noarch
effect estimate given observed data and a hypothesis about the distribution of
future data. / GPL-2
r-piton 0.1.1 A wrapper around the ‘Parsing Expression Grammar Template Library’, a C11 linux-
library for generating Parsing Expression Grammars, that makes it accessible 64,
within Rcpp. With this, developers can implement their own grammars and osx-
easily expose them in R packages. / MIT 64,
win-
64
r-pivotalr 0.1.18.3.1
Provides an R interface for the Pivotal Data stack running on ‘PostgreSQL’, linux-
‘Greenplum’ or ‘Apache HAWQ (incubating)’ databases with parallel and dis- 64,
tributed computation ability for big data processing. ‘PivotalR’ provides an R osx-
interface to various database operations on tables or views. These operations 64,
are almost the same as the corresponding native R operations. Thus users of win-
R do not need to learn ‘SQL’ when they operate on objects in the database. It 64
also provides a wrapper for ‘Apache MADlib (incubating)’, which is an open-
source library for parallel and scalable in-database analytics. / GPL-2
r-pivotaltrackr 0.1.0 ‘Pivotal Tracker’ <https://www.pivotaltracker.com> is a project management noarch
software-as-a-service that provides a REST API. This package provides an R
interface to that API, allowing you to query it and work with its responses. /
MIT
r-pixels 0.1.0 Provides tools to show and draw image pixels using ‘HTML’ widgets and noarch
‘Shiny’ applications. It can be used to visualize the ‘MNIST’ dataset for hand-
written digit recognition or to create new image recognition datasets. / MIT
r-pixmap 0.4_11Functions for import, export, plotting and other manipulations of bitmapped noarch
images. / GPL-2
r-pk 1.3_4 Estimation of pharmacokinetic parameters using non-compartmental theory. / noarch
GPL-2


Name Version
r-pkconverter 1.3 Pharmacokinetics is the study of drug absorption, distribution, metabolism, noarch
and excretion. The pharmacokinetics model explains that how the drug con-
centration change as the drug moves through the different compartments of
the body. For pharmacokinetic modeling and analysis, it is essential to
understand the basic pharmacokinetic parameters. All parameters are con-
sidered, but only some of parameters are used in the model. Therefore,
we need to convert the estimated parameters to the other parameters after
fitting the specific pharmacokinetic model. This package is developed to
help this converting work. For more detailed explanation of pharmacoki-
netic parameters, see Gabrielsson and Weiner (2007), ISBN-10: 9197651001;
Benet and Zia-Amirhosseini (1995) <DOI: 10.1177/019262339502300203>;
Mould and Upton (2012) <doi:10.1038/psp.2012.4>; Mould and Upton (2013)
<doi:10.1038/psp.2013.14>. / GPL-2
r-pkgbuild 1.0.3 Provides functions used to build R packages. Locates compilers needed to linux-
build R packages on various platforms and ensures the PATH is configured 64,
appropriately so R can use them. / GPL-3 noarch,
osx-
64,
win-
32,
win-
64
r-pkgcond 0.1.0 This provides utilities for creating classed error and warning conditions based noarch
on where the error originated. / GPL-2
r-pkgconfig 2.0.2 Set configuration options on a per-package basis. Options set by a given pack- linux-
age only apply to that package, other packages are unaffected. / MIT file 32,
LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-pkgdown 1.4.1 Generate an attractive and useful website from a source package. ‘pkgdown’ noarch
converts your documentation, vignettes, ‘README’, and more to ‘HTML’
making it easy to share information about your package online. / MIT
r-pkgkitten 0.1.4 Provides a function kitten() which creates cute little packages which pass R noarch
package checks. This sets it apart from package.skeleton() which it calls, and
which leaves imperfect files behind. As this is not exactly helpful for begin-
ners, kitten() offers an alternative. / GPL-2
r-pkgload 1.0.2 Simulates the process of installing a package and then attaching it. This is linux-
a key part of the ‘devtools’ package as it allows you to rapidly iterate while64,
developing a package. / GPL-3 osx-
64,
win-
32,
win-
64


Name Version
r-pkgmaker 0.27 Provides some low-level utilities to use for package development. It currently linux-
provides managers for multiple package specific options and registries, vi- 32,
gnette, unit test and bibtex related utilities. It serves as a base package for linux-
packages like NMF, RcppOctave, doRNG, and as an incubator package for 64,
other general purposes utilities, that will eventually be packaged separately. It noarch,
is still under heavy development and changes in the interface(s) are more than osx-
likely to happen. / GPL (>= 2) 64,
win-
32,
win-
64
r-pki 0.1_5.1
PKI functions such as verifying certificates, RSA encription and signing which linux-
can be used to build PKI infrastructure and perform cryptographic tasks. / 32,
GPL-2 | GPL-3 | file LICENSE linux-
64,
osx-
64,
win-
32,
win-
64
r-pkmon 1.0 We implement two least-squares estimators under k-monotony constraint us- noarch
ing a method based on the Support Reduction Algorithm from Groeneboom et
al (2008) <DOI:10.1111/j.1467-9469.2007.00588.x>. The first one is a pro-
jection estimator on the set of k-monotone discrete functions. The second one
is a projection on the set of k-monotone discrete probabilities. This package
provides functions to generate samples from the spline basis from Lefevre and
Loisel (2013) <DOI:10.1239/jap/1378401239>, and from mixtures of splines.
/ CC BY 4.0
r-pkpdmodels 0.3.2 Provides functions to evaluate common pharmacokinetic/pharmacodynamic noarch
models and their gradients. / GPL-2
r-pksea 0.0.1 A tool for inferring kinase activity changes from phosphoproteomics data. noarch
‘pKSEA’ uses kinase-substrate prediction scores to weight observed changes
in phosphopeptide abundance to calculate a phosphopeptide-level contri-
bution score, then sums up these contribution scores by kinase to ob-
tain a phosphoproteome-level kinase activity change score (KAC score).
‘pKSEA’ then assesses the significance of changes in predicted substrate
abundances for each kinase using permutation testing. This results in a
permutation score (pKSEA significance score) reflecting the likelihood of
a similarly high or low KAC from random chance, which can then be
interpreted in an analogous manner to an empirically calculated p-value.
‘pKSEA’ contains default databases of kinase-substrate predictions from ‘Net-
worKIN’ (NetworKINPred_db) <http://networkin.info> Horn, et. al (2014)
<doi:10.1038/nmeth.2968> and of known kinase-substrate links from ‘Phos-
phoSitePlus’ (KSEAdb) <https://www.phosphosite.org/> Hornbeck PV, et. al
(2015) <doi:10.1093/nar/gku1267>. / MIT


Name Version
r-pla 0.2 Parallel Line Assays: Completely randomized design, Randomized Block de- noarch
sign, and Latin squares design. Balanced data are fitted as described in the
Ph.Eur. In the presence of missing values complete data analysis can be per-
formed (with computation of Fieller’s confidence intervals for the estimated
potency), or imputation of values can be applied. The package contains a
script such that a pdf-document with a report of an analysis of an assay can be
produced from an input file with data of the assay. Here no knowledge of R is
needed by the user. / GPL-2
r-plac 0.1.1 A semi-parametric estimation method for the Cox model with left-truncated linux-
data using augmented information from the marginal of truncation times. / 64,
GPL-3 osx-
64,
win-
64
r-plan 0.4_3 Supports the creation of ‘burndown’ charts and ‘gantt’ diagrams. / GPL-2 noarch
r-planesmuestra 0.1 Calculates an acceptance sampling plan, (sample size and acceptance number) noarch
based in MIL STD 105E, Dodge Romig and MIL STD 414 tables and proce-
dures. The arguments for each function are related to lot size, inspection level
and quality level. The specific plan operating curve (OC), is calculated by the
binomial distribution. / GPL-2
r-planets 0.1.0 The goal of ‘planets’ is to provide of very simple and accessible data contain- noarch
ing basic information from all known planets. / MIT
r-planor 1.5_1 Automatic generation of regular factorial designs, including fractional designs, linux-
orthogonal block designs, row-column designs and split-plots. / GPL-2 64,
osx-
64,
win-
64
r-plantecophys 1.4_4 Coupled leaf gas exchange model, A-Ci curve simulation and fitting, Ball- noarch
Berry stomatal conductance models, leaf energy balance using Penman-
Monteith, Cowan-Farquhar optimization, humidity unit conversions. See Du-
ursma (2015) <doi:10.1371/journal.pone.0143346>. / GPL-3
r-plaqr 2.0 Estimation, prediction, thresholding, transformation, and plotting for partially noarch
linear additive quantile regression. Intuitive functions for fitting and plotting
partially linear additive quantile regression models. Uses and works with func-
tions from the ‘quantreg’ package. / GPL-2
r-playerratings 1.0_3 Implements schemes for estimating player or team skill based on dynamic up- linux-
dating. Implemented methods include Elo, Glicko, Glicko-2 and Stephenson. 64,
Contains pdf documentation of a reproducible analysis using approximately osx-
two million chess matches. / GPL-3 64,
win-
64
r-plde 0.1.2 We present a penalized log-density estimation method using Legendre poly- noarch
nomials with lasso penalty to adjust estimate’s smoothness. Re-expressing
the logarithm of the density estimator via a linear combination of Legendre
polynomials, we can estimate parameters by maximizing the penalized log-
likelihood function. Besides, we proposed an implementation strategy that
builds on the coordinate decent algorithm, together with the Bayesian infor-
mation criterion (BIC). / GPL-2


Name Version
r-plfm 2.2.2 Functions for estimating probabilistic latent feature models with a disjunctive, linux-
conjunctive or additive mapping rule on (aggregated) binary three-way data. / 64,
GPL-2 osx-
64,
win-
64
r-pliable 1.1 Fits a pliable lasso model. For details see Tibshirani and Friedman (2018) linux-
<arXiv:1712.00484>. / GPL-3 64,
osx-
64,
win-
64
r-plis 1.1 PLIS is a multiple testing procedure for testing several groups of hypotheses. noarch
Linear dependency is expected from the hypotheses within the same group
and is modeled by hidden Markov Models. It is noted that, for PLIS, a smaller
p value does not necessarily imply more significance because of dependency
among the hypotheses. A typical application of PLIS is to analyze genome
wide association studies datasets, where SNPs from the same chromosome are
treated as a group and exhibit strong linear genomic dependency. / GPL-3
r-plm 1.7_0 A set of estimators and tests for panel data econometrics. / GPL (>= 2) linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-pln 0.2_1 Performs bivariate composite likelihood and full information maximum like- linux-
lihood estimation for polytomous logit-normit (graded logistic) item response 64,
theory (IRT) models. / GPL-3 osx-
64,
win-
64
r-plogr 0.2.0 A simple header-only logging library for C. Add ‘LinkingTo: plogr’ to ‘DE- linux-
SCRIPTION’, and ‘#include <plogr.h>’ in your C modules to use it. / MIT file 32,
LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-plordprob 1.1 Multivariate ordered probit model, i.e. the extension of the scalar ordered linux-
probit model where the observed variables have dimension greater than one. 64,
Estimation of the parameters is done via maximization of the pairwise like- osx-
lihood, a special case of the composite likelihood obtained as product of bi- 64,
variate marginal distributions. The package uses the Fortran 77 subroutine win-
SADMVN by Alan Genz, with minor adaptations made by Adelchi Azzalini 64
in his mvnormt package for evaluating the two-dimensional Gaussian integrals
involved in the pairwise log-likelihood. Optimization of the latter objective
function is performed via quasi-Newton box-constrained optimization algo-
rithm, as implemented in nlminb. / GPL-2
r-plot.matrix 1.2 Visualizes a matrix object plainly as heatmap. It provides S3 functions to plot noarch
simple matrices and loading matrices. / GPL-3
r-plotcontour 0.1.0 This function plots a contour line with a user-defined probability and tightness noarch
of fit. / GPL-2
r-plotfunctions 1.3 When analyzing data, plots are a helpful tool for visualizing data and interpret- noarch
ing statistical models. This package provides a set of simple tools for building
plots incrementally, starting with an empty plot region, and adding bars, data
points, regression lines, error bars, gradient legends, density distributions in
the margins, and even pictures. The package builds further on R graphics by
simply combining functions and settings in order to reduce the amount of code
to produce for the user. As a result, the package does not use formula input or
special syntax, but can be used in combination with default R plot functions.
Note: Most of the functions were part of the package ‘itsadug’, which is now
split in two packages: 1. the package ‘itsadug’, which contains the core func-
tions for visualizing and evaluating nonlinear regression models, and 2. the
package ‘plotfunctions’, which contains more general plot functions. / GPL-2
r-plotly 4.9.0 Create interactive web graphics from ‘ggplot2’ graphs and/or a custom inter- linux-
face to the (MIT-licensed) JavaScript library ‘plotly.js’ inspired by the gram- 32,
mar of graphics. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-plotlygeoassets 0.0.2 Includes ‘JavaScript’ files that allow ‘plotly’ maps to render without an internet noarch
connection. / MIT
r-plotmcmc 2.0_0 Markov chain Monte Carlo diagnostic plots. The purpose of the package is noarch
to combine existing tools from the ‘coda’ and ‘lattice’ packages, and make it
easy to adjust graphical details. / GPL-2
r-plotpc 1.0.4 Plot principal component histograms around a bivariate scatter plot. / GPL-3 noarch
r- 1.0 Creates an envelope around a set of plotted points. The envelope is compact noarch
plotregionhighlighter with a boundary that is continuous, smooth and convex. Each point is repre-
sented as a circle and the circles and connecting lines are the solution to the
multiple pulley problem. This method can be used to highlight regions in a
two-dimensional space. / GPL-2
r-plotrix 3.7_6 Lots of plots, various labeling, axis and color scaling functions. / GPL-2 noarch


Name Version
r-plotscale 0.1.6 Figures rendered on graphics devices are usually rescaled to fit pre-determined noarch
device dimensions. ‘plotscale’ implements the reverse: desired plot di-
mensions are specified and device dimensions are calculated to accommo-
date marginal material, giving consistent proportions for plot elements. De-
fault methods support grid graphics such as lattice and ggplot. See exam-
ple(‘devsize’) and vignette(‘plotscale’). / GPL-3
r-plotwidgets 0.4 Small self-contained plots for use in larger plots or to delegate plotting in other noarch
functions. Also contains a number of alternative color palettes and HSL color
space based tools to modify colors or palettes. / GPL (>= 2.0)
r-plrasch 1.0 Fit Log Linear by Linear Association models and Rasch family models by noarch
pseudolikelihood estimation / GPL-2
r-plrmodels 1.1 This package provides statistical inference tools applied to Partial Linear Re- noarch
gression (PLR) models. Specifically, point estimation, confidence intervals es-
timation, bandwidth selection, goodness-of-fit tests and analysis of covariance
are considered. Kernel-based methods, combined with ordinary least squares
estimation, are used and time series errors are allowed. In addition, these tech-
niques are also implemented for both parametric (linear) and nonparametric
regression models. / GPL-3
r-pls 2.7_1 Multivariate regression methods Partial Least Squares Regression (PLSR), linux-
Principal Component Regression (PCR) and Canonical Powered Partial Least 64,
Squares (CPPLS). / GPL-2 noarch,
osx-
64,
win-
32,
win-
64
r-plsbiplot1 0.1 Principal Component Analysis (PCA) biplots, Covariance monoplots and bi- noarch
plots, Partial Least Squares (PLS) biplots, Partial Least Squares for General-
ized Linear Model (PLS-GLM) biplots, Sparse Partial Least Squares (SPLS)
biplots and Sparse Partial Least Squares for Generalized Linear Model (SPLS-
GLM) biplots. / GPL-2
r-plsdepot 0.1.17plsdepot contains different methods for PLS analysis of one or two data tables noarch
such as Tucker’s Inter-Battery, NIPALS, SIMPLS, SIMPLS-CA, PLS Regres-
sion, and PLS Canonical Analysis. The main reference for this software is
the awesome book (in French) ‘La Regression PLS: Theorie et Pratique’ by
Michel Tenenhaus. / GPL-3
r-plsdof 0.2_9 The plsdof package provides Degrees of Freedom estimates for Partial Least noarch
Squares (PLS) Regression. Model selection for PLS is based on various in-
formation criteria (aic, bic, gmdl) or on cross-validation. Estimates for the
mean and covariance of the PLS regression coefficients are available. They
allow the construction of approximate confidence intervals and the application
of test procedures. Further, cross-validation procedures for Ridge Regression
and Principal Components Regression are available. / GPL-2
r-plugdensity 0.8_3 Kernel density estimation with global bandwidth selection via plug-in. / GPL- linux-
2 64,
osx-
64,
win-
64


Name Version
r-plumber 0.4.6 Gives the ability to automatically generate and serve an HTTP API from R linux-
functions using the annotations in the R documentation around your functions. 32,
64,
noarch,
osx-
64,
win-
32,
win-
64
r-plus 1.0 Efficient procedures for fitting an entire regression sequences with different noarch
model types. / GPL-2
r-pluscode 0.1.0 Retrieves a ‘pluscode’ by inputting latitude and longitude. Includes additional noarch
functions to retrieve neighbouring ‘pluscodes’. / GPL-2
r-plusser 0.4_0 plusser provides an API interface to Google so that posts, profiles and pages noarch
can be automatically retrieved. / GPL-3
r-plyr 1.8.4 A set of tools that solves a common set of problems: you need to break a linux-
big problem down into manageable pieces, operate on each piece and then put 32,
all the pieces back together. For example, you might want to fit a model to linux-
each spatial location or time point in your study, summarise data by panels or 64,
collapse high-dimensional arrays to simpler summary statistics. The develop- osx-
ment of ‘plyr’ has been generously supported by ‘Becton Dickinson’. / MIT 64,
file LICENSE win-
32,
win-
64
r-pmcmr 4.3 Note, that the ‘PMCMR’ package is superseded by the novel ‘PMCMRplus’ noarch
package. The ‘PMCMRplus’ package contains all functions from ‘PMCMR’
and many more parametric and non-parametric multiple comparison proce-
dures, one-factorial trend tests, as well as improved method functions, such as
print, summary and plot. The ‘PMCMR’ package is no longer maintained, but
kept for compatibility of reverse depending packages for some time. / GPL-3
r-pmml 2.0.0 The Predictive Model Markup Language (PMML) is an XML-based language noarch
which provides a way for applications to define machine learning, statistical
and data mining models and to share models between PMML compliant ap-
plications. More information about the PMML industry standard and the Data
Mining Group can be found at <http://www.dmg.org>. The generated PMML
can be imported into any PMML consuming application, such as Zementis
Predictive Analytics products, which integrate with web services, relational
database systems and deploy natively on Hadoop in conjunction with Hive,
Spark or Storm, as well as allow predictive analytics to be executed for IBM z
Systems mainframe applications and real-time, streaming analytics platforms.
The package isofor (used for anomaly detection) can be installed with dev-
tools::install_github(Zelazny7/isofor). / GPL-3


Name Version
r- 1.3.3 Allows for data to be transformed before using it to construct models. Builds noarch
pmmltransformations structures to allow functions in the PMML package to output transformation
details in addition to the model in the resulting PMML file. The Predictive
Model Markup Language (PMML) is an XML-based language which provides
a way for applications to define machine learning, statistical and data mining
models and to share models between PMML compliant applications. More in-
formation about the PMML industry standard and the Data Mining Group can
be found at <http://www.dmg.org>. The generated PMML can be imported
into any PMML consuming application, such as Zementis Predictive Analyt-
ics products, which integrate with web services, relational database systems
and deploy natively on Hadoop in conjunction with Hive, Spark or Storm, as
well as allow predictive analytics to be executed for IBM z Systems mainframe
applications and real-time, streaming analytics platforms. / GPL (>= 2.1)
r-pmr 1.2.5 Descriptive statistics (mean rank, pairwise frequencies, and marginal ma- noarch
trix), Analytic Hierarchy Process models (with Saaty’s and Koczkodaj’s in-
consistencies), probability models (Luce models, distance-based models, and
rank-ordered logit models) and visualization with multidimensional preference
analysis for ranking data are provided. Current, only complete rankings are
supported by this package. / GPL-2
r-pmsampsize 1.0.1 Computes the minimum sample size required for the development of a new noarch
multivariable prediction model using the criteria proposed by Riley et al.
(2018) <doi: 10.1002/sim.7992>. pmsampsize can be used to calculate
the minimum sample size for the development of models with continuous,
binary or survival (time-to-event) outcomes. Riley et al. (2018) <doi:
10.1002/sim.7992> lay out a series of criteria the sample size should meet.
These aim to minimise the overfitting and to ensure precise estimation of key
parameters in the prediction model. / GPL-3
r-pmultinom 1.0.0 Implements multinomial CDF (P(N1<=n1, . . . , Nk<=nk)) and tail probabil- noarch
ities (P(N1>n1, . . . , Nk>nk)), as well as probabilities with both constraints
(P(l1<N1<=u1, . . . , lk<Nk<=uk)). Uses a method suggested by Bruce Levin
(1981) <doi:10.1214/aos/1176345593>. / AGPL-3
r-png 0.1_7 This package provides an easy and simple way to read, write and display linux-
bitmap images stored in the PNG format. It can read and write both files and 32,
in-memory raw vectors. / GPL-2 | GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64
r-pnmtrem 1.3 An R package for Probit-Normal Marginalized Transition Random Effects noarch
Models / GPL-2


Name Version
r-pnn 1.0.1 The program pnn implements the algorithm proposed by Specht (1990). It is noarch
written in the R statistical language. It solves a common problem in automatic
learning. Knowing a set of observations described by a vector of quantitative
variables, we classify them in a given number of groups. Then, the algo-
rithm is trained with this datasets and should guess afterwards the group of
any new observation. This neural network has the main advantage to begin
generalization instantaneously even with a small set of known observations. It
is delivered with four functions (learn, smooth, perf and guess) and a dataset.
The functions are documented with examples and provided with unit tests. /
AGPL-3
r-pocrm 0.12 Provides functions to implement and simulate the partial order continual re- noarch
assessment method (PO-CRM) of Wages, Conaway and O’Quigley (2011)
<doi:10.1177/1740774511408748> for use in Phase I trials of combinations
of agents. Provides a function for generating a set of initial guesses (skeleton)
for the toxicity probabilities at each combination that correspond to the set of
possible orderings of the toxicity probabilities specified by the user. / GPL-2
r-pod 1.1.4 This tool computes the probability of detection (POD) curve and the limit of noarch
detection (LOD), i.e. the number of copies of the target DNA sequence re-
quired to ensure a 95 % probability of detection (LOD95). Other quantiles of
the LOD can be specified. This is a reimplementation of the mathematical-
statistical modelling of the validation of qualitative polymerase chain reaction
(PCR) methods within a single laboratory as provided by the commercial tool
‘PROLab’ <http://quodata.de/>. The modelling itself has been described by
Uhlig et al. (2015) <doi:10.1007/s00769-015-1112-9>. / GPL-3
r-poet 2.0 Estimate large covariance matrices in approximate factor models by threshold- noarch
ing principal orthogonal complements. / GPL-2
r-poibin 1.3 Implementation of both the exact and approximation methods for computing linux-
the cdf of the Poisson binomial distribution. It also provides the pmf, quantile 64,
function, and random number generation for the Poisson binomial distribution. osx-
/ GPL-2 64,
win-
64
r-poiclaclu 1.0.2.1Implements the methods described in the paper, Witten (2011) Classification noarch
and Clustering of Sequencing Data using a Poisson Model, Annals of Applied
Statistics 5(4) 2493-2518. / GPL-2
r-poilog 0.4 Functions for obtaining the density, random deviates and maximum likelihood linux-
estimates of the Poisson lognormal distribution and the bivariate Poisson log- 64,
normal distribution. / GPL-3 osx-
64,
win-
64
r-pointdensityp 0.3.4 The function pointdensity returns a density count and the temporal average for noarch
every point in the original list. The dataframe returned includes four columns:
lat, lon, count, and date_avg. The lat column is the original latitude data; the
lon column is the original longitude data; the count is the density count of the
number of points within a radius of radius*grid_size (the neighborhood); and
the date_avg column includes the average date of each point in the neighbor-
hood. / MIT


Name Version
r-poisbinnonnor 1.3.1 Generation of multiple count, binary and continuous variables simultaneously noarch
given the marginal characteristics and association structure. Throughout the
package, the word ‘Poisson’ is used to imply count data under the assumption
of Poisson distribution. / GPL-2 | GPL-3
r-poisbinom 1.0.1 Provides the probability, distribution, and quantile functions and random num- linux-
ber generator for the Poisson-Binomial distribution. This package relies on 64,
FFTW to implement the discrete Fourier transform, so that it is much faster osx-
than the existing implementation of the same algorithm in R. / GPL-2 64,
win-
64
r- 1.1 Functions to create confidence intervals for ratios of Poisson rates under mis- linux-
poisdoublesamp classification using double sampling. / GPL-2 64,
osx-
64,
win-
64
r-poisnonnor 1.6.1 Generation of count (assuming Poisson distribution) and continuous data (us- noarch
ing Fleishman polynomials) simultaneously. / GPL-2 | GPL-3
r-poisnor 1.3.1 Generates multivariate data with count and continuous variables with a pre- noarch
specified correlation matrix. The count and continuous variables are assumed
to have Poisson and normal marginals, respectively. The data generation mech-
anism is a combination of the normal to anything principle and a connection
between Poisson and normal correlations in the mixture. / GPL-2
r-poisson 1.0 Contains functions and classes for simulating, plotting and analysing homoge- noarch
nous and non-homogenous Poisson processes. / GPL-2
r- 1.2 High dimensional mixtures of Poisson Generalized Linear models with three noarch
poisson.glm.mix different parameterizations of Poisson means are considered. Moreover, par-
titioning the response variables into a set of blocks is possible. The package
estimates parameters via EM algorithm. For an efficient initialization, a ran-
dom splitting small-EM is introduced. / GPL-2
r-poissonpca 1.0.2 For a multivariate dataset with independent Poisson measurement error, calcu- linux-
lates principal components of transformed latent Poisson means. T. Kenney, 64,
T. Huang, H. Gu (2019) <arXiv:1904.11745>. / GPL-3 osx-
64,
win-
64
r-poissonseq 1.1.2 This package implements a method for normalization, testing, and false dis- noarch
covery rate estimation for RNA-sequencing data. The description of the
method is in Li J, Witten DM, Johnstone I, Tibshirani R (2012). Normal-
ization, testing, and false discovery rate estimation for RNA-sequencing data.
Biostatistics 13(3): 523-38. We estimate the sequencing depths of experi-
ments using a new method based on Poisson goodness-of-fit statistic, calcu-
late a score statistic on the basis of a Poisson log-linear model, and then esti-
mate the false discovery rate using a modified version of permutation plug-in
method. A more detailed instruction as well as sample data is available at
http://www.stanford.edu/~junli07/research.html. In this version, we changed
the way of calculating log foldchange for two-class data. The FDR estimation
part remains unchanged. / GPL-2
r-poistweedie 1.0 Simulation of models Poisson-Tweedie. / GPL-2 noarch


r-poker 0.8.8 Type testRoundOfPoker() to demonstrate the game of Texas Hold â C~Em noarch
poker. Rotate the dealer button, deal cards, rank each hand, compare ranks,
break ties (if necessary), determine the winner, output a textual summary, and
output a graphical user interface. / GPL-2
r-polidata 0.1.0.1This package provides easy access to various political data APIs directly noarch
from R. For example, you can access Google Civic Information API <https://
developers.google.com/civic-information/> or Sunlight Congress API <https:
//sunlightlabs.github.io/congress/> for US Congress data, and POPONG API
<http://data.popong.com/> for South Korea National Assembly data. / MIT
r-politicaldata 0.1.3 Provides useful functions for obtaining commonly-used data in political anal- noarch
ysis and political science, including from sources such as the Compara-
tive Agendas Project <https://www.comparativeagendas.net>, which provides
data on politics and policy from 20 countries, the MIT Election and Data
Science Lab <https://www.electionlab.mit.edu>, and FiveThirtyEight <https:
//www.FiveThirtyEight.com>. / MIT
r-pollstr 2.0.1 Client for the HuffPost Pollster API, which provides access to U.S. polls on noarch
elections and political opinion. / GPL-2
r-polspline 1.1.14Routines for the polynomial spline fitting routines hazard regression, hazard linux-
estimation with flexible tails, logspline, lspec, polyclass, and polymars, by C. 32,
Kooperberg and co-authors. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
r-polyaaeppli 2.0 Functions for evaluating the mass density, cumulative distribution function, noarch
quantile function and random variate generation for the Polya-Aeppli distribu-
tion, also known as the geometric compound Poisson distribution. / GPL-2
r-polyclip 1.10_0R port of Angus Johnson’s open source library Clipper. Performs polygon linux-
clipping operations (intersection, union, set minus, set difference) for polyg- 64,
onal regions of arbitrary complexity, including holes. Computes offset poly- osx-
gons (spatial buffer zones, morphological dilations, Minkowski dilations) for 64,
polygonal regions and polygonal lines. Computes Minkowski Sum of general win-
polygons. There is a function for removing self-intersections from polygon 64
data. / BSL
r-polycor 0.7_10Computes polychoric and polyserial correlations by quick two-step methods noarch
or ML, optionally with standard errors; tetrachoric and biserial correlations
are special cases. / GPL-2
r-polycub 0.7.1 Numerical integration of continuously differentiable functions f(x,y) over linux-
simple closed polygonal domains. The following cubature methods are 64,
implemented: product Gauss cubature (Sommariva and Vianello, 2007, osx-
<doi:10.1007/s10543-007-0131-2>), the simple two-dimensional midpoint 64,
rule (wrapping ‘spatstat’ functions), adaptive cubature for radially symmetric win-
functions via line integrate() along the polygon boundary (Meyer and Held, 64
2014, <doi:10.1214/14-AOAS743>, Supplement B), and integration of the bi-
variate Gaussian density based on polygon triangulation. For simple integra-
tion along the axes, the ‘cubature’ package is more appropriate. / GPL-2


Name Version
r-polyfreqs 1.0.2 Implements a Gibbs sampling algorithm to perform Bayesian inference on linux-
biallelic SNP frequencies, genotypes and heterozygosity (observed and ex- 64,
pected) in a population of autopolyploids. See the published paper in osx-
Molecular Ecology Resources: Blischak et al. (2016) <doi:10.1111/1755- 64,
0998.12493>. / GPL-2 win-
64
r-polylabelr 0.1.0 A wrapper around the C library ‘polylabel’ from ‘Mapbox’, providing an effi- linux-
cient routine for finding the approximate pole of inaccessibility of a polygon, 64,
which usually serves as an excellent candidate for labeling of a polygon. / MIT osx-
64,
win-
64
r-polynom 1.4_0 A collection of functions to implement a class for univariate polynomial ma- noarch
nipulations. / GPL-2
r-polynomf 2.0_2 Implements univariate polynomial operations in R, including polynomial arith- linux-
metic, finding zeros, plotting, and some operations on lists of polynomials. / 64,
GPL-2 osx-
64,
win-
64
r-polypatex 0.9.2 Functions to perform paternity exclusion via allele matching, in autopolyploid noarch
species having ploidy 4, 6, or 8. The marker data used can be genotype data
(copy numbers known) or ‘allelic phenotype data’ (copy numbers not known).
/ GPL-3
r-polysat 1.7_4 A collection of tools to handle microsatellite data of any ploidy (and sam- linux-
ples of mixed ploidy) where allele copy number is not known in partially het- 64,
erozygous genotypes. It can import and export data in ABI ‘GeneMapper’, osx-
‘Structure’, ‘ATetra’, ‘Tetrasat’/’Tetra’, ‘GenoDive’, ‘SPAGeDi’, ‘POPDIST’, 64,
‘STRand’, and binary presence/absence formats. It can calculate pairwise dis- win-
tances between individuals using a stepwise mutation model or infinite al- 64
leles model, with or without taking ploidies and allele frequencies into ac-
count. These distances can be used for the calculation of clonal diversity
statistics or used for further analysis in R. Allelic diversity statistics and
Polymorphic Information Content are also available. polysat can assist the
user in estimating the ploidy of samples, and it can estimate allele frequen-
cies in populations, calculate pairwise or global differentiation statistics based
on those frequencies, and export allele frequencies to ‘SPAGeDi’ and ‘ade-
genet’. Functions are also included for assigning alleles to isoloci in cases
where one pair of microsatellite primers amplifies alleles from two or more
independently segregating isoloci. polysat is described by Clark and Jasie-
niuk (2011) <doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier
(2017) <doi:10.1111/1755-0998.12639>. / GPL-2
r-polysegratio 0.2_5 Perform classic chi-squared tests and Ripol et al(1999) binomial confidence noarch
interval approach for autopolyploid dominant markers. Also, dominant mark-
ers may be generated for families of offspring where either one or both of the
parents possess the marker. Missing values and misclassified markers may be
generated at random. / GPL-3


Name Version
r-polytrend 1.2 This algorithm classifies the trends into linear, quadratic, cubic, concealed and noarch
no-trend types. The concealed trends are those trends that possess quadratic or
cubic forms, but the net change from the start of the time period to the end of
the time period hasn’t been significant. The no-trend category includes simple
linear trends with statistically in-significant slope coefficient. / GPL-2
r-pomaspu 1.0.0 POM-aSPU test evaluates an association between an ordinal re- linux-
sponse and multiple phenotypes, for details see Kim and Pan (2017) 64,
<DOI:10.1002/gepi.22033>. / GPL-3 osx-
64,
win-
64
r-pomdp 0.9.1_1
Provides an interface to pomdp-solve, a solver for Partially Observable linux-
Markov Decision Processes (POMDP). The package enables the user to sim- 64,
ply define all components of a POMDP model and solve the problem using osx-64
several methods. The package also contains functions to analyze and visualize
the POMDP solutions (e.g., the optimal policy). / GPL-3
r-pomic 1.0.4 Calculations of an information criterion are proposed to check the quality of noarch
simulations results of Agent-based models (ABM/IBM) or other non-linear
rule-based models. The POMDEV measure (Pattern Oriented Modelling DE-
Viance) is based on the Kullback-Leibler divergence and likelihood theory. It
basically indicates the deviance of simulation results from field observations.
Once POMDEV scores and metropolis-hasting sampling on different model
versions are effectuated, POMIC scores (Pattern Oriented Modelling Informa-
tion Criterion) can be calculated. This method could be further developed to
incorporate multiple patterns assessment. Piou C, U Berger and V Grimm
(2009) <doi:10.1016/j.ecolmodel.2009.05.003>. / GPL-2
r-pomp 2.3 Tools for data analysis with partially observed Markov process (POMP) mod- linux-
els (also known as stochastic dynamical systems, hidden Markov models, and 64,
nonlinear, non-Gaussian, state-space models). The package provides facilities osx-
for implementing POMP models, simulating them, and fitting them to time se- 64,
ries data by a variety of frequentist and Bayesian methods. It is also a versatile win-
platform for implementation of inference methods for general POMP models. 64
/ GPL-3
r-pooh 0.3_2 Finds equivalence classes corresponding to a symmetric relation or undirected linux-
graph. Finds total order consistent with partial order or directed graph (so- 64,
called topological sort). / MIT osx-
64,
win-
64
r-pool 0.1.4.2Enables the creation of object pools, which make it less computationally ex- linux-
pensive to fetch a new object. Currently the only supported pooled objects are 32,
‘DBI’ connections. / GPL-3 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r- 1.0 Calculates the pooled mean group (PMG) estimator for dynamic noarch
pooledmeangroup panel data models, as described by Pesaran, Shin and Smith (1999)
<doi:10.1080/01621459.1999.10474156>. / GPL-2
r-poolfstat 1.1.0 Functions for the computation of F-statistics from Pool-Seq data in population noarch
genomics studies. The package also includes several utilities to manipulate
Pool-Seq data stored in standard format (‘vcf’ or ‘rsync’ files generated by the
the ‘PoPoolation’ software) and perform conversion to alternative format (as
used in the ‘BayPass’ and ‘SelEstim’ software). / GPL-2
r-pop 0.1 Population dynamic models underpin a range of analyses and applications in noarch
ecology and epidemiology. The various approaches for analysing population
dynamics models (MPMs, IPMs, ODEs, POMPs, PVA) each require the model
to be defined in a different way. This makes it difficult to combine different
modelling approaches and data types to solve a given problem. ‘pop’ aims to
provide a flexible and easy to use common interface for constructing popula-
tion dynamic models and enabling to them to be fitted and analysed in lots of
different ways. / MIT
r-pop.wolf 0.1 Simulate the dynamic of wolf populations using a specific Individual-Based linux-
Model (IBM) compiled in C. / GPL-3 64,
osx-
64,
win-
64
r-popbio 2.4.4 Construct and analyze projection matrix models from a demography study of noarch
marked individuals classified by age or stage. The package covers methods
described in Matrix Population Models by Caswell (2001) and Quantitative
Conservation Biology by Morris and Doak (2002). / GPL-3
r-popdemog 1.0.3 Plot demographic graphs for single/multiple populations from coalescent sim- noarch
ulation program input. Currently, this package can support the ‘ms’, ‘msHot’,
‘MaCS’, ‘msprime’, ‘SCRM’, and ‘Cosi2’ simulation programs. It does not
check the simulation program input for correctness, but assumes the simulation
program input has been validated by the simulation program. More features
will be added to this package in the future, please check the ‘GitHub’ page for
the latest updates: <https://github.com/YingZhou001/POPdemog>. / GPL-2
r-popgenkit 1.0 There are two main purposes to this package. The first is to allow batch con- noarch
version of Genepop (Rousset 2008) input files for use with Arlequin (Excoffier
and Lischer 2010), which has a simple GUI to analyze batch files. Two com-
monly used simulation software, BottleSim (Kuo & Janzen 2003) and Easy-
pop (Balloux 2001) produce Genepop output files that can be analyzed this
way. There are also functions to convert to and from BottleSim format, to
quickly produce allele frequency tables or to convert a file directly for use in
ordination analyses (e.g. principal component analysis). This package also in-
cludes functions to calculate allele rarefaction curves, confidence intervals on
heterozygosity and allelic richness with resampling strategies (bootstrap and
jackknife). / GPL-2
r-popkin 1.2.2 Provides functions to estimate the kinship matrix of individuals from a large linux-
set of biallelic SNPs, and extract inbreeding coefficients and the generalized 64,
FST (Wright’s fixation index). Method described in Ochoa and Storey (2016) osx-
<doi:10.1101/083923>. / GPL-3 64,
win-
64


Name Version
r-popkorn 0.3_0 Provides a suite of tools for various methods of estimating confidence intervals noarch
for the mean of selected populations. / MIT
r-poprange 1.1.3 Runs a forward genetic simulator / MIT noarch
r-popreconstruct 1.0_5 Implements the Bayesian hierarchical model described by Wheldon, Raftery, noarch
Clark and Gerland (see: <doi:10.1080/01621459.2012.737729>) for simul-
taneously estimating age-specific population counts, fertility rates, mortality
rates and net international migration flows, at the national level. / GPL-3
r-poptrend 0.1.0 Functions to estimate and plot smooth or linear population trends, or popula- noarch
tion indices, from animal or plant count survey data. / GPL-3
r-population 0.2 Run population simulations using an Individual-Based Model (IBM) compiled linux-
in C. / GPL-3 64,
osx-
64,
win-
64
r-portfolio 0.4_7 Classes for analysing and implementing equity portfolios. / GPL-2 noarch
r-portsort 0.1.0 Designed to aid both academic researchers and asset managers in conducting noarch
factor based portfolio sorts. Provides functionality to sort assets into portfolios
for up to three factors via a conditional or unconditional sorting procedure. /
GPL-2
r-posi 1.0 In linear LS regression, calculate for a given design matrix the multiplier K of noarch
coefficient standard errors such that the confidence intervals [b - K*SE(b), b
K*SE(b)] have a guaranteed coverage probability for all coefficient estimates
b in any submodels after performing arbitrary model selection. / GPL-3
r-postcodesior 0.1.1 Free UK geocoding using data from Office for National Statistics. It is using noarch
several functions to get information about post codes, outward codes, reverse
geocoding, nearest post codes/outward codes, validation, or randomly generate
a post code. API wrapper around <https://postcodes.io>. / GPL-3
r-postinfectious 0.1.0 Functions to estimate the incubation period distribution of post-infectious syn- noarch
drome which is defined as the time between the symptom onset of the an-
tecedent infection and that of the post-infectious syndrome. / GPL-2
r-postlogic 0.1.0 Provides adds postfix and infix logic operators for if, then, unless, and other- noarch
wise. / GPL-2
r-pot 1.1_7 Some functions useful to perform a Peak Over Threshold analysis in univariate linux-
and bivariate cases, see Beirlant et al. (2004) <doi:10.1002/0470012382>. A 64,
user’s guide is available. / GPL-2 osx-
64,
win-
64
r-potts 0.5_8 Do Markov chain Monte Carlo (MCMC) simulation of Potts models (Potts, linux-
1952, <doi:10.1017/S0305004100027419>), which are the multi-color gen- 64,
eralization of Ising models (so, as as special case, also simulates Ising osx-
models). Use the Swendsen-Wang algorithm (Swendsen and Wang, 1987, 64,
<doi:10.1103/PhysRevLett.58.86>) so MCMC is fast. Do maximum compos- win-
ite likelihood estimation of parameters (Besag, 1975, <doi:10.2307/2987782>, 64
Lindsay, 1988, <doi:10.1090/conm/080>). / GPL-2


Name Version
r-power 1.0.7 Functions for the computation of power and level tables for hypothesis tests, linux-
in Latex format, functions to build explanatory graphs for studying power of 64,
test statistics. / GPL-2 osx-
64,
win-
64
r-poweranalysis 0.2.1 Basic functions for power analysis and effect size calculation. / GPL-2 noarch
r-powercomprisk 1.0.1 A power analysis tool for jointly testing the cause-1 cause-specific hazard and noarch
the any-cause hazard with competing risks data. / GPL-2
r- 0.1.0 An implementation for using powerful algorithm to compute the maximal noarch
powerfulmaxeigenpair eigenpair of Hermitizable tridiagonal matrices in R. It provides two algorithms
to find the maximal and the next to maximal eigenpairs under the tridiagonal
matrix. Besides, it also provides two auxiliary algorithms to generate tridi-
agonal matrix and solve the linear equation by Thomas algorithm. Several
examples are included in the vignettes to illustrate the usage of the functions.
/ MIT
r-powerlaw 0.70.2An implementation of maximum likelihood estimators for a variety of heavy noarch
tailed distributions, including both the discrete and continuous power law dis-
tributions. Additionally, a goodness-of-fit based approach is used to estimate
the lower cut-off for the scaling region. / GPL-2 | GPL-3
r-powerlmm 0.4.0 Calculate power for the ‘time x treatment’ effect in two- and three-level mul- noarch
tilevel longitudinal studies with missing data. Both the third-level factor (e.g.
therapists, schools, or physicians), and the second-level factor (e.g. subjects),
can be assigned random slopes. Studies with partially nested designs, un-
equal cluster sizes, unequal allocation to treatment arms, and different dropout
patterns per treatment are supported. For all designs power can be calcu-
lated both analytically and via simulations. The analytical calculations ex-
tends the method described in Galbraith et al. (2002) <doi:10.1016/S0197-
2456(02)00205-2>, to three-level models. Additionally, the simulation tools
provides flexible ways to investigate bias, Type I errors and the consequences
of model misspecification. / GPL-3
r- 0.2.9 Functions to calculate power and sample size for testing (1) mediation effects; noarch
powermediation (2) the slope in a simple linear regression; (3) odds ratio in a simple logistic
regression; (4) mean change for longitudinal study with 2 time points; (5)
interaction effect in 2-way ANOVA; and (6) the slope in a simple Poisson
regression. / GPL-2
r-powernormal 1.2.0 Miscellaneous functions for a descriptive analysis and initial Bayesian and noarch
classical inference for the power parameter of the the Power Normal (PN)
distribution. This miscellaneous will be extend for more distributions into the
power family and the three-parameter model. / GPL-2


Name Version
r-powerpkg 1.5 noarch
(1) To estimate the power of testing for linkage using an affected sib pair
design, as a function of the recurrence risk ratios. We will use analytical
power formulae as implemented in R. These are based on a Mathemat-
ica notebook created by Martin Farrall. (2) To examine how the power
of the transmission disequilibrium test (TDT) depends on the disease al-
lele frequency, the marker allele frequency, the strength of the linkage
disequilibrium, and the magnitude of the genetic effect. We will use
an R program that implements the power formulae of Abel and Muller-
Myhsok (1998). These formulae allow one to quickly compute power of
the TDT approach under a variety of different conditions. This R pro-
gram was modeled on Martin Farrall’s Mathematica notebook. / GPL-2
r-powersurvepi 0.1.0 Functions to calculate power and sample size for testing main effect or interac- noarch
tion effect in the survival analysis of epidemiological studies (non-randomized
studies), taking into account the correlation between the covariate of the inter-
est and other covariates. Some calculations also take into account the compet-
ing risks and stratified analysis. This package also includes a set of functions to
calculate power and sample size for testing main effect in the survival analysis
of randomized clinical trials. / GPL-2
r-powerupr 1.0.4 Includes tools to calculate statistical power, minimum detectable effect size noarch
(MDES), MDES difference (MDESD), and minimum required sample size
for various multilevel randomized experiments with continuous outcomes.
Some of the functions can assist with planning two- and three-level cluster-
randomized trials (CRTs) sensitive to multilevel moderation and mediation
(2-1-1, 2-2-1, and 3-2-1). See ‘PowerUp!’ Excel series at <https://www.
causalevaluation.org/>. / GPL-3
r-pp 0.6.2 The PP package includes estimation of (MLE, WLE, MAP, EAP, ROBUST) linux-
person parameters for the 1,2,3,4-PL model and the GPCM (generalized partial 64,
credit model). The parameters are estimated under the assumption that the osx-
item parameters are known and fixed. The package is useful e.g. in the case 64,
that items from an item pool / item bank with known item parameters are win-
administered to a new population of test-takers and an ability estimation for 64
every test-taker is needed. / GPL-3


Name Version
r-pp3 1.2 Exploratory projection pursuit is a method to discovers structure in multi- linux-
variate data. At heart this package uses a projection index to evaluate how 64,
interesting a specific three-dimensional projection of multivariate data (with osx-
more than three dimensions) is. Typically, the main structure finding algo- 64,
rithm starts at a random projection and then iteratively changes the projection win-
direction to move to a more interesting one. In other words, the projection 64
index is maximised over the projection direction to find the most interesting
projection. This maximum is, though, a local maximum. So, this code has the
ability to restart the algorithm from many different starting positions automat-
ically. Routines exist to plot a density estimate of projection indices over the
runs, this enables the user to obtain an idea of the distribution of the projec-
tion indices, and, hence, which ones might be interesting. Individual projec-
tion solutions, including those identified as interesting, can be extracted and
plotted individually. The package can make use of the mclapply() function
to execute multiple runs in parallel to speed up index discovery. Projection
pursuit is similar to independent component analysis. This package uses a
projection index that maximises an entropy measure to look for projections
that exhibit non-normality, and operates on sphered data. Hence, information
from this package is different from that obtained from principal components
analysis, but the rationale behind both methods is similar. Nason, G. P. (1995)
<doi:10.2307/2986135>. / GPL-2
r-ppcc 1.1 Calculates the Probability Plot Correlation Coefficient (PPCC) between a con- linux-
tinuous variable X and a specified distribution. The corresponding com- 64,
posite hypothesis test that was first introduced by Filliben (1975) <doi: osx-
10.1080/00401706.1975.10489279> can be performed to test whether the 64,
sample X is element of either the Normal, log-Normal, Exponential, Uniform, win-
Cauchy, Logistic, Generalized Logistic, Gumbel (GEVI), Weibull, General- 64
ized Extreme Value, Pearson III (Gamma 2), Mielke’s Kappa, Rayleigh or
Generalized Logistic Distribution. The PPCC test is performed with a fast
Monte-Carlo simulation. / GPL-3
r-ppcor 1.1 Calculates partial and semi-partial (part) correlations along with p-value. / noarch
GPL-2
r-ppls 1.6_1.1
Contains linear and nonlinear regression methods based on Partial Least noarch
Squares and Penalization Techniques. Model parameters are selected via
cross-validation, and confidence intervals ans tests for the regression coeffi-
cients can be conducted via jackknifing. / GPL-2
r-ppmr 1.0 Efficient statistical inference of two-sample MR (Mendelian Randomization) linux-
analysis. It can account for the correlated instruments and the horizontal 64,
pleiotropy, and can provide the accurate estimates of both causal effect and osx-
horizontal pleiotropy effect as well as the two corresponding p-values. There 64,
are two main functions in the ‘PPMR’ package. One is PMR_individual() for win-
individual level data, the other is PMR_summary() for summary data. / GPL-3 64
r-pps 0.94 The pps package contains functions to select samples using PPS (probability noarch
proportional to size) sampling. It also includes a function for stratified sim-
ple random sampling, a function to compute joint inclusion probabilities for
Sampford’s method of PPS sampling, and a few utility functions. The user’s
guide pps-ug.pdf is included. / GPL-2


Name Version
r-pqantimalarials 0.2 This package allows users to calculate the number of under-five child deaths noarch
caused by consumption of poor quality antimalarials across 39 sub-Saharan
nations. The package supports one function, that starts an interactive web tool
created using the shiny R package. The web tool runs locally on the user’s
machine. The web tool allows users to set input parameters (prevalence of
poor quality antimalarials, case fatality rate of children who take poor quality
antimalarials, and sample size) which are then used to perform an uncertainty
analysis following the Latin hypercube sampling scheme. Users can down-
load the output figures as PDFs, and the output data as CSVs. Users can also
download their input parameters for reference. This package was designed
to accompany the analysis presented in: J. Patrick Renschler, Kelsey Walters,
Paul Newton, Ramanan Laxminarayan Estimated under-five deaths associated
with poor-quality antimalarials in sub-Saharan Africa, 2014. Paper submitted.
/ GPL-3
r-pqlseq 1.1 An efficient tool designed for differential analysis of large-scale RNA sequenc- linux-
ing (RNAseq) data and Bisulfite sequencing (BSseq) data in the presence of 64,
individual relatedness and population structure. ‘PQLseq’ first fits a Gener- osx-
alized Linear Mixed Model (GLMM) with adjusted covariates, predictor of 64,
interest and random effects to account for population structure and individual win-
relatedness, and then performs Wald tests for each gene in RNAseq or site in 64
BSseq. / GPL-2
r-pracma 2.2.5 Provides a large number of functions from numerical analysis and linear al- noarch
gebra, numerical optimization, differential equations, time series, plus some
well-known special mathematical functions. Uses ‘MATLAB’ function names
where appropriate to simplify porting. / GPL-3
r-practools 1.2 Functions and datasets to support Valliant, Dever, and Kreuter, ‘‘Practical noarch
Tools for Designing and Weighting Survey Samples” (2nd edition, 2018).
Contains functions for sample size calculation for survey samples using strat-
ified or clustered one-, two-, and three-stage sample designs. Other functions
compute variance components for multistage designs and sample sizes in two-
phase designs. A number of example data sets are included. / GPL-2
r-pragma 0.1.3 pragma allows for the use of pragma (also sometimes called directives or key- noarch
words. These allow assigning arbitrary functionality to a word without requir-
ing the standard function call syntax i.e. with parens. / GPL-2
r-prais 1.1.1 The Prais-Winsten estimator (Prais & Winsten, 1954) takes into account AR(1) noarch
serial correlation of the errors in a linear regression model. The procedure re-
cursively estimates the coefficients and the error autocorrelation of the speci-
fied model until sufficient convergence of the AR(1) coefficient is attained. /
GPL-2
r-praise 1.0.0 Build friendly R packages that praise their users if they have done something linux-
good, or they just need it to feel better. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-praktikum 0.1 Kasulikud funktsioonid kvantitatiivsete mudelite kursuse (SHPH.00.004) noarch
jaoks / GPL-2
r-praznik 6.0.0 A collection of feature selection filters performing greedy optimisation linux-
of mutual information-based usefulness criteria, inspired by the overview 64,
by Brown, Pocock, Zhao and Lujan (2012) <http://www.jmlr.org/papers/ osx-
v13/brown12a.html>. Implements, among other, minimum redundancy 64,
maximal relevancy (‘mRMR’) method by Peng, Long and Ding (2005) win-
<doi:10.1109/TPAMI.2005.159>; joint mutual information (‘JMI’) method by 64
Yang and Moody (1999) <http://papers.nips.cc/paper/1779-data-visualization-
and-feature-selection-new-algorithms-for-nongaussian-data>; double input
symmetrical relevance (‘DISR’) method by Meyer and Bontempi (2006)
<doi:10.1007/11732242_9> as well as joint mutual information max-
imisation (‘JMIM’) method by Bennasar, Hicks and Setchi (2015)
<doi:10.1016/j.eswa.2015.07.007>. / GPL-3
r-prclust 1.3 Clustering is unsupervised and exploratory in nature. Yet, it can be per- linux-
formed through penalized regression with grouping pursuit. In this package, 64,
we provide two algorithms for fitting the penalized regression-based cluster- osx-
ing (PRclust) with non-convex grouping penalties, such as group truncated 64,
lasso, MCP and SCAD. One algorithm is based on quadratic penalty and dif- win-
ference convex method. Another algorithm is based on difference convex and 64
ADMM, called DC-ADD, which is more efficient. Generalized cross valida-
tion and stability based method were provided to select the tuning parameters.
Rand index, adjusted Rand index and Jaccard index were provided to estimate
the agreement between estimated cluster memberships and the truth. / GPL-2
| GPL-3
r-precisesums 0.3 Most of the time floating point arithmetic does approximately the right thing. linux-
When adding sums or having products of numbers that greatly differ in mag- 64,
nitude, the floating point arithmetic may be incorrect. This package im- osx-
plements the Kahan (1965) sum <doi:10.1145/363707.363723>, Neumaier 64,
(1974) sum <doi:10.1002/zamm.19740540106>, pairwise-sum (adapted from win-
‘NumPy’, See Castaldo (2008) <doi:10.1137/070679946> for a discussion of 64
accuracy), and arbitrary precision sum (adapted from the fsum in ‘Python’ ;
Shewchuk (1997) <http://www.cs.berkeley.edu/~jrs/papers/robustr.pdf>). In
addition, products are changed to long double precision for accuracy, or
changed into a log-sum for accuracy. / GPL-2
r-prediction 0.3.14A one-function package containing ‘prediction()’, a type-safe alternative to noarch
‘predict()’ that always returns a data frame. The ‘summary()’ method pro-
vides a data frame with average predictions, possibly over counterfactual ver-
sions of the data (a la the ‘margins’ command in ‘Stata’). Marginal effect es-
timation is provided by the related package, ‘margins’ <https://cran.r-project.
org/package=margins>. The package currently supports common model types
(e.g., lm, glm) from the ‘stats’ package, as well as numerous other model
classes from other add-on packages. See the README or main package doc-
umentation page for a complete listing. / MIT
r- 0.1_4 Three prediction algorithms described in the paper On-line predictive linear re- noarch
predictiveregression gression Annals of Statistics 37, 1566 - 1590 (2009) / file LICENSE (Restricts
use)


Name Version
r-predkmeans 0.1.0 Implements the predictive k-means method for clustering observations, using a linux-
mixture of experts model to allow covariates to influence cluster centers. Moti- 64,
vated by air pollution epidemiology settings, where cluster membership needs osx-
to be predicted across space. Includes functions for predicting cluster member- 64,
ship using spatial splines and principal component analysis (PCA) scores using win-
either multinomial logistic regression or support vector machines (SVMs). For 64
method details see Keller et al. (2017) <doi:10.1214/16-AOAS992>. / GPL-3
r-predmixcor 1.1_1 train_predict_mix predicts the binary response with binary features / GPL-2 noarch
r- 0.1.0 Dynamize headers or R code within ‘Rmd’ files to prevent proliferation of noarch
preknitposthtmlrender ‘Rmd’ files for similar reports. Add in external HTML document within
‘rmarkdown’ rendered HTML doc. / GPL-2
r-preputils 1.0.2 Miscellaneous small utilities are provided to mitigate issues with messy, in- noarch
consistent or high dimensional data and help for preprocessing and preparing
analyses. / GPL-3
r-prereg 0.4.0 Provides a collection of templates to author preregistration documents for sci- noarch
entific studies in PDF format. / GPL-3
r- 1.1.9 This package provides a set of functions useful when evaluating the results of noarch
presenceabsence presence-absence models. Package includes functions for calculating thresh-
old dependent measures such as confusion matrices, pcc, sensitivity, speci-
ficity, and Kappa, and produces plots of each measure as the threshold is var-
ied. It will calculate optimal threshold choice according to a choice of opti-
mization criteria. It also includes functions to plot the threshold independent
ROC curves along with the associated AUC (area under the curve). / Unlimited
r-prettyb 0.2.1 Drop-in replacements for standard base graphics functions. The replacements noarch
are prettier versions of the originals. / GPL-2 | GPL-3
r-prettycode 1.0.2 Replace the standard print method for functions with one that performs syntax noarch
highlighting, using ANSI colors, if the terminal supports them. / MIT
r-prettydoc 0.3.0 Creating tiny yet beautiful documents and vignettes from R Markdown. The noarch
package provides the ‘html_pretty’ output format as an alternative to the
‘html_document’ and ‘html_vignette’ engines that convert R Markdown into
HTML pages. Various themes and syntax highlight styles are supported. /
Apache License (>= 2.0)
r-prettygraphs 2.1.6 Simple and crisp publication-quality graphics for the ExPosition family of noarch
packages. See An ExPosition of the Singular Value Decomposition in R
(Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>. / GPL-2
r-prettymapr 0.2.2 Automates the process of creating a scale bar and north arrow in any package noarch
that uses base graphics to plot in R. Bounding box tools help find and manip-
ulate extents. Finally, there is a function to automate the process of setting
margins, plotting the map, scale bar, and north arrow, and resetting graphic
parameters upon completion. / GPL-2
r-prettyr 2.2_3 Functions for conventionally formatting descriptive stats, reshaping data noarch
frames and formatting R output as HTML. / GPL-2


Name Version
r-prettyunits 1.0.2 Pretty, human readable formatting of quantities. Time intervals: 1337000 -> linux-
15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 32,
1337 -> 1.34 kB. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-prevederer 0.0.1 Easy and efficient access to the API provided by ‘Prevedere’, an industry in- noarch
sights and predictive analytics company. Query and download indicators, mod-
els and workbenches built with ‘Prevedere’ for further analysis and reporting
<https://www.prevedere.com/>. / MIT
r-primefactr 0.1.1 Use Prime Factorization for simplifying computations, for instance for ratios noarch
of large factorials. / GPL-3
r-primes 0.1.0 Functions to test whether a number is prime and generate the prime numbers linux-
within a specified range. Based around an implementation of Wilson’s theorem 64,
for testing for an integer’s primality. / MIT osx-
64,
win-
64
r-primme 3.0_0 R interface to PRIMME, a C library for computing a few eigenvalues and their linux-
corresponding eigenvectors of a real symmetric or complex Hermitian matrix. 64,
It can also compute singular values and vectors of a square or rectangular osx-64
matrix. It can find largest, smallest, or interior singular/eigenvalues and can
use preconditioning to accelerate convergence. / GPL-3
r-princurve 2.1.4 Fitting a principal curve to a data matrix in arbitrary dimensions. Hastie and linux-
Stuetzle (1989) <doi:10.2307/2289936>. / GPL-2 64,
osx-
64,
win-
64
r-prinsimp 0.8_8 Provides capabilities beyond principal components analysis to focus on find- noarch
ing structure in low variability subspaces. Constructs and plots simple basis
vectors for pre-defined and user-defined measures of simplicity. / AGPL-3
r-printr 0.1 Extends the S3 generic function knit_print() in ‘knitr’ to automatically print noarch
some objects using an appropriate format such as Markdown or LaTeX. For
example, data frames are automatically printed as tables, and the help() pages
can also be rendered in ‘knitr’ documents. / GPL-3
r-priogene 0.99.0In gene sequencing methods, the topological features of protein-protein in- noarch
teraction (PPI) networks are often used, such as ToppNet <https://toppgene.
cchmc.org>. In this study, a candidate gene prioritization method was pro-
posed for non-communicable diseases considering disease risks transferred
between genes in weighted disease PPI networks with weights for nodes and
edges based on functional information. / Artistic-2.0
r-prioritizrdata 0.2.2 Conservation planning data sets for learning how to use the ‘prioritizr’ package noarch
<https://CRAN.R-project.org/package=prioritizr>. / GPL-3
r-prioritylasso 0.2.2 Fits successive Lasso models for several blocks of (omics) data with different noarch
priorities and takes the predicted values as an offset for the next block. / GPL-2


Name Version
r-prism.forecast 0.1.6 Implements Penalized Regression with Inferred Seasonality Module (PRISM) noarch
to generate forecast estimation of weekly unemployment initial claims using
‘Google Trends’ data. It includes required data and tools for backtesting the
performance in 2007-2016. / GPL-2
r-prithulib 1.0.2 Enables user to perform the following: 1. Roll ‘n’ number of die/dice (roll()). noarch
2. Toss ‘n’ number of coin(s) (toss()). 3. Play the game of Rock, Paper,
Scissors. 4. Choose ‘n’ number of card(s) from a pack of 52 playing cards
(Joker optional). / GPL-3
r-privatelr 1.2_22Implements two differentially private algorithms for estimating L2- noarch
regularized logistic regression coefficients. A randomized algorithm F is
epsilon-differentially private (C. Dwork, Differential Privacy, ICALP 2006
<DOI:10.1007/11681878_14>), if |log(P(F(D) in S)) - log(P(F(D’) in S))| <=
epsilon for any pair D, D’ of datasets that differ in exactly one record, any
measurable set S, and the randomness is taken over the choices F makes. /
GPL-2
r-prnsamplr 0.1.0 Survey sampling using permanent random numbers (PRN’s). A solution to noarch
the problem of unknown overlap between survey samples, which leads to a
low precision in estimates when the survey is repeated or combined with other
surveys. The PRN solution is to supply the U(0, 1) random numbers to the
sampling procedure, instead of having the sampling procedure generate them.
In Lindblom (2014) <doi:10.2478/jos-2014-0047>, and therein cited articles,
it is shown how this is carried out and how it improves the estimates. This
package supports two common fixed-size sampling procedures (simple ran-
dom sampling and probability-proportional-to-size sampling) and includes a
function for transforming the PRN’s in order to control the sample overlap. /
MIT
r-pro 0.1.1 Optogenetics is a new tool to study neuronal circuits that have been genetically noarch
modified to allow stimulation by flashes of light. This package implements the
methodological framework, Point-process Response model for Optogenetics
(PRO), for analyzing data from these experiments. This method provides ex-
plicit nonlinear transformations to link the flash point-process with the spiking
point-process. Such response functions can be used to provide important and
interpretable scientific insights into the properties of the biophysical process
that governs neural spiking in response to optogenetic stimulation. / GPL-2
r-probemod 0.2.1 Contains functions that are useful for probing moderation effects (or inter- noarch
actions) including techniques such as pick-a-point (also known as spotlight
analysis) and Johnson-Neyman (also known as floodlight analysis). Plot func-
tion is also provided to facilitate visualization of results from each of these
techniques. / GPL-3
r-probfda 1.0.1 Probabilistic Fisher discriminant analysis (pFDA) is a probabilistic version of noarch
the popular and powerful Fisher linear discriminant analysis for dimensionality
reduction and classification. / GPL-2
r-probhat 0.1.1 Computes nonparametric probability distributions (probability density func- noarch
tions, cumulative distribution functions and quantile functions) using kernel
smoothing. Supports univariate, multivariate and conditional distributions,
and weighted data (possibly useful mixed with fuzzy clustering or frequency
data). Also, supports empirical continuous cumulative distribution functions
and their inverses, and random number generation. / GPL-2
r-probsvm 1.00 This package provides multiclass conditional probability estimation for the noarch
SVM, which is distributional assumption free. / GPL-2


Name Version
r-proc 1.14.0Tools for visualizing, smoothing and comparing receiver operating character- linux-
istic (ROC curves). (Partial) area under the curve (AUC) can be compared with 32,
statistical tests based on U-statistics or bootstrap. Confidence intervals can be linux-
computed for (p)AUC or ROC curves. / GPL (>= 3) 64,
osx-
64,
win-
32,
win-
64
r-proccalibrad 0.14 Package for processing downloaded MODIS Calibrated radiances Product noarch
HDF files. Specifically, MOD02 calibrated radiance product files, and the
associated MOD03 geolocation files (for MODIS-TERRA). The package will
be most effective if the user installs MRTSwath (MODIS Reprojection Tool
for swath products; <https://lpdaac.usgs.gov/tools/modis_reprojection_tool_
swath>, and adds the directory with the MRTSwath executable to the default
R PATH by editing ~/.Rprofile. / GPL-2
r-processcontrol 0.1.0 Generate time series chart for individual values with mean and /- 3 standard noarch
deviation lines and the corresponding mR chart with the upper control limit.
Also execute the 8 Shewhart stability run tests and display the violations. /
MIT
r-processx 3.3.0 Portable tools to run system processes in the background. It can check if a linux-
background process is running; wait on a background process to finish; get the 32,
exit status of finished processes; kill background processes and their children; linux-
restart processes. It can read the standard output and error of the processes, 64,
using non-blocking connections. ‘processx’ can poll a process for standard osx-
output or error, with a timeout. It can also poll several processes at once. / 64,
MIT file LICENSE win-
32,
win-
64
r-prodigenr 0.5.0 Create a project directory structure, along with typical files for that project. noarch
This allows projects to be quickly and easily created, as well as for them to
be standardized. Designed specifically with scientists in mind (mainly bio-
medical researchers, but likely applies to other fields). / MIT
r-prodlim 2018.04.18
Fast and user friendly implementation of nonparametric estimators for cen- linux-
sored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen 32,
method. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
r-profdpm 3.3 This package facilitates profile inference (inference at the posterior mode) for linux-
a class of product partition models (PPM). The Dirichlet process mixture is 64,
currently the only available member of this class. These methods search for osx-
the maximum posterior (MAP) estimate for the data partition in a PPM. / GPL- 64,
2 win-
64


Name Version
r- 1.1 This package provides profile likelihoods for a parameter of interest in com- noarch
profilelikelihood monly used statistical models. The models include linear models, generalized
linear models, proportional odds models, linear mixed-effects models, and lin-
ear models for longitudinal responses fitted by generalized least squares. The
package also provides plots for normalized profile likelihoods as well as the
maximum profile likelihood estimates and the kth likelihood support intervals.
/ GPL-3
r-profilemodel 0.6.0 Provides tools that can be used to calculate, evaluate, plot and use for infer- linux-
ence the profiles of arbitrary inference functions for arbitrary ‘glm’-like fitted 32,
models with linear predictors. More information on the methods that are im- linux-
plemented can be found in Kosmidis (2008) <https://www.r-project.org/doc/ 64,
Rnews/Rnews_2008-2.pdf>. / GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64
r-profmem 0.5.0 A simple and light-weight API for memory profiling of R expressions. The noarch
profiling is built on top of R’s built-in memory profiler (‘utils::Rprofmem()’),
which records every memory allocation done by R (also native code). / LGPL-
2.1
r-profr 0.3.3 An alternative data structure and visual rendering for the profiling information noarch
generated by Rprof. / MIT
r-proftools 0.99_2Tools for examining Rprof profile output. / GPL-3 noarch
r-profvis 0.3.5 Interactive visualizations for profiling R code. / GPL-3 | file LICENSE linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-prognosticroc 0.7 Prognostic ROC curve is an alternative graphical approach to represent the dis- noarch
criminative capacity of the marker: a receiver operating characteristic (ROC)
curve by plotting 1 minus the survival in the high-risk group against 1 minus
the survival in the low-risk group. This package contains functions to assess
prognostic ROC curve. The user can enter the survival according to a model
previously estimated or the user can also enter individual survival data for
estimating the prognostic ROC curve by using Kaplan-Meier estimator. The
area under the curve (AUC) corresponds to the probability that a patient in
the low-risk group has a longer lifetime than a patient in the high-risk group.
The prognostic ROC curve provides complementary information compared to
survival curves. The AUC is assessed by using the trapezoidal rules. When
survival curves do not reach 0, the prognostic ROC curve is incomplete and
the extrapolations of the AUC are performed by assuming pessimist, optimist
and non-informative situations. / GPL-2


Name Version
r-progress 1.2.0 Configurable Progress bars, they may include percentage, elapsed time, and/or noarch
the estimated completion time. They work in terminals, in ‘Emacs’ ‘ESS’,
‘RStudio’, ‘Windows’ ‘Rgui’ and the ‘macOS’ ‘R.app’. The package also
provides a ‘C’ ‘API’, that works with or without ‘Rcpp’. / MIT file LICENSE
r-proj4 1.0_8.1
A simple interface to lat/long projection and datum transformation of the linux-
PROJ.4 cartographic projections library. It allows transformation of geo- 64,
graphic coordinates from one projection and/or datum to another. / GPL-2 osx-64
r- 0.9.0 Provides functions to automatically build a directory structure for a new R noarch
projecttemplate project. Using this structure, ‘ProjectTemplate’ automates data loading, pre-
processing, library importing and unit testing. / GPL-3
r-projmgr 0.1.0 Provides programmatic access to ‘GitHub’ API with a focus on project man- noarch
agement. Key functionality includes setting up issues and milestones from R
objects or ‘YAML’ configurations, querying outstanding or completed tasks,
and generating progress updates in tables, charts, and RMarkdown reports.
Useful for those using ‘GitHub’ in personal, professional, or academic set-
tings with an emphasis on streamlining the workflow of data analysis projects.
/ MIT
r- 1.0.1 Provides functions for calculating and analyzing the proliferative index (PI) noarch
proliferativeindex from an RNA-seq dataset. As described in Ramaker & Lasseigne, et al.
bioRxiv, 2016 <doi:10.1101/063057>. / MIT
r-promethee 1.1 Functions which can be used to support the Multicriteria Decision Analysis noarch
(MCDA) process involving multiple criteria, by PROMETHEE (Preference
Ranking Organization METHod for Enrichment of Evaluations). / GPL-3
r-promises 1.0.1 Provides fundamental abstractions for doing asynchronous programming in R linux-
using promises. Asynchronous programming is useful for allowing a single R 32,
process to orchestrate multiple tasks in the background while also attending linux-
to something else. Semantics are similar to ‘JavaScript’ promises, but with a 64,
syntax that is idiomatic R. / MIT file LICENSE osx-
64,
win-
32,
win-
64
r-promote 1.1.1 Deploy, maintain, and invoke predictive models using the ‘Alteryx Promote’ noarch
REST API. ‘Alteryx Promote’ is available at the URL: <https://www.alteryx.
com/products/alteryx-promote>. / FreeBSD
r-propcis 0.3_0 Computes two-sample confidence intervals for single, paired and independent noarch
proportions. / GPL-3
r-properties 0.0_9 Allows to parse ‘Java’ properties files in the context of ‘R Service Bus’ appli- noarch
cations. / GPL-2
r-propscrrand 1.1 This package contains functions to run propensity-biased allocation to balance noarch
covariate distributions in sequential trials and propensity-constrained random-
ization to balance covariate distributions in trials with known baseline covari-
ates at time of randomization. Currently this package only supports trials com-
paring two groups. / GPL-3


Name Version
r-proscorertools 0.0.1 Provides a reliable and flexible toolbox to score patient-reported outcome noarch
(PRO), Quality of Life (QOL), and other psychometric measures. The guiding
philosophy is that scoring errors can be eliminated by using a limited num-
ber of well-tested, well-behaved functions to score PRO-like measures. The
workhorse of the package is the ‘scoreScale’ function, which can be used
to score most single-scale measures. It can reverse code items that need to
be reversed before scoring and pro-rate scores for missing item data. Cur-
rently, three different types of scores can be output: summed item scores, mean
item scores, and scores scaled to range from 0 to 100. The ‘PROscorerTools’
functions can be used to write new functions that score more complex mea-
sures. In fact, ‘PROscorerTools’ functions are the building blocks of the scor-
ing functions in the ‘PROscorer’ package (which is a repository of functions
that score specific commonly-used instruments). Users are encouraged to use
‘PROscorerTools’ to write scoring functions for their favorite PRO-like instru-
ments, and to submit these functions for inclusion in ‘PROscorer’ (a tutorial
vignette will be added soon). The long-term vision for the ‘PROscorerTools’
and ‘PROscorer’ packages is to provide an easy-to-use system to facilitate the
incorporation of PRO measures into research studies in a scientifically rigorous
and reproducible manner. These packages and their vignettes are intended to
help establish and promote best practices for scoring and describing PRO-like
measures in research. / MIT
r-prospectr 0.1.3 The package provides functions for pretreatment and sample selection of visi- linux-
ble and near infrared diffuse reflectance spectra / GPL-3 64,
osx-
64,
win-
64
r-prosper 0.3.0 An environment to simulate the development of annual plant populations with noarch
regard to population dynamics and genetics, especially herbicide resistance. It
combines genetics on the individual level (Renton et al. 2011) with a stochas-
tic development on the population level (Daedlow, 2015). Renton, M, Diggle,
A, Manalil, S and Powles, S (2011) <doi:10.1016/j.jtbi.2011.05.010> Daed-
low, Daniel (2015, doctoral dissertation: University of Rostock, Faculty of
Agriculture and Environmental Sciences.) / GPL-3
r- 0.1.0 An implementation of protein descriptors in R. These descriptors combine the noarch
proteindescriptors advantages of being fixed length and including partial sequential effect: Vari-
ous length of protein sequences are described with fixed length vectors that are
suitable for machine learning algorithms, and still includes partial sequential
effect. / BSD_3_clause
r- 2.0 This package provides functions to identify the optimal solution that maxi- noarch
proteomicdesign mizes numbers of detectable differentiated proteins from a multi-stage clinical
proteomic study. / GPL-3


Name Version
r-proto 1.0.0 An object oriented system using object-based, also called prototype-based, linux-
rather than class-based object oriented ideas. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-protoclass 1.0 Greedy algorithm described in Bien and Tibshirani (2011) Prototype Selection noarch
for Interpretable Classification. Annals of Applied Statistics. 5(4). 2403-2424
/ GPL-3
r-protoclust 1.6.3 Performs minimax linkage hierarchical clustering. Every cluster has an asso- linux-
ciated prototype element that represents that cluster as described in Bien, J., 64,
and Tibshirani, R. (2011), Hierarchical Clustering with Prototypes via Mini- osx-
max Linkage, The Journal of the American Statistical Association, 106(495), 64,
1075-1084. / GPL-2 win-
64
r-protolidar 0.1 PROTOLIDAR package contains functions for analyze the LIDAR scan of noarch
plants (grapevine) and make 3D maps in GRASS GIS. / GPL-3
r-protolite 1.9 Optimized C implementations for reading and writing protocol-buffers. Cur- linux-
rently supports ‘rexp.proto’ for serializing R objects and ‘geobuf.proto’ for 64,
geojson data. This lightweight package is complementary to the much larger osx-
‘RProtoBuf’ package which provides a full featured toolkit for working with 64,
protocol-buffers in R. / MIT win-
64
r-proton 1.0 ‘The Proton Game’ is a console-based data-crunching game for younger and noarch
older data scientists. Act as a data-hacker and find Slawomir Pietraszko’s cre-
dentials to the Proton server. You have to solve four data-based puzzles to find
the login and password. There are many ways to solve these puzzles. You
may use loops, data filtering, ordering, aggregation or other tools. Only basics
knowledge of R is required to play the game, yet the more functions you know,
the more approaches you can try. The knowledge of dplyr is not required but
may be very helpful. This game is linked with the „Pietraszko’s Cave” story
available at http://biecek.pl/BetaBit/Warsaw. It’s a part of Beta and Bit series.
You will find more about the Beta and Bit series at http://biecek.pl/BetaBit. /
GPL-2
r-protr 1.6_2 Comprehensive toolkit for generating various numeri- noarch
cal features of protein sequences described in Xiao et
al. (2015) <DOI:10.1093/bioinformatics/btv042>. For
full functionality, the software ‘ncbi-blast’ is needed, see
<https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download>
for more information. / BSD_3_clause
r-protviz 0.4.0 Helps with quality checks, visualizations and analysis of mass spectrometry linux-
data, coming from proteomics experiments. The package is developed, tested 64,
and used at the Functional Genomics Center Zurich. We use this package osx-
mainly for prototyping, teaching, and having fun with proteomics data. But it 64,
can also be used to do data analysis for small scale data sets. / GPL-3 win-
64


Name Version
r-provparser 0.2 R functions to access provenance information collected by ‘rdt’ or ‘rdtLite’. noarch
The information is stored inside a ‘ProvInfo’ object and can be accessed
through a collection of functions that will return the requested data. The ex-
act format of the JSON created by ‘rdt’ and ‘rdtLite’ is described in <https:
//github.com/End-to-end-provenance/ExtendedProvJson>. / GPL-3
r-provviz 1.0.6 Displays provenance graphically for provenance collected by the ‘rdt’ or noarch
‘rdtLite’ packages, or other tools providing compatible PROV JSON output.
The exact format of the JSON created by ‘rdt’ and ‘rdtLite’ is described in
<https://github.com/End-to-end-provenance/ExtendedProvJson>. More infor-
mation about rdtLite and associated tools is available at <https://github.com/
End-to-end-provenance/> and Barbara Lerner, Emery Boose, and Luis Perez
(2018), Using Introspection to Collect Provenance in R, Informatics, <doi:
10.3390/informatics5010012>. / GPL-3
r-proxy 0.4_23Provides an extensible framework for the efficient calculation of auto- and linux-
cross-proximities, along with implementations of the most popular ones. / 64,
GPL-2 osx-
64,
win-
64
r-prroc 1.3.1 Computes the areas under the precision-recall (PR) and ROC curve for noarch
weighted (e.g., soft-labeled) and unweighted data. In contrast to other imple-
mentations, the interpolation between points of the PR curve is done by a non-
linear piecewise function. In addition to the areas under the curves, the curves
themselves can also be computed and plotted by a specific S3-method. Ref-
erences: Davis and Goadrich (2006) <doi:10.1145/1143844.1143874>; Keil-
wagen et al. (2014) <doi:10.1371/journal.pone.0092209>; Grau et al. (2015)
<doi:10.1093/bioinformatics/btv153>. / GPL-3
r-prsr 3.1.1 Tests periodicity in short time series using response surface regression. / GPL-
linux-
2 64,
osx-
64,
win-
64
r-pryr 0.1.4 Useful tools to pry back the covers of R and understand the language at a linux-
deeper level. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-ps 1.3.0 List, query and manipulate all system processes, on ‘Windows’, ‘Linux’ and linux-
‘macOS’. / BSD_3_clause file LICENSE 64,
osx-
64,
win-
32,
win-
64


Name Version
r-psagraphics 2.1.1 A collection of functions that primarily produce graphics to aid in a Propensity noarch
Score Analysis (PSA). Functions include: cat.psa and box.psa to test balance
within strata of categorical and quantitative covariates, circ.psa for a represen-
tation of the estimated effect size by stratum, loess.psa that provides a graphic
and loess based effect size estimate, and various balance functions that provide
measures of the balance achieved via a PSA in a categorical covariate. / GPL-2
r-pscl 1.5.2 Bayesian analysis of item-response theory (IRT) models, roll call analysis; linux-
computing highest density regions; maximum likelihood estimation of zero- 64,
inflated and hurdle models for count data; goodness-of-fit measures for GLMs; osx-
data sets used in writing and teaching at the Political Science Computational 64,
Laboratory; seats-votes curves. / GPL-2 win-
64
r-pseval 1.3.1 Contains the core methods for the evaluation of principal surrogates in a single noarch
clinical trial. Provides a flexible interface for defining models for the risk
given treatment and the surrogate, the models for integration over the missing
counterfactual surrogate responses, and the estimation methods. Estimated
maximum likelihood and pseudo-score can be used for estimation, and the
bootstrap for inference. A variety of post-estimation summary methods are
provided, including print, summary, plot, and testing. / MIT
r-psi 1.1 This package contains functions to calculate the Specificity Index statis- noarch
tic, which can be used for comparative quantitative analysis to iden-
tify genes enriched in specific cell populations across a large num-
ber of profiles, as well as perform numerous post-processing operations.
NOTE:Supplementary data (human & mouse expression sets, calculated pSI
datasets, etc.) can be found in pSI.data package located at the following URL:
http://genetics.wustl.edu/jdlab/psi_package/ / GPL-2
r-pso 1.0.3 The package provides an implementation of PSO consistent with the standard noarch
PSO 2007/2011 by Maurice Clerc et al. Additionally a number of ancillary
routines are provided for easy testing and graphics. / LGPL-3
r-psoptim 1.0 Particle swarm optimization - a basic variant. / GPL (>= 2.0) noarch
r-pspearman 0.3_0 Spearman’s rank correlation test with precomputed exact null distribution forlinux-
n <= 22. / GPL-3 64,
osx-
64,
win-
64
r-pspline 1.0_18Smoothing splines with penalties on order m derivatives. / Unlimited linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
r-pstat 1.2 Calculating Pst values to assess differentiation among populations from a set noarch
of quantitative traits is the primary purpose of such a package. The bootstrap
method provides confidence intervals and distribution histograms of Pst. Vari-
ations of Pst in function of the parameter c/h^2 are studied as well. Finally, the
package proposes different transformations especially to eliminate any vari-
ation resulting from allometric growth (calculation of residuals from linear
regressions, Reist standardizations or Aitchison transformation). / GPL-2
r-psumtsim 0.4 Functions to simulate Poisson or Normally distributed responses relative to a noarch
baseline and compute achieved significance level and powers for tests on the
simulated responses. / GPL-3
r-psy 1.1 Kappa, ICC, Cronbach alpha, screeplot, mtmm / GPL-2 noarch
r-psych 1.8.12A general purpose toolbox for personality, psychometric theory and experi- linux-
mental psychology. Functions are primarily for multivariate analysis and scale 32,
construction using factor analysis, principal component analysis, cluster anal- linux-
ysis and reliability analysis, although others provide basic descriptive statis- 64,
tics. Item Response Theory is done using factor analysis of tetrachoric and noarch,
polychoric correlations. Functions for analyzing data at multiple levels in- osx-
clude within and between group statistics, including correlations and factor 64,
analysis. Functions for simulating and testing particular item and test struc- win-
tures are included. Several functions serve as a useful front end for struc- 32,
tural equation modeling. Graphical displays of path diagrams, factor anal- win-
ysis and structural equation models are created using basic graphics. Some 64
of the functions are written to support a book on psychometric theory as
well as publications in personality research. For more information, see the
<https://personality-project.org/r> web page. / GPL (>= 2)
r-psychotools 0.5_0 Infrastructure for psychometric modeling such as data classes (for item re- linux-
sponse data and paired comparisons), basic model fitting functions (for 64,
Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit, rat- osx-
ing scale, multinomial processing tree models), extractor functions for dif- 64,
ferent types of parameters (item, person, threshold, discrimination, guessing, win-
upper asymptotes), unified inference and visualizations, and various datasets 64
for illustration. Intended as a common lightweight and efficient toolbox for
psychometric modeling and a common building block for fitting psychome-
tric mixture models in package psychomix and trees based on psychometric
models in package psychotree. / GPL-2 | GPL-3
r-psychtools 1.9.5.26
Support functions, data sets, and vignettes for the ‘psych’ package. Contains noarch
several of the biggest data sets for the ‘psych’ package as well as one vignette.
A few helper functions for file manipulation are included as well. For more
information, see the <https://personality-project.org/r> web page. / GPL-2
r-psymonitor 0.0.2 Apply the popular real-time monitoring strategy proposed by Phillips, Shi noarch
and Yu (2015a,b;PSY) <doi:10.1111/iere.12132>, <doi:10.1111/iere.12131>,
along with a new bootstrap procedure designed to mitigate the potential impact
of heteroskedasticity and to effect family-wise size control in recursive testing
algorithms (Phillips and Shi, forthcoming). / GPL-3
r-psyphy 0.1_9 An assortment of functions that could be useful in analyzing data from psy- noarch
chophysical experiments. It includes functions for calculating d’ from several
different experimental designs, links for m-alternative forced-choice (mafc)
data to be used with the binomial family in glm (and possibly other contexts)
and self-Start functions for estimating gamma values for CRT screen calibra-
tions. / GPL-3


Name Version
r-pte 1.7 We provide inference for personalized medicine models. Namely, we answer noarch
the questions: (1) how much better does a purported personalized recommen-
dation engine for treatments do over a business-as-usual approach and (2) is
that difference statistically significant? / GPL-3
r-ptest 1.0_8 Implements p-value computations using an approximation to the cumulative linux-
distribution function for a variety of tests for periodicity. These tests include 64,
harmonic regression tests with normal and double exponential errors as well osx-
as modifications of Fisher’s g test. An accompanying vignette illustrates the 64,
application of these tests. / GPL-2 win-
64
r-ptprocess 3.3_13Fits and analyses time dependent marked point process models with an empha- noarch
sis on earthquake modelling. For a more detailed introduction to the package,
see the topic PtProcess. A list of recent changes can be found in the topic
Change Log. / GPL-2
r-pts2polys 0.1.1 Various applications in invasive species biology, conservation biology, epi- linux-
demiology and elsewhere involve sampling of sets of 2D points from a pos- 64,
terior distribution. The number of such point sets may be large, say 1000 or osx-
10000. This package facilitates visualisation of such output by constructing 64,
seven nested polygons representing the location and variability of the point win-
sets. This can be used, for example, to visualise the range boundary of a 64
species, and uncertainty in the location of that boundary. / GPL-2
r-ptsuite 1.0.0 Various estimation methods for the shape parameter of Pareto distributed linux-
data. This package contains functions for various estimation methods such 64,
as maximum likelihood (Newman, 2005)<doi:10.1016/j.cities.2012.03.001>, osx-
Hill’s estimator (Hill, 1975)<doi:10.1214/aos/1176343247>, least squares 64,
(Zaher et al., 2014)<doi:10.9734/BJMCS/2014/10890>, method of moments win-
(Rytgaard, 1990)<doi:10.2143/AST.20.2.2005443>, percentiles (Bhatti et 64
al., 2018)<doi:10.1371/journal.pone.0196456>, and weighted least squares
(Nair et al., 2019) to estimate the shape parameter of Pareto dis-
tributed data. It also provides both a heuristic method (Hubert et al.,
2013)<doi:10.1016/j.csda.2012.07.011> and a goodness of fit test (Gulati and
Shapiro, 2008)<doi:10.1007/978-0-8176-4619-6> for testing for Pareto data
as well as a method for generating Pareto distributed data. / GPL-3
r-ptw 1.9_13Parametric Time Warping aligns patterns, i.e. it aims to put corresponding fea- linux-
tures at the same locations. The algorithm searches for an optimal polynomial 64,
describing the warping. It is possible to align one sample to a reference, several osx-
samples to the same reference, or several samples to several references. One 64,
can choose between calculating individual warpings, or one global warping for win-
a set of samples and one reference. Two optimization criteria are implemented: 64
RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). Both
warping of peak profiles and of peak lists are supported. / GPL-2
r-ptwikiwords 0.0.3 Contains a dataset of words used in 15.000 randomly extracted pages from the noarch
Portuguese Wikipedia (<https://pt.wikipedia.org/>). / MIT
r-ptycho 1.1_4 Bayesian variable selection for linear regression models using hierarchical pri- noarch
ors. There is a prior that combines information across responses and one that
combines information across covariates, as well as a standard spike and slab
prior for comparison. An MCMC samples from the marginal posterior distri-
bution for the 0-1 variables indicating if each covariate belongs to the model
for each response. / GPL-2


Name Version
r-publish 2018.04.17
A bunch of convenience functions that transform the results of some basic noarch
statistical analyses into table format nearly ready for publication. This includes
descriptive tables, tables of logistic regression and Cox regression results as
well as forest plots. / GPL-2
r-pullword 0.2 R Interface to Pullword Service for natural language processing in Chinese. It linux-
enables users to extract valuable words from text by deep learning models. For 64,
more details please visit the official site (in Chinese) http://pullword.com/. / osx-
LGPL-3 64,
win-
64
r-pulsar 0.3.6 Model selection for penalized graphical models using the Stability Approach noarch
to Regularization Selection (‘StARS’), with options for speed-ups includ-
ing Bounded StARS (B-StARS), batch computing, and other stability met-
rics (e.g., graphlet stability G-StARS). Christian L. Müller, Richard Bonneau,
Zachary Kurtz (2016) <arXiv:1605.07072>. / GPL-2
r-pumilior 1.3.1 R package to query and get data out of a Pumilio sound archive system (http: noarch
//ljvillanueva.github.io/pumilio/). / GPL-3
r-purge 0.2.1 Enables the removal of training data from fitted R models while retaining pre- noarch
dict functionality. The purged models are more portable as their memory foot-
prints do not scale with the training sample size. / MIT
r-purging 1.0.0 Simple method of purging independent variables of mediating effects. First, noarch
regress the direct variable on the indirect variable. Then, used the stored resid-
uals as the new purged (direct) variable in the updated specification. This purg-
ing process allows for use of a new direct variable uncorrelated with the indi-
rect variable. Please cite the method and/or package using Waggoner, Philip
D. (2018) <doi:10.1177/1532673X18759644>. / MIT
r-purrr 0.3.2 A complete and consistent functional programming toolkit for R. / GPL-3 | file linux-
LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-pushbar 0.1.0 Create sliders from left, right, top and bottom which may include any html or noarch
‘Shiny’ input or output. / MIT
r-pushoverr 1.0.0 Send push notifications to mobile devices or the desktop using Pushover. noarch
These notifications can display job status, results, scraped web data, or any
other text or numeric data. / BSD_2_clause
r-pvclass 1.4 Computes nonparametric p-values for the potential class memberships of new noarch
observations as well as cross-validated p-values for the training data. The
p-values are based on permutation tests applied to an estimated Bayesian like-
lihood ratio, using a plug-in statistic for the Gaussian model, ‘k nearest neigh-
bors’, ‘weighted nearest neighbors’ or ‘penalized logistic regression’. Ad-
ditionally, it provides graphical displays and quantitative analyses of the p-
values. / GPL-2


Name Version
r-pvclust 2.0_0 An implementation of multiscale bootstrap resampling for assessing the un- noarch
certainty in hierarchical cluster analysis. It provides AU (approximately unbi-
ased) p-value as well as BP (bootstrap probability) value for each cluster in a
dendrogram. / GPL-2
r-pvsr 0.3 The pvsR package facilitates data retrieval from Project Vote Smart’s rich on- noarch
line data base on US politics via the Project Vote Smart application program-
ming interface (PVS API). The functions in this package cover most PVS API
classes and methods and return the requested data in a data frame. / GPL-2
r-pwr 1.2_2 Power analysis functions along the lines of Cohen (1988). / GPL-3 noarch
r-pwr2 1.0 User friendly functions for power and sample size analysis at one-way and noarch
two-way ANOVA settings take either effect size or delta and sigma as argu-
ments. They are designed for both one-way and two-way ANOVA settings. In
addition, a function for plotting power curves is available for power compari-
son, which can be easily visualized by statisticians and clinical researchers. /
GPL-2
r-pwrab 0.1.0 Power analysis for AB testing. The calculations are based on the Welch’s un- noarch
equal variances t-test, which is generally preferred over the Student’s t-test
when sample sizes and variances of the two groups are unequal, which is fre-
quently the case in AB testing. In such situations, the Student’s t-test will give
biased results due to using the pooled standard deviation, unlike the Welch’s
t-test. / GPL-3
r-pwrrasch 0.1_2 Statistical power simulation for testing the Rasch Model based on a three-way noarch
analysis of variance design with mixed classification. / GPL-3
r-pwt 7.1_1 The Penn World Table provides purchasing power parity and national income noarch
accounts converted to international prices for 189 countries for some or all of
the years 1950-2010. / GPL-2
r-pwt8 8.1_1 The Penn World Table 8.x provides information on relative levels of income, noarch
output, inputs, and productivity for 167 countries between 1950 and 2011. /
GPL-2 | GPL-3
r-pwt9 9.1_0 The Penn World Table 9.x (<http://www.ggdc.net/pwt/>) provides information noarch
on relative levels of income, output, inputs, and productivity for 182 countries
between 1950 and 2017. / GPL-2 | GPL-3
r-pxr 0.42.2Provides a set of functions for reading and writing PC-Axis files, used by noarch
different statistical organizations around the globe for data dissemination. /
GPL-3
r-pxweb 0.9.1 Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis API noarch
is used by organizations such as Statistics Sweden and Statistics Finland to
disseminate data. The R package can interact with all PX-Web/PC-Axis APIs
to fetch information about the data hierarchy, extract metadata and extract and
parse statistics to R data.frame format. PX-Web is a solution to disseminate
PC-Axis data files in dynamic tables on the web. Since 2013 PX-Web contains
an API to disseminate PC-Axis files. / BSD_2_clause
r-pymturkr 1.1 Provides access to the latest ‘Amazon Mechanical Turk’ (‘MTurk’) <https: noarch
//www.mturk.com> Requester API (version ‘2017–01–17’), replacing the now
deprecated ‘MTurkR’ package. / GPL-2
r-pyramid 1.5 Drawing population pyramid using (1) data.frame or (2) vectors. The for- noarch
mer is named as pyramid() and the latter pyramids(), as wrapper function of
pyramid(). pyramidf() is the function to draw population pyramid within the
specified frame. / GPL-2
r-pzfx 0.2.0 Read and write ‘GraphPad Prism’ ‘.pzfx’ files in R. / MIT noarch


Name Version
r-qaig 0.1.5 A tool for automatic generation of sibling items from a parent item model noarch
defined by the user. It is an implementation of the process automatic item
generation (AIG) focused on generating quantitative multiple-choice type of
items (see Embretson, Kingston (2018) <doi:10.1111/jedm.12166>). / GPL-3
r-qboxplot 0.2 Produce quantile-based box-and-whisker plot(s). / GPL-2 noarch
r- 1.1.1 Implements tests for Type I error in Qualitative Comparative Analysis (QCA) noarch
qcafalsepositive that take into account the multiple hypothesis tests inherent in the procedure.
Tests can be carried out on three variants of QCA: crisp-set QCA (csQCA),
multi-value QCA (mvQCA) and fuzzy-set QCA (fsQCA). For fsQCA, the
fsQCApermTest() command implements a permutation test that provides 95%
confidence intervals for the number of counterexamples and degree of consis-
tency, respectively. The distributions of permuted values can be plotted against
the observed values. For csQCA and mvQCA, simple binomial tests are im-
plemented in csQCAbinTest() and mvQCAbinTest(), respectively. / GPL-3
r-qcba 0.3.1 CBA postprocessing algorithm that creates smaller models for datasets con- noarch
taining quantitative (numerical) attributes. Article describing QCBA is pub-
lished in Tomas Kliegr (2017) <arXiv:1711.10166>. / AGPL-3
r-qcc 2.7 Shewhart quality control charts for continuous, attribute and count data. noarch
Cusum and EWMA charts. Operating characteristic curves. Process capa-
bility analysis. Pareto chart and cause-and-effect chart. Multivariate control
charts. / GPL-2
r-qcewas 1.2_2 Tools for (automated and manual) quality control of the results of Epigenome- noarch
Wide Association Studies. / GPL-3
r-qcgwas 1.0_8 Tools for (automated and manual) quality control of the results of Genome noarch
Wide Association Studies / GPL-3
r-qcsis 0.1 Quantile correlation-sure independence screening (QC-SIS) and composite noarch
quantile correlation-sure independence screening (CQC-SIS) for ultrahigh-
dimensional data. / GPL-2
r-qcv 1.0 Primarily, the ‘qcv’ package computes key indices related to the Quan- noarch
tifying Construct Validity procedure (QCV; Westen & Rosenthal, 2003
<doi:10.1037/0022-3514.84.3.608>; see also Furr & Heuckeroth, in press).
The qcv() function is the heart of the ‘qcv’ package, but additional functions
in the package provide useful ancillary information related to the QCV proce-
dure. / GPL-2
r- 1.0.7 A collection of text analysis dictionaries and word lists for use with the ‘qdap’ noarch
qdapdictionaries package. / GPL-2
r-qdapregex 0.7.2 A collection of regular expression tools associated with the ‘qdap’ package noarch
that may be useful outside of the context of discourse analysis. Tools include
removal/extraction/replacement of abbreviations, dates, dollar amounts, email
addresses, hash tags, numbers, percentages, citations, person tags, phone num-
bers, times, and zip codes. / GPL-2
r-qdaptools 1.3.3 A collection of tools associated with the ‘qdap’ package that may be useful noarch
outside of the context of text analysis. / GPL-2
r-qdcomparison 3.0 Allows practitioners to determine (i) if two univariate distributions (which can noarch
be continuous, discrete, or even mixed) are equal, (ii) how two distributions
differ (shape differences, e.g., location, scale, etc.), and (iii) where two distri-
butions differ (at which quantiles), all using nonparametric LP statistics. The
primary reference is Jungreis, D. (2019, Technical Report). / GPL-2


Name Version
r-qdm 0.1_0 This package provides different specifications of a Quadrilateral Dissimilar- noarch
ity Model which can be used to fit same-different judgments in order to get
a predicted matrix that satisfies regular minimality [Colonius & Dzhafarov,
2006, Measurement and representations of sensations, Erlbaum]. From such a
matrix, Fechnerian distances can be computed. / GPL-2
r-qfrm 1.0.1 Option pricing (financial derivatives) techniques mainly following textbook noarch
‘Options, Futures and Other Derivatives’, 9ed by John C.Hull, 2014. Prentice
Hall. Implementations are via binomial tree option model (BOPM), Black-
Scholes model, Monte Carlo simulations, etc. This package is a result of
Quantitative Financial Risk Management course (STAT 449 and STAT 649)
at Rice University, Houston, TX, USA, taught by Oleg Melnikov, statistics
PhD student, as of Spring 2015. / GPL-2
r-qgglmm 0.7.2 Compute various quantitative genetics parameters from a Generalised Linear noarch
Mixed Model (GLMM) estimates. Especially, it yields the observed pheno-
typic mean, phenotypic variance and additive genetic variance. / GPL-2
r-qgtools 1.0 Two linear mixed model approaches: REML(restricted maximum likelihood) noarch
and MINQUE (minimum norm quadratic unbiased estimation) approaches and
several resampling techniques are integrated for various quantitative genetics
analyses. With these two types of approaches, various unbalanced data struc-
tures, missing data, and any irregular genetic mating designs can be analyzed
and statistically tested. This package also offers fast computations for many
large data sets. Other functions will be added to this R tool in the future. /
GPL-2
r-qhot 0.1.0 This function produces both the numerical and graphical summaries of the noarch
QTL hotspot detection in the genomes that are available on the worldwide
web including the flanking markers of QTLs. / GPL-3
r-qiitr 0.1.0 Qiita is a technical knowledge sharing and collaboration platform for program- noarch
mers. See <https://qiita.com/api/v2/docs> for more information. / MIT
r-qkerntool 1.19 Nonlinear machine learning tool for classification, clustering and dimension- noarch
ality reduction. It integrates 12 q-kernel functions and 15 conditional negative
definite kernel functions and includes the q-kernel and conditional negative
definite kernel version of density-based spatial clustering of applications with
noise, spectral clustering, generalized discriminant analysis, principal compo-
nent analysis, multidimensional scaling, locally linear embedding, sammon’s
mapping and t-Distributed stochastic neighbor embedding. / GPL-2
r-qlearn 1.0 Functions to implement Q-learning for estimating optimal dynamic treatment noarch
regimes from two stage sequentially randomized trials, and to perform infer-
ence via m-out-of-n bootstrap for parameters indexing the optimal regime. /
GPL-2
r-qlearning 0.1.1 Implements Q-Learning, a model-free form of reinforcement learning, de- noarch
scribed in work by Strehl, Li, Wiewiora, Langford & Littman (2006)
<doi:10.1145/1143844.1143955>. / GPL-3
r-qmrparser 0.1.5 Basic functions for building parsers, with an application to PC-AXIS format noarch
files. / GPL-3


Name Version
r-qpdf 1.1 Content-preserving transformations transformations of PDF files such as split, linux-
combine, and compress. This package interfaces directly to the ‘qpdf’ C API 64,
and does not require any command line utilities. Note that ‘qpdf’ does not read osx-
actual content from PDF files: to extract text and data you need the ‘pdftools’ 64,
package. / Apache License 2.0 win-
32,
win-
64
r-qqman 0.1.4 Create Q-Q and manhattan plots for GWAS data from PLINK results. / GPL-3 noarch
r-qqperm 1.0.1 Provides users the necessary utility functions to generate permutation-based noarch
QQ plots and also estimate inflation factor based on the empirical NULL dis-
tribution. While it has general utility, it is particularly helpful when the skew-
ness of the Fisher’s Exact test in sparse data situations with imbalanced case-
control sample sizes renders the reliance on the uniform chi-square expected
distribution inappropriate. / GPL-2
r-qqvases 1.0.0 Presents an explanatory animation of normal quantile-quantile plots based on noarch
a water-filling analogy. The animation presents a normal QQ plot as the para-
metric plot of the water levels in vases defined by two distributions. The dis-
tributions decorate the axes in the normal QQ plot and are optionally shown as
vases adjacent to the plot. The package draws QQ plots for several distribu-
tions, either as samples or continuous functions. / GPL-2
r-qrage 1.0 Tools that create D3 JavaScript force directed graph from R. D3 JavaScript noarch
was created by Michael Bostock. See http://d3js.org/ and, more specifically
for Force Directed Graph https://github.com/mbostock/d3/wiki/Force-Layout.
/ MIT
r-qrank 1.0 A Quantile Rank-score based test for the identification of expression quantita- noarch
tive trait loci. / GPL-2
r-qrcode 0.1.1 Create QRcode in R. / GPL-3 noarch
r-qrm 0.4_13Accompanying package to the book Quantitative Risk Management: Con- linux-
cepts, Techniques and Tools by Alexander J. McNeil, RÃ¼diger Frey, and 64,
Paul Embrechts. / GPL (>= 2) osx-
64,
win-
32,
win-
64
r-qrmdata 2016_01_03_1
Various data sets (stocks, stock indices, constituent data, FX, zero-coupon noarch
bond yield curves, volatility, commodities) for Quantitative Risk Management
practice. / GPL-2 | GPL-3
r-qrmix 0.9.0 Implements the robust algorithm for fitting finite mixture models based on noarch
quantile regression proposed by Emir et al., 2017 (unpublished). / LGPL-3
r-qrnn 2.0.4 Fit quantile regression neural network models with optional left censor- noarch
ing, partial monotonicity constraints, generalized additive model constraints,
and the ability to fit multiple non-crossing quantile functions follow-
ing Cannon (2011) <doi:10.1016/j.cageo.2010.07.005> and Cannon (2018)
<doi:10.1007/s00477-018-1573-6>. / GPL-2


Name Version
r-qrsvm 0.2.1 Quantile Regression (QR) using Support Vector Machines under the Pinball- noarch
Loss. Estimation is based on Nonparametric Quantile Regression by I.
Takeuchi, Q.V.Le , T. Sears, A.J.Smola (2004). Implementation relies on
‘quadprog’ package, package ‘kernlab’ Kernelfunctions and package ‘Matrix’
nearPD to find next Positive definite Kernelmatrix. Package estimates quan-
tiles individually but an Implementation of non crossing constraints coming
soon. Function multqrsvm() now supports parallel backend for faster fitting. /
GPL-2
r-qsardata 1.3 Molecular descriptors and outcomes for several public domain data sets / GPL- noarch
3
r-qtlbook 0.18_8Datasets for the book, A Guide to QTL Mapping with R/qtl. Broman and Sen noarch
(2009) <doi:10.1007/978-0-387-92125-9>. / GPL-3
r-qtldesign 0.941 Tools for the design of QTL experiments / GPL-3 noarch
r-quadprog 1.5_5 This package contains routines and documentation for solving quadratic pro- linux-
gramming problems. / GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-quadprogxt 0.0.4 Extends the quadprog package to solve quadratic programs with absolute value noarch
constraints and absolute values in the objective function. / GPL-2
r-qualci 0.1 Exact one-sided p-values and confidence intervals for an outcome variable de- noarch
fined on an interval measurement scale with only qualitative and ordinal infor-
mation available. / GPL-2
r-qualvar 0.2.0 Implements indices of qualitative variation proposed by Wilcox (1973). / GPL- noarch
3
r-quandl 2.10.0Functions for interacting directly with the Quandl API to offer data in a num- noarch
ber of formats usable in R, downloading a zip with all data from a Quandl
database, and the ability to search. This R package uses the Quandl API. For
more information go to <https://www.quandl.com/docs/api>. For more help
on the package itself go to <https://www.quandl.com/help/r>. / MIT
r-quantileda 1.1 Code for centroid, median and quantile classifiers. / GPL-3 noarch


Name Version
r-quantilegrader 0.1.1 Implementation of the food safety restaurant grading system adopted by Public noarch
Health - Seattle & King County (see Ashwood, Z.C., Elias, B., and Ho. D.E.
Improving the Reliability of Food Safety Disclosure: A Quantile Adjusted
Restaurant Grading System for Seattle-King County (working paper)). As re-
ported in the accompanying paper, this package allows jurisdictions to easily
implement refinements that address common challenges with unadjusted grad-
ing systems. First, in contrast to unadjusted grading, where the most recent
single routine inspection is the primary determinant of a grade, grading inputs
are allowed to be flexible. For instance, it is straightforward to base the grade
on average inspection scores across multiple inspection cycles. Second, the
package can identify quantile cutoffs by inputting substantively meaningful
regulatory thresholds (e.g., the proportion of establishments receiving suffi-
cient violation points to warrant a return visit). Third, the quantile adjustment
equalizes the proportion of establishments in a flexible number of grading cat-
egories (e.g., A/B/C) across areas (e.g., ZIP codes, inspector areas) to account
for inspector differences. Fourth, the package implements a refined quantile
adjustment that addresses two limitations with the stats::quantile() function
when applied to inspection score datasets with large numbers of score ties.
The quantile adjustment algorithm iterates over quantiles until, over all restau-
rants in all areas, grading proportions are within a tolerance of desired global
proportions. In addition the package allows a modified definition of quantile
from Nearest Rank. Instead of requiring that at least p[1]% of restaurants re-
ceive the top grade and at least (p[1]p[2])% of restaurants receive the top or
second best grade for quantiles p, the algorithm searches for cutoffs so that as
close as possible p[1]% of restaurants receive the top grade, and as close as
possible to p[2]% of restaurants receive the second top grade. / GPL-2
r-quantilenpci 0.9.0 Based on Alan D. Hutson (1999) <doi:10.1080/02664769922458>, Calculat- noarch
ing nonparametric confidence intervals for quantiles using fractional order
statistics, Journal of Applied Statistics, 26:3, 343-353. / GPL-3
r-quantmod 0.4_14Specify, build, trade, and analyse quantitative financial trading strategies. / linux-
GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-quantnorm 1.0.5 Modifies the distance matrix obtained from data with batch effects, so noarch
as to improve the performance of sample pattern detection, such as clus-
tering, dimension reduction, and construction of networks between sub-
jects. The method has been published in Bioinformatics (Fei et al,
2018, <doi:10.1093/bioinformatics/bty117>). Also available on ‘GitHub’
<https://github.com/tengfei-emory/QuantNorm>. / GPL-2
r-quantpsyc 1.5 Contains functions useful for data screening, testing moderation, mediation noarch
and estimating power. / GPL-2


Name Version
r-quantreg 5.38 Estimation and inference methods for models of conditional quantiles: Lin- linux-
ear and nonlinear parametric and non-parametric (total variation penalized) 32,
models for conditional quantiles of a univariate response and several meth- linux-
ods for handling censored survival data. Portfolio selection methods based on 64,
expected shortfall risk are also included. / GPL (>= 2) osx-
64,
win-
32,
win-
64
r- 0.4_3 Fits non-crossing regression quantiles as a function of linear covariates and noarch
quantreggrowth multiple smooth terms via B-splines with L1-norm difference penalties.
Monotonicity constraints on the fitted curves are allowed. See Muggeo,
Sciandra, Tomasello and Calvo (2013) <doi:10.1007/s10651-012-0232-1> and
<doi:10.13140/RG.2.2.12924.85122> for some code example. / GPL-3
r-quantumops 2.5.3 Contains basic structures and operations used frequently in quantum com- noarch
puting. Intended to be a convenient tool to help learn quantum mechan-
ics and algorithms. Can create arbitrarily sized kets and bras and imple-
ments quantum gates, inner products, and tensor products. Creates arbi-
trarily controlled versions of all gates and can simulate complete or partial
measurements of kets. Has functionality to convert functions into equiva-
lent quantum gates. Includes larger applications, such as Steane error cor-
rection <DOI:10.1103/physrevlett.77.793>, Quantum Fourier Transform and
Shor’s algorithm (Shor 1999), Grover’s algorithm (1996), Quantum Approx-
imation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann
2014) <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018)
<arXiv:1804.00633>. / GPL-3
r-quclu 0.1.0 Various quantile-based clustering algorithms: algorithm CU (Common theta noarch
and Unscaled variables), algorithm CS (Common theta and Scaled variables
through lambda_j), algorithm VU (Variable-wise theta_j and Unscaled vari-
ables) and algorithm VW (Variable-wise theta_j and Scaled variables through
lambda_j). Hennig, Viroli, Anderlucci (2018) <arXiv:1806.10403v1>. / GPL-
2 | GPL-3
r-queryparser 0.1.1 Translate ‘SQL’ ‘SELECT’ statements into lists of ‘R’ expressions. / Apache noarch
License 2.0
r-queueing 0.2.11It provides versatile tools for analysis of birth and death based Markovian noarch
Queueing Models and Single and Multiclass Product-Form Queueing Net-
works. It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K,
M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K, Multi-
ple Channel Open Jackson Networks, Multiple Channel Closed Jackson Net-
works, Single Channel Multiple Class Open Networks, Single Channel Mul-
tiple Class Closed Networks and Single Channel Multiple Class Mixed Net-
works. Also it provides a B-Erlang, C-Erlang and Engset calculators. This
work is dedicated to the memory of D. Sixto Rios Insua. / GPL-2


Name Version
r-quiddich 1.0.0 Provides tools for an automated identification of diagnostic molecular char- noarch
acters, i.e. such columns in a given nucleotide or amino acid alignment that
allow to distinguish taxa from each other. These characters can then be used
to complement the formal descriptions of the taxa, which are often based on
morphological and anatomical features. Especially for morphologically cryp-
tic species, this will be helpful. QUIDDICH distinguishes between four dif-
ferent types of diagnostic characters. For more information, see Kuehn, A.L.,
Haase, M. 2019. QUIDDICH: QUick IDentification of DIagnostic CHaracters.
/ GPL-3
r-quietr 0.1.0 Simplifies output suppression logic in R packages, as it’s common to develop noarch
some form of it in R. ‘quietR’ intends to simplify that problem and allow a set
of simple toggle functions to be used to suppress console output. / MIT
r-quran 0.1.0 Full text, in data frames containing one row per verse, of the Qur’an in Arabic noarch
(with and without vowels) and in English (the Yusuf Ali and Saheeh Interna-
tional translations), formatted to be convenient for text analysis. / MIT
r-qvcalc 0.9_1 Functions to compute quasi variances and associated measures of approxima- linux-
tion error. / GPL-2 | GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-r.blip 1.1 Allows the user to learn Bayesian networks from datasets con- noarch
taining thousands of variables. It focuses on score-based learn-
ing, mainly the ‘BIC’ and the ‘BDeu’ score functions. It pro-
vides state-of-the-art algorithms for the following tasks: (1) parent
set identification - Mauro Scanagatta (2015) <http://papers.nips.cc/
paper/5803-learning-bayesian-networks-with-thousands-of-variables>;
(2) general structure optimization - Mauro Scanagatta (2018)
<doi:10.1007/s10994-018-5701-9>, Mauro Scanagatta (2018)
<http://proceedings.mlr.press/v73/scanagatta17a.html>; (3) bounded
treewidth structure optimization - Mauro Scanagatta (2016)
<http://papers.nips.cc/paper/6232-learning-treewidth-bounded-bayesian-
networks-with-thousands-of-variables>; (4) structure learning on incomplete
data sets - Mauro Scanagatta (2018) <doi:10.1016/j.ijar.2018.02.004>.
Distributed under the LGPL-3 by IDSIA. / LGPL-3
r-r.cache 0.13.0Memoization can be used to speed up repetitive and computational expensive noarch
function calls. The first time a function that implements memoization is called
the results are stored in a cache memory. The next time the function is called
with the same set of parameters, the results are momentarily retrieved from the
cache avoiding repeating the calculations. With this package, any R object can
be cached in a key-value storage where the key can be an arbitrary set of R
objects. The cache memory is persistent (on the file system). / LGPL-2.1


Name Version
r-r.devices 2.16.0Functions for creating plots and image files in a unified way regardless of out- noarch
put format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options
as well as scales and aspect ratios are controlled in a uniform way across all
device types. Switching output format requires minimal changes in code. This
package is ideal for large-scale batch processing, because it will never leave
open graphics devices or incomplete image files behind, even on errors or user
interrupts. / LGPL-2.1
r-r.huge 0.9.0 DEPRECATED. Do not start building new projects based on this package. noarch
Cross-platform alternatives are the following packages: bigmemory (CRAN),
ff (CRAN), BufferedMatrix (Bioconductor). The main usage of it was inside
the aroma.affymetrix package. (The package currently provides a class repre-
senting a matrix where the actual data is stored in a binary format on the local
file system. This way the size limit of the data is set by the file system and not
the memory.) / LGPL-2.1
r-r.matlab 3.6.2 Methods readMat() and writeMat() for reading and writing MAT files. For noarch
user with MATLAB v6 or newer installed (either locally or on a remote host),
the package also provides methods for controlling MATLAB (trademark) via
R and sending and retrieving data between R and MATLAB. / LGPL-2.1
r-r.methodss3 1.7.1 Methods that simplify the setup of S3 generic functions and S3 methods. Ma- linux-
jor effort has been made in making definition of methods as simple as possible
32,
with a minimum of maintenance for package developers. For example, generic linux-
functions are created automatically, if missing, and naming conflict are auto-
64,
matically solved, if possible. The method setMethodS3() is a good start for noarch,
those who in the future may want to migrate to S4. This is a cross-platform osx-
package implemented in pure R that generates standard S3 methods. / LGPL 64,
(>= 2.1) win-
32,
win-
64
r-r.oo 1.22.0Methods and classes for object-oriented programming in R with or without linux-
references. Large effort has been made on making definition of methods as 32,
simple as possible with a minimum of maintenance for package developers. linux-
The package has been developed since 2001 and is now considered very stable. 64,
This is a cross-platform package implemented in pure R that defines standard noarch,
S3 classes without any tricks. / LGPL (>= 2.1) osx-
64,
win-
32,
win-
64
r-r.utils 2.8.0 Utility functions useful when programming and developing R packages. / linux-
LGPL (>= 2.1) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-r0 1.2_6 Estimation of reproduction numbers for disease outbreak, based on incidence noarch
data. The R0 package implements several documented methods. It is there-
fore possible to compare estimations according to the methods used. Depend-
ing on the methods requested by user, basic reproduction number (commonly
denoted as R0) or real-time reproduction number (referred to as R(t)) is com-
puted, along with a 95% Confidence Interval. Plotting outputs will give differ-
ent graphs depending on the methods requested : basic reproductive number
estimations will only show the epidemic curve (collected data) and an adjusted
model, whereas real-time methods will also show the R(t) variations through-
out the outbreak time period. Sensitivity analysis tools are also provided, and
allow for investigating effects of varying Generation Time distribution or time
window on estimates. / GPL-2
r-r1magic 0.3.2 Utilities for sparse signal recovery suitable for compressed sensing. L1, L2 noarch
and TV penalties, DFT basis matrix, simple sparse signal generator, mutual
cumulative coherence between two matrices and examples, Lp complex norm,
scaling back regression coefficients. / GPL-3
r-r2admb 0.7.16A series of functions to call ‘AD Model Builder’ (i.e., compile and run models) noarch
from within R, read the results back into R as ‘admb’ objects, and provide
standard accessors (i.e. coef(), vcov(), etc.) / GPL-3
r-r2beat 1.0.0 Multivariate optimal allocation for different domains in one and two noarch
stages stratified sample design. R2BEAT extends the Neyman (1934)
<doi:10.2307/2342192> – Tschuprow (1923) allocation method to the case
of several variables, adopting a generalization of the Bethel’s proposal (1989).
R2BEAT develops this methodology but, moreover, it allows to determine the
sample allocation in the multivariate and multi-domains case of estimates for
two-stage stratified samples. / EUPL
r-r2d2 1.0_0 This package provides generic functions to analyze the distribution of two con- noarch
tinuous variables: ‘conf2d’ to calculate a smooth empirical confidence region,
and ‘freq2d’ to calculate a frequency distribution. / GPL-2
r-r2d3 0.2.3 Suite of tools for using ‘D3’, a library for producing dynamic, interactive data noarch
visualizations. Supports translating objects into ‘D3’ friendly data structures,
rendering ‘D3’ scripts, publishing ‘D3’ visualizations, incorporating ‘D3’ in R
Markdown, creating interactive ‘D3’ applications with Shiny, and distributing
‘D3’ based ‘htmlwidgets’ in R packages. / BSD_3_clause file LICENSE
r-r2dgc 1.0.3 Provides functions for aligning 2D gas chromatography mass spectrometry noarch
derived metabolite peaks obtained from primary processing and generates an
alignment table that allows for a comparison of common peaks across samples
and metabolite identification. Publication describing the package in detail is
available at the following citation: Ryne C. Ramaker, Emily Gordon, Sara J.
Cooper (2017) <doi:10.1101/179168>. / MIT
r-r2dt 0.1 Some heavily used base R functions are reconstructed to also be compliant to noarch
data.table objects. Also, some general helper functions that could be of interest
for working with data.table objects are included. / GPL-3
r-r2html 2.3.2 Includes HTML function and methods to write in an HTML file. Thus, mak- noarch
ing HTML reports is easy. Includes a function that allows redirection on the
fly, which appears to be very useful for teaching purpose, as the student can
keep a copy of the produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML reports for sta-
tistical analysis. Finally, a driver for ‘Sweave’ allows to parse HTML flat files
containing R code and to automatically write the corresponding outputs (tables
and graphs). / GPL-2


Name Version
r-r2openbugs 3.2_3.2
Using this package, it is possible to call a BUGS model, summarize inferences noarch
and convergence in a table and graph, and save the simulations in arrays for
easy access in R. / GPL-2
r-r2pmml 0.23.0R wrapper for the JPMML-R library <https://github.com/jpmml/jpmml-r>, noarch
which converts R models to Predictive Model Markup Language (PMML).
/ AGPL-3
r-r2stl 1.0.0 r2stl, R package for visualizing data using a 3D printer Package r2stl converts noarch
R data to STL (stereolithography) files that can be used to feed a 3-dimensional
printer. The 3-dimensional output from an R function can be materialized into
a solid surface in a plastic material, therefore allowing more detailed exami-
nation. There are many possible uses for this new R tool, such as to examine
mathematical expressions with very irregular shapes, to aid teaching people
with impaired vision, to create raised relief maps from digital elevation maps
(DEMs), to bridge the gap between mathematical tools and rapid prototyp-
ing, and many more. Ian Walker created the function r2stl and Jose’ Gama
assembled the package. / CC BY-NC-SA 3.0
r-r2winbugs 2.1_21Invoke a ‘BUGS’ model in ‘OpenBUGS’ or ‘WinBUGS’, a class bugs for noarch
‘BUGS’ results and functions to work with that class. Function write.model()
allows a ‘BUGS’ model file to be written. The class and auxiliary functions
could be used with other MCMC programs, including ‘JAGS’. / GPL-2
r-r3port 0.1.1 Create and combine HTML and PDF reports from within R. Possibility to noarch
design tables and listings for reporting and also include R plots. / GPL-2
r-r4couchdb 0.7.5 Provides a collection of functions for basic database and document manage- noarch
ment operations such as add, get, list access or delete. Every cdbFunction()
gets and returns a list() containing the connection setup. Such a list can be
generated by cdbIni(). / MIT
r-r6 2.4.0 Creates classes with reference semantics, similar to R’s built-in reference linux-
classes. Compared to reference classes, R6 classes are simpler and lighter- 32,
weight, and they are not built on S4 classes so they do not require the methods linux-
package. These classes allow public and private members, and they support 64,
inheritance, even when the classes are defined in different packages. / MIT file noarch,
LICENSE osx-
64,
win-
32,
win-
64
r-r62s3 1.3.1 After defining an R6 class, R62S3 is used to automatically generate optional noarch
S3/S4 generics and methods for dispatch. Also allows piping for R6 objects. /
MIT
r-r6ds 1.2.0 Provides reference classes implementing some useful data structures. The noarch
package implements these data structures by using the reference class R6.
Therefore, the classes of the data structures are also reference classes which
means that their instances are passed by reference. The implemented data
structures include stack, queue, double-ended queue, doubly linked list, set,
dictionary and binary search tree. See for example <https://en.wikipedia.org/
wiki/Data_structure> for more information about the data structures. / GPL-3


Name Version
r-radanalysis 0.5.5 It has tools for normalization of rank abundance distributions (RAD) to a de- noarch
sired number of ranks using MaxRank Normalization method. RADs are com-
monly used in biology/ecology and mathematically equivalent to complemen-
tary cumulative distributions (CCDFs) which are used in physics, linguistics
and sociology and more generally in data science. / GPL-3
r-radar 1.0.0 Fundamental formulas for Radar, for attenuation, range, velocity, effective- noarch
ness, power, scatter, doppler, geometry, radar equations, etc. Based on Nick
Guy’s Python package PyRadarMet / GPL-3
r-radarboxplot 1.0.0 Creates the radar-boxplot, a plot that was created by the author during his doc- noarch
toring in forest resources. The radar-boxplot is a visualization feature suited
for multivariate classification/clustering. It provides an intuitive deep under-
standing of the data. / MIT
r-radarchart 0.3.1 Create interactive radar charts using the ‘Chart.js’ ‘JavaScript’ library and the noarch
‘htmlwidgets’ package. ‘Chart.js’ <http://www.chartjs.org/> is a lightweight
library that supports several types of simple chart using the ‘HTML5’ canvas
element. This package provides an R interface specifically to the radar chart,
sometimes called a spider chart, for visualising multivariate data. / MIT
r-raddata 1.0.0 Nuclear Decay Data for Dosimetric Calculations from the International Com- noarch
mission on Radiological Protection from ICRP Publication 107. Ann. ICRP 38
(3). Eckerman, Keith and Endo, Akira 2008 <doi:10.1016/j.icrp.2008.10.004>
<http://www.icrp.org/publication.asp?id=ICRP%20Publication%20107>.
This is a database of the physical data needed in calculations of radionuclide-
specific protection and operational quantities. The data is prescribed by the
ICRP, the international authority on radiation dose standards, for estimating
dose from the intake of or exposure to radionuclides in the workplace
and the environment. The database contains information on the half-lives,
decay chains, and yields and energies of radiations emitted in nuclear
transformations of 1252 radionuclides of 97 elements. / GPL-2
r-radiosonde 1.4 RadioSonde is a collection of programs for reading and plotting SKEW-T,log noarch
p diagrams and wind profiles for data collected by radiosondes (the typi-
cal weather balloon-borne instrument), which we will call flights, sondes,
or profiles throughout the associated documentation. The raw data files are
in a common format that has a header followed by specific variables. Use
help(ExampleSonde) for the full explanation of the data files. / GPL-2
r-radjust 0.1.0 Calculates adjusted p-values for the null hypothesis of no replicability across noarch
studies for two study designs: (i) a primary and follow-up study, where the fea-
tures in the follow-up study are selected from the primary study, as described
in Bogomolov and Heller (2013) <doi:10.1080/01621459.2013.829002> and
Heller, Bogomolov and Benjamini (2014) <doi:10.1073/pnas.1314814111>;
(ii) two independent studies, where the features for replicability are first se-
lected in each study separately, as described in Bogomolov and Heller (2018)
<doi:10.1093/biomet/asy029>. The latter design is the one encountered in a
typical meta-analysis of two studies, but the inference is for replicability rather
than for identifying the features that are non-null in at least one study. / GPL-3


Name Version
r-radviz 0.7.0 An implementation of the radviz projection in R. It enables the visualiza- noarch
tion of multidimensional data while maintaining the relation to the original
dimensions. This package provides functions to create and plot radviz projec-
tions, and a number of summary plots that enable comparison and analysis.
For reference see Ankerst et al. (1996) <http://citeseer.ist.psu.edu/viewdoc/
summary?doi=10.1.1.68.1811> for original implementation, see Di Caro et al.
(2010) <DOI:10.1007/978-3-642-13672-6_13> for the original method for di-
mensional anchor arrangements. / CC BY-NC-SA 4.0
r-radwords 0.1.18Aims at loading Google Adwords data into R. Adwords is an online advertis- noarch
ing service that enables advertisers to display advertising copy to web users
(see <https://developers.google.com/adwords/> for more information). There-
fore the package implements three main features. First, the package provides
an authentication process for R with the Google Adwords API (see <https:
//developers.google.com/adwords/api/> for more information) via OAUTH2.
Second, the package offers an interface to apply the Adwords query language
in R and query the Adwords API with ad-hoc reports. Third, the received data
are transformed into suitable data formats for further data processing and data
analysis. / MIT
r-rafalib 1.0.0 A series of shortcuts for routine tasks originally developed by Rafael A. noarch
Irizarry to facilitate data exploration. / Artistic-2.0
r-rahrefs 0.1.4 Enables downloading detailed reports from <https://ahrefs.com> about back- noarch
links from pointing to website, provides authentication with an API key as well
as ordering, grouping and filtering functionalities. / MIT
r- 0.1.0 Determination of rainfall-runoff erosivity factor. / GPL-2 noarch
rainfallerosivityfactor
r-rainfarmr 0.1 An implementation of the RainFARM (Rainfall Filtered Autoregressive noarch
Model) stochastic precipitation downscaling method (Rebora et al. (2006)
<doi:10.1175/JHM517.1>). Adapted for climate downscaling according to
D’Onofrio et al. (2018) <doi:10.1175/JHM-D-13-096.1> and for complex to-
pography as in Terzago et al. (2018) <doi:10.5194/nhess-18-2825-2018>. The
RainFARM method is based on the extrapolation to small scales of the Fourier
spectrum of a large-scale precipitation field, using a fixed logarithmic slope
and random phases at small scales, followed by a nonlinear transformation of
the resulting linearly correlated stochastic field. RainFARM allows to generate
ensembles of spatially downscaled precipitation fields which conserve precip-
itation at large scales and whose statistical properties are consistent with the
small-scale statistics of observed precipitation, based only on knowledge of
the large-scale precipitation field. / Apache License 2.0
r-raltmetric 0.7.0 Provides a programmatic interface to the citation information and alternate noarch
metrics provided by ‘Altmetric’. Data from Altmetric allows researchers to
immediately track the impact of their published work, without having to wait
for citations. This allows for faster engagement with the audience interested in
your work. For more information, visit <https://www.altmetric.com/>. / MIT
r-ramble 0.1.1 Parser generator for R using combinatory parsers. It is inspired by combina- noarch
tory parsers developed in Haskell. / MIT


Name Version
r-ramchoice 1.1 It is widely documented in psychology, economics and other disciplines that noarch
socio-economic agent may not pay full attention to all available alternatives,
rendering standard revealed preference theory invalid. This package imple-
ments the estimation and inference procedures of Cattaneo, Ma, Masatlioglu
and Suleymanov (2019) <arXiv:1712.03448>, which utilizes standard choice
data to partially identify and estimate a decision maker’s preference. For in-
ference, several simulation-based critical values are provided. / GPL-2
r-ramify 0.3.3 Additional matrix functionality for R including: (1) wrappers for the base ma- noarch
trix function that allow matrices to be created from character strings and lists
(the former is especially useful for creating block matrices), (2) better print-
ing of large matrices via the generic pretty print function, and (3) a number of
convenience functions for users more familiar with other scientific languages
like ‘Julia’, ‘Matlab’/’Octave’, or ‘Python”NumPy’. / GPL-2
r-rampath 0.4 We rewrite of RAMpath software developed by John McArdle and Steven noarch
Boker as an R package. In addition to performing regular SEM analysis
through the R package lavaan, RAMpath has unique features. First, it can
generate path diagrams according to a given model. Second, it can display
path tracing rules through path diagrams and decompose total effects into their
respective direct and indirect effects as well as decompose variance and covari-
ance into individual bridges. Furthermore, RAMpath can fit dynamic system
models automatically based on latent change scores and generate vector field
plots based upon results obtained from a bivariate dynamic system. Starting
version 0.4, RAMpath can conduct power analysis for both univariate and bi-
variate latent change score models. / GPL-2
r-randcorr 1.0 Implements the algorithm by Pourahmadi and Wang (2015) noarch
<doi:10.1016/j.spl.2015.06.015> for generating a random p x p correla-
tion matrix. Briefly, the idea is to represent the correlation matrix using
Cholesky factorization and p(p-1)/2 hyperspherical coordinates (i.e., angles),
sample the angles from a particular distribution and then convert to the
standard correlation matrix form. The angles are sampled from a distribution
with pdf proportional to sin^k(theta) (0 < theta < pi, k >= 1) using the efficient
sampling algorithm described in Enes Makalic and Daniel F. Schmidt (2018)
<arXiv:1809.05212>. / GPL-3
r-randgeo 0.3.0 Generate random positions (latitude/longitude), Well-known text (‘WKT’) noarch
points or polygons, or ‘GeoJSON’ points or polygons. / MIT
r-randmeta 0.1.0 A novel numerical algorithm that provides functionality for estimating the ex- noarch
act 95% confidence interval of the location parameter in the random effects
model, and is much faster than the naive method. Works best when the num-
ber of studies is between 6-20. / GPL-2
r-random 0.2.6 The true random number service provided by the RANDOM.ORG website noarch
created by Mads Haahr samples atmospheric noise via radio tuned to an unused
broadcasting frequency together with a skew correction algorithm due to John
von Neumann. More background is available in the included vignette based on
an essay by Mads Haahr. In its current form, the package offers functions to
retrieve random integers, randomized sequences and random strings. / GPL-2


Name Version
r-randomforest 4.6_14Classification and regression based on a forest of trees using random inputs, linux-
based on Breiman (2001) <DOI:10.1023/A:1010933404324>. / GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-randomglm 1.02_1The package implements a bagging predictor based on general linear models / noarch
GPL-2
r-randomizebe 0.3_5 Contains a function to randomize subjects, patients in groups of sequences noarch
(treatment sequences). If a blocksize is given, the randomization will be done
within blocks. The randomization may be controlled by a Wald-Wolfowitz
runs test. Functions to obtain the p-value of that test are included. The package
is mainly intended for randomization of bioequivalence studies but may be
used also for other clinical crossover studies. Contains two helper functions
sequences() and williams() to get the sequences of commonly used designs in
BE studies. / GPL (>= 2.0)
r-randtests 1.0 Several non parametric randomness tests for numeric sequences / GPL-2 noarch
r-rangemodelr 1.0.4 Generates expected values of species richness, with continuous or scattered noarch
ranges, for data across one or two dimensions. / GPL-2
r-ranger 0.11.2A fast implementation of Random Forests, particularly suited for high dimen- linux-
sional data. Ensembles of classification, regression, survival and probability 32,
prediction trees are supported. Data from genome-wide association studies can linux-
be analyzed efficiently. In addition to data frames, datasets of class ‘gwaa.data’ 64,
(R package ‘GenABEL’) and ‘dgCMatrix’ (R package ‘Matrix’) can be di- osx-
rectly analyzed. / GPL-3 64,
win-
32,
win-
64
r-rankfd 0.0.3 The rankFD() function calculates the Wald-type statistic (WTS) and the noarch
ANOVA-type statistic (ATS) for nonparametric factorial designs, e.g., for
count, ordinal or score data in a crossed design with an arbitrary number of
factors. / GPL-2 | GPL-3
r-rankhazard 1.1.0 Rank-hazard plots Karvanen and Harrell (2009) <DOI:10.1002/sim.3591> vi- noarch
sualize the relative importance of covariates in a proportional hazards model.
The key idea is to rank the covariate values and plot the relative hazard as a
function of ranks scaled to interval [0,1]. The relative hazard is plotted in re-
spect to the reference hazard, which can bee.g. the hazard related to the median
of the covariate. / GPL-2
r-rankingproject 0.1.1 Functions to generate plots and tables for comparing independently- sampled noarch
populations. Companion package to A Primer on Visualizations for Compar-
ing Populations, Including the Issue of Overlapping Confidence Intervals by
Wright, Klein, and Wieczorek (2017, in press). / GPL-2
r-rankresponse 3.1.1 Methods for ranking responses of a single response question or a multiple noarch
response question / GPL-2
r-rap 1.1 To find the reversal association between variables. / GPL-2 noarch


Name Version
r-rapiclient 0.1.2 Access services specified in OpenAPI (formerly Swagger) format. It is not a noarch
code generator. Client is generated dynamically as a list of R functions. / MIT
r-rapidjsonr 1.1 Provides JSON parsing capability through the ‘Rapidjson’ ‘C’ header-only li- noarch
brary. / MIT
r-rapidxmlr 0.1.0 Provides XML parsing capability through the ‘Rapidxml’ ‘C’ header-only li- noarch
brary. / MIT
r-rappdirs 0.3.1 An easy way to determine which directories on the users computer you should linux-
use to save data, caches and logs. A port of Python’s ‘Appdirs’ (url{https: 32,
//github.com/ActiveState/appdirs}) to R. / MIT file LICENSE linux-
64,
osx-
64,
win-
32,
win-
64
r-raptor 1.0.0 Performs wood cell anatomical data analyses on spatially explicit xylem (tra- noarch
cheids) datasets derived from thin sections of woody tissue. The package
includes functions for visualisation, detection and alignment of continuous
tracheid radial file (defined as rows) and individual tracheid position within
an annual ring of coniferous species. This package is designed to be used
with elaborate cell output, e.g. as provided with ROXAS (von Arx & Carrer,
2014 <doi:10.1016/j.dendro.2013.12.001>). The package has been validated
for Picea abies, Larix Siberica, Pinus cembra and Pinus sylvestris. / GPL-2
r-rarity 1.3_6 Allows calculation of rarity weights for species and indices of rarity for as- noarch
semblages of species according to different methods (Leroy et al. 2012, Insect.
Conserv. Divers. 5:159-168 <doi:10.1111/j.1752-4598.2011.00148.x>; Leroy
et al. 2013, Divers. Distrib. 19:794-803 <doi:10.1111/ddi.12040>). / GPL
(>= 2.0)
r-rasciidoc 2.0.0 Inspired by Karl Broman‘s reader on using ‘knitr’ with ‘asciidoc’ (<http:// noarch
kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is merely a wrapper
to ‘knitr’ and ‘asciidoc’. / BSD_2_clause
r-raster 2.8_19Reading, writing, manipulating, analyzing and modeling of gridded spatial linux-
data. The package implements basic and high-level functions. Processing of 32,
very large files is supported. / GPL (>= 3) linux-
64,
osx-
64,
win-
32,
win-
64
r-rasterize 0.1 Provides R functions to selectively rasterize components of ‘grid’ output. / noarch
GPL-3
r-rasterlist 0.5.8 A S4 class has been created such that complex operations can be executed on noarch
each cells of a raster map. The raster of objects contains the traditional raster
map with the addition of a list of generic objects: one object for each raster
cells. It allows to write few lines of R code for complex map algebra. Two
environmental applications about frequency analysis of raster map of precip-
itation and creation of a raster map of soil water retention curves have been
presented. / GPL-3


Name Version
r-rastervis 0.46 Methods for enhanced visualization and interaction with raster data. It imple- noarch
ments visualization methods for quantitative data and categorical data, both
for univariate and multivariate rasters. It also provides methods to display spa-
tiotemporal rasters, and vector fields. See the website for examples. / GPL-3
r-ratedistortion 1.01 An implementation of routines for solving rate-distortion problems. Rate- noarch
distortion theory is a field within information theory that examines optimal
lossy compression. That is, given that some information must be lost, how can
a communication channel be designed that minimizes the cost of communica-
tion error? Rate-distortion theory is concerned with the optimal (minimal cost)
solution to such tradeoffs. An important tool for solving rate-distortion prob-
lems is the Blahut algorithm, developed by Richard Blahut and described in:
. Blahut, R. E. (1972). Computation of channel capacity and rate-distortion
functions. IEEE Transactions on Information Theory, IT-18(4), 460-473. .
This package implements the basic Blahut algorithm, and additionally con-
tains a number of ‘helper’ functions, including a routine for searching for an
information channel that minimizes cost subject to a constraint on information
rate. / GPL-2
r-ratelimitr 0.4.1 Allows to limit the rate at which one or more functions can be called. / MIT noarch
r-rateratio.test 1.0_2 A function which performs exact rate ratio tests and returns an object of class noarch
htest. / GPL-3
r-raters 2.0.1 The kappa statistic implemented by Fleiss is a very popular index for assess- noarch
ing the reliability of agreement among multiple observers. It is used both in
the psychological and in the psychiatric field. Other fields of application are
typically medicine, biology and engineering. Unfortunately,the kappa statistic
may behave inconsistently in case of strong agreement between raters, since
this index assumes lower values than it would have been expected. We pro-
pose a modification kappa implemented by Fleiss in case of nominal and or-
dinal variables. Monte Carlo simulations are used both to testing statistical
hypotheses and to calculating percentile bootstrap confidence intervals based
on proposed statistic in case of nominal and ordinal data. / GPL-2
r-ratesci 0.3_0 Computes confidence intervals for the rate (or risk) difference (‘RD’) or noarch
rate ratio (or relative risk, ‘RR’) for binomial proportions or Poisson rates,
or for odds ratio (‘OR’, binomial only). Also confidence intervals for
a single binomial or Poisson rate, and intervals for matched pairs. In-
cludes skewness-corrected asymptotic score (‘SCAS’) methods, which have
been developed in Laud (2017) <doi:10.1002/pst.1813> from Miettinen &
Nurminen (1985) <doi:10.1002/sim.4780040211> and Gart & Nam (1988)
<doi:10.2307/2531848>. Also includes MOVER methods (Method Of Vari-
ance Estimates Recovery) for all contrasts, derived from the Newcombe
method but using equal-tailed Jeffreys intervals, and generalised for Bayesian
applications incorporating prior information. So-called ‘exact’ methods for
strictly conservative coverage are approximated using continuity corrections.
Also includes methods for stratified calculations (e.g. meta-analysis), either
assuming fixed effects or incorporating stratum heterogeneity. / GPL-3
r-ratios 1.2.0 Calculation of ratios between two data sets containing environmental data like noarch
element concentrations by different methods. Additionally plant element con-
centrations can be corrected for adhering particles (soil, airborne dust). / GPL-
3
r-rattle.data 1.0.2 Contains the datasets used as default examples by the rattle package. The noarch
datasets themselves can be used independently of the rattle package to illus-
trate analytics, data mining, and data science tasks. / GPL-3


Name Version
r-raw 0.1.6 In order to facilitate R instruction for actuaries, we have organized several noarch
sets of publicly available data of interest to non-life actuaries. In addition, we
suggest a set of packages, which most practicing actuaries will use routinely.
Finally, there is an R markdown skeleton for basic reserve analysis. / CC0
r-rbenchmark 1.0.0 rbenchmark is inspired by the Perl module Benchmark, and is intended to noarch
facilitate benchmarking of arbitrary R code. The library consists of just one
function, benchmark, which is a simple wrapper around system.time. Given a
specification of the benchmarking process (counts of replications, evaluation
environment) and an arbitrary number of expressions, benchmark evaluates
each of the expressions in the specified environment, replicating the evaluation
as many times as specified, and returning the results conveniently wrapped into
a data frame. / GPL-2
r-rbiouml 1.8 Functions for connecting to BioUML server, querying BioUML repository and noarch
launching BioUML analyses. / GPL-2
r-rbit 1.0.0 A simple implementation of Binary Indexed Tree by R. The BinaryIn- noarch
dexedTree class supports construction of Binary Indexed Tree from a vector,
update of a value in the vector and query for the sum of a interval of the vector.
/ MIT
r-rbitcoin 0.9.2 Utilities related to Bitcoin. Unified markets API interface (bitstamp, kraken, noarch
btce, bitmarket). Both public and private API calls. Integration of data struc-
tures for all markets. Support SSL. Read Rbitcoin documentation (command:
?btc) for more information. / MIT
r- 1.0.4 An R package for the BitCoinCharts.com API. / LGPL-3 noarch
rbitcoinchartsapi
r-rbldatalicense 0.2.1 R interface to access prices and market data with the ‘Bloomberg Data noarch
License’ service from <https://www.bloomberg.com/professional/product/
data-license/>. As a prerequisite, a valid Data License from ‘Bloomberg’ is
needed together with the corresponding SFTP credentials and whitelisting of
the IP from which accessing the service. This software and its author are in no
way affiliated, endorsed, or approved by ‘Bloomberg’ or any of its affiliates.
‘Bloomberg’ is a registered trademark. / GPL-3
r-rbmn 0.9_2 Creation, manipulation, simulation of linear Gaussian Bayesian networks from noarch
text files and more. . . / GPL-2
r-rbokeh 0.6.3 A native R plotting library that provides a flexible declarative interface for linux-
creating interactive web-based graphics, backed by the Bokeh visualization 32,
library <http://bokeh.pydata.org/>. / MIT file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rbtc 0.1_6 Implementation of the RPC-JSON API for Bitcoin and utility functions for noarch
address creation and content analysis of the blockchain. / GPL-3


Name Version
r-rbtt 0.1.0 Tu & Zhou (1999) <doi:10.1002/(SICI)1097- noarch
0258(19991030)18:20%3C2749::AID-SIM195%3E3.0.CO;2-C> showed
that comparing the means of populations whose data-generating distributions
are non-negative with excess zero observations is a problem of great impor-
tance in the analysis of medical cost data. In the same study, Tu & Zhou
discuss that it can be difficult to control type-I error rates of general-purpose
statistical tests for comparing the means of these particular data sets. This
package allows users to perform a modified bootstrap-based t-test that aims to
better control type-I error rates in these situations. / GPL-3
r-rca 2.0 Relational Class Analysis (RCA) is a method for detecting heterogeneity in noarch
attitudinal data (as described in Goldberg A., 2011, Am. J. Soc, 116(5)). /
GPL-2
r-rcane 1.0 There are different numeric optimizations which are used in order to esti- noarch
mate coefficients in models such as linear regression and neural networks.
This package covers parameter estimation in linear regression using dif-
ferent methods such as batch gradient descent, stochastic gradient descent,
minibatch gradient descent and coordinate descent. Kiwiel, Krzysztof C
(2001) <doi:10.1007/PL00011414> Yu Nesterov (2004) <ISBN:1-4020-7553-
7> Ferguson, Thomas S (1982) <doi:10.1080/01621459.1982.10477894>
Zeiler, Matthew D (2012) <arXiv:1212.5701> Wright, Stephen J (2015)
<arXiv:1502.04759>. / MIT
r-rcapture 1.4_2 Estimation of abundance and other of demographic parameters for closed pop- noarch
ulations, open populations and the robust design in capture-recapture experi-
ments using loglinear models. / GPL-2
r-rcarbon 1.2.0 Enables the calibration and analysis of radiocarbon dates, often but not noarch
exclusively for the purposes of archaeological research. It includes
functions not only for basic calibration, uncalibration, and plotting of
one or more dates, but also a statistical framework for building demo-
graphic and related longitudinal inferences from aggregate radiocarbon
date lists, including: Monte-Carlo simulation test (Timpson et al 2014
<doi:10.1016/j.jas.2014.08.011>), random mark permutation test (Crema et
al 2016 <doi:10.1371/journal.pone.0154809>) and spatial permutation tests
(Crema, Bevan, and Shennan 2017 <doi:10.1016/j.jas.2017.09.007>). / GPL-2
r-rcarto 0.8 This package makes some maps using shapefiles and dataframes. Five kinds noarch
of maps are available : proportionnal circles, proportionnal circles colored by
a discretized quantitative variable, proportionnal circles colored by the modal-
ities of a qualitative variable, choropleth and typology. / GPL (>= 2.0)
r-rcbalance 1.8.5 Tools for large, sparse optimal matching of treated units and control units in noarch
observational studies. Provisions are made for refined covariate balance con-
straints, which include fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to network optimiza-
tion problems rather than greedy algorithms. / MIT
r-rcbsubset 1.1.4 Tools for optimal subset matching of treated units and control units in obser- noarch
vational studies, with support for refined covariate balance constraints, (in-
cluding fine and near-fine balance as special cases). A close relative is the
‘rcbalance’ package. / MIT
r-rcc 1.0.0 Functions to implement the parametric and non-parametric bootstrap noarch
confidence interval methods described in Morrison and Simon (2017)
<arXiv:1702.06986>. / GPL-2


r-rcdklibs 2.0 An R interface to the Chemistry Development Kit, a Java library for chemoin- noarch
formatics. Given the size of the library itself, this package is not expected to
change very frequently. To make use of the CDK within R, it is suggested that
you use the ‘rcdk’ package. Note that it is possible to directly interact with
the CDK using ‘rJava’. However ‘rcdk’ exposes functionality in a more id-
iomatic way. The CDK library itself is released as LGPL and the sources can
be obtained from <https://github.com/cdk/cdk>. / LGPL-3
r-rceim 0.3 An implementation of a stochastic heuristic method for performing multidi- noarch
mensional function optimization. The method is inspired in the Cross-Entropy
Method. It does not relies on derivatives, neither imposes particularly strong
requirements into the function to be optimized. Additionally, it takes profit
from multi-core processing to enable optimization of time-consuming func-
tions. / GPL-2
r-rcelldata 1.3_2 Example dataset for ‘Rcell’ package. Contains images and cell data object. / noarch
GPL-2
r-rcereal 1.2.1 To facilitate using ‘cereal’ with Rcpp. ‘cereal’ is a header-only C11 serializa- noarch
tion library. ‘cereal’ takes arbitrary data types and reversibly turns them into
different representations, such as compact binary encodings, XML, or JSON.
‘cereal’ was designed to be fast, light-weight, and easy to extend - it has no
external dependencies and can be easily bundled with other code or used stan-
dalone. Please see <http://uscilab.github.io/cereal> for more information. /
BSD_2_clause
r-rcgmin 2013_2.21
Conjugate gradient minimization of nonlinear functions with box constraints noarch
incorporating the Dai/Yuan update. This implementation should be used in
place of the CG algorithm of the optim() function. / GPL-2
r-rchallenge 1.3.0 A simple data science challenge system using R Markdown and Dropbox noarch
<https://www.dropbox.com/>. It requires no network configuration, does not
depend on external platforms like e.g. Kaggle <https://www.kaggle.com/> and
can be easily installed on a personal computer. / GPL-2
r-rcheology 3.6.1.0Provides a dataset of functions in all base packages of R versions 1.0.1 on- noarch
wards. / CC0
r-rchoicedialogs 1.0.6 Collection of portable choice dialog widgets / LGPL-2.1 noarch
r-rcircos 1.2.1 A simple and flexible way to generate Circos 2D track plot images for genomic noarch
data visualization is implemented in this package. The types of plots include:
heatmap, histogram, lines, scatterplot, tiles and plot items for further decora-
tions include connector, link (lines and ribbons), and text (gene) label. All
functions require only R graphics package that comes with R base installation.
/ GPL-2
r-rcites 1.0.1 A programmatic interface to the Species <https://speciesplus.net/> database noarch
via the Species/CITES Checklist API <https://api.speciesplus.net/>. / MIT
r-rclean 1.0.0 To create clearer, more concise code provides this toolbox helps coders to noarch
isolate the essential parts of a script that produces a chosen result, such as an
object, tables and figures written to disk and even warnings and errors. This
work was funded by US National Science Foundation grant SSI-1450277 for
applications of End-to-End Data Provenance. / GPL-3
r-rclinicalcodes 1.0.1 R tools for integrating with the www.clinicalcodes.org web repository / GPL-2 noarch
r-rclipboard 0.1.2 Leverages the functionality of ‘clipboard.js’, a JavaScript library for HMTL5- noarch
based copy to clipboard from web pages (see <https://clipboardjs.com> for
more information), and provides a reactive copy-to-clipboard UI button com-
ponent, called ‘rclipButton’, for ‘shiny’ R applications. / MIT


Name Version
r-rclone 1.0.2 R version of ‘GenClone’ (a computer program to analyse genotypic data, noarch
test for clonality and describe spatial clonal organization, Arnaud-Haond &
Belkhir 2007, <http://wwz.ifremer.fr/clonix/content/download/68205/903914/
file/GenClone2.0.setup.zip>), this package allows clone handling as ‘Gen-
Clone’ does, plus the possibility to work with several populations, Multi-
Locus Lineages (MLL) custom definition and use, and p-value calculation
for psex statistic (probability of originating from distinct sexual events) and
psex_Fis statistic (taking account of Hardy-Weinberg equilibrium departure)
as ‘MLGsim’/’MLGsim2’ (a program for detecting clones using a simulation
approach, Stenberg et al. 2003). / GPL (>= 2.0)
r-rcma 1.1 Tool for providing access to the Java version ‘CMAEvolutionStrategy’ of noarch
Nikolaus Hansen. ‘CMA-ES’ is the Covariance Matrix Adaptation Evolution
Strategy, see https://www.lri.fr/~hansen/cmaes_inmatlab.html#java. / GPL-3
r-rcmdcheck 1.3.2 Run ‘R CMD check’ from ‘R’ programmatically, and capture the results of the noarch
individual checks. / MIT file LICENSE
r-rcolombos 2.0.2 Provides programmatic access to Colombos, a web based interface for explor- noarch
ing and analyzing comprehensive organism-specific cross-platform expression
compendia of bacterial organisms. / GPL-3
r-rcolorbrewer 1.1_2 Provides color schemes for maps (and other graphics) designed by Cynthia linux-
Brewer as described at http://colorbrewer2.org / Apache License 2.0 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rconics 1.0 Solve some conic related problems (intersection of conics with lines and con- noarch
ics, arc length of an ellipse, polar lines, etc.). / GPL-2
r-rcorpora 2.0.0 A collection of small text corpora of interesting data. It contains all data sets noarch
from ‘dariusk/corpora’. Some examples: names of animals: birds, dinosaurs,
dogs; foods: beer categories, pizza toppings; geography: English towns, rivers,
oceans; humans: authors, US presidents, occupations; science: elements, plan-
ets; words: adjectives, verbs, proverbs, US president quotes. / CC0
r-rcpp 1.0.1 The ‘Rcpp’ package provides R functions as well as C classes which offer linux-
a seamless integration of R and C. Many R data types and objects can be 32,
mapped back and forth to C equivalents which facilitates both writing of new linux-
code as well as easier integration of third-party libraries. Documentation about 64,
‘Rcpp’ is provided by several vignettes included in this package, via the ‘Rcpp osx-
Gallery’ site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Fran- 64,
cois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013, win-
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Bal- 32,
amuta (2017, <doi:10.7287/peerj.preprints.3188v1>); see ‘citation(Rcpp)’ for win-
details. / GPL (>= 2) 64
r-rcpp11 3.1.2.0Rcpp11 includes a header only C11 library that facilitates integration between noarch
R and modern C. / MIT


Name Version
r-rcpparmadillo 0.9.300.2.0
‘Armadillo’ is a templated C linear algebra library (by Conrad Sanderson) that linux-
aims towards a good balance between speed and ease of use. Integer, float- 32,
ing point and complex numbers are supported, as well as a subset of trigono- linux-
metric and statistics functions. Various matrix decompositions are provided 64,
through optional integration with LAPACK and ATLAS libraries. The ‘Rcp- osx-
pArmadillo’ package includes the header files from the templated ‘Armadillo’ 64,
library. Thus users do not need to install ‘Armadillo’ itself in order to use ‘Rcp- win-
pArmadillo’. From release 7.800.0 on, ‘Armadillo’ is licensed under Apache 32,
License 2; previous releases were under licensed as MPL 2.0 from version win-
3.800.0 onwards and LGPL-3 prior to that; ‘RcppArmadillo’ (the ‘Rcpp’ bind- 64
ings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later,
as is the rest of ‘Rcpp’. Note that Armadillo requires a fairly recent compiler;
for the g family at least version 4.6.* is required. / GPL (>= 2)
r-rcppeigen 0.3.3.5.0
R and ‘Eigen’ integration using ‘Rcpp’. ‘Eigen’ is a C template library for linux-
linear algebra: matrices, vectors, numerical solvers and related algorithms. 32,
It supports dense and sparse matrices on integer, floating point and complex linux-
numbers, decompositions of such matrices, and solutions of linear systems. Its 64,
performance on many algorithms is comparable with some of the best imple- osx-
mentations based on ‘Lapack’ and level-3 ‘BLAS’. The ‘RcppEigen’ package 64,
includes the header files from the ‘Eigen’ C template library (currently ver- win-
sion 3.3.4). Thus users do not need to install ‘Eigen’ itself in order to use 32,
‘RcppEigen’. Since version 3.1.1, ‘Eigen’ is licensed under the Mozilla Pub- win-
lic License (version 2); earlier version were licensed under the GNU LGPL 64
version 3 or later. ‘RcppEigen’ (the ‘Rcpp’ bindings/bridge to ‘Eigen’) is li-
censed under the GNU GPL version 2 or later, as is the rest of ‘Rcpp’. / GPL
(>= 2) | file LICENSE
r-rcppprogress 0.4.1 Allows to display a progress bar in the R console for long running computa- noarch
tions taking place in c code, and support for interrupting those computations
even in multithreaded code, typically using OpenMP. / GPL (>= 3)
r-rcpproll 0.3.0 Provides fast and efficient routines for common rolling / windowed operations. linux-
Routines for the efficient computation of windowed mean, median, sum, prod- 32,
uct, minimum, maximum, standard deviation and variance are provided. / GPL linux-
(>= 2) 64,
osx-
64,
win-
32,
win-
64
r-rcppthread 0.5.3 Provides a C11-style thread class and thread pool that can safely be interrupted noarch
from R; see, Nagler (2018) <arXiv:1811.00450>. / MIT
r-rcppxptrutils 0.1.1 Provides the means to compile user-supplied C functions with ‘Rcpp’ and re- noarch
trieve an ‘XPtr’ that can be passed to other C components. / MIT
r-rcreds 0.6.6 Tools to write a list of credentials to an encrypted file and later read from noarch
that file into R. The goal is to have a useful alternative to including user-
name/passwords as part of a script or even stored in the clear in a separate text
file. Additional tools provided which are specific for connecting to a database.
/ MIT


Name Version
r-rcriteo 1.0.2 Aims at loading Criteo online advertising campaign data into R. Criteo <http: noarch
//www.criteo.com/> is an online advertising service that enables advertisers
to display commercial ads to web users. The package provides an authen-
tication process for R with the Criteo API <http://kb.criteo.com/ advertis-
ing/content/5/27/en/api.html>. Moreover, the package features an interface
to query campaign data from the Criteo API. The data can be downloaded and
will be transformed into a R data frame. / GPL-2 | MIT
r-rcriticor 2.0 Goldwin-Pierre correlogram. Research of critical periods in the past. Inte- noarch
grates a time series in a given window. / GPL-2
r-rcrypt 0.1.1 Provides easy symmetric file encryption using GPG with cryptographically noarch
strong defaults. Only symmetric encryption is supported. GPG is pre-installed
with most Linux distributions. Windows users will need to install ‘Gpg4win’
(http://www.gpg4win.org/). OS X users will need to install ‘GPGTools’ (https:
//gpgtools.org/). / MIT
r-rcssplot 0.3.0 Provides a means to style plots through cascading style sheets. This separates noarch
the aesthetics from the data crunching in plots and charts. / GPL-2
r-rcube 0.5 Provides simplified methods for managing classic Rubik’s cubes and many noarch
other modifications of it (such as NxNxN size cubes, void cubes and 8-
coloured cubes - so called octa cubes). Includes functions of handling special
syntax for managing such cubes; and different approach to plotting 3D cubes
without using external libraries (for example ‘OpenGL’). / GPL-3
r-rcur 1.3 Functions and objects for CUR matrix decomposition. / GPL-2 noarch
r-rcurl 1.95_4.12
A wrapper for ‘libcurl’ <http://curl.haxx.se/libcurl/> Provides functions to al- linux-
low one to compose general HTTP requests and provides convenient functions 32,
to fetch URIs, get & post forms, etc. and process the results returned by the linux-
Web server. This provides a great deal of control over the HTTP/FTP/. . . con- 64,
nection and the form of the request while providing a higher-level interface osx-
than is available just using R socket connections. Additionally, the underlying 64,
implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads win-
and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, 32,
redirects, authentication, etc. / BSD win-
64
r-rd2md 0.0.2 The native R functionalities only allow PDF exports of reference manuals. noarch
This shall be extended by converting the package documentation files into
markdown files and combining them into a markdown version of the package
reference manual. / GPL-3
r-rd2roxygen 1.8 Functions to convert Rd to ‘roxygen’ documentation. It can parse an Rd file to noarch
a list, create the ‘roxygen’ documentation and update the original R script (e.g.
the one containing the definition of the function) accordingly. This package
also provides utilities that can help developers build packages using ‘roxygen’
more easily. The ‘formatR’ package can be used to reformat the R code in the
examples sections so that the code will be more readable. / GPL-3
r-rda 1.0.2_2.1
Shrunken Centroids Regularized Discriminant Analysis for the classification noarch
purpose in high dimensional data. / GPL-2
r-rdatacanvas 0.1 Provides basic functionalities for writing a module for http://datacanvas.io. noarch
The http://datacanvas.io is a big data analytics platform that helps data sci-
entists to build, manage and share data pipelines. / BSD_3_clause
r-rdataretriever 2.0.0 Provides an R interface to the Data Retriever <http://data-retriever.org/> via noarch
the Data Retriever’s command line interface. The Data Retriever automates
the tasks of finding, downloading, and cleaning public datasets, and then stores
them in a local database. / MIT


Name Version
r-rdbnomics 0.4.7 R access to hundreds of millions data series from DBnomics API (<https://db. noarch
nomics.world/>). / AGPL-3
r-rde 0.1.0 Allows caching of raw data directly in R code. This allows R scripts and R noarch
Notebooks to be shared and re-run on a machine without access to the original
data. Cached data is encoded into an ASCII string that can be pasted into R
code. When the code is run, the data is automatically loaded from the cached
version if the original data file is unavailable. Works best for small datasets (a
few hundred observations). / GPL-3
r-rdetools 1.0 The package provides functions for estimating the relevant dimension of a data noarch
set in feature spaces, applications to model selection, graphical illustrations
and prediction. / GPL-2
r-rdian 0.1.1 A client library for ‘The Guardian’ (https://www.guardian.com/) and their API, noarch
this package allows users to search for Guardian articles and retrieve both the
content and metadata. / MIT
r-rdice 1.0.0 A collection of functions to simulate dice rolls and the like. In particular, noarch
experiments and exercises can be performed looking at combinations and per-
mutations of values in dice rolls and coin flips, together with the corresponding
frequencies of occurrences. When applying each function, the user has to in-
put the number of times (rolls, flips) to toss the dice. Needless to say, the
more the tosses, the more the frequencies approximate the actual probabilities.
Moreover, the package provides functions to generate non-transitive sets of
dice (like Efron’s) and to check whether a given set of dice is non-transitive
with given probability. / GPL-2
r-rdidq 1.0 The package has many function that helps to perform various quality check on noarch
the data.It basically provides many function that helps in performing Extrap-
olative data analysis. / GPL-2
r-rdistance 2.1.3 Distance-sampling is a popular method for estimating density and abundance noarch
of organisms in ecology. Rdistance contains routines that assist with analysis
of distance-sampling data collected on point or line transects. Distance models
are specified using regression-like formula (similar to lm, glm, etc.). Abun-
dance routines perform automated bootstrapping and automated detection-
function selection. Overall (study area) and site-level (transect or point) abun-
dance estimates are available. A large suite of classical, parametric detection
functions are included along with some uncommon parametric functions (e.g.,
Gamma, negative exponential) and non-parametric smoothed distance func-
tions. Custom (user-defined) detection functions are easily implemented (see
vignette). The help files and vignettes have been vetted by multiple authors
and tested in workshop settings. / GPL-3
r-rdnase 1.1_1 Comprehensive toolkit for generating various numerical representation noarch
schemes of DNA sequence. The descriptors and similarity scores included
are extensively used in bioinformatics and chemogenomics. / GPL-2
r-rdnb 0.1_3 A wrapper for the ‘Deutsche Nationalbibliothek (German National Library) noarch
API’, available at <http://www.dnb.de>. The German National Library is the
German central archival library, collecting, archiving, bibliographically clas-
sifying all German and German-language publications, foreign publications
about Germany, translations of German works, and the works of German-
speaking emigrants published abroad between 1933 and 1945. A personal
access token is required for usage. / MIT


Name Version
r- 0.8.2 Wraps around the default help functionality in R. Instead of plain docu- noarch
rdocumentation mentation files, documentation will show up as it does on <https://www.
rdocumentation.org>, a platform that shows R documentation from ‘CRAN’,
‘GitHub’ and ‘Bioconductor’, together with informative stats to assess the
package quality. / GPL-2
r-rdota2 0.1.6 An R API Client for Valve’s Dota2. RDota2 can be easily used to connect to noarch
the Steam API and retrieve data for Valve’s popular video game Dota2. You
can find out more about Dota2 at <http://store.steampowered.com/app/570/>.
/ MIT
r-rdrobust 0.99.4Regression-discontinuity (RD) designs are quasi-experimental research de- noarch
signs popular in social, behavioral and natural sciences. The RD design is
usually employed to study the (local) causal effect of a treatment, intervention
or policy. This package provides tools for data-driven graphical and analytical
statistical inference in RD designs: rdrobust() to construct local-polynomial
point estimators and robust confidence intervals for average treatment effects
at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform
bandwidth selection for the different procedures implemented, and rdplot() to
conduct exploratory data analysis (RD plots). / GPL-2
r-rdroolsjars 1.0.1 External jars required for package ‘Rdrools’. / Apache License 2.0 noarch
r-rdsm 2.1.1 Provides a threads-type programming environment for R. The package gives linux-
the R programmer the clearer, more concise shared memory world view, and in 64
some cases gives superior performance as well. In addition, it enables parallel
processing on very large, out-of-core matrices. / GPL-2
r-rdstk 1.1 This package provides an R interface to Pete Warden’s Data Science Toolkit. noarch
See www.datasciencetoolkit.org for more information. The source code for
this package can be found at github.com/rtelmore/RDSTK Happy hacking! /
BSD_2_clause
r-rdstreeboot 1.0 A tree bootstrap method for estimating uncertainty in respondent-driven sam- noarch
ples (RDS). Quantiles are estimated by multilevel resampling in such a way
that preserves the dependencies of and accounts for the high variability of the
RDS process. / GPL-2 | GPL-3
r-reactlog 1.0.0 Building interactive web applications with R is incredibly easy with ‘shiny’. noarch
Behind the scenes, ‘shiny’ builds a reactive graph that can quickly be-
come intertwined and difficult to debug. ‘reactlog’ (Schloerke 2019)
<doi:10.5281/zenodo.2591517> provides a visual insight into that black box
of ‘shiny’ reactivity by constructing a directed dependency graph of the appli-
cation’s reactive state at any time point in a reactive recording. / GPL-3
r-reactr 0.4.1 Make it easy to use ‘React’ in R with ‘htmlwidget’ scaffolds, helper depen- noarch
dency functions, an embedded ‘Babel’ ‘transpiler’, and examples. / MIT
r-read.gb 1.6 Opens complete record(s) with .gb extension from the NCBI/GenBank Nu- noarch
cleotide database and returns a list containing shaped record(s). These kind
of files contains detailed records of DNA samples (locus, organism, type of
sequence, source of the sequence. . . ). An example of record can be found at
<https://www.ncbi.nlm.nih.gov/nuccore/HE799070>. / GPL (>= 2.0)
r-readabf 1.0.1 Loads Axon Binary Files (both ‘ABF’ and ‘ABF2’) created by Axon Instru- noarch
ments/Molecular Devices software such as ‘pClamp’. / GPL-3
r- 1.8.5 Reads data files acquired by Bruker Daltonics’ matrix-assisted laser noarch
readbrukerflexdata desorption/ionization-time-of-flight mass spectrometer of the *flex series. /
GPL-3


Name Version
r-readbulk 1.1.2 Combine multiple data files from a common directory. The data files will be noarch
read into R and bound together, creating a single large data.frame. A general
function is provided along with a specific function for data that was collected
using the open-source experiment builder ‘OpenSesame’ <http://osdoc.cogsci.
nl/>. / GPL-3
r-readhac 1.0 Read Acoustic HAC format. / GPL-2 noarch
r-readjdx 0.3.250
Import data written in the JCAMP-DX format. This is an instrument- noarch
independent format used in the field of spectroscopy. Examples include IR,
NMR, and Raman spectroscopy. See the vignette for background and sup-
ported formats. The official JCAMP-DX site is <http://www.jcamp-dx.org/>.
/ GPL-3
r-readmldata 0.9_7 Functions for reading data sets in different formats for testing machine learning noarch
tools are provided. This allows to run a loop over several data sets in their
original form, for example if they are downloaded from UCI Machine Learning
Repository. The data are not part of the package and have to be downloaded
separately. / GPL-3
r-readmnist 1.0.6 You can use the function Read.mnist() to read data and arrange them prop- noarch
erly from MNIST dataset (the open handwriting digit database <http://yann.
lecun.com/exdb/mnist/>). With this package, you can conveniently get all of
necessary informations and then immediately start to check whether your ma-
chine learning algorithm works well. It can automatically recognize the type
of dataset and returns the informations in corresponding structure. / GPL-3
r-readmzxmldata 2.8.1 Functions for reading mass spectrometry data in mzXML format. / GPL-3 noarch
r-readoffice 0.2.2 Reads in text from ‘unstructured’ modern Microsoft Office files (XML based noarch
files) such as Word and PowerPoint. This does not read in structured data
(from Excel or Access) as there are many other great packages to that do so
already. / Unlimited
r-readr 1.3.1 The goal of ‘readr’ is to provide a fast and friendly way to read rectangular
linux-
data (like ‘csv’, ‘tsv’, and ‘fwf’). It is designed to flexibly parse many types
32,
of data found in the wild, while still cleanly failing when data unexpectedly
linux-
changes. / GPL (>= 2) | file LICENSE 64,
osx-
64,
win-
32,
win-
64
r-readxl 1.3.1 Import excel files into R. Supports ‘.xls’ via the embedded ‘libxls’ C li- linux-
brary <https://github.com/evanmiller/libxls> and ‘.xlsx’ via the embedded 32,
‘RapidXML’ C library <https://rapidxml.sourceforge.net>. Works on Win- linux-
dows, Mac and Linux without external dependencies. / GPL-3 64,
osx-
64,
win-
32,
win-
64


Name Version
r-realvams 0.4_3 Fits a multivariate value-added model (VAM), see Broatch, Green, and linux-
Karl (2018) <doi:10.32614/RJ-2018-033> and Broatch and Lohr (2012) 64,
<doi:10.3102/1076998610396900>, with normally distributed test scores and osx-
a binary outcome indicator. A pseudo-likelihood approach, Wolfinger 64,
(1993) <doi:10.1080/00949659308811554>, is used for the estimation of win-
this joint generalized linear mixed model. The inner loop of the pseudo- 64
likelihood routine (estimation of a linear mixed model) occurs in the frame-
work of the EM algorithm presented by Karl, Yang, and Lohr (2013)
<DOI:10.1016/j.csda.2012.10.004>. This material is based upon work sup-
ported by the National Science Foundation under grants DRL-1336027 and
DRL-1336265. / GPL-2
r-reams 0.1 Resampling methods for adaptive linear model selection. These can be thought noarch
of as extensions of the Akaike information criterion that account for searching
among candidate models. / GPL-2
r-rearrangement 2.1 The rearrangement operator (Hardy, Littlewood, and Polya 1952) for univari- noarch
ate, bivariate, and trivariate point estimates of monotonic functions. The pack-
age additionally provides a function that creates simultaneous confidence in-
tervals for univariate functions and applies the rearrangement operator to these
confidence intervals. / GPL-2
r-reat 3.0.1 Collection of models and analysis methods used in regional and urban eco- noarch
nomics and (quantitative) economic geography, e.g. measures of inequality,
regional disparities and convergence, regional specialization as well as acces-
sibility and spatial interaction models. / GPL-2
r-rebmix 2.10.3R functions for random univariate and multivariate finite mixture model gener- linux-
ation, estimation, clustering, latent class analysis and classification. Variables 64,
can be continuous, discrete, independent or dependent and may follow normal, osx-
lognormal, Weibull, gamma, binomial, Poisson, Dirac or circular von Mises 64,
parametric families. / GPL-2 win-
64
r-rebus.base 0.0_3 Build regular expressions piece by piece using human readable code. This noarch
package contains core functionality, and is primarily intended to be used by
package developers. / Unlimited
r-reca 1.7 Relevant Component Analysis (RCA) tries to find a linear transformation of noarch
the feature space such that the effect of irrelevant variability is reduced in the
transformed space. / GPL-3
r-rechonest 1.2 The ‘Echo nest’ <http://the.echonest.com> is the industry’s leading music in- noarch
telligence company, providing developer with deepest understanding of music
content and music fans. This package can be used to access artist’s data in-
cluding songs, blogs, news, reviews etc. Song’s data including audio summary,
style, danceability, tempo etc can also be accessed. / MIT
r-recipa 3.0 Pathways in a database could have many redundancies among them. This noarch
package allows the user to set a maximum value for the proportion of these
redundancies. / GPL-2


Name Version
r-recipes 0.1.5 An extensible framework to create and preprocess design matrices. Recipes linux-
consist of one or more data manipulation and analysis steps. Statistical param- 32,
eters for the steps can be estimated from an initial data set and then applied to linux-
other data sets. The resulting design matrices can then be used as inputs into 64,
statistical or machine learning models. / GPL-2 noarch,
osx-
64,
win-
32,
win-
64
r-recoder 0.1 Simple, easy to use, and flexible functionality for recoding variables. It allows noarch
for simple piecewise definition of transformations. / GPL-2
r-recombinator 1.0.1 Turns nested lists into data.frames in an orderly manner. / MIT noarch
r-recommended 3.6.0 R is a free software environment for statistical computing and graphics. / GPL- linux-
3.0 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-reconstructr 2.0.2 Functions to reconstruct sessions from web log or other user trace data and linux-
calculate various metrics around them, producing tabular, output that is com- 64,
patible with ‘dplyr’ or ‘data.table’ centered processes. / MIT osx-
64,
win-
64
r-recorder 0.8.2 A lightweight toolkit to validate new observations when computing their pre- noarch
dictions with a predictive model. The validation process consists of two steps:
(1) record relevant statistics and meta data of the variables in the original train-
ing data for the predictive model and (2) use these data to run a set of basic
validation tests on the new set of observations. / MIT
r-records 1.0 Functions for generating k-record values and k-record times / GPL-2 noarch
r-recosystem 0.4.2 R wrapper of the ‘libmf’ library <http://www.csie.ntu.edu.tw/~cjlin/libmf/> linux-
for recommender system using matrix factorization. It is typically used to ap- 64,
proximate an incomplete matrix using the product of two matrices in a latent osx-
space. Other common names for this task include collaborative filtering, ma- 64,
trix completion, matrix recovery, etc. High performance multi-core parallel win-
computing is supported in this package. / BSD_3_clause 64
r-recurse 1.1.0 Computes revisitation metrics for trajectory data, such as the number of revis- linux-
itations for each location as well as the time spent for that visit and the time 64,
since the previous visit. Also includes functions to plot data. / MIT osx-
64,
win-
64
r-redas 0.9.3 Provides functions used in the ‘R: Einführung durch angewandte Statistik’ noarch
(second edition). / GPL-2


Name Version
r-redm 0.7.2 A new implementation of EDM algorithms based on research software previ- linux-
ously developed for internal use in the Sugihara Lab (UCSD/SIO). Contains 64,
C compiled objects that use time delay embedding to perform state-space re- osx-
construction and nonlinear forecasting and an R interface to those objects us- 64,
ing ‘Rcpp’. It supports both the simplex projection method from Sugihara win-
& May (1990) <DOI:10.1038/344734a0> and the S-map algorithm in Sug- 64
ihara (1994) <DOI:10.1098/rsta.1994.0106>. In addition, this package im-
plements convergent cross mapping as described in Sugihara et al. (2012)
<DOI:10.1126/science.1227079> and multiview embedding as described in
Ye & Sugihara (2016) <DOI:10.1126/science.aag0863>. / file LICENSE
r-redmonder 0.2.0 Provide color schemes for maps (and other graphics) based on the color noarch
palettes of several Microsoft(r) products. Forked from ‘RColorBrewer’ v1.1-2.
/ Apache License 2.0
r-reemtree 0.90.3This package estimates regression trees with random effects as a way to use noarch
data mining techniques to describe longitudinal or panel data. / GPL-3
r-reffreeewas 2.2 Reference-free method for conducting EWAS while deconvoluting DNA noarch
methylation arising as mixtures of cell types. The older method (Houseman
et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to surrogate vari-
able analysis (SVA and ISVA), except that it makes additional use of a bi-
ological mixture assumption. The newer method (Houseman et al., 2016,
<doi:10.1186/s12859-016-1140-4>) is similar to non-negative matrix factor-
ization, with additional constraints and additional utilities. / GPL-2
r-refinr 0.3.1 These functions take a character vector as input, identify and cluster similar linux-
values, and then merge clusters together so their values become identical. The 64,
functions are an implementation of the key collision and ngram fingerprint osx-
algorithms from the open source tool Open Refine <http://openrefine.org/>. 64,
More info on key collision and ngram fingerprint can be found here <https: win-
//github.com/OpenRefine/OpenRefine/wiki/Clustering-In-Depth>. / GPL-3 64
r-refmanager 1.2.12Provides tools for importing and working with bibliographic references. It noarch
greatly enhances the ‘bibentry’ class by providing a class ‘BibEntry’ which
stores ‘BibTeX’ and ‘BibLaTeX’ references, supports ‘UTF-8’ encoding, and
can be easily searched by any field, by date ranges, and by various formats
for name lists (author by last names, translator by full names, etc.). Entries
can be updated, combined, sorted, printed in a number of styles, and exported.
‘BibTeX’ and ‘BibLaTeX’ ‘.bib’ files can be read into ‘R’ and converted to
‘BibEntry’ objects. Interfaces to ‘NCBI Entrez’, ‘CrossRef’, and ‘Zotero’ are
provided for importing references and references can be created from locally
stored ‘PDF’ files using ‘Poppler’. Includes functions for citing and generating
a bibliography with hyperlinks for documents prepared with ‘RMarkdown’ or
‘RHTML’. / GPL-2 | GPL-3 | BSD_3_clause
r-refnr 0.1.0 A tool for refining data frame with formulas. / Apache License 2.0 | file LI- noarch
CENSE
r-refset 0.1.1 Provides subsets with reference semantics, i.e. subsets which automatically noarch
reflect changes in the original object, and which optionally update the original
object when they are changed. / GPL-2
r-regclust 1.0 This package clusters regression coefficients using the methods of clustering noarch
through linear regression models (CLM) (Qin and Self 2006). Maximum like-
lihood approach is used to infer the parameters for each cluster. Bayesian
information criterion (BIC) combined with Bootstrapped maximum volume
(BMV) criterion are used to determine the number of clusters. / Artistic-2.0


Name Version
r-regent 1.0.6 Produces population distribution of disease risk and statistical risk categories, noarch
and predicts risks for individuals with genotype information. / GPL-3
r-regexpipes 0.0.1 Provides wrappers around base::grep() where the first argument is standardized noarch
to take the data object. This makes it less of a pain to use regular expressions
with ‘magrittr’ or other pipe operators. / GPL-2
r-regexselect 1.0.0 ‘shiny’ extension that adds regular expression filtering capabilities to the noarch
choice vector of the select list. / GPL-2 | GPL-3
r-registry 0.5_1 Provides a generic infrastructure for creating and using registries. / GPL-2 linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-reglogit 1.2_6 Regularized (polychotomous) logistic regression by Gibbs sampling. The linux-
package implements subtly different MCMC schemes with varying efficiency 64,
depending on the data type (binary v. binomial, say) and the desired es- osx-
timator (regularized maximum likelihood, or Bayesian maximum a posteri- 64,
ori/posterior mean, etc.) through a unified interface. / LGPL-3 win-
64
r-regnet 0.4.0 Network-based regularization has achieved success in variable selection linux-
for high-dimensional biological data due to its ability to incorporate cor- 64,
relations among genomic features. This package provides procedures of osx-
network-based variable selection for generalized linear models (Ren et 64,
al. (2017) <doi:10.1186/s12863-017-0495-5> and Ren et al. (2019) win-
<doi:10.1002/gepi.22194>). Two recent additions are the robust network reg- 64
ularization for the survival response and the network regularization for contin-
uous response. Functions for other regularization methods will be included in
the forthcoming upgraded versions. / GPL-2
r-regpro 0.1.1 Tools are provided for (1) nonparametric regression (kernel, local linear), (2) noarch
semiparametric regression (single index, additive models), and (3) quantile
regression (linear, kernel). / GPL-2
r-regress 1.3_15Functions to fit Gaussian linear model by maximising the residual log like- noarch
lihood where the covariance structure can be written as a linear combination
of known matrices. Can be used for multivariate models and random effects
models. Easy straight forward manner to specify random effects models, in-
cluding random interactions. Code now optimised to use Sherman Morrison
Woodbury identities for matrix inversion in random effects models. We’ve
added the ability to fit models using any kernel as well as a function to return
the mean and covariance of random effects conditional on the data (BLUPs). /
GPL-3


Name Version
r- 0.7.2 The expander functions rely on the mathematics developed for the Hessian- noarch
regressionfactory definiteness invariance theorem for linear projection transformations of vari-
ables, described in authors’ paper, to generate the full, high-dimensional gra-
dient and Hessian from the lower-dimensional derivative objects. This greatly
relieves the computational burden of generating the regression-function deriva-
tives, which in turn can be fed into any optimization routine that utilizes
such derivatives. The theorem guarantees that Hessian definiteness is pre-
served, meaning that reasoning about this property can be performed in the
low-dimensional space of the base distribution. This is often a much easier
task than its equivalent in the full, high-dimensional space. Definiteness of
Hessian can be useful in selecting optimization/sampling algorithms such as
Newton-Raphson optimization or its sampling equivalent, the Stochastic New-
ton Sampler. Finally, in addition to being a computational tool, the regression
expansion framework is of conceptual value by offering new opportunities to
generate novel regression problems. / GPL-2
r-regsel 0.2 Functions for fitting linear and generalized linear models with variable selec- noarch
tion. The functions can automatically do Stepwise Regression, Lasso or Elas-
tic Net as variable selection methods. Lasso and Elastic net are improved and
handle factors better (they can either include or exclude all factor levels). /
GPL-2
r-regspec 2.4 Computes linear Bayesian spectral estimates from multirate data for second- noarch
order stationary time series. Provides credible intervals and methods for plot-
ting various spectral estimates. / GPL-2
r-regsubseq 0.12 For a sequence of event occurence times, we are interested in finding sub- noarch
sequences in it that are too regular. We define regular as being significantly
different from a homogeneous Poisson process. The departure from the Pois-
son process is measured using a L1 distance. See Di and Perlman 2007 for
more details. / GPL-2
r-regtest 0.05 Functions for unary and binary regression tests / file LICENSE (Restricts use) noarch
r-rehh.data 1.0.0 Contains example data for the ‘rehh’ package. / GPL-2 noarch
r-reinforcelearn 0.2.1 Implements reinforcement learning environments and algorithms as described noarch
in Sutton & Barto (1998, ISBN:0262193981). The Q-Learning algorithm
can be used with function approximation, eligibility traces (Singh & Sut-
ton (1996) <doi:10.1007/BF00114726>) and experience replay (Mnih et al.
(2013) <arXiv:1312.5602>). / MIT
r-reins 1.0.8 Functions from the book Reinsurance: Actuarial and Statistical Aspects (2017) linux-
by Hansjoerg Albrecher, Jan Beirlant and Jef Teugels <http://www.wiley.com/ 64,
WileyCDA/WileyTitle/productCd-0470772689.html>. / GPL-2 osx-
64,
win-
64
r-reinstallr 0.1.4 Search R files for not installed packages and run install.packages. / GPL-3 noarch
r-rel 1.3.1 Derives point estimates with confidence intervals for Bennett et als S, Cohen’s noarch
kappa, Conger’s kappa, Fleiss’ kappa, Gwet’s AC, intraclass correlation coef-
ficients, Krippendorff’s alpha, Scott’s pi, the standard error of measurement,
and weighted kappa. / GPL-3
r-rela 4.1 Item analysis with alpha standard error and principal axis factoring for contin- noarch
uous variable scales (with plots). / Artistic-2.0


Name Version
r-relabeloadings 1.0 In confirmatory factor analysis (CFA), structural constraints typically ensure noarch
that the model is identified up to all possible reflections, i.e., column sign
changes of the matrix of loadings. Such reflection invariance is problematic
for Bayesian CFA when the reflection modes are not well separated in the
posterior distribution. Imposing rotational constraints – fixing some loadings
to be zero or positive in order to pick a factor solution that corresponds to one
reflection mode – may not provide a satisfactory solution for Bayesian CFA.
The function ‘relabel’ uses the relabeling algorithm of Erosheva and Curtis to
correct for sign invariance in MCMC draws from CFA models. The MCMC
draws should come from Bayesian CFA models that are fit without rotational
constraints. / GPL-2
r-relatable 1.0.0 Functions to safely map from a vector of keys to a vector of values, determine noarch
properties of a given relation, or ensure a relation conforms to a given type,
such as many-to-many, one-to-many, injective, surjective, or bijective. Permits
default return values for use similar to a vectorised switch statement, as well
as safely handling large vectors, NAs, and duplicate mappings. / MIT
r-relatedness 2.0 Inference of relatedness coefficients from a bi-allelic genotype matrix using linux-
a Maximum Likelihood estimation, Laporte, F., Charcosset, A. and Mary- 64,
Huard, T. (2017) <doi:10.1111/biom.12634>. / AGPL-3 osx-
64,
win-
64
r-relaxnet 0.3_2 Extends the glmnet package with relaxation, done by running glmnet once on noarch
the entire predictor matrix, then again on each different subset of variables
from along the regularization path. Relaxation may lead to improved predic-
tion accuracy for truly sparse data generating models, as well as fewer false
positives (i.e. fewer noncontributing predictors in the final model). Penalty
may be lasso (alpha = 1) or elastic net (0 < alpha < 1). For this version, family
may be gaussian or binomial only. Takes advantage of fast FORTRAN code
from the glmnet package. / GPL-2
r-relaxo 0.1_2 Relaxed Lasso is a generalisation of the Lasso shrinkage technique for lin- noarch
ear regression. Both variable selection and parameter estimation is achieved
by regular Lasso, yet both steps do not necessarily use the same penalty pa-
rameter. The results include all standard Lasso solutions but allow often for
sparser models while having similar or even slightly better predictive perfor-
mance if many predictor variables are present. The package depends on the
LARS package. / GPL-3
r-relen 1.0.1 This function computes the relative entropy (H) as an index for qualitative noarch
variation of a factor. / GPL-2
r-reliability 0.0_2 Functions for estimating parameters in software reliability models. Only infi- noarch
nite failure models are implemented so far. / Unlimited
r-reliar 0.01 A collection of utilities for some reliability models/probability distributions. / noarch
GPL-2
r-relimp 1.0_5 Functions to facilitate inference on the relative importance of predictors in a noarch
linear or generalized linear model, and a couple of useful Tcl/Tk widgets. /
GPL-2


Name Version
r-relsurv 2.2_3 Contains functions for analysing relative survival data, including nonparamet- linux-
ric estimators of net (marginal relative) survival, relative survival ratio, crude 64,
mortality, methods for fitting and checking additive and multiplicative regres- osx-
sion models, transformation approach, methods for dealing with population 64,
mortality tables. / GPL-3 win-
64
r-relvalanalysis 1.0 Classes and functions for analyzing the performance of portfolios relative to a noarch
benchmark. / GPL-2 | GPL-3
r-rem 1.3.1 Calculate endogenous network effects in event sequences and fit relational linux-
event models (REM): Using network event sequences (where each tie between 64,
a sender and a target in a network is time-stamped), REMs can measure how osx-
networks form and evolve over time. Endogenous patterns such as popular- 64,
ity effects, inertia, similarities, cycles or triads can be calculated and analyzed win-
over time. / GPL-2 64
r-rematch 1.0.1 A small wrapper on ‘regexpr’ to extract the matches and captured groups from linux-
the match of a regular expression to a character vector. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rematch2 2.1.0 Wrappers on ‘regexpr’ and ‘gregexpr’ to return the match results in tidy data noarch
frames. / MIT
r-remindr 0.0.1 Insert/extract text reminders into/from function source code comments or as noarch
the comment attribute of any object. The former can be handy in development
as reminders of e.g. argument requirements, expected objects in the calling
environment, required options settings, etc. The latter can be used to provide
information of the object and as simple manual tooltips for users, among other
things. / GPL-2 | GPL-3
r-remmap 0.2_0 remMap is developed for fitting multivariate response regression models under linux-
the high-dimension-low-sample-size setting / GPL-2 64,
osx-
64,
win-
64
r-remotes 2.0.4 Download and install R packages stored in ‘GitHub’, ‘BitBucket’, or plain noarch
‘subversion’ or ‘git’ repositories. This package provides the ‘install_*’ func-
tions in ‘devtools’. Indeed most of the code was copied over from ‘devtools’.
/ GPL (>= 2)
r-renpow 0.1_1 Supports calculations and visualization for renewable power systems and the noarch
environment. Analysis and graphical tools for DC and AC circuits and their
use in electric power systems. Analysis and graphical tools for thermodynamic
cycles and heat engines, supporting efficiency calculations in coal-fired power
plants, gas-fired power plants. Calculations of carbon emissions and atmo-
spheric CO2 dynamics. Analysis of power flow and demand for the grid, as
well as power models for microgrids and off-grid systems. Provides resource
and power generation for hydro power, wind power, and solar power. / GPL-2


Name Version
r-rentrez 1.2.2 Provides an R interface to the NCBI’s ‘EUtils’ API, allowing users to noarch
search databases like ‘GenBank’ <https://www.ncbi.nlm.nih.gov/genbank/>
and ‘PubMed’ <https://www.ncbi.nlm.nih.gov/pubmed/>, process the results
of those searches and pull data into their R sessions. / MIT
r-reordercluster 1.0 Tools for performing the leaf reordering for the dendrogram that preserves the linux-
hierarchical clustering result and at the same time tries to group instances from 64,
the same class together. / GPL-3 osx-
64,
win-
64
r- 2.0.0 Global tests for expression data of high-dimensional sets of molecular features. noarch
repeatedhighdim / GPL-2
r-repec 0.1.0 Utilities for accessing RePEc (Research Papers in Economics) through a noarch
RESTful API. You can request a code and get detailed information at the fol-
lowing page: <https://ideas.repec.org/api.html>. / MIT
r-repfdr 1.2.3 Estimation of Bayes and local Bayes false discovery rates for replicability linux-
analysis (Heller & Yekutieli, 2014 <doi:10.1214/13-AOAS697> ; Heller at 64,
al., 2015 <doi: 10.1093/bioinformatics/btu434>). / GPL-2 osx-
64,
win-
64
r-repo 2.1.3 A data manager meant to avoid manual storage/retrieval of data to/from the noarch
file system. It builds one (or more) centralized repository where R objects are
stored with rich annotations, including corresponding code chunks, and easily
searched and retrieved. / GPL-3
r-repogenerator 0.0.1 Generates a project and repo for easy initialization of a GitHub repo for R noarch
workshops. The repo includes a README with instructions to ensure that all
users have the needed packages, an ‘RStudio’ project with the right directories
and the proper data. The repo can then be used for hosting code taught during
the workshop. / MIT
r-repolr 3.4 Fits linear models to repeated ordinal scores using GEE methodology. / GPL-3 linux-
64,
osx-
64,
win-
64
r-reportreg 0.3.0 Provides an easy way to report the results of regression analysis, including: 1. noarch
Proportional hazards regression from function ‘coxph’ of package ‘survival’;
2. Conditional logistic regression from function ‘clogit’ of package ‘survival’;
3. Ordered logistic regression from function ‘polr’ of package ‘MASS’; 4.
Binary logistic regression from function ‘glm’ of package ‘stats’; 5. Linear
regression from function ‘lm’ of package ‘stats’; 6. Risk regression model
for survival analysis with competing risks from function ‘FGR’ of package
‘riskRegression’; 7. Multilevel model from function ‘lme’ of package ‘nlme’.
/ GPL-3
r-reportroc 3.4 Provides an easy way to report the results of ROC analysis, including: 1. an noarch
ROC curve. 2. the value of Cutoff, AUC (Area Under Curve), ACC (ac-
curacy), SEN (sensitivity), SPE (specificity), PLR (positive likelihood ratio),
NLR (negative likelihood ratio), PPV (positive predictive value), NPV (nega-
tive predictive value). / GPL-3


Name Version
r-reports 0.1.4 Assists in writing reports and presentations by providing a frame work that noarch
brings together existing R, LaTeX/.docx and Pandoc tools. The package is
designed to be used with RStudio, MiKTex/Tex Live/LibreOffice, knitr, knitc-
itations, Pandoc and pander. The user will want to download these free pro-
grams/packages to maximize the effectiveness of the reports package. Func-
tions with two letter names are general text formatting functions for copying
text from articles for inclusion as a citation. / GPL-2
r-reporttools 1.1.2 These functions are especially helpful when writing reports of data analysis noarch
using Sweave. / GPL-2
r-repr 0.19.2String and binary representations of objects for several formats / mime types. linux-
/ GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-represent 1.0 Contains workhorse function jrparams(), as well as two helper functions noarch
Mboxtest() and JRsMahaldist(), and four example data sets. / GPL-3
r-represtools 0.1.2 Reproducible research tools automates the creation of an analysis directory noarch
structure and work flow. There are R markdown skeletons which encapsulate
typical analytic work flow steps. Functions will create appropriate modules
which may pass data from one step to another. / GPL-3
r-reprex 0.2.1 Convenience wrapper that uses the ‘rmarkdown’ package to render small linux-
snippets of code to target formats that include both code and output. The 32,
goal is to encourage the sharing of small, reproducible, and runnable ex- linux-
amples on code-oriented websites, such as <https://stackoverflow.com> and 64,
<https://github.com>, or in email. The user’s clipboard is the default source noarch,
of input code and the default target for rendered output. ‘reprex’ also extracts osx-
clean, runnable R code from various common formats, such as copy/paste from 64,
an R session. / MIT file LICENSE win-
32,
win-
64
r-reqs 0.8_12This package contains the function run.eqs() which calls an EQS script file, noarch
executes the EQS estimation, and, finally, imports the results as R objects.
These two steps can be performed separately: call.eqs() calls and executes
EQS, whereas read.eqs() imports existing EQS outputs as objects into R. It
requires EQS 6.2 (build 98 or higher). / GPL-3
r-request 0.1.0 High level and easy ‘HTTP’ client for ‘R’. Provides functions for building noarch
‘HTTP’ queries, including query parameters, body requests, headers, authen-
tication, and more. / MIT
r-requirer 1.0.0.1Modularizes source code. Keeps the global environment clean, explicifies in- noarch
terdependencies. Inspired by ‘RequireJS’<http://requirejs.org/>. / MIT
r-rerefact 1.0 Executes a post-rotation algorithm that REorders and/or REflects FACTors noarch
(REREFACT) for each replication of a simulation study with exploratory fac-
tor analysis. / GPL-2


Name Version
r-resample 0.4 Bootstrap, permutation tests, and other resampling functions, featuring easy- noarch
to-use syntax. / BSD_3_clause
r-resampledata 0.3.1 Package of data sets from Mathematical Statistics with Resampling in R (1st noarch
Ed. 2011, 2nd Ed. 2018) by Laura Chihara and Tim Hesterberg. / CC0
r-resemble 1.2.2 Implementation of functions for spectral similarity/dissimilarity analysis and linux-
memory-based learning (MBL) for non-linear modeling in complex spectral 64,
datasets. In chemometrics MBL is also known as local modeling. / GPL-3 osx-
64,
win-
64
r-reservoir 1.1.5 Measure single-storage water supply system performance using resilience, noarch
reliability, and vulnerability metrics; assess storage-yield-reliability relation-
ships; determine no-fail storage with sequent peak analysis; optimize release
decisions for water supply, hydropower, and multi-objective reservoirs using
deterministic and stochastic dynamic programming; generate inflow replicates
using parametric and non-parametric models; evaluate inflow persistence us-
ing the Hurst coefficient. / GPL-2
r-reshape 0.8.8 Flexibly restructure and aggregate data using just two functions: melt and cast. linux-
/ MIT file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-reshape2 1.4.3 Flexibly restructure and aggregate data using just two functions: melt and linux-
‘dcast’ (or ‘acast’). / MIT file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-resistorarray 1.0_32Electrical properties of resistor networks using matrix methods. / GPL-2 noarch
r-ress 1.3 Contains three functions that query AuriQ Systems’ Essentia Database and re- noarch
turn the results in R. ‘essQuery’ takes a single Essentia command and captures
the output in R, where you can save the output to a dataframe or stream it di-
rectly into additional analysis. ‘read.essentia’ takes an Essentia script and cap-
tures the output csv data into R, where you can save the output to a dataframe
or stream it directly into additional analysis. ‘capture.essentia’ takes a file
containing any number of Essentia commands and captures the output of the
specified statements into R dataframes. Essentia can be downloaded for free
at http://www.auriq.com/documentation/source/install/index.html. / LGPL-3


Name Version
r-restimizeapi 1.0.0 Provides the user with functions to develop their trading strategy, uncover ac- noarch
tionable trading ideas, and monitor consensus shifts with crowdsourced earn-
ings and economic estimate data directly from <www.estimize.com>. Further
information regarding the web services this package invokes can be found at
<www.estimize.com/api>. / LGPL-3
r-restorepoint 0.2 Debugging with restore points instead of break points. A restore point stores noarch
all local variables when called inside a function. The stored values can later be
retrieved and evaluated in a modified R console that replicates the function’s
environment. To debug step by step, one can simply copy & paste the function
body from the R script. Particularly convenient in combination with RStudio.
See the Github page inst/vignettes for a tutorial. / GPL-2
r-restrictedmvn 1.0 A fast Gibbs sampler for multivariate normal with affine constraints. / GPL-2 linux-
64,
osx-
64,
win-
64
r-rethinker 1.1.0 Simple, native ‘RethinkDB’ client. / GPL-3 noarch
r-reticulate 1.12 Interface to ‘Python’ modules, classes, and functions. When calling into linux-
‘Python’, R data types are automatically converted to their equivalent ‘Python’ 32,
types. When values are returned from ‘Python’ to R they are converted back linux-
to R types. Compatible with all versions of ‘Python’ >= 2.7. / Apache License 64,
2.0 osx-
64,
win-
32,
win-
64
r-retimes 0.1_2 Reaction time analysis by maximum likelihood / GPL-3 linux-
64,
osx-
64,
win-
64
r-retrodesign 0.1.0 Provides tools for working with Type S (Sign) and Type M (Mag- noarch
nitude) errors, as proposed in Gelman and Tuerlinckx (2000)
<doi.org/10.1007/s001800000040> and Gelman & Carlin (2014)
<doi.org/10.1177/1745691614551642>. In addition to simply calculating the
probability of Type S/M error, the package includes functions for calculating
these errors across a variety of effect sizes for comparison, and recommended
sample size given tolerances for Type S/M errors. To improve the speed of
these calculations, closed forms solutions for the probability of a Type S/M
error from Lu, Qiu, and Deng (2018) <doi.org/10.1111/bmsp.12132> are
implemented. As of 1.0.0, this includes support only for simple research
designs. See the package vignette for a fuller exposition on how Type S/M
errors arise in research, and how to analyze them using the type of design
analysis proposed in the above papers. / MIT
r-reval 2.0.0 Simplified scenario testing and sensitivity analysis with R via a generalized noarch
function for one-factor-at-a-time (OFAT) sensitivity analysis, evaluation of pa-
rameter sets and (sampled) parameter permutations. Options for formatting
output and parallel processing are also provided. / GPL-3


Name Version
r-revealjs 0.9 R Markdown format for ‘reveal.js’ presentations, a framework for easily cre- noarch
ating beautiful presentations using HTML. / MIT
r-revecor 0.99.3An implementation of the reverse ecology framework. Reverse ecology refers noarch
to the use of genomics to study ecology with no a priori assumptions about the
organism(s) under consideration, linking organisms to their environment. It
allows researchers to reconstruct the metabolic networks and study the ecology
of poorly characterized microbial species from their genomic information, and
has substantial potentials for microbial community ecological analysis. / GPL-
2
r-revgeo 0.15 Function revgeo() allows you to use the Photon geocoder for OpenStreetMap noarch
<http://photon.komoot.de>, Google Maps <http://maps.google.com>, and
Bing <https://www.bingmapsportal.com> to reverse geocode coordinate pairs
with minimal hassle. / GPL (>= 3.0)
r-revoioq 10.0.0Test suite for Microsoft R Services. / GPL-2 linux-
64,
osx-
64,
win-
64
r-revomods 11.0.0Microsoft modifications and extensions to standard R functions / GPL-2 linux-
64,
osx-
64,
win-
64
r-revoutils 11.0.0Utility functions for Microsoft R / GPL-2 linux-
64,
osx-
64,
win-
64
r-revoutilsmath 11.0.0Utility functions for managing math threading. / file LICENSE linux-
64,
win-
64
r-reweight 1.2.1 Adjusts the weights of survey respondents so that the marginal distributions noarch
of certain variables fit more closely to those from a more precise source (e.g.
Census Bureau’s data). / GPL-2
r-rex 1.1.2 A friendly interface for the construction of regular expressions. / MIT file linux-
LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-rexperigen 0.2.1 Provides convenience functions to communicate with an Experigen server: Ex- linux-
perigen (<http://github.com/aquincum/experigen>) is an online framework for 64,
creating linguistic experiments, and it stores the results on a dedicated server. osx-
This package can be used to retrieve the results from the server, and it is es- 64,
pecially helpful with registered experiments, as authentication with the server win-
has to happen. / GPL-3 64
r-rexpokit 0.26.6.4
Wraps some of the matrix exponentiation utilities from EXPOKIT (<http: linux-
//www.maths.uq.edu.au/expokit/>), a FORTRAN library that is widely rec- 64,
ommended for matrix exponentiation (Sidje RB, 1998. Expokit: A Software osx-
Package for Computing Matrix Exponentials. ACM Trans. Math. Softw. 64,
24(1): 130-156). EXPOKIT includes functions for exponentiating both small, win-
dense matrices, and large, sparse matrices (in sparse matrices, most of the 64
cells have value 0). Rapid matrix exponentiation is useful in phylogenetics
when we have a large number of states (as we do when we are inferring the
history of transitions between the possible geographic ranges of a species), but
is probably useful in other ways as well. / GPL-2
r-rfacebook 0.6.15Provides an interface to the Facebook API. / GPL-2 noarch
r-rfdsn 0.0.0 This package facilitates searching for and downloading seismic time series in noarch
miniSEED format (a minimalist version of the Standard for the Exchange of
Earthquake Data) from International Federation of Digital Seismograph Net-
works repositories. This package can also be used to gather information about
seismic networks (stations, channels, locations, etc) and find historical earth-
quake data (origins, magnitudes, etc). / GPL-3
r-rferns 3.0.0 Provides the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua linux-
(2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label 64,
classification and featuring OOB error approximation and importance measure osx-
as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>. / GPL-3 64,
win-
64
r-rfgls 1.1 RFGLS uses a generalized least-squares method to perform single-marker as- noarch
sociation analysis, in datasets of nuclear families containing parents, twins,
and/or adoptees / GPL-2
r-rfinanceyj 0.3.1 Japanese stock market from Yahoo!-finance-Japan / BSD_3_clause noarch
r-rfinterval 1.0.0 An integrated package for constructing random forest prediction in- noarch
tervals using a fast implementation package ‘ranger’. This package
can apply the following three methods described in Haozhe Zhang,
Joshua Zimmerman, Dan Nettleton, and Daniel J. Nordman (2019)
<doi:10.1080/00031305.2019.1585288>: the out-of-bag prediction interval,
the split conformal method, and the quantile regression forest. / GPL-3
r-rfit 0.23.0R estimation and inference for linear models. Estimation is for general scores linux-
and a library of commonly used score functions is included. / GPL-2 64,
osx-
64,
win-
64
r-rflights 0.1.102
Query plane tickets, from several airlines, using the ‘Kiwi’ API (similar to noarch
‘Google Flights’). The API is documented at <https://docs.kiwi.com/>. / GPL-
3
r-rflptools 1.6 RFLPtools provides functions to analyse DNA fragment samples (i.e. derived noarch
from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence
analysis). / LGPL-3


Name Version
r-rfml 0.1.0 Functionality required to efficiently use R with MarkLogic NoSQL Database noarch
Server, <http://www.marklogic.com/what-is-marklogic/>. Many basic and
complex R operations are pushed down into the database, which removes the
main memory boundary of R and allows to make full use of MarkLogic server.
In order to use the package you need a MarkLogic Server version 8 or higher.
/ GPL-3
r-rfoaas 2.0.0 R access to the ‘FOAAS’ (F. . . Off As A Service) web service is provided. / noarch
GPL-2
r-rfolding 1.0 The basic algorithm to perform the folding test of unimodality. Given a dataset noarch
X (d dimensional, n samples), the test checks whether the distribution of the
data are rather unimodal or rather multimodal. This package stems from the
following research publication: Siffer Alban, Pierre-Alain Fouque, Alexandre
Termier, and Christine LargouÃ«t. Are your data gathered? In Proceedings of
the 24th ACM SIGKDD International Conference on Knowledge Discovery
Data Mining, pp. 2210-2218. ACM, 2018. <doi:10.1145/3219819.3219994>.
/ GPL-3
r-rforcecom 1.1 Insert, update, retrieve, delete and bulk operate datasets with a SaaS based noarch
CRM Salesforce.com and a PaaS based application platform Force.com from
R. / Apache License 2.0
r-rfordummies 0.1.4 Contains all the code examples in the book R for Dummies (2nd edition) by noarch
Andrie de Vries and Joris Meys. You can view the table of contents as well as
the sample code for each chapter. / GPL-2 | GPL-3
r- 1.3.1 A modified version (with great help from Ian J. Wilson) of Ian J. Wilson’s linux-
rforensicbatwing program BATWING for calculating forensic trace-suspect match probabilities. 64,
/ GPL-3 osx-
64,
win-
64
r-rformatter 0.1.1 The R Formatter formats R source code. It is very much based on formatR, noarch
but tries to improve it by heuristics. For example, spaces can be forced around
the division operator /. / GPL-3
r-rfreak 0.3_0 An R interface to a modified version of the Free Evolutionary Algorithm Kit noarch
FrEAK. FrEAK is a toolkit written in Java to design and analyze evolution-
ary algorithms. Both the R interface and an extended version of FrEAK
are contained in the RFreak package. For more information on FrEAK see
http://sourceforge.net/projects/freak427/. / GPL-2
r-rfutilities 2.1_4 Utilities for Random Forest model selection, class balance correction, signifi- noarch
cance test, cross validation and partial dependency plots. / GPL-3
r-rga 0.4.2 Provides functions for accessing and retrieving data from the Google Analyt- noarch
ics APIs (https://developers.google.com/analytics/). Supports OAuth 2.0 au-
thorization. Package provides access to the Management, Core Reporting,
Multi-Channel Funnels Reporting, Real Time Reporting and Metadata APIs.
Access to all the Google Analytics accounts which the user has access to.
Auto-pagination to return more than 10,000 rows of the results by combining
multiple data requests. Also package provides shiny app to explore the core
reporting API dimensions and metrics. / GPL-2
r-rga4gh 0.1.1 An Interface to the GA4GH API that allows users to easily GET responses and noarch
POST requests to GA4GH Servers. See <http://ga4gh.org> for more informa-
tion about the GA4GH project. / GPL-2


Name Version
r-rgabriel 0.7 This package was created to analyze multi-level one-way experimental de- noarch
signs. It is designed to handle vectorized observation and factor data where
there are unequal sample sizes and population variance homogeneity can not
be assumed. To conduct the Gabriel test, create two vectors: one for your
observations and one for the factor level of each observation. The function,
rgabriel, conduct the test and save the output as a vector to input into the
gabriel.plot function, which produces a confidence interval plot for Multiple
Comparison. / GPL-2
r-rgammagamma 1.0.12This package implements a Gamma convolution model for background cor- noarch
rection. / GPL (>= 2.0)
r-rgb 1.6.1 Classes and methods to efficiently handle (slice, annotate, draw . . . ) genomic linux-
features (such as genes or transcripts), and an interactive interface to browse 64,
them. / GPL-3 osx-
64,
win-
64
r-rgbm 1.0_8 Provides an implementation of Regularized LS-TreeBoost & LAD-TreeBoost linux-
algorithm for Regulatory Network inference from any type of expression data 64,
(Microarray/RNA-seq etc). See Mall et al (2017) <doi:10.1101/132670>. / osx-
GPL-3 64,
win-
64
r-rgcca 2.1.2 Multiblock data analysis concerns the analysis of several sets of variables noarch
(blocks) observed on the same group of individuals. The main aims of the
RGCCA package are: (i) to study the relationships between blocks and (ii) to
identify subsets of variables of each block which are active in their relation-
ships with the other blocks. / GPL-2
r-rgdal 1.4_4 Provides bindings to the ‘Geospatial’ Data Abstraction Library (‘GDAL’) (>= osx-
1.11.4) and access to projection/transformation operations from the ‘PROJ.4’ 64,
library. The ‘GDAL’ and ‘PROJ.4’ libraries are external to the package, win-
and, when installing the package from source, must be correctly installed 64
first. From ‘rgdal’ 1.4.1, provision is made for ‘PROJ6’ accommodation, with
‘PROJ6’ functionality to follow; from 1.4.1 ‘rgdal’ will build and function
when ‘PROJ’ >= 6. Both ‘GDAL’ raster and ‘OGR’ vector map data can be
imported into R, and ‘GDAL’ raster data and ‘OGR’ vector data exported. Use
is made of classes defined in the ‘sp’ package. Windows and Mac Intel OS X
binaries (including ‘GDAL’, ‘PROJ.4’ and ‘Expat’) are provided on ‘CRAN’.
/ GPL-2
r-rgdax 1.0.0 Allow access to both public and private end points to Coinbase Pro (erstwhile noarch
GDAX) cryptocurrency exchange. For authenticated flow, users must have
valid api, secret and passphrase to be able to connect. / MIT
r-rgeckoboard 0.1_5 Provides an interface to Geckoboard. / MIT noarch
r-rgen 0.0.1 Provides popular sampling distributions C routines based in armadillo through noarch
a header file approach. / GPL-2


Name Version
r-rgendata 1.0 The GenDataSample() and GenDataPopulation() functions create, respec- noarch
tively, a sample or population of multivariate nonnormal data using meth-
ods described in Ruscio and Kaczetow (2008). Both of these functions call
a FactorAnalysis() function to reproduce a correlation matrix. The EFACom-
pData() function allows users to determine how many factors to retain in an
exploratory factor analysis of an empirical data set using a method described
in Ruscio and Roche (2012). The latter function uses populations of com-
parison data created by calling the GenDataPopulation() function. <DOI:
10.1080/00273170802285693>. <DOI: 10.1037/a0025697>. / MIT
r-rgenetics 0.1 R packages for genetics research / GPL-2 noarch
r-rgenoud 5.8_3.0
A genetic algorithm plus derivative optimizer. / GPL-3 linux-
64,
osx-
64,
win-
64
r-rgeode 0.1.0 Provides the hybrid Bayesian method Geometric Density Estimation. On linux-
the one hand, it scales the dimension of our data, on the other it performs 64,
inference. The method is fully described in the paper Scalable Geomet- osx-
ric Density Estimation by Y. Wang, A. Canale, D. Dunson (2016) <http: 64,
//proceedings.mlr.press/v51/wang16e.pdf>. / GPL-2 win-
64
r-rgeos 0.5_1 Interface to Geometry Engine - Open Source (‘GEOS’) using the C ‘API’ for linux-
topology operations on geometries. The ‘GEOS’ library is external to the 64,
package, and, when installing the package from source, must be correctly in- osx-
stalled first. Windows and Mac Intel OS X binaries are provided on ‘CRAN’. 64,
(‘rgeos’ >= 0.5-1): Up to and including ‘GEOS’ 3.7.1, topological operations win-
succeeded with some invalid geometries for which the same operations fail 64
from and including ‘GEOS’ 3.7.2. The ‘checkValidity=’ argument defaults
and structure have been changed, from default FALSE to integer default ‘0L’
for ‘GEOS’ < 3.7.2 (no check), ‘1L’ ‘GEOS’ >= 3.7.2 (check and warn).
A value of ‘2L’ is also provided that may be used, assigned globally using
‘set_RGEOS_CheckValidity(2L)’, or locally using the ‘checkValidity=2L’ ar-
gument, to attempt zero-width buffer repair if invalid geometries are found.
The previous default (FALSE, now ‘0L’) is fastest and used for ‘GEOS’ <
3.7.2, but will not warn users of possible problems before the failure of topo-
logical operations that previously succeeded. / GPL-2
r-rgexf 0.15.3Create, read and write GEXF (Graph Exchange XML Format) graph files (used linux-
in Gephi and others). Using the XML package, it allows the user to easily 32,
build/read graph files including attributes, GEXF viz attributes (such as color, linux-
size, and position), network dynamics (for both edges and nodes) and edge 64,
weighting. Users can build/handle graphs element-by-element or massively osx-
through data-frames, visualize the graph on a web browser through sigmajs (a 64,
javascript library) and interact with the igraph package. / GPL (>= 3) win-
32,
win-
64
r-rgf 1.0.6 Regularized Greedy Forest wrapper of the ‘Regularized Greedy Forest’ <https: noarch
//github.com/RGF-team/rgf/tree/master/python-package> ‘python’ package,
which also includes a Multi-core implementation (FastRGF) <https://github.
com/RGF-team/rgf/tree/master/FastRGF>. / MIT


Name Version
r-rgift 0.1_5 This package provides some functions to create quizzes in the GIFT format. noarch
This format is used by several Virtual Learning Environments such as Moodle.
/ GPL-2
r-rgl 0.100.19
Provides medium to high level functions for 3D interactive graphics, includ- linux-
ing functions modelled on base graphics (plot3d(), etc.) as well as functions 32,
for constructing representations of geometric objects (cube3d(), etc.). Out- linux-
put may be on screen using OpenGL, or to various standard 3D file formats 64,
including WebGL, PLY, OBJ, STL as well as 2D image formats, including osx-
PNG, Postscript, SVG, PGF. / GPL 64,
win-
32,
win-
64
r-rglobi 0.2.19A programmatic interface to the web service methods provided by Global Bi- noarch
otic Interactions (GloBI). GloBI provides access to spatial-temporal species
interaction records from sources all over the world. rglobi provides methods to
search species interactions by location, interaction type, and taxonomic name.
In addition, it supports Cypher, a graph query language, to allow for executing
custom queries on the GloBI aggregate species interaction data set. / MIT
r-rglwidget 0.2.1 The contents of this package have been merged into rgl, so it is no longer linux-
needed. / GPL-2 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rgooddata 0.1.1 Export raw reports from ‘GoodData’ business intelligence platform (see <http: noarch
//www.gooddata.com> for more information). / GPL-3
r- 0.1.6 Provides functions for accessing and retrieving data from the Google Analytics noarch
rgoogleanalytics API. / Apache License 2.0
r- 0.1.1 It fires a query to the API to get the unsampled data in R for Google Analytics noarch
rgoogleanalyticspremium Premium Accounts. It retrieves data from the Google drive document and
stores it into the local drive. The path to the excel file is returned by this
package. The user can read data from the excel file into R using read.csv()
function. / Apache License 2.0
r-rgooglefit 0.3.1 Provides interface to Google Fit REST API v1 (see <https://developers.google. noarch
com/fit/rest/v1/reference/>). / MIT
r-rgooglemaps 1.4.4 Serves two purposes: (i) Provide a comfortable R interface to query the Google noarch
server for static maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling. / GPL-3
r-rgoogleslides 0.3.1 Previously, when one is working with in the Google Ecosystem (Using Google noarch
Drive etc), there is hardly any good workflow of getting the values calculated
from R and getting that into Google Slides. The normal and easy way out
would be to just copy your work over but when you have a number of analysis
to present with a lot of changes between each environment, it just becomes
quite cumbersome. / MIT


Name Version
r-rgr 1.1.15Geological Survey of Canada (GSC) functions for exploratory data analysis noarch
with applied geochemical data, with special application to the estimation of
background ranges and identification of outliers, ‘anomalies’, to support min-
eral exploration and environmental studies. Additional functions are provided
to support analytical data QA/QC, ANOVA for investigations of field sam-
pling and analytical variability, and utility tasks. NOTE: function caplot() for
concentration-area plots employs package ‘akima’, however, ‘akima’ is only
licensed for not-for-profit use. Therefore, not-for-profit users of ‘rgr’ will have
to independently make package ‘akima’ available through library(. . . .); and
use of function caplot() by for-profit users will fail. / GPL-2
r-rgrass7 0.2_1 Interpreted interface between ‘GRASS’ 7 geographical information system noarch
and R, based on starting R from within the ‘GRASS’ ‘GIS’ environment, or
running free-standing R in a temporary ‘GRASS’ location; the package pro-
vides facilities for using all ‘GRASS’ commands from the R command line.
This package may not be used for ‘GRASS’ 6, for which ‘spgrass6’ should be
used. / GPL-2
r-rgroovy 1.3 Integrates the Groovy scripting language with the R Project for Statistical noarch
Computing. / LGPL-3
r-rgw 0.1.0 Implementation of the affine-invariant method of Goodman & Weare (2010) noarch
<DOI:10.2140/camcos.2010.5.65>, a method of producing Monte-Carlo sam-
ples from a target distribution. / MIT
r-rh2 0.2.4 DBI/RJDBC interface to h2 database. h2 version 1.3.175 is included. / Mozilla noarch
Public License 1.1
r-rhandsontable 0.3.7 An R interface to the ‘Handsontable’ JavaScript library, which is a minimalist noarch
Excel-like data grid editor. See <https://handsontable.com/> for details. / MIT
r-rhealthdatagov 1.0.1 An R interface for the HealthData.gov data API. For each data resource, you noarch
can filter results (server-side) to select subsets of data. / GPL-2
r-rhive 2.0_0.10
RHive is an R extension facilitating distributed computing via HIVE query. It linux-
provides an easy to use HQL like SQL and R objects and functions in HQL. / 32,
Apache License (== 2.0) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rhli 0.0.2 Complete access from ‘R’ to the FIS ‘MarketMap C-Toolkit’ (‘FAME C- linux-
HLI’). ‘FAME’ is a fully integrated software and database management sys- 64,
tem from FIS that provides the following capabilities: Time series and cross- osx-
sectional data management; Financial calculation, data analysis, economet- 64,
rics, and forecasting; Table generation and detailed multicolor, presentation- win-
quality report writing; Multicolor, presentation-quality graphics; What-if anal- 64
ysis; Application development and structured programming; Data transfer to
and from other applications; Tools for building customized graphical user in-
terfaces. / AGPL-3
r-rhmc 1.0.0 Implements simple Hamiltonian Monte Carlo routines in R for sampling from noarch
any desired target distribution which is continuous and smooth. See Neal
(2017) <arXiv:1701.02434> for further details on Hamiltonian Monte Carlo.
Automatic parameter selection is not supported. / GPL-3


r-rhnerm 1.1 Performs the random heteroscedastic nested error regression model noarch
described in Kubokawa, Sugasawa, Ghosh and Chaudhuri (2016)
<doi:10.5705/ss.202014.0070>. / GPL-2
r-rhor 1.2.1.1Rho is used to test the generalization of inter rater reliability (IRR) statistics. noarch
Calculating rho starts by generating a large number of simulated, fully-coded
data sets: a sizable collection of hypothetical populations, all of which have
a kappa value below a given threshold – which indicates unacceptable agree-
ment. Then kappa is calculated on a sample from each of those sets in the
collection to see if it is equal to or higher than the kappa in then real sample.
If less than five percent of the distribution of samples from the simulated data
sets is greater than actual observed kappa, the null hypothesis is rejected and
one can conclude that if the two raters had coded the rest of the data, we would
have acceptable agreement (kappa above the threshold). / GPL-3
r-rhosp 1.10 Evaluating risk (that a patient arises a side effect) during hospitalization is the noarch
main purpose of this package. Several methods (Parametric, non parametric
and De Vielder estimation) to estimate the risk constant (R) are implemented
in this package. There are also functions to simulate the different models of
this issue in order to quantify the previous estimators. It is necessary to read at
least the first six pages of the report to understand the topic. / GPL-2
r- 0.1.0 Microbenchmarks for determining the run time performance of aspects of the noarch
rhpcbenchmark R programming environment and packages relevant to high-performance com-
putation. The benchmarks are divided into three categories: dense matrix lin-
ear algebra kernels, sparse matrix linear algebra kernels, and machine learning
functionality. / Apache License 2.0 | file LICENSE
r-rhpcblasctl 0.18_205
Control the number of threads on ‘BLAS’ (Aka ‘GotoBLAS’, ‘OpenBLAS’, linux-
‘ACML’, ‘BLIS’ and ‘MKL’). And possible to control the number of threads 64,
in ‘OpenMP’. Get a number of logical cores and physical cores if feasible. / osx-
AGPL-3 64,
win-
64
r-rhpcc 1.0 rHpcc is an R package providing an Interface between R and noarch
HPCC.Familiarity with ECL (Enterprise Control Language) is a must to
use this package.HPCC is a massive parallel-processing computing platform
that solves Big Data problems.ECL is the Enterprise Control Language
designed specifically for huge data projects using the HPCC platform.Its
extreme scalability comes from a design that allows you to leverage every
query you create for re-use in subsequent queries as needed. To do this, ECL
takes a dictionary approach to building queries wherein each ECL definition
defines an Attribute. Each previously defined Attribute can then be used in
succeeding ECL Attribute definitions as the language extends itself as you use
it. / GPL-2
r-rht 1.0 This package offers functions to perform regularized Hotelling’s T-square test noarch
for pathway or gene set analysis. The package is tailored for but not limited to
proteomics data, in which sample sizes are often small, a large proportion of
the data are missing and/or correlations may be present. / GPL-3
r-rhymer 1.0.0 Wrapper for ‘Datamuse’ API to find rhyming and other associated words. This noarch
includes words of similar meaning, spelling, or other related words. Learn
more about the ‘Datamuse’ API here <http://www.datamuse.com/api/>. / MIT


Name Version
r-ri 0.9 This package provides a set of tools for conducting exact or approximate noarch
randomization-based inference for experiments of arbitrary design. The pri-
mary functionality of the package is in the generation, manipulation and use
of permutation matrices implied by given experimental designs. Among other
features, the package facilitates estimation of average treatment effects, con-
stant effects variance estimation, randomization inference for significance test-
ing against sharp null hypotheses and visualization of data and results. / GPL-2
r-ri2by2 1.3 Computes attributable effects based confidence interval, permutation test con- linux-
fidence interval, or asymptotic confidence interval for the the average treatment 64,
effect on a binary outcome. / GPL-3 osx-
64,
win-
64
r-ridge 2.4 Linear and logistic ridge regression functions. Additionally includes special linux-
functions for genome-wide single-nucleotide polymorphism (SNP) data. / 64,
GPL-2 osx-
64,
win-
64
r-ridgefusion 1.0_3 This package implements ridge fusion methodology for inverse covariance ma- noarch
trix estimation for use in quadratic discriminant analysis. The package also
contains function for model based clustering using ridge fusion for inverse
matrix estimation, as well as tuning parameter selection functions. We have
also implemented QDA using joint inverse covariance estimation. / MIT
r-ridigbio 0.3.5 An interface to iDigBio’s search API that allows downloading specimen noarch
records. Searches are returned as a data.frame. Other functions such as the
metadata end points return lists of information. iDigBio is a US project fo-
cused on digitizing and serving museum specimen collections on the web. See
<https://www.idigbio.org> for information on iDigBio. / MIT
r-ridit 1.1 An extension of the Kruskal-Wallis Test that allow selection of arbitrary refer- noarch
ence group. Also provide Mean Ridit for each group. Mean Ridit of a group is
an estimate of probability a random observation from that group will be greater
than or equal to a random observation from reference group. / GPL-2 | GPL-3
r-ridittools 0.1 Functions to compute ridit scores of vectors, compute mean ridits and their noarch
standard errors for vectors compared to a reference vector, as described in
Fleiss (1981, ISBN:0-471-06428-9), and compute means/SEs for multiple
groups in matrices. Data can be either counts or proportions. Emphasis is on
ridit analysis of ordered categorical data such as Likert items and pain-rating
scales. / GPL-2 | GPL-3 | MIT
r-rifle 1.0 Implements the algorithms for solving sparse generalized eigenvalue problem noarch
by Tan, et. al. (2018). Sparse Generalized Eigenvalue Problem: Optimal
Statistical Rates via Truncated Rayleigh Flow. To appear in Journal of the
Royal Statistical Society: Series B. <arXiv:1604.08697>. / GPL-2
r-rifs 0.1_5 RIFS package provides functionality for generating & plotting prefractals in noarch
R^n with various protofractal sets and partition coefficient for iterative seg-
ments / GPL-3


Name Version
r-rimpact 1.0 The metrics() function calculates measures of scholarly impact. These include noarch
conventional measures, such as the number of publications and the total cita-
tions to all publications, as well as modern and robust metrics based on the
vector of citations associated with each publication, such as the h index and
many of its variants or rivals. These methods are described in Ruscio et al.
(2012) <DOI: 10.1080/15366367.2012.711147>. / MIT
r-ring 1.0.0 Circular / ring buffers in R and C. There are a couple of different buffers here linux-
with different implementations that represent different trade-offs. / MIT 64,
osx-
64,
win-
64
r-rinside 0.2.15C classes to embed R in C applications A C class providing the R interpreter is linux-
offered by this package making it easier to have R inside your C application. 64,
As R itself is embedded into your application, a shared library build of R is osx-
required. This works on Linux, OS X and even on Windows provided you use 64,
the same tools used to build R itself. d Numerous examples are provided in the win-
eight subdirectories of the examples/ directory of the installed package: stan- 64
dard, ‘mpi’ (for parallel computing), ‘qt’ (showing how to embed ‘RInside’
inside a Qt GUI application), ‘wt’ (showing how to build a web-application
using the Wt toolkit), ‘armadillo’ (for ‘RInside’ use with ‘RcppArmadillo’)
and ‘eigen’ (for ‘RInside’ use with ‘RcppEigen’). The examples use ‘GNU-
makefile(s)’ with GNU extensions, so a GNU make is required (and will use
the ‘GNUmakefile’ automatically). ‘Doxygen’-generated documentation of
the C classes is available at the ‘RInside’ website as well. / GPL-2
r-rinsp 1.2.3 Functions to calculate several ecological indices of individual and population linux-
niche width (Araujo’s E, clustering and pairwise similarity among individu- 64,
als, IS, Petraitis’ W, and Roughgarden’s WIC/TNW) to assess individual spe- osx-
cialization based on data of resource use. Resource use can be quantified by 64,
counts of categories, measures of mass/lenght or proportions. Monte Carlo re- win-
sampling procedures are available for hypothesis testing against multinomial 64
null models. / GPL-2
r-rintervaltree 0.1.0 This tool can be used to build binary interval trees using real number inputs. noarch
The tree supports queries of intervals overlapping a single number or an inter-
val (start, end). Intervals with same bounds but different names are treated as
distinct intervals. Insertion of intervals is also allowed. Deletion of intervals is
not implemented at this point. See Mark de Berg, Otfried Cheong, Marc van
Kreveld, Mark Overmars (2008). Computational Geometry: Algorithms and
Applications, for a reference. / GPL-2
r-rintrojs 0.2.2 A wrapper for the ‘Intro.js’ library (For more info: <http://www.introjs.com>). noarch
This package makes it easy to include step-by-step introductions, and clickable
hints in a ‘Shiny’ application. It supports both static introductions in the UI,
and programmatic introductions from the server-side. / AGPL-3


Name Version
r-rio 0.5.16Streamlined data import and export by making assumptions that the user is linux-
probably willing to make: ‘import()’ and ‘export()’ determine the data struc- 32,
ture from the file extension, reasonable defaults are used for data import and linux-
export (e.g., ‘stringsAsFactors=FALSE’), web-based import is natively sup- 64,
ported (including from SSL/HTTPS), compressed files can be read directly noarch,
without explicit decompression, and fast import packages are used where ap- osx-
propriate. An additional convenience function, ‘convert()’, provides a simple 64,
method for converting between file types. / GPL-2 win-
32,
win-
64
r-rip46 1.0.2 Utility functions and S3 classes for IPv4 and IPv6 addresses, including con- linux-
version to and from binary representation. / GPL-3 64,
osx-64
r-rising 0.1.0 Fits an Ising model to a binary dataset using L1 regularized logistic regres- linux-
sion and extended BIC. Also includes a fast lasso logistic regression function 64,
for high-dimensional problems. Uses the ‘libLBFGS’ optimization library by osx-
Naoaki Okazaki. / GPL-2 64,
win-
64
r-risk 1.0 Computes 26 financial risk measures for any continuous distribu- noarch
tion. The 26 financial risk measures include value at risk, ex-
pected shortfall due to Artzner et al. (1999) <DOI:10.1007/s10957-
011-9968-2>, tail conditional median due to Kou et al. (2013)
<DOI:10.1287/moor.1120.0577>, expectiles due to Newey and Powell (1987)
<DOI:10.2307/1911031>, beyond value at risk due to Longin (2001)
<DOI:10.3905/jod.2001.319161>, expected proportional shortfall due to
Belzunce et al. (2012) <DOI:10.1016/j.insmatheco.2012.05.003>, ele-
mentary risk measure due to Ahmadi-Javid (2012) <DOI:10.1007/s10957-
011-9968-2>, omega due to Shadwick and Keating (2002), sortino ra-
tio due to Rollinger and Hoffman (2013), kappa due to Kaplan and
Knowles (2004), Wang (1998)’s <DOI:10.1080/10920277.1998.10595708>
risk measures, Stone (1973)’s <DOI:10.2307/2978638> risk measures,
Luce (1980)’s <DOI:10.1007/BF00135033> risk measures, Sarin (1987)’s
<DOI:10.1007/BF00126387> risk measures, Bronshtein and Kurelenkova
(2009)’s risk measures. / GPL-2


Name Version
r- 0.2.0 Fast design of risk parity portfolios for financial investment. The goal of the linux-
riskparityportfolio risk parity portfolio formulation is to equalize or distribute the risk contribu- 64,
tions of the different assets, which is missing if we simply consider the overall osx-
volatility of the portfolio as in the mean-variance Markowitz portfolio. In ad- 64,
dition to the vanilla formulation, where the risk contributions are perfectly win-
equalized subject to no shortselling and budget constraints, many other formu- 64
lations are considered that allow for box constraints and shortselling, as well as
the inclusion of additional objectives like the expected return and overall vari-
ance. See vignette for a detailed documentation and comparison, with several
illustrative examples. The package is based on the papers: Y. Feng, and D. P.
Palomar (2015). SCRIP: Successive Convex Optimization Methods for Risk
Parity Portfolio Design. IEEE Trans. on Signal Processing, vol. 63, no. 19,
pp. 5285-5300. <doi:10.1109/TSP.2015.2452219>. F. Spinu (2013), An Al-
gorithm for Computing Risk Parity Weights. <doi:10.2139/ssrn.2297383>. T.
Griveau-Billion, J. Richard, and T. Roncalli (2013). A fast algorithm for com-
puting High-dimensional risk parity portfolios. <arXiv:1311.4057>. / GPL-3
r-riskportfolios 2.1.2 Collection of functions designed to compute risk-based portfolios as described noarch
in Ardia et al. (2017) <doi:10.1007/s10479-017-2474-7> and Ardia et al.
(2017) <doi:10.21105/joss.00171>. / GPL-2
r-riskr 1.1 Computes risk measures from data, as well as performs risk management pro- noarch
cedures. / GPL-2
r-risksetroc 1.0.4 Compute time-dependent Incident/dynamic accuracy measures (ROC curve, noarch
AUC, integrated AUC )from censored survival data under proportional or non-
proportional hazard assumption of Heagerty & Zheng (Biometrics, Vol 61 No
1, 2005, PP 92-105). / GPL-2
r-riskyr 0.2.0 Risk-related information (like the prevalence of conditions and the sensitivity noarch
and specificity of diagnostic tests or treatment decisions) can be expressed in
terms of probabilities or frequencies. By providing a toolbox of methods and
metrics, ‘riskyr’ computes, translates, and visualizes risk-related information
in a variety of ways. Offering multiple complementary perspectives on the
interplay between key parameters renders teaching and training of risk literacy
more transparent. / GPL-2 | GPL-3
r-rismed 2.1.7 A set of tools to extract bibliographic content from the National Center for noarch
Biotechnology Information (NCBI) databases, including PubMed. The name
RISmed is a portmanteau of RIS (for Research Information Systems, a com-
mon tag format for bibliographic data) and PubMed. / GPL-2
r-riverbuilder 0.1.1 Generates graphs, CSV files, and coordinates related to river valleys when noarch
calling the riverbuilder() function. / GPL-3
r-riverload 1.0.1 Implements several of the most popular load estimation procedures, including noarch
averaging methods, ratio estimators and regression methods. The package pro-
vides an easy-to-use tool to rapidly calculate the load for various compounds
and to compare different methods. The package also supplies additional func-
tions to easily organize and analyze the data. / GPL-2
r-rivernet 1.2 Functions for reading, analysing and plotting river networks. For this package, noarch
river networks consist of sections and nodes with associated attributes, e.g. to
characterise their morphological, chemical and biological state. The package
provides functions to read this data from text files, to analyse the network
structure and network paths and regions consisting of sections and nodes that
fulfill prescribed criteria, and to plot the river network and associated proper-
ties. / GPL-3


Name Version
r-riverplot 0.6 Sankey plots are a type of diagram that is convenient to illustrate how flow noarch
of information, resources etc. separates and joins, much like observing how
rivers split and merge. For example, they can be used to compare different
clusterings. / GPL (>= 2.0)
r-rivervis 0.46.0This R package is a flexible and efficient tool to visualise both quantitative and noarch
qualitative data from river surveys. It can be used to produce diagrams with
the topological structure of the river network. / GPL-2
r-rivr 1.2_1 A tool for undergraduate and graduate courses in open-channel hydraulics. linux-
Provides functions for computing normal and critical depths, steady-state wa- 64,
ter surface profiles (e.g. backwater curves) and unsteady flow computations osx-
(e.g. flood wave routing). / GPL-3 64,
win-
64
r-rjacgh 2.0.4 Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models. linux-
The selection of the number of states is made via their posterior probability 64,
computed by Reversible Jump Markov Chain Monte Carlo Methods. Also osx-
returns probabilistic common regions for gains/losses. / GPL-3 64,
win-
64
r-rjava 0.9_11Low-level interface to Java VM very much like .C/.Call and friends. Allows linux-
creation of objects, calling methods and accessing fields. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-rjazz 0.1.7 This is the official ‘Jazz’ client. ‘Jazz’ is a lightweight modular data pro- noarch
cessing framework, including a web server. It provides data persistence and
computation capabilities accessible from ‘R’ and ‘Python’ and also through
a REST API. <https://github.com/bbvadata/Jazz> See ?rjazz::rjazz to get a
‘Jazz’ server. / Apache License (== 2.0)
r-rjdbc 0.2_7.1
The RJDBC package is an implementation of R’s DBI interface using JDBC linux-
as a back-end. This allows R to connect to any DBMS that has a JDBC driver. 32,
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rjdemetra 0.1.3 Interface around ‘JDemetra’ (<https://github.com/jdemetra/jdemetra-app>), noarch
the seasonal adjustment software officially recommended to the members of
the European Statistical System (ESS) and the European System of Central
Banks. It offers full access to all options and outputs of ‘JDemetra’, in-
cluding the two leading seasonal adjustment methods TRAMO/SEATS and
X-12ARIMA/X-13ARIMA-SEATS. / EUPL


Name Version
r-rje 1.10.10
A series of functions in some way considered useful to the author. These linux-
include functions for subsetting tables and generating indices for arrays, con- 64,
ditioning and intervening in probability distributions, generating combinations osx-
and more. . . / GPL-2 64,
win-
64
r-rjsdmx 2.1_0 Provides functions to retrieve data and metadata from providers that dissem- noarch
inate data by means of SDMX web services. SDMX (Statistical Data and
Metadata eXchange) is a standard that has been developed with the aim of
simplifying the exchange of statistical information. More about the SDMX
standard and the SDMX Web Services can be found at: <http://sdmx.org>. /
EUPL
r-rjson 0.2.20Converts R object into JSON objects and vice-versa / GPL-2 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-rjsonio 1.3_1.1
This is a package that allows conversion to and from data in Javascript linux-
object notation (JSON) format. This allows R objects to be inserted into 32,
Javascript/ECMAScript/ActionScript code and allows R programmers to read linux-
and convert JSON content to R objects. This is an alternative to rjson pack- 64,
age. Originally, that was too slow for converting large R objects to JSON and osx-
was not extensible. rjson’s performance is now similar to this package, and 64,
perhaps slightly faster in some cases. This package uses methods and is read- win-
ily extensible by defining methods for different classes, vectorized operations, 32,
and C code and callbacks to R functions for deserializing JSON objects to R. win-
The two packages intentionally share the same basic interface. This package 64
(RJSONIO) has many additional options to allow customizing the generation
and processing of JSON content. This package uses libjson rather than imple-
menting yet another JSON parser. The aim is to support other general projects
by building on their work, providing feedback and benefit from their ongoing
development. / BSD_3_clause file LICENSE
r-rjsplot 2.5 Creates interactive graphs with ‘R’. It joins the data analysis power of R and noarch
the visualization libraries of JavaScript in one package. / CC BY-NC-SA 4.0
r-rjstat 0.3.0 Read and write the ‘JSON-stat’ format (http://json-stat.org) to and from (lists noarch
of) R data frames. Not all features are supported, especially the extensive
metadata features of ‘JSON-stat’. / MIT
r-rjwsacruncher 0.1.0 ‘JDemetra’ (<https://github.com/jdemetra/jdemetra-app>) is the seasonal ad- noarch
justment software officially recommended to the members of the European
Statistical System and the European System of Central Banks. Seasonal ad-
justment models performed with ‘JDemetra’ can be stored into workspaces.
‘JWSACruncher’ (<https://github.com/jdemetra/jwsacruncher/releases>) is a
console tool that re-estimates all the multi-processing defined in a workspace
and to export the result. ‘rjwsacruncher’ allows to launch easily the
‘JWSACruncher’. / GPL-3
r-rjython 0.0_4 R interface to Python via Jython allowing R to call python code. / GPL-2 noarch


Name Version
r-rkeajars 5.0_3 External jars required for package RKEA. / GPL-2 noarch
r-rkeeldata 1.0.5 ‘KEEL’ is a popular Java software for a large number of different knowledge noarch
data discovery tasks. Furthermore, ‘RKEEL’ is a package with a R code layer
between R and ‘KEEL’, for using ‘KEEL’ in R code. This package includes
the datasets from ‘KEEL’ in .dat format for its use in ‘RKEEL’ package. For
more information about ‘KEEL’, see <http://www.keel.es/>. / GPL-3
r-rkeeljars 1.0.19‘KEEL’ is a popular Java software for a large number of different knowledge noarch
data discovery tasks. Furthermore, ‘RKEEL’ is a package with a R code layer
between R and ‘KEEL’, for using ‘KEEL’ in R code. This package downloads
and install the .jar files necessary for ‘RKEEL’ algorithms execution. For more
information about ‘KEEL’, see <http://www.keel.es/>. / GPL-3
r-rkelly 1.0 Calculates the Kelly criterion (Kelly, J.L. (1956) <doi:10.1002/j.1538- noarch
7305.1956.tb03809.x>) for bets given quoted prices, model predictions and
commissions. Additionally it contains helper functions to calculate the proba-
bilities for wins and draws in multi-leg games. / MIT
r-rklout 1.0 An interface of R to Klout API v2. It fetches Klout Score for a Twitter User- noarch
name/handle in real time. Klout is a website and mobile app that uses social
media analytics to rank its users according to online social influence via the
Klout Score, which is a numerical value between 1 and 100. In determining
the user score, Klout measures the size of a user’s social media network and
correlates the content created to measure how other users interact with that
content. / GPL-2
r-rkmetrics 1.3 Hybrid Mortality Modelling (HMM) provides a framework in which mortality noarch
around the accident hump and at very old ages can be modelled under a single
model. The graphics’ codes necessary for visualization of the models’ output
are included here. Specifically, the graphics are based on the assumption that,
the mortality rates can be expressed as a function of the area under the curve
between the crude mortality rates plots and the tangential transform of the
force of mortality. / GPL-3
r-rknn 1.2_1 Random knn classification and regression are implemented. Random knn linux-
based feature selection methods are also included. The approaches are mainly 64,
developed for high-dimensional data with small sample size. / GPL-2 osx-
64,
win-
64
r-rkt 1.5 Contains function rkt which computes the Mann-Kendall test (MK) and the noarch
Seasonal and the Regional Kendall Tests for trend (SKT and RKT) and Theil-
Sen’s slope estimator. / GPL-2
r-rkum 0.1.1 Robust kernel center matrix, robust kernel cross-covariance operator for noarch
kernel unsupervised methods, kernel canonical correlation analysis, influ-
ence function of identifying significant outliers or atypical objects from
multimodal datasets. Alam, M. A, Fukumizu, K., Wang Y.-P. (2018)
<doi:10.1016/j.neucom.2018.04.008>. Alam, M. A, Calhoun, C. D., Wang
Y.-P. (2018) <doi:10.1016/j.csda.2018.03.013>. / GPL-3
r-rkvo 0.1 This package provides functionality to read files containing observations linux-
which consist of arbitrary key/value pairs. / GPL-3 64,
osx-
64,
win-
64
r-rlab 2.15.1Functions and Datasets Required for ST370 class / GPL-2 noarch


Name Version
r-rlabkey 2.3.1 The ‘LabKey’ client library for R makes it easy for R users to load live data linux-
from a ‘LabKey’ Server, <http://www.labkey.com/>, into the R environment 64,
for analysis, provided users have permissions to read the data. It also enables osx-
R users to insert, update, and delete records stored on a ‘LabKey’ Server, pro- 64,
vided they have appropriate permissions to do so. / Apache License 2.0 win-
64
r-rlakeanalyzer 1.11.4.1
Standardized methods for calculating common important derived physical fea- noarch
tures of lakes including water density based based on temperature, thermal
layers, thermocline depth, lake number, Wedderburn number, Schmidt stabil-
ity and others. / GPL-2
r-rlang 0.3.4 A toolbox for working with base types, core R features like the condition sys- linux-
tem, and core ‘Tidyverse’ features like tidy evaluation. / GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-rlas 1.3.3 Read and write ‘las’ and ‘laz’ binary file formats. The LAS file format is linux-
a public file format for the interchange of 3-dimensional point cloud data 64,
between data users. The LAS specifications are approved by the Ameri- osx-
can Society for Photogrammetry and Remote Sensing <https://www.asprs.org/ 64,
committee-general/laser-las-file-format-exchange-activities.html>. The LAZ win-
file format is an open and lossless compression scheme for binary LAS format 64
versions 1.0 to 1.3 <https://www.laszip.org/>. / GPL-3
r-rld 1.0 Analyzes data from repeated low-dose challenge experiments and provide vac- noarch
cine efficacy estimates. In addition, this package can provide guidance to de-
sign repeated low-dose challenge studies. / GPL-2
r-rlda 0.2.6 Estimates the Bayesian LDA model for mixed-membership clustering based linux-
on different types of data (i.e., Multinomial, Bernoulli, and Binomial en- 64,
tries). Albuquerque, Valle and Li (2019) <doi:10.1016/j.knosys.2018.10.024>. osx-
/ GPL-2 64,
win-
64
r-rldcp 1.0.2 Linguistic Descriptions of Complex Phenomena (LDCP) is an architecture noarch
and methodology that allows us to model complex phenomena, interpret-
ing input data, and generating automatic text reports customized to the user
needs (see <doi:10.1016/j.ins.2016.11.002> and <doi:10.1007/s00500-016-
2430-5>). The proposed package contains a set of methods that facilitates
the development of LDCP systems. It main goal is increasing the visibility
and practical use of this research line. / GPL-2
r-rleafangle 1.0 Leaf angle distribution is described by a number of functions (e.g. el- noarch
lipsoidal, Beta and rotated ellipsoidal). The parameters of leaf angle dis-
tributions functions are estimated through different empirical relationship.
This package includes estimations of parameters of different leaf angle
distribution function, plots and evaluates leaf angle distribution functions,
calculates extinction coefficients given leaf angle distribution. Reference:
Wang(2007)<doi:10.1016/j.agrformet.2006.12.003>. / GPL-3


Name Version
r-rleafmap 0.2 Display spatial data with interactive maps powered by the open-source noarch
JavaScript library ‘Leaflet’ (see <http://leafletjs.com/>). Maps can be rendered
in a web browser or displayed in the HTML viewer pane of ‘RStudio’. This
package is designed to be easy to use and can create complex maps with vector
and raster data, web served map tiles and interface elements. / GPL-3
r-rlecuyer 0.3_4 Provides an interface to the C implementation of the random number gener- linux-
ator with multiple independent streams developed by L’Ecuyer et al (2002). 64,
The main purpose of this package is to enable the use of this random number osx-
generator in parallel R applications. / GPL-2 64,
win-
64
r-rlibeemd 1.4.1 An R interface for libeemd (Luukko, Helske, Räsänen, 2016) linux-
<doi:10.1007/s00180-015-0603-9>, a C library of highly efficient par- 64,
allelizable functions for performing the ensemble empirical mode de- osx-
composition (EEMD), its complete variant (CEEMDAN), the regular 64,
empirical mode decomposition (EMD), and bivariate EMD (BEMD). win-
Due to the possible portability issues CRAN version no longer sup- 64
ports OpenMP, you can install OpenMP-supported version from GitHub:
<https://github.com/helske/Rlibeemd/>. / GPL-3
r-rlinkedin 0.2 A series of functions that allow users to access the ‘LinkedIn’ API to get infor- noarch
mation about connections, search for people and jobs, share updates with their
network, and create group discussions. For more information about using the
API please visit <https://developer.linkedin.com/>. / GPL-2
r-rlist 0.4.6.1Provides a set of functions for data manipulation with list objects, including linux-
mapping, filtering, grouping, sorting, updating, searching, and other useful 32,
functions. Most functions are designed to be pipeline friendly so that data linux-
processing with lists can be chained. / MIT file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-rlm 1.2 Robust fitting of linear model which can take response in matrix form. / GPL-2 linux-
64,
osx-
64,
win-
64
r-rlmdatadriven 0.3.0 Data driven approach for robust regression estimation in ho- noarch
moscedastic and heteroscedastic context. See Wang et al. (2007),
<doi:10.1198/106186007X180156> regarding homoscedastic framework. /
GPL (>= 2.0)
r-rlme 0.5 Estimates robust rank-based fixed effects and predicts robust random effects linux-
in two- and three- level random effects nested models. The methodology is 64,
described in Bilgic & Susmann (2013) <https://journal.r-project.org/archive/ osx-
2013/RJ-2013-027/>. / GPL-2 64,
win-
64


Name Version
r-rlof 1.1.1 R parallel implementation of Local Outlier Factor(LOF) which uses multiple linux-
CPUs to significantly speed up the LOF computation for large datasets. (Note: 64,
The overall performance depends on the computers especially the number of osx-
the cores).It also supports multiple k values to be calculated in parallel, as well 64,
as various distance measures in addition to the default Euclidean distance. / win-
GPL-2 64
r-rlrsim 3.1_3 Rapid, simulation-based exact (restricted) likelihood ratio tests for testing linux-
the presence of variance components/nonparametric terms for models fit with 64,
nlme::lme(),lme4::lmer(), lmeTest::lmer(), gamm4::gamm4(), mgcv::gamm() osx-
and SemiPar::spm(). / GPL-3 64,
win-
64
r-rlt 3.2.2 Random forest with a variety of additional features for regression, classifi- linux-
cation and survival analysis. The features include: parallel computing with 64,
OpenMP, embedded model for selecting the splitting variable (based on Zhu, osx-
Zeng & Kosorok, 2015), subject weight, variable weight, tracking subjects 64,
used in each tree, etc. / GPL-2 win-
64
r-rltp 0.1.4 R interface to the ‘LTP’-Cloud service for Natural Language Processing in linux-
Chinese (http://www.ltp-cloud.com/). / LGPL-3 64,
osx-
64,
win-
64
r-rm2006 0.1.0 Estimation the conditional covariance matrix using the RiskMetrics 2006 noarch
methodology of Zumbach (2007) <doi:10.2139/ssrn.1420185>. / GPL-2
r-rmaf 3.0.1 Uses refined moving average filter based on the optimal and data-driven mov- noarch
ing average lag q or smoothing spline to estimate trend and seasonal compo-
nents, as well as irregularity (residuals) for univariate time series or data. /
GPL-2
r-rmake 1.1.0 Creates and maintains a build process for complex analytic tasks in R. Package noarch
allows to easily generate Makefile for the (GNU) ‘make’ tool, which drives
the build process by (in parallel) executing build commands in order to update
results accordingly to given dependencies on changed data or updated source
files. / GPL (>= 3.0)
r-rmallow 1.0 An EM algorithm to fit Mallows’ Models to full or partial rankings, with or noarch
without ties. / GPL-2
r-rmalschains 0.2_5 An implementation of an algorithm family for continuous optimization called linux-
memetic algorithms with local search chains (MA-LS-Chains). Memetic al- 64,
gorithms are hybridizations of genetic algorithms with local search methods. osx-
They are especially suited for continuous optimization. / GPL-3 64,
win-
64


Name Version
r-rmargint 1.0.2 Three robust marginal integration procedures for additive models based on lo- linux-
cal polynomial kernel smoothers. As a preliminary estimator of the multivari- 64,
ate function for the marginal integration procedure, a first approach uses local osx-
constant M-estimators, a second one uses local polynomials of order 1 over all 64,
the components of covariates, and the third one uses M-estimators based on win-
local polynomials but only in the direction of interest. For this last approach, 64
estimators of the derivatives of the additive functions can be obtained. All
three procedures can compute predictions for points outside the training set if
desired. See Boente and Martinez (2017) <doi:10.1007/s11749-016-0508-0>
for details. / GPL (>= 3.0)
r-rmariadb 1.0.6 Implements a ‘DBI’-compliant interface to ‘MariaDB’ (<https://mariadb. linux-
org/>) and ‘MySQL’ (<https://www.mysql.com/>) databases. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-rmarkdown 1.12 Convert R Markdown documents into a variety of formats. / GPL-3 linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rmatio 0.14.0Read and write ‘Matlab’ MAT files from R. The ‘rmatio’ package supports linux-
reading MAT version 4, MAT version 5 and MAT compressed version 5. The 64,
‘rmatio’ package can write version 5 MAT files and version 5 files with vari- osx-
able compression. / GPL-3 64,
win-
64
r-rmawgen 1.3.3 S3 and S4 functions are implemented for spatial multi-site stochastic genera- noarch
tion of daily time series of temperature and precipitation. These tools make
use of Vector AutoRegressive models (VARs). The weather generator model
is then saved as an object and is calibrated by daily instrumental Gaussianized
time series through the ‘vars’ package tools. Once obtained this model, it can
it can be used for weather generations and be adapted to work with several
climatic monthly time series. / GPL-2
r-rmcorr 0.3.0 Compute the repeated measures correlation, a statistical technique for deter- noarch
mining the overall within-individual relationship among paired measures as-
sessed on two or more occasions, first introduced by Bland and Altman (1995).
Includes functions for diagnostics, p-value, effect size with confidence interval
including optional bootstrapping, as well as graphing. Also includes several
example datasets. / GPL-2


r-rmdfiltr 0.1.0 A collection of ‘Lua’ filters that extend the functionality of R Markdown tem- noarch
plates (e.g., count words or post-process ‘pandoc-citeproc’- citations). / MIT
r-rmdplugr 0.4.0 Formats for R Markdown that undo modifications by ‘pandoc’ and ‘rmark- noarch
down’ to original ‘latex’ templates, such as smaller margins, paragraph spac-
ing, and compact titles. In addition, enhancements such as author blocks with
affiliations and headers and footers are introduced. All of this functionality is
built around plugins that modify the default ‘pandoc’ template without relying
on custom templates. / GPL-3
r-rmdshower 2.1.1 ‘R’ ‘Markdown’ format for ‘shower’ presentations, see <https://github.com/ noarch
shower/shower>. / MIT
r-rmea 1.1.0 A suite of tools useful to read, visualize and export bivariate motion energy noarch
time-series. Lagged synchrony between subjects can be analyzed through win-
dowed cross-correlation. Surrogate data generation allows an estimation of
pseudosynchrony that helps to estimate the effect size of the observed synchro-
nization. Ramseyer & Tschacher (2011) <doi:10.1037/a0023419>. / GPL-3
r-rmecabko 0.1.6.2An ‘Rcpp’ interface for Eunjeon project <http://eunjeon.blogspot.com/>. The win-
‘mecab-ko’ and ‘mecab-ko-dic’ is based on a C library, and part-of-speech 64
tagging with them is useful when the spacing of source Korean text is not cor-
rect. This package provides part-of-speech tagging and tokenization function
for Korean text. / GPL-2
r-rmediation 1.1.4 We provide functions to compute confidence intervals (CIs) for a well-defined noarch
nonlinear function of the model parameters (e.g., product of k coefficients) in
single–level and multilevel structural equation models. / GPL-2
r-rmeta 3.0 Functions for simple fixed and random effects meta-analysis for two-sample noarch
comparisons and cumulative meta-analyses. Draws standard summary plots,
funnel plots, and computes summaries and tests for association and hetero-
geneity. / GPL-2
r-rmi 0.1.1 Provides mutual information estimators based on k-nearest neighbor estima- linux-
tors by A. Kraskov, et al. (2004) <doi:10.1103/PhysRevE.69.066138>, S. Gao, 64,
et al. (2015) <http://proceedings.mlr.press/v38/gao15.pdf> and local density osx-
estimators by W. Gao, et al. (2017) <doi:10.1109/ISIT.2017.8006749>. / 64,
GPL-3 win-
64
r-rmio 0.1.2 Provides header files of ‘mio’, a cross-platform C11 header-only library for noarch
memory mapped file IO <https://github.com/mandreyel/mio>. / GPL-3
r-rmisc 1.5 The Rmisc library contains many functions useful for data analysis and utility noarch
operations. / GPL-3
r-rmixmod 2.1.2.2Interface of ‘MIXMOD’ software for supervised, unsupervised and semi- linux-
supervised classification with mixture modelling. / GPL-3 64,
osx-
64,
win-
64
r-rmixpanel 0.7_1 Provides an interface to many endpoints of Mixpanel’s Data Export, Engage noarch
and JQL API. The R functions allow for event and profile data export as well as
for segmentation, retention, funnel and addiction analysis. Results are always
parsed into convenient R objects. Furthermore it is possible to load and update
profiles. / MIT


Name Version
r-rmixtcompio 4.0.1 Mixture Composer <https://github.com/modal-inria/MixtComp> is a project linux-
to build mixture models with heterogeneous data sets and partially missing 64,
data management. It includes models for real, categorical, counting, functional osx-
and ranking data. This package contains the minimal R interface of the C 64,
‘MixtComp’ library. / AGPL-3 win-
64
r-rmkdiscrete 0.1 Sundry discrete probability distributions and helper functions. / GPL-2 linux-
64,
osx-
64,
win-
64
r-rmoajars 1.0.1 External jars required for package RMOA. RMOA is a framework to build data noarch
stream models on top of MOA (Massive Online Analysis - <http://moa.cms.
waikato.ac.nz>). The jar files are put in this R package, the modelling logic
can be found in the RMOA package. / GPL-3
r-rmonad 0.5.0 A monadic solution to pipeline analysis. All operations – and the errors, warn- noarch
ings and messages they emit – are merged into a directed graph. Infix binary
operators mediate when values are stored, how exceptions are handled, and
where pipelines branch and merge. The resulting structure may be queried for
debugging or report generation. ‘rmonad’ complements, rather than competes
with, non-monadic pipeline packages like ‘magrittr’ or ‘pipeR’. This work is
funded by the NSF (award number 1546858). / GPL-3
r-rmosek 1.3.5 This is a meta-package designed to support the installation of Rmosek (>= 6.0) noarch
and bring the optimization facilities of MOSEK (>= 6.0) to the R-language.
The interface supports large-scale optimization of many kinds: Mixed-integer
and continuous linear, second-order cone, exponential cone and power cone
optimization, as well as continuous semidefinite optimization. Rmosek and
the R-language are open-source projects. MOSEK is a proprietary product,
but unrestricted trial and academic licenses are available. / LGPL-2.1
r-rmpfr 0.7_2 Arithmetic (via S4 classes and methods) for arbitrary precision floating point linux-
numbers, including transcendental (special) functions. To this end, the pack- 64,
age interfaces to the ‘LGPL’ licensed ‘MPFR’ (Multiple Precision Floating- osx-64
Point Reliable) Library which itself is based on the ‘GMP’ (GNU Multiple
Precision) Library. / GPL-2
r-rmpw 0.0.4 We implement causal mediation analysis using the methods proposed by Hong noarch
(2010) and Hong, Deutsch & Hill (2015) <doi:10.3102/1076998615583902>.
It allows the estimation and hypothesis testing of causal mediation effects
through ratio of mediator probability weights (RMPW). This strategy conve-
niently relaxes the assumption of no treatment-by-mediator interaction while
greatly simplifying the outcome model specification without invoking strong
distributional assumptions. We also implement a sensitivity analysis by ex-
tending the RMPW method to assess potential bias in the presence of omitted
pretreatment or posttreatment covariates. The sensitivity analysis strategy was
proposed by Hong, Qin, and Yang (2018) <doi:10.3102/1076998617749561>.
/ GPL-2


Name Version
r-rmr 1.1.0 Analysis of oxygen consumption data generated by Loligo (R) Systems noarch
respirometry equipment. The package includes a function for loading data
output by Loligo’s ‘AutoResp’ software (get.witrox.data()), functions for cal-
culating metabolic rates over user-specified time intervals, extracting critical
points from data using broken stick regressions based on Yeager and Ultsch
(<DOI:10.1086/physzool.62.4.30157935>), and easy functions for converting
between different units of barometric pressure. / GPL-3
r-rmr2 3.3.1 Supports the map reduce programming model on top of hadoop streaming / linux-
Apache 2.0 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-rms 5.1_3.1
Regression modeling, testing, estimation, validation, graphics, prediction, and linux-
typesetting by storing enhanced model design attributes in the fit. ‘rms’ is 32,
a collection of functions that assist with and streamline modeling. It also linux-
contains functions for binary and ordinal logistic regression models, ordi- 64,
nal models for continuous Y with a variety of distribution families, and the osx-
Buckley-James multiple regression model for right-censored responses, and 64,
implements penalized maximum likelihood estimation for logistic and ordi- win-
nary linear models. ‘rms’ works with almost any regression model, but it was 32,
especially written to work with binary or ordinal regression models, Cox re- win-
gression, accelerated failure time models, ordinary linear models, the Buckley- 64
James model, generalized least squares for serially or spatially correlated ob-
servations, generalized linear models, and quantile regression. / GPL (>= 2)
r-rms.gof 1.0 This package can be used to test any simple null hypothesis using the root- noarch
mean-square goodness of fit test. Monte Carlo estimation is used to calculate
the associated P-value. / GPL-3
r-rmsfact 0.0.3 Display a randomly selected quote about Richard M. Stallman based on the noarch
collection in the ‘GNU Octave’ function ‘fact()’ which was aggregated by
Jordi GutiÃ©rrez Hermoso based on the (now defunct) site stallmanfacts.com
(which is accessible only via <http://archive.org>). / GPL-3
r-rmthreshold 1.1 An algorithm which can be used to determine an objective threshold for signal- noarch
noise separation in large random matrices (correlation matrices, mutual infor-
mation matrices, network adjacency matrices) is provided. The package makes
use of the results of Random Matrix Theory (RMT). The algorithm incre-
ments a suppositional threshold monotonically, thereby recording the eigen-
value spacing distribution of the matrix. According to RMT, that distribution
undergoes a characteristic change when the threshold properly separates signal
from noise. By using the algorithm, the modular structure of a matrix - or of
the corresponding network - can be unraveled. / GPL-3


Name Version
r-rmtl 0.9 Efficient solvers for 10 regularized multi-task learning algorithms applicable noarch
for regression, classification, joint feature selection, task clustering, low-rank
learning, sparse learning and network incorporation. Based on the acceler-
ated gradient descent method, the algorithms feature a state-of-art computa-
tional complexity O(1/k^2). Sparse model structure is induced by the solving
the proximal operator. The detail of the package is described in the paper of
Han Cao and Emanuel Schwarz (2018) <doi:10.1093/bioinformatics/bty831>.
/ GPL-3
r-rmtstat 0.3 Functions for working with the Tracy-Widom laws and other distributions re- noarch
lated to the eigenvalues of large Wishart matrices. The tables for computing the
Tracy-Widom densities and distribution functions were computed by Momar
Dieng’s MATLAB package RMLab (formerly available on his homepage at
http://math.arizona.edu/~momar/research.htm ). This package is part of a col-
laboration between Iain Johnstone, Zongming Ma, Patrick Perry, and Morteza
Shahram. It will soon be replaced by a package with more accuracy and built-
in support for relevant statistical tests. / BSD_3_clause
r-rmumps 5.2.1_5
Some basic features of MUMPS (Multifrontal Massively Parallel sparse di- linux-
rect Solver) are wrapped in a class whose methods can be used for se- 64,
quentially solving a sparse linear system (symmetric or not) with one or osx-
many right hand sides (dense or sparse). There is a possibility to do sep- 64,
arately symbolic analysis, LU (or LDL^t) factorization and system solv- win-
ing. Third part ordering libraries are included and can be used: PORD, 64
METIS, SCOTCH. MUMPS method was first described in Amestoy et
al. (2001) <doi:10.1137/S0895479899358194> and Amestoy et al. (2006)
<doi:10.1016/j.parco.2005.07.004>. / GPL-2
r-rmutil 1.1.3 A toolkit of functions for nonlinear regression and repeated measurements not linux-
to be used by itself but called by other Lindsey packages such as ‘gnlm’, ‘sta- 64,
ble’, ‘growth’, ‘repeated’, and ‘event’ (available at <http://www.commanster. osx-
eu/rcode.html>). / GPL-2 64,
win-
64
r-rmvp 0.99.15
A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide linux-
Association Study (GWAS) tool. It can (1) effectively process large data, (2) 64,
rapidly evaluate population structure, (3) efficiently estimate variance compo- osx-
nents several algorithms, (4) implement parallel-accelerated association tests 64,
of markers three methods, (5) globally efficient design on GWAS process com- win-
puting, (6) enhance visualization of related information. ‘rMVP’ contains 64
three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jian-
ming Yu (2006) <DOI:10.1038/ng1702>) and FarmCPU (Xiaolei Liu (2016)
<doi:10.1371/journal.pgen.1005767>); variance components estimation meth-
ods EMMAX (Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;),
FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>,
R implementation from ‘GAPIT2’: You Tang and Xiaolei Liu (2016)
<DOI:10.1371/journal.pone.0107684> and ‘SUPER’: Qishan Wang and Feng
Tian (2014) <DOI:10.1371/journal.pone.0107684>), and HE regression (Xi-
ang Zhou (2017) <DOI:10.1214/17-AOAS1052>). / Apache License 2.0


Name Version
r-rmysql 0.10.15
A ‘DBI’ interface to ‘MySQL’ / ‘MariaDB’. The ‘RMySQL’ package con- linux-
tains an old implementation based on legacy code from S-PLUS which being 32,
phased out. A modern ‘MySQL’ client based on ‘Rcpp’ is available from the linux-
‘RMariaDB’ package. / GPL-2 64,
osx-
64,
win-
64
r-rnaseqwrapper 1.0_1 This package is designed to streamline several of the common steps for RNA- noarch
seq analysis, including differential expression and variant discovery. For the
development build, or to contribute changes to this package, please see our
repository at https://bitbucket.org/petersmp/rnaseqwrapper/ / GPL-3
r-rnassqs 0.5.0 Interface to access data via the United States Department of Agriculture’s noarch
National Agricultural Statistical Service (NASS) ‘Quick Stats’ web API
<https://quickstats.nass.usda.gov/api>. Convenience functions facilitate build-
ing queries based on available parameters and valid parameter values. / MIT
r- 0.1.0 Vector map data from <http://www.naturalearthdata.com/>. Access functions noarch
rnaturalearthdata are provided in the accompanying package ‘rnaturalearth’. / CC0
r- 0.0.4 Image data used as examples in the loon R package. / GPL-2 noarch
rnavgraphimagedata
r-rnavicell 0.2 Provides a set of functions to access a data visualization web service. For noarch
more information and a tutorial on how to use it, see https://navicell.curie.fr/
pages/nav_web_service.html and https://github.com/sysbio-curie/RNaviCell.
/ LGPL-2.1
r-rnbp 0.1.0 Use the <http://api.nbp.pl/> API through R. Retrieve currency exchange rates noarch
and gold prices data published by the National Bank of Poland in form of
convenient R objects. / GPL-3
r-rncbieutilslibs 0.9 Provides the libraries of the EUtils operations for the RNCBI package. / GPL- noarch
3
r-rnd 1.2 Extract the implied risk neutral density from options using various methods. / noarch
GPL-2
r-rndtexexams 1.5 Using as input a ‘LaTeX’ file with a multiple choice exam, this package will noarch
produce several versions with randomized contents of the same exam. Func-
tions for grading are also available. / GPL-2
r-rnentropy 1.2.2 An implementation of a method based on information theory devised for the noarch
identification of genes showing a significant variation of expression across
multiple conditions. Given expression estimates from any number of RNA-
Seq samples and conditions it identifies genes or transcripts with a signifi-
cant variation of expression across all the conditions studied, together with the
samples in which they are over- or under-expressed. Zambelli et al. (2018)
<doi:10.1093/nar/gky055>. / GPL-3
r-rneos 0.3_2 Within this package the XML-RPC API to NEOS <https://neos-server.org/ noarch
neos/> is implemented. This enables the user to pass optimization problems to
NEOS and retrieve results within R. / GPL-2
r-rnetcarto 0.2.4 It provides functions to compute the modularity and modularity-related roles linux-
in networks. It is a wrapper around the rgraph library (Guimera & Amaral, 64,
2005, doi:10.1038/nature03288). / GPL-2 osx-64


Name Version
r-rnetcdf 1.9_1 An interface to the NetCDF file format designed by Unidata for efficient stor- linux-
age of array-oriented scientific data and descriptions. The R interface is closely 64,
based on the C API of the NetCDF library, and it includes calendar conversions osx-
from the Unidata UDUNITS library. The current implementation supports all 64,
operations on NetCDF datasets in classic and 64-bit offset file formats, and win-
NetCDF4-classic format is supported for reading and modification of existing 64
files. / GPL-2
r-rnetlogo 1.0_4 Interface to use and access Wilensky’s ‘NetLogo’ (Wilensky 1999) from R us- noarch
ing either headless (no GUI) or interactive GUI mode. Provides functions to
load models, execute commands, and get values from reporters. Mostly anal-
ogous to the ‘NetLogo’ ‘Mathematica’ Link <https://github.com/NetLogo/
Mathematica-Link>. / GPL-2
r-rngforgpd 1.0.2 Generation of univariate and multivariate data that follow the generalized Pois- noarch
son distribution. The details of the univariate part are explained in Demirtas
(2017), and the multivariate part is an extension of the correlated Poisson data
generation routine that was introduced in Yahav and Shmueli (2012). / GPL-2
| GPL-3
r-rngsetseed 0.3_2 A function setVectorSeed() is provided. Its argument is a numeric vector of linux-
an arbitrary nonzero length, whose components have integer values from [0, 64,
2^32-1]. The input vector is transformed using AES (Advanced Encryption osx-
Standard) algorithm into an initial state of Mersenne-Twister random number 64,
generator. The function provides a better alternative to the R base function win-
set.seed(), if the input vector is a single integer. Initializing a stream of random 64
numbers with a vector is a convenient way to obtain several streams, each of
which is identified by several integer indices. / GPL-3
r-rngtools 1.3.1 Provides a set of functions for working with Random Number Generators linux-
(RNGs). In particular, a generic S4 framework is defined for getting/setting the
32,
current RNG, or RNG data that are embedded into objects for reproducibility. linux-
Notably, convenient default methods greatly facilitate the way current RNG 64,
settings can be changed. / GPL-3 noarch,
osx-
64,
win-
32,
win-
64
r-rngwell 0.10_5It is a dedicated package to WELL pseudo random generators, which were linux-
introduced in Panneton et al. (2006), ‘‘Improved Long-Period Generators 64,
Based on Linear Recurrences Modulo 2”, ACM Transactions on Mathemat- osx-
ical Software. But this package is not intended to be used directly, you are 64,
strongly __encouraged__ to use the ‘randtoolbox’ package, which depends on win-
this package. / BSD_3_clause 64


Name Version
r-rngwell19937 0.6_0 Long period linear random number generator WELL19937a by F. Panneton, P. linux-
L’Ecuyer and M. Matsumoto. The initialization algorithm allows to seed the 64,
generator with a numeric vector of an arbitrary length and uses MRG32k5a by osx-
P. L’Ecuyer to achieve good quality of the initialization. The output function 64,
may be set to provide numbers from the interval (0,1) with 53 (the default) or win-
32 random bits. WELL19937a is of similar type as Mersenne Twister and has 64
the same period. WELL19937a is slightly slower than Mersenne Twister, but
has better equidistribution and bit-mixing properties and faster recovery from
states with prevailing zeros than Mersenne Twister. All WELL generators with
orders 512, 1024, 19937 and 44497 can be found in randtoolbox package. /
file LICENSE (Restricts use)
r-rnifti 0.11.1Provides very fast read and write access to images stored in the NIfTI-1 and linux-
ANALYZE-7.5 formats, with seamless synchronisation between compiled C 64,
and interpreted R code. Also provides a C/C API that can be used by other osx-
packages. Not to be confused with ‘RNiftyReg’, which performs image regis- 64,
tration. / GPL-2 win-
64
r-rnomni 0.7.1 Genetic association tests that use the rank-based inverse normal transformation linux-
(INT). These tests are recommend for continuous traits with non-normally dis- 64,
tributed residuals. INT-based tests robustly control the type I error in settings osx-
where standard linear regression does not. Moreover, INT-based tests domi- 64,
nate standard linear regression in terms of power. INT-based tests may be clas- win-
sified into two types: tests that directly transform the phenotype (D-INT) and 64
tests that transform phenotypic residuals (I-INT). Our omnibus test (O-INT)
adaptively combines D-INT and I-INT into a single robust and statistically
powerful approach. / GPL-3
r-rnpn 0.1.0 Programmatic interface to the Web Service methods provided by the National noarch
‘Phenology’ Network (<https://usanpn.org/>), which includes data on various
life history events that occur at specific times. / MIT
r-rnr 0.2.1 Apply sensitivity analysis for offline policy evaluation, as implemented in Jung noarch
et al. (2017) <arXiv:1702.04690> based on Rosenbaum and Rubin (1983)
<http://www.jstor.org/stable/2345524>. / GPL-3
r-rnumerai 0.3 Routines to interact with the Numerai Machine Learning Tournament API noarch
<https://numer.ai>. The functionality includes the ability to automatically
download the current tournament data, submit predictions, and to get infor-
mation for your user. General ‘GraphQL’ queries can also be executed. /
GPL-3
r-roauth 0.9.6 Provides an interface to the OAuth 1.0 specification allowing users to authen- noarch
ticate via OAuth to the server of their choice. / Artistic-2.0
r-robastrda 1.2.0 Includes ‘sysdata.rda’ file for packages of the ‘RobASt’ - family of packages; noarch
is currently used by package ‘RobExtremes’ only. / LGPL-3
r-robcor 0.1_6 Robust pairwise correlations based on estimates of scale, particularly on noarch
FastQn one-step M-estimate. / GPL-2
r-robcp 0.2.4 Provides robust methods to detect change-points in uni- or multivariate time linux-
series. They can cope with corrupted data and heavy tails. One can detect 64,
changes in location, scale and dependence structure of a possibly multivariate osx-
time series. Procedures are based on Huberized versions of CUSUM tests 64,
proposed in Duerre and Fried (2019) <arXiv:1905.06201>. / GPL-3 win-
64


Name Version
r-robeth 2.7_5 Locations problems, M-estimates of coefficients and scale in linear regression, linux-
Weights for bounded influence regression, Covariance matrix of the coeffi- 64,
cient estimates, Asymptotic relative efficiency of regression M-estimates, Ro- osx-
bust testing in linear models, High breakdown point regression, M-estimates 64,
of covariance matrices, M-estimates for discrete generalized linear models. / win-
GPL-2 64
r-robfilter 4.1.1 A set of functions to filter time series based on concepts from robust statistics. linux-
/ GPL-2 64,
osx-
64,
win-
64
r-robfitcongraph 0.1.0 Contains a single function named robFitConGraph() which includes two al- linux-
gorithms for robust estimation of scatter matrices subject to zero-constraints 64,
in its inverse. The methodology is described in Vogel & Tyler (2014) osx-
<doi:10.1093/biomet/asu041>. See robFitConGraph() function documenta- 64,
tion for further details. / GPL-3 win-
64
r-robrsvd 1.0 This package provides the function to calculate SVD, regularized SVD, robust noarch
SVD and robust regularized SVD method. The robust SVD methods use al-
ternating iteratively reweighted least squares methods. The regularized SVD
uses generalized cross validation to choose the optimal smoothing parameters.
/ GPL-3
r-robumeta 2.0 Functions for conducting robust variance estimation (RVE) meta-regression noarch
using both large and small sample RVE estimators under various weighting
schemes. These methods are distribution free and provide valid point esti-
mates, standard errors and hypothesis tests even when the degree and structure
of dependence between effect sizes is unknown. Also included are functions
for conducting sensitivity analyses under correlated effects weighting and pro-
ducing RVE-based forest plots. / GPL-2
r-robustaft 1.4_4 R functions for the computation of the truncated maximum likelihood and the linux-
robust accelerated failure time regression for gaussian and log-Weibull case. / 64,
GPL-2 osx-
64,
win-
64
r-robustbase 0.93_4Essential Robust Statistics. Tools allowing to analyze data with robust meth- linux-
ods. This includes regression methodology including model selections and 32,
multivariate statistics where we strive to cover the book Robust Statistics, The- linux-
ory and Methods by ‘Maronna, Martin and Yohai’; Wiley 2006. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64


Name Version
r-robustblme 0.1.3 Bayesian robust fitting of linear mixed effects models through weighted like- linux-
lihood equations and approximate Bayesian computation as proposed by Ruli 64,
et al. (2017) <arXiv:1706.01752>. / GPL-2 osx-
64,
win-
64
r-robustetm 1.0 Testing homogeneity for generalized exponential tilt model. This package in- linux-
cludes a collection of functions for (1) implementing methods for testing ho- 64,
mogeneity for generalized exponential tilt model; and (2) implementing exist- osx-
ing methods under comparison. / GPL-2 64,
win-
64
r-robustgam 0.1.7 This package provides robust estimation for generalized additive models. It linux-
implements a fast and stable algorithm in Wong, Yao and Lee (2013). The 64,
implementation also contains three automatic selection methods for smoothing osx-
parameter. They are designed to be robust to outliers. For more details, see 64,
Wong, Yao and Lee (2013). / GPL-2 win-
64
r-robustgasp 0.5.7 Robust parameter estimation and prediction of Gaussian stochastic process linux-
emulators. It allows for robust parameter estimation and prediction using 64,
Gaussian stochastic process emulator. It also implements the parallel par- osx-
tial Gaussian stochastic process emulator for computer model with massive 64,
outputs See the reference: Mengyang Gu and Jim Berger, 2016, Annals of Ap- win-
plied Statistics; Mengyang Gu, Xiaojing Wang and Jim Berger, 2018, Annals 64
of Statistics. / GPL-2 | GPL-3
r- 1.1 Methods for aggregating ranked lists, especially lists of genes. It implements noarch
robustrankaggreg the Robust Rank Aggregation (Kolde et. al in preparation) and some other
simple algorithms for the task. RRA method uses a probabilistic model for
aggregation that is robust to noise and also facilitates the calculation of signif-
icance probabilities for all the elements in the final ranking. / GPL-2
r-robustreg 0.1_11Linear regression functions using Huber and bisquare psi functions. Optimal linux-
weights are calculated using IRLS algorithm. / GPL-2 64,
osx-
64,
win-
64
r-robustx 1.2_4 Robustness – ‘eXperimental’, ‘eXtraneous’, or ‘eXtraordinary’ Functionality noarch
for Robust Statistics. In other words, methods which are not yet well estab-
lished, often related to methods in package ‘robustbase’. / GPL-2
r-rocc 1.2 Functions for a classification method based on receiver operating characteris- noarch
tics (ROC). Briefly, features are selected according to their ranked AUC value
in the training set. The selected features are merged by the mean value to form
a metagene. The samples are ranked by their metagene value and the meta-
gene threshold that has the highest accuracy in splitting the training samples
is determined. A new sample is classified by its metagene value relative to the
threshold. In the first place, the package is aimed at two class problems in gene
expression data, but might also apply to other problems. / GPL-2


Name Version
r-roccv 1.2 Cross validate large genetic data while specifying clinical variables that should noarch
always be in the model using the function cv(). An ROC plot from the cross
validation data with AUC can be obtained using rocplot(), which also can be
used to compare different models. Framework was built to handle genetic data,
but works for any data. / MIT
r-rocit 1.1.1 Sensitivity (or recall or true positive rate), false positive rate, specificity, pre- noarch
cision (or positive predictive value), negative predictive value, misclassifica-
tion rate, accuracy, F-score- these are popular metrics for assessing perfor-
mance of binary classifier for certain threshold. These metrics are calculated
at certain threshold values. Receiver operating characteristic (ROC) curve is
a common tool for assessing overall diagnostic ability of the binary classifier.
Unlike depending on a certain threshold, area under ROC curve (also known
as AUC), is a summary statistic about how well a binary classifier performs
overall for the classification task. ROCit package provides flexibility to eas-
ily evaluate threshold-bound metrics. Also, ROC curve, along with AUC, can
be obtained using different methods, such as empirical, binormal and non-
parametric. ROCit encompasses a wide variety of methods for constructing
confidence interval of ROC curve and AUC. ROCit also features the option of
constructing empirical gains table, which is a handy tool for direct marketing.
The package offers options for commonly used visualization, such as, ROC
curve, KS plot, lift plot. Along with in-built default graphics setting, there are
rooms for manual tweak by providing the necessary values as function argu-
ments. ROCit is a powerful tool offering a range of things, yet it is very easy
to use. / GPL-3
r-rocnit 1.0 Non-inferiority test and diagnostic test are very important in clinical trails. noarch
This package is to get a p value from the non-inferiority test for ROC curves
from diagnostic test. / GPL-3
r-rococo 1.1.7 Provides the robust gamma rank correlation coefficient as introduced by linux-
Bodenhofer, Krone, and Klawonn (2013) <DOI:10.1016/j.ins.2012.11.026> 64,
along with a permutation-based rank correlation test. The rank correlation co- osx-
efficient and the test are explicitly designed for dealing with noisy numerical 64,
data. / GPL-2 win-
64
r-rocr 1.0_7 ROC graphs, sensitivity/specificity curves, lift charts, and precision/recall linux-
plots are popular examples of trade-off visualizations for specific pairs of per- 32,
formance measures. ROCR is a flexible tool for creating cutoff-parameterized linux-
2D performance curves by freely combining two from over 25 performance 64,
measures (new performance measures can be added using a standard inter- noarch,
face). Curves from different cross-validation or bootstrapping runs can be av- osx-
eraged by different methods, and standard deviations, standard errors or box 64,
plots can be used to visualize the variability across the runs. The parameteri- win-
zation can be visualized by printing cutoff values at the corresponding curve 32,
positions, or by coloring the curve according to cutoff. All components of a win-
performance plot can be quickly adjusted using a flexible parameter dispatch- 64
ing mechanism. Despite its flexibility, ROCR is easy to use, with only three
commands and reasonable default values for all optional parameters. / GPL
(>= 2)
r-rocwogs 1.0 Function to estimate the ROC Curve of a continuous-scaled diagnostic test noarch
with the help of a second imperfect diagnostic test with binary responses. /
GPL-2


Name Version
r-rodam 0.1.6 ‘ODAM’ (Open Data for Access and Mining) is a framework that imple- noarch
ments a simple way to make research data broadly accessible and fully avail-
able for reuse, including by a script language such as R. The main purpose
is to make a data set accessible online with a minimal effort from the data
provider, and to allow any scientists or bioinformaticians to be able to ex-
plore the data set and then extract a subpart or the totality of the data accord-
ing to their needs. The Rodam package has only one class, ‘odamws’, that
provides methods to allow you to retrieve online data using ‘ODAM’ Web
Services. This obviously requires that data are implemented according the
‘ODAM’ approach , namely that the data subsets were deposited in the suitable
data repository in the form of TSV files associated with their metadata also
described in TSV files. See <http://www.slideshare.net/danieljacob771282/
odam-open-data-access-and-mining>. / LGPL-3
r-rodbc 1.3_15An ODBC database interface. / GPL-2 | GPL-3 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-rodbcdbi 0.1.1 An implementation of R’s DBI interface using ODBC package as a back-end. noarch
This allows R to connect to any DBMS that has a ODBC driver. / MIT
r-rodbcext 0.3.1 An extension for RODBC package adding support for parameterized queries. linux-
/ GPL-2 | GPL-3 64,
osx-
64,
win-
64
r-rode 0.99.6Show physics, math and engineering students how an ODE solver is made noarch
and how effective R classes can be for the construction of the equations that
describe natural phenomena. Inspiration for this work comes from the book
on Computer Simulations in Physics by Harvey Gould, Jan Tobochnik, and
Wolfgang Christian. Book link: <http://www.compadre.org/osp/items/detail.
cfm?ID=7375>. / GPL-2
r-rodeo 0.7.4 Provides an R6 class and several utility methods to facilitate the implementa- linux-
tion of models based on ordinary differential equations. The heart of the pack- 64,
age is a code generator that creates compiled ‘Fortran’ (or ‘R’) code which can osx-
be passed to a numerical solver. There is direct support for solvers contained 64,
in packages ‘deSolve’ and ‘rootSolve’. / GPL-2 win-
64


Name Version
r-rodm 1.1 This package implements an interface to Oracle Data Mining (ODM). It pro- noarch
vides an ideal environment for rapid development of demos and proof of con-
cept data mining studies. It facilitates the prototyping of vertical applications
and makes ODM and the RDBMS environment easily accessible to statisti-
cians and data analysts familiar with R but not fluent in SQL or familiar with
the database environment. It also facilitates the benchmarking and testing of
ODM functionality including the production of summary statistics, perfor-
mance metrics and graphics. It enables the scripting and control of produc-
tion data mining methodologies from a high-level environment. Oracle Data
Mining (ODM) is an option of Oracle Relational Database Management Sys-
tem (RDBMS) Enterprise Edition (EE). It contains several data mining and
data analysis algorithms for classification, prediction, regression, clustering,
associations, feature selection, anomaly detection, feature extraction, and spe-
cialized analytics. It provides means for the creation, management and oper-
ational deployment of data mining models inside the database environment.
For more information consult the entry for Oracle Data Mining in Wikipedia
(en.wikipedia.org). / LGPL-2
r-roi 0.3_2 The R Optimization Infrastructure (‘ROI’) is a sophisticated framework for noarch
handling optimization problems in R. More information can be found on the
‘ROI’ homepage <http://roi.r-forge.r-project.org/>. / GPL-3
r-rollbar 0.1.0 Reports errors and messages to Rollbar, the error tracking platform <https: noarch
//rollbar.com>. / MIT
r-rolldown 0.1 R Markdown output formats based on JavaScript libraries such as ‘Scrollama’ noarch
(<https://github.com/russellgoldenberg/scrollama>) for storytelling. / MIT
r-rollregres 0.1.2 Methods for fast rolling and expanding linear regression models. That is, series linux-
of linear regression models estimated on either an expanding window of data or 64,
a moving window of data. The methods use rank-one updates and downdates osx-
of the upper triangular matrix from a QR decomposition (see Dongarra, Moler, 64,
Bunch, and Stewart (1979) <doi:10.1137/1.9781611971811>). / GPL-2 win-
64
r-roloc 0.1_1 Functions to convert an R colour specification to a colour name. The user can noarch
select and create different lists of colour names and different colour metrics
for the conversion. / GPL-2 | GPL-3
r-rolr 1.0.0 Provides fast procedures for exploring all pairs of cutpoints of a single covari- noarch
ate with respect to survival and determining optimal cutpoints using a hierar-
chical method and various ordered logrank tests. / GPL-3
r-ronfhir 0.3.1 R on FHIR is an easy to use wrapper around the ‘HL7 FHIR’ REST API (STU noarch
3). It provides tools to easily read and search resources on a FHIR server and
brings the results into the R environment. R on FHIR is based on the FhirClient
of the official ‘HL7 FHIR .NET API’, also made by Firely. / BSD_3_clause
r-rook 1.1_1 This package contains the Rook specification and convenience software for linux-
building and running Rook applications. To get started, be sure and read the 32,
‘Rook’ help file first. / GPL-2 linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
r-rootsolve 1.7 Routines to find the root of nonlinear functions, and to perform steady-state linux-
and equilibrium analysis of ordinary differential equations (ODE). Includes 64,
routines that: (1) generate gradient and jacobian matrices (full and banded), osx-
(2) find roots of non-linear equations by the ‘Newton-Raphson’ method, (3) 64,
estimate steady-state conditions of a system of (differential) equations in full, win-
banded or sparse form, using the ‘Newton-Raphson’ method, or by dynami- 64
cally running, (4) solve the steady-state conditions for uni-and multicompo-
nent 1-D, 2-D, and 3-D partial differential equations, that have been converted
to ordinary differential equations by numerical differencing (using the method-
of-lines approach). Includes fortran code. / GPL-2
r-rootwishart 0.4.1 Functions for hypothesis testing in single and double Wishart settings, linux-
based on Roy’s largest root. This test statistic is especially use- 64,
ful in multivariate analysis. The computations are based on results osx-
by Chiani (2014) <DOI:10.1016/j.jmva.2014.04.002> and Chiani (2016) 64,
<DOI:10.1016/j.jmva.2015.10.007>. They use the fact that the CDF is related win-
to the Pfaffian of a matrix that can be computed in a finite number of iterations. 64
This package takes advantage of the Boost and Eigen C libraries to perform
multi-precision linear algebra. / GPL-2
r-rop 1.0 Trees Classification and Regression using multivariate nodes calculated by noarch
an exhaustive numerical approach. We propose a new concept of deci-
sion tree, including multivariate knots and non hierarchical pathway. This
package’s model uses a multivariate nodes tree that calculates directly a
risk score for each observation for the state Y observed. Nguyen JM,
Gaultier A, Antonioli D (2015) <doi:10.1016/j.respe.2018.03.088> Castillo
JM, Knol AC, Nguyen JM, Khammari A, Saint Jean M, Dreno B (2016)
<doi:10.1684/ejd.2016.2826> Vildy S, Nguyen JM, Gaultier A, Khammari A,
Dreno B (2017) <doi:10.1684/ejd.2016.2955> Nguyen JM, Gaultier A, Anto-
nioli D (2018) <doi:10.1016/j.respe.2018.03.088>. / GPL (>= 2.0)
r-rope 1.0 Selects one model with variable selection FDR controlled at a specified level. noarch
A q-value for each potential variable is also returned. The input, variable selec-
tion counts over many bootstraps for several levels of penalization, is modeled
as coming from a beta-binomial mixture distribution. / GPL-3
r-ropendata 0.1.0 ‘Rapid7’ collects ‘cybersecurity’ data and makes it available via their ‘Open noarch
Data’ <http://opendata.rapid7.com> portal which has an API. Tools are pro-
vided to assist in querying for available data sets and downloading any data set
authorized to a free, registered account. / MIT
r-ropendota 0.1.2 Provides a client for the API of OpenDota. OpenDota is a web service which noarch
is provide DOTA2 real time data. Data is collected through the Steam We-
bAPI. With ROpenDota you can easily grab the latest DOTA2 statistics in R
programming such as latest match on official international competition, an-
alyzing your or enemy performance to learn their strategies,etc. Please see
<https://github.com/rosdyana/ROpenDota> for more information. / MIT
r-ropenfigi 0.2.8 Provide a simple interface to Bloomberg’s OpenFIGI API. Please see <https: noarch
//openfigi.com> for API details and registration. You may be eligible to have
an API key to accelerate your loading process. / GPL-3
r- 1.0.1 An R package for the OpenSecrets.org web services API. / LGPL-3 noarch
ropensecretsapi
r- 1.1 OpenWeatherMap (OWM) <http://openweathermap.org/api> is a service pro- noarch
ropenweathermap viding weather related data. This package can be used to access current
weather data for one location or several locations. It can also be used to fore-
cast weather for 5 days with data for every 3 hours. / MIT


Name Version
r-roperators 1.1.0 Provides string arithmetic, reassignment operators, logical operators that han- noarch
dle missing values, and extra logical operators such as floating point equality
and all or nothing. The intent is to allow R users to write code that is easier
to read, write, and maintain while providing a friendlier experience to new R
users from other language backgrounds (such as ‘Python’) who are used to
concepts such as x = 1 and ‘foo’ ‘bar’. / MIT
r-roptimizely 0.2.0 R package extracts optimizely test results and test information using Opti- noarch
mizely REST API. Only read functionality is supported for analysis and re-
porting. / GPL-2
r-rose 0.0_3 The package provides functions to deal with binary classification problems in noarch
the presence of imbalanced classes. Synthetic balanced samples are generated
according to ROSE (Menardi and Torelli, 2013). Functions that implement
more traditional remedies to the class imbalance are also provided, as well
as different metrics to evaluate a learner accuracy. These are estimated by
holdout, bootstrap or cross-validation methods. / GPL-2
r-rosetteapi 1.12.1‘Rosette’ is an API for multilingual text analysis and information extraction. noarch
More information can be found at <https://developer.rosette.com>. / Apache
License 2.0 | file LICENSE
r-rotationforest 0.1.3 Fit and deploy rotation forest models (Rodriguez, J.J., Kuncheva, L.I., 2006. noarch
Rotation forest: A new classifier ensemble method. IEEE Trans. Pattern
Anal. Mach. Intell. 28, 1619-1630 <doi:10.1109/TPAMI.2006.211>) for bi-
nary classification. Rotation forest is an ensemble method where each base
classifier (tree) is fit on the principal components of the variables of random
partitions of the feature set. / GPL-2
r-rotor 0.2.3 Conditionally rotate or back-up files based on their size or the date of the last noarch
backup; inspired by the ‘Linux’ utility ‘logrotate’. / MIT
r- 0.1 Rough Sets were introduced by Zdzislaw Pawlak on his book Rough Sets: noarch
roughsetknowledgereduction
Theoretical Aspects of Reasoning About Data. Rough Sets provide a formal
method to approximate crisp sets when the set-element belonging relationship
is either known or undetermined. This enables the use of Rough Sets for rea-
soning about incomplete or contradictory knowledge. A decision table is a
prescription of the decisions to make given some conditions. Such decision
tables can be reduced without losing prescription ability. This package pro-
vides the classes and methods for knowledge reduction from decision tables as
presented in the chapter 7 of the aforementioned book. This package provides
functions for calculating the both the discernibility matrix and the essential
parts of decision tables. / MIT
r-roundhouse 0.0.1 An R wrapper to the ‘Internet Chuck Norris database’ (‘ICNDb’) API for gen- noarch
erating random Chuck Norris facts. / GPL-2
r-rowr 1.1.3 Provides utilities which interact with all R objects as if they were arranged in noarch
rows. It allows more consistent and predictable output to common functions,
and generalizes a number of utility functions to to be failsafe with any number
and type of input objects. / GPL-3


Name Version
r-roxygen2 6.1.1 Generate your Rd documentation, ‘NAMESPACE’ file, and collation field us- linux-
ing specially formatted comments. Writing documentation in-line with code 32,
makes it easier to keep your documentation up-to-date as your requirements linux-
change. ‘Roxygen2’ is inspired by the ‘Doxygen’ system for C. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64
r-rpaci 0.1.1 Analysis of corneal data obtained from a Placido disk corneal topographer noarch
with calculation of irregularity indices. A corneal topographer is an oph-
thalmic clinical device that obtains measurements in the cornea (the anterior
part of the eye). A Placido disk corneal topographer makes use of the Placido
disk (Rowsey et al. (1981), <doi:10.1001/archopht.1981.03930011093022>,
Rand et al. (1997), <doi:10.1016/S0886-3350(99)00355-7>), which pro-
duce a circular pattern of measurement nodes. The raw information
measured by such a topographer is used by practitioners to analyze
curvatures, to study optical aberrations, or to diagnose specific condi-
tions of the eye. The rPACI package allows the calculation of the
corneal irregularity indices described in Ramos-Lopez et al. (2013),
<doi:10.1097/OPX.0b013e3182843f2a>, and that were firstly introduced in
Ramos-Lopez et al. (2011), <doi:10.1097/OPX.0b013e3182843f2a>. It pro-
vides a simple interface to read corneal topography data files as exported by
a typical Placido disk topographer, to compute the irregularity indices men-
tioned before, and to display summary plots that are easy to interpret for a
clinician. / GPL-3
r-rpanel 1.1_4 A set of functions to build simple GUI controls for R functions. These are built linux-
on the ‘tcltk’ package. Uses could include changing a parameter on a graph by 32,
animating it with a slider or a doublebutton, up to more sophisticated control linux-
panels. Some functions for specific graphical tasks, referred to as ‘cartoons’, 64,
are provided. / GPL (>= 2) noarch,
osx-
64,
win-
32,
win-
64
r-rpart 4.1_15Recursive partitioning for classification, regression and survival trees. An im- linux-
plementation of most of the functionality of the 1984 book by Breiman, Fried- 32,
man, Olshen and Stone. / GPL-2 | GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64
r-rpart.plot 3.0.8 Plot ‘rpart’ models. Extends plot.rpart() and text.rpart() in the ‘rpart’ package. noarch
/ GPL-3


Name Version
r-rpart.utils 0.5 This package contains additional tools for working with rpart objects. Most noarch
importantly, it includes methods for converting rpart rules into a series of
structured tables sufficient for executing the decision tree completely in SQL.
/ GPL-3
r-rpartscore 1.0_1 This package contains functions that allow to build classification trees for or- noarch
dinal responses within the CART framework. The trees are grown using the
Generalized Gini impurity function, where the misclassification costs are given
by the absolute or squared differences in scores assigned to the categories of
the response. Pruning is based on the total misclassification rate or on the total
misclassification cost. / GPL-2
r-rpca 0.2.3 Suppose we have a data matrix, which is the superposition of a low-rank com- noarch
ponent and a sparse component. Candes, E. J., Li, X., Ma, Y., & Wright, J.
(2011). Robust principal component analysis?. Journal of the ACM (JACM),
58(3), 11. prove that we can recover each component individually under some
suitable assumptions. It is possible to recover both the low-rank and the sparse
components exactly by solving a very convenient convex program called Prin-
cipal Component Pursuit; among all feasible decompositions, simply mini-
mize a weighted combination of the nuclear norm and of the L1 norm. This
package implements this decomposition algorithm resulting with Robust PCA
approach. / GPL-2 | GPL-3
r-rpclr 1.0 This package implements the R-PCLR (Random-Penalized Conditional Logis- noarch
tic Regression) algorithm for obtaining variable importance. The algorithm is
applicable for the analysis of high dimensional data from matched case-control
studies. / GPL-2
r-rpensemble 0.4 Implements the methodology of Cannings, T. I. and Samworth, R. J. (2017) noarch
Random-projection ensemble classification, J. Roy. Stat. Soc., Ser. B. (with
discussion), 79, 959–1035. The random projection ensemble classifier is a
general method for classification of high-dimensional data, based on careful
combination of the results of applying an arbitrary base classifier to random
projections of the feature vectors into a lower-dimensional space. The random
projections are divided into non-overlapping blocks, and within each block the
projection yielding the smallest estimate of the test error is selected. The ran-
dom projection ensemble classifier then aggregates the results of applying the
base classifier on the selected projections, with a data-driven voting threshold
to determine the final assignment. / GPL-3
r-rpexe.rpext 0.0.1 This reduced piecewise exponential survival software implements the noarch
likelihood ratio test and backward elimination procedure in Han,
Schell, and Kim (2012 <doi:10.1080/19466315.2012.698945>, 2014
<doi:10.1002/sim.5915>), and Han et al. (2016 <doi:10.1111/biom.12590>).
Inputs to the program can be either times when events/censoring occur or the
vectors of total time on test and the number of events. Outputs of the programs
are times and the corresponding p-values in the backward elimination. Details
about the model and implementation are given in Han et al. 2014. This
program can run in R version 3.2.2 and above. / GPL-3
r-rphylip 0.1_23Rphylip provides an R interface for the PHYLIP package. All users of Rphylip noarch
will thus first have to install the PHYLIP phylogeny methods program package
(Felsenstein 2013). See http://www.phylip.com for more information about
installing PHYLIP. / GPL-2
r-rpinterest 0.3.1 Get information (boards, pins and users) from the Pinterest <http://www. noarch
pinterest.com> API. / GPL-3


Name Version
r-rpipedrive 0.1.1 R interaction with ‘pipedrive.com API’. All functions were created and doc- noarch
umented according to <https://developers.pipedrive.com/docs/api/v1/>. Cre-
ated with the objective of offering integration and even the development
of ‘APIs’. Making possible to create workflows and easily downloading
databases for analysis. / GPL-2
r-rpivottable 0.3.0 Build powerful pivot tables (aka Pivot Grid, Pivot Chart, Cross-Tab) and dy- noarch
namically slice & dice / drag ‘n’ drop your data. ‘rpivotTable’ is a wrapper
of ‘pivottable’, a powerful open-source Pivot Table library implemented in
‘JavaScript’ by Nicolas Kruchten. Aligned to ‘pivottable’ v2.19.0. / MIT
r-rplotengine 1.0_7 Generate basic charts either by custom applications, or from a small script noarch
launched from the system console, or within the R console. Two ASCII text
files are necessary: (1) The graph parameters file, which name is passed to
the function ‘rplotengine()’. The user can specify the titles, choose the type
of the graph, graph output formats (e.g. png, eps), proportion of the X-axis
and Y-axis, position of the legend, whether to show or not a grid at the back-
ground, etc. (2) The data to be plotted, which name is specified as a parameter
(‘data_filename’) in the previous file. This data file has a tabulated format,
with a single character (e.g. tab) between each column, and a headers line
located in the first row. Optionally, the file could include data columns for
showing confidence intervals. / GPL-2
r-rpmg 2.2_2 Really Poor Man’s Graphical User Interface, used to create interactive R anal- noarch
ysis sessions with simple R commands. / GPL-2
r-rpmm 1.25 Recursively Partitioned Mixture Model for Beta and Gaussian Mixtures. This noarch
is a model-based clustering algorithm that returns a hierarchy of classes, simi-
lar to hierarchical clustering, but also similar to finite mixture models. / GPL-2
r-rpnf 1.0.5 A set of functions to analyze and print the development of a commodity using noarch
the Point and Figure (P&F) approach. A P&F processor can be used to calcu-
late daily statistics for the time series. These statistics can be used for deeper
investigations as well as to create plots. Plots can be generated as well known
X/O Plots in plain text format, and additionally in a more graphical format. /
GPL-3
r-rpoet 1.1.0 Wrapper for the ‘PoetryDB’ API <http://poetrydb.org> that allows for interac- noarch
tion and data extraction from the database in an R interface. The ‘PoetryDB’
API is a database of poetry and poets implemented with ‘MongoDB’ to enable
developers and poets to easily access one of the most comprehensive poetry
databases currently available. / GPL-2
r- 1.0 Using some association schemes to obtain a new series of resolvable partially noarch
rppairwisedesign pairwise balanced designs (RPPBD) and space-filling designs. / GPL-3
r-rprime 0.1.0 ‘Eprime’ is a set of programs for administering psychological experiments by noarch
computer. This package provides functions for loading, parsing, filtering and
exporting data in the text files produced by ‘Eprime’ experiments. / GPL-2
r-rprintf 0.2.1 Provides a set of functions to facilitate building formatted strings under various noarch
replacement rules: C-style formatting, variable-based formatting, and number-
based formatting. C-style formatting is basically identical to built-in function
‘sprintf’. Variable-based formatting allows users to put variable names in a
formatted string which will be replaced by variable values. Number-based
formatting allows users to use index numbers to represent the corresponding
argument value to appear in the string. / MIT


Name Version
r-rprobsup 2.1 The A() function calculates the A statistic, a nonparametric measure of ef- noarch
fect size for two independent groups thatâ C™s also known as the probabil-
ity of superiority (Ruscio, 2008), along with its standard error and a confi-
dence interval constructed using bootstrap methods (Ruscio & Mullen, 2012).
Optional arguments can be specified to calculate variants of the A statis-
tic developed for other research designs (e.g., related samples, more than
two independent groups or related samples; Ruscio & Gera, 2013). <DOI:
10.1037/1082-989X.13.1.19>. <DOI: 10.1080/00273171.2012.658329>.
<DOI: 10.1080/00273171.2012.738184>. / MIT
r-rprojroot 1.3_2 Robust, reliable and flexible paths to files below a project root. The ‘root’ of a linux-
project is defined as a directory that matches a certain criterion, e.g., it contains 32,
a certain regular file. / GPL-3 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rpsychi 0.8 The rpsychi offers a number of functions for psychiatry, psychiatric nursing, noarch
clinical psychology. Functions are primarily for statistical significance testing
using published work. For example, you can conduct a factorial analysis of
variance (ANOVA), which requires only the mean, standard deviation, and
sample size for each cell, rather than the individual data. This package covers
fundamental statistical tests such as t-test, chi-square test, analysis of variance,
and multiple regression analysis. With some exceptions, you can obtain effect
size and its confidence interval. These functions help you to obtain effect size
from published work, and then to conduct a priori power analysis or meta-
analysis, even if a researcher do not report effect size in a published work. /
GPL-2
r-rpublica 0.1.3 Client for accessing data journalism APIs from ProPublica <http://www. noarch
propublica.org/>. / GPL-2
r-rpushbullet 0.3.2 An R interface to the Pushbullet messaging service which provides fast and ef- noarch
ficient notifications (and file transfer) between computers, phones and tablets.
An account has to be registered at the site <http://www.pushbullet.com> site
to obtain a (free) API key. / GPL-2
r-rqcc 0.19.8.2
Constructs robust quality control chart based on the median and Hodges- noarch
Lehmann estimators (location) and the median absolute deviation (MAD) and
Shamos estimators (scale) which are unbiased with a sample of finite size. For
more details, see Park, Kim and Wang (2019)<arXiv:1908.00462>. This work
was partially supported by the National Research Foundation of Korea (NRF)
grant funded by the Korea government (No. NRF-2017R1A2B4004169). /
GPL-2 | GPL-3
r-rrate 1.0 Replication Rate (RR) is the probability of replicating a statistically signifi- noarch
cant association in genome-wide association studies. This R-package provide
the estimation method for replication rate which makes use of the summary
statistics from the primary study. We can use the estimated RR to determine
the sample size of the replication study, and to check the consistency between
the results of the primary study and those of the replication study. / GPL-3


Name Version
r-rrblup 4.6 Software for genomic prediction with the RR-BLUP mixed model (Endelman noarch
2011, <doi:10.3835/plantgenome2011.08.0024>). One application is to esti-
mate marker effects by ridge regression; alternatively, BLUPs can be calcu-
lated based on an additive relationship matrix or a Gaussian kernel. / GPL-3
r-rrna 1.0 Functions for creating and manipulating RNA secondary structure plots. / noarch
GPL-3
r-rroad 0.0.5 Computation of the International Roughness Index (IRI) given a longitudinal noarch
road profile. The IRI can be calculated for a single road segment or for a
sequence of segments with a fixed length (e. g. 100m). For the latter, an
overlap of the segments can be selected. The IRI and likewise the algorithms
for its determination are defined in Sayers, Michael W; Gillespie, Thomas D;
Queiroz, Cesar A.V. 1986. The International Road Roughness Experiment
(IRRE) : establishing correlation and a calibration standard for measurements.
World Bank technical paper; no. WTP 45. Washington, DC : The World
Bank. (ISBN 0-8213-0589-1) available from <http://documents.worldbank.
org/curated/en/326081468740204115>. / MIT
r-rromeo 0.1.0 Fetches information from the ‘SHERPA/RoMEO’ API <http://www.sherpa. noarch
ac.uk/romeo/apimanual.php> which indexes policies of journal regarding the
archival of scientific manuscripts before and/or after peer-review as well as
formatted manuscripts. / GPL-3
r-rrpp 0.4.2 Linear model calculations are made for many random versions of data. Us- noarch
ing residual randomization in a permutation procedure, sums of squares are
calculated over many permutations to generate empirical probability distribu-
tions for evaluating model effects. This packaged is described by Collyer &
Adams (2018) <doi:10.1111/2041-210X.13029>. Additionally, coefficients,
statistics, fitted values, and residuals generated over many permutations can
be used for various procedures including pairwise tests, prediction, classifi-
cation, and model comparison. This package should provide most tools one
could need for the analysis of high-dimensional data, especially in ecology and
evolutionary biology, but certainly other fields, as well. / GPL-2
r-rrreg 0.7.0 Univariate and multivariate methods to analyze randomized response (RR) noarch
survey designs (e.g., Warner, S. L. (1965). Randomized response: A sur-
vey technique for eliminating evasive answer bias. Journal of the American
Statistical Association, 60, 63–69, <doi:10.2307/2283137>). Besides univari-
ate estimates of true proportions, RR variables can be used for correlations,
as dependent variable in a logistic regression (with or without random ef-
fects), or as predictors in a linear regression (Heck, D. W., & Moshagen,
M. (2018). RRreg: An R package for correlation and regression analyses
of randomized response data. Journal of Statistical Software, 85(2), 1–29,
<doi:10.18637/jss.v085.i02>). For simulations and the estimation of statisti-
cal power, RR data can be generated according to several models. The im-
plemented methods also allow to test the link between continuous covariates
and dishonesty in cheating paradigms such as the coin-toss or dice-roll task
(Moshagen, M., & Hilbig, B. E. (2017). The statistical analysis of cheating
paradigms. Behavior Research Methods, 49, 724–732, <doi:10.3758/s13428-
016-0729-x>). / GPL-3
r-rrscale 0.1.3 Non-linear transformations of data to better discover latent effects. Applies noarch
a sequence of three transformations (1) a Gaussianizing transformation, (2) a
Z-score transformation, and (3) an outlier removal transformation. / GPL-3
r-rsadbe 1.0 The package contains all the data sets related to the book written by the main- noarch
tainer of the package. / GPL-2


Name Version
r-rsampling 0.1.1 Resampling Stats (http://www.resample.com) is an add-in for running random- noarch
ization tests in Excel worksheets. The workflow is (1) to define a statistic of
interest that can be calculated from a data table, (2) to randomize rows ad/or
columns of a data table to simulate a null hypothesis and (3) and to score the
value of the statistic from many randomizations. The relative frequency dis-
tribution of the statistic in the simulations is then used to infer the probability
of the observed value be generated by the null process (probability of Type I
error). This package intends to translate this logic for R for teaching purposes.
Keeping the original workflow is favored over performance. / GPL-2
r-rsarules 1.0 Implements the Gibbs sampling algorithm to randomly sample association noarch
rules with one pre-chosen item as the consequent from a transaction dataset.
The Gibbs sampling algorithm was proposed in G. Qian, C.R. Rao, X. Sun and
Y. Wu (2016) <DOI:10.1073/pnas.1604553113>. / GPL-3
r-rsatscan 0.3.9200
SaTScan(TM) (http://www.satscan.org) is software for finding regions in noarch
Time, Space, or Time-Space that have excess risk, based on scan statistics,
and uses Monte Carlo hypothesis testing to generate P-values for these regions.
The rsatscan package provides functions for writing R data frames in SaTScan-
readable formats, for setting SaTScan parameters, for running SaTScan in the
OS, and for reading the files that SaTScan creates. / GPL-3
r-rsaucelabs 0.1.6 Retrieve, update, delete job information from <https://saucelabs.com/>. Poll noarch
the ‘SauceLabs’ services current status and access supported platforms. Send
and retrieve files from ‘SauceLabs’ and manage tunnels associated with
‘SauceConnect’. / GPL-3
r-rsca 3.0 A statistical tool for multivariate modeling and clustering using stepwise clus- noarch
ter analysis. The modeling output of rSCA is constructed as a cluster tree to
represent the complicated relationships between multiple dependent and in-
dependent variables. A free tool (named rSCA Tree Generator) for visualiz-
ing the cluster tree from rSCA is also released and it can be downloaded at
<https://rscatree.weebly.com/>. / GPL-2
r-rscala 3.2.15‘Scala’ <http://www.scala-lang.org/> is embedded in ‘R’ and callbacks from noarch
‘Scala’ to ‘R’ are available. Support is provided to write ‘R’ packages that
access ‘Scala’. After installation, please run ‘rscala::scalaConfig()’. / Apache
License 2.0 | file LICENSE
r-rsconnect 0.8.13Programmatic deployment interface for ‘RPubs’, ‘shinyapps.io’, and ‘RStudio linux-
Connect’. Supported content types include R Markdown documents, Shiny 32,
applications, Plumber APIs, plots, and static web content. / GPL-2 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rsdmx 0.5_13Set of classes and methods to read data and metadata documents exchanged noarch
through the Statistical Data and Metadata Exchange (SDMX) framework, cur-
rently focusing on the SDMX XML standard format (SDMX-ML). / GPL-2


Name Version
r-rse 1.3 A Bayesian-weighted estimator and two unweighted estimators are developed noarch
to estimate the number of newly found rare species in additional ecological
samples. Among these methods, the Bayesian-weighted estimator and an un-
weighted (Chao-derived) estimator are of high accuracy and recommended for
practical applications. Technical details of the proposed estimators have been
well described in the following paper: Shen TJ, Chen YH (2018) A Bayesian
weighted approach to predicting the number of newly discovered rare species.
Conservation Biology, In press. / GPL-3
r-rseedcalc 1.3 Estimate the percentage of seeds in a seedlot that contain stacks of genetically noarch
modified traits. Estimates are calculated using a multinomial group testing
model with maximum likelihood estimation of the parameters. / GPL-2
r-rsem 0.4.6 A robust procedure is implemented to estimate means and covariance matrix of noarch
multiple variables with missing data using Huber weight and then to estimate
a structural equation model. / GPL-2
r-rserve 1.7_3.1
Rserve acts as a socket server (TCP/IP or local sockets) which allows binary linux-
requests to be sent to R. Every connection has a separate workspace and work- 32,
ing directory. Client-side implementations are available for popular languages linux-
such as C/C and Java, allowing any application to use facilities of R without 64,
the need of linking to R code. Rserve supports remote connection, user au- osx-
thentication and file transfer. A simple R client is included in this package as 64,
well. / GPL-2 | file LICENSE win-
32,
win-
64
r-rsfa 1.04 Slow Feature Analysis in R, ported to R based on the matlab versions SFA noarch
toolkit 1.0 by Pietro Berkes and SFA toolkit 2.8 by Wolfgang Konen for mat-
lab. / GPL-2
r-rsitecatalyst 1.4.15Functions for interacting with the Adobe Analytics API V1.4 (<https://api. noarch
omniture.com/admin/1.4/rest/>). / MIT
r-rskey 0.4.1 Create custom keyboard shortcuts to examine code selected in the ‘Rstudio’ noarch
editor. F3 can for example yield ‘str(selection)’ and F7 open the source code
of CRAN and base package functions on ‘github’. / GPL-2
r-rslp 0.1.0 Implements the Stemming Algorithm for the Portuguese Language noarch
<DOI:10.1109/SPIRE.2001.10024>. / MIT
r-rslurm 0.4.0 Functions that simplify submitting R scripts to a Slurm workload manager, in noarch
part by automating the division of embarrassingly parallel calculations across
cluster nodes. / GPL-3
r-rsm 2.10 Provides functions to generate response-surface designs, fit first- and second- noarch
order response-surface models, make surface plots, obtain the path of steepest
ascent, and do canonical analysis. A good reference on these methods is Chap-
ter 10 of Wu, C-F J and Hamada, M (2009) Experiments: Planning, Analysis,
and Parameter Design Optimization ISBN 978-0-471-69946-0. / GPL-2
r-rsmartlyio 0.1.3 Aims at loading Facebook and Instagram advertising data from ‘Smartly.io’ noarch
into R. ‘Smartly.io’ is an online advertising service that enables advertisers to
display commercial ads on social media networks (see <http://www.smartly.
io/> for more information). The package offers an interface to query the
‘Smartly.io’ API and loads data directly into R for further data processing and
data analysis. / MIT


Name Version
r-rsocrata 1.7.9_5
Provides easier interaction with ‘Socrata’ open data portals <http://dev.socrata. noarch
com>. Users can provide a ‘Socrata’ data set resource URL, or a ‘Socrata’
Open Data API (SoDA) web query, or a ‘Socrata’ human-friendly URL, re-
turns an R data frame. Converts dates to ‘POSIX’ format and manages throt-
tling by ‘Socrata’. Users can upload data to ‘Socrata’ portals directly from R.
/ MIT
r-rsoi 0.5.0 Downloads Southern Oscillation Index, Oceanic Nino Index, North Pacific noarch
Gyre Oscillation data, North Atlantic Oscillation and Arctic Oscillation. Data
sources are described in the README file. / GPL-3
r-rspc 1.2.2 Implementation of Nelson rules for control charts in ‘R’. The ‘Rspc’ imple- noarch
ments some Statistical Process Control methods, namely Levey-Jennings type
of I (individuals) chart, Shewhart C (count) chart and Nelson rules (as de-
scribed in Montgomery, D. C. (2013) Introduction to statistical quality control.
Hoboken, NJ: Wiley.). Typical workflow is taking the time series, specify the
control limits, and list of Nelson rules you want to evaluate. There are several
options how to modify the rules (one sided limits, numerical parameters of
rules, etc.). Package is also capable of calculating the control limits from the
data (so far only for i-chart and c-chart are implemented). / GPL-3
r-rspde 0.4.6 Functions that compute rational approximations of fractional elliptic stochastic noarch
partial differential equations. The package also contains functions for common
statistical usage of these approximations. The main reference for the methods
is Bolin and Kirchner (2019) <arXiv:1711.04333>, which can be generated by
the citation function in R. / GPL-3
r-rspincalc 1.0.2 Conversion between attitude representations: DCM, Euler angles, Quater- noarch
nions, and Euler vectors. Plus conversion between 2 Euler angle set types (xyx,
yzy, zxz, xzx, yxy, zyz, xyz, yzx, zxy, xzy, yxz, zyx). Fully vectorized code,
with warnings/errors for Euler angles (singularity, out of range, invalid angle
order), DCM (orthogonality, not proper, exceeded tolerance to unity determi-
nant) and Euler vectors(not unity). Also quaternion and other useful functions.
Based on SpinCalc by John Fuller and SpinConv by Paolo de Leva. / GPL-3
r-rsps 1.0 Provides functions for estimating power or sample size for RNA-Seq studies. noarch
Empirical approach is used and the data is assumed to be count in nature. The
underlying distribution of data is assumed to be Poisson or negative binomial.
The package contains 6 function; 4 functions provide estimates of sample size
or power for Poisson and Negative Binomial distribution; 2 functions provide
plots of power for given sample size or sample size for given power. / GPL-2
r-rsq 1.1 Calculate generalized R-squared, partial R-squared, and partial correlation co- noarch
efficients for generalized linear models (including quasi models with well de-
fined variance functions). / GPL-2
r-rsqlite 2.1.1 Embeds the ‘SQLite’ database engine in R and provides an interface compliant linux-
with the ‘DBI’ package. The source for the ‘SQLite’ engine is included. / 32,
LGPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
r-rssop 1.1 Reservoir Systems Standard Operation Policy. A system for simulation of noarch
supply reservoirs. It proposes functionalities for plotting and evaluation of
supply reservoirs systems. / GPL-2
r-rstack 1.0.0 An extremely simple stack data type, implemented with ‘R6’ classes. The size noarch
of the stack increases as needed, and the amortized time complexity is O(1).
The stack may contain arbitrary objects. / MIT
r-rstackdeque 1.1.1 Provides fast, persistent (side-effect-free) stack, queue and deque (double- noarch
ended-queue) data structures. While deques include a superset of function-
ality provided by queues, in these implementations queues are more efficient
in some specialized situations. See the documentation for rstack, rdeque, and
rpqueue for details. / MIT
r-rstan 2.18.2User-facing R functions are provided to parse, compile, test, estimate, and an- linux-
alyze Stan models by accessing the header-only Stan library provided by the 32,
‘StanHeaders’ package. The Stan project develops a probabilistic program- linux-
ming language that implements full Bayesian statistical inference via Markov 64,
Chain Monte Carlo, rough Bayesian inference via ‘variational’ approximation, osx-
and (optionally penalized) maximum likelihood estimation via optimization. 64,
In all three cases, automatic differentiation is used to quickly and accurately win-
evaluate gradients without burdening the user with the need to derive the par- 32,
tial derivatives. / GPL (>= 3) win-
64
r-rstantools 1.5.1 Provides various tools for developers of R packages interfacing with ‘Stan’ noarch
<http://mc-stan.org>, including functions to set up the required package struc-
ture, S3 generics and default methods to unify function naming across ‘Stan’-
based R packages, and vignettes with recommendations for developers. / GPL-
3
r-rstata 1.1.1 A simple R -> Stata interface allowing the user to execute Stata commands noarch
(both inline and from a .do file) from R. / GPL-3
r-rstatscn 1.1.3 R interface for china national data <http://data.stats.gov.cn/>, some convenient noarch
functions for accessing the national data are provided. / Apache License 2.0
r-rstorm 1.0 While streaming processing provides opportunities to deal with extremely noarch
large and ever growing data sets in (near) real time, the development of stream-
ing algorithms for complex models is often cumbersome: the software pack-
ages that facilitate streaming processing in production environments do not
provide statisticians with the simulation, estimation, and plotting tools they
are used to. Developers of streaming algorithms would thus benefit from the
flexibility of [R] to create, plot and compute data while developing streaming
algorithms. Package RStorm implements a streaming architecture modeled
on Storm for easy development and testing of streaming algorithms in [R].
RStorm is not intended as a production package, but rather a development tool
for streaming algorithms. / GPL-2
r-rstripe 0.1 A convenience interface for communicating with the Stripe payment processor noarch
to accept payments online. See <https://stripe.com> for more information. /
MIT


Name Version
r-rstudioapi 0.10 Access the RStudio API (if available) and provide informative error messages linux-
when it’s not. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rsubgroup 0.6 A collection of efficient and effective tools and algorithms for subgroup noarch
discovery and analytics. The package integrates an R interface to the
org.vikamine.kernel library of the VIKAMINE system (http://www.vikamine.
org) implementing subgroup discovery, pattern mining and analytics in Java. /
GPL-3
r-rsurfer 0.2 The software suite, ‘Freesurfer’, is a open-source software suite involving the noarch
segmentation of brain MRIs (see <http://freesurfer.net/> for more informa-
tion). This package provides functionality to import the data generated by
‘Freesurfer’; functions to easily manipulate the data; and provides brain spe-
cific normalisation commonly used when studying structural brain MRIs. This
package has been designed using an installation of and data generated from
‘Freesurfer’ version 5.3. / MIT
r-rsurrogate 2.0 Provides functions to estimate the proportion of treatment effect on the primary noarch
outcome that is explained by the treatment effect on the surrogate marker. /
GPL-3
r-rsvd 1.0.2 Low-rank matrix decompositions are fundamental tools and widely used for noarch
data analysis, dimension reduction, and data compression. Classically, highly
accurate deterministic matrix algorithms are used for this task. However, the
emergence of large-scale data has severely challenged our computational abil-
ity to analyze big data. The concept of randomness has been demonstrated
as an effective strategy to quickly produce approximate answers to familiar
problems such as the singular value decomposition (SVD). The rsvd package
provides several randomized matrix algorithms such as the randomized sin-
gular value decomposition (rsvd), randomized principal component analysis
(rpca), randomized robust principal component analysis (rrpca), randomized
interpolative decomposition (rid), and the randomized CUR decomposition
(rcur). In addition several plot functions are provided. The methods are dis-
cussed in detail by Erichson et al. (2016) <arXiv:1608.02148>. / GPL-3
r-rt.test 1.18.7.9
Performs one-sample t-test based on robustified statistics using median/MAD noarch
(TA) and Hodges-Lehmann/Shamos (TB). For more details, see Park and
Wang (2018)<arXiv:1807.02215>. This work was partially supported by the
National Research Foundation of Korea (NRF) grant funded by the Korea gov-
ernment (No. NRF-2017R1A2B4004169). / GPL-2 | GPL-3
r-rt3 0.1.2 Play the classic game of tic-tac-toe (naughts and crosses). / MIT noarch


Name Version
r-rtape 2.2 Storing huge data in RData format causes problems because of the necessity noarch
to load the whole file to the memory in order to access and manipulate objects
inside such file; rtape is a simple solution to this problem. The package con-
tains several wrappers of R built-in serialize/unserialize mechanism allowing
user to quickly append objects to a tape-like file and later iterate over them
requiring only one copy of each stored object to reside in memory a time. /
GPL-2
r-rtauchen 1.0 Discretize AR(1) process following Tauchen (1986) <http://www. noarch
sciencedirect.com/science/article/pii/0165176586901680>. A discrete
Markov chain that approximates in the sense of weak convergence a
continuous-valued univariate Autoregressive process of first order is gener-
ated. It is a popular method used in economics and in finance. / GPL-2
r-rtaxometrics 2.3 We provide functions to perform taxometric analyses. This package contains noarch
44 functions, but only 5 should be called directly by users. CheckData() should
be run prior to any taxometric analysis to ensure that the data are appropriate
for taxometric analysis. RunTaxometrics() performs taxometric analyses for
a sample of data. RunCCFIProfile() performs a series of taxometric analyses
to generate a CCFI profile. CreateData() generates a sample of categorical or
dimensional data. ClassifyCases() assigns cases to groups using the base-rate
classification method. / MIT
r-rtconnect 0.1.4 Tools for analyzing sales report files of iTunes Connect. / GPL-3 noarch
r-rtde 0.2_0 Robust tail dependence estimation for bivariate models. This package is based noarch
on two papers by the authors:’Robust and bias-corrected estimation of the
coefficient of tail dependence’ and ‘Robust and bias-corrected estimation of
probabilities of extreme failure sets’. This work was supported by a research
grant (VKR023480) from VILLUM FONDEN and an international project for
scientific cooperation (PICS-6416). / GPL-2
r-rtematres 0.2 Exploit controlled vocabularies organized on tematres servers. / GPL-3 noarch
r-rtensor 1.4 A set of tools for creation, manipulation, and modeling of tensors with arbi- noarch
trary number of modes. A tensor in the context of data analysis is a multidi-
mensional array. rTensor does this by providing a S4 class ‘Tensor’ that wraps
around the base ‘array’ class. rTensor provides common tensor operations as
methods, including matrix unfolding, summing/averaging across modes, cal-
culating the Frobenius norm, and taking the inner product between two tensors.
Familiar array operations are overloaded, such as index subsetting via ‘[’ and
element-wise operations. rTensor also implements various tensor decompo-
sition, including CP, GLRAM, MPCA, PVD, and Tucker. For tensors with 3
modes, rTensor also implements transpose, t-product, and t-SVD, as defined in
Kilmer et al. (2013). Some auxiliary functions include the Khatri-Rao prod-
uct, Kronecker product, and the Hamadard product for a list of matrices. /
GPL-2
r-rtephra 0.1 Models and displays tephra transport through custom (windy, turbulent, het- noarch
erogeneous) atmosphere over custom topography. Includes a Lagrangian
(particle-tracking) tephra transport model and a function to save snapshots of
model as png files. / GPL-3
r-rtexturemetrics 1.1 This package contains several functions for calculation of texture metrics for noarch
Grey Level Co-occurrence matrices / GPL-2
r-rtf 0.4_14A set of R functions to output Rich Text Format (RTF) files with high reso- noarch
lution tables and graphics that may be edited with a standard word processor
such as Microsoft Word. / GPL-2


Name Version
r-rticles 0.10 A suite of custom R Markdown formats and templates for authoring journal noarch
articles and conference submissions. / GPL-3
r-rtika 1.22 Extract text or metadata from over a thousand file types, using Apache Tika noarch
<https://tika.apache.org/>. Get either plain text or structured XHTML content.
/ Apache License 2.0 | file LICENSE
r-rtnmin 2016_7.7
Truncated Newton function minimization with bounds constraints based on the noarch
‘Matlab’/’Octave’ codes of Stephen Nash. / GPL-2
r-rtorch 0.0.3 ‘R’ implementation and interface of the Machine Learning platform ‘PyTorch’ noarch
<https://pytorch.org/> developed in ‘Python’. It requires a ‘conda’ environ-
ment with ‘torch’ and ‘torchvision’ to provide ‘PyTorch’ functions, methods
and classes. The key object in ‘PyTorch’ is the tensor which is in essence a
multidimensional array. These tensors are fairly flexible to perform calcula-
tions in CPUs as well as ‘GPUs’ to accelerate the process. / MIT
r-rtrim 2.0.6 The TRIM model is widely used for estimating growth and decline noarch
of animal populations based on (possibly sparsely available) count
data. The current package is a reimplementation of the original
TRIM software developed at Statistics Netherlands by Jeroen Pan-
nekoek. See <https://www.cbs.nl/en-gb/society/nature-and-environment/
indices-and-trends%2d%2dtrim%2d%2d> for more information about TRIM.
/ EUPL
r-rts 1.0_49This framework aims to provide classes and methods for manipulating and noarch
processing of raster time series data (e.g. a time series of satellite images). /
GPL-3
r-rtson 1.3 TSON, short for Typed JSON, is a binary-encoded serialization of JSON noarch
like document that support JavaScript typed data (https://github.com/tercen/
TSON). / Apache License Version 2.0
r-rtsplot 0.1.1 A fast and elegant time series visualization package. In addition to the standard noarch
R plot types, this package supports candle sticks, open-high-low-close, and
volume plots. Useful for visualizing any time series data, e.g., stock prices
and technical indicators. / MIT
r-rtwalk 1.8.0 The ‘t-walk’ is a general-purpose MCMC sampler for arbitrary continuous noarch
distributions that requires no tuning. / GPL-3
r-rtype 0.1_1 A strong type system for R which supports symbol declaration and assignment noarch
with type checking and condition checking. / MIT
r-runit 0.4.32R functions implementing a standard Unit Testing framework, with additional linux-
code inspection and report generation tools. / GPL-2 64,
noarch,
osx-
64,
win-
64
r-runiversal 1.0.2 This package contains some functions for converting R objects to Java style noarch
variables and XML. Generated Java code is interpretable by dynamic Java
libraries such as Beanshell. Calling R externally and handling the Java or XML
output is an other way to call R from other languages without native interfaces.
For a Java implementation of this approach visit http://www.mhsatman.com/
rcaller.php and http://stdioe.blogspot.com/search/label/rcaller / GPL-3


Name Version
r-runstats 1.0.1 Provides methods for fast computation of running sample statistics for time noarch
series. These include: (1) mean, (2) standard deviation, and (3) variance over
a fixed-length window of time-series, (4) correlation, (5) covariance, and (6)
Euclidean distance (L2 norm) between short-time pattern and time-series. Im-
plemented methods utilize Convolution Theorem to compute convolutions via
Fast Fourier Transform (FFT). / GPL-3
r-ruta 1.1.0 Implementation of several unsupervised neural networks, from building noarch
their architecture to their training and evaluation. Available networks
are auto-encoders including their main variants: sparse, contractive, de-
noising, robust and variational, as described in Charte et al. (2018)
<doi:10.1016/j.inffus.2017.12.007>. / GPL-3
r-rv 2.3.3 Implements a simulation-based random variable class and a suite of methods noarch
for extracting parts of random vectors, calculating extremes of random vec-
tors, and generating random vectors under a variety of distributions following
Kerman and Gelman (2007) <doi:10.1007/s11222-007-9020-4>. / GPL-2
r-rvcheck 0.1.3 Check latest release version of R and R package (both in ‘CRAN’, ‘Biocon- noarch
ductor’ or ‘Github’). / Artistic-2.0
r-rversions 1.1.0 Query the main ‘R’ ‘SVN’ repository to find the versions ‘r-release’ and ‘r- linux-
oldrel’ refer to, and also all previous ‘R’ versions and their release dates. / 32,
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rvest 0.3.3 Wrappers around the ‘xml2’ and ‘httr’ packages to make it easy to download, linux-
then manipulate, HTML and XML. / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-rvhpdt 3.0 To detecting rare variants for binary traits using general pedigrees, the pedi- noarch
gree disequilibrium tests are proposed by collapsing rare haplotypes/variants
with/without weights. To run the test, MERLIN is needed in Linux for haplo-
typing. / GPL-2
r-rviennacl 1.7.1.8‘ViennaCL’ is a free open-source linear algebra library for computations on noarch
many-core architectures (GPUs, MIC) and multi-core CPUs. The library
is written in C and supports ‘CUDA’, ‘OpenCL’, and ‘OpenMP’ (including
switches at runtime). I have placed these libraries in this package as a more ef-
ficient distribution system for CRAN. The idea is that you can write a package
that depends on the ‘ViennaCL’ library and yet you do not need to distribute a
copy of this code with your package. / GPL-3


Name Version
r-rviewgraph 1.2 This is an ‘R’ interface to Alun Thomas’s ‘ViewGraph’ ‘Java’ graph viewing noarch
program. It takes a graph specified as an incidence matrix, list of edges, or in
‘igraph’ format and runs a graphical user interface that shows an animation of
a force directed algorithm positioning the vertices in two dimensions. It works
well for graphs of various structure of up to a few thousand vertices. It’s not
fazed by graphs that comprise several components. The coordinates can be
read as an ‘igraph’ style layout matrix at any time. The user can mess with
the layout using a mouse, preferably one with 3 buttons, and some keyed com-
mands. The ‘Java’ program ‘ViewGraph’ is contained in Alun Thomas’s ‘JPS-
GCS’ collection of ‘Java’ programs for statistical genetics and computational
statistics. The homepage for ‘JPSGCS’ is <http://www-genepi.med.utah.edu/
~alun/software/index.html>. The documentation page for ‘ViewGraph’ is at
<http://www-genepi.med.utah.edu/~alun/software/docs/ViewGraph.html>. /
GPL-2
r-rvtdt 1.0 Used to compute population controls weighted rare variants transmission dis- noarch
tortion test / GPL-3
r-rwars 1.0.0 Provides functions to retrieve and reformat data from the ‘Star Wars’ API noarch
(SWAPI) <https://swapi.co/>. / MIT
r-rwc 1.11 Code to facilitate simulation and inference when connectivity is de- noarch
fined by underlying random walks. Methods for spatially-correlated
pairwise distance data are especially considered. This provides core
code to conduct analyses similar to that in Hanks and Hooten (2013)
<doi:10.1080/01621459.2012.724647>. / GPL-2
r-rweblogo 1.0.3 RWebLogo is a wrapper for the WebLogo python package that allows gener- noarch
ating of customised sequence logos. Sequence logos are graphical representa-
tions of the sequence conservation of nucleotides (in a strand of DNA/RNA) or
amino acids (in protein sequences). Each logo consists of stacks of symbols,
one stack for each position in the sequence. The overall height of the stack in-
dicates the sequence conservation at that position, while the height of symbols
within the stack indicates the relative frequency of each amino or nucleic acid
at that position. In general, a sequence logo provides a richer and more precise
description of, for example, a binding site, than would a consensus sequence.
/ BSD_3_clause
r-rwekajars 3.9.3_1
External jars required for package ‘RWeka’. / GPL-2 noarch
r-rwhois 1.0.3 Queries data from WHOIS servers. / MIT noarch
r-rwinsteps 1.0_1.1
Facilitates communication between R and the Rasch modeling software Win- noarch
steps. Currently includes functions for reading and writing command files,
sending them to Winsteps, reading and writing data according to command
file specifications, reading output into R, and plotting various results. / GPL-2
r-rwishart 0.1.1 An expansion of R’s ‘stats’ random wishart matrix generation. This noarch
package allows the user to generate singular, Uhlig and Harald (1994)
<doi:10.1214/aos/1176325375>, and pseudo wishart, Diaz-Garcia, et
al.(1997) <doi:10.1006/jmva.1997.1689>, matrices. In addition the user
can generate wishart matrices with fractional degrees of freedom, Ad-
hikari (2008) <doi:10.1061/(ASCE)0733-9399(2008)134:12(1029)>, com-
monly used in volatility modeling. Users can also use this package to create
random covariance matrices. / GPL-2
r-rworldxtra 1.01 High resolution vector country boundaries derived from Natural Earth data, noarch
can be plotted in rworldmap. / GPL-2


Name Version
r-rxkcd 1.8_2 Visualize your favorite XKCD comic strip directly from R. XKCD <https: noarch
//xkcd.com> web comic content is provided under the Creative Commons
Attribution-NonCommercial 2.5 License. / GPL-2
r-rxnat 1.0.6 Allows communication with Extensible Neuroimaging Archive Toolkit <https: noarch
//www.xnat.org>. ‘Rxnat’ is using the ‘XNAT’ REST API to perform data
queries and download images. / GPL-2
r-rxseq 0.99.3Analysis of combined total and allele specific reads from the reciprocal cross noarch
study with RNA-seq data. / GPL-2
r-rxshrink 1.1 Identify and display TRACEs for a specified shrinkage path and determine the noarch
extent of shrinkage most likely, under normal distribution theory, to produce
an optimal reduction in MSE Risk in estimates of regression (beta) coeffi-
cients. Alternative estimates are also provided when ill-conditioned (nearly
multicollinear) models yield OLS estimates with wrong numerical signs. /
GPL-3
r- 1.0 ‘Yandex Translate’ (https://translate.yandex.com/) is a statistical machine noarch
ryandextranslate translation system. The system translates separate words, complete texts, and
webpages. This package can be used to detect language from text and to trans-
late it to supported target language. For more info: https://tech.yandex.com/
translate/doc/dg/concepts/About-docpage/ . / MIT
r-rym 0.5.2 Allows work with ‘Management API’ for load counters, segments, filters, noarch
user permissions and goals list from Yandex Metrica, ‘Reporting API’ al-
lows you to get information about the statistics of site visits and other data
without using the web interface, ‘Logs API’ allows to receive non-aggregated
data and ‘Compatible with Google Analytics Core Reporting API v3’ allows
receive information about site traffic and other data using field names from
Google Analytics Core API. For more information see official documents
<https://tech.yandex.ru/metrika/doc/api2/concept/about-docpage/>. / GPL-2
r- 1.0 You can use this package to translate thousands of words. The Youdao trans- noarch
ryoudaotranslate lation open API is applied in this package. But, it just translates less than 1000
English words into Chinese. / GPL-2
r-ryoutheria 1.0.3 A programmatic interface to web-services of YouTheria. YouTheria is an on- noarch
line database of mammalian trait data <http://www.utheria.org/>. / MIT
r-rzabbix 0.1.0 R interface to the ‘Zabbix API’ data <https://www.zabbix.com/documentation/ noarch
3.0/manual/api/reference>. Enables easy and direct communication with ‘Zab-
bix API’ from ‘R’. / GPL-2
r-rzeit2 0.2.3 Interface to gather newspaper articles from ‘DIE ZEIT’ and ‘ZEIT ONLINE’, noarch
based on a multilevel query <http://developer.zeit.de/>. A personal API key is
required for usage. / MIT
r-rzmq 0.9.6 Interface to the ‘ZeroMQ’ lightweight messaging kernel (see <http://www. linux-
zeromq.org/> for more information). / GPL-3 32,
linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
r-s20x 3.1_28A set of functions used in teaching STATS 201/208 Data Analysis at the Uni- noarch
versity of Auckland. The functions are designed to make parts of R more
accessible to a large undergraduate population who are mostly not statistics
majors. / GPL-2
r-sabarsi 0.1.0 Implements a new approach ‘SABARSI’ described in Wang et al., A Statistical noarch
Approach of Background Removal and Spectrum Identification for SERS Data
(Unpublished). Sabarsi forms a pipeline for SERS (surface-enhanced Raman
scattering) data analysis including background removal, signal detection, sig-
nal integration, and cross-experiment comparison. The background removal
algorithm, the very first step of SERS data analysis, takes into account the
change of background shape. / GPL-3
r-sac 1.0.1 Semiparametric empirical likelihood ratio based test of changepoint with one- noarch
change or epidemic alternatives with data-based model diagnostic / GPL-2
r-sacobra 1.1 Performs surrogate-assisted optimization for expensive black-box constrained noarch
problems. / GPL-2
r-sadeg 1.0.0 We analyzed the nucleotide composition of genes with a special emphasis on noarch
stability of DNA sequences. Besides, in a variety of different organisms un-
equal use of synonymous codons, or codon usage bias, occurs which also show
variation among genes in the same genome. Seemingly, codon usage bias is
affected by both selective constraints and mutation bias which allows and en-
ables us to examine and detect changes in these two evolutionary forces be-
tween genomes or along one genome. Therefore, we determined the codon
adaptation index (CAI), effective number of codons (ENC) and codon usage
analysis with calculation of the relative synonymous codon usage (RSCU),
and subsequently predicted the translation efficiency and accuracy through
GC-rich codon usages. Furthermore, we estimated the relative stability of the
DNA sequence following calculation of the average free energy (Delta G) and
Dimer base-stacking energy level. / GPL-3
r-sae 1.2 Functions for small area estimation. / GPL-2 noarch
r-saemix 2.2 The SAEMIX package implements the Stochastic Approximation EM algo- noarch
rithm for parameter estimation in (non)linear mixed effects models. The
SAEM algorithm: - computes the maximum likelihood estimator of the pop-
ulation parameters, without any approximation of the model (linearisation,
quadrature approximation,. . . ), using the Stochastic Approximation Expecta-
tion Maximization (SAEM) algorithm, - provides standard errors for the max-
imum likelihood estimator - estimates the conditional modes, the conditional
means and the conditional standard deviations of the individual parameters,
using the Hastings-Metropolis algorithm. Several applications of SAEM in
agronomy, animal breeding and PKPD analysis have been published by mem-
bers of the Monolix group (<http://group.monolix.org/>). / GPL-2
r-saery 1.0 A complete set of functions to calculate several EBLUP (Empirical Best Linear noarch
Unbiased Predictor) estimators and their mean squared errors. All estimators
are based on an area-level linear mixed model introduced by Rao and Yu in
1994 (see documentation). The REML method is used for fitting this model. /
GPL-2


Name Version
r-safd 2.1 The aim of the package is to provide some basic functions for doing statistics noarch
with one dimensional Fuzzy Data (in the form of polygonal fuzzy numbers). In
particular, the package contains functions for the basic operations on the class
of fuzzy numbers (sum, scalar product, mean, median, Hukuhara difference) as
well as for calculating (Bertoluzza) distance and sample variance. Moreover a
function to simulate fuzzy random variables and bootstrap tests for the equality
of means is included. Version 2.1 fixes some bugs of previous versions. / GPL-
2
r-saic 1.0 Computes the Akaike information criterion for the generalized linear models noarch
(logistic regression, Poisson regression, and Gaussian graphical models) esti-
mated by the lasso. / GPL-2
r-saltsampler 1.1.0 The SALTSampler package facilitates Monte Carlo Markov Chain (MCMC) noarch
sampling of random variables on a simplex. A Self-Adjusting Logit Transform
(SALT) proposal is used so that sampling is still efficient even in difficult cases,
such as those in high dimensions or with parameters that differ by orders of
magnitude. Special care is also taken to maintain accuracy even when some
coordinates approach 0 or 1 numerically. Diagnostic and graphic functions
are included in the package, enabling easy assessment of the convergence and
mixing of the chain within the constrained space. / BSD_3_clause
r-salty 0.1.0 Take real or simulated data and salt it with errors commonly found in the wild, noarch
such as pseudo-OCR errors, Unicode problems, numeric fields with nonsensi-
cal punctuation, bad dates, etc. / MIT
r-sample.size 1.0 Computes the required sample size using the optimal designs with multiple noarch
constraints proposed in Mayo et al.(2010). This optimal method is designed
for two-arm, randomized phase II clinical trials, and the required sample size
can be optimized either using fixed or flexible randomization allocation ratios.
/ GPL-2
r-samplesize 0.2_4 Computes sample size for Student’s t-test and for the Wilcoxon-Mann- noarch
Whitney test for categorical data. The t-test function allows paired and un-
paired (balanced / unbalanced) designs as well as homogeneous and heteroge-
neous variances. The Wilcoxon function allows for ties. / GPL-2
r- 0.1.0 The design of phase 3 clinical trials can be classified into 4 types: (1) Testing noarch
samplesize4clinicaltrials for equality;(2) Superiority trial;(3) Non-inferiority trial; and (4) Equivalence
trial according to the goals. Given that none of the available packages com-
bines these designs in a single package, this package has made it possible for
researchers to calculate sample size when comparing means or proportions in
phase 3 clinical trials with different designs. The ssc function can calculate
the sample size with pre-specified type 1 error rate,statistical power and effect
size according to the hypothesis testing framework. Furthermore, effect size
is comprised of true treatment difference and non-inferiority or equivalence
margins which can be set in ssc function. (Reference: Yin, G. (2012). Clini-
cal Trial Design: Bayesian and Frequentist Adaptive Methods. John Wiley &
Sons.) / GPL-2
r-samplesizecmh 0.0.0 Calculates the power and sample size for Cochran-Mantel-Haenszel tests. noarch
There are also several helper functions for working with probability, odds,
relative risk, and odds ratio values. / GPL-2 | GPL-3
r- 0.0.6 To determine sample size for case-control studies to be analyzed using logistic noarch
samplesizelogisticcasecontrol
regression. / GPL-2


Name Version
r- 1.1 A set of R functions for calculating sample size requirements using three dif- noarch
samplesizemeans ferent Bayesian criteria in the context of designing an experiment to estimate
a normal mean or the difference between two normal means. Functions for
calculation of required sample sizes for the Average Length Criterion, the Av-
erage Coverage Criterion and the Worst Outcome Criterion in the context of
normal means are provided. Functions for both the fully Bayesian and the
mixed Bayesian/likelihood approaches are provided. / GPL-2
r- 1.0 A set of R functions for calculating sample size requirements using three dif- noarch
samplesizeproportions ferent Bayesian criteria in the context of designing an experiment to estimate
the difference between two binomial proportions. Functions for calculation of
required sample sizes for the Average Length Criterion, the Average Coverage
Criterion and the Worst Outcome Criterion in the context of binomial obser-
vations are provided. In all cases, estimation of the difference between two
binomial proportions is considered. Functions for both the fully Bayesian and
the mixed Bayesian/likelihood approaches are provided. / GPL-2
r- 1.0 Package provides the possibility to sampling complete datasets from a normal noarch
samplingdatacrt distribution to simulate cluster randomized trails for different study designs. /
GPL-3
r-sandwich 2.5_1 Model-robust standard error estimators for cross-sectional, time series, clus- linux-
tered, panel, and longitudinal data. / GPL-2 | GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-sanon 1.5 There are several functions to implement the method for analysis in a ran- noarch
domized clinical trial with strata with following key features. A stratified
Mann-Whitney estimator addresses the comparison between two randomized
groups for a strictly ordinal response variable. The multivariate vector of such
stratified Mann-Whitney estimators for multivariate response variables can be
considered for one or more response variables such as in repeated measure-
ments and these can have missing completely at random (MCAR) data. Non-
parametric covariance adjustment is also considered with the minimal assump-
tion of randomization. The p-value for hypothesis test and confidence interval
are provided. / GPL-2
r-sarp.moodle 0.3.10Provides a set of basic functions for creating Moodle XML output files suited noarch
for importing questions in Moodle (a learning management system, see <https:
//moodle.org/> for more information). / Artistic-2.0
r-sas7bdat 0.5 Read SAS files in the sas7bdat data format. / GPL-2 noarch
r-sascii 1.0 Using any importation code designed for SAS users to read ASCII files into noarch
sas7bdat files, the SAScii package parses through the INPUT block of a (.sas)
syntax file to design the parameters needed for a read.fwf function call. This
allows the user to specify the location of the ASCII (often a .dat) file and the
location of the .sas syntax file, and then load the data frame directly into R in
just one step. / GPL-2
r-sasmarkdown 0.4.3 Settings and functions to extend the ‘knitr’ ‘SAS’ engine. / MIT noarch


Name Version
r-sasmixed 1.0_4 Data sets and sample lmer analyses corresponding to the examples in Littell, noarch
Milliken, Stroup and Wolfinger (1996), SAS System for Mixed Models, SAS
Institute. / GPL-2
r-saspect 0.1_1 A statistical method for significant analysis of comparative proteomics based noarch
on LC-MS/MS Experiments / GPL-2
r-sautomata 0.1.0 Machine learning provides algorithms that can learn from data and make in- noarch
ferences or predictions. Stochastic automata is a class of input/output de-
vices which can model components. This work provides implementation an
inference algorithm for stochastic automata which is similar to the Viterbi al-
gorithm. Moreover, we specify a learning algorithm using the expectation-
maximization technique and provide a more efficient implementation of the
Baum-Welch algorithm for stochastic automata. This work is based on In-
ference and learning in stochastic automata was by Karl-Heinz Zimmer-
mann(2017) <doi:10.12732/ijpam.v115i3.15>. / GPL-3
r-saver 1.1.1 An implementation of a regularized regression prediction and empirical Bayes noarch
method to recover the true gene expression profile in noisy and sparse single-
cell RNA-seq data. See Huang M, et al (2018) <doi:10.1038/s41592-018-
0033-z> for more details. / GPL-2
r-saves 0.5 The purpose of this package is to be able to save and load only the needed noarch
variables/columns of a dataframe in special binary files (tar archives) - which
seems to be a lot faster method than loading the whole binary object (RData
files) via load() function, or than loading columns from SQLite/MySQL
databases via SQL commands (see vignettes). Performance gain on SSD
drives is a lot more sensible compared to basic load() function. The perfor-
mance improvement gained by loading only the chosen variables in binary
format can be useful in some special cases (e.g. where merging data tables is
not an option and very different datasets are needed for reporting), but be sure
if using this package that you really need this, as non-standard file formats are
used! / AGPL-3
r-sbf 1.1.1 Smooth Backfitting for additive models using Nadaraya-Watson estimator / noarch
GPL-2
r-sbgcop 0.980 Estimation and inference for parameters in a Gaussian copula model, treating noarch
the univariate marginal distributions as nuisance parameters as described in
Hoff (2007) <doi:10.1214/07-AOAS107>. This package also provides a semi-
parametric imputation procedure for missing multivariate data. / GPL-2
r-sbl 0.1.0 Implements sparse Bayesian learning method for QTL mapping and genome- noarch
wide association studies. / GPL-3


Name Version
r-sbrect 0.26 The package uses fitting axes-aligned rectangles to a time series in order to noarch
find structural breaks. The algorithm enclose the time series in a number of
axes-aligned rectangles and tries to minimize their area and number. As these
are conflicting aims, the user has to specify a parameter alpha in [0.0,1.0]. Val-
ues close to 0 result in more breakpoints, values close to 1 in fewer. The left
edges of the rectangles are the breakpoints. The package supplies two meth-
ods, computeBreakPoints(series,alpha) which returns the indices of the break
points and computeRectangles(series,alpha) which returns the rectangles. The
algorithm is randomised; it uses a genetic algorithm. Therefore, the break
point sequence found can be different in different executions of the method on
the same data, especially when used on longer series of some thousand obser-
vations. The algorithm uses a range-tree as background data structure which
makes i very fast and suited to analyse series with millions of observations. A
detailed description can be found in Paul Fischer, Astrid Hilbert, Fast detection
of structural breaks, Proceedings of Compstat 2014. / GPL-2
r-sbsdiff 0.1.0 Calculates a Satorra-Bentler scaled chi-squared difference test between nested noarch
models that were estimated using maximum likelihood (ML) with robust stan-
dard errors, which cannot be calculated the traditional way. For details see
Satorra & Bentler (2001) <doi:10.1007/bf02296192> and Satorra & Bentler
(2010) <doi:10.1007/s11336-009-9135-y>. This package may be particularly
helpful when used in conjunction with ‘Mplus’ software, specifically when
implementing the complex survey option. In such cases, the model estimator
in ‘Mplus’ defaults to ML with robust standard errors. / MIT
r-scagnostics 0.2_4.1
Calculates graph theoretic scagnostics. Scagnostics describe various measures noarch
of interest for pairs of variables, based on their appearance on a scatterplot.
They are useful tool for discovering interesting or unusual scatterplots from
a scatterplot matrix, without having to look at every individual plot. / file
LICENSE (FOSS)
r-scales 1.0.0 Graphical scales map data to aesthetics, and provide methods for automatically linux-
determining breaks and labels for axes and legends. / MIT file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-scalreg 1.0.1 Algorithms for fitting scaled sparse linear regression and estimating precision noarch
matrices. / GPL-2
r-scam 1.2_5 Routines for generalized additive modelling under shape constraints on noarch
the component functions of the linear predictor (Pya and Wood, 2015)
<doi:10.1007/s11222-013-9448-7>. Models can contain multiple shape con-
strained (univariate and/or bivariate) and unconstrained terms. The routines of
gam() in package ‘mgcv’ are used for setting up the model matrix, printing
and plotting the results. Penalized likelihood maximization based on Newton-
Raphson method is used to fit a model with multiple smoothing parameter
selection by GCV or UBRE/AIC. / GPL-2
r-scatterd3 0.9 Creates ‘D3’ ‘JavaScript’ scatterplots from ‘R’ with interactive features : pan- noarch
ning, zooming, tooltips, etc. / GPL-3
r-scatterplot3d 0.3_41Plots a three dimensional (3D) point cloud. / GPL-2 noarch


Name Version
r-scbmeanfd 1.2.2 Statistical methods for estimating and inferring the mean of functional data. noarch
The methods include simultaneous confidence bands, local polynomial fitting,
bandwidth selection by plug-in and cross-validation, goodness-of-fit tests for
parametric models, equality tests for two-sample problems, and plotting func-
tions. / GPL-3
r-scdensity 1.0.2 Implements methods for obtaining kernel density estimates subject to a va- noarch
riety of shape constraints (unimodality, bimodality, symmetry, tail mono-
tonicity, bounds, and constraints on the number of inflection points). En-
forcing constraints can eliminate unwanted waves or kinks in the esti-
mate, which improves its subjective appearance and can also improve sta-
tistical performance. The main function scdensity() is very similar to the
density() function in ‘stats’, allowing shape-restricted estimates to be ob-
tained with little effort. The methods implemented in this package are de-
scribed in Wolters and Braun (2017) <doi:10.1080/03610918.2017.1288247>,
Wolters (2012) <doi:10.18637/jss.v047.i06>, and Hall and Huang (2002)
<http://www3.stat.sinica.edu.tw/statistica/j12n4/j12n41/j12n41.htm>. See the
scdensity() help for for full citations. / GPL-2
r-scdhlm 0.3.1 Provides a set of tools for estimating hierarchical linear models and effect noarch
sizes based on data from single-case designs. Functions are provided for
calculating standardized mean difference effect sizes that are directly com-
parable to standardized mean differences estimated from between-subjects
randomized experiments, as described in Hedges, Pustejovsky, and Shadish
(2012) <DOI:10.1002/jrsm.1052>; Hedges, Pustejovsky, and Shadish (2013)
<DOI:10.1002/jrsm.1086>; and Pustejovsky, Hedges, and Shadish (2014)
<DOI:10.3102/1076998614547577>. Includes an interactive web interface.
/ GPL-3
r-scenario 1.0 Uses the neural gas algorithm to construct a scenario tree for use in multi- noarch
stage stochastic programming. The primary input is a set of initial scenarios
or realizations of a disturbance. The scenario tree nodal structure must be
predefined using a scenario tree nodal partition matrix. / GPL-2
r-schoenberg 2.0.2 Functions for creating and manipulating 12-tone (i.e., dodecaphonic) musical noarch
matrices using Arnold Schoenberg’s (1923) serialism technique. This package
can generate random 12-tone matrices and can generate matrices using a pre-
determined sequence of notes. / GPL-3
r-schoolmath 0.4 This package contains functions and datasets for math taught in school. A noarch
main focus is set to prime-calculation / GPL-2
r-schorsch 1.6 Offers a helping hand to psychologists and other behavioral scientists who rou- noarch
tinely deal with experimental data from factorial experiments. It includes sev-
eral functions to format output from other R functions according to the style
guidelines of the APA (American Psychological Association). This format-
ted output can be copied directly into manuscripts to facilitate data reporting.
These features are backed up by a toolkit of several small helper functions, e.g.,
offering out-of-the-box outlier removal. The package lends its name to Georg
Schorsch Schuessler, ingenious technician at the Department of Psychology
III, University of Wuerzburg. For details on the implemented methods, see
Roland Pfister and Markus Janczyk (2016) <doi: 10.20982/tqmp.12.2.p147>.
/ GPL-3


Name Version
r-schumaker 1.1 This is a shape preserving spline <doi:10.1137/0720057> which is guaranteed noarch
to be monotonic and concave or convex if the data is monotonic and concave or
convex. It does not use any optimisation and is therefore quick and smoothly
converges to a fixed point in economic dynamics problems including value
function iteration. It also automatically gives the first two derivatives of the
spline and options for determining behaviour when evaluated outside the in-
terpolation domain. / MIT
r-scico 1.1.0 Colour choice in information visualisation is important in order to avoid being noarch
mislead by inherent bias in the used colour palette. The ‘scico’ package pro-
vides access to the perceptually uniform and colour-blindness friendly palettes
developed by Fabio Crameri and released under the Scientific Colour-Maps
moniker. The package contains 24 different palettes and includes both diverg-
ing and sequential types. / MIT
r-scientotext 0.1 It involves bibliometric indicators calculation from bibliometric data.It also noarch
deals pattern analysis using the text part of bibliometric data.The bibliometric
data are obtained from mainly Web of Science and Scopus. / GPL-3
r-scifigure 0.2 Users may specify what fundamental qualities of a new study have or have not noarch
changed in an attempt to reproduce or replicate an original study. A compar-
ison of the differences is visualized. Visualization approach follows ‘Patil’,
‘Peng’, and ‘Leek’ (2016) <doi:10.1101/066803>. / MIT
r-scina 1.2.0 An automatic cell type detection and assignment algorithm for single cell noarch
RNA-Seq and Cytof/FACS data. ‘SCINA’ is capable of assigning cell type
identities to a pool of cells profiled by scRNA-Seq or Cytof/FACS data
with prior knowledge of markers, such as genes and protein symbols that
are highly or lowly expressed in each category. See Zhang Z, et al (2019)
<doi:10.3390/genes10070531> for more details. / GPL-2
r-sciplot 1.1_1 A collection of functions that creates graphs with error bars for data collected noarch
from one-way or higher factorial designs. / GPL-2
r-sciviews 0.9_13Functions to install SciViews additions to R, and more tools. / GPL-2 noarch
r-scma 1.3.0 Perform meta-analysis of single-case experiments, including calculating vari- noarch
ous effect size measures (SMD, PND, PEM and NAP) and probability combin-
ing (additive and multiplicative method), as discussed in Bulte and Onghena
(2013) <doi:10.22237/jmasm/1383280020>. / GPL-2
r-scoreggum 1.0 Estimate GGUM Person Parameters Using Pre-Calibrated Item Parameters noarch
and Binary or Graded Disagree-Agree Responses / GPL-2
r-scorer2 0.99.0This package contains the functions necessary to run the SCORER 2.0 algo- noarch
rithm. SCORER 2.0 can be used to differentiate between parallel dimeric and
trimeric coiled-coil sequence, which are the two most more frequent coiled-
coil structures observed naturally. As such, SCORER 2.0 is particularly useful
for researchers looking to characterize novel coiled-coil sequences. It may
also be used to assist in the structural characterization of synthetic coiled-coil
sequences. Also included in this package are functions that allows the user to
retrain the SCORER 2.0 algorithm using user-defined training data. / GPL-2
r-scoring 0.6 Evaluating probabilistic forecasts via proper scoring rules. scoring implements noarch
the beta, power, and pseudospherical families of proper scoring rules, along
with ordered versions of the latter two families. Included among these fam-
ilies are popular rules like the Brier (quadratic) score, logarithmic score, and
spherical score. For two-alternative forecasts, also includes functionality for
plotting scores that one would obtain under specific scoring rules. / GPL-2
r-scottknott 1.2_7 Division of an ANOVA experiment treatment means into homogeneous dis- noarch
tinct groups using the clustering method of Scott & Knott. / GPL-2


Name Version
r-scperf 1.1.1 Implements different inventory models, the bullwhip effect and other supply noarch
chain performance variables. Marchena Marlene (2010) <arXiv:1009.3977>.
/ GPL-3
r-scrabblescore 1.0 Given a word will produce that word’s scrabble score. Unlike many naive noarch
implementations this package takes into consideration the distribution of letter
in scrabble. So a word like ‘zzz’ will be scored ‘10’ rather than ‘30’. / MIT
License
r-scraep 1.1 A utility to webscrape the in-house careers of members of the European par- noarch
liament, from its website <http://www.europarl.europa.eu>. / GPL-3
r-scraper 0.1.6 Tools for Scraping Data from Web-Based Documents / GPL-2 noarch
r-screenclean 1.0.1 Routines for a collection of screen-and-clean type variable selection proce- noarch
dures, including UPS and GS. / GPL-2
r-scrime 1.3.5 Tools for the analysis of high-dimensional data developed/implemented at noarch
the group Statistical Complexity Reduction In Molecular Epidemiology
(SCRIME). Main focus is on SNP data. But most of the functions can also
be applied to other types of categorical data. / GPL-2
r-scriptests 1.0_16Support for using .Rt (transcript) tests in the tests directory of a package. Pro- noarch
vides more convenience and features than the standard .R/.Rout.save tests.
Tests can be run under R CMD check and also interactively. Provides
source.pkg() for quickly loading code, DLLs, and data from a package for
use in an edit/compile/test development cycle. / GPL-3
r-scriptexec 0.3.1 Run complex native scripts with a single command, similar to system com- noarch
mands. / Apache License 2.0
r-scriptname 1.0.1 A small set of functions wrapping up the call stack and command line inspec- noarch
tion needed to determine a running script’s filename from within the script
itself. / MIT
r-scripturs 0.1.0 Full text, in data frames containing one row per verse, of the Standard Works noarch
of The Church of Jesus Christ of Latter-day Saints (LDS). These are the Old
Testament, (KJV), the New Testament (KJV), the Book of Mormon, the Doc-
trine and Covenants, and the Pearl of Great Price. / MIT
r-scrobbler 0.1.0 ‘Last.fm’<https://www.last.fm> is a music platform focussed on building a de- noarch
tailed profile of a users listening habits. It does this by ‘scrobbling’ (recording)
every track you listen to on other platforms (‘spotify’, ‘youtube’, ‘soundcloud’
etc) and transferring them to your ‘Last.fm’ database. This allows ‘Last.fm’ to
act as a complete record of your entire listening history. ‘scrobbler’ provides
helper functions to download and analyse your listening history in R. / GPL-3
r-scrselect 1.3_3 Contains four functions used in the DIC-tau_g procedure. SCRSELECT() noarch
and SCRSELECTRUN() uses Stochastic Search Variable Selection to select
important covariates in the three hazard functions of a semi-competing risks
model. These functions perform the Gibbs sampler for variable selection and
a Metropolis-Hastings-Green sampler for the number of split points and pa-
rameters for the three baseline hazard function. The function SCRSELECT()
returns the posterior sample of all quantities sampled in the Gibbs sampler
after a burn-in period to a desired file location, while the function SCRSE-
LECTRUN() returns posterior values of important quantities to the DIC-Tau_g
procedure in a list. The function DICTAUG() returns a list containing the
DIC values for the unique models visited by the DIC-Tau_g grid search. The
function ReturnModel() uses SCRSELECTRUN() and DICTAUG() to return a
summary of the posterior coefficient vectors for the optimal model along with
saving this posterior sample to a desired path location. / GPL-2


Name Version
r-scrt 1.3.0 Design single-case phase, alternation and multiple-baseline experiments, and noarch
conduct randomization tests on data gathered by means of such designs, as
discussed in Bulte and Onghena (2013) <doi:10.22237/jmasm/1383280020>.
/ GPL-2
r-sdaa 0.1_3 Functions and Datasets from Lohr, S. (1999), Sampling: Design and Analysis, noarch
Duxbury. / GPL-3
r-sdat 1.1 Test the global null in linear models using marginal approach. / GPL-2 linux-
64,
osx-
64,
win-
64
r-sdcspatial 0.1.1 Privacy protected raster maps can be created from spatial point data. Protec- noarch
tion methods include smoothing of dichotomous variables by de Jonge and de
Wolf (2016) <doi:10.1007/978-3-319-45381-1_9>, continuous variables by de
Wolf and de Jonge (2018) <doi:10.1007/978-3-319-99771-1_23>, suppressing
revealing values and a generalization of the quad tree method by Suñé, Rovira,
Ibáñez and Farré (2017) <doi:10.2901/EUROSTAT.C2017.001>. / GPL-2
r-sdde 1.0.1 Compares the evolution of an original network X to an augmented network linux-
Y by counting the number of Shortcuts, Detours, Dead Ends (SDDE), equal 64,
paths and disconnected nodes. / GPL-3 osx-
64,
win-
64
r-sddpack 0.9 The semidiscrete decomposition (SDD) approximates a matrix as a weighted noarch
sum of outer products formed by vectors with entries constrained to be in the
set {-1, 0, 1}. / GPL-2
r-sdef 1.7 Performs two tests to evaluate if the experiments are associated and returns a noarch
list of interesting features common to all the experiments. / GPL-2
r-sdm 1.0_67An extensible framework for developing species distribution models using in- noarch
dividual and community-based approaches, generate ensembles of models,
evaluate the models, and predict species potential distributions in space and
time. For more information, please check the following paper: Naimi, B.,
Araujo, M.B. (2016) <doi:10.1111/ecog.01881>. / GPL-3
r-sdmtools 1.1_221.1
This packages provides a set of tools for post processing the outcomes of osx-
species distribution modeling exercises. It includes novel methods for com- 64,
paring models and tracking changes in distributions through time. It further win-
includes methods for visualizing outcomes, selecting thresholds, calculating 64
measures of accuracy and landscape fragmentation statistics, etc.. This pack-
age was made possible in part by financial support from the Australian Re-
search Council & ARC Research Network for Earth System Science. / GPL-3
r-sdmvspecies 0.3.2 A software package help user to create virtual species for species distribution noarch
modelling. It includes several methods to help user to create virtual species
distribution map. Those maps can be used for Species Distribution Modelling
(SDM) study. SDM use environmental data for sites of occurrence of a species
to predict all the sites where the environmental conditions are suitable for the
species to persist, and may be expected to occur. / AGPL-3


Name Version
r-sdnet 2.4.1 Fitting discrete Bayesian networks using soft-discretized data. Soft- linux-
discretization is based on mixture of normal distributions. Also implemented 64,
is a supervised Bayesian network learning employing Kullback-Leibler diver- osx-
gence. For more information see Balov (2013) <DOI:10.1186/1755-8794-6- 64,
S3-S1>. / GPL-2 win-
64
r-sdpt3r 0.3 Solves the general Semi-Definite Linear Programming formulation using linux-
an R implementation of SDPT3 (K.C. Toh, M.J. Todd, and R.H. Tu- 64,
tuncu (1999) <doi:10.1080/10556789908805762>). This includes prob- osx-
lems such as the nearest correlation matrix problem (Higham (2002) 64,
<doi:10.1093/imanum/22.3.329>), D-optimal experimental design (Smith win-
(1918) <doi:10.2307/2331929>), Distance Weighted Discrimination (Marron 64
and Todd (2012) <doi:10.1198/016214507000001120>), as well as graph the-
ory problems including the maximum cut problem. Technical details surround-
ing SDPT3 can be found in R.H Tutuncu, K.C. Toh, and M.J. Todd (2003)
<doi:10.1007/s10107-002-0347-5>. / GPL-2 | GPL-3
r-sdt 1.0.0 Functions for self-determination motivation theory (SDT) to compute mea- noarch
sures of motivation internalization, motivation simplex structure, and of the
original and adjusted self-determination or relative autonomy index. SDT was
introduced by Deci and Ryan (1985) <doi:10.1007/978-1-4899-2271-7>. See
package?SDT for an overview. / GPL-2
r-sdtoolkit 2.33_1Implements algorithms to help with scenario discovery - currently only modi- noarch
fied version of the the Patient Rule Induction Method. / GPL-3
r-sdwd 1.0.2 Formulates a sparse distance weighted discrimination (SDWD) for high- linux-
dimensional classification and implements a very fast algorithm for computing 64,
its solution path with the L1, the elastic-net, and the adaptive elastic-net penal- osx-
ties. / GPL-2 64,
win-
64
r-seacarb 3.2.12Calculates parameters of the seawater carbonate system and assists the design linux-
of ocean acidification perturbation experiments. / GPL (>= 2) 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-sealasso 0.1_2 Standard error adjusted adaptive lasso (SEA-lasso) is a version of the adap- noarch
tive lasso, which incorporates OLS standard error to the L1 penalty weight.
This method is intended for variable selection under linear regression settings
(n > p). This new weight assignment strategy is especially useful when the
collinearity of the design matrix is a concern. / GPL-2
r-searchable 0.3.3.1Provides functionality for searching / subsetting and slicing named objects noarch
using ‘stringr/i’-style modifiers by case (in)sensitivity, regular expressions or
fixed expressions; searches uses the standard ‘[’ operator and allows specifica-
tion of default search behavior to either the search target (named object) and/or
the search pattern. / GPL-2


Name Version
r-searcher 0.0.4 Provides a search interface to look up terms on ‘Google’, ‘Bing’, ‘Duck- noarch
DuckGo’, ‘Startpage’, ‘StackOverflow’, ‘RStudio Community’, ‘GitHub’, and
‘BitBucket’. Upon searching, a browser window will open with the aforemen-
tioned search results. / GPL-2
r-searchtrees 0.5.2 This package provides an implementation of the QuadTree data structure. It linux-
uses this to implement fast k-Nearest Neighbor and Rectangular range lookups 64,
in 2 dimenions. The primary target is high performance interactive graphics. / osx-
LGPL-3 64,
win-
64
r-seas 0.5_2 Capable of deriving seasonal statistics, such as normals, and analysis of sea- linux-
sonal data, such as departures. This package also has graphics capabilities for 64,
representing seasonal data, including boxplots for seasonal parameters, and osx-
bars for summed normals. There are many specific functions related to clima- 64,
tology, including precipitation normals, temperature normals, cumulative pre- win-
cipitation departures and precipitation interarrivals. However, this package is 64
designed to represent any time-varying parameter with a discernible seasonal
signal, such as found in hydrology and ecology. / GPL-2
r-seasic 0.1 This package conducts Score Equity Assessment (SEA; Dorans, 2004) by cal- noarch
culating and plotting multiple SEA indices as introduced by a variety of au-
thors and summarized by Huggins and Penfield (2012). / GPL-3
r-seasonal 1.7.0 Easy-to-use interface to X-13-ARIMA-SEATS, the seasonal adjustment soft- noarch
ware by the US Census Bureau. It offers full access to almost all options
and outputs of X-13, including X-11 and SEATS, automatic ARIMA model
search, outlier detection and support for user defined holiday variables, such
as Chinese New Year or Indian Diwali. A graphical user interface can be
used through the ‘seasonalview’ package. Uses the X-13-binaries from the
‘x13binary’ package. / GPL-3
r-secr 3.2.1 Functions to estimate the density and size of a spatially distributed animal linux-
population sampled with an array of passive detectors, such as traps, or by 64,
searching polygons or transects. Models incorporating distance-dependent de- osx-
tection are fitted by maximizing the likelihood. Tools are included for data 64,
manipulation and model selection. / GPL-2 win-
64
r-secret 1.0.0 Allow sharing sensitive information, for example passwords, ‘API’ keys, etc., noarch
in R packages, using public key cryptography. / MIT
r-secure 0.5 Sequential factor extraction via co-sparse unit-rank estimation (SeCURE). / linux-
GPL (>= 3.0) 64,
osx-
64,
win-
64
r-securitytxt 0.1.1 When security risks in web services are discovered by independent security re- linux-
searchers who understand the severity of the risk, they often lack the channels 64,
to properly disclose them. As a result, security issues may be left unreported. osx-
The ‘security.txt’ ‘Web Security Policies’ specification defines an ‘IETF’ draft 64,
standard <https://tools.ietf.org/html/draft-foudil-securitytxt-00> to help orga- win-
nizations define the process for security researchers to securely disclose secu- 64
rity vulnerabilities. Tools are provided to help identify and parse ‘security.txt’
files to enable analysis of the usage and adoption of these policies. / MIT


Name Version
r-seeclickfixr 1.1.0 Provides a wrapper to access data from the SeeClickFix web API for R. noarch
SeeClickFix is a central platform employed by many cities that allows citi-
zens to request their city’s services. This package creates several functions to
work with all the built-in calls to the SeeClickFix API. Allows users to down-
load service request data from numerous locations in easy-to-use dataframe
format manipulable in standard R functions. / GPL-3
r-seedcalc 1.0.0 Functions to calculate seed germination and seedling emergence and growth noarch
indexes. The main indexes for germination and seedling emergence, consid-
ering the time for seed germinate are: T10, T50 and T90, in Farooq et al.
(2005) <10.1111/j.1744-7909.2005.00031.x>; and MGT, in Labouriau (1983).
Considering the germination speed are: Germination Speed Index, in Maguire
(1962), Mean Germination Rate, in Labouriau (1983); considering the homo-
geneity of germination are: Coefficient of Variation of the Germination Time,
in Carvalho et al. (2005) <10.1590/S0100-84042005000300018>, and Vari-
ance of Germination, in Labouriau (1983); Uncertainty, in Labouriau and Val-
adares (1976) <ISSN:0001-3765>; and Synchrony, in Primack (1980). The
main seedling indexes are Growth, in Sako (2001), Uniformity, in Sako (2001)
and Castan et al. (2018) <doi:10.1590/1678-992x-2016-0401>; and Vigour,
in Medeiros and Pereira (2018) <doi:10.1590/1983-40632018v4852340>. /
GPL-2
r-seedwater 1.0 Bringing together tools for modeling drying and soaking (rehydration) kinetics noarch
of seeds. This package contains several widely used predictive models (e.g.:
da Silva et al., 2018). As these are nonlinear, the functions are interactive-
based and easy-to-use. Least squares estimates are obtained with just a few
visual adjustments of the initial parameter values. Reference: da Silva AR et
al. (2018) <doi:10.2134/agronj2017.07.0373>. / GPL-2
r-seer2r 1.0 read and write SEER*STAT data files / GPL-2 noarch
r- 1.2.0 Provides supplemental 2010 census tract boundary package for 23 states with- noarch
seermapper2010east out Seer Registries that are east of the Mississippi river for use with the
‘SeerMapper’ package. The data contained in this package is derived from
U. S. Census data and is in public domain. / GPL-2
r- 1.2.0 Provides supplemental 2010 census tract boundaries of the 15 states containing noarch
seermapper2010regs Seer Registries for use with the ‘SeerMapper’ package. The data contained in
this package is derived from U. S. 2010 Census data and is in public domain.
/ GPL-2
r- 1.2.0 Provides supplemental 2010 census tract boundaries for the 14 states without noarch
seermapper2010west Seer Registries that are west of the Mississippi river for use with the ‘SeerMap-
per’ package. The data contained in this package is derived from U. S. 2010
Census data and is in public domain. / GPL-2
r-seermappereast 1.2.0 Provides supplemental 2000 census tract boundaries for the 23 states without noarch
Seer Registries that are east of the Mississippi river for use with the ‘SeerMap-
per’ package. The data contained in this package is derived from U. S. Census
data and is in the public domain. / GPL-2
r- 1.2.0 Provides supplemental 2000 census tract boundaries for the 15 states contain- noarch
seermapperregs ing Seer Registries for use with the ‘SeerMapper’ package. The data contained
in this package is derived from U. S. Census data and is in the public domain.
/ GPL-2
r- 1.2.0 Provides supplemental 2000 census tract boundaries for the 14 states without noarch
seermapperwest Seer Registries that are west of the Mississippi river for use with the ‘SeerMap-
per’ package. The data contained in this package is derived from U. S. Census
data and is in the public domain. / GPL-2


Name Version
r-segmag 1.2.4 Contains functions that help to determine event boundaries in event segmen- linux-
tation experiments by bootstrapping a critical segmentation magnitude under 64,
the null hypothesis that all key presses were randomly distributed across the osx-
experiment. Segmentation magnitude is defined as the sum of Gaussians cen- 64,
tered at the times of the segmentation key presses performed by the partici- win-
pants. Within a participant, the maximum of the overlaid Gaussians is used to 64
prevent an excessive influence of a single participant on the overall outcome
(e.g. if a participant is pressing the key multiple times in succession). Further
functions are included, such as plotting the results. / GPL-3
r-segmented 1.0_0 Given a regression model, segmented ‘updates’ it by adding one or noarch
more segmented (i.e., piece-wise linear) relationships. Several vari-
ables with multiple breakpoints are allowed. The estimation method is
discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and illustrated in
Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>).
An approach for hypothesis testing is presented in Muggeo (2016,
<doi:10.1080/00949655.2016.1149855>), and interval estimation for the
breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>). / GPL-
3
r-segmentier 0.1.2 A dynamic programming solution to segmentation based on maximization linux-
of arbitrary similarity measures within segments. The general idea, the- 64,
ory and this implementation are described in Machne, Murray & Stadler osx-
(2017) <doi:10.1038/s41598-017-12401-8>. In addition to the core algo- 64,
rithm, the package provides time-series processing and clustering functions win-
as described in the publication. These are generally applicable where a k- 64
means clustering yields meaningful results, and have been specifically devel-
oped for clustering of the Discrete Fourier Transform of periodic gene expres-
sion data (‘circadian’ or ‘yeast metabolic oscillations’). This clustering ap-
proach is outlined in the supplemental material of Machne & Murray (2012)
<doi:10.1371/journal.pone.0037906>), and here is used as a basis of segment
similarity measures. Notably, the time-series processing and clustering func-
tions can also be used as stand-alone tools, independent of segmentation, e.g.,
for transcriptome data already mapped to genes. / GPL-2
r- 2.0 Performs a fast exact segmentation on data and allows for use of various cost linux-
segmentor3isback functions. / GPL-2 64,
osx-
64,
win-
64
r-segmentr 0.2.0 Given a likelihood provided by the user, this package applies it to a given ma- linux-
trix dataset in order to find change points in the data that maximize the sum 64,
of the likelihoods of all the segments. This package provides a handful of osx-
algorithms with different time complexities and assumption compromises so 64,
the user is able to choose the best one for the problem at hand. The imple- win-
mentation of the segmentation algorithms in this package are based on the pa- 64
per by Bruno M. de Castro, Florencia Leonardi (2018) <arXiv:1501.01756>.
The Berlin weather sample dataset was provided by Deutscher Wetterdienst
<https://dwd.de/>. You can find all the references in the Acknowledgments
section of this package’s repository via the URL below. / MIT


Name Version
r-segmgarch 1.2 Implements a segmentation algorithm for multiple change-point detection in linux-
high-dimensional GARCH processes. It simultaneously segments GARCH 64,
processes by identifying ‘common’ change-points, each of which can be osx-
shared by a subset or all of the component time series as a change-point in 64,
their within-series and/or cross-sectional correlation structure. / GPL-2 win-
64
r-segregation 0.2.0 Computes entropy-based segregation indices, as developed by Theil (1971) noarch
<isbn:978-0471858454>, with a focus on the Mutual Information Index (M)
and Theil’s Information Index (H). The M, further described by Mora and
Ruiz-Castillo (2011) <doi:10.1111/j.1467-9531.2011.01237.x> and Frankel
and Volij (2011) <doi:10.1016/j.jet.2010.10.008>, is a measure of segregation
that is highly decomposable. The package provides tools to decompose the in-
dex by units and groups (local segregation), and by within and between terms.
Includes standard error estimation by bootstrapping. / MIT
r-seismic 1.0 An implementation of self-exciting point process model for information cas- noarch
cades, which occurs when many people engage in the same acts after observing
the actions of others (e.g. post resharings on Facebook or Twitter). It provides
functions to estimate the infectiousness of an information cascade and predict
its popularity given the observed history. See http://snap.stanford.edu/seismic/
for more information and datasets. / GPL-3
r-seismicroll 1.1.3 Fast versions of seismic analysis functions that ‘roll’ over a vector of values. linux-
See the ‘RcppRoll’ package for alternative versions of basic statistical func- 64,
tions such as rolling mean, median, etc. / GPL-2 osx-
64,
win-
64
r-sejong 0.01 Sejong(http://www.sejong.or.kr/) corpus and Hannanum(http://semanticweb. noarch
kaist.ac.kr/home/index.php/HanNanum) dictionaries for KoNLP / GPL-3
r-sel 1.0_2 This package implements a novel method for fitting a bounded probability dis- linux-
tribution to quantiles (for example stated by an expert), see Bornkamp and 64,
Ickstadt (2009) for details. For this purpose B-splines are used, and the den- osx-
sity is obtained by penalized least squares based on a Brier entropy penalty. 64,
The package provides methods for fitting the distribution as well as methods win-
for evaluating the underlying density and cdf. In addition methods for plot- 64
ting the distribution, drawing random numbers and calculating quantiles of the
obtained distribution are provided. / GPL-3
r-selectapref 0.1.1 Provides indices such as Manly’s alpha, foraging ratio, and Ivlev’s selectivity noarch
to allow for analysis of dietary selectivity and preference. Can accommodate
multiple experimental designs such as constant prey number of prey deple-
tion.Please contact the package maintainer with any publications making use
of this package in an effort to maintain a repository of dietary selections stud-
ies. / GPL-2


Name Version
r-selectiongain 2.0.591
Multi-stage selection is practiced in numerous fields of life and social sciences noarch
and particularly in breeding. A special characteristic of multi-stage selection is
that candidates are evaluated in successive stages with increasing intensity and
effort, and only a fraction of the superior candidates is selected and promoted
to the next stage. For the optimum design of such selection programs, the
selection gain plays a crucial role. It can be calculated by integration of a trun-
cated multivariate normal (MVN) distribution. While mathematical formulas
for calculating the selection gain and the variance among selected candidates
were developed long time ago, solutions for numerical calculation were not
available. This package can also be used for optimizing multi-stage selection
programs for a given total budget and different costs of evaluating the candi-
dates in each stage. / GPL-2
r-selectmeta 1.0.8 Publication bias, the fact that studies identified for inclusion in a meta analysis noarch
do not represent all studies on the topic of interest, is commonly recognized
as a threat to the validity of the results of a meta analysis. One way to ex-
plicitly model publication bias is via selection models or weighted probability
distributions. In this package we provide implementations of several paramet-
ric and nonparametric weight functions. The novelty in Rufibach (2011) is
the proposal of a non-increasing variant of the nonparametric weight function
of Dear & Begg (1992). The new approach potentially offers more insight in
the selection process than other methods, but is more flexible than paramet-
ric approaches. To maximize the log-likelihood function proposed by Dear &
Begg (1992) under a monotonicity constraint we use a differential evolution
algorithm proposed by Ardia et al (2010a, b) and implemented in Mullen et al
(2009). In addition, we offer a method to compute a confidence interval for
the overall effect size theta, adjusted for selection bias as well as a function
that computes the simulation-based p-value to assess the null hypothesis of no
selection as described in Rufibach (2011, Section 6). / GPL-2
r-selectr 0.4_1 Translates a CSS3 selector into an equivalent XPath expression. This allows linux-
us to use CSS selectors when working with the XML package as it can only 32,
evaluate XPath expressions. Also provided are convenience functions useful linux-
for using CSS selectors on XML nodes. This package is a port of the Python 64,
package ‘cssselect’ (<https://cssselect.readthedocs.io/>). / BSD_3_clause file noarch,
LICENCE osx-
64,
win-
32,
win-
64
r-selemix 1.0.1 Detection of outliers and influential errors using a latent variable model. / noarch
EUPL
r-seleniumpipes 0.3.7 The W3C WebDriver specification defines a way for out-of-process programs noarch
to remotely instruct the behaviour of web browsers. It is detailed at <https:
//w3c.github.io/webdriver/webdriver-spec.html>. This package provides an R
client implementing the W3C specification. / GPL-3


Name Version
r-selfingtree 0.2 A probability tree allows to compute probabilities of complex events, such noarch
as genotype probabilities in intermediate generations of inbreeding through
recurrent self-fertilization (selfing). This package implements functionality to
compute probability trees for two- and three-marker genotypes in the F2 to
F7 selfing generations. The conditional probabilities are derived automatically
and in symbolic form. The package also provides functionality to extract and
evaluate the relevant probabilities. / BSD_3_clause
r-semicomprisks 3.3 Hierarchical multistate models are considered to perform the analysis of linux-
independent/clustered semi-competing risks data. The package allows to 64,
choose the specification for model components from a range of options giv- osx-
ing users substantial flexibility, including: accelerated failure time or pro- 64,
portional hazards regression models; parametric or non-parametric specifica- win-
tions for baseline survival functions and cluster-specific random effects dis- 64
tribution; a Markov or semi-Markov specification for terminal event following
non-terminal event. While estimation is mainly performed within the Bayesian
paradigm, the package also provides the maximum likelihood estimation ap-
proach for several parametric models. The package also includes functions for
univariate survival analysis as complementary analysis tools. / GPL-2
r-semid 0.3.2 Provides routines to check identifiability or non-identifiability of linear noarch
structural equation models as described in Drton, Foygel, and Sullivant
(2011) <DOI:10.1214/10-AOS859>, Foygel, Draisma, and Drton (2012)
<DOI:10.1214/12-AOS1012>, and other works. The routines are based on
the graphical representation of structural equation models by a path dia-
gram/mixed graph. / GPL-2
r-seminr 0.7.0 A powerful, easy to write and easy to modify syntax for specifying and noarch
estimating Partial Least Squares (PLS) path models allowing for the latest
estimation methods for Consistent PLS as per Dijkstra & Henseler (2015,
MISQ 39(2): 297-316), adjusted interactions as per Henseler & Chin (2010)
<doi:10.1080/10705510903439003> and bootstrapping utilizing parallel pro-
cessing as per Hair et al. (2017, ISBN:978-1483377445). / GPL-3
r-semipar 1.0_4.2
Functions for semiparametric regression analysis, to complement the book: noarch
Ruppert, D., Wand, M.P. and Carroll, R.J. (2003). Semiparametric Regression.
Cambridge University Press. / GPL-2
r-semmodcomp 1.0 Conduct tests of difference in fit for mean and covariance structure models as noarch
in structural equation modeling (SEM) / GPL-3
r- 0.1.3 Implements dictionaries that can be used in the ‘SemNetCleaner’ package. noarch
semnetdictionaries Also includes several functions aimed at facilitating the text cleaning analysis
in the ‘SemNetCleaner’ package. This package is designed to integrate and
update word lists and dictionaries based on each user’s individual needs by
allowing users to store and save their own dictionaries. Dictionaries can be
added to the ‘SemNetDictionaries’ package by submitting user-defined dictio-
naries to <https://github.com/AlexChristensen/SemNetDictionaries>. / GPL
(>= 3.0)
r-sempls 1.0_10Fits structural equation models using partial least squares (PLS). The PLS ap- noarch
proach is referred to as ‘soft-modeling’ technique requiring no distributional
assumptions on the observed data. / GPL-2
r-sempower 1.0.0 Provides a-priori, post-hoc, and compromise power-analyses for noarch
structural equation models (SEM). Moshagen & Erdfelder (2016)
<doi:10.1080/10705511.2014.950896>. / LGPL-3


Name Version
r-semver 0.2.0 Tools and functions for parsing, rendering and operating on semantic version linux-
strings. Semantic versioning is a simple set of rules and requirements that 64,
dictate how version numbers are assigned and incremented as outlined at <http: osx-
//semver.org>. / MIT 64,
win-
64
r-sendmailr 1.2_1 Package contains a simple SMTP client which provides a portable solution for noarch
sending email, including attachment, from within R. / GPL-2
r-sensemakr 0.1.2 Implements a suite of sensitivity analysis tools that extends the traditional noarch
omitted variable bias framework and makes it easier to understand the im-
pact of omitted variables in regression models, as discussed in Cinelli and Ha-
zlett (2018) <https://www.researchgate.net/publication/322509816_Making_
Sense_of_Sensitivity_Extending_Omitted_Variable_Bias>. / GPL-3
r-sensibo.sky 1.0.0 Provides an interface to the ‘Sensibo Sky’ API which allows to remotely con- noarch
trol non-smart air conditioning units. See <https://sensibo.com> for more in-
formations. / MIT
r- 1.01 Performs exact or approximate adaptive or nonadaptive Cochran-Mantel- noarch
sensitivity2x2xk Haenszel-Birch tests and sensitivity analyses for one or two 2x2xk tables in
observational studies. / GPL-2
r- 2.1 This package performs sensitivity analysis for case-control studies in which noarch
sensitivitycasecontrol some cases may meet a more narrow definition of being a case compared to
other cases which only meet a broad definition. The sensitivity analyses are de-
scribed in Small, Cheng, Halloran and Rosenbaum (2013, Case Definition and
Sensitivity Analysis, Journal of the American Statistical Association, 1457-
1468). The functions sens.analysis.mh and sens.analysis.aberrant.rank provide
sensitivity analyses based on the Mantel-Haenszel test statistic and aberrant
rank test statistic as described in Rosenbaum (1991, Sensitivity Analysis for
Matched Case Control Studies, Biometrics); see also Section 1 of Small et
al. The function adaptive.case.test provides adaptive inferences as described
in Section 5 of Small et al. The function adaptive.noether.brown provides a
sensitivity analysis for a matched cohort study based on an adaptive test. The
other functions in the package are internal functions. / GPL-2
r-sensitivityfull 1.5.6 Sensitivity to unmeasured biases in an observational study that is a full match. noarch
Function senfm() performs tests and function senfmCI() creates confidence
intervals. The method uses Huber’s M-statistics, including least squares,
and is described in Rosenbaum (2007, Biometrics) <DOI:10.1111/j.1541-
0420.2006.00717.x>. / GPL-2
r-sensitivitymult 1.0.2 Sensitivity analysis for multiple outcomes in observational studies. For in- noarch
stance, all linear combinations of several outcomes may be explored using
Scheffe projections in the comparison() function; see Rosenbaum (2016, An-
nals of Applied Statistics) <doi:10.1214/16-AOAS942>. Alternatively, atten-
tion may focus on a few principal components in the principal() function. The
package includes parallel methods for individual outcomes, including tests in
the senm() function and confidence intervals in the senmCI() function. / GPL-2
r-sensitivitymv 1.4.3 The package performs a sensitivity analysis in an observational study using noarch
an M-statistic, for instance, the mean. The main function in the package is
senmv(), but amplify() and truncatedP() are also useful. The method is de-
veloped in Rosenbaum Biometrics, 2007, 63, 456-464, <doi:10.1111/j.1541-
0420.2006.00717.x>. / GPL-2
r-sensitivitymw 1.1 Sensitivity analysis analysis in matched observational studies with multiple noarch
controls using weighted M-statistics to increase design sensitivity. / GPL-2


Name Version
r- 1.0_6 This package provides functions to perform principal stratification sensitivity linux-
sensitivitypstrat analyses on datasets. / GPL-3 64,
osx-
64,
win-
64
r-sensmediation 0.3.0 We implement functions to estimate and perform sensitivity analysis to unob- noarch
served confounding of direct and indirect effects introduced in Lindmark, de
Luna and Eriksson (2018) <doi:10.1002/sim.7620>. The estimation and sen-
sitivity analysis are parametric, based on probit and/or linear regression mod-
els. Sensitivity analysis is implemented for unobserved confounding of the
exposure-mediator, mediator-outcome and exposure-outcome relationships. /
GPL-2
r-sensory 1.1 Contains the function CUUimpute() which performs model-based clustering noarch
and imputation simultaneously. / GPL-2
r-sensr 1.5_1 Provides methods for sensory discrimination methods; duotrio, tetrad, triangle, noarch
2-AFC, 3-AFC, A-not A, same-different, 2-AC and degree-of-difference. This
enables the calculation of d-primes, standard errors of d-primes, sample size
and power computations, and comparisons of different d-primes. Methods for
profile likelihood confidence intervals and plotting are included. / GPL-2 |
GPL-3
r-sensrivastava 2015.6.25
Collection of datasets from Sen & Srivastava: Regression Analysis, Theory, noarch
Methods and Applications, Springer. Sources for individual data files are more
fully documented in the book. / GPL-2
r-senstrat 1.0.3 Sensitivity analysis in unmatched observational studies, with or with- noarch
out strata. The main functions are sen2sample() and senstrat(). See
Rosenbaum, P. R. and Krieger, A. M. (1990), JASA, 85, 493-498,
<doi:10.1080/01621459.1990.10476226> and Gastwirth, Krieger and Rosen-
baum (2000), JRSS-B, 62, 545â C“555 <doi:10.1111/1467-9868.00249> . /
GPL-2
r-separate 0.2.1 It combines maximum likelihood estimation of the parameters of matrix noarch
and 3rd-order tensor normal distributions with unstructured factor variance-
covariance matrices, two procedures, and unbiased modified likelihood ratio
testing of simple and double separability for variance-covariance structures,
two procedures. / MIT
r-separationplot 1.1 Functions to generate separation plots for evaluation of model fit. / Artistic-2.0 noarch
r-seqalloc 1.0 Potential randomization schemes are prospectively evaluated when units are noarch
assigned to treatment arms upon entry into the experiment. The schemes are
evaluated for balance on covariates and on predictability (i.e., how well could
a site worker guess the treatment of the next unit enrolled). / GPL-2
r-seqcbs 1.2.1 This is a method for DNA Copy Number Profiling using Next-Generation Se- linux-
quencing. It has new model and test statistics based on non-homogeneous 64,
Poisson Processes with change point models. It uses an adaptation of Circu- osx-
lar Binary Segmentation. Also included are methods for point-wise Bayesian 64,
Confidence Interval and model selection method for the change-point model. win-
A case and a control sample reads (normal and tumor) are required. / GPL-2 64


Name Version
r-seqdesign 1.2 A modification of the preventive vaccine efficacy trial design of Gilbert, Grove noarch
et al. (2011, Statistical Communications in Infectious Diseases) is imple-
mented, with application generally to individual-randomized clinical trials
with multiple active treatment groups and a shared control group, and a study
endpoint that is a time-to-event endpoint subject to right-censoring. The design
accounts for the issues that the efficacy of the treatment/vaccine groups may
take time to accrue while the multiple treatment administrations/vaccinations
are given; there is interest in assessing the durability of treatment efficacy over
time; and group sequential monitoring of each treatment group for potential
harm, non-efficacy/efficacy futility, and high efficacy is warranted. The de-
sign divides the trial into two stages of time periods, where each treatment is
first evaluated for efficacy in the first stage of follow-up, and, if and only if
it shows significant treatment efficacy in stage one, it is evaluated for longer-
term durability of efficacy in stage two. The package produces plots and tables
describing operating characteristics of a specified design including an uncon-
ditional power for intention-to-treat and per-protocol/as-treated analyses; trial
duration; probabilities of the different possible trial monitoring outcomes (e.g.,
stopping early for non-efficacy); unconditional power for comparing treatment
efficacies; and distributions of numbers of endpoint events occurring after the
treatments/vaccinations are given, useful as input parameters for the design
of studies of the association of biomarkers with a clinical outcome (surrogate
endpoint problem). The code can be used for a single active treatment versus
control design and for a single-stage design. / GPL-2
r-seqicp 1.1 Contains an implementation of invariant causal prediction for sequential data. noarch
The main function in the package is ‘seqICP’, which performs linear sequential
invariant causal prediction and has guaranteed type I error control. For non-
linear dependencies the package also contains a non-linear method ‘seqICPnl’,
which allows to input any regression procedure and performs tests based on
a permutation approach that is only approximately correct. In order to test
whether an individual set S is invariant the package contains the subroutines
‘seqICP.s’ and ‘seqICPnl.s’ corresponding to the respective main methods. /
GPL-3
r-seqmade 1.0 A network module-based generalized linear model for differential expression noarch
analysis with the count-based sequence data from RNA-Seq. / GPL-2
r-seqmeta 1.6.7 Computes necessary information to meta analyze region-based tests for rare linux-
genetic variants (e.g. SKAT, T1) in individual studies, and performs meta 64,
analysis. / GPL-2 osx-
64,
win-
64
r-seqminer 7.1 Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta- linux-
analysis results in R. This package can help you (1) read VCF/BCF/BGEN 64,
files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL sum- osx-
mary statistics files; (3) read tables from a tabix-indexed files; (4) annotate 64,
VCF/BCF files; (5) create customized workflow based on Makefile. / GPL-3 win-
64
r-seqmon 2.3 S4 class object for creating and managing group sequential designs. It calcu- noarch
lates the efficacy and futility boundaries at each look. It allows modifying the
design and tracking the design update history. / MIT


Name Version
r-seqrflp 1.0.1 This package includes functions for handling DNA sequences, especially sim- noarch
ulated RFLP and TRFLP pattern based on selected restriction enzyme and
DNA sequences. / GPL-2
r-seqtest 0.1_0 Sequential triangular test for the arithmetic mean in one- and twosamples, noarch
proportions in one- and two-samples, and the Pearson’s correlation coefficient.
/ GPL-3
r-sequences 0.5.9 Educational package used in R courses to illustrate object-oriented program- linux-
ming and package development. Using biological sequences (DNA and RNA) 64,
as a working example. / GPL-3 osx-
64,
win-
64
r-sequential 3.0.1 Functions to calculate exact critical values, statistical power, expected time noarch
to signal, and required sample sizes for performing exact sequential analysis.
All these calculations can be done for either Poisson or binomial data, for
continuous or group sequential analyses, and for different types of rejection
boundaries. In case of group sequential analyses, the group sizes do not have
to be specified in advance and the alpha spending can be arbitrarily settled. /
GPL-2
r-sequoia 1.3.3 Fast multi-generational pedigree inference from incomplete data on hundreds linux-
of SNPs, including parentage assignment and sibship clustering. See Huisman 64,
(2017) (DOI:10.1111/1755-0998.12665, citation(‘sequoia’)) for more infor- osx-
mation. / GPL-2 64,
win-
64
r-serial 2.1.4 Enables reading and writing binary and ASCII data to RS232/RS422/RS485 noarch
or any other virtual serial interfaces of the computer. / GPL-2
r-serieslcb 0.4.0 Calculate and compare lower confidence bounds for binomial series system noarch
reliability. The R ‘shiny’ application, launched by the function launch_app(),
weaves together a workflow of customized simulations and delta coverage cal-
culations to output recommended lower confidence bound methods. / GPL-3
r-seroincidence 2.0.0 Translates antibody levels measured in a (cross-sectional) population sample noarch
into an estimate of the frequency with which seroconversions (infections) oc-
cur in the sampled population. / GPL-3
r-servr 0.15 Start an HTTP server in R to serve static files, or dynamic documents that can noarch
be converted to HTML files (e.g., R Markdown) under a given directory. /
GPL-3
r-sesem 1.0.2 Structural equation modeling is a powerful statistical approach for the testing noarch
of networks of direct and indirect theoretical causal relationships in complex
data sets with inter-correlated dependent and independent variables. Here we
implement a simple method for spatially explicit structural equation model-
ing based on the analysis of variance co-variance matrices calculated across a
range of lag distances. This method provides readily interpreted plots of the
change in path coefficients across scale. / GPL-2
r-session 1.0.3 Utility functions for interacting with R processes from external programs. This noarch
package includes functions to save and restore session information (including
loaded packages, and attached data objects), as well as functions to evaluate
strings containing R commands and return the printed results or an execution
transcript. / GPL-2


Name Version
r-sessioninfo 1.1.1 Query and print information about the current R session. It is similar to noarch
‘utils::sessionInfo()’, but includes more information about packages, and
where they were installed from. / GPL-2
r-setpath 1.0 Tests gene expression data from a biological pathway for biologically mean- noarch
ingful differences in the eigenstructure between two classes. Specifically, it
tests the null hypothesis that the two classes’ leading eigenvalues and sums of
eigenvalues are equal. A pathway’s leading eigenvalue arguably represents the
total variability due to variability in pathway activity, while the sum of all its
eigenvalues represents the variability due to pathway activity and to other, un-
regulated causes. Implementation of the method described in Danaher (2015),
Covariance-based analyses of biological pathways. / GPL-2
r-setrank 1.1.0 Implements an algorithm to conduct advanced gene set enrichment analysis on noarch
the results of genomics experiments. / GPL-3
r-setrng 2013.9_1
SetRNG provides utilities to help set and record the setting of the seed and the noarch
uniform and normal generators used when a random experiment is run. The
utilities can be used in other functions that do random experiments to simplify
recording and/or setting all the necessary information for reproducibility. See
the vignette and reference manual for examples. / GPL-2
r-sets 1.0_18Data structures and basic operations for ordinary sets, generalizations such as linux-
fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals. / 64,
GPL-2 osx-
64,
win-
64
r-setter 0.0_1 Mutators to set attributes of variables, that work well in a pipe (much like noarch
stats::setNames()). / Unlimited
r-settest 0.2.0 It provides cumulative distribution function (CDF), quantile, p-value, sta- noarch
tistical power calculator and random number generator for a collection of
group-testing procedures, including the Higher Criticism tests, the one-sided
Kolmogorov-Smirnov tests, the one-sided Berk-Jones tests, the one-sided phi-
divergence tests, etc. The input are a group of p-values. The null hypothesis is
that they are i.i.d. Uniform(0,1). In the context of signal detection, the null hy-
pothesis means no signals. In the context of the goodness-of-fit testing, which
contrasts a group of i.i.d. random variables to a given continuous distribu-
tion, the input p-values can be obtained by the CDF transformation. The null
hypothesis means that these random variables follow the given distribution.
For reference, see Hong Zhang, Jiashun Jin and Zheyang Wu. Distributions
and Statistical Power of Optimal Signal-Detection Methods In Finite Cases,
submitted. / GPL-2
r-settings 0.2.4 Provides option settings management that goes beyond R’s default ‘options’ noarch
function. With this package, users can define their own option settings man-
ager holding option names, default values and (if so desired) ranges or sets of
allowed option values that will be automatically checked. Settings can then
be retrieved, altered and reset to defaults with ease. For R programmers and
package developers it offers cloning and merging functionality which allows
for conveniently defining global and local options, possibly in a multilevel
options hierarchy. See the package vignette for some examples concerning
functions, S4 classes, and reference classes. There are convenience functions
to reset par() and options() to their ‘factory defaults’. / GPL-3


Name Version
r-severity 2.0 This package contains functions for calculating severity and generating sever- noarch
ity curves. Specifically, the simple case of the one-parameter Normal distribu-
tion (i.e., with known variance) is considered. / GPL-2
r-sf 0.6_3 Support for simple features, a standardized way to encode spatial vector data. linux-
Binds to ‘GDAL’ for reading and writing data, to ‘GEOS’ for geometrical op- 32,
erations, and to ‘PROJ’ for projection conversions and datum transformations. linux-
/ GPL-2 | MIT file LICENSE 64,
osx-
64,
win-
64
r-sfa 1.0_1 Stochastic Frontier Analysis introduced by Aigner, Lovell and Schmidt (1976) noarch
and Battese and Coelli (1992, 1995). / GPL-2
r-sfinx 1.7.99The straightforward filtering index (SFINX) identifies true positive protein in- noarch
teractions in a fast, user-friendly, and highly accurate way. It is not only useful
for the filtering of affinity purification - mass spectrometry (AP-MS) data, but
also for similar types of data resulting from other co-complex interactomics
technologies, such as TAP-MS, Virotrap and BioID. SFINX can also be used
via the website interface at <http://sfinx.ugent.be>. / Apache License 2.0
r-sfs 0.1.4 An implementation of the Similarity-First Search algorithm (SFS), a combi- linux-
natorial algorithm which can be used to solve the seriation problem and to 64,
recognize some structured weighted graphs. The SFS algorithm represents a osx-
generalization to weighted graphs of the graph search algorithm Lexicographic 64,
Breadth-First Search (Lex-BFS), a variant of Breadth-First Search. The SFS win-
algorithm reduces to Lex-BFS when applied to binary matrices (or, equiv- 64
alently, unweighted graphs). Hence this library can be also considered for
Lex-BFS applications such as recognition of graph classes like chordal or unit
interval graphs. In fact, the SFS seriation algorithm implemented in this pack-
age is a multisweep algorithm, which consists in repeating a finite number of
SFS iterations (at most n sweeps for a matrix of size n). If the data matrix
has a Robinsonian structure, then the ranking returned by the multistep SFS
algorithm is a Robinson ordering of the input matrix. Otherwise the algorithm
can be used as a heuristic to return a ranking partially satisfying the Robinson
property. / GPL-3
r-sfsmisc 1.1_3 Useful utilities [‘goodies’] from Seminar fuer Statistik ETH Zurich, some of linux-
which were ported from S-plus in the 1990’s. For graphics, have pretty (Log- 32,
scale) axes, an enhanced Tukey-Anscombe plot, combining histogram and linux-
boxplot, 2d-residual plots, a ‘tachoPlot()’, pretty arrows, etc. For robustness, 64,
have a robust F test and robust range(). For system support, notably on Linux, noarch,
provides ‘Sys.*()’ functions with more access to system and CPU information. osx-
Finally, miscellaneous utilities such as simple efficient prime numbers, integer 64,
codes, Duplicated(), toLatex.numeric() and is.whole(). / GPL (>= 2) win-
32,
win-
64


Name Version
r-sgb 1.0 Main properties and regression procedures using a generalization of the noarch
Dirichlet distribution called Simplicial Generalized Beta distribution. It is a
new distribution on the simplex (i.e. on the space of compositions or positive
vectors with sum of components equal to 1). The Dirichlet distribution can be
constructed from a random vector of independent Gamma variables divided by
their sum. The SGB follows the same construction with generalized Gamma
instead of Gamma variables. The Dirichlet exponents are supplemented by
an overall shape parameter and a vector of scales. The scale vector is itself a
composition and can be modeled with auxiliary variables through a log-ratio
transformation. Graf, M. (2017, ISBN: 978-84-947240-0-8). See also the vi-
gnette enclosed in the package. / GPL-2
r-sgee 0.6_0 Stagewise techniques implemented with Generalized Estimating Equations to noarch
handle individual, group, bi-level, and interaction selection. Stagewise ap-
proaches start with an empty model and slowly build the model over several
iterations, which yields a ‘path’ of candidate models from which model selec-
tion can be performed. This ‘slow brewing’ approach gives stagewise tech-
niques a unique flexibility that allows simple incorporation of Generalized Es-
timating Equations; see Vaughan, G., Aseltine, R., Chen, K., Yan, J., (2017)
<doi:10.1111/biom.12669> for details. / GPL-3
r-sgeostat 1.0_27An Object-oriented Framework for Geostatistical Modeling in S containing linux-
functions for variogram estimation, variogram fitting and kriging as well as 64,
some plot functions. Written entirely in S, therefore works only for small data osx-
sets in acceptable computing time. / GPL-2 64,
win-
64
r-sgl 1.2 Fit a regularized generalized linear model via penalized maximum likelihood. linux-
The model is fit for a path of values of the penalty parameter. Fits linear, 64,
logistic and Cox models. / GPL-3 osx-
64,
win-
64
r-sglasso 1.2.3 RCON(V, E) models are a kind of restriction of the Gaussian Graphical Mod- linux-
els defined by a set of equality constraints on the entries of the concentration 64,
matrix. ‘sglasso’ package implements the structured graphical lasso (sglasso) osx-
estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized 64,
RCON(V, E) model. Two cyclic coordinate algorithms are implemented to win-
compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) 64
and a cyclic coordinate descent (CCD) algorithm. / GPL-2
r-sgloptim 1.3.8 Fast generic solver for sparse group lasso optimization problems. The loss linux-
(objective) function must be defined in a C module. The optimization problem 64,
is solved using a coordinate gradient descent algorithm. Convergence of the osx-
algorithm is established (see reference) and the algorithm is applicable to a 64,
broad class of loss functions. Use of parallel computing for cross validation win-
and subsampling is supported through the ‘foreach’ and ‘doParallel’ packages. 64
Development version is on GitHub, please report package issues on GitHub. /
GPL-2


Name Version
r-sgmcmc 0.2.4 Provides functions that performs popular stochastic gradient Markov chain noarch
Monte Carlo (SGMCMC) methods on user specified models. The required
gradients are automatically calculated using ‘TensorFlow’ <https://www.
tensorflow.org/>, an efficient library for numerical computation. This means
only the log likelihood and log prior functions need to be specified. The meth-
ods implemented include stochastic gradient Langevin dynamics (SGLD),
stochastic gradient Hamiltonian Monte Carlo (SGHMC), stochastic gradient
Nose-Hoover thermostat (SGNHT) and their respective control variate ver-
sions for increased efficiency. References: M. Welling, Y. W. Teh (2011)
<http://www.icml-2011.org/papers/398_icmlpaper.pdf>; T. Chen, E. B. Fox,
C. E. Guestrin (2014) <arXiv:1402.4102>; N. Ding, Y. Fang, R. Babbush,
C. Chen, R. D. Skeel, H. Neven (2014) <https://papers.nips.cc/paper/5592-
bayesian-sampling-using-stochastic-gradient-thermostats>; J. Baker, P. Fearn-
head, E. B. Fox, C. Nemeth (2017) <arXiv:1706.05439>. / GPL-3
r-sgpdata 21.0_0.0
Data sets utilized by the ‘SGP’ package as exemplars for users to conduct their noarch
own student growth percentiles (SGP) analyses. / GPL-3
r-sgr 1.3 The package for Sample Generation by Replacement simulations (SGR; Lom- noarch
bardi & Pastore, 2014; Pastore & Lombardi, 2014). The package can be used
to perform fake data analysis according to the sample generation by replace-
ment approach. It includes functions for making simple inferences about dis-
crete/ordinal fake data. The package allows to study the implications of fake
data for empirical results. / GPL-2
r-sgrsea 0.1 Provides functions to implement sgRSEA (single-guide RNA Set Enrichment noarch
Analysis), which is a robust test for identification of essential genes from
genetic screening data using CRISPR (clustered regularly interspaced short
palindromic repeats) and Cas9 (CRISPR-associated nuclease 9) system. /
GPL-2
r-shades 1.4.0 Functions for easily manipulating colours, creating colour scales and calculat- noarch
ing colour distances. / BSD_3_clause
r-shape 1.4.4 Functions for plotting graphical shapes such as ellipses, circles, cylinders, ar- noarch
rows, . . . / GPL-3
r-shapechange 1.4 In a scatterplot where the response variable is Gaussian, Poisson or binomial, noarch
we consider the case in which the mean function is smooth with a change-
point, which is a mode, an inflection point or a jump point. The main routine
estimates the mean curve and the change-point as well using shape-restricted
B-splines. An optional subroutine delivering a bootstrap confidence interval
for the change-point is incorporated in the main routine. / GPL-2
r-shapefiles 0.7 Functions to read and write ESRI shapefiles / GPL-3 noarch
r-sharpdata 1.2 Functions and data sets inspired by data sharpening - data perturbation to linux-
achieve improved performance in nonparametric estimation, as described in 64,
Choi, E., Hall, P. and Rousson, V. (2000) <doi:10.1214/aos/1015957396>. osx-
Capabilities for enhanced local linear regression function and derivative es- 64,
timation are included, as well as an asymptotically correct iterated data sharp- win-
ening estimator for any degree of local polynomial regression estimation. A 64
cross-validation-based bandwidth selector is included which, in concert with
the iterated sharpener, will often provide superior performance, according to
a median integrated squared error criterion. Sample data sets are provided to
illustrate function usage. / Unlimited


r-sharpr2 1.1.1.0An algorithm for identifying high-resolution driver elements for datasets from noarch
a high-definition reporter assay library. Xinchen Wang, Liang He, Sarah
Goggin, Alham Saadat, Li Wang, Melina Claussnitzer, Manolis Kellis (2017)
<doi:10.1101/193136>. / GPL-2
r-shiftr 1.5 Fast enrichment analysis for locally correlated statistics via circular permuta- linux-
tions. The analysis can be performed at multiple significance thresholds for 64,
both primary and auxiliary data sets with efficient correction for multiple test- osx-
ing. / LGPL-3 64,
win-
64
r-shiftsharese 1.0.0 Provides confidence intervals in least-squares regressions when the variable noarch
of interest has a shift-share structure, and in instrumental variables regres-
sions when the instrument has a shift-share structure. The confidence intervals
implement the AKM and AKM0 methods developed in Adão, Kolesár, and
Morales (2019) <doi:10.1093/qje/qjz025>. / GPL-3
r-shiny 1.3.2 Makes it incredibly easy to build interactive web applications with R. Auto- linux-
matic reactive binding between inputs and outputs and extensive prebuilt wid- 32,
gets make it possible to build beautiful, responsive, and powerful applications linux-
with minimal effort. / GPL-3 | file LICENSE 64,
noarch,
osx-
64,
win-
32,
win-
64
r-shiny.i18n 0.1.0 It provides easy internationalization of Shiny applications. It can be used as noarch
standalone translation package to translate reports, interactive visualizations
or graphical elements as well. / MIT
r-shiny.router 0.1.1 The minimal router for your Shiny apps. It allows you to create dynamic noarch
web applications with real-time user interface and easily share URLs to pages
within your Shiny apps. / MIT
r-shiny.semantic 0.2.1 Creating a great user interface for your Shiny apps can be a hassle, especially noarch
if you want to work purely in R and don’t want to use, for instance HTML
templates. This package adds support for a powerful UI library Semantic UI
- <http://semantic-ui.com/>. It also supports universal UI input binding that
works with various DOM elements. / MIT
r-shinyace 0.4.0 Ace editor bindings to enable a rich text editing environment within Shiny. / noarch
MIT
r-shinyaframe 1.0.1 Make R data available in Web-based virtual reality experiences for immer- noarch
sive, cross-platform data visualizations. Includes the ‘gg-aframe’ JavaScript
package for a Grammar of Graphics declarative HTML syntax to create 3-
dimensional data visualizations with ‘Mozilla A-Frame’ <https://aframe.io>. /
AGPL-3
r-shinyalert 1.0 Easily create pretty popup messages (modals) in ‘Shiny’. A modal can contain noarch
text, images, OK/Cancel buttons, an input to get a response from the user, and
many more customizable options. / MIT
r-shinyanimate 0.3.0 An extension of ‘animate.css’ that allows user to easily add animations to any noarch
UI element in ‘shiny’ app using the elements id. / MIT


Name Version
r- 0.2.1 Provides Bootstrap 2 web components for use with the Shiny package. With noarch
shinybootstrap2 versions of Shiny prior to 0.11, these Bootstrap 2 components were included
as part of the package. Later versions of Shiny include Bootstrap 3, so the
Bootstrap 2 components have been moved into this package for those uses
who rely on features specific to Bootstrap 2. / GPL-3
r-shinybs 0.61 Adds additional Twitter Bootstrap components to Shiny. / GPL-3 linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-shinybusy 0.1.3 Add a global indicator (spinner, progress bar, gif) in your ‘shiny’ applications noarch
to show the user that the server is busy. / GPL-3
r- 0.2.0 Create a lightweight Shiny wrapper for the css-loaders created by Luke Hass linux-
shinycssloaders <https://github.com/lukehaas/css-loaders>. Wrapping a Shiny output will au- 32,
tomatically show a loader when the output is (re)calculating. / GPL-3 linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r- 0.9.0 A custom css/html or gif/image file for the loading screen in R ‘shiny’. It also noarch
shinycustomloader can use the marquee to have custom text loading screen. / GPL-3
r- 0.7.1 Create dashboards with ‘Shiny’. This package provides a theme on top of linux-
shinydashboard ‘Shiny’, making it easy to create attractive dashboards. / GPL (>= 2) | file 32,
LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r- 0.7.0 Extend ‘shinydashboard’ with ‘AdminLTE2’ components. ‘AdminLTE2’ is a noarch
shinydashboardplus free ‘Bootstrap 3’ dashboard template available at <https://adminlte.io>. Cus-
tomize boxes, add timelines and a lot more. / GPL-2
r-shinydnd 0.1.0 Add functionality to create drag and drop div elements in shiny. / GPL-3 noarch
r-shinyeffects 0.1.0 Add fancy CSS effects to your ‘shinydashboards’ or ‘shiny’ apps. 100% com- noarch
patible with ‘shinydashboardPlus’ and ‘bs4Dash’. / GPL-2
r-shinyfeedback 0.1.0 Easily display user feedback next to Shiny inputs. The feedback message is noarch
displayed when the feedback condition evaluates to TRUE. / GPL-3


Name Version
r-shinyglide 0.1.1 Insert Glide JavaScript component into Shiny applications for carousel or noarch
assistant-like user interfaces. / GPL-3
r-shinyhelper 0.3.1 Creates a lightweight way to add markdown helpfiles to ‘shiny’ apps, using noarch
modal dialog boxes, with no need to observe each help button separately. /
GPL-3
r-shinyjqui 0.3.2 An extension to shiny that brings interactions and animation effects from noarch
‘jQuery UI’ library. / MIT
r-shinyjs 1.0 Perform common useful JavaScript operations in Shiny apps that will greatly linux-
improve your apps without having to know any JavaScript. Examples include: 32,
hiding an element, disabling an input, resetting an input back to its original linux-
value, delaying code execution by a few seconds, and many more useful func- 64,
tions for both the end user and the developer. ‘shinyjs’ can also be used to noarch,
easily call your own custom JavaScript functions from R. / AGPL-3 osx-
64,
win-
32,
win-
64
r-shinylp 1.1.2 Provides functions that wrap HTML Bootstrap components code to enable the noarch
design and layout of informative landing home pages for Shiny applications.
This can lead to a better user experience for the users and writing less HTML
for the developer. / MIT
r-shinymaterial 0.5.5 Allows shiny developers to incorporate UI elements based on Google’s Ma- noarch
terial design. See <https://material.io/guidelines/> for more information. /
GPL-3
r-shinymatrix 0.2.0 Implements a custom matrix input field. / MIT noarch
r-shinyshortcut 0.1.0 Provides function shinyShortcut() that, when given the base directory of a noarch
shiny application, will produce an executable file that runs the shiny app di-
rectly in the user’s default browser. Tested on both windows and unix ma-
chines. Inspired by and borrowing from <http://www.mango-solutions.com/
wp/2017/03/shiny-based-tablet-or-desktop-app/>. / GPL-3
r-shinysky 2.0.0 A set of Shiny UI components includings alerts and styled buttons / MIT linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
r-shinythemes 1.1.2 Themes for use with Shiny. Includes several Bootstrap themes from <http: linux-
//bootswatch.com/>, which are packaged for use with Shiny applications. / 32,
GPL-3 | file LICENSE linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-shinytime 1.0.1 Provides a time input widget for Shiny. This widget allows intuitive time in- noarch
put in the ‘[hh]:[mm]:[ss]’ or ‘[hh]:[mm]’ (24H) format by using a separate
numeric input for each time component. The interface with R uses date-time
objects. See the project page for more information and examples. / GPL-3
r-shinytoastr 2.1.1 Browser notifications in ‘Shiny’ apps, using ‘toastr’: <https://github.com/ noarch
CodeSeven/toastr#readme>. / MIT
r-shinytree 0.2.7 Exposes bindings to jsTree – a JavaScript library that supports interactive trees noarch
– to enable a rich, editable trees in Shiny. / MIT
r-shinywidgets 0.4.9 Collection of custom input controls and user interface components for ‘Shiny’ noarch
applications. Give your applications a unique and colorful style ! / GPL-3
r-ship 1.0.2 The SHIP-package allows the estimation of various types of shrinkage covari- noarch
ance matrices. These types differ in terms of the so-called covariance target
(to be chosen by the user), the highly structured matrix which the standard
unbiased sample covariance matrix is shrunken towards and which optionally
incorporates prior biological knowledge extracted from the database KEGG.
The shrinkage intensity is obtained via an analytical procedure. / GPL-2
r-shipunov 1.2 A collection of functions for data manipulation, plotting and statistical com- noarch
puting, to use separately or with the book Visual Statistics. Use R!: Shipunov
(2019) <http://ashipunov.info/shipunov/software/r/r-en.htm>. Most useful
functions are probably Bclust(), Jclust() and BootA() which bootstrap hier-
archical clustering; Recode. . . () which multiple recode in a fast, flexible and
simple way; Misclass() which outputs confusion matrix even if classes are not
concerted; Overlap() which calculates overlaps of convex hulls from any pro-
jection; and Pleiad() which is fast and flexible correlogram. In fact, there are
much more useful functions, please see documentation. / GPL-2
r-shopifyr 1.0.0 An interface to the Admin API of the E-commerce service Shopify, (<https: noarch
//help.shopify.com/en/api/reference>). / GPL-3
r-shotgroups 0.7.5.1Analyzes shooting data with respect to group shape, precision, and accu- noarch
racy. This includes graphical methods, descriptive statistics, and inference
tests using standard, but also non-parametric and robust statistical methods.
Implements distributions for radial error in bivariate normal variables. Works
with files exported by ‘OnTarget PC/TDS’, ‘Silver Mountain’ e-target, ‘Shot-
Marker’ e-target, or ‘Taran’, as well as with custom data files in text format.
Supports inference from range statistics like extreme spread. Includes a set of
web-based graphical user interfaces. / GPL-2
r-showimage 1.0.0 Sometimes it is handy to be able to view an image file on an ‘R’ graphics noarch
device. This package just does that. Currently it supports ‘PNG’ files. / GPL-
2 | GPL-3


Name Version
r-shp2graph 0_5 Functions for converting network data from a SpatialLinesDataFrame object linux-
to an ‘igraph’-Class object. / GPL-2 64,
osx-
64,
win-
64
r-shrinkcovmat 1.4.0 Provides nonparametric Steinian shrinkage estimators of the covariance ma- linux-
trix that are suitable in high dimensional settings, that is when the number of 64,
variables is larger than the sample size. / GPL-2 | GPL-3 osx-
64,
win-
64
r-shuffle 1.0.1 Implementation of the shuffle estimator, a non-parametric estimator for signal noarch
and noise variance under mild noise correlations. / GPL (>= 2.0)
r-shutterstock 0.1.0 Access ‘Shutterstock’ API from R. The ‘Shutterstock’ API presents access noarch
to search, view, license and download the media and information from the
‘Shutterstock’s library <https://api-reference.shutterstock.com/>. / MIT
r-si 0.2.0 An implementation of four stochastic methods of integrating in R, includ- noarch
ing: 1. Stochastic Point Method (or Monte Carlo Method); 2. Mean Value
Method; 3. Important Sampling Method; 4. Stratified Sampling Method.
It can be used to estimate one-dimension or multi-dimension integration by
Monte Carlo methods. And the estimated variance (precision) is given. Refer-
ence: Caflisch, R. E. (1998) <doi:10.1017/S0962492900002804>. / GPL-3
r-siebanxicor 1.0.0 Allows to retrieve time series of all indicators available in the Bank noarch
of Mexico’s Economic Information System (<http://www.banxico.org.mx/
SieInternet/>). / MIT
r-sier 0.1.0 Methods for regression with high-dimensional predictors and univariate or noarch
maltivariate response variables. It considers the decomposition of the coef-
ficient matrix that leads to the best approximation to the signal part in the
response given any rank, and estimates the decomposition by solving a penal-
ized generalized eigenvalue problem followed by a least squares procedure.
Ruiyan Luo and Xin Qi (2017) <doi:10.1016/j.jmva.2016.09.005>. / GPL-2


Name Version
r-sieveph 1.0.0 Implements semiparametric estimation and testing procedures for a continu- noarch
ous, possibly multivariate, mark-specific hazard ratio (treatment/placebo) of an
event of interest in a randomized treatment efficacy trial with a time-to-event
endpoint, as described in Juraska M and Gilbert PB (2013), Mark-specific haz-
ard ratio model with multivariate continuous marks: an application to vaccine
efficacy. Biometrics 69(2):328 337, and in Juraska M and Gilbert PB (2015),
Mark-specific hazard ratio model with missing multivariate marks. Lifetime
Data Analysis 22(4): 606-25. The former considers continuous multivari-
ate marks fully observed in all subjects who experience the event of interest,
whereas the latter extends the previous work to allow multivariate marks that
are subject to missingness-at-random. For models with missing marks, two
estimators are implemented based on (i) inverse probability weighting (IPW)
of complete cases, and (ii) augmentation of the IPW estimating functions by
leveraging correlations between the mark and auxiliary data to ‘impute’ the ex-
pected profile score vectors for subjects with missing marks. The augmented
IPW estimator is doubly robust and recommended for use with incomplete
mark data. The methods make two key assumptions: (i) the time-to-event is
assumed to be conditionally independent of the mark given treatment, and (ii)
the weight function in the semiparametric density ratio/biased sampling model
is assumed to be exponential. Diagnostic testing procedures for evaluating va-
lidity of both assumptions are implemented. Summary and plotting functions
are provided for estimation and inferential results. / GPL-2
r-sievetest 1.2.3 Functions for making particle-size analysis. Sieve tests are widely used to noarch
obtain particle-size distribution of powders or granular materials. / GPL-2
r-sig 0.0_5 Print function signatures and find overly complicated code. / Unlimited noarch
r-sigclust 1.1.0 SigClust is a statistical method for testing the significance of clustering re- noarch
sults. SigClust can be applied to assess the statistical significance of splitting
a data set into two clusters. For more than two clusters, SigClust can be used
iteratively. / GPL-2
r- 1.3 Uses logistic regression to model the probability of detection as a function of noarch
sightabilitymodel covariates. This model is then used with observational survey data to estimate
population size, while accounting for uncertain detection. See Steinhorst and
Samuel (1989). / GPL-2
r-sigmanet 1.1.0 Create interactive graph visualizations using ‘Sigma.js’ <http://sigmajs.org/>. noarch
This package is meant to be used in conjunction with ‘igraph’, replacing the
(somewhat underwhelming) plotting features of the package. The idea is to
quickly render graphs, regardless of their size, in a way that allows for easy, it-
erative modification of aesthetics. Because ‘Sigma.js’ is a ‘javascript’ library,
the visualizations are inherently interactive and are well suited for integration
with ‘Shiny’ apps. While there are several ‘htmlwidgets’ focused on network
visualization, they tend to underperform on medium to large sized graphs.
‘Sigma.js’ was designed for larger network visualizations and this package
aims to make those strengths available to ‘R’ users. / MIT
r-sigmoid 0.3.0 Several different sigmoid functions are implemented, including a wrapper noarch
function, SoftMax preprocessing and inverse functions. / GPL-3
r-signal 0.7_6 A set of signal processing functions originally written for ‘Matlab’ and ‘Oc- linux-
tave’. Includes filter generation utilities, filtering functions, resampling rou-64,
tines, and visualization of filter models. It also includes interpolation func- osx-
tions. / GPL-2 64,
win-
64


r-signifreg 2.1 Provide consistent significance controlled variable selection procedure with noarch
different directions (forward, backward, stepwise) based on diverse criteria
(AIC, BIC, adjusted r-square, and p-value). The algorithm selects a final model
with only significant variables based on a correction choice of False Discovery
Rate, Bonferroni, or no correction. / GPL-2
r- 1.5.1 Perform sign test on one-sample data, which is one of the oldest non- noarch
signmedian.test parametric statistical methods. Assume that X comes from a continuous dis-
tribution with median = v ( unknown ). Test the null hypothesis H0: median
of X v = mu ( mu is the location parameter and is given in the test ) v.s. the
alternative hypothesis H1: v > mu ( or v < mu or v != mu ) and calculate the
p-value. When the sample size is large, perform the asymptotic sign test. In
both ways, calculate the R-estimate of location of X and the distribution free
confidence interval for mu. / GPL-2
r-sigoptr 0.0.1 Interfaces with the ‘SigOpt’ API. More info at <https://sigopt.com>. / MIT noarch
r-sigora 3.0.5 Pathway Analysis is the process of statistically linking observations on the noarch
molecular level to biological processes or pathways on the systems(i.e. organ-
ism, organ, tissue, cell) level. Traditionally, pathway analysis methods regard
pathways as collections of single genes and treat all genes in a pathway as
equally informative. This can lead to identification of spurious pathways as
statistically significant, since components are often shared amongst pathways.
SIGORA seeks to avoid this pitfall by focusing on genes or gene-pairs that are
(as a combination) specific to a single pathway. In relying on such pathway
gene-pair signatures (Pathway-GPS), SIGORA inherently uses the status of
other genes in the experimental context to identify the most relevant pathways.
The current version allows for pathway analysis of human and mouse datasets
and contains pre-computed Pathway-GPS data for pathways in the KEGG and
Reactome pathway repositories as well as mechanisms for extracting GPS for
user supplied repositories. / GPL-2
r-sii 1.0.3.1This package calculates ANSI S3.5-1997 Speech Intelligibility Index (SII), noarch
a standard method for computing the intelligibility of speech from acoustical
measurements of speech, noise, and hearing thresholds. This package includes
data frames corresponding to Tables 1 - 4 in the ANSI standard as well as a
function utilizing these tables and user-provided hearing threshold and noise
level measurements to compute the SII score. The methods implemented here
extend the standard computations to allow calculation of SII when the mea-
sured frequencies do not match those required by the standard by applying
interpolation to obtain values for the required frequencies – Development of
this package was funded by the Center for Bioscience Education and Technol-
ogy (CBET) of the Rochester Institute of Technology (RIT). / GPL-2
r-sim.diffproc 4.4 It provides users with a wide range of tools to simulate, estimate, analyze, linux-
and visualize the dynamics of stochastic differential systems in both forms Ito 64,
and Stratonovich. Statistical analysis with parallel Monte Carlo and moment osx-
equations methods of SDE’s. Enabled many searchers in different domains to 64,
use these equations to modeling practical problems in financial and actuarial win-
modeling and other areas of application, e.g., modeling and simulate of first 64
passage time problem in shallow water using the attractive center (Boukhetala
K, 1996) ISBN:1-56252-342-2. / GPL-2


Name Version
r-simboot 0.2_6 Provides estimation of simultaneous bootstrap and asymptotic confidence in- noarch
tervals for diversity indices, namely the Shannon and the Simpson index. Sev-
eral pre–specified multiple comparison types are available to choose. Further
user–defined contrast matrices are applicable. In addition, simboot estimates
adjusted as well as unadjusted p–values for two of the three proposed bootstrap
methods. Further simboot allows for comparing biological diversities of two
or more groups while simultaneously testing a user-defined selection of Hill
numbers of orders q, which are considered as appropriate and useful indices
for measuring diversity. / GPL-2
r-simcausal 0.5.5 A flexible tool for simulating complex longitudinal data using structural equa- noarch
tions, with emphasis on problems in causal inference. Specify interventions
and simulate from intervened data generating distributions. Define and eval-
uate treatment-specific means, the average treatment effects and coefficients
from working marginal structural models. User interface designed to facili-
tate the conduct of transparent and reproducible simulation studies, and allows
concise expression of complex functional dependencies for a large number of
time-varying nodes. See the package vignette for more information, documen-
tation and examples. / GPL-2
r-simcdm 0.1.1 Provides efficient R and ‘C’ routines to simulate cognitive diagnos- linux-
tic model data for Deterministic Input, Noisy And Gate (‘DINA’) 64,
and reduced Reparameterized Unified Model (‘rRUM’) from Culpep- osx-
per and Hudson (2017) <doi: 10.1177/0146621617707511>, Culpep- 64,
per (2015) <doi:10.3102/1076998615595403>, and de la Torre (2009) win-
<doi:10.3102/1076998607309474>. / GPL-2 64
r-simcop 0.7.0 Provides a framework to generating random variates from arbitrary multivari- noarch
ate copulae, while concentrating on (bivariate) extreme value copulae. Par-
ticularly useful if the multivariate copulae are not available in closed form. /
GPL-2
r-simctest 2.5 Algorithms for the implementation and evaluation of Monte Carlo tests, as linux-
well as for their use in multiple testing procedures. / GPL-2 64,
osx-
64,
win-
64
r-simdistr 1.0.1 Assessment of the distributions of baseline continuous and categorical vari- noarch
ables in randomised trials. This method is based on the Carlisle-Stouffer
method with Monte Carlo simulations. It calculates p-values for each trial
baseline variable, as well as combined p-values for each trial - these p-values
measure how compatible are distributions of trials baseline variables with ran-
dom sampling. This package also allows for graphically plotting the cumu-
lative frequencies of computed p-values. Please note that code was partly
adapted from Carlisle JB, Loadsman JA. (2017) <doi:10.1111/anae.13650>.
/ GPL-2
r-simecol 0.8_13An object oriented framework to simulate ecological (and other) dynamic sys- linux-
tems. It can be used for differential equations, individual-based (or agent- 64,
based) and other models as well. It supports structuring of simulation scenar- osx-
ios (to avoid copy and paste) and aims to improve readability and re-usability 64,
of code. / GPL-2 win-
64


r-simex 1.8 Implementation of the SIMEX-Algorithm by Cook & Stefanski (1994) noarch
<doi:10.1080/01621459.1994.10476871> and MCSIMEX by Küchenhoff,
Mwalili & Lesaffre (2006) <doi:10.1111/j.1541-0420.2005.00396.x>. / GPL-
3
r-simexaft 1.0.7.1Implement of the Simulation-Extrapolation (SIMEX) algorithm for the accel- noarch
erated failure time (AFT) with covariates subject to measurement error. / GPL-
3
r-simframe 0.5.3 A general framework for statistical simulation. / GPL-2 linux-
64,
osx-
64,
win-
64
r-simhaz 0.1 Generate power for the Cox proportional hazards model by simulating survival noarch
events data with time dependent exposure status for subjects. A dichotomous
exposure variable is considered with a single transition from unexposed to
exposed status during the subject’s time on study. / GPL-2
r-similar 1.0.6 An implementation of a novel method to quantify the similarity the code-base linux-
of R functions by means of program dependence graphs. Possible use cases 64,
include detection of code clones for improving software quality and of plagia- osx-
rism among students’ homework assignments. / GPL-3 64,
win-
64
r- 1.4 Functions to run and assist four different similarity measures. The similarity noarch
similaritymeasures measures included are: longest common subsequence (LCSS), Frechet dis-
tance, edit distance and dynamic time warping (DTW). Each of these simi-
larity measures can be calculated from two n-dimensional trajectories, both in
matrix form. / GPL-3
r-simile 1.3.3 Allows a Simile model saved as a compiled binary to be loaded, parameter- noarch
ized, executed and interrogated. This version works with Simile v5.97 on. /
Unlimited
r-siminf 6.3.0 Provides an efficient and very flexible framework to conduct data-driven epi- linux-
demiological modeling in realistic large scale disease spread simulations. The 64,
framework integrates infection dynamics in subpopulations as continuous-time osx-
Markov chains using the Gillespie stochastic simulation algorithm and in- 64,
corporates available data such as births, deaths and movements as scheduled win-
events at predefined time-points. Using C code for the numerical solvers and 64
‘OpenMP’ (if available) to divide work over multiple processors ensures high
performance when simulating a sample outcome. One of our design goals was
to make the package extendable and enable usage of the numerical solvers
from other R extension packages in order to facilitate complex epidemiologi-
cal research. The package contains template models and can be extended with
user-defined models. / GPL-3


Name Version
r-simmer 4.3.0 A process-oriented and trajectory-based Discrete-Event Simulation (DES) linux-
package for R. It is designed as a generic yet powerful framework. The ar- 64,
chitecture encloses a robust and fast simulation core written in ‘C’ with au- osx-
tomatic monitoring capabilities. It provides a rich and flexible R API that 64,
revolves around the concept of trajectory, a common path in the simulation win-
model for entities of the same type. Documentation about ‘simmer’ is provided 64
by several vignettes included in this package, via the paper by Ucar, Smeets &
Azcorra (2019, <doi:10.18637/jss.v090.i02>), and the paper by Ucar, Hernán-
dez, Serrano & Azcorra (2018, <doi:10.1109/MCOM.2018.1700960>); see
‘citation(simmer)’ for details. / GPL-2
r-simml 0.1.0 A major challenge in estimating treatment decision rules from a random- noarch
ized clinical trial dataset with covariates measured at baseline lies in detect-
ing relatively small treatment effect modification-related variability (i.e., the
treatment-by-covariates interaction effects on treatment outcomes) against a
relatively large non-treatment-related variability (i.e., the main effects of co-
variates on treatment outcomes). The class of Single-Index Models with
Multiple-Links is a novel single-index model specifically designed to esti-
mate a single-index (a linear combination) of the covariates associated with the
treatment effect modification-related variability, while allowing a nonlinear as-
sociation with the treatment outcomes via flexible link functions. The models
provide a flexible regression approach to developing treatment decision rules
based on patients’ data measured at baseline. We refer to Petkova, Tarpey,
Su, and Ogden (2017) <doi: 10.1093/biostatistics/kxw035> and A constrained
single-index model for estimating interactions between a treatment and co-
variates (under review, 2019) for detail. The main function of this package is
simml(). / GPL-3
r-simms 1.2.0 Algorithms to create prognostic biomarkers using biological genesets or net- noarch
works. / GPL-2
r-simone 1.0_4 Implements the inference of co-expression networks based on partial correla- linux-
tion coefficients from either steady-state or time-course transcriptomic data. 64,
Note that with both type of data this package can deal with samples collected osx-
in different experimental conditions and therefore not identically distributed. 64,
In this particular case, multiple but related networks are inferred on one simone win-
run. / GPL-2 64
r-simphe 0.2.0 Provides functions to simulate single or multiple, independent or correlated noarch
phenotype(s) with additive, dominance effects and their interactions. Also
includes functions to generate phenotype(s) with specific heritability. Flexible
and user-friendly options for simulation. / GPL-2
r-simpleboot 1.1_7 Simple bootstrap routines. / GPL-2 noarch
r-simplecache 0.4.1 Provides intuitive functions for caching R objects, encouraging reproducible, noarch
restartable, and distributed R analysis. The user selects a location to store
caches, and then provides nothing more than a cache name and instructions
(R code) for how to produce the R object. Also provides some advanced op-
tions like environment assignments, recreating or reloading caches, and cluster
compute bindings (using the ‘batchtools’ package) making it flexible enough
for use in large-scale data analysis projects. / BSD_2_clause
r-simplegraph 1.0.0 Simple classic graph algorithms for simple graph classes. Graphs may possess noarch
vertex and edge attributes. ‘simplegraph’ has so dependencies and it is written
entirely in R, so it is easy to install. / MIT
r-simpleneural 0.1.1 Trains neural networks (multilayer perceptrons with one hidden layer) for bi- noarch
or multi-class classification. / MIT


Name Version
r-simplercache 0.3.2 Simple result caching in R based on R.cache. The global environment is not noarch
considered when caching results simplifying moving files between multiple
instances of R. Relies on more base functions than R.cache (e.g. cached results
are saved using saveRDS() and readRDS()). / LGPL-3
r-simplesetup 0.1.0 When working across multiple machines and, similarly for reproducible re- noarch
search, it can be time consuming to ensure that you have all of the needed
packages installed and loaded and that the correct working directory is set.
‘simpleSetup’ provides simple functions for making these tasks more straight-
forward. / GPL-3
r- 1.2 Provides methods to integrate functions over m-dimensional simplices in n- noarch
simplicialcubature dimensional Euclidean space. There are exact methods for polynomials and
adaptive methods for integrating an arbitrary function. Dirichlet probabilities
are calculated in certain cases. / GPL-2
r-simputation 0.2.3 Easy to use interfaces to a number of imputation methods that fit in the not-a- linux-
pipe operator of the ‘magrittr’ package. / GPL-3 64,
osx-
64,
win-
64
r-simsalapar 1.0_10Tools for setting up (design), conducting, and evaluating large-scale simulation noarch
studies with graphics and tables, including parallel computations. / GPL-2 |
GPL-3
r- 0.1.1 Contains two functions for simulating survival data from piecewise exponen- noarch
simscrpiecewise tial hazards with a proportional hazards adjustment for covariates. The first
function SimUNIVPiecewise simulates univariate survival data based on a
piecewise exponential hazard, covariate matrix and true regression vector. The
second function SimSCRPiecewise semi-competing risks data based on three
piecewise exponential hazards, three true regression vectors and three matrices
of patient covariates (which can be different or the same). This simulates from
the Semi-Markov model of Lee et al (2015) given patient covariates, regression
parameters, patient frailties and baseline hazard functions. / GPL-2
r-simsem 0.5_14Provides an easy framework for Monte Carlo simulation in structural equation noarch
modeling, which can be used for various purposes, such as such as model fit
evaluation, power analysis, or missing data handling and planning. / GPL-2
r-simsurv 0.2.3 Simulate survival times from standard parametric survival distributions (ex- noarch
ponential, Weibull, Gompertz), 2-component mixture distributions, or a user-
defined hazard, log hazard, cumulative hazard, or log cumulative hazard func-
tion. Baseline covariates can be included under a proportional hazards as-
sumption. Time dependent effects (i.e. non-proportional hazards) can be in-
cluded by interacting covariates with linear time or a user-defined function
of time. Clustered event times are also accommodated. The 2-component
mixture distributions can allow for a variety of flexible baseline hazard func-
tions reflecting those seen in practice. If the user wishes to provide a user-
defined hazard or log hazard function then this is possible, and the result-
ing cumulative hazard function does not need to have a closed-form solu-
tion. Note that this package is modelled on the ‘survsim’ package avail-
able in the ‘Stata’ software (see Crowther and Lambert (2012) <http://www.
stata-journal.com/sjpdf.html?articlenum=st0275> or Crowther and Lambert
(2013) <doi:10.1002/sim.5823>). / GPL-3


Name Version
r-simtimer 4.0.0 Handles datetimes as integers for the usage inside Discrete-Event Simu- noarch
lations (DES). The conversion is made using the internally generic func-
tion as.numeric() of the base package. DES is described in Simula-
tion Modeling and Analysis by Averill Law and David Kelton (1999)
<doi:10.2307/2288169>. / GPL-3
r-simulator 0.2.0 A framework for performing simulations such as those common in method- noarch
ological statistics papers. The design principles of this package are described
in greater depth in Bien, J. (2016) The simulator: An Engine to Stream-
line Simulations, which is available at <http://faculty.bscb.cornell.edu/~bien/
simulator.pdf>. / GPL-3
r-simule 1.3.0 This is an R implementation of a constrained l1 minimization approach for noarch
estimating multiple Sparse Gaussian or Nonparanormal Graphical Models
(SIMULE). The SIMULE algorithm can be used to estimate multiple re-
lated precision matrices. For instance, it can identify context-specific gene
networks from multi-context gene expression datasets. By performing data-
driven network inference from high-dimensional and heterogenous data sets,
this tool can help users effectively translate aggregated data into knowledge
that take the form of graphs among entities. Please run demo(simuleDemo) to
learn the basic functions provided by this package. For further details, please
read the original paper: Beilun Wang, Ritambhara Singh, Yanjun Qi (2017)
<DOI:10.1007/s10994-017-5635-7>. / GPL-2
r-sin 0.6 This package provides routines to perform SIN model selection as described noarch
in Drton & Perlman (2004, 2008). The selected models are represented in the
format of the ‘ggm’ package, which allows in particular parameter estimation
in the selected model. / GPL-2
r-sinaplot 1.1.0 The sinaplot is a data visualization chart suitable for plotting any single vari- noarch
able in a multiclass data set. It is an enhanced jitter strip chart, where the
width of the jitter is controlled by the density distribution of the data within
each class. / GPL-2
r-sinib 1.0.0 Density, distribution function, quantile function and random generation for noarch
the sum of independent non-identical binomial distribution with parameters
code{size} and code{prob}. / GPL-3
r-sirad 2.3_3 Calculating daily global solar radiation at horizontal surface using several noarch
well-known models (i.e. Angstrom-Prescott, Supit-Van Kappel, Hargreaves,
Bristow and Campbell, and Mahmood-Hubbard), and model calibration based
on ground-truth data, and (3) model auto-calibration. The FAO Penmann-
Monteith equation to calculate evapotranspiration is also included. / GPL-2
r-sisvive 1.4 Selects invalid instruments amongst a candidate of potentially bad instruments. noarch
The algorithm selects potentially invalid instruments and provides an estimate
of the causal effect between exposure and outcome. / GPL-2
r-sitmo 2.0.1 Provided within are two high quality and fast PPRNGs that may be used in an linux-
‘OpenMP’ parallel environment. In addition, there is a generator for one di- 64,
mensional low-discrepancy sequence. The objective of this library to consoli- osx-
date the distribution of the ‘sitmo’ (C98 & C11), ‘threefry’ and ‘vandercorput’ 64,
(C11-only) engines on CRAN by enabling others to link to the header files win-
inside of ‘sitmo’ instead of including a copy of each engine within their indi- 64
vidual package. Lastly, the package contains example implementations using
the ‘sitmo’ package and three accompanying vignette that provide additional
information. / MIT
r-sitools 1.4 Format a number (or a list of numbers) to a string (or a list of strings) with SI noarch
prefix. Use SI prefixes as constants like (4 * milli)^2 / GPL-3


r-sitree 0.1_7 Forecasts plots at tree level. / GPL-2 noarch
r-sizer 0.1_5 Calculates and plots the SiZer map for scatterplot data. A SiZer map is a way noarch
of examining when the p-th derivative of a scatterplot-smoother is significantly
negative, possibly zero or significantly positive across a range of smoothing
bandwidths. / GPL-2
r-sjdbc 1.6.0 Provides a database-independent JDBC interface. / BSD_3_clause noarch
r-skat 1.3.2.1Functions for kernel-regression-based association tests including Burden test, linux-
SKAT and SKAT-O. These methods aggregate individual SNP score statistics 64,
in a SNP set and efficiently compute SNP-set level p-values. / GPL-2 osx-
64,
win-
64
r-skda 0.1 Sparse (Multicategory) Kernel Discriminant Analysis does variable selection linux-
for nonparametric classification / GPL-2 64,
osx-
64,
win-
64
r-skeletor 1.0.4 A tool for bootstrapping new packages with useful defaults, including a test noarch
suite outline that passes checks and helpers for running tests, checking test
coverage, building vignettes, and more. Package skeletons it creates are set
up for pushing your package to ‘GitHub’ and using other hosted services for
building and test automation. / MIT
r-skellam 0.2.0 Functions for the Skellam distribution, including: density (pmf), cdf, quantiles noarch
and regression. / GPL-2
r-skewt 0.1 Density, distribution function, quantile function and random generation for the noarch
skewed t distribution of Fernandez and Steel. / GPL-3
r-skmeans 0.2_11Algorithms to compute spherical k-means partitions. Features several meth- noarch
ods, including a genetic and a fixed-point algorithm and an interface to the
CLUTO vcluster program. / GPL-2
r-skywatchr 0.8_2 Query and download satellite imagery and climate/atmospheric datasets us- noarch
ing the SkyWatch API. Search datasets by wavelength (band), cloud cover,
resolution, location, date, etc. Get the query results as data frame and as
HTML. To learn more about the SkyWatch API, see <https://github.com/
skywatchspaceapps/api>. / GPL-2
r-slam 0.1_45Data structures and algorithms for sparse arrays and matrices, based on index linux-
arrays and simple triplet representations, respectively. / GPL-2 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-slc 0.3 Estimates the slope and level change present in data after removing phase A noarch
trend. Represents graphically the original and the detrended data. / GPL-2


Name Version
r-sldassay 1.8 Calculates maximum likelihood estimate, exact and asymptotic confidence in- noarch
tervals, and exact and asymptotic goodness of fit p-values for concentration
of infectious units from serial limiting dilution assays. This package uses the
likelihood equation, exact goodness of fit p-values, and exact confidence inter-
vals described in Meyers et al. (1994) <http://jcm.asm.org/content/32/3/732.
full.pdf>. This software is also implemented as a web application through the
Shiny R package <https://iupm.shinyapps.io/sldassay/>. / GPL-3
r-sleekts 1.0.2 Compute Time series Resistant Smooth 4253H, twice smoothing method. / noarch
GPL-3
r-sleepr 0.3.0 Use behavioural variables to score activity and infer sleep from bouts of im- noarch
mobility. It is primarily designed to score sleep in fruit flies from Drosophila
Activity Monitor (TriKinetics) and Ethoscope data. It implements sleep scor-
ing using the five-minute rule (Hendricks et al. (2000) <DOI:10.1016/S0896-
6273(00)80877-6>), activity classification for Ethoscopes (Geissmann et al.
(2017) <DOI:10.1371/journal.pbio.2003026>) and a new algorithm to detect
when animals are dead. / GPL-3
r-sleuth2 2.0_5 Data sets from Ramsey, F.L. and Schafer, D.W. (2002), The Statistical Sleuth: noarch
A Course in Methods of Data Analysis (2nd ed), Duxbury. / GPL-2
r-sleuth3 1.0_3 Data sets from Ramsey, F.L. and Schafer, D.W. (2013), The Statistical Sleuth: noarch
A Course in Methods of Data Analysis (3rd ed), Cengage Learning. / GPL-2
r-slfm 1.0.0 Set of tools to find coherent patterns in microarray data using a Bayesian linux-
Sparse Latent Factor Model - SLFM; see Duarte and Mayrink (2015) 64,
<DOI:10.1007/978-3-319-12454-4_15>. Considerable effort has been put into osx-
making slfm fast and memory efficient, turning it an interesting alternative to 64,
simpler methods in terms of execution time. It implements versions of the win-
SLFM based on two type of mixtures priors for the loadings: one relying on 64
a degenerate component at zero and the other using a small variance normal
distribution for the spike part of the mixture. It also implements additional
functions to allow pre-processing procedures for the data and to fit the model
for a large number of probesets or genes. / GPL-2
r-slhd 2.1_1 Generate the optimal Latin Hypercube Designs (LHDs) for computer exper- linux-
iments with quantitative factors and the optimal Sliced Latin Hypercube De- 64,
signs (SLHDs) for computer experiments with both quantitative and qualitative osx-
factors. Details of the algorithm can be found in Ba, S., Brenneman, W. A. and 64,
Myers, W. R. (2015), Optimal Sliced Latin Hypercube Designs, Technomet- win-
rics. Important function in this package is maximinSLHD. / LGPL-2.1 64
r-slickr 0.2.4 Create and customize interactive carousels using the ‘Slick’ JavaScript library noarch
and the ‘htmlwidgets’ package. The carousels can contain plots produced in
R, images, ‘iframes’, videos and other ‘htmlwidgets’. These carousels can
be used directly from the R console, from ‘RStudio’, in Shiny apps and R
Markdown documents. / MIT
r-slide 1.0.0 This statistical method uses the nearest neighbor algorithm to estimate abso- noarch
lute distances between single cells based on a chosen constellation of surface
proteins, with these distances being a measure of the similarity between the
two cells being compared. Based on Sen, N., Mukherjee, G., and Arvin, A.M.
(2015) <DOI:10.1016/j.ymeth.2015.07.008>. / GPL-3
r-slideview 0.1.0 Create a side-by-side view of raster(image)s with an interactive slider to switch noarch
between regions of the images. This can be especially useful for image com-
parison of the same region at different time stamps. / MIT


Name Version
r-slim 0.1.1 Fits singular linear models to longitudinal data. Singular linear models are noarch
useful when the number, or timing, of longitudinal observations may be in-
formative about the observations themselves. They are described in Farewell
(2010) <doi:10.1093/biomet/asp068>, and are extensions of the linear incre-
ments model <doi:10.1111/j.1467-9876.2007.00590.x> to general longitudi-
nal data. / GPL-3
r-slippymath 0.3.1 Provides functions for performing common tasks when working with slippy noarch
map tile service APIs e.g. Google maps, Open Street Map, Mapbox, Stamen,
among others. Functionality includes converting from latitude and longitude
to tile numbers, determining tile bounding boxes, and compositing tiles to a
georeferenced raster image. / MIT
r-slope 0.1.3 Efficient procedures for Sorted L1 Penalized Estimation (SLOPE). The sorted linux-
L1 norm is useful for statistical estimation and testing, particularly for variable 64,
selection in the linear model. / GPL-3 osx-
64,
win-
64
r-slouch 2.1.2 An implementation of a phylogenetic comparative method. It can fit uni- noarch
variate among-species Ornstein-Uhlenbeck models of phenotypic trait evolu-
tion, where the trait evolves towards a primary optimum. The optimum can
be modelled as a single parameter, as multiple discrete regimes on the phy-
logenetic tree, and/or with continuous covariates. See also Hansen (1997)
doi:10.2307/2411186, Butler & King (2004) doi:10.1086/426002, Hansen et
al. (2008) doi:10.1111/j.1558-5646.2008.00412.x. / GPL-2
r-slp 1.0_5 Interface for creation of ‘slp’ class smoother objects for use in Generalized linux-
Additive Models (as implemented by packages ‘gam’ and ‘mgcv’). / GPL-2 64,
osx-
64,
win-
64
r-sm 2.2_5.6
This is software linked to the book ‘Applied Smoothing Techniques for Data linux-
Analysis - The Kernel Approach with S-Plus Illustrations’ Oxford University 64,
Press. / GPL-2 osx-
64,
win-
64
r-smaa 0.3_0 Implementation of the Stochastic Multi-Criteria Acceptability Analysis linux-
(SMAA) family of Multiple Criteria Decision Analysis (MCDA) methods. / 64,
GPL-3 osx-
64,
win-
64
r-smac 1.0 This package provides a solution path for L1-penalized angle-based classifi- linux-
cation. Three loss functions are implemented in smac, including the deviance 64,
loss in logistic regression, the exponential loss in boosting, and the proximal osx-
support vector machine loss. / GPL-2 64,
win-
64
r-smallarea 0.1 Inference techniques for Fay Herriot Model. / GPL-2 noarch


Name Version
r-smartsizer 1.0.1 A set of tools for determining the necessary sample size in order to identify the noarch
optimal dynamic treatment regime in a sequential, multiple assignment, ran-
domized trial (SMART). Utilizes multiple comparisons with the best method-
ology to adjust for multiple comparisons. Designed for an arbitrary SMART
design. Please see Artman (2018) <arXiv:1804.04587> for more details. /
GPL-3
r-smatr 3.4_8 Methods for fitting bivariate lines in allometry using the major axis (MA) noarch
or standardised major axis (SMA), and for making inferences about such
lines. The available methods of inference include confidence intervals and
one-sample tests for slope and elevation, testing for a common slope or el-
evation amongst several allometric lines, constructing a confidence interval
for a common slope or elevation, and testing for no shift along a common
axis, amongst several samples. See Warton et al. 2012 <doi:10.1111/j.2041-
210X.2011.00153.x> for methods description. / GPL-2
r-smc 1.1 particle filtering, auxiliary particle filtering and sequential Monte Carlo algo- linux-
rithms / GPL-2 64,
osx-
64,
win-
64
r-smcfcs 1.4.0 Implements multiple imputation of missing covariates by Substantive Model noarch
Compatible Fully Conditional Specification. This is a modification of the pop-
ular FCS/chained equations multiple imputation approach, and allows impu-
tation of missing covariate values from models which are compatible with the
user specified substantive model. / GPL-3
r-smco 0.1 This package is for optimizing non-linear complex functions based on Monte noarch
Carlo random sampling. / GPL-2
r-smcrm 0.0_3 Data Sets for Kumar and Petersen (2012). Statistical Methods in Customer noarch
Relationship Management, Wiley: New York. / GPL-3
r-smcure 2.0 An R-package for Estimating Semiparametric PH and AFT Mixture Cure noarch
Models / GPL-2
r-smdata 1.2 Contains data files to accompany Smithson & Merkle (2013), Generalized Lin- noarch
ear Models for Categorical and Continuous Limited Dependent Variables. /
GPL-2
r-smds 1.0 Symbolic multidimensional scaling for interval-valued dissimilarities. The hy- linux-
persphere model and the hyperbox model are available. / GPL-2 64,
osx-
64,
win-
64
r-sme 1.0.2 Fit smoothing-splines mixed-effects models to replicated functional data sets linux-
and visualise the results. / GPL-3 64,
osx-
64,
win-
64
r-smfilter 1.0.3 Provides the filtering algorithms for the state space models on the Stiefel man- noarch
ifold as well as the corresponding sampling algorithms for uniform, vector
Langevin-Bingham and matrix Langevin-Bingham distributions on the Stiefel
manifold. / GPL-3


Name Version
r-smfsb 1.3 Code and data for modelling and simulation of stochastic kinetic biochemical linux-
network models. It contains the code and data associated with the second and 64,
third editions of the book Stochastic Modelling for Systems Biology, published osx-
by Chapman & Hall/CRC Press. / LGPL-3 64,
win-
64
r-smirnov 1.0_1 This tiny package contains one function smirnov() which calculates two scaled noarch
taxonomic coefficients, Txy (coefficient of similarity) and Txx (coefficient of
originality). These two characteristics may be used for the analysis of similar-
ities between any number of taxonomic groups, and also for assessing unique-
ness of giving taxon. It is possible to use smirnov() output as a distance mea-
sure: convert it to distance by as.dist(1 - smirnov(x)). / GPL-2
r-smisc 0.3.9.1A collection of functions for statistical computing and data manipulation in linux-
R. Includes routines for data ingestion, operating on dataframes and matri- 64,
ces, conversion to and from lists, converting factors, filename manipulation, osx-
programming utilities, parallelization, plotting, statistical and mathematical 64,
operations, and time series. / BSD_3_clause win-
64
r- 1.0.1 Constructs a yield curve by the Smith-Wilson method from a table of LIBOR noarch
smithwilsonyieldcurve and SWAP rates / GPL-3
r-smitidvisu 0.0.6 Visualisation tools for ‘SMITIDstruct’ package. Allow to visualize host time- linux-
line, transmission tree, index diversities and variant graph using HTMLwid- 64,
gets. It mainly using D3JS javascript framework. / GPL-3 osx-
64,
win-
64
r-smloutliers 0.1 Local Correlation Integral (LOCI) method for outlier identification is imple- noarch
mented here. The LOCI method developed here is invented in Breunig, et al.
(2000), see <doi:10.1145/342009.335388>. / GPL-2
r-smma 1.0.2 Efficient design matrix free procedure for solving a soft maximin problem linux-
for large scale array-tensor structured models. Currently Lasso and SCAD 64,
penalized estimation is implemented. / GPL-2 osx-
64,
win-
64
r-smoother 1.1 A collection of methods for smoothing numerical data, commencing with a noarch
port of the Matlab gaussian window smoothing function. In addition, several
functions typically used in smoothing of financial data are included. / GPL-2
r-smoothhazard 1.4.1 Estimation of two-state (survival) models and irreversible illness- death mod- linux-
els with possibly interval-censored,left-truncated and right-censored data. Pro- 64,
portional intensities regression models can be specified to allow for covariates osx-
effects separately for each transition. We use either a parametric approach with 64,
Weibull baseline intensities or a semi-parametric approach with M-splines ap- win-
proximation of baseline intensities in order to obtain smooth estimates of the 64
hazard functions. Parameter estimates are obtained by maximum likelihood in
the parametric approach and by penalized maximum likelihood in the semi-
parametric approach. / GPL-2


Name Version
r-smoothhr 1.0.2 Provides flexible hazard ratio curves allowing non-linear relationships between noarch
continuous predictors and survival. To better understand the effects that each
continuous covariate has on the outcome, results are ex pressed in terms of
hazard ratio curves, taking a specific covariate value as reference. Confidence
bands for these curves are also derived. / GPL-2
r-smoothie 1.0_1 Functions to smooth two-dimensional fields using FFT and the convolution noarch
theorem / GPL-2
r-smoothmest 0.1_2 Some M-estimators for 1-dimensional location (Bisquare, ML for the Cauchy noarch
distribution, and the estimators from application of the smoothing principle
introduced in Hampel, Hennig and Ronchetti (2011) to the above, the Huber
M-estimator, and the median, main function is smoothm), and Pitman estima-
tor. / GPL-3
r-smoothsurv 2.0.1 Contains, as a main contribution, a function to fit a regression model with pos- linux-
sibly right, left or interval censored observations and with the error distribution 64,
expressed as a mixture of G-splines. Core part of the computation is done in osx-
compiled C written using the Scythe Statistical Library Version 0.3. / GPL-2 64,
win-
64
r-smpracticals 1.4_3 Contains the datasets and a few functions for use with the practicals out- noarch
lined in Appendix A of the book Statistical Models (Davison, 2003, Cam-
bridge University Press). The practicals themselves can be found at <http:
//statwww.epfl.ch/davison/SM/>. / GPL-2
r-smr 2.0.1 Computes the studentized midrange distribution (pdf, cdf and quantile) and noarch
generates random numbers / GPL-2
r-sms 2.3.1 Produce small area population estimates by fitting census data to survey data. noarch
/ GPL-3
r-smss 1.0_2 Datasets used in Statistical Methods for the Social Sciences (SMSS) by Alan noarch
Agresti and Barbara Finlay. / GPL-3
r-smvar 1.3.3 Implements the structural model for variances in order to detect differentially noarch
expressed genes from gene expression data / GPL-3
r-sn 1.5_4 Build and manipulate probability distributions of the skew-normal family and noarch
some related ones, notably the skew-t family, and provide related statistical
methods for data fitting and model diagnostics, in the univariate and the mul-
tivariate case. / GPL-2 | GPL-3
r-snakecase 0.11.0A consistent, flexible and easy to use tool to parse and convert strings into noarch
cases like snake or camel among others. / GPL-3
r-snakecharmr 1.0.7.1Run ‘Python’ code, make function calls, assign and retrieve variables, etc. linux-
from R. A fork from ‘rPython’ which uses ‘jsonlite’, ‘Rcpp’ and has several 64,
fixes and improvements. / GPL-2 osx-64
r- 2.1.0 Plays the game of Snakes and Ladders and has tools for analyses. The tools noarch
snakesandladdersanalysis included allow you to find the average moves to win, frequency of each square,
importance of the snakes and the ladders, the most common square and the
plotting of the game played. / GPL-2
r-snappier 0.1.0 Compression and decompression with ‘Snappy’. / BSD_3_clause linux-
64,
osx-
64,
win-
64


Name Version
r-snapshot 0.1.2 Functions for reading and writing Gadget N-body snapshots. The Gadget code noarch
is popular in astronomy for running N-body / hydrodynamical cosmological
and merger simulations. To find out more about Gadget see the main distribu-
tion page at www.mpa-garching.mpg.de/gadget/ / GPL-2
r-snem 0.1.0 Efficient estimation of multivariate skew-normal distribution in closed form. / noarch
GPL-2
r-snipem 1.0.1 Snipping methods optimally removing scattered cells for robust estimation and linux-
cluster analysis. / GPL-2 64,
osx-
64,
win-
64
r-snn 1.1 Implement K-nearest neighbor classifier, weighted nearest neighbor classifier, noarch
bagged nearest neighbor classifier, optimal weighted nearest neighbor clas-
sifier and stabilized nearest neighbor classifier, and perform model selection
via 5 fold cross-validation for them. This package also provides functions for
computing the classification error and classification instability of a classifica-
tion procedure. / GPL-3
r-snnr 1.0 Solve the problem of over-parameterization in neural networks for genomic se- linux-
lection. Daniel Gianola, Hayrettin OkutEmail, Kent A Weigel and Guilherme 64,
JM Rosa (2011) <doi:10.1186/1471-2156-12-87>. / GPL-2 osx-
64,
win-
64
r-snow 0.4_3 Support for simple parallel computing in R. / GPL-3 noarch
r-snowballc 0.6.0 An R interface to the C libstemmer library that implements Porter’s word linux-
stemming algorithm for collapsing words to a common root to aid compari- 32,
son of vocabulary. Currently supported languages are Danish, Dutch, English, linux-
Finnish, French, German, Hungarian, Italian, Norwegian, Portuguese, Roma- 64,
nian, Russian, Spanish, Swedish and Turkish. / BSD_3_clause file LICENSE osx-
64,
win-
32,
win-
64
r-snowflakes 1.0.0 The function generates and plots random snowflakes. Each snowflake is noarch
defined by a given diameter, width of the crystal, color, and random seed.
Snowflakes are plotted in such way that they always remain round, no matter
what the aspect ratio of the plot is. Snowflakes can be created using transparent
colors, which creates a more interesting, somewhat realistic, image. Images of
the snowflakes can be separately saved as svg files and used in websites as
static or animated images. / GPL-2
r-snpar 1.0 contains several supplementary non-parametric statistics methods including noarch
quantile test, Cox-Stuart trend test, runs test, normal score test, kernel PDF
and CDF estimation, kernel regression estimation and kernel Kolmogorov-
Smirnov test. / GPL-2
r-snpmaxsel 1.0_3 This package implements asymptotic methods related to maximally selected noarch
statistics, with applications to SNP data. / GPL-2


Name Version
r-sns 1.1.2 Stochastic Newton Sampler (SNS) is a Metropolis-Hastings-based, Markov noarch
Chain Monte Carlo sampler for twice differentiable, log-concave probability
density functions (PDFs) where the proposal density function is a multivari-
ate Gaussian resulting from a second-order Taylor-series expansion of log-
density around the current point. The mean of the Gaussian proposal is the
full Newton-Raphson step from the current point. A Boolean flag allows for
switching from SNS to Newton-Raphson optimization (by choosing the mean
of proposal function as next point). This can be used during burn-in to get
close to the mode of the PDF (which is unique due to concavity). For high-
dimensional densities, mixing can be improved via ‘state space partitioning’
strategy, in which SNS is applied to disjoint subsets of state space, wrapped in
a Gibbs cycle. Numerical differentiation is available when analytical expres-
sions for gradient and Hessian are not available. Facilities for validation and
numerical differentiation of log-density are provided. / GPL-2
r-soar 0.99_11
Allows objects to be stored on disc and automatically recalled into memory, as noarch
required, by delayed assignment. / GPL-2 | GPL-3
r-sobolsequence 1.0 R implementation of S. Joe and F. Y. Kuo(2008) <DOI:10.1137/070709359>. linux-
The implementation is based on the data file new-joe-kuo-6.21201 64,
<http://web.maths.unsw.edu.au/~fkuo/sobol/>. / BSD_3_clause osx-
64,
win-
64
r-soccer 0.1.1 Functions for evaluating tournament predictions, simulating results from in- linux-
dividual soccer matches and tournaments. See <http://sandsynligvis.dk/2018/ 64,
08/03/world-cup-prediction-winners/> for more information. / GPL-2 osx-
64,
win-
64
r-social 1.0 A set of functions to quantify and visualise social autocorrelation. / GPL-2 linux-
64,
osx-
64,
win-
64
r-socialnetworks 1.1 Generates social networks using either of two approaches: using either pair- linux-
wise distances or territorial area intersections. / GPL-3 64,
osx-
64,
win-
64
r-socialposition 1.0.1 Provides to sociologists (and related scientists) a toolbox to facilitate the con- noarch
struction of social position indicators from survey data. Social position indica-
tors refer to what is commonly known as social class and social status. There
exists in the sociological literature many theoretical conceptualisation and em-
pirical operationalization of social class and social status. This first version of
the package offers tools to construct the International Socio-Economic Index
of Occupational Status (ISEI) and the Oesch social class schema. It also pro-
vides tools to convert several occupational classifications (PCS82, PCS03, and
ISCO08) into a common one (ISCO88) to facilitate data harmonisation work,
and tools to collapse (i.e. group) modalities of social position indicators. /
GPL-2 | GPL-3


Name Version
r-soda 1.0_6 Functions, examples and other software related to the book Software for Data linux-
Analysis: Programming with R. See package?SoDA for an overview. / GPL-2 64,
osx-
64,
win-
64
r-sodavis 1.2 Variable and interaction selection are essential to classification in high- noarch
dimensional setting. In this package, we provide the implementation of SODA
procedure, which is a forward-backward algorithm that selects both main and
interaction effects under logistic regression and quadratic discriminant anal-
ysis. We also provide an extension, S-SODA, for dealing with the variable
selection problem for semi-parametric models with continuous responses. /
GPL-2
r-sofia 1.0 Software that leverages the capabilities of Circos by manipulating data, prepar- noarch
ing configuration files, and running the Perl-native Circos directly from the
R environment with minimal user intervention. Circos is a novel software
that addresses the challenges in visualizing genetic data by creating circu-
lar ideograms composed of tracks of heatmaps, scatter plots, line plots, his-
tograms, links between common markers, glyphs, text, and etc. Please see
<http://www.circos.ca>. / GPL-3
r-softclustering 1.1902.2
It contains soft clustering algorithms, in particular approaches derived from noarch
rough set theory: Lingras & West original rough k-means, Peters’ refined
rough k-means, and PI rough k-means. It also contains classic k-means and a
corresponding illustrative demo. / GPL-2
r-softimpute 1.4 Iterative methods for matrix completion that use nuclear-norm regulariza- linux-
tion. There are two main approaches.The one approach uses iterative soft- 64,
thresholded svds to impute the missing values. The second approach uses osx-
alternating least squares. Both have an EM flavor, in that at each iteration the 64,
matrix is completed with the current estimate. For large matrices there is a win-
special sparse-matrix class named Incomplete that efficiently handles all com- 64
putations. The package includes procedures for centering and scaling rows,
columns or both, and for computing low-rank SVDs on large sparse centered
matrices (i.e. principal components) / GPL-2
r-softmaxreg 1.2 Implementation of ‘softmax’ regression and classification models with multi- noarch
ple layer neural network. It can be used for many tasks like word embedding
based document classification, ‘MNIST’ dataset handwritten digit recognition
and so on. Multiple optimization algorithm including ‘SGD’, ‘Adagrad’, ‘RM-
Sprop’, ‘Moment’, ‘NAG’, etc are also provided. / GPL-2
r- 0.1.0 Performs random forests for soft decision trees for a classification problem. linux-
softrandomforest Current limitations are for a maximum depth of 5 resulting in 16 terminal 64,
nodes. Some data cleaning is required before input. Final graphic output osx-
requires currently requires exporting to ‘Microsoft Excel’ for visualization. 64,
Method based on Irsoy, Yildiz and Alpaydin (2012, ISBN: 978-4-9906441-1- win-
6). / CC0 64


Name Version
r-soilhyp 0.1.3 Provides functions for (1) soil water retention (SWC) and unsaturated hy- noarch
draulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-
Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parame-
ter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation
and (3) calculation of soil hydraulic properties (Ku and soil water contents)
based on the simplified evaporation method (SEM) [6, 7]. Main references: [1]
van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>,
Mualem (1976) <doi:10.1029/WR012i003p00513>, [3] Pe-
ters (2013) <doi:10.1002/wrcr.20548>, Iden and Durner
(2013) <doi:10.1002/2014WR015937>, [5] Peters (2014)
<doi:10.1002/2014WR015937>, [6] Wind G. P. (1966), [7] Peters and
Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and [8] Brooks and
Corey (1964). / GPL-2
r-soilphysics 3.1 Basic and model-based soil physical analyses. / GPL-2 noarch
r-soiltexture 1.5.1 The Soil Texture Wizard is a set of R functions designed to produce texture noarch
triangles (also called texture plots, texture diagrams, texture ternary plots),
classify and transform soil textures data. These functions virtually allows to
plot any soil texture triangle (classification) into any triangle geometry (isosce-
les, right-angled triangles, etc.). This set of function is expected to be useful
to people using soil textures data from different soil texture classification or
different particle size systems. Many (> 15) texture triangles from all around
the world are predefined in the package. A simple text based graphical user
interface is provided: soiltexture_gui(). / AGPL-3
r-soilwater 1.0.5 It implements parametric formulas of soil water retention or conductivity noarch
curve. At the moment, only Van Genuchten (for soil water retention curve)
and Mualem (for hydraulic conductivity) were implemented. See reference
(<http://en.wikipedia.org/wiki/Water_retention_curve>). / GPL-2
r-sokoban 0.1.0 Interactively play a game of sokoban ,which has nine game levels.Sokoban is noarch
a type of transport puzzle, in which the player pushes boxes or crates around
in a warehouse, trying to get them to storage locations. / GPL-3
r-solar 0.44 Calculation methods of solar radiation and performance of photovoltaic sys- noarch
tems from daily and intradaily irradiation data sources. / GPL-3
r-solarpos 1.0 Calculation of solar zenith and azimuth angles. / GPL-2 noarch
r-solartime 0.0.1 Provide utilities to work with solar time, i.e. where noon is exactly when noarch
sun culminates. Provides functions for computing sun position and times of
sunrise and sunset. / GPL-3
r-solomon 1.0_1 Parentage analysis using Bayes’ theorem / GPL-2 noarch
r-solrad 1.0.0 For surface energy models and estimation of solar positions and components noarch
with varying topography, time and locations. The functions calculate solar
top-of-atmosphere, open, diffuse and direct components, atmospheric trans-
mittance and diffuse factors, day length, sunrise and sunset, solar azimuth,
zenith, altitude, incidence, and hour angles, earth declination angle, equation
of time, and solar constant. Details about the methods and equations are ex-
plained in Seyednasrollah, Bijan, Mukesh Kumar, and Timothy E. Link. ‘On
the role of vegetation density on net snow cover radiation at the forest floor.’
Journal of Geophysical Research: Atmospheres 118.15 (2013): 8359-8374,
<doi:10.1002/jgrd.50575>. / AGPL-3
r- 0.1.0 Given a symmetric positive definite matrix Q and a non-singular matrix L, noarch
solverationalmatrixequation
find symmetric positive definite solution X such that X = Q L (X inv) L^T.
Reference: Benner, P., Faßbender, H. On the Solution of the Rational Matrix
Equation. Benner, Faßbender (2007) <doi:10.1155/2007/21850>. / GPL-2


Name Version
r-som 0.3_5.1
Self-Organizing Map (with application in gene clustering). / GPL-3 linux-
64,
osx-
64,
win-
64
r-somebm 0.1 some Brownian motions simulation functions / MIT noarch
r-somekfwer 1.2 This package collects some procedures controlling the Generalized Family- noarch
wise Error Rate. / GPL-2
r-somemtp 1.4.1 It’s a collection of functions for Multiplicity Correction and Multiple Testing. noarch
/ GPL-2
r-sommer 4.0.4 Structural multivariate-univariate linear mixed model solver for estima- linux-
tion of multiple random effects and unknown variance-covariance struc- 64,
tures (i.e. heterogeneous and unstructured variance models) (Covarrubias- osx-
Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 64,
<doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained us- win-
ing the Direct-Inversion Newton-Raphson and Direct-Inversion Average In- 64
formation algorithms. Designed for genomic prediction and genome wide as-
sociation studies (GWAS), particularly focused in the p > n problem (more
coefficients than observations) and dense known covariance structures for lev-
els of random effects. Spatial models can also be fitted using i.e. the two-
dimensional spline functionality available in sommer. / GPL-2
r-somplot 1.6.4 The package provides the plot function som.plot() to create high quality visu- noarch
alisations of hexagonal Kohonen maps (self-organising maps). / GPL-2
r-sonar 1.0.2 Formulas for calculating sound velocity, water pressure, depth, density, ab- noarch
sorption and sonar equations. / GPL-3
r-soniclength 1.4.6 Estimate the abundance of cell clones from the distribution of lengths of DNA noarch
fragments (as created by sonication, whence ‘sonicLength’). The algorithm in
Estimating abundances of retroviral insertion sites from DNA fragment length
data by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bush-
man FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The ex-
perimental setting and estimation details are described in detail there. Briefly,
integration of new DNA in a host genome (due to retroviral infection or gene
therapy) can be tracked using DNA sequencing, potentially allowing character-
ization of the abundance of individual cell clones bearing distinct integration
sites. The locations of integration sites can be determined by fragmenting the
host DNA (via sonication or fragmentase), breaking the newly integrated DNA
at a known sequence, amplifying the fragments containing both host and in-
tegrated DNA, sequencing those amplicons, then mapping the host sequences
to positions on the reference genome. The relative number of fragments con-
taining a given position in the host genome estimates the relative abundance of
cells hosting the corresponding integration site, but that number is not avail-
able and the count of amplicons per fragment varies widely. However, the
expected number of distinct fragment lengths is a function of the abundance
of cells hosting an integration site at a given position and a certain nuisance
parameter. The algorithm implicitly estimates that function to estimate the
relative abundance. / GPL-2


Name Version
r-soobench 1.0_73Collection of different single objective test functions useful for benchmarks linux-
and algorithm development. / BSD 64,
osx-
64,
win-
64
r-sopie 1.5 Provides functions to non-parametrically estimate the off-pulse interval of a noarch
source function originating from a pulsar. The technique is based on a sequen-
tial application of P-values obtained from goodness-of-fit tests for the uniform
distribution, such as the Kolmogorov-Smirnov, Cramer-von Mises, Anderson-
Darling and Rayleigh goodness-of-fit tests. / GPL-3
r-soql 0.1.1 Used to construct the URLs and parameters of ‘Socrata Open Data API’ noarch
<https://dev.socrata.com> calls, using the API’s ‘SoQL’ parameter format. Has
method-chained and sensical syntax. Plays well with pipes. / MIT
r-sor 0.23.1Estimation for longitudinal data following outcome dependent sampling us- noarch
ing the sequential offsetted regression technique. Includes support for bi-
nary, count, and continuous data. The first regression is a logistic regression,
which uses a known ratio (the probability of being sampled given that the
subject/observation was referred divided by the probability of being sampled
given that the subject/observation was no referred) as an offset to estimate the
probability of being referred given outcome and covariates. The second regres-
sion uses this estimated probability to calculate the mean population response
given covariates. / GPL-3
r- 0.1.0 Provides tools to efficiently analyze and visualize laboratory data from aque- noarch
sorptionanalysis ous static adsorption experiments. The package provides functions to plot
Langmuir, Freundlich, and Temkin isotherms and functions to determine the
statistical conformity of data points to the Langmuir, Freundlich, and Temkin
adsorption models through statistical characterization of the isothermic least
squares regressions lines. Scientific Reference: Dada, A.O, Olalekan, A.,
Olatunya, A. (2012) <doi:10.9790/5736-0313845>. / GPL-2
r- 0.1_3 SortableHTMLTables writes a data frame to an HTML file that contains a noarch
sortablehtmltables sortable table. The sorting is done using the jQuery plugin Tablesorter. The
appearance is controlled through a CSS file and several GIF’s. / MIT
r-sotkanet 0.9.48Access data from the sotkanet open data portal <https://www.sotkanet.fi/ noarch
sotkanet/fi/index>. / BSD_2_clause
r-sotu 1.0.2 The President of the United States is constitutionally obligated to provide a noarch
report known as the ‘State of the Union’. The report summarizes the current
challenges facing the country and the president’s upcoming legislative agenda.
While historically the State of the Union was often a written document, in re-
cent decades it has always taken the form of an oral address to a joint session
of the United States Congress. This package provides the raw text from every
such address with the intention of being used for meaningful examples of text
analysis in R. The corpus is well suited to the task as it is historically impor-
tant, includes material intended to be read and material intended to be spoken,
and it falls in the public domain. As the corpus spans over two centuries it is
also a good test of how well various methods hold up to the idiosyncrasies of
historical texts. Associated data about each address, such as the year, presi-
dent, party, and format, are also included. / GPL-2
r-sound 1.4.5 Basic functions for dealing with wav files and sound samples. / GPL-2 noarch


Name Version
r-soundexbr 1.2 The SoundexBR package provides an algorithm for decoding names into pho- linux-
netic codes, as pronounced in Portuguese. The goal is for homophones to be 64,
encoded to the same representation so that they can be matched despite minor osx-
differences in spelling. The algorithm mainly encodes consonants; a vowel 64,
will not be encoded unless it is the first letter. The soundex code resultant win-
consists of a four digits long string composed by one letter followed by three 64
numerical digits: the letter is the first letter of the name, and the digits encode
the remaining consonants. / GPL-2
r-source.gist 1.0.0 Analogous to source(), but works when given a Gist URL or ID. / MIT noarch
r-sourcetools 0.1.7 Tools for the reading and tokenization of R code. The ‘sourcetools’ pack- linux-
age provides both an R and C interface for the tokenization of R code, and 32,
helpers for interacting with the tokenized representation of R code. / MIT file linux-
LICENSE 64,
osx-
64,
win-
32,
win-
64
r-sp 1.3_1 Classes and methods for spatial data; the classes document where the spatial linux-
location information resides, for 2D or 3D data. Utility functions are provided, 32,
e.g. for plotting data as maps, spatial selection, as well as methods for retriev- linux-
ing coordinates, for subsetting, print, summary, etc. / GPL (>= 2) 64,
osx-
64,
win-
32,
win-
64
r-sp23design 0.9 Provides methods for generating, exploring and executing seamless Phase II- noarch
III designs of Lai, Lavori and Shih using generalized likelihood ratio statistics.
Includes pdf and source files that describe the entire R implementation with
the relevant mathematical details. / LGPL-3
r-spa3g 1.0 The package implements the model-based kernel machine method for detect- noarch
ing gene-centric gene-gene interactions of Li and Cui (2012). / GPL-3
r-spaa 0.2.2 Miscellaneous functions for analysing species association and niche overlap. / noarch
GPL-2
r-space 0.1_1 Partial correlation estimation with joint sparse regression model / GPL-2 linux-
64,
osx-
64,
win-
64
r-spacejam 1.1 This package provides an extension of conditional independence (CIG) and linux-
directed acyclic graph (DAG) estimation to the case where conditional rela- 64,
tionships are (non-linear) additive models. / GPL-2 osx-
64,
win-
64


Name Version
r-spacesrgb 1.2_2 Standard RGB spaces included are sRGB, ‘Adobe’ RGB, ‘ProPhoto’ RGB, noarch
BT.709, and others. User-defined RGB spaces are also possible. There is
partial support for ACES Color workflows. / GPL-3
r-spacesxyz 1.0_4 Functions for converting among CIE XYZ, xyY, Lab, and Luv. The XYZs noarch
of some standard illuminants and some standard linear chromatic adaptation
transforms (CATs) are included. Compute CCT and the Planckian and daylight
loci. Three different standard color difference metrics are included. / GPL-3
r-spacyr 1.2 An R wrapper to the ‘Python’ ‘spaCy’ ‘NLP’ library, from <http://spacy.io>. / noarch
GPL-3
r-spaddins 0.2.0 A set of RStudio addins that are designed to be used in combination with noarch
user-defined RStudio keyboard shortcuts. These addins either: 1) insert text
at a cursor position (e.g. insert operators %>%, <<-, %$%, etc.), 2) replace
symbols in selected pieces of text (e.g., convert backslashes to forward slashes
which results in stings like c:dataconverted into c:/data/) or 3) enclose text with
special symbols (e.g., converts bold into bold) which is convenient for editing
R Markdown files. / MIT
r-spader 0.1.1 Estimation of various biodiversity indices and related (dis)similarity mea- noarch
sures based on individual-based (abundance) data or sampling-unit-based (in-
cidence) data taken from one or multiple communities/assemblages. / GPL-3
r-spaero 0.5.0 Implements methods for anticipating the emergence and eradication of infec- noarch
tious diseases from surveillance time series. Also provides support for com-
putational experiments testing the performance of such methods. / GPL-2
r-spam 2.2_2 Set of functions for sparse matrix algebra. Differences with other sparse ma- linux-
trix packages are: (1) we only support (essentially) one sparse matrix format, 64,
(2) based on transparent and simple structure(s), (3) tailored for MCMC cal- osx-
culations within G(M)RF. (4) and it is fast and scalable (with the extension 64,
package spam64). / LGPL-2 | BSD_3_clause win-
64
r-spam64 2.2_2 Provides the Fortran code of the R package ‘spam’ with 64-bit integers. Load- linux-
ing this package together with the R package spam enables the sparse matrix 64,
class spam to handle huge sparse matrices with more than 2^31-1 non-zero osx-
elements. / LGPL-2 | BSD_3_clause 64,
win-
64
r-spanel 0.1 Fit the spatial panel data models: the fixed effects, random effects and between noarch
models. / GPL-3
r-spanish 0.4.2 Character vector to numerical translation in Euros from Spanish spelled mon- noarch
etary quantities. Reverse translation from integer to Spanish. Upper limit is up
to the millions range. Geocoding via Cadastral web site. / GPL-3
r-spar 0.1 This package performs robust nonparametric tests for rare variants association noarch
analysis using summation of partition approaches that incorporate gene-gene
and gene-environmental interactions / GPL-2
r-sparcl 1.0.4 Implements the sparse clustering methods of Witten and Tibshirani (2010): linux-
A framework for feature selection in clustering; published in Journal of the 64,
American Statistical Association 105(490): 713-726. / GPL-2 osx-
64,
win-
64
r-sparkline 2.0 Include interactive sparkline charts <http://omnipotent.net/jquery.sparkline> noarch
in all R contexts with the convenience of ‘htmlwidgets’. / MIT


Name Version
r-sparklyr 1.0.0 R interface to Apache Spark, a fast and general engine for big data processing, linux-
see <http://spark.apache.org>. This package supports connecting to local and 32,
remote Apache Spark clusters, provides a ‘dplyr’ compatible back-end, and linux-
provides an interface to Spark’s built-in machine learning algorithms. / Apache 64,
License 2.0 | file LICENSE noarch,
osx-
64,
win-
32,
win-
64
r-sparkr 2.4.4 Provides an R Front end for ‘Apache Spark’ <https://spark.apache.org>. / noarch
Apache License (== 2.0)
r-sparktex 0.1 Generate syntax for use with the sparklines package for LaTeX. / GPL-2 noarch
r-sparql 1.16 Use SPARQL to pose SELECT or UPDATE queries to an end-point. / GPL-3 noarch
r-sparsebnutils 0.0.7 A set of tools for representing and estimating sparse Bayesian networks from noarch
continuous and discrete data, as described in Aragam, Gu, and Zhou (2017)
<arXiv:1703.04025>. / GPL-2
r-sparsedc 0.1.17Implements the algorithm described in Barron, M., Zhang, S. and Li, J. noarch
2017, A sparse differential clustering algorithm for tracing cell type changes
via single-cell RNA-sequencing data, Nucleic Acids Research, gkx1113,
<doi:10.1093/nar/gkx1113>. This algorithm clusters samples from two differ-
ent populations, links the clusters across the conditions and identifies marker
genes for these changes. The package was designed for scRNA-Seq data but
is also applicable to many other data types, just replace cells with samples and
genes with variables. The package also contains functions for estimating the
parameters for SparseDC as outlined in the paper. We recommend that users
further select their marker genes using the magnitude of the cluster centers. /
GPL-3
r-sparseeigen 0.1.0 Computation of sparse eigenvectors of a matrix (aka sparse PCA) with running noarch
time 2-3 orders of magnitude lower than existing methods and better final per-
formance in terms of recovery of sparsity pattern and estimation of numerical
values. Can handle covariance matrices as well as data matrices with real or
complex-valued entries. Different levels of sparsity can be specified for each
individual ordered eigenvector and the method is robust in parameter selection.
See vignette for a detailed documentation and comparison, with several illus-
trative examples. The package is based on the paper: K. Benidis, Y. Sun, P.
Babu, and D. P. Palomar (2016). Orthogonal Sparse PCA and Covariance Esti-
mation via Procrustes Reformulation, IEEE Transactions on Signal Processing
<doi:10.1109/TSP.2016.2605073>. / GPL-3
r-sparsegrid 0.8.2 SparseGrid is a package to create sparse grids for numerical integration, based noarch
on code from www.sparse-grids.de / GPL-3
r- 0.3.3.4Estimates Hessian of a scalar-valued function, and returns it in a sparse Matrix
linux-
sparsehessianfd format. The sparsity pattern must be known in advance. The algorithm is espe- 64,
cially efficient for hierarchical models with a large number of heterogeneous osx-
units. See Braun, M. (2017) <doi:10.18637/jss.v082.i10>. / MPL (== 2.0) 64,
win-
64


Name Version
r- 0.1.1 Computation of sparse portfolios for financial index tracking, i.e., joint selec- noarch
sparseindextracking tion of a subset of the assets that compose the index and computation of their
relative weights (capital allocation). The level of sparsity of the portfolios, i.e.,
the number of selected assets, is controlled through a regularization parame-
ter. Different tracking measures are available, namely, the empirical tracking
error (ETE), downside risk (DR), Huber empirical tracking error (HETE), and
Huber downside risk (HDR). See vignette for a detailed documentation and
comparison, with several illustrative examples. The package is based on the
paper: K. Benidis, Y. Feng, and D. P. Palomar, Sparse Portfolios for High-
Dimensional Financial Index Tracking, IEEE Trans. on Signal Processing,
vol. 66, no. 1, pp. 155-170, Jan. 2018. <doi:10.1109/TSP.2017.2762286>. /
GPL-3
r-sparsem 1.77 Some basic linear algebra functionality for sparse matrices is provided: includ- linux-
ing Cholesky decomposition and backsolving as well as standard R subsetting 32,
and Kronecker products. / GPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
r-sparsemdc 0.99.5Implements the algorithm described in Barron, M., and Li, J. (Not yet pub- noarch
lished). This algorithm clusters samples from multiple ordered populations,
links the clusters across the conditions and identifies marker genes for these
changes. The package was designed for scRNA-Seq data but is also applicable
to many other data types, just replace cells with samples and genes with vari-
ables. The package also contains functions for estimating the parameters for
SparseMDC as outlined in the paper. We recommend that users further select
their marker genes using the magnitude of the cluster centers. / GPL-3
r-sparsemse 1.2.1 Implements the routines and algorithms developed and analysed in Multiple noarch
systems estimation for Sparse Capture Data: Inferential Challenges when there
are Non-Overlapping Lists Chan, L, Silverman, B. W., Vincent, K (2019)
<arXiv:1902.05156>. This package explicitly handles situations where there
are pairs of lists which have no observed individuals in common. / GPL-2
r-sparsemvn 0.2.1.1Computes multivariate normal (MVN) densities, and samples from MVN dis- noarch
tributions, when the covariance or precision matrix is sparse. / MPL (>= 2.0)
r-sparsepp 1.22 Provides interface to ‘sparsepp’ - fast, memory efficient hash map. It is derived noarch
from Google’s excellent ‘sparsehash’ implementation. We believe ‘sparsepp’
provides an unparalleled combination of performance and memory usage,
and will outperform your compiler’s unordered_map on both counts. Only
Google’s ‘dense_hash_map’ is consistently faster, at the cost of much greater
memory usage (especially when the final size of the map is not known in ad-
vance). / BSD_3_clause
r-sparsesem 2.5 Sparse-aware maximum likelihood for structural equation models in inferring linux-
gene regulatory networks / GPL-3 64,
osx-
64,
win-
64


Name Version
r-sparsestep 1.0.0 Implements the SparseStep model for solving regression problems with a spar- noarch
sity constraint on the parameters. The SparseStep regression model was pro-
posed in Van den Burg, Groenen, and Alfons (2017) <https://arxiv.org/abs/
1701.06967>. In the model, a regularization term is added to the regression
problem which approximates the counting norm of the parameters. By itera-
tively improving the approximation a sparse solution to the regression problem
can be obtained. In this package both the standard SparseStep algorithm is im-
plemented as well as a path algorithm which uses golden section search to
determine solutions with different values for the regularization parameter. /
GPL-2
r-sparsesvd 0.2 Wrapper around the ‘SVDLIBC’ library for (truncated) singular value decom- linux-
position of a sparse matrix. Currently, only sparse real matrices in Matrix 64,
package format are supported. / BSD_3_clause osx-
64,
win-
64
r-sparsesvm 1.1_6 Fast algorithm for fitting solution paths of sparse SVM models with lasso or linux-
elastic-net regularization. / GPL-3 64,
osx-
64,
win-
64
r-sparsio 1.0.0 Fast ‘SVMlight’ reader and writer. ‘SVMlight’ is most commonly used format linux-
for storing sparse matrices (possibly with some target variable) on disk. For ad- 64,
ditional information about ‘SVMlight’ format see <http://svmlight.joachims. osx-
org/>. / GPL-2 64,
win-
64
r-spatest 3.0.0 Performs score test using saddlepoint approximation to estimate the null dis- noarch
tribution. Also prepares summary statistics for meta-analysis and performs
meta-analysis to combine multiple association results. For the latest version,
please check <https://github.com/leeshawn/SPAtest>. / GPL-2
r-spatgraphs 3.2_1 Graphs (or networks) and graph component calculations for spatial locations linux-
in 1D, 2D, 3D etc. / GPL-2 64,
osx-
64,
win-
64
r-spatial 7.3_11Functions for kriging and point pattern analysis. / GPL-2 | GPL-3 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64


Name Version
r-spatialacc 0.1_3 Provides a set of spatial accessibility measures from a set of locations (de- noarch
mand) to another set of locations (supply). It aims, among others, to support
research on spatial accessibility to health care facilities. Includes the locations
and some characteristics of major public hospitals in Greece. / GPL-2
r- 0.6_9 Functions that compute the spatial covariance matrix for the matern and power noarch
spatialcovariance classes of spatial models, for data that arise on rectangular units. This code can
also be used for the change of support problem and for spatial data that arise
on irregularly shaped regions like counties or zipcodes by laying a fine grid of
rectangles and aggregating the integrals in a form of Riemann integration. /
GPL-3
r-spatialml 0.1.3 Implements a spatial extension of the random forest algorithm (Georganos et noarch
al. (2019) <doi:10.1080/10106049.2019.1595177>). Future updates include
more local machine learning methods as well as a geographically weighted
random forest. / GPL-2
r-spatialnp 1.1_3 Test and estimates of location, tests of independence, tests of spheric- linux-
ity and several estimates of shape all based on spatial signs, symmetrized 64,
signs, ranks and signed ranks. For details, see Oja and Randles (2004) osx-
<doi:10.1214/088342304000000558> and Oja (2010) <doi:10.1007/978-1- 64,
4419-0468-3>. / GPL-2 win-
64
r-spatialpack 0.3_8 Tools to assess the association between two spatial processes. Currently, sev- linux-
eral methodologies are implemented: A modified t-test to perform hypothesis 64,
testing about the independence between the processes, a suitable nonparamet- osx-
ric correlation coefficient, the codispersion coefficient, and an F test for as- 64,
sessing the multiple correlation between one spatial process and several others. win-
Functions for image processing and computing the spatial association between 64
images are also provided. SpatialPack gives methods to complement method-
ologies that are available in geoR for one spatial process. / GPL (>= 2.0)
r-spatimeclus 1.0 Mixture model is used to achieve the clustering goal. Each component is itself linux-
a mixture model of polynomial autoregressive regressions whose the logistic 64,
weights consider the spatial and temporal information. / GPL-2 osx-
64,
win-
64
r-spatiotemporal 1.1.9.1Utilities that estimate, predict and cross-validate the spatio-temporal model linux-
developed for MESA Air. / GPL-2 64,
osx-
64,
win-
64
r-spatstat.utils 1.13_0Contains utility functions for the ‘spatstat’ package which may also be useful linux-
for other purposes. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-spbayes 0.4_2 Fits univariate and multivariate spatio-temporal random effects models for linux-
point-referenced data using Markov chain Monte Carlo (MCMC). Details are 64,
given in Finley, Banerjee, and Gelfand (2015) <doi:10.18637/jss.v063.i13> osx-
and Finley, Banerjee, and Cook (2014) <doi:10.1111/2041-210X.12189>. / 64,
GPL-2 win-
64
r-spbsampling 1.3.0 Selection of spatially balanced samples. In particular, the implemented sam- linux-
pling designs allow to select probability samples well spread over the popu- 64,
lation of interest, in any dimension and using any distance function (e.g. Eu- osx-
clidean distance, Manhattan distance). For more details, Benedetti R and Pier- 64,
simoni F (2017) <doi:10.1002/bimj.201600194> and Benedetti R and Piersi- win-
moni F (2017) <arXiv:1710.09116>. The implementation has been done in C 64
through the use of ‘Rcpp’ and ‘RcppArmadillo’. / GPL-3
r-spcadjust 1.1 Calibration of thresholds of control charts such as CUSUM charts based on noarch
past data, taking estimation error into account. / GPL-2
r-spcalda 1.0 A new reduced-rank LDA method which works for high dimensional multi- noarch
class data. / GPL-2
r-spcavrp 0.4 Implements the SPCAvRP algorithm, developed and analysed in Sparse prin- noarch
cipal component analysis via random projections Gataric, M., Wang, T. and
Samworth, R. J. (2018) <arXiv:1712.05630>. The algorithm is based on the
aggregation of eigenvector information from carefully-selected random pro-
jections of the sample covariance matrix. / GPL-3
r-spcdanalyze 0.1.0 Programs to find the sample size or power of studies using the Sequential noarch
Parallel Comparison Design (SPCD) and programs to analyze such stud-
ies. This is a clinical trial design where patients initially on placebo who
did not respond are re-randomized between placebo and active drug in a
second phase and the results of the two phases are pooled. The method
of analyzing binary data with this design is described in Fava,Evins, Dorer
and Schoenfeld(2003) <doi:10.1159/000069738>, and the method of ana-
lyzing continuous data is described in Chen, Yang, Hung and Wang (2011)
<doi:10.1016/j.cct.2011.04.006>. / Unlimited
r-spcov 1.01 Provides a covariance estimator for multivariate normal data that is sparse and noarch
positive definite. Implements the majorize-minimize algorithm described in
Bien, J., and Tibshirani, R. (2011), Sparse Estimation of a Covariance Matrix,
Biometrika. 98(4). 807–820. / GPL-2
r-spd 2.0_1 The Semi Parametric Piecewise Distribution blends the Generalized Pareto noarch
Distribution for the tails with a kernel based interior. / GPL-3
r-spdata 0.3.0 Diverse spatial datasets for demonstrating, benchmarking and teaching spatial linux-
data analysis. It includes R data of class sf (defined by the package ‘sf’), Spa- 32,
tial (‘sp’), and nb (‘spdep’). Unlike other spatial data packages such as ‘rnat- linux-
uralearth’ and ‘maps’, it also contains data stored in a range of file formats 64,
including GeoJSON, ESRI Shapefile and GeoPackage. Some of the datasets noarch,
are designed to illustrate specific analysis techniques. cycle_hire() and cy- osx-
cle_hire_osm(), for example, is designed to illustrate point pattern analysis 64,
techniques. / CC0 win-
32,
win-
64
r-spdownscale 0.1.0 Spatial downscaling of climate data (Global Circulation Models/Regional Cli- noarch
mate Models) using quantile-quantile bias correction technique. / GPL-2


Name Version
r-spearmanci 1.0 Functions for conducting jackknife Euclidean / empirical likelihood noarch
inference for Spearman’s rho (de Carvalho and Marques (2012)
<10.1080/10920277.2012.10597644>). / GPL-3
r-spec 0.1.7 Creates a data specification that describes the columns of a table noarch
(data.frame). Provides methods to read, write, and update the specifica-
tion. Checks whether a table matches its specification. See specifica-
tion.data.frame(),read.spec(), write.spec(), as.csv.spec(), respecify.character(),
and %matches%.data.frame(). / GPL-3
r-speccalt 0.1.1 Alternative to the kernlab::specc function. Includes a spectral clustering imple- noarch
mentation, a locally adapted kernel function akin to what is already proposed
in kernlab, and an optional procedure that automatically estimates the optimal
number of clusters. Several sample data sets are also included. / LGPL-3
r-specdetec 1.0.0 Calculate change point based on spectral clustering with the option to auto- noarch
matically calculate the number of clusters if this information is not available.
/ GPL-3
r-spectralgp 1.3.3 Routines for creating, manipulating, and performing Bayesian inference about noarch
Gaussian processes in one and two dimensions using the Fourier basis approx-
imation: simulation and plotting of processes, calculation of coefficient vari-
ances, calculation of process density, coefficient proposals (for use in MCMC).
It uses R environments to store GP objects as references/pointers. / GPL-2
r-spedinstabr 1.8 From output files obtained from the software ‘ModestR’, the relative contri- noarch
bution of factors to explain species distribution is depicted using several plots.
A global geographic raster file for each environmental variable may be also
obtained with the mean relative contribution, considering all species present
in each raster cell, of the factor to explain species distribution. Finally, for
each variable it is also possible to compare the frequencies of any variable ob-
tained in the cells where the species is present with the frequencies of the same
variable in the cells of the extent. / GPL-2
r-speedglm 0.3_2 Fitting linear models and generalized linear models to large data sets by up- noarch
dating algorithms. / GPL-3
r-speff2trial 1.0.4 The package performs estimation and testing of the treatment effect in a 2- noarch
group randomized clinical trial with a quantitative, dichotomous, or right-
censored time-to-event endpoint. The method improves efficiency by lever-
aging baseline predictors of the endpoint. The inverse probability weighting
technique of Robins, Rotnitzky, and Zhao (JASA, 1994) is used to provide
unbiased estimation when the endpoint is missing at random. / GPL-2
r-spelling 2.1 Spell checking common document formats including latex, markdown, manual noarch
pages, and description files. Includes utilities to automate checking of docu-
mentation and vignettes as a unit test during ‘R CMD check’. Both British
and American English are supported out of the box and other languages can
be added. In addition, packages may define a ‘wordlist’ to allow custom ter-
minology without having to abuse punctuation. / MIT
r-spgrass6 0.8_9 Interpreted interface between GRASS 6 geographical information system and noarch
R, based on starting R from within the GRASS environment, or running free-
standing R in a temporary GRASS location; the package provides facilities for
using all GRASS commands from the R command line. This package may not
be used for GRASS 7, for which rgrass7 should be used. / GPL-2
r-sphericalk 1.2 Spherical K-function for point-pattern analysis on the sphere. / GPL-2 noarch
r-spi 1.1 Compute the SPI index using R / GPL-2 noarch


Name Version
r-spiassay 1.1.0 The SNP Panel Identification Assay (SPIA) is a package that enables an accu- noarch
rate determination of cell line identity from the genotype of single nucleotide
polymorphisms (SNPs). The SPIA test allows to discern when two cell lines
are close enough to be called similar and when they are not. Details about
the method are available at Demichelis et al. (2008) SNP panel identification
assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic
Acids Res., 3, 2446-2456. / GPL-2
r-spiders 1.2 Fits and simulates data from our predator preferences model, noarch
<DOI:10.1007/s10651-016-0341-3>. / GPL (>= 2.0)
r-spikes 1.1 Applies re-sampled kernel density method to detect vote fraud. It estimates noarch
the proportion of coarse vote-shares in the observed data relative to the null
hypothesis of no fraud. / GPL-2
r-spin 1.1 An optimal weighting strategy to compute simulation-efficient shortest proba- noarch
bility intervals (spins). / GPL-2
r-spina 4.1.0 Calculates constant structure parameters of endocrine homeostatic systems noarch
from equilibrium hormone concentrations. Methods and equations have been
described in Dietrich et al. (2012) <doi:10.1155/2012/351864> and Dietrich
et al. (2016) <doi:10.3389/fendo.2016.00057>. / BSD_3_clause
r-spinyreg 0.1_0 Implements a generative model that uses a spike-and-slab like prior distribu- noarch
tion obtained by multiplying a deterministic binary vector. Such a model al-
lows an EM algorithm, optimizing a type-II log-likelihood. / GPL-2
r-spiritr 0.1.1 Contains an R Markdown template for a clinical trial protocol adhering to the noarch
SPIRIT statement. The SPIRIT (Standard Protocol Items for Interventional
Trials) statement outlines recommendations for a minimum set of elements
to be addressed in a clinical trial protocol. Also contains functions to create
a xml document from the template and upload it to clinicaltrials.gov<https:
//www.clinicaltrials.gov/> for trial registration. / MIT
r-splines2 0.2.8 Constructs B-splines and its integral, monotone splines (M-splines) and noarch
its integral (I-splines), convex splines (C-splines), and their derivatives of
given order. Piecewise constant basis is allowed for B-splines and M-
splines. See De Boor (1978) <doi:10.1002/zamm.19800600129>, Ramsay
(1988) <doi:10.1214/ss/1177012761>, and Meyer (2008) <doi:10.1214/08-
AOAS167> for more information. / GPL-3
r-splitfeas 0.1.0 An implementation of the majorization-minimization (MM) algorithm intro- noarch
duced by Xu, Chi, Yang, and Lange (2017) <arXiv:1612.05614> for solving
multi-set split feasibility problems. In the multi-set split feasibility problem,
we seek to find a point x in the intersection of multiple closed sets and whose
image under a mapping also must fall in the intersection of several closed sets.
/ MIT
r-splitstackshape 1.4.8 Online data collection tools like Google Forms often export multiple-response noarch
questions with data concatenated in cells. The concat.split (cSplit) family of
functions splits such data into separate cells. The package also includes func-
tions to stack groups of columns and to reshape wide data, even when the data
are unbalanced—something which reshape (from base R) does not handle, and
which melt and dcast from reshape2 do not easily handle. / GPL-3
r-splot 0.5.0 Automates common plotting tasks to ease data exploration. Makes density noarch
plots (potentially overlaid on histograms), scatter plots with prediction lines,
or bar or line plots with error bars. For each type, y, or x and y variables can
be plotted at levels of other variables, all with minimal specification. / GPL-2


Name Version
r-spls 2.2_3 Provides functions for fitting a sparse partial least squares (SPLS) re- noarch
gression and classification (Chun and Keles (2010) <doi:10.1111/j.1467-
9868.2009.00723.x>). / GPL-2
r-spongebob 0.4.0 Convert text (and text in R objects) to Mocking SpongeBob case <https: noarch
//knowyourmeme.com/memes/mocking-spongebob> and show them off in fun
ways. CoNVErT TexT (AnD TeXt In r ObJeCtS) To MOCkINg SpoNge-
bOb CAsE <https://knowyourmeme.com/memes/mocking-spongebob> aND
shOw tHem OFf IN Fun WayS. / BSD_3_clause
r-sporm 1.1 R implementation of the methods described in A rank-based empirical likeli- noarch
hood approach to two-sample proportional odds model and its goodness-of-fit
by Zhong Guan and Cheng Peng, Journal of Nonparametric Statistics, to ap-
pear. / GPL-2
r-sportsanalytics 0.2 The aim of this package is to provide infrastructure for sports analysis. Any- noarch
way, currently it is a selection of data sets, functions to fetch sports data, ex-
amples, and demos – with the ambition to develop bit by bit a set of classes to
represent general concepts of sports analysis. / GPL-2
r-spreda 1.1 The Statistical Package for REliability Data Analysis (SPREDA) implements noarch
recently-developed statistical methods for the analysis of reliability data. Mod-
ern technological developments, such as sensors and smart chips, allow us to
dynamically track product/system usage as well as other environmental vari-
ables, such as temperature and humidity. We refer to these variables as dy-
namic covariates. The package contains functions for the analysis of time-
to-event data with dynamic covariates and degradation data with dynamic co-
variates. The package also contains functions that can be used for analyzing
time-to-event data with right censoring, and with left truncation and right cen-
soring. Financial support from NSF and DuPont are acknowledged. / GPL-2
r-sprsmdl 0.1_0 R functions to mine sparse models from data. / GPL-2 noarch
r-sprt 1.0 Perform Wald’s Sequential Probability Ratio Test on variables with a Normal, noarch
Bernoulli, Exponential and Poisson distribution. Plot acceptance and continu-
ation regions, or create your own with the help of closures. / BSD_2_clause
r-spsl 0.1_9 Provides basic functionality for labeling iso- & anisotropic percolation clusters noarch
on 2D & 3D square lattices with various lattice sizes, occupation probabilities,
von Neumann & Moore (1,d)-neighborhoods, and random variables weighting
the percolation lattice sites. / GPL-3
r-spurs 2.0.2 Provides functions and datasets from Jones, O.D., R. Maillardet, and A.P. noarch
Robinson. 2014. An Introduction to Scientific Programming and Simulation,
Using R. 2nd Ed. Chapman And Hall/CRC. / GPL-3
r-spyvsspy 0.1.1 Data on the Spy vs. Spy comic strip of Mad magazine, created and written by noarch
Antonio Prohias. / LGPL-3
r-sqlrender 1.6.2 A rendering tool for parameterized SQL that also translates into different SQL noarch
dialects. These dialects include ‘Microsoft Sql Server’, ‘Oracle’, ‘PostgreSql’,
‘Amazon RedShift’, ‘Apache Impala’, ‘IBM Netezza’, ‘Google BigQuery’,
‘Microsoft PDW’, and ‘SQLite’. / Apache License 2.0
r-sqlutils 1.2 This package provides utilities for working with a library of SQL files. / GPL- noarch
3
r-sqrl 0.6.3 Facilitates interaction with ODBC data sources by managing communications noarch
on behalf of the user. Supports multi-statement SQL scripts, with or without
embedded R. / GPL-3


Name Version
r-squarem 2017.10_1
Algorithms for accelerating the convergence of slow, monotone sequences linux-
from smooth, contraction mapping such as the EM algorithm. It can be used 32,
to accelerate any smooth, linearly convergent acceleration scheme. A tuto- linux-
rial style introduction to this package is available in a vignette on the CRAN 64,
download page or, when the package is loaded in an R session, with vi- noarch,
gnette(SQUAREM). / GPL (>= 2) osx-
64,
win-
32,
win-
64
r-squash 1.0.8 Functions for color-based visualization of multivariate data, i.e. colorgrams noarch
or heatmaps. Lower-level functions map numeric values to colors, display
a matrix as an array of colors, and draw color keys. Higher-level plotting
functions generate a bivariate histogram, a dendrogram aligned with a color-
coded matrix, a triangular distance matrix, and more. / Artistic-2.0
r-sra 0.1.1 This package (sra) provides a set of tools to analyse artificial-selection re- noarch
sponse datasets. The data typically feature for several generations the average
value of a trait in a population, the variance of the trait, the population size and
the average value of the parents that were chosen to breed. Sra implements
two families of models aiming at describing the dynamics of the genetic ar-
chitecture of the trait during the selection response. The first family relies
on purely descriptive (phenomenological) models, based on an autoregres-
sive framework. The second family provides different mechanistic models,
accounting e.g. for inbreeding, mutations, genetic and environmental canal-
ization, or epistasis. The parameters underlying the dynamics of the time se-
ries are estimated by maximum likelihood. The sra package thus provides (i) a
wrapper for the R functions mle() and optim() aiming at fitting in a convenient
way a predetermined set of models, and (ii) some functions to plot and analyze
the output of the models. / GPL-2
r-srcs 1.1 Implementation of the SRCS method for a color-based visualization of the noarch
results of multiple pairwise tests on a large number of problem configura-
tions, proposed in: I.G. del Amo, D.A. Pelta. SRCS: a technique for compar-
ing multiple algorithms under several factors in dynamic optimization prob-
lems. In: E. Alba, A. Nakib, P. Siarry (Eds.), Metaheuristics for Dynamic
Optimization. Series: Studies in Computational Intelligence 433, Springer,
Berlin/Heidelberg, 2012. / LGPL-3
r-srda 1.0.0 Sparse redundancy analysis for high dimensional (biomedical) data. Direc- noarch
tional multivariate analysis to express the maximum variance in the predicted
data set by a linear combination of variables of the predictive data set. Imple-
mented in a partial least squares framework, for more details see Csala et al.
(2017) <doi:10.1093/bioinformatics/btx374>. / MIT
r-srttools 1.2.0 Srt file is a common subtitle format for videos, it contains subtitle and when noarch
the subtitle showed. This package is for align time of srt file, and also change
color, style and position of subtitle in videos, the srt file will be read as a vector
into R, and can be write into srt file after modified using this package. / GPL-2
r-ssanv 1.1 A set of functions to calculate sample size for two-sample difference in means noarch
tests. Does adjustments for either nonadherence or variability that comes from
using data to estimate parameters. / GPL-3


Name Version
r-ssbtools 0.4.0 Functions used by other packages from Statistics Norway are gathered. Gen- noarch
eral data manipulation functions, and functions for hierarchical computations
are included. The hierarchy specification functions are useful within statistical
disclosure control. / Apache License 2.0 | file LICENSE
r-sscor 0.2 Provides the spatial sign correlation and the two-stage spatial sign correlation noarch
as well as a one-sample test for the correlation coefficient. / GPL-2 | GPL-3
r-ssd 0.3 ssd calculates the sample size needed to detect the differences between two noarch
sets of unordered categorical data. / GPL-2
r-ssdr 1.2.0 Performs structured OLS (sOLS) and structured SIR (sSIR). / GPL-2 noarch
r-sse 0.7_13Provides functions to evaluate user-defined power functions for a parameter noarch
range, and draws a sensitivity plot. It also provides a resampling procedure for
semi-parametric sample size estimation and methods for adding information
to a Sweave report. / GPL-3
r-ssh.utils 1.0 This package provides utility functions for system command execution, both linux-
locally and remotely using ssh/scp. The command output is captured and pro- 64
vided to the caller. This functionality is intended to streamline calling shell
commands from R, retrieving and using their output, while instrumenting the
calls with appropriate error handling. NOTE: this first version is limited to
unix with local and remote systems running bash as the default shell. / Apache
License (== 2.0)
r-ssize.fdr 1.2 This package contains a set of functions that calculates appropriate sample noarch
sizes for one-sample t-tests, two-sample t-tests, and F-tests for microarray ex-
periments based on desired power while controlling for false discovery rates.
For all tests, the standard deviations (variances) among genes can be assumed
fixed or random. This is also true for effect sizes among genes in one-sample
and two sample experiments. Functions also output a chart of power versus
sample size, a table of power at different sample sizes, and a table of critical
test values at different sample sizes. / GPL-3
r-ssm 1.0.1 Creates an S4 class SSM and defines functions for fitting smooth supersatu- noarch
rated models, a polynomial model with spline-like behaviour. Functions are
defined for the computation of Sobol indices for sensitivity analysis and plot-
ting the main effects using FANOVA methods. It also implements the estima-
tion of the SSM metamodel error using a GP model with a variety of defined
correlation functions. / GPL-3
r-sss 0.1_0 Tools to import survey files in the .sss (triple-s) format. The package provides noarch
the function read.sss() that reads the .asc (or .csv) and .sss files of a triple-s
survey data file. / GPL-2 | GPL-3
r-sssimple 0.6.4 Simulate, solve state space models / GPL-2 noarch
r-ssvd 1.0 Fast iterative thresholding sparse SVD, together with an initialization algo- noarch
rithm / GPL-2
r-stabledist 0.7_1 Density, Probability and Quantile functions, and random number generation linux-
for (skew) stable distributions, using the parametrizations of Nolan. / GPL 32,
(>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-stableestim 2.1 Estimate the four parameters of stable laws using maximum likelihood noarch
method, generalised method of moments with finite and continuum number of
points, iterative Koutrouvelis regression and Kogon-McCulloch method. The
asymptotic properties of the estimators (covariance matrix, confidence inter-
vals) are also provided. / GPL-2
r-stabm 1.1.0 An implementation of many measures for the assessment of the stability of noarch
feature selection. Both simple measures and measures which take into ac-
count the similarities between features are available, see Bommert et al. (2017)
<doi:10.1155/2017/7907163>. / LGPL-3
r-stabs 0.6_3 Resampling procedures to assess the stability of selected variables with addi- noarch
tional finite sample error control for high-dimensional variable selection pro-
cedures such as Lasso or boosting. Both, standard stability selection (Mein-
shausen & Buhlmann, 2010, <doi:10.1111/j.1467-9868.2010.00740.x>) and
complementary pairs stability selection with improved error bounds (Shah
& Samworth, 2013, <doi:10.1111/j.1467-9868.2011.01034.x>) are imple-
mented. The package can be combined with arbitrary user specified variable
selection approaches. / GPL-2
r-stackoverflow 0.3.0 Helper functions collected from StackOverflow.com, a question and answer noarch
site for professional and enthusiast programmers. / CC BY-SA 4.0
r-stacomirtools 0.5.3 S4 class wrappers for the ‘ODBC’ connection, also provides some utilities to noarch
paste small datasets to clipboard, rename columns. It is used by the package
‘stacomiR’ for connections to the database. Development versions of ‘sta-
comiR’ are available in R-forge. / GPL-2
r- 1.0.0 Analyzing a mixture of two-stage logistic regressions with noarch
stagedchoicesplinemix fixed candidate knots. See Bruch, E., F. Feinberg, K. Lee (in
press)<DOI:10.1073/pnas.1522494113>. / GPL-2
r- 1.2 Proposes an original instrument for measuring stakeholder influence on the noarch
stakeholderanalysis development of an infrastructure project that is carried through by a munici-
pality, drawing on stakeholder classifications (Mitchell, Agle, & Wood, 1997)
and input-output modelling (Hester & Adams, 2013). Mitchell R., Agle B.R.,
& Wood D.J. <doi:10.2307/259247> Hester, P.T., & Adams, K.M. (2013)
<doi:10.1016/j.procs.2013.09.282>. / GPL-2
r-stand 2.0 Provides functions for the analysis of occupational and environmental data noarch
with non-detects. Maximum likelihood (ML) methods for censored log-
normal data and non-parametric methods based on the product limit estimate
(PLE) for left censored data are used to calculate all of the statistics recom-
mended by the American Industrial Hygiene Association (AIHA) for the com-
plete data case. Functions for the analysis of complete samples using exact
methods are also provided for the lognormal model. Revised from 2007-11-05
‘survfit~1’. / GPL-2
r-standardize 0.2.1 Tools which allow regression variables to be placed on similar scales, offering noarch
computational benefits as well as easing interpretation of regression output. /
GPL-3
r-standardizetext 1.0 Standardizes text according to a template; particularly useful for country noarch
names. / GPL-3


Name Version
r-stanheaders 2.18.1The C header files of the Stan project are provided by this package, but it linux-
contains no R code, vignettes, or function documentation. There is a shared 32,
object containing part of the ‘CVODES’ library, but it is not accessible from linux-
R. ‘StanHeaders’ is only useful for developers who want to utilize the ‘Link- 64,
ingTo’ directive of their package’s DESCRIPTION file to build on the Stan osx-
library without incurring unnecessary dependencies. The Stan project devel- 64,
ops a probabilistic programming language that implements full or approximate win-
Bayesian statistical inference via Markov Chain Monte Carlo or ‘variational’ 32,
methods and implements (optionally penalized) maximum likelihood estima- win-
tion via optimization. The Stan library includes an advanced automatic dif- 64
ferentiation scheme, ‘templated’ statistical and linear algebra functions that
can handle the automatically ‘differentiable’ scalar types (and doubles, ‘ints’,
etc.), and a parser for the Stan language. The ‘rstan’ package provides user-
facing R functions to parse, compile, test, estimate, and analyze Stan models.
/ BSD_3_clause file LICENSE
r-staplr 2.9.0 Provides function to manipulate PDF files: fill out PDF forms; merge multiple noarch
PDF files into one; remove selected pages from a file; rename multiple files in a
directory; rotate entire pdf document; rotate selected pages of a pdf file; Select
pages from a file; splits single input PDF document into individual pages;
splits single input PDF document into parts from given points. / GPL-3
r-stargazer 5.2.2 Produces LaTeX code, HTML/CSS code and ASCII text for well-formatted noarch
tables that hold regression analysis results from several models side-by-side,
as well as summary statistics. / GPL-2
r-startup 0.12.0Adds support for R startup configuration via ‘.Renviron.d’ and ‘.Rprofile.d’ di- noarch
rectories in addition to ‘.Renviron’ and ‘.Rprofile’ files. This makes it possible
to keep private / secret environment variables separate from other environment
variables. It also makes it easier to share specific startup settings by simply
copying a file to a directory. / LGPL-2.1
r-startupmsg 0.9.6 Provides utilities to create or suppress start-up messages. / LGPL-3 noarch
r-stat2data 2.0.0 Datasets for the textbook Stat2: Modeling with Regression and ANOVA (sec- noarch
ond edition). The package also includes data for the first edition, Stat2: Build-
ing Models for a World of Data and a few functions for plotting diagnostics. /
GPL-3
r-statdataml 1.0_26Support for reading and writing files in StatDataML—an XML-based data ex- noarch
change format. / GPL-2
r-statgraph 0.2.0 Contains statistical methods to analyze graphs, such as graph parameter es- noarch
timation, model selection based on the GIC (Graph Information Criterion),
statistical tests to discriminate two or more populations of graphs (ANOGVA
-Analysis of Graph Variability), correlation between graphs, and clustering of
graphs. / GPL-3
r-statmeasures 1.0 Offers useful functions to perform day-to-day data manipulation operations, noarch
data quality checks and post modelling statistical checks. One can effortlessly
change class of a number of variables to factor, remove duplicate observations
from the data, create deciles of a variable, perform data quality checks for
continuous (integer or numeric), categorical (factor) and date variables, and
compute goodness of fit measures such as auc for statistical models. The func-
tions are consistent for objects of class ‘data.frame’ and ‘data.table’, which is
an enhanced ‘data.frame’ implemented in the package ‘data.table’. / GPL-2


Name Version
r-statpermeco 0.1.0 Statistical performance measures used in the econometric literature to evaluate noarch
conditional covariance/correlation matrix estimates (MSE, MAE, Euclidean
distance, Frobenius distance, Stein distance, asymmetric loss function, eigen-
value loss function and the loss function defined in Eq. (4.6) of Engle et
al. (2016) <doi:10.2139/ssrn.2814555>). Additionally, compute Eq. (3.1)
and (4.2) of Li et al. (2016) <doi:10.1080/07350015.2015.1092975> to com-
pare the factor loading matrix. The statistical performance measures imple-
mented have been previously used in, for instance, Laurent et al. (2012)
<doi:10.1002/jae.1248>, Amendola et al. (2015) <doi:10.1002/for.2322> and
Becker et al. (2015) <doi:10.1016/j.ijforecast.2013.11.007>. / GPL-2
r-statprograms 0.2.0 A small collection of data on graduate statistics programs from the United noarch
States. / MIT
r-stcov 0.1.0 Estimates a covariance matrix using Stein’s isotonized covariance estimator, noarch
or a related estimator suggested by Haff. / GPL-2
r-stddiff 2.0 Contains three main functions including stddiff.numeric(), stddiff.binary() and noarch
stddiff.category(). These are used to calculate the standardized difference be-
tween two groups. It is especially used to evaluate the balance between two
groups before and after propensity score matching. / GPL-3
r-steinernet 3.0.1 A set of functions for finding and analysing Steiner trees. It has applications noarch
in biological pathway network analysis. Sadeghi (2013) <doi:10.1186/1471-
2105-14-144>. / GPL-3
r-steiniv 0.1_1 Routines for computing different types of linear estimators, based on noarch
instrumental variables (IVs), including the semi-parametric Stein-like
(SPS) estimator, originally introduced by Judge and Mittelhammer (2004)
<DOI:10.1198/016214504000000430>. / GPL-2
r-stellar 0.3_3 A package to manage and display stellar tracks and isochrones from Pisa low- noarch
mass database. Includes tools for isochrones construction and tracks interpo-
lation. / GPL-2
r-stem 1.0 Estimation of the parameters of a spatio-temporal model using the EM al- noarch
gorithm, estimation of the parameter standard errors using a spatio-temporal
parametric bootstrap, spatial mapping. / GPL-2
r-stemmatology 0.3.2 Explore and analyse the genealogy of textual or musical traditions, noarch
from their variants, with various stemmatological methods, mainly the
disagreement-based algorithms suggested by Camps and Cafiero (2015)
<doi:10.1484/M.LECTIO-EB.5.102565>. / GPL-3
r-stevedore 0.9.1 Work with containers over the Docker API. Rather than using system calls to noarch
interact with a docker client, using the API directly means that we can receive
richer information from docker. The interface in the package is automatically
generated using the ‘OpenAPI’ (a.k.a., ‘swagger’) specification, and all return
values are checked in order to make them type stable. / MIT
r-stheoreme 1.2 Functions implementing the procedure of entropy comparison between two noarch
data samples after the renormalization of respective probability distributions
with the algorithm designed by Klimontovich (Zeitschrift fur Physik B Con-
densed Matter. 1987, Volume 66, Issue 1, pp 125-127) and extended by An-
ishchenko (Proc. SPIE 2098, Computer Simulation in Nonlinear Optics. 1994,
pp.130-136). The package also includes data preparation tools which can also
be used separately for various applications. / GPL-2


Name Version
r-sticky 0.5.2 In base R, object attributes are lost when objects are modified by common noarch
data operations such as subset, filter, slice, append, extract etc. This packages
allows objects to be marked as ‘sticky’ and have attributes persisted during
these operations or when inserted into or extracted from recursive (i.e. list- or
table-like) objects. / GPL-2
r-stinepack 1.4 A consistently well behaved method of interpolation based on piecewise ratio- noarch
nal functions using Stineman’s algorithm. / GPL-2
r-stmgp 1.0.1 Rapidly build accurate genetic prediction models for genome-wide asso- noarch
ciation or whole-genome sequencing study data by smooth-threshold mul-
tivariate genetic prediction (STMGP) method. Variable selection is per-
formed using marginal association test p-values with an optimal p-value cut-
off selected by Cp-type criterion. Quantitative and binary traits are mod-
eled respectively via linear and logistic regression models. A function that
works through PLINK software (Purcell et al. 2007 <DOI:10.1086/519795>,
Chang et al. 2015 <DOI:10.1186/s13742-015-0047-8>) <https://www.cog-
genomics.org/plink2> is provided. Covariates can be included in regression
model. / GPL-2
r-stochprofml 1.2 This is an R package accompanying the paper Parameterizing cell-to-cell reg- noarch
ulatory heterogeneities via stochastic transcriptional profiles by Sameer S Ba-
jikar, Christiane Fuchs, Andreas Roller, Fabian J Theis and Kevin A Janes
(PNAS 2014, 111(5), E626-635). In this paper, we measure expression pro-
files from small heterogeneous populations of cells, where each cell is assumed
to be from a mixture of lognormal distributions. We perform maximum likeli-
hood estimation in order to infer the mixture ratio and the parameters of these
lognormal distributions from the cumulated expression measurements. / GPL-
2
r-stockchina 0.3.1 With this package, users can obtain the real-time price and volume information noarch
of stocks in China market, as well as the information of the stock index. This
package adopted the API from Sina Finance (http://finance.sina.com.cn/). /
GPL-2
r-stoichcalc 1.1_3 Given a list of substance compositions, a list of substances involved in a pro- noarch
cess, and a list of constraints in addition to mass conservation of elementary
constituents, the package contains functions to build the substance composi-
tion matrix, to analyze the uniqueness of process stoichiometry, and to calcu-
late stoichiometric coefficients if process stoichiometry is unique. (See Re-
ichert, P. and Schuwirth, N., A generic framework for deriving process sto-
ichiometry in enviromental models, Environmental Modelling and Software
25, 1241-1251, 2010 for more details.) / GPL-2
r-stopes 0.1 A variable selection procedure for low to moderate size linear regressions mod- noarch
els. This method repeatedly splits the data into two sets, one for estimation and
one for validation, to obtain an empirically optimized threshold which is then
used to screen for variables to include in the final model. / GPL-2


Name Version
r-stopwords 0.9.0 Provides multiple sources of stopwords, for use in text analysis and natural linux-
language processing. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-storr 1.2.1 Creates and manages simple key-value stores. These can use a variety of ap- noarch
proaches for storing the data. This package implements the base methods and
support for file system, in-memory and DBI-based database stores. / MIT
r-strategy 1.0.1 Users can build and test customized quantitative trading strategies. Some noarch
quantitative trading strategies are already implemented, e.g. various moving-
average filters with trend following approaches. The implemented class called
Strategy allows users to access several methods to analyze performance fig-
ures, plots and backtest the strategies. Furthermore, custom strategies can be
added, a generic template is available. The custom strategies require a certain
input and output so they can be called from the Strategy-constructor. / GPL-3
r- 0.3.0 Performs Stratified Covariate Balancing with Markov blanket feature selec- noarch
stratifiedbalancing tion and use of synthetic cases. See Alemi et al. (2016) <DOI:10.1111/1475-
6773.12628>. / GPL-2
r- 1.1.2 I provide functions to calculate Gross Primary Productivity, Net Ecosystem noarch
streammetabolism Production, and Ecosystem Respiration from single station diurnal Oxygen
curves. / GPL-3
r-stressr 1.0.0 Forms queries to submit to the Cleveland Federal Reserve Bank web site’s noarch
financial stress index data site. Provides query functions for both the composite
stress index and the components data. By default the download includes daily
time series data starting September 25, 1991. The functions return a class of
either type easing or cfsi which contain a list of items related to the query
and its graphical presentation. The list includes the time series data as an xts
object. The package provides four lattice time series plots to render the time
series data in a manner similar to the bank’s own presentation. / MIT
r-stressstrength 1.0.2 Reliability of (normal) stress-strength models and for building two-sided or noarch
one-sided confidence intervals according to different approximate procedures.
/ GPL-3
r- 0.1.0 Takes a list of character strings and forms an adjacency matrix for the times noarch
string2adjmatrix the specified characters appear together in the strings provided. For use in
social network analysis and data wrangling. Simple package, comprised of
three functions. / GPL-3


r-stringb 0.1.13Base R already ships with string handling capabilities ‘out- of-the-box’ but noarch
lacks streamlined function names and workflow. The ‘stringi’ (‘stringr’) pack-
age on the other hand has well named functions, extensive Unicode support
and allows for a streamlined workflow. On the other hand it adds depen-
dencies and regular expression interpretation between base R functions and
‘stringi’ functions might differ. This packages aims at providing a solution
to the use case of unwanted dependencies on the one hand but the need for
streamlined text processing on the other. The packages’ functions are solely
based on wrapping base R functions into ‘stringr’/’stringi’ like function names.
Along the way it adds one or two extra functions and last but not least provides
all functions as generics, therefore allowing for adding methods for other text
structures besides plain character vectors. / MIT
r-stringdist 0.9.5.1Implements an approximate string matching version of R’s native ‘match’ linux-
function. Can calculate various string distances based on edits (Damerau- 32,
Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q- linux-
gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An 64,
implementation of soundex is provided as well. Distances can be computed osx-
between character vectors while taking proper care of encoding or between 64,
integer vectors representing generic sequences. / GPL-3 win-
32,
win-
64
r-stringformattr 0.1.2 Pass named and unnamed character vectors into specified positions in strings. noarch
This represents an attempt to replicate some of python’s string formatting. /
MIT
r-stringi 1.4.3 Allows for fast, correct, consistent, portable, as well as convenient charac- linux-
ter string/text processing in every locale and any native encoding. Owing 32,
to the use of the ICU library, the package provides R users with platform- linux-
independent functions known to Java, Perl, Python, PHP, and Ruby program- 64,
mers. Available features include: pattern searching (e.g., with ICU Java-like osx-
regular expressions or the Unicode Collation Algorithm), random string gen- 64,
eration, case mapping, string transliteration, concatenation, Unicode normal- win-
ization, date-time formatting and parsing, etc. / file LICENSE (FOSS) 32,
win-
64
r-stringr 1.4.0 A consistent, simple and easy to use set of wrappers around the fantastic linux-
‘stringi’ package. All function and argument names (and positions) are con- 32,
sistent, all functions deal with NA’s and zero length vectors in the same way, linux-
and the output from one function is easy to feed into the input of another. / 64,
GPL-2 | file LICENSE noarch,
osx-
64,
win-
32,
win-
64
r-strip 1.0.0 The strip function deletes components of R model outputs that are useless for noarch
specific purposes, such as predict[ing], print[ing], summary[izing], etc. / MIT


Name Version
r-stripless 1.0_3 For making Trellis-type conditioning plots without strip labels. This is useful noarch
for displaying the structure of results from factorial designs and other studies
when many conditioning variables would clutter the display with layers of
redundant strip labels. Settings of the variables are encoded by layout and
spacing in the trellis array and decoded by a separate legend. The functionality
is implemented by a single S3 generic strucplot() function that is a wrapper
for the Lattice package’s xyplot() function. This allows access to all Lattice
graphics capabilities in the usual way. / GPL-2 | GPL-3
r-strucchange 1.5_1 Testing, monitoring and dating structural changes in (linear) regression mod- linux-
els. strucchange features tests/methods from the generalized fluctuation test 32,
framework as well as from the F test (Chow test) framework. This includes linux-
methods to fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM, re- 64,
cursive/moving estimates) and F statistics, respectively. It is possible to mon- noarch,
itor incoming data online using fluctuation processes. Finally, the breakpoints osx-
in regression models with structural changes can be estimated together with 64,
confidence intervals. Emphasis is always given to methods for visualizing the win-
data. / GPL-2 | GPL-3 32,
win-
64
r-structfdr 1.3 Perform more powerful false discovery control (FDR) for microbiome data, noarch
taking into account the prior phylogenetic relationship among bacteria species.
As a general methodology, it is applicable to any type of (genomic) data with
prior structure information. / GPL-2
r-stsm.class 1.3 This package defines an S4 class for structural time series models and provides noarch
some basic methods to work with it. / GPL-2
r-stuart 0.8.0 Construct subtests from a pool of items by using ant-colony-optimization, noarch
genetic algorithms, brute force, or random sampling. Schultze (2017)
<doi:10.17169/refubium-622>. / GPL-3
r-stubthat 1.2.1 Create stubs of functions for use while testing. / MIT noarch
r-stv 1.0.1 Implementations of the Single Transferable Vote counting system. By default, noarch
it uses the Cambridge method for surplus allocation and Droop method for
quota calculation. Fractional surplus allocation and the Hare quota are avail-
able as options. / LGPL-3
r-stylest 0.1.0 Estimates distinctiveness in speakers’ (authors’) style. Fits models that can be noarch
used for predicting speakers of new texts. Methods developed in Spirling et al
(2018) <doi:10.2139/ssrn.3235506> (working paper). / GPL-3
r-subcopem2d 1.3 Calculate empirical subcopula and dependence measures from a given bivari- noarch
ate sample, and Bernstein copula approximations. / GPL-3
r-subcultcon 1.0 The three functions in the package compute the maximum likelihood estimates noarch
of the informants’ competence scores, tests for two answer keys with known
groups, and finds best split of the informants into sub-culture groups. / GPL-2
| GPL-3
r-subdetect 1.1 A test for the existence of a subgroup with enhanced treatment effect. And, a noarch
sample size calculation procedure for the subgroup detection test. / GPL-3
r-subgroup 1.1 Produces various measures of expected treatment effect heterogeneity under noarch
an assumption of homogeneity across subgroups. Graphical presentations are
created to compare these expected differences with the observed differences. /
GPL-2 | GPL-3


Name Version
r- 0.2.1 Developed to assist in discovering interesting subgroups in high-dimensional noarch
subgroup.discovery data. The PRIM implementation is based on the 1998 paper Bump hunt-
ing in high-dimensional data by Jerome H. Friedman and Nicholas I. Fisher.
<doi:10.1023/A:1008894516817> PRIM involves finding a set of rules which
combined imply unusually large (or small) values of some other target vari-
able. Specifically one tries to find a set of sub regions in which the target vari-
able is substantially larger than overall mean. The objective of bump hunting
in general is to find regions in the input (attribute/feature) space with relatively
high (low) values for the target variable. The regions are described by simple
rules of the type if: condition-1 and . . . and condition-n then: estimated target
value. Given the data (or a subset of the data), the goal is to produce a box B
within which the target mean is as large as possible. There are many problems
where finding such regions is of considerable practical interest. Often these are
problems where a decision maker can in a sense choose or select the values of
the input variables so as to optimize the value of the target variable. In bump
hunting it is customary to follow a so-called covering strategy. This means that
the same box construction (rule induction) algorithm is applied sequentially to
subsets of the data. / GPL-3
r-subgxe 0.9.0 Classical methods for combining summary data from genome-wide associa- noarch
tion studies (GWAS) only use marginal genetic effects and power can be com-
promised in the presence of heterogeneity. ‘subgxe’ is a R package that im-
plements p-value assisted subset testing for association (pASTA), a method
developed by Yu et al. (2019) <doi:10.1159/000496867>. pASTA general-
izes association analysis based on subsets by incorporating gene-environment
interactions into the testing procedure. / GPL-3
r-subniche 0.9.7 Complementary indexes calculation to the Outlying Mean Index analysis to noarch
explore niche shift of a community and biological constraint within an Eu-
clidean space, with graphical displays. / GPL-2
r- 1.0 Routines for identifying metabolic subpathways mediated by microRNAs noarch
subpathwaygmir (miRNAs) through topologically locating miRNAs and genes within recon-
structed Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic path-
way graphs embedded by miRNAs. (1) This package can obtain the re-
constructed KEGG metabolic pathway graphs with genes and miRNAs as
nodes, through converting KEGG metabolic pathways to graphs with genes
as nodes and compounds as edges, and then integrating miRNA-target interac-
tions verified by low-throughput experiments from four databases (TarBase,
miRecords, mirTarBase and miR2Disease) into converted pathway graphs.
(2) This package can locate metabolic subpathways mediated by miRNAs by
topologically analyzing the lenient distance of miRNAs and genes within re-
constructed KEGG metabolic pathway graphs.(3) This package can identify
significantly enriched miRNA-mediated metabolic subpathways based on lo-
cated subpathways by hypergenomic test. (4) This package can support six
species for metabolic subpathway identification, such as caenorhabditis ele-
gans, drosophila melanogaster, danio rerio, homo sapiens, mus musculus and
rattus norvegicus, and user only need to update interested organism-specific
environment variables. / GPL-2


Name Version
r-subsamp 0.1.0 This subsample winner algorithm (SWA) for regression with a large-p data noarch
(X, Y) selects the important variables (or features) among the p features X in
explaining the response Y. The SWA first uses a base procedure, here a linear
regression, on each of subsamples randomly drawn from the p variables, and
then computes the scores of all features, i.e., the p variables, according to the
performance of these features collected in each of the subsample analyses. It
then obtains the ‘semifinalist’ of the features based on the resulting scores and
determines the ‘finalists’, i.e., the important features, from the ‘semifinalist’.
Fan, Sun and Qiao (2017) <http://sr2c.case.edu/swa-reg/>. / GPL-2 | GPL-3
r-sudoku 2.6 Generates, plays, and solves Sudoku puzzles. The GUI playSudoku() needs noarch
package tkrplot if you are not on Windows. / GPL-3
r-sudokualt 0.2_0 Tools for making, retrieving, displaying and solving sudoku games. This noarch
package is an alternative to the earlier sudoku-solver package, ‘sudoku’. The
present package uses a slightly different algorithm, has a simpler coding and
presents a few more sugar tools, such as plot and print methods. Solved su-
doku games are of some interest in Experimental Design as examples of Latin
Square designs with additional balance constraints. / GPL-2
r-sue 1.0 This is a package for the subsampling method of robust estimation of linear noarch
regression models / GPL-2
r-suncalc 0.5.0 Get sun position, sunlight phases (times for sunrise, sunset, dusk, etc.), moon noarch
position and lunar phase for the given location and time. Most calculations are
based on the formulas given in Astronomy Answers articles about position of
the sun and the planets : <https://www.aa.quae.nl/en/reken/zonpositie.html>.
/ GPL-2
r-sunclarco 1.0.0 Survival analysis for unbalanced clusters using Archimedean copulas (Prenen noarch
et al. (2016) <DOI:10.1111/rssb.12174>). / GPL-3
r-suntersampling 1.0.1 Functions for drawing samples according to Sunter’s sampling design, and for noarch
computing first and second order inclusion probabilities / GPL-3
r-supcluster 1.0 Clusters features under the assumption that each cluster has a random effect noarch
and there is an outcome variable that is related to the random effects by a lin-
ear regression. In this way the cluster analysis is ‘‘supervised” by the outcome
variable. An alternate specification is that features in each cluster have the
same compound symmetric normal distribution, and the conditional distribu-
tion of the outcome given the features has the same coefficient for each feature
in a cluster. / GPL-2
r-superdiag 1.1 A Comprehensive Test Suite for Markov Chain Nonconvergence. / GPL-3 noarch
r-supermds 1.0.2 Witten and Tibshirani (2011) Supervised multidimensional scaling for visu- noarch
alization, classification, and bipartite ranking. Computational Statistics and
Data Analysis 55(1): 789-801. / GPL-2
r-supernova 2.0.0 Produces ANOVA tables in the format used by Judd, McClelland, and Ryan noarch
(2017, ISBN:978-1138819832) in their introductory textbook, Data Analysis.
This includes proportional reduction in error and formatting to improve ease
the transition between the book and R. / GPL-3
r-superpc 1.09 Supervised principal components for regression and survival analsysis. Espe- noarch
cially useful for high-dimnesional data, including microarray data. / GPL-2


Name Version
r-suppdists 1.1_9.4
Ten distributions supplementing those built into R. Inverse Gauss, Kruskal- linux-
Wallis, Kendall’s Tau, Friedman’s chi squared, Spearman’s rho, maximum F 32,
ratio, the Pearson product moment correlation coefficient, Johnson distribu- linux-
tions, normal scores and generalized hypergeometric distributions. In addition 64,
two random number generators of George Marsaglia are included. / GPL (>= osx-
2) 64,
win-
32,
win-
64
r-support.bws 0.2_0 Provides three basic functions that support an implementation of object case noarch
(Case 1) best-worst scaling: one for converting a two-level orthogonal main-
effect design/balanced incomplete block design into questions; one for creat-
ing a data set suitable for analysis; and one for calculating count-based scores.
/ GPL-2
r-support.bws2 0.2_2 Provides three basic functions that support an implementation of Case 2 (pro- noarch
file case) best-worst scaling. The first is to convert an orthogonal main-effect
design into questions, the second is to create a dataset suitable for analysis,
and the third is to calculate count-based scores. / GPL-2
r- 1.0 Provides functions to estimate the proportion of treatment effect on a censored noarch
surrogateoutcome primary outcome that is explained by the treatment effect on a censored sur-
rogate outcome/event. All methods are described in detail in Assessing the
Value of a Censored Surrogate Outcome by Parast L, Tian L, and Cai T which
is currently in press at Lifetime Data Analysis. The main functions are (1)
R.q.event() which calculates the proportion of the treatment effect (the differ-
ence in restricted mean survival time at time t) explained by surrogate outcome
information observed up to a selected landmark time, (2) R.t.estimate() which
calculates the proportion of the treatment effect explained by primary outcome
information only observed up to a selected landmark time, and (3) IV.event()
which calculates the incremental value of the surrogate outcome information.
/ GPL-3
r-surrogatetest 1.1 Provides functions to test for a treatment effect in terms of the difference in sur- noarch
vival between a treatment group and a control group using surrogate marker
information obtained at some early time point in a time-to-event outcome set-
ting. Nonparametric kernel estimation is used to estimate the test statistic and
perturbation resampling is used for variance estimation. More details will be
available in the future in: Parast L, Cai T, Tian L (2019). Using a Surrogate
Marker for Early Testing of a Treatment Effect. Biometrics, In press. / GPL-3
r-surrosurvroc 0.1.0 Nonparametric and semiparametric estimations of the time-dependent ROC noarch
curve for an incomplete failure time data with surrogate failure time endpoints.
/ GPL-2
r-surtex 0.9 suRtex was designed for easy descriptive statistic reporting of categorical sur- noarch
vey data (e.g., Likert scales) in LaTeX. suRtex takes a matrix or data frame
and produces the LaTeX code necessary for a sideways table creation. Mean,
median, standard deviation, and sample size are optional. / GPL-3
r-survawkmt2 1.0.0 Tests for equality of two survival functions based on integrated weighted dif- noarch
ferences of two Kaplan-Meier curves. / GPL-2


Name Version
r- 1.0 Three new methods to perform outlier detection in a survival context. In total noarch
survbootoutliers there are six methods provided, the first three methods are traditional residual-
based outlier detection methods, the second three are the concordance-based.
Package developed during the work on the two following publications: Pinto
J., Carvalho A. and Vinga S. (2015) <doi:10.5220/0005225300750082>; Pinto
J.D., Carvalho A.M., Vinga S. (2015) <doi:10.1007/978-3-319-27926-8_22>.
/ GPL-2
r-survexp.fr 1.0 Relative survival, AER and SMR based on French death rates / GPL-2 noarch
r-surveyeditor 1.0 Help generate slides for surveys or experiments. The resulted slides allow the noarch
subject to respond with the use of the mouse (usual keyboard input is replaced
with clicking on a virtual keyboard on the slide). Subjects’ responses are saved
to the user- specified location in the form of R-readable text file. To allow flex-
ibility, each function in this package generates a particular type of slides thus
general R function writing skills are required to compile these edited slides. /
GPL-2
r-surveyoutliers 0.1 At present, the only functionality is the calculation of optimal one-sided win- noarch
sorizing cutoffs. The main function is optimal.onesided.cutoff.bygroup. It
calculates the optimal tuning parameter for one-sided winsorisation, and so
calculates winsorised values for a variable of interest. See the help file for this
function for more details and an example. / GPL-2 | GPL-3
r-survgini 1.0 The Gini concentration test for survival data is a nonparametric test based on noarch
the Gini index for testing the equality of two survival distributions from the
point of view of concentration. The package compares different nonparametric
tests (asymptotic Gini test, permutation Gini test, log-rank test, Gray-Tsiatis
test and Wilcoxon test) and computes their p-values. / GPL-2
r-survival 2.44_1.1
Contains the core survival analysis routines, including definition of Surv ob- linux-
jects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and 32,
parametric accelerated failure time models. / LGPL (>= 2) linux-
64,
osx-
64,
win-
32,
win-
64
r-survjamda.data 1.0.2 Three breast cancer gene expression data sets that can be used for package noarch
‘survJamda’. This package contains the gene expression and phenotype data
of GSE1992, GSE3143 and GSE4335. / GPL-2
r-survlong 1.0 Kernel weighting methods for estimation of proportional hazards models with noarch
intermittently observed longitudinal covariates. / GPL-2
r-survregcenscov 1.4 The main function of this package allows estimation of a Weibull Regression noarch
for a right-censored endpoint, one interval-censored covariate, and an arbi-
trary number of non-censored covariates. Additional functions allow to switch
between different parametrizations of Weibull regression used by different R
functions, inference for the mean difference of two arbitrarily censored Nor-
mal samples, and estimation of canonical parameters from censored samples
for several distributional assumptions. / GPL-2


Name Version
r-survrm2 1.0_2 Performs two-sample comparisons using the restricted mean survival time noarch
(RMST) as a summary measure of the survival time distribution. Three kinds
of between-group contrast metrics (i.e., the difference in RMST, the ratio of
RMST and the ratio of the restricted mean time lost (RMTL)) are computed. It
performs an ANCOVA-type covariate adjustment as well as unadjusted analy-
ses for those measures. / GPL-2
r-survrm2adapt 1.0_1 Performs the procedure proposed by Horiguchi et al. (2018) noarch
<doi:10.1002/sim.7661>. The method specifies a set of truncation time
points tau’s for calculating restricted mean survival times (RMST), performs
testing for equality, and estimates the difference in RMST between two groups
at the specified tau’s. Multiplicity by specifying several tau’s is taken into
account in this procedure. / GPL-2
r-survtrunc 0.1.0 Package performs Cox regression and survival distribution function estima- noarch
tion when the survival times are subject to double truncation. The estima-
tion procedure for each method involves inverse probability weighting, where
the weights correspond to the inverse of the selection probabilities and are
estimated using the survival times and truncation times only. Both methods
require that the survival and truncation times are quasi-independent. A test
for checking this independence assumption is also included in this package.
The functions available in this package for Cox regression, survival distribu-
tion function estimation, and testing independence under double truncation
are based on the following methods, respectively: Rennert and Xie (2017)
<doi:10.1111/biom.12809>, Shen (2010) <doi:10.1007/s10463-008-0192-2>,
Martin and Betensky (2005) <doi:10.1198/016214504000001538>. / GPL-2
r-svapls 1.4 Accurate identification of genes that are truly differentially expressed over two noarch
sample varieties, after adjusting for hidden subject-specific effects of residual
heterogeneity. / GPL-3
r-svdvisual 1.1 Some visualization tools based on Singular Value Decomposition / GPL-2 noarch
r-svenssonm 0.1.0 Obtain parameters of Svensson’s Method, including percentage agreement, noarch
systematic change and individual change. Also, the contingency table can
be generated. Svensson’s Method is a rank-invariant nonparametric method
for the analysis of ordered scales which measures the level of change both
from systematic and individual aspects. For the details, please refer to Svens-
son E. Analysis of systematic and random differences between paired ordinal
categorical data [dissertation]. Stockholm: Almqvist & Wiksell International;
1993. / GPL-3
r-svgpanzoom 0.3.3 This ‘htmlwidget’ provides pan and zoom interactivity to R graphics, including noarch
‘base’, ‘lattice’, and ‘ggplot2’. The interactivity is provided through the ‘svg-
pan-zoom.js’ library. Various options to the widget can tailor the pan and zoom
experience to nearly any user desire. / MIT
r-svgui 1.0.0 The SciViews svGUI package eases the management of Graphical User Inter- noarch
faces (GUI) in R. It is independent from any particular GUI widgets (Tk, Gtk2,
native, . . . ). It centralizes info about GUI elements currently used, and it dis-
patches GUI calls to the particular toolkits in use in function of the context (is
R run at the terminal, within a Tk application, a HTML page?). / GPL-2
r-svmisc 1.1.0 Miscellaneous functions for SciViews or general use: manage a temporary noarch
environment attached to the search path for temporary variables you do not
want to save() or load(), test if Aqua, Mac, Win, . . . Show progress bar, etc. /
GPL-2


Name Version
r-svmplus 1.0.1 Implementation of Support Vector Machines Plus (SVM) noarch
for classification problems. See (Vladimir et. al, 2009,
<doi:10.1016/j.neunet.2009.06.042>) for theoretical details and see (Li
et. al, 2016, <https://github.com/okbalefthanded/svmplus_matlab>) for
implementation details in ‘MATLAB’. / GPL-3
r-svn 1.0 Determines networks of significant synchronization between the discrete states noarch
of nodes; see Tumminello et al <doi:10.1371/journal.pone.0017994>. / GPL
(>= 2.0)
r-svs 1.1.0 Various tools for semantic vector spaces, such as correspondence analysis noarch
(simple, multiple and discriminant), latent semantic analysis, probabilistic la-
tent semantic analysis, non-negative matrix factorization, latent class analysis
and EM clustering. Furthermore, there are specialized distance measures, plot-
ting functions and some helper functions. / GPL-3
r-svsweave 0.9_8 Supporting functions for the GUI API (Sweave functions) / GPL-2 noarch
r-svunit 0.7_12A complete unit test system and functions to implement its GUI part / GPL-2 noarch
r-swagger 3.9.2 A collection of ‘HTML’, ‘JavaScript’, and ‘CSS’ assets that dynamically noarch
generate beautiful documentation from a ‘Swagger’ compliant API: <https:
//swagger.io/specification/>. / Apache License 2.0 | file LICENSE
r-swapclass 1.0.1 A null model randomizing semi-quantitative multi-classes (or ordinal) data by noarch
swapping sub-matrices while both the row and the column marginal sums are
held constant. / GPL-3
r-swcrtdesign 3.0 A set of tools for examining the design and analysis aspects of stepped wedge noarch
cluster randomized trials (SW CRT) based on a repeated cross-sectional sam-
pling scheme (Hussey MA and Hughes JP (2007) Contemporary Clinical Tri-
als 28:182-191. <doi:10.1016/j.cct.2006.05.007>). / GPL-2
r-swdft 1.0.0 Implements the Sliding Window Discrete Fourier Transform (SWDFT). Also noarch
provides statistical methods based on the SWDFT, and graphical tools to dis-
play the outputs. / MIT
r-sweidnumbr 1.4.1 Structural handling of identity numbers used in the Swedish administration noarch
such as personal identity numbers (‘personnummer’) and organizational iden-
tity numbers (‘organisationsnummer’). / BSD_2_clause
r-swirl 2.4.4 Use the R console as an interactive learning environment. Users receive im- noarch
mediate feedback as they are guided through self-paced lessons in data science
and R programming. / MIT
r-swissair 1.1.5 Ozone, NOx (= Sum of nitrogen monoxide and nitrogen dioxide), nitrogen noarch
monoxide, ambient temperature, dew point, wind speed and wind direction at
3 sites around lake of Lucerne in Central Switzerland in 30 min time resolution
for year 2004. / GPL-3
r-swissmrp 0.62 Provides a number of useful functions to employ MrP for small area prediction noarch
in Switzerland. Based on a hierarchical model and survey data one can derive
cantonal preference measures. The package allows to automatize the predic-
tion and post-stratification steps. It further provides adequate print, summary,
map, and plot functions for objects of its class. / GPL-2
r-switchr 0.13.5Provides an abstraction for managing, installing, and switching between sets noarch
of installed R packages. This allows users to maintain multiple package li-
braries simultaneously, e.g. to maintain strict, package-version-specific re-
producibility of many analyses, or work within a development/production re-
lease paradigm. Introduces a generalized package installation process which
supports multiple repository and non-repository sources and tracks package
provenance. / Artistic-2.0


Name Version
r-sybil 2.1.5 This Systems Biology Package (Gelius-Dietrich et. al. (2012) noarch
<doi:10.1186/1752-0509-7-125>) implements algorithms for constraint based
analyses of metabolic networks, e.g. flux-balance analysis (FBA), mini-
mization of metabolic adjustment (MOMA), regulatory on/off minimization
(ROOM), robustness analysis and flux variability analysis. The package is eas-
ily extendable for additional algorithms. Most of the current LP/MILP solvers
are supported via additional packages. / GPL-3
r-sylly 0.1_5 Provides the hyphenation algorithm used for ‘TeX’/’LaTeX’ and similar soft- noarch
ware, as proposed by Liang (1983, <https://tug.org/docs/liang/>). Mainly con-
tains the function hyphen() to be used for hyphenation/syllable counting of text
objects. It was originally developed for and part of the ‘koRpus’ package, but
later released as a separate package so it’s lighter to have this particular func-
tionality available for other packages. Support for various languages needs
be added on-the-fly or by plugin packages (<https://undocumeantit.github.io/
repos>); this package does not include any language specific data. Due to
some restrictions on CRAN, the full package sources are only available from
the project homepage. To ask for help, report bugs, request features, or discuss
the development of the package, please subscribe to the koRpus-dev mailing
list (<http://korpusml.reaktanz.de>). / GPL-3
r-sym.arma 1.0 Functions for fitting the Autoregressive and Moving Average Symmetric noarch
Model for univariate time series introduced by Maior and Cysneiros (2018),
<doi:10.1007/s00362-016-0753-z>. Fitting method: conditional maximum
likelihood estimation. For details see: Wei (2006), Time Series Analysis: Uni-
variate and Multivariate Methods, Section 7.2. / GPL-2
r-synbreeddata 1.5 Data sets for the ‘synbreed’ package with three data sets from cattle, maize noarch
and mice to illustrate the functions in the ‘synbreed’ R package. All data
sets are stored in the gpData format introduced in the ‘synbreed’ package.
This research was funded by the German Federal Ministry of Education and
Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and
animal breeding (FKZ 0315528A). / GPL-2
r-synchrony 0.3.7 Methods for computing spatial, temporal, and spatiotemporal statistics includ- noarch
ing: empirical univariate, bivariate and multivariate variograms; fitting vari-
ogram models; phase locking and synchrony analysis; generating autocorre-
lated and cross-correlated matrices. / GPL-2
r-syncmove 0.1_0 The function ‘syncSubsample’ subsamples temporal data of different entities noarch
so that the result only contains synchronal events. The function ‘mci’ cal-
culates the Movement Coordination Index (MCI, see reference on help page
for function ‘mci’) of a data set created with the function ‘syncSubsample’. /
GPL-2
r-synet 2.0 Infers sympatry matrices from distributional data and analyzes them in order noarch
to identify groups of species cohesively connected. / GPL-3
r-syntaxr 0.8.0 A set of functions for generating ‘SPSS’ syntax files from the R environment. noarch
/ MIT
r-sys 3.2 Drop-in replacements for the base system2() function with fine control and linux-
consistent behavior across platforms. Supports clean interruption, timeout, 64,
background tasks, and streaming STDIN / STDOUT / STDERR over binary osx-
or text connections. Arguments on Windows automatically get encoded and 64,
quoted to work on different locales. / MIT file LICENSE win-
32,
win-
64


Name Version
r-t2eq 1.1 Contains functions for applying the T^2-test for equivalence. The T^2- noarch
test for equivalence is a multivariate two-sample equivalence test. Dis-
tance measure of the test is the Mahalanobis distance. For mul-
tivariate normally distributed data the T^2-test for equivalence is ex-
act and UMPI. The function T2EQ() implements the T^2-test for
equivalence according to Wellek (2010) <DOI:10.1201/ebk1439808184>.
The function T2EQ.dissolution.profiles.hoffelder() implements a vari-
ant of the T^2-test for equivalence according to Hoffelder (2016)
<http://www.ecv.de/suse_item.php?suseId=Z|pi|8430> for the equivalence
comparison of highly variable dissolution profiles. / GPL-3
r-tablaxlsx 1.2.2 Some functions are included in this package for writing tables in Excel format noarch
suitable for distribution. / GPL-3
r-table1 1.1 Create HTML tables of descriptive statistics, as one would expect to see as the noarch
first table (i.e. Table 1) in a medical/epidemiological journal article. / GPL-3
r-table1heatmap 1.1 Table 1 is the classical way to describe the patients in a clinical study. The noarch
amount of splits in the data in such a table is limited. Table1Heatmap draws
a heatmap of all crosstables that can be generated with the data. Users can
choose between showing the actual crosstables or direction of effect of associ-
ations, and highlight associations by number of patients or p-values. / LGPL-3
r-tablehtml 2.0.0 A tool to create and style HTML tables with CSS. These can be exported noarch
and used in any application that accepts HTML (e.g. ‘shiny’, ‘rmarkdown’,
‘PowerPoint’). It also provides functions to create CSS files (which also work
with shiny). / MIT
r-tablematrix 0.82.0Provides two classes extending ‘data.table’ class. Simple ‘tableList’ class noarch
wraps ‘data.table’ and any additional structures together. More complex
‘tableMatrix’ class combines ‘data.table’ and ‘matrix’. See <http://github.
com/InferenceTechnologies/tableMatrix> for more information and examples.
/ GPL-2
r-tablemonster 1.7 Provides a user friendly interface to generation of booktab style tables using noarch
‘xtable’. / GPL-2
r-tableplot 0.3_5 Description: / GPL-3 noarch
r-tablerdash 0.1.0 ‘R’ interface to the ‘Tabler’ HTML template. See more here <https://tabler. noarch
io>. ‘tablerDash’ is a light ‘Bootstrap 4’ dashboard template. There are differ-
ent layouts available such as a one page dashboard or a multi page template,
where the navigation menu is contained in the navigation bar. A fancy example
is available at <https://dgranjon.shinyapps.io/shinyMons/>. / GPL-2
r- 1.3.2 A wrapper to a set of algorithms designed to recognise positional cues present noarch
tabletolongform in hierarchical for-human Tables (which would normally be interpreted visu-
ally by the human brain) to decompose, then reconstruct the data into machine-
readable LongForm Dataframes. / GPL-3
r-tabulizerjars 1.0.1 ‘Java’ .jar files for the ‘Tabula’ <http://tabula.technology/> ‘Java’ library, noarch
which are required by the ‘tabulizer’ R package. The version numbering of
this package corresponds to versions of ‘tabula-java’ library releases <https:
//github.com/tabulapdf/tabula-java/releases/>. / MIT
r-tabulog 0.1.1 Convert semi-structured log files (such as ‘Apache’ access.log files) into a tab- noarch
ular format (data.frame) using a standard template system. / MIT
r-tabusearch 1.1.1 Tabu search algorithm for binary configurations. A basic version of the al- noarch
gorithm as described by Fouskakis and Draper (2007) <doi:10.1111/j.1751-
5823.2002.tb00174.x>. / GPL-2


Name Version
r-tactile 0.2.0 Extensions to ‘lattice’, providing new high-level functions, methods for exist- noarch
ing functions, panel functions, and a theme. / GPL-3
r-tailloss 1.0 Set of tools to estimate the probability in the upper tail of the aggregate loss noarch
distribution using different methods: Panjer recursion, Monte Carlo simula-
tions, Markov bound, Cantelli bound, Moment bound, and Chernoff bound. /
GPL-2 | GPL-3
r-taipan 0.1.2 A tool to help create shiny apps for selecting and annotating elements of im- noarch
ages. Users must supply images, questions, and answer choices. The user
interface is a dynamic shiny app, that displays the images and questions and
answer choices. The data generated can be saved to a file that can be used for
subsequent analysis. The original purpose was to annotate still images from
tennis video for face recognition and emotion detection purposes. / GPL-3
r-tandem 1.0.2 A two-stage regression method that can be used when various input data types noarch
are correlated, for example gene expression and methylation in drug response
prediction. In the first stage it uses the upstream features (such as methyla-
tion) to predict the response variable (such as drug response), and in the sec-
ond stage it uses the downstream features (such as gene expression) to pre-
dict the residuals of the first stage. In our manuscript (Aben et al., 2016,
<doi:10.1093/bioinformatics/btw449>), we show that using TANDEM pre-
vents the model from being dominated by gene expression and that the features
selected by TANDEM are more interpretable. / GPL-2
r-tangram 0.4 Provides an extensible formula system to quickly and easily create production noarch
quality tables. The steps of the process are formula parser, statistical content
generation from data, to rendering. Each step of the process is separate and
user definable thus creating a set of building blocks for highly extensible table
generation. A user is not limited by any of the choices of the package creator
other than the formula grammar. For example, one could chose to add a dif-
ferent S3 rendering function and output a format not provided in the default
package. Or possibly one would rather have Gini coefficients for their sta-
tistical content. Routines to achieve New England Journal of Medicine style,
Lancet style and Hmisc::summaryM() statistics are provided. The package
contains rendering for HTML5, Rmarkdown and an indexing format for use in
tracing and tracking are provided. / GPL-3
r- 1.0 Art-like behavior based on randomness / Unlimited noarch
taoteprogramming
r-tapkee 1.0 Wrapper for using ‘tapkee’ command line utility, it allows to run it from inside noarch
R and catch the results for further analysis and plotting. ‘Tapkee’ is a program
for fast dimension reduction (see <http://tapkee.lisitsyn.me/> for more details).
/ GPL-2
r-tar 1.0 Identification and estimation of the autoregressive threshold models with noarch
Gaussian noise, as well as positive-valued time series. The package pro-
vides the identification of the number of regimes, the thresholds and the au-
toregressive orders, as well as the estimation of remain parameters. The
package implements the methodology from the 2005 paper: Modeling Bi-
variate Threshold Autoregressive Processes in the Presence of Missing Data
<DOI:10.1081/STA-200054435>. / GPL-2


r-tariff 1.0.5 Implement the Tariff algorithm for coding cause-of-death from verbal au- noarch
topsies. The Tariff method was originally proposed in James et al (2011)
<DOI:10.1186/1478-7954-9-31> and later refined as Tariff 2.0 in Serina, et
al. (2015) <DOI:10.1186/s12916-015-0527-9>. Note that this package was
not developed by authors affiliated with the Institute for Health Metrics and
Evaluation and thus unintentional discrepancies may exist between the this
implementation and the implementation available from IHME. / GPL-2
r-tarifx 1.0.6.1A collection of various utility and convenience functions. / GPL-2 noarch
r-tatest 1.0 The ta-test is a modified two-sample or two-group t-test of Gosset (1908). In noarch
small samples with less than 15 replicates,the ta-test significantly reduces type
I error rate but has almost the same power with the t-test and hence can greatly
enhance reliability or reproducibility of discoveries in biology and medicine.
The ta-test can test single null hypothesis or multiple null hypotheses without
needing to correct p-values. / GPL-3
r-tatoo 1.1.1 Functions to combine data.frames in ways that require additional effort in base noarch
R, and to add metadata (id, title, . . . ) that can be used for printing and xlsx
export. The ‘Tatoo_report’ class is provided as a convenient helper to write
several such tables to a workbook, one table per worksheet. Tatoo is built on
top of ‘openxlsx’, but intimate knowledge of that package is not required to
use tatoo. / MIT
r-taup.r 1.5 Evaluates traveltimes and ray paths using predefined Earth (or other planet) noarch
models. Includes phase plotting routines. The IASP91 (Kennett and Engdahl,
1991 <doi:10.1111/j.1365-246X.1991.tb06724.x>) and AK135 (Kennett et al.,
1995 <doi:10.1111/j.1365-246X.1995.tb03540.x>) Earth models are included,
and most important arrival phases can be evaluated. / GPL-3
r-taxicabca 0.1.0 Computation and visualization of Taxicab Correspondence Analysis, noarch
Choulakian (2006) <doi:10.1007/s11336-004-1231-4>. Classical correspon-
dence analysis (CA) is a statistical method to analyse 2-dimensional tables of
positive numbers and is typically applied to contingency tables (Benzecri, J.-P.
(1973). L’Analyse des Donnees. Volume II. L’Analyse des Correspondances.
Paris, France: Dunod). Classical CA is based on the Euclidean distance. Taxi-
cab CA is like classical CA but is based on the Taxicab or Manhattan distance.
For some tables, Taxicab CA gives more informative results than classical CA.
/ GPL-2
r-tbd 0.1.0 Estimation of the survivor average causal effect under outcomes truncated by noarch
death, which requires the existence of a substitution variable. It can be applied
to both experimental and observational data. / GPL-2
r-tbdiag 0.1 This package provides functions to assist researchers working in the field noarch
of tuberculosis diagnostics. Functions for the interpretation of two popular
interferon-gamma release assays are provided, and additional functionality is
planned. / MIT
r-tcgaretriever 1.3 The Cancer Genome Atlas (TCGA) is a program aimed at improving our noarch
understanding of Cancer Biology. Several TCGA Datasets are available on-
line. ‘TCGAretriever’ helps accessing and downloading TCGA data hosted on
‘cBioPortal’ via its Web Interface (see <http://www.cbioportal.org/web_api.
jsp> for more information). Features of ‘TCGAretriever’ include: 1) it is very
simple to use (get all the TCGA data you need with a few lines of code); 2)
performance (smooth and reliable data download via ‘httr’); 3) it is tailored for
downloading large volumes of data. / GPL-2


r-tciapathfinder 1.0.5 A wrapper for The Cancer Imaging Archive’s REST API. The Cancer Imag- noarch
ing Archive (TCIA) hosts de-identified medical images of cancer available
for public download, as well as rich metadata for each image series. TCIA
provides a REST API for programmatic access to the data. This package pro-
vides simple functions to access each API endpoint. For more information,
see <https://github.com/pamelarussell/TCIApathfinder> and TCIA’s website.
/ MIT
r-tcltk2 1.2_11A series of additional Tcl commands and Tk widgets with style and various noarch
functions (under Windows: DDE exchange, access to the registry and icon
manipulation) to supplement the tcltk package / LGPL-3
r-tdamapper 1.0 Topological Data Analysis using Mapper (discrete Morse theory). Generate a noarch
1-dimensional simplicial complex from a filter function defined on the data:
1. Define a filter function (lens) on the data. 2. Perform clustering within
within each level set and generate one node (vertex) for each cluster. 3. For
each pair of clusters in adjacent level sets with a nonempty intersection, gen-
erate one edge between vertices. The function mapper1D uses a filter function
with codomain R, while the the function mapper2D uses a filter function with
codomain R^2. / GPL-3
r-tdcor 0.1_2 The Time-Delay Correlation algorithm (TDCor) reconstructs the topology of noarch
a gene regulatory network (GRN) from time-series transcriptomic data. The
algorithm is described in details in Lavenus et al., Plant Cell, 2015. It was ini-
tially developed to infer the topology of the GRN controlling lateral root for-
mation in Arabidopsis thaliana. The time-series transcriptomic dataset which
was used in this study is included in the package to illustrate how to use it. /
GPL-2
r-tdpanalysis 0.99 Set of functions designed to help in the analysis of TDP sensors. Features noarch
includes dates and time conversion, weather data interpolation, daily maxi-
mum of tension analysis and calculations required to convert sap flow den-
sity data to sap flow rates at the tree and plot scale (For more informa-
tion see : Granier (1985) <DOI:10.1051/forest:19850204> & Granier (1987)
<DOI:10.1093/treephys/3.4.309>). / GPL-2
r-tdroc 1.0 Compute time-dependent ROC curve from censored survival data using non- noarch
parametric weight adjustments. / GPL-2
r-tdsc 1.0.0.1Functions for performing time domain signal coding as used in Chesmore noarch
(2001) <doi:10.1016/S0003-682X(01)00009-3>, and related tasks. This pack-
age creates the standard S-matrix and A-matrix (with variable lag), has tools
to convert coding matrices into distributed matrices, provides published code-
books and allows for extraction of code sequences. / GPL-3
r-teachingdemos 2.10 Demonstration functions that can be used in a classroom to demonstrate sta- noarch
tistical concepts, or on your own to better understand the concepts or the pro-
gramming. / Artistic-2.0
r- 3.4.2 Allows the user to draw probabilistic samples and make inferences from a noarch
teachingsampling finite population based on several sampling designs. / GPL-2
r-teachnet 0.7.1 Can fit neural networks with up to two hidden layer and two different error noarch
functions. Also able to handle a weight decay. But just able to compute one
output neuron and very slow. / GPL-2
r-teamr 0.0.1 Package of wrapper functions using R6 class to send requests to Mi- noarch
crosoft ‘Teams’ <https://products.office.com/en-us/microsoft-teams/
group-chat-software> through webhooks. When you need to share in-
formation or data from R to ‘Teams’, rather than copying/pasting, you can use
this package to send well-formatted output from multiple R objects. / MIT


r-teda 0.1.1 The typicality and eccentricity data analysis (TEDA) framework was put for- noarch
ward by Angelov (2013) <DOI:10.14313/JAMRIS_2-2014/16>. It has been
further developed into multiple different techniques since, and provides a non-
parametric way of determining how similar an observation, from a process that
is not purely random, is to other observations generated by the process. This
package provides code to use the batch and recursive TEDA methods that have
been published. / GPL-3
r-teereg 1.1 For fitting multiple linear regressions, the ordinary least squares approach is noarch
sensitive to outliers and/or violations of model assumptions. The trimmed el-
emental estimators are more robust to such situations. This package contains
functions for computing the trimmed elemental estimates, as well as for creat-
ing the bias-corrected and accelerated bootstrap confidence intervals based on
elemental regressions. / GPL-2
r-tejapi 1.0.1 Functions for interacting directly with the Taiwan Economic Journal API to noarch
offer data in R. For more information go to <https://api.tej.com.tw>. / MIT
r-telegram 0.6.0 R wrapper around the Telegram Bot API (http://core.telegram.org/bots/api) to noarch
access Telegram’s messaging facilities with ease (e.g. you send messages,
images, files from R to your smartphone). / GPL-3
r-telegram.bot 2.3.1 Provides a pure interface for the ‘Telegram Bot API’ <http://core.telegram.org/ noarch
bots/api>. In addition to the pure API implementation, it features a number of
tools to make the development of ‘Telegram’ bots with R easy and straight-
forward, providing an easy-to-use interface that takes some work off the pro-
grammer. / GPL-3
r-tempcont 0.1.0 Method to estimate the effect of the trend in predictor variables on the observed noarch
trend of the response variable using mixed models with temporal autocorrela-
tion. See Fernández-Martínez et al. (2017 and 2019) <doi:10.1038/s41598-
017-08755-8> <doi:10.1038/s41558-018-0367-7>. / GPL-2
r-tempcyclesdata 1.0.1 This is the data companion package to the package tempcycles. This pack- noarch
age includes the metadata, linear, and cycling parameters from Recent geo-
graphic convergence in diurnal and annual temperature cycling flattens global
thermal profiles, Wang & Dillon, Nature Climate Change, 4, 988-992 (2014).
doi:10.1038/nclimate2378. / GPL-2
r-tempdisagg 0.25.0Temporal disaggregation methods are used to disaggregate and interpolate a noarch
low frequency time series to a higher frequency series, where either the sum,
the average, the first or the last value of the resulting high frequency series
is consistent with the low frequency series. Temporal disaggregation can be
performed with or without one or more high frequency indicator series. Con-
tains the methods of Chow-Lin, Santos-Silva-Cardoso, Fernandez, Litterman,
Denton and Denton-Cholette. / GPL-3
r-tempor 1.0.4.4TEMPO (TEmporal Modeling of Pathway Outliers) is a pathway-based out- noarch
lier detection approach for finding pathways showing significant changes
in temporal expression patterns across conditions. Given a gene expres-
sion data set where each sample is characterized by an age or time point
as well as a phenotype (e.g. control or disease), and a collection of gene
sets or pathways, TEMPO ranks each pathway by a score that characterizes
how well a partial least squares regression (PLSR) model can predict age
as a function of gene expression in the controls and how poorly that same
model performs in the disease. TEMPO v1.0.3 is described in Pietras (2018)
<doi:10.1145/3233547.3233559>. / GPL-3


Name Version
r-tempr 0.9.9.15
Analysis and visualization of data from temporal sensory methods, including noarch
for temporal check-all-that-apply (TCATA) and temporal dominance of sensa-
tions (TDS). / GPL-2
r-tenispolar 0.1.4 Implementation of ZENIT-POLAR substitution cipher method of encryption noarch
using by default the TENIS-POLAR cipher. This last cipher of encryption be-
came famous through the collection of Brazilian books Os Karas by the author
Pedro Bandeira. For more details, see A Cryptographic Dictionary (GC&CS,
1944). / GPL-3
r-tensor 1.5 The tensor product of two arrays is notionally an outer product of the arrays noarch
collapsed in specific extents by summing along the appropriate diagonals. /
GPL-2
r-tensorflow 1.13.1Interface to ‘TensorFlow’ <https://www.tensorflow.org/>, an open source soft- linux-
ware library for numerical computation using data flow graphs. Nodes in the 32,
graph represent mathematical operations, while the graph edges represent the linux-
multidimensional data arrays (tensors) communicated between them. The flex- 64,
ible architecture allows you to deploy computation to one or more ‘CPUs’ or noarch,
‘GPUs’ in a desktop, server, or mobile device with a single ‘API’. ‘Tensor- osx-
Flow’ was originally developed by researchers and engineers working on the 64,
Google Brain Team within Google’s Machine Intelligence research organiza- win-
tion for the purposes of conducting machine learning and deep neural networks 32,
research, but the system is general enough to be applicable in a wide variety win-
of other domains as well. / Apache License 2.0 64
r-tensorr 0.1.1 Provides methods to manipulate and store sparse tensors. Tensors are multi- noarch
dimensional generalizations of matrices (two dimensional) and vectors (one
dimensional). / GPL-3
r-tensr 1.0.1 A collection of functions for Kronecker structured covariance estimation noarch
and testing under the array normal model. For estimation, maximum like-
lihood and Bayesian equivariant estimation procedures are implemented.
For testing, a likelihood ratio testing procedure is available. This pack-
age also contains additional functions for manipulating and decompos-
ing tensor data sets. This work was partially supported by NSF grant
DMS-1505136. Details of the methods are described in Gerard and
Hoff (2015) <doi:10.1016/j.jmva.2015.01.020> and Gerard and Hoff (2016)
<doi:10.1016/j.laa.2016.04.033>. / GPL-3
r-teqr 6.0_0 The TEQR package contains software to calculate the operating characteristics noarch
for the TEQR and the ACT designs.The TEQR (toxicity equivalence range)
design is a toxicity based cumulative cohort design with added safety rules.
The ACT (Activity constrained for toxicity) design is also a cumulative cohort
design with additional safety rules. The unique feature of this design is that
dose is escalated based on lack of activity rather than on lack of toxicity and is
de-escalated only if an unacceptable level of toxicity is experienced. / GPL-2
r-teraplusb 1.0 This package is for the comparison of various types of AB escalation rules for noarch
dose finding trials. / LGPL-2.1
r-ternary 1.1.1 Plots ternary diagrams using the standard graphics functions. An alternative to noarch
‘ggtern’, which uses the ‘ggplot2’ family of plotting functions. / GPL-2
r-ternvis 1.2 A suite of functions for visualising ternary probabilistic forecasts, as discussed noarch
in the paper by Jupp (2012) <doi:10.1098/rsta.2011.0350>. / GPL-2


Name Version
r-testassay 0.1.0 A common way of validating a biological assay for is through a procedure, noarch
where m levels of an analyte are measured with n replicates at each level, and
if all m estimates of the coefficient of variation (CV) are less than some pre-
specified level, then the assay is declared validated for precision within the
range of the m analyte levels. Two limitations of this procedure are: there is
no clear statistical statement of precision upon passing, and it is unclear how to
modify the procedure for assays with constant standard deviation. We provide
tools to convert such a procedure into a set of m hypothesis tests. This refram-
ing motivates the m:n:q procedure, which upon completion delivers a 100q%
upper confidence limit on the CV. Additionally, for a post-validation assay out-
put of y, the method gives an ‘‘effective standard deviation interval” of log(y)
plus or minus r, which is a 68% confidence interval on log(mu), where mu is
the expected value of the assay output for that sample. Further, the m:n:q pro-
cedure can be straightforwardly applied to constant standard deviation assays.
We illustrate these tools by applying them to a growth inhibition assay. / MIT
r-testdriver 0.5.1 Provides data sets for teaching statistics and data science courses. It includes noarch
a sample of data from John Edmund Kerrich’s famous coinflip experiment.
These are data that I use for teaching SOC 4015 / SOC 5050 at Saint Louis
University (SLU). The package also contains an R Markdown template with
the required formatting for assignments in my courses SOC 4015, SOC 4650,
SOC 5050, and SOC 5650 at SLU. / GPL-3
r-testequavar 0.1.2 Tests the hypothesis that variances are homogeneous or not using boot- noarch
strap. The procedure uses a variance-based statistic, and is derived from
a normal-theory test. The test equivalently expressed the hypothesis as a
function of the log contrasts of the population variances. A box-type ac-
ceptance region is constructed to test the hypothesis. See Cahoy (2010)
<doi:10.1016/j.csda.2010.04.012>. / GPL-3
r-tester 0.1.7 tester allows you to test characteristics of common R objects. / GPL-3 noarch
r-testfunctions 0.2.0 Test functions are often used to test computer code. They are used in opti- noarch
mization to test algorithms and in metamodeling to evaluate model predictions.
This package provides test functions that can be used for any purpose. Some
functions are taken from <https://www.sfu.ca/~ssurjano>, but their R code is
not used. / GPL-3
r- 1.1 Provides a bootstrap test which decides whether two dose response curves noarch
testingsimilarity can be assumed as equal concerning their maximum absolute deviation. A
plenty of choices for the model types are available, which can be found in
the ‘DoseFinding’ package, which is used for the fitting of the models. See
<doi:10.1080/01621459.2017.1281813> for details. / GPL-3
r-testit 0.9 Provides two convenience functions assert() and test_pkg() to facilitate testing linux-
R packages. / GPL 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-testscorer 1.7.2 GUI for entering test items and obtaining raw and transformed scores. The re- noarch
sults are shown on the console and can be saved to a tabular text file for further
statistical analysis. The user can define his own tests and scoring procedures
through a GUI. / GPL-2
r-testthat 2.1.1 Software testing is important, but, in part because it is frustrating and boring, linux-
many of us avoid it. ‘testthat’ is a testing framework for R that is easy learn 32,
and use, and integrates with your existing ‘workflow’. / MIT file LICENSE linux-
64,
osx-
64,
win-
32,
win-
64
r-texreg 1.36.23
Converts coefficients, standard errors, significance stars, and goodness-of-fit noarch
statistics of statistical models into LaTeX tables or HTML tables/MS Word
documents or to nicely formatted screen output for the R console for easy
model comparison. A list of several models can be combined in a single table.
The output is highly customizable. New model types can be easily imple-
mented. / GPL-2 | GPL-3
r-textgrid 1.0.1 The software application Praat can be used to annotate waveform data (e.g., noarch
to mark intervals of interest or to label events). (See <http://www.fon.hum.
uva.nl/praat/> for more information about Praat.) These annotations are stored
in a Praat TextGrid object, which consists of a number of interval tiers and
point tiers. An interval tier consists of sequential (i.e., not overlapping) labeled
intervals. A point tier consists of labeled events that have no duration. The
‘textgRid’ package provides S4 classes, generics, and methods for accessing
information that is stored in Praat TextGrid objects. / GPL-3
r-textile 0.1.2 Contains real images of the same textile material with/without noarch
local defects, which were used in Bui and Apley (2017)
<doi:10.1080/00401706.2017.1302362>. / GPL-2
r-textometry 0.1.4 Statistical exploration of textual corpora using several methods from French noarch
‘Textometrie’ (new name of ‘Lexicometrie’) and French ‘Data Analysis’
schools. It includes methods for exploring irregularity of distribution of lex-
icon features across text sets or parts of texts (Specificity analysis); multi-
dimensional exploration (Factorial analysis), etc. Those methods are used in
the TXM software. / GPL-3
r-textrank 0.3.0 The ‘textrank’ algorithm is an extension of the ‘Pagerank’ algorithm for text. noarch
The algorithm allows to summarize text by calculating how sentences are re-
lated to one another. This is done by looking at overlapping terminology used
in sentences in order to set up links between sentences. The resulting sentence
network is next plugged into the ‘Pagerank’ algorithm which identifies the
most important sentences in your text and ranks them. In a similar way ‘tex-
trank’ can also be used to extract keywords. A word network is constructed by
looking if words are following one another. On top of that network the ‘Pager-
ank’ algorithm is applied to extract relevant words after which relevant words
which are following one another are combined to get keywords. More infor-
mation can be found in the paper from Mihalcea, Rada & Tarau, Paul (2004)
<http://www.aclweb.org/anthology/W04-3252>. / MPL-2.0


Name Version
r-textreg 0.1.5 Function for sparse regression on raw text, regressing a labeling vector onto a linux-
feature space consisting of all possible phrases. / MIT 64,
osx-
64,
win-
64
r-textshape 1.6.0 Tools that can be used to reshape and restructure text data. / GPL-2 noarch
r-texttinyr 1.1.3 It offers functions for splitting, parsing, tokenizing and creating a vocabulary linux-
for big text data files. Moreover, it includes functions for building a document- 64,
term matrix and extracting information from those (term-associations, most osx-
frequent terms). It also embodies functions for calculating token statistics 64,
(collocations, look-up tables, string dissimilarities) and functions to work with win-
sparse matrices. Lastly, it includes functions for Word Vector Representa- 64
tions (i.e. ‘GloVe’, ‘fasttext’) and incorporates functions for the calculation of
(pairwise) text document dissimilarities. The source code is based on ‘C11’
and exported in R through the ‘Rcpp’, ‘RcppArmadillo’ and ‘BH’ packages. /
GPL-3
r-textutils 0.1_11Utilities for handling character vectors that store human-readable text (either noarch
plain or with markup, such as HTML or LaTeX). The package provides, in
particular, functions that help with the preparation of plain-text reports (e.g.
for expanding and aligning strings that form the lines of such reports); the
package also provides generic functions for transforming R objects to HTML
and to plain text. / GPL-3
r-tfcox 0.1.0 In Cox’s proportional hazard model, covariates are modeled as linear function linux-
and may not be flexible. This package implements additive trend filtering Cox 64,
proportional hazards model as proposed in Jiacheng Wu & Daniela Witten osx-
(2019) Flexible and Interpretable Models for Survival Data, Journal of Com- 64,
putational and Graphical Statistics, <DOI:10.1080/10618600.2019.1592758>. win-
The fitted functions are piecewise polynomial with adaptively chosen knots. / 64
GPL-2
r-tfdatasets 1.13.1Interface to ‘TensorFlow’ Datasets, a high-level library for building complex noarch
input pipelines from simple, re-usable pieces. See <https://www.tensorflow.
org/programmers_guide/datasets> for additional details. / Apache License 2.0
r-tfer 1.1 Statistical interpretation of forensic glass transfer (Simulation of the probabil- noarch
ity distribution of recovered glass fragments). / GPL-2
r-tfmpvalue 0.0.8 In putative Transcription Factor Binding Sites (TFBSs) identification from linux-
sequence/alignments, we are interested in the significance of certain match 64,
score. TFMPvalue provides the accurate calculation of P-value with score osx-
threshold for Position Weight Matrices, or the score with given P-value. It 64,
is an interface to code originally made available by Helene Touzet and Jean- win-
Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007) 64
<DOI:10.1186/1748-7188-2-15>. / GPL-2
r-tframe 2015.12_1.1
A kernel of functions for programming time series methods in a way that is noarch
relatively independently of the representation of time. Also provides plotting,
time windowing, and some other utility functions which are specifically in-
tended for time series. See the Guide distributed as a vignette, or ?tframe.Intro
for more details. (User utilities are in package tfplot.) / GPL-2


Name Version
r-tfruns 1.4 Create and manage unique directories for each ‘TensorFlow’ training run. Pro- linux-
vides a unique, time stamped directory for each run along with functions to 32,
retrieve the directory of the latest run or latest several runs. / Apache License linux-
2.0 64,
noarch,
osx-
64,
win-
32,
win-
64
r-tfse 0.5.0 A collection of useful tools for programming and writing-scripts. Several func- noarch
tions are simple wrappers around base R functions that extend their function-
ality while also providing some convenient propertiesâC“regular expression
functions that automatically detect look-ahead and look-behind statements, a
read-line function that suppresses incomplete-final-line warnings and automat-
ically opens and closes connections, a version of substrings that starts from the
end of strings, etc. Other functions are useful for checking whether packages
are installed, omitting missing data, and showing in-use connections. / MIT
r-tfx 0.1.0 Connects R to TrueFX(tm) for free streaming real-time and historical tick-by- noarch
tick market data for dealable interbank foreign exchange rates with millisecond
detail. / GPL-3
r-tgcd 2.1 Deconvolving thermoluminescence glow curves according to various kinetic linux-
models (first-order, second-order, general-order, and mixed-order) using a 64,
modified Levenberg-Marquardt algorithm. It provides the possibility of setting osx-
constraints or fixing any of parameters. It offers an interactive way to initialize 64,
parameters by clicking with a mouse on a plot at positions where peak maxima win-
should be located. The optimal estimate is obtained by trial-and-error. It also 64
provides routines for simulating first-order, second-order, and general-order
glow peaks. / GPL-2 | GPL-3
r-tggd 0.1.1 Density, distribution function, quantile function and random generation for the noarch
Truncated Generalised Gamma Distribution (also in log10(x) and ln(x) space).
/ GPL-3
r-tgram 0.2_3 Functions to compute and plot tracheidograms, as in De Soto et al. (2011) noarch
<doi:10.1139/x11-045>. / GPL-2
r-th.data 1.0_10Contains data sets used in other packages Torsten Hothorn maintains. / GPL-3 linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-thankr 1.0.0 Find out who maintains the packages you use in your current session or in your noarch
package library and maybe say ‘thank you’. / MIT
r-thankyoustars 0.2.0 A tool for starring GitHub repositories. / MIT noarch


Name Version
r-thermindex 0.2.0 Calculates several thermal comfort indexes using temperature, wind speed and noarch
relative humidity values, calculating indexes such as Humidex, windchill, Dis-
comfort Index and others. / GPL-2
r-thermocouple 1.0.2 Temperature measurement data, equations and methods for thermocouples, noarch
wire RTD, thermistors, IC thermometers, bimetallic strips and the ITS-90. /
GPL-3
r-thgenetics 0.4_2 A step-up test for genetic rare variants in a gene or in a pathway. The linux-
method determines an optimal grouping of rare variants analytically. The 64,
method has been described in Hoffmann TJ, Marini NJ, and Witte JS (2010) osx-
<doi:10.1371/journal.pone.0013584>. / GPL-3 64,
win-
64
r-thinknum 1.3.0 This package interacts directly with the Thinknum API to offer data in a num- noarch
ber of formats usable in R / GPL-2
r- 1.0_3 Design and analyze three-arm non-inferiority or superiority trials which linux-
threearmedtrials follow a gold-standard design, i.e. trials with an experimental treatment, an 64,
active, and a placebo control. Method for the following distributions are osx-
implemented: Poisson (Mielke and Munk (2009) <arXiv:0912.4169>), 64,
negative binomial (Muetze et al. (2016) <doi:10.1002/sim.6738>), win-
normal (Pigeot et al. (2003) <doi:10.1002/sim.1450>; Hasler et al. 64
(2009) <doi:10.1002/sim.3052>), binary (Friede and Kieser (2007)
<doi:10.1002/sim.2543>), nonparametric (Muetze et al. (2017)
<doi:10.1002/sim.7176>), exponential (Mielke and Munk (2009)
<arXiv:0912.4169>). / GPL-2
r-threeboost 1.1 This package implements a thresholded version of the EEBoost algorithm de- noarch
scribed in [Wolfson (2011, JASA)]. EEBoost is a general-purpose method for
variable selection which can be applied whenever inference would be based on
an estimating equation. The package currently implements variable selection
based on the Generalized Estimating Equations, but can also accommodate
user-provided estimating functions. Thresholded EEBoost is a generalization
which allows multiple variables to enter the model at each boosting step. /
GPL-3
r-threegroups 0.21 Implements the Maximum Likelihood estimator for baseline, placebo, and noarch
treatment groups (three-group) experiments with non-compliance proposed by
Gerber, Green, Kaplan, and Kern (2010). / GPL-2
r-threejs 0.3.1 Create interactive 3D scatter plots, network plots, and globes using the linux-
‘three.js’ visualization library (<https://threejs.org>). / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-threeway 1.1.3 Component analysis for three-way data arrays by means of Cande- noarch
comp/Parafac, Tucker3, Tucker2 and Tucker1 models. / GPL-2
r-threewords 0.1.0 A connector to the ‘What3Words’ (http://what3words.com/) service, which noarch
represents each 3m by 3m square on earth with a unique trio of English-
language words. / MIT


Name Version
r-threg 1.0.3 Fit a threshold regression model based on the first-hitting-time of a boundary noarch
by the sample path of a Wiener diffusion process. The threshold regression
methodology is well suited to applications involving survival and time-to-event
data. / GPL-2
r-thregi 1.0.4 Fit a threshold regression model for Interval Censored Data based on the first- noarch
hitting-time of a boundary by the sample path of a Wiener diffusion process.
The threshold regression methodology is well suited to applications involving
survival and time-to-event data. / GPL-2
r-thresholdroc 2.7 Functions that provide point and interval estimations of optimum thresholds noarch
for continuous diagnostic tests. The methodology used is based on minimizing
an overall cost function in the two- and three-state settings. The package also
provides functions for sample size determination and estimation of diagnostic
accuracy measures. It also includes graphical tools. / GPL-2
r-thsls 0.1 Fit the Simultaneous Systems of Linear Equations using Three-stage Least noarch
Squares. / GPL-3
r-tibble 2.1.1 Provides a ‘tbl_df’ class (the ‘tibble’) that provides stricter checking and better linux-
formatting than the traditional data frame. / MIT file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-tibbrconnector 1.5.1 Post messages to tibbr from within R. / BSD_3_clause noarch
r-tickexec 1.1 Functions to execute orders in backtesting using tick data. A testing platform noarch
was established by the four major execution functions, namely ‘LimitBuy’,
‘LimitSell’, ‘MarketBuy’ and ‘MarketSell’, which enclosed all tedious aspects
(such as queueing for order executions and calculate actual executed volumes)
for order execution using tick data. Such that one can focus on the logic of
strategies, rather than its execution. / GPL-3
r-tictoc 1.0 This package provides the timing functions ‘tic’ and ‘toc’ that can be nested. noarch
One can record all timings while a complex script is running, and examine
the values later. It is also possible to instrument the timing calls with custom
callbacks. In addition, this package provides class ‘Stack’, implemented as a
vector, and class ‘List’, implemented as a list, both of which support opera-
tions ‘push’, ‘pop’, ‘first’, ‘last’ and ‘clear’. / Apache License (== 2.0) | file
LICENSE
r-tiddlywikir 1.0.1 Utilities to generate wiki reports in TiddlyWiki format. / GPL-2 noarch
r-tideharmonics 0.1_1 Implements harmonic analysis of tidal and sea-level data. Over 400 harmonic noarch
tidal constituents can be estimated, all with daily nodal corrections. Time-
varying mean sea-levels can also be used. / BSD_3_clause
r-tides 2.1 Calculate Characteristics of Quasi-Periodic Time Series, e.g. Estuarine Water noarch
Levels. / GPL-3
r-tidetables 0.0.2 Tide analysis and prediction of predominantly semi-diurnal tides with two high noarch
waters and two low waters during one lunar day (~24.842 hours, ~1.035 days).
The analysis should preferably cover an observation period of at least 19 years.
For shorter periods, for example, the nodal cycle can not be taken into account,
which particularly affects the height calculation. The main objective of this
package is to produce tide tables. / GPL-3


Name Version
r-tidyr 0.8.3 An evolution of ‘reshape2’. It’s designed specifically for data tidying (not linux-
general reshaping or aggregating) and works well with ‘dplyr’ data pipelines. 32,
64,
osx-
64,
win-
32,
win-
64
r-tidyselect 0.2.5 A backend for the selecting functions of the ‘tidyverse’. It makes it easy to im- linux-
plement select-like functions in your own packages in a way that is consistent 32,
with other ‘tidyverse’ interfaces for selection. / GPL-3 linux-
64,
osx-
64,
win-
32,
win-
64
r-tidytext 0.2.0 Text mining for word processing and sentiment analysis using ‘dplyr’, ‘gg- linux-
plot2’, and other tidy tools. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-tidyverse 1.2.1 The ‘tidyverse’ is a set of packages that work in harmony because they share linux-
common data representations and ‘API’ design. This package is designed to 32,
make it easy to install and load multiple ‘tidyverse’ packages in a single step. linux-
Learn more about the ‘tidyverse’ at <https://tidyverse.org>. / GPL-3 | file LI- 64,
CENSE noarch,
osx-
64,
win-
32,
win-
64
r-tiff 0.1_5 This package provides an easy and simple way to read, write and display linux-
bitmap images stored in the TIFF format. It can read and write both files 64,
and in-memory raw vectors. / GPL-2 | GPL-3 osx-
64,
win-
64
r-tightclust 1.1 The functions needed to perform tight clustering Algorithm. / GPL-2 noarch


Name Version
r-tilegramsr 0.2.0 R spatial objects for Tilegrams. Tilegrams are tiled maps where the region size linux-
is proportional to the certain characteristics of the dataset. / MIT file LICENSE 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-tilting 1.1.1 Implements an algorithm for variable selection in high-dimensional linear re- noarch
gression using the tilted correlation, a new way of measuring the contribution
of each variable to the response which takes into account high correlations
among the variables in a data-driven way. / GPL-2
r-timechange 0.0.1 Efficient routines for manipulation of date-time objects while accounting for linux-
time-zones and daylight saving times. The package includes utilities for up- 64,
dating of date-time components (year, month, day etc.), modification of time- osx-
zones, rounding of date-times, period addition and subtraction etc. Parts of the 64,
‘CCTZ’ source code, released under the Apache 2.0 License, are included in win-
this package. See <https://github.com/google/cctz> for more details. / GPL-3 64
r-timedate 3043.102
The ‘timeDate’ class fulfils the conventions of the ISO 8601 standard as well linux-
as of the ANSI C and POSIX standards. Beyond these standards it provides 32,
the Financial Center concept which allows to handle data records collected in linux-
different time zones and mix them up to have always the proper time stamps 64,
with respect to your personal financial center, or alternatively to the GMT noarch,
reference time. It can thus also handle time stamps from historical data records osx-
from the same time zone, even if the financial centers changed day light saving 64,
times at different calendar dates. / GPL (>= 2) win-
32,
win-
64
r-timedelay 1.0.8 We provide a toolbox to estimate the time delay between the brightness time noarch
series of gravitationally lensed quasar images via Bayesian and profile like-
lihood approaches. The model is based on a state-space representation for
irregularly observed time series data generated from a latent continuous-time
Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically mo-
tivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sam-
pler, producing posterior samples of the model parameters that include the
time delay. A profile likelihood of the time delay is a simple approximation to
the marginal posterior distribution of the time delay. Both Bayesian and pro-
file likelihood approaches complement each other, producing almost identical
results; the Bayesian way is more principled but the profile likelihood is easier
to implement. / GPL-2
r-timeordered 0.9.9 Approaches for incorporating time into network analysis. Methods include: noarch
construction of time-ordered networks (temporal graphs); shortest-time and
shortest-path-length analyses; resource spread calculations; data resampling
and rarefaction for null model construction; reduction to time-aggregated net-
works with variable window sizes; application of common descriptive statis-
tics to these networks; vector clock latencies; and plotting functionalities. The
package supports <doi:10.1371/journal.pone.0020298>. / GPL-3


Name Version
r-timeprojection 0.2.0 Extract useful time components of a date object, such as day of week, week- noarch
end, holiday, day of month, etc, and put it in a data frame. This can be used to
create many predictor variables out of a single time variable, which can then
be used in a regression or decision tree. Also includes function plotCalen-
darHeatmap which draws a calendar and overlays a heatmap based on values.
/ GPL-3
r-timer 1.1.0 Provides a ‘timeR’ class that makes timing codes easier. One can create noarch
‘timeR’ objects and use them to record all timings, and extract recordings as
data frame for later use. / Apache License (== 2.0) | file LICENSE
r-timereg 1.9.4 Programs for Martinussen and Scheike (2006), ‘Dynamic Regression Models linux-
for Survival Data’, Springer Verlag. Plus more recent developments. Addi- 64,
tive survival model, semiparametric proportional odds model, fast cumulative osx-
residuals, excess risk models and more. Flexible competing risks regression 64,
including GOF-tests. Two-stage frailty modelling. PLS for the additive risk win-
model. Lasso in the ‘ahaz’ package. / GPL-2 64
r-timesboot 1.0 Computes bootstrap CI for the sample ACF and periodogram / GPL-2 noarch
r-timeseries 3042.102
Provides a class and various tools for financial time series. This includes basic linux-
functions such as scaling and sorting, subsetting, mathematical operations and 32,
statistical functions. / GPL (>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-timetools 1.14 Objects to manipulate sequential and seasonal time series. Sequential time linux-
series based on time instants and time durations are handled. Both can be reg- 64,
ularly or unevenly spaced (overlapping durations are allowed). Only POSIX* osx-
format are used for dates and times. The following classes are provided : 64,
‘POSIXcti’, ‘POSIXctp’, ‘TimeIntervalDataFrame’, ‘TimeInstantDataFrame’, win-
‘SubtimeDataFrame’ ; methods to switch from a class to another and to modify 64
the time support of series (hourly time series to daily time series for instance)
are also defined. Tools provided can be used for instance to handle environ-
mental monitoring data (not always produced on a regular time base). / GPL-3
r-timevis 0.5 Create rich and fully interactive timeline visualizations. Timelines can be in- noarch
cluded in Shiny apps and R markdown documents, or viewed from the R con-
sole and ‘RStudio’ Viewer. ‘timevis’ includes an extensive API to manipulate
a timeline after creation, and supports getting data out of the visualization into
R. Based on the ‘vis.js’ Timeline module and the ‘htmlwidgets’ R package. /
MIT


Name Version
r-timevtree 0.3.1 Estimates time varying regression effects under Cox type models in survival noarch
data using classification and regression tree. The codes in this package were
originally written in S-Plus for the paper Survival Analysis with Time-Varying
Regression Effects Using a Tree-Based Approach, by Xu, R. and Adak, S.
(2002) <doi:10.1111/j.0006-341X.2002.00305.x>, Biometrics, 58: 305-315.
Development of this package was supported by NIH grants AG053983 and
AG057707, and by the UCSD Altman Translational Research Institute, NIH
grant UL1TR001442. The content is solely the responsibility of the authors
and does not necessarily represent the official views of the NIH. The exam-
ple data are from the Honolulu Heart Program/Honolulu Asia Aging Study
(HHP/HAAS). / GPL-2
r-timewarp 1.0.15Date sequence, relative date calculations, and date manipulation with business noarch
days and holidays. Works with Date and POSIXt classes. / GPL-3
r-timsac 1.3.6 Functions for statistical analysis, prediction and control of time series based linux-
mainly on Akaike and Nakagawa (1988) <ISBN 978-90-277-2786-2>. / GPL- 64,
2 osx-
64,
win-
64
r-tinflex 1.5 A universal non-uniform random number generator for quite arbitrary distri- linux-
butions with piecewise twice differentiable densities. / GPL-2 64,
osx-
64,
win-
64
r-tinsel 0.0.1 Instead of nesting function calls, annotate and transform functions using #. noarch
comments. / MIT
r-tint 0.1.2 A ‘tufte’-alike style for ‘rmarkdown’. A modern take on the ‘Tufte’ design noarch
for pdf and html vignettes, building on the ‘tufte’ package with additional
contributions from the ‘knitr’ and ‘ggtufte’ package, and also acknowledging
the key influence of ‘envisioned css’. / GPL-3
r-tinyproject 0.6.1 Creates useful files and folders for data analysis projects and provides func- noarch
tions to manage data, scripts and output files. Also provides a project template
for ‘Rstudio’. / GPL-2
r-tinytest 1.0.0 Provides a lightweight (zero-dependency) and easy to use unit testing frame- noarch
work. Main features: install tests with the package. Test results are treated as
data that can be stored and manipulated. Test files are R scripts interspersed
with test commands, that can be programmed over. Fully automated build-
install-test sequence for packages. Skip tests when not run locally (e.g. on
CRAN). Flexible and configurable output printing. Compare computed output
with output stored with the package. Run tests in parallel. Extensible by other
packages. Report side effects. / GPL-3
r-tinytex 0.12 Helper functions to install and maintain the ‘LaTeX’ distribution named ‘Tiny- linux-
TeX’ (<https://yihui.name/tinytex/>), a lightweight, cross-platform, portable, 64,
and easy-to-maintain version of ‘TeX Live’. This package also contains helper noarch,
functions to compile ‘LaTeX’ documents, and install missing ‘LaTeX’ pack- osx-
ages automatically. / MIT file LICENSE 64,
win-
32,
win-
64


Name Version
r-tiobeindexr 0.1.1 Get latest ‘TIOBE’ Programming Index Tables. The ‘TIOBE’ Programming noarch
Community index is an indicator of the popularity of programming languages
from <https://www.tiobe.com/tiobe-index/>. / AGPL-3
r-tipom 1.0.2_1
TIPOM is based on a methodology that was developed in the 1960s by noarch
Bernardino Bagolini. The basic idea is to use the three simple dimensions of
length, width and thickness of each lithic artefact to classify them in discrete
groups and infer their function. / GPL-3
r-tippy 0.0.1 ‘Htmlwidget’ of ‘Tippyjs’ to add tooltips to ‘Shiny’ apps and ‘R markdown’ noarch
documents. / MIT
r-tis 1.37.1Functions and S3 classes for time indexes and time indexed series, which are linux-
compatible with FAME frequencies. / Unlimited 64,
osx-
64,
win-
64
r-titan 1.0_16GUI to analyze mass spectrometric data on the relative abundance of two sub- noarch
stances from a titration series. / GPL-2
r-titanic 0.1.0 This data set provides information on the fate of passengers on the fatal maiden noarch
voyage of the ocean liner Titanic, summarized according to economic status
(class), sex, age and survival. Whereas the base R Titanic data found by call-
ing data(Titanic) is an array resulting from cross-tabulating 2201 observations,
these data sets are the individual non-aggregated observations and formatted
in a machine learning context with a training sample, a testing sample, and
two additional data sets that can be used for deeper machine learning analysis.
These data sets are also the data sets downloaded from the Kaggle competition
and thus lowers the barrier to entry for users new to R or machine learing. /
CC0
r-titrationcurves 0.1.0 A collection of functions to plot acid/base titration curves (pH vs. volume noarch
of titrant), complexation titration curves (pMetal vs. volume of EDTA), re-
dox titration curves (potential vs.volume of titrant), and precipitation titration
curves (either pAnalyte or pTitrant vs. volume of titrant). Options include the
titration of mixtures, the ability to overlay two or more titration curves, and
the ability to show equivalence points. / GPL-2
r-tkrgl 0.8 Provides ‘TK’ widget tools for the ‘rgl’ package. / GPL linux-
32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-tkrplot 0.0_24simple mechanism for placing R graphics in a Tk widget / GPL linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-tkrplotr 0.1.1 Display a plot in a Tk canvas. / GPL-2 noarch
r-tlemix 0.1.3 TLE implements a general framework for robust fitting of finite mixture mod- noarch
els. Parameter estimation is performed using the EM algorithm. / GPL-3
r-tlm 0.1.5 Computation of effects under linear, logistic and Poisson regression models noarch
with transformed variables. Logarithm and power transformations are allowed.
Effects can be displayed both numerically and graphically in both the original
and the transformed space of the variables. / GPL-2
r-tlmec 0.0_2 Fit a linear mixed effects model for censored data with Student-t or normal noarch
distributions. The errors are assumed independent and identically distributed.
/ GPL (>= 3.0)
r-tls 0.1.0 Functions for point and interval estimation in error-in-variables mod- noarch
els via total least squares or generalized total least squares method.
See Golub and Van Loan (1980) <doi:10.1137/0717073>, Gleser (1981)
<https://www.jstor.org/stable/2240867>, Ivan Markovsky and Huffel (2007)
<doi:10.1016/j.sigpro.2007.04.004> for more information. / GPL-3
r-tm 0.7_6 A framework for text mining applications within R. / GPL-3 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r- 1.1 This package provides a tm Source to create corpora from a corpus prepared noarch
tm.plugin.alceste in the format used by the Alceste application (i.e. a single text file with in-
line meta-data). It is able to import both text contents and meta-data (starred)
variables. / GPL-2
r-tm.plugin.dc 0.2_8 A plug-in for the text mining framework tm to support text mining in a dis- noarch
tributed way. The package provides a convenient interface for handling dis-
tributed corpus objects based on distributed list objects. / GPL-2
r- 1.4 Provides a ‘tm’ Source to create corpora from articles exported from the ‘Eu- noarch
tm.plugin.europresse ropresse’ content provider as HTML files. It is able to read both text content
and meta-data information (including source, date, title, author and pages). /
GPL-2
r- 1.7 Provides a ‘tm’ Source to create corpora from articles exported from the Dow noarch
tm.plugin.factiva Jones ‘Factiva’ content provider as XML or HTML files. It is able to read
both text content and meta-data information (including source, date, title, au-
thor, subject, geographical coverage, company, industry, and various provider-
specific fields). / GPL-2


Name Version
r- 1.4.0 Provides a ‘tm’ Source to create corpora from articles exported from the ‘Lex- noarch
tm.plugin.lexisnexis isNexis’ content provider as HTML files. It is able to read both text content
and meta-data information (including source, date, title, author and pages).
Note that the file format is highly unstable: there is no warranty that this pack-
age will work for your corpus, and you may have to adjust the code to adapt it
to your particular format. / GPL-2
r-tm.plugin.mail 0.2_1 A plug-in for the tm text mining framework providing mail handling function- noarch
ality. / GPL-3
r- 1.3 Facilitate text retrieval from feed formats like XML (RSS, ATOM) and JSON. noarch
tm.plugin.webmining Also direct retrieval from HTML is supported. As most (news) feeds only
incorporate small fractions of the original text tm.plugin.webmining even re-
trieves and extracts the text of the original text source. / GPL-3
r-tm1r 1.1.2 Useful functions to connect to ‘TM1’ <https://www.ibm.com/uk-en/ noarch
marketplace/planning-and-analytics> instance from R via REST API. With
the functions in the package, data can be imported from ‘TM1’ via mdx view
or native view, data can be sent to ‘TM1’, processes and chores can be exe-
cuted, and cube and dimension metadata information can be taken. / GPL-2
r-tmb 1.7.15With this tool, a user should be able to quickly implement complex random linux-
effect models through simple C templates. The package combines ‘CppAD’ 64,
(C automatic differentiation), ‘Eigen’ (templated matrix-vector library) and osx-
‘CHOLMOD’ (sparse matrix routines available from R) to obtain an efficient 64,
implementation of the applied Laplace approximation with exact derivatives. win-
Key features are: Automatic sparseness detection, parallelism through ‘BLAS’ 64
and parallel user templates. / GPL-2
r-tmcalculator 1.0.0 The melting temperature of nucleic acid sequences can be calcu- noarch
lated in three method, the Wallace rule (Thein & Wallace (1986)
<doi:10.1016/S0140-6736(86)90739-7>), empirical formulas based
on G and C content (Marmur J. (1962) <doi:10.1016/S0022-
2836(62)80066-7>, Schildkraut C. (2010) <doi:10.1002/bip.360030207>,
Wetmur J G (1991) <10.3109/10409239109114069>, Unter-
gasser,A. (2012) <doi:10.1093/nar/gks596>, von Ahsen N
(2001) <PMID:11673362>) and nearest neighbor thermody-
namics (Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>,
Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>, Allawi H
(1998) <doi:10.1093/nar/26.11.2694>, SantaLucia J (2004)
<doi:10.1146/annurev.biophys.32.110601.141800>, Freier S (1986)
<doi:10.1073/pnas.83.24.9373>, Xia T (1998) <doi:10.1021/bi9809425>,
Chen JL (2012) <doi:10.1021/bi3002709>, Bommarito S (2000)
<doi:10.1093/nar/28.9.1929>, Turner D H (2010) <doi:10.1093/nar/gkp892>,
Sugimoto N (1995) <doi:10.1016/S0048-9697(98)00088-6>, Allawi
H T (1997) <doi:10.1021/bi962590c>, Santalucia N (2005)
<doi:10.1093/nar/gki918>), and it can also be corrected with salt ions
and chemical compound (SantaLucia J (1996) <doi:10.1021/bi951907q>,
SantaLucia J(1998) <doi:10.1073/pnas.95.4.1460>, Owczarzy R (2004)
<doi:10.1021/bi034621r>, Owczarzy R (2008) <doi:10.1021/bi702363u>). /
GPL-2


Name Version
r-tmcn 0.2_13A Text mining toolkit for Chinese, which includes facilities for Chinese linux-
string processing, Chinese NLP supporting, encoding detecting and convert- 64,
ing. Moreover, it provides some functions to support ‘tm’ package in Chinese. osx-
/ LGPL-3 64,
win-
64
r-tmdb 1.0 Provides an R-interface to the TMDb API (see TMDb API on <http://docs. noarch
themoviedb.apiary.io/#>). The Movie Database (TMDb) is a popular user
editable database for movies and TV shows (see <https://www.themoviedb.
org>). / Artistic-2.0
r-tmg 0.3 Random number generation of truncated multivariate Gaussian distributions linux-
using Hamiltonian Monte Carlo. The truncation is defined using linear and/or 64,
quadratic polynomials. / GPL-2 osx-
64,
win-
64
r-tmpm 1.0.3 Trauma Mortality prediction for ICD-9, ICD-10, and AIS lexicons in long or noarch
wide format based on Dr. Alan Cook’s tmpm mortality model. / GPL-2
r-tmvmixnorm 1.0.2 Efficient sampling of truncated multivariate (scale) mixtures of normals un- noarch
der linear inequality constraints is nontrivial due to the analytically in-
tractable normalizing constant. Meanwhile, traditional methods may sub-
ject to numerical issues, especially when the dimension is high and de-
pendence is strong. Algorithms proposed by Li and Ghosh (2015) <doi:
10.1080/15598608.2014.996690> are adopted for overcoming difficulties in
simulating truncated distributions. Efficient rejection sampling for simulat-
ing truncated univariate normal distribution is included in the package, which
shows superiority in terms of acceptance rate and numerical stability compared
to existing methods and R packages. An efficient function for sampling from
truncated multivariate normal distribution subject to convex polytope restric-
tion regions based on Gibbs sampler for conditional truncated univariate dis-
tribution is provided. By extending the sampling method, a function for sam-
pling truncated multivariate Student’s t distribution is also developed. More-
over, the proposed method and computation remain valid for high dimensional
and strong dependence scenarios. Empirical results in Li and Ghosh (2015)
<doi: 10.1080/15598608.2014.996690> illustrated the superior performance
in terms of various criteria (e.g. mixing and integrated auto-correlation time).
/ GPL-2
r-tmvnsim 1.0_2 Importance sampling from the truncated multivariate normal using the GHK linux-
(Geweke-Hajivassiliou-Keane) simulator. Unlike Gibbs sampling which can 64,
get stuck in one truncation sub-region depending on initial values, this package osx-
allows truncation based on disjoint regions that are created by truncation of 64,
absolute values. The GHK algorithm uses simple Cholesky transformation win-
followed by recursive simulation of univariate truncated normals hence there 64
are also no convergence issues. Importance sample is returned along with
sampling weights, based on which, one can calculate integrals over truncated
regions for multivariate normals. / GPL-2


Name Version
r-tnc 0.1.0 Node centrality measures for temporal networks. Available measures noarch
are temporal degree centrality, temporal closeness centrality and tem-
poral betweenness centrality defined by Kim and Anderson (2012)
<doi:10.1103/PhysRevE.85.026107>. Applying the REN algorithm by Hanke
and Foraita (2017) <doi:10.1186/s12859-017-1677-x> when calculating the
centrality measures keeps the computational running time linear in the number
of graph snapshots. Further, all methods can run in parallel up to the number
of nodes in the network. / GPL-3
r-tnet 3.0.14R package for analyzing weighted, two-mode, and longitudinal networks. / noarch
GPL-3
r-todor 0.0.5 This is a simple addin to ‘RStudio’ that finds all ‘TODO’, ‘FIX ME’, noarch
‘CHANGED’ etc. comments in your project and shows them as a markers
list. / MIT
r-tokenbrowser 0.1.0 Create browsers for reading full texts from a token list format. Information linux-
obtained from text analyses (e.g., topic modeling, word scaling) can be used 64,
to annotate the texts. / GPL-3 osx-
64,
win-
64
r-tokenizers 0.2.1 Convert natural language text into tokens. Includes tokenizers for shingled linux-
n-grams, skip n-grams, words, word stems, sentences, paragraphs, characters, 32,
shingled characters, lines, tweets, Penn Treebank, regular expressions, as well linux-
as functions for counting characters, words, and sentences, and a function for 64,
splitting longer texts into separate documents, each with the same number of osx-
words. The tokenizers have a consistent interface, and the package is built on 64,
the ‘stringi’ and ‘Rcpp’ packages for fast yet correct tokenization in ‘UTF-8’. win-
win-
64
r-tokenizers.bpe 0.1.0 Unsupervised text tokenizer focused on computational efficiency. Wraps linux-
the ‘YouTokenToMe’ library <https://github.com/VKCOM/YouTokenToMe> 64,
which is an implementation of fast Byte Pair Encoding (BPE) <https://www. osx-
aclweb.org/anthology/P16-1162>. / MPL-2.0 64,
win-
64
r-toordinal 1.1_0.0
Language specific cardinal to ordinal number conversion. / GPL-3 noarch
r-topicmodels 0.2_9 Provides an interface to the C code for Latent Dirichlet Allocation (LDA) mod- linux-
els and Correlated Topics Models (CTM) by David M. Blei and co-authors and 64,
the C code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan osx-
and co-authors. / GPL-2 64,
win-
64
r-topmodel 0.7.3 Set of hydrological functions including an R implementation of the hydrolog- linux-
ical model TOPMODEL, which is based on the 1995 FORTRAN version by 64,
Keith Beven. From version 0.7.0, the package is put into maintenance mode. / osx-
GPL-2 64,
win-
64
r-topsis 1.0 Evaluation of alternatives based on multiple criteria using TOPSIS method. / noarch
GPL-2
r-tosls 1.0 Fit an Instrumental Variables Two Stage Least Squares model / Artistic-2.0 noarch


Name Version
r-totalcensus 0.6.1 Download summary files from Census Bureau <https://www2.census.gov/> noarch
and extract data, in particular high resolution data at block, block group, and
tract level, from decennial census and American Community Survey 1-year
and 5-year estimates. / MIT
r- 1.0.1 For a given phylogenetic tree, calculates the Total Cophenetic Index. Refer- noarch
totalcopheneticindex ence: A. Mir, F. Rossello, L. A. Rotger (2013). A new balance index for phylo-
genetic trees. Math. Biosci. 241, 125-136 <doi:10.1016/j.mbs.2012.10.005>.
/ Unlimited
r-touch 0.1_4 R implementation of the software tools developed in the H-CUP (Healthcare linux-
Cost and Utilization Project) <https://www.hcup-us.ahrq.gov> and AHRQ 64,
(Agency for Healthcare Research and Quality) <https://www.ahrq.gov>. It osx-
currently contains functions for mapping ICD-9 codes to the AHRQ comor- 64,
bidity measures and translating ICD-9 (resp. ICD-10) codes to ICD-10 (resp. win-
ICD-9) codes based on GEM (General Equivalence Mappings) from CMS 64
(Centers for Medicare and Medicaid Services). / GPL-3
r-tourr 0.5.6 Implements geodesic interpolation and basis generation functions that allow noarch
you to create new tour methods from R. / MIT
r-toxtestd 2.0 Calculates sample size and dose allocation for binary toxicity tests, using the noarch
Fish Embryo Toxicity Test as example. An optimal test design is obtained
by running (i) spoD (calculate the number of individuals to test under control
conditions), (ii) setD (estimate the minimal sample size per treatment given
the users precision requirements) and (iii) doseD (construct an individual dose
scheme). / GPL-2
r-tp.idm 1.5 Estimation of transition probabilities for the illness-death model. Both linux-
the Aalen-Johansen estimator for a Markov model and a novel non- 64,
Markovian estimator by de Una-Alvarez and Meira-Machado (2015) osx-
<doi:10.1111/biom.12288>, see also Balboa and de Una-Alvarez (2018) 64,
<doi:10.18637/jss.v083.i10>, are included. / GPL-2 win-
64
r-tpauc 2.1.1 Tools for estimating and inferring two-way partial area under receiver oper- noarch
ating characteristic curves (two-way pAUC), partial area under receiver oper-
ating characteristic curves (pAUC), and partial area under ordinal dominance
curves (pODC). Methods includes Mann-Whitney statistic and Jackknife, etc.
/ GPL-2
r-tpe 1.0.1 This package implements the greedy approximation for tree preserving em- noarch
bedding. / MIT
r-tpes 1.0.0 A bioinformatics tool for the estimation of the tumor purity from sequencing noarch
data. It uses the set of putative clonal somatic single nucleotide variants within
copy number neutral segments to call tumor cellularity. / MIT
r-tpmsm 1.2.2 Estimation of transition probabilities for the illness-death model and or the linux-
three-state progressive model. / GPL-2 64,
osx-
64,
win-
64


Name Version
r-tracerer 2.0.1 ‘BEAST2’ (<http://www.beast2.org>) is a widely used Bayesian phyloge- linux-
netic tool, that uses DNA/RNA/protein data and many model priors to cre- 64,
ate a posterior of jointly estimated phylogenies and parameters. ‘Tracer’ osx-
(<http://tree.bio.ed.ac.uk/software/tracer/>) is a GUI tool to parse and analyze 64,
the files generated by ‘BEAST2’. This package provides a way to parse and win-
analyze ‘BEAST2’ input files without active user input, but using R function 64
calls instead. / GPL-3
r-track 1.1.9 Automatically stores objects in files on disk so that files are rewritten when noarch
objects are changed, and so that objects are accessible but do not occupy mem-
ory until they are accessed. Keeps track of times when objects are created and
modified, and caches some basic characteristics of objects to allow for fast
summaries of objects. Also provides a command history mechanism that saves
the last command to a history file after each command completes. / GPL-3
r-trading 1.2 Contains trades from the five major assets classes and also functionality to use noarch
pricing curves, rating tables, CSAs and add-on tables. The implementation
follows an object oriented logic whereby each trade inherits from more abstract
classes while also the curves/tables are objects. There is a lot of functionality
focusing on the counterparty credit risk calculations however the package can
be used for trading applications in general. / GPL-3
r-trampr 1.0_8 Matching terminal restriction fragment length polymorphism (‘TRFLP’) pro- noarch
files between unknown samples and a database of known samples. TRAMPR
facilitates analysis of many unknown profiles at once, and provides tools
for working directly with electrophoresis output through to generating sum-
maries suitable for community analyses with R’s rich set of statistical func-
tions. TRAMPR also resolves the issues of multiple ‘TRFLP’ profiles within
a species, and shared ‘TRFLP’ profiles across species. / GPL-2
r-transcriber 0.0.0 Transcribes audio to text with the HP IDOL API. Includes functions to upload noarch
files, retrieve transcriptions, and monitor jobs. / GPL-3
r-translation.ko 0.0.1.5.2
R version 2.1.0 and later support Korean translations of program messages. noarch
The continuous efforts have been made by <http://developer.r-project.org/
TranslationTeams.html> The R Documentation files are licensed under the
General Public License, version 2 or 3. This means that the pilot project to
translate them into Korean has permission to reproduce them and translate
them. This work is done with GNU ‘gettext’ utilities. The portable object
template is updated a weekly basis or whenever changes are necessary. Com-
ments and corrections via email to the maintainer is of course most welcome.
In order to voluntarily participate in or offer your help with this translation,
please contact the maintainer. To check the change and progress of Korean
translation, please visit <http://www.openstatistics.net>. / GPL-2
r-transmodel 2.1 A unified estimation procedure for the analysis of right censored data using noarch
linear transformation models. / GPL-2
r-transp 0.1 Implementation of two transportation problem algorithms. 1. North West noarch
Corner Method 2. Minimum Cost Method or Least cost method. For more
technical details about the algorithms please refer below URLs. <http://
www.universalteacherpublications.com/univ/ebooks/or/Ch5/nw.htm>. <http:
//personal.maths.surrey.ac.uk/st/J.F/chapter7.pdf>. / GPL-2


Name Version
r-transport 0.12_1Solve optimal transport problems. Compute Wasserstein distances (a.k.a. linux-
Kantorovitch, Fortet–Mourier, Mallows, Earth Mover’s, or minimal L_p dis- 64,
tances), return the corresponding transference plans, and display them graph- osx-
ically. Objects that can be compared include grey-scale images, (weighted) 64,
point patterns, and mass vectors. / GPL-2 win-
64
r-transurv 1.2.0 A structural transformation model for a latent, quasi-independent truncation linux-
time as a function of the observed dependent truncation time and the event 64,
time, and an unknown dependence parameter. The dependence parameter is osx-
chosen to minimize the conditional Kendall’s tau (Martin and Betensky, 2005) 64,
<doi:10.1198/016214504000001538>. The marginal distribution for the trun- win-
cation time and the event time are completely left unspecified. / GPL-3 64
r-trapezoid 2.0_0 The trapezoid package provides dtrapezoid, ptrapezoid, qtrapezoid, and rtrape- linux-
zoid functions for the trapezoidal distribution. / GPL-3 64,
osx-
64,
win-
64
r-tree 1.0_40Classification and regression trees. / GPL-2 | GPL-3 linux-
64,
osx-
64,
win-
64
r-treebase 0.1.4 Interface to the API for ‘TreeBASE’ <http://treebase.org> from ‘R.’ ‘Tree- noarch
BASE’ is a repository of user-submitted phylogenetic trees (of species, popu-
lation, or genes) and the data used to create them. / CC0
r-treeclust 1.1_7 Create a measure of inter-point dissimilarity useful for clustering mixed data, noarch
and, optionally, perform the clustering. / GPL-2
r-treecm 1.2.2 The centre of mass is a crucial data for arborists in order to consolidate a noarch
tree using steel or dynamic cables. Given field-recorded data on branchiness
of a tree, the package: (i) computes and plots the centre of mass of the tree
itself, (ii) computes branches slenderness coefficient in order to aid the arborist
identify potentially dangerous branches, and (iii) computes the force acting on
a ground plinth and its best position relating to the tree centre of mass, should
the tree need to be stabilized by a steel cable. / GPL-2
r-treelet 1.1 Treelets provides a novel construction of multi-scale bases that extends noarch
wavelets to non-smooth signals. It returns a multi-scale orthonormal basis,
where the final computed basis functions are supported on nested clusters in a
hierarchical tree. Both the tree and the basis, which are constructed simultane-
ously, reflect the internal structure of the data. / GPL-2
r-treeman 1.1.3 S4 class and methods for intuitive and efficient phylogenetic tree manipulation. linux-
/ GPL-2 64,
osx-
64,
win-
64


Name Version
r-treeperm 1.6 An implementation of permutation tests in R, supporting both exact and linux-
asymptotic K sample test of data locations. The p value of exact tests is found 64,
using tree algorithms. Tree algorithms treat permutations of input data as tree osx-
nodes and perform constraint depth-first searches for permutations that fall 64,
into the critical region of a test systematically. Pruning of tree search and win-
optimisations at C level enable exact tests for certain large data sets. / GPL-2 64
r-trekfont 0.9.3 Provides a collection of true type and open type Star Trek-themed fonts. / noarch
GPL-3
r-trendchange 0.1.0 Innovative Trend Analysis is a graphical method to examine the trends in time noarch
series data. Sequential Mann-Kendall test uses the intersection of prograde and
retrograde series to indicate the possible change point in time series data. Dis-
tribution free cumulative sum charts indicate location and significance of the
change point in time series. Zekai, S. (2011). <doi:10.1061/(ASCE)HE.1943-
5584.0000556>. Grayson, R. B. et al. (1996). Hydrological Recipes: Esti-
mation Techniques in Australian Hydrology. Cooperative Research Centre for
Catchment Hydrology, Australia, p. 125. Sneyers, S. (1990). On the statistical
analysis of series of observations. Technical note no 5 143, WMO No 725
415. Secretariat of the World Meteorological Organization, Geneva, 192 pp. /
GPL-3
r-trendsegmentr 1.0.0 Performs the detection of point anomalies and linear trend changes for univari- noarch
ate time series by implementing the bottom-up unbalanced wavelet transfor-
mation proposed by H. Maeng and P. Fryzlewicz (2019) <http://personal.lse.
ac.uk/maengh/>. The estimated number and locations of the change-points are
returned with the piecewise-linear estimator for signal. / GPL-3
r-trialsize 1.3 functions and examples in Sample Size Calculation in Clinical Research. / linux-
GPL (>= 2.15.1) 64,
osx-
64,
win-
64
r-triangle 0.12 Provides the r, q, p, and d distribution functions for the triangle distribution. / noarch
GPL-2
r-triangulation 0.5.0 Measuring angles between points in a landscape is much easier than measur- noarch
ing distances. When the location of three points is known the position of the
observer can be determined based solely on the angles between these points as
seen by the observer. This task (known as triangulation) however requires
onerous calculations - these calculations are automated by this package. /
LGPL-3
r-triebeard 0.3.0 ‘Radix trees’, or ‘tries’, are key-value data structures optimised for efficient linux-
lookups, similar in purpose to hash tables. ‘triebeard’ provides an implemen- 64,
tation of ‘radix trees’ for use in R programming and in developing packages osx-
with ‘Rcpp’. / MIT 64,
win-
64
r-trimcluster 0.1_2.1
Trimmed k-means clustering. / GPL-3 noarch
r-trimr 1.0.1 Provides various commonly-used response time trimming methods, including noarch
the recursive / moving-criterion methods reported by Van Selst and Jolicoeur
(1994). By passing trimming functions raw data files, the package will return
trimmed data ready for inferential testing. / GPL-3


Name Version
r-triosgl 1.1.0 Fit a trio model via penalized maximum likelihood. The model is fit for a path linux-
of values of the penalty parameter. This package is based on Noah Simon, et 64,
al. (2011) <doi:10.1080/10618600.2012.681250>. / GPL-3 osx-
64,
win-
64
r-tripack 1.3_8 A constrained two-dimensional Delaunay triangulation package providing linux-
both triangulation and generation of voronoi mosaics of irregular spaced data. 64,
/ ACM | file LICENSE (Restricts use) osx-
64,
win-
64
r-tripsanddipr 0.1.0 Uses read counts for biallelic single nucleotide polymorphisms (SNPs) to com- noarch
pare the likelihoods for the observed read counts given that a sample is either
diploid or triploid. It allows parameters to be specified to account for sequenc-
ing error rates and allelic bias. For details of the algorithm, please see Delomas
(2019) <doi:10.1111/1755-0998.13073>. / MIT
r-tropalgebra 0.1.1 It includes functions like tropical addition, tropical multiplication for vectors noarch
and matrices. In tropical algebra, the tropical sum of two numbers is their min-
imum and the tropical product of two numbers is their ordinary sum. For more
information see also I. Simon (1988) Recognizable sets with multiplicities in
the tropical semi ring: Volume 324 Lecture Notes I Computer Science, pages
107-120 <doi: 10.1007/BFb0017135>. / GPL-3
r-tropicalsparse 0.1.0 Some of the basic tropical algebra functionality is provided for sparse matrices noarch
by applying sparse matrix storage techniques. Some of these are addition and
multiplication of vectors and matrices, dot product of the vectors in tropical
form and some general equations are also solved using tropical algebra. /
GPL-3
r-trotter 0.6 Class definitions and constructors for pseudo-vectors containing all permu- noarch
tations, combinations and subsets of objects taken from a vector. Simplifies
working with structures commonly encountered in combinatorics. / GPL-3
r-trueskill 0.1 An implementation of the TrueSkill algorithm (Herbrich, R., Minka, T. and noarch
Grapel, T) in R; a Bayesian skill rating system with inference by approxi-
mate message passing on a factor graph. Used by Xbox to rank gamers and
identify appropriate matches. http://research.microsoft.com/en-us/projects/
trueskill/default.aspx Current version allows for one player per team. Will
update as time permits. Requires R version 3.0 as it is written with Reference
Classes. URL: https://github.com/bhoung/trueskill-in-r Acknowledgements to
Doug Zongker and Heungsub Lee for their python implementations of the
algorithm and for the liberal reuse of Doug’s code comments (@dougz and
@sublee on github). / GPL-3
r-truncgof 0.6_0 Goodness-of-fit tests and some adjusted exploratory tools allowing for left linux-
truncated data / GPL-2 64,
osx-
64,
win-
64


Name Version
r-truncnorm 1.0_8 Density, probability, quantile and random number generation functions for the linux-
truncated normal distribution. / GPL-2 64,
osx-
64,
win-
64
r-truncreg 0.2_5 Estimation of models for truncated Gaussian variables by maximum likeli- noarch
hood. / GPL-2
r-trust 0.1_7 Does local optimization using two derivatives and trust regions. Guaranteed to noarch
converge to local minimum of objective function. / MIT
r- 0.2.6 Trusted Timestamps (tts) are created by incorporating a hash of a file or dataset noarch
trustedtimestamping into a transaction on the decentralized blockchain (Stellar network). The pack-
age makes use of a free service provided by <https://stellarapi.io>. / AGPL-3
r-trustoptim 0.8.6.2Trust region algorithm for nonlinear optimization. Efficient when the Hessian linux-
of the objective function is sparse (i.e., relatively few nonzero cross-partial 64,
derivatives). See Braun, M. (2014) <doi:10.18637/jss.v060.i04>. / MPL (>= osx-
2.0) 64,
win-
64
r-trycatchlog 1.1.4 Advanced tryCatch() and try() functions for better error handling (logging, noarch
stack trace with source code references and support for post-mortem analysis
via dump files). / GPL-3
r-tsallisqexp 0.9_3 Tsallis distribution also known as the q-exponential family distribution. Pro- noarch
vide distribution d, p, q, r functions, fitting and testing functions. Project initi-
ated by Paul Higbie and based on Cosma Shalizi’s code. / GPL-2
r-tsbox 0.2.0 Time series toolkit with identical behavior for all time series classes: ‘ts’,’xts’, noarch
‘data.frame’, ‘data.table’, ‘tibble’, ‘zoo’, ‘timeSeries’, ‘tsibble’, ‘tis’ or ‘irts’.
Also converts reliably between these classes. / GPL-3
r-tsc 1.0_3 Performs the two-sample comparisons using the following exact test proce- linux-
dures: the exact likelihood-ratio test (LRT) for equality of two normal popu- 64,
lations proposed in Zhang et al. (2012); the combined test based on the LRT osx-
and Shapiro-Wilk test for normality via the Bonferroni correction technique; 64,
the newly proposed density-based empirical likelihood (DBEL) ratio test. To win-
calculate p-values of the DBEL procedures, three procedures are used: (a) the 64
traditional Monte Carlo (MC) method implemented in C, (b) a new interpola-
tion method based on regression techniques to operate with tabulated critical
values of the test statistic; (c) a Bayesian type method that uses the tabulated
critical values as the prior information and MC generated DBEL-test-statistic’s
values as data. / GPL-2
r-tsdata 2016.8_1
Illustrates the various ‘TSdbi’ packages with a vignette using time series data noarch
from several sources. The vignette also illustrates some simple time series
manipulation and plotting using packages ‘tframe’ and ‘tfplot’. / GPL-2
r-tsdecomp 0.2 ARIMA-model-based decomposition of quarterly and monthly time se- noarch
ries data. The methodology is developed and described, among others,
in Burman (1980) <DOI:10.2307/2982132> and Hillmer and Tiao (1982)
<DOI:10.2307/2287770>. / GPL-2
r-tsdf 1.1_7 Calculate optimal Zhong’s two-/three-stage Phase II designs (see Zhong noarch
(2012) <doi:10.1016/j.cct.2012.07.006>). Generate Target Toxicity decision
table for Phase I dose-finding (two-/three-stage). This package also allows
users to run dose-finding simulations based on customized decision table. /
GPL-2


Name Version
r-tsdfgs 1.0 Determining training set for genomic selection using a genetic algorithm linux-
(Holland J.H. (1975) <DOI:10.1145/1216504.1216510>) or simple exchange 64,
algorithm (change an individual every iteration). Three different crite- osx-
ria are used in both algorithms, which are r-score (Ou J.H., Liao C.T. 64,
(2018) <DOI:10.6342/NTU201802290>), PEV-score (Akdemir D. et al. win-
(2015) <DOI:10.1186/s12711-015-0116-6>) and CD-score (Laloe D. (1993) 64
<DOI:10.1186/1297-9686-25-6-557>). Phenotypic data for candidate set is
not necessary for all these methods. By using it, one may readily determine a
training set that can be expected to provide a better training set comparing to
random sampling. / GPL-3
r-tsdisagg2 0.1.0 Disaggregates low frequency time series data to higher frequency series. noarch
Implements the following methods for temporal disaggregation: Boot,
Feibes and Lisman (1967) <DOI:10.2307/2985238>, Chow and Lin (1971)
<DOI:10.2307/1928739>, Fernandez (1981) <DOI:10.2307/1924371> and
Litterman (1983) <DOI:10.2307/1391858>. / GPL-2
r-tse 0.1.0 Calculates total survey error (TSE) for one or more surveys, using com- noarch
mon scale-dependent and/or scale-independent metrics. On TSE, see:
Weisberg, Herbert (2005, ISBN:0-226-89128-3); Biemer, Paul (2010)
<doi:10.1093/poq/nfq058>. / GPL-2
r-tseind 0.1.0 Calculates total survey error (TSE) for one or more surveys, using both noarch
scale-dependent and scale-independent metrics. Package works directly
from the data set, with no hand calculations required: just upload a prop-
erly structured data set (see TESTIND and its documentation), properly in-
put column names (see functions documentation), and run your functions.
For more on TSE, see: Weisberg, Herbert (2005, ISBN:0-226-89128-3);
Biemer, Paul (2010) <doi:10.1093/poq/nfq058>; Biemer, Paul et.al. (2017,
ISBN:9781119041672); etc. / GPL-2
r-tsentropies 0.9 Computes various entropies of given time series. This is the initial version linux-
that includes ApEn() and SampEn() functions for calculating approximate en- 64,
tropy and sample entropy. Approximate entropy was proposed by S.M. Pincus osx-
in Approximate entropy as a measure of system complexity, Proceedings of 64,
the National Academy of Sciences of the United States of America, 88, 2297- win-
2301 (March 1991). Sample entropy was proposed by J. S. Richman and J. R. 64
Moorman in Physiological time-series analysis using approximate entropy and
sample entropy, American Journal of Physiology, Heart and Circulatory Phys-
iology, 278, 2039-2049 (June 2000). This package also contains FastApEn()
and FastSampEn() functions for calculating fast approximate entropy and fast
sample entropy. These are newly designed very fast algorithms, resulting from
the modification of the original algorithms. The calculated values of these
entropies are not the same as the original ones, but the entropy trend of the an-
alyzed time series determines equally reliably. Their main advantage is their
speed, which is up to a thousand times higher. A scientific article describing
their properties has been submitted to The Journal of Supercomputing and in
present time it is waiting for the acceptance. / GPL-3


Name Version
r-tseries 0.10_46
Time series analysis and computational finance. / GPL-2 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-tserieschaos 0.1_13.1
Routines for the analysis of nonlinear time series. This work is largely in- linux-
spired by the TISEAN project, by Rainer Hegger, Holger Kantz and Thomas 64,
Schreiber: <http://www.mpipks-dresden.mpg.de/~tisean/>. / GPL-2 osx-
64,
win-
64
r-tseriesmma 0.1.1 Multiscale multifractal analysis (MMA) (GieraÅ‚towski et al., noarch
2012)<DOI:10.1103/PhysRevE.85.021915> is a time series analysis method,
designed to describe scaling properties of fluctuations within the signal
analyzed. The main result of this procedure is the so called Hurst surface
h(q,s) , which is a dependence of the local Hurst exponent h (fluctuation
scaling exponent) on the multifractal parameter q and the scale of observation
s (data window width). / GPL-2
r-tsetools 0.1.3 Tools for downloading and organizing data from Tehran Stock Exchange noarch
(TSE) <http://new.tse.ir/en/>. It also performs some descriptive data analy-
sis for assets. / BSD_2_clause
r-tsewgt 0.1.0 Calculates total survey error (TSE) for a survey under multiple, different noarch
weighting schemes, using both scale-dependent and scale-independent met-
rics. Package works directly from the data set, with no hand calculations re-
quired: just upload a properly structured data set (see TESTWGT and its doc-
umentation), properly input column names (see functions documentation), and
run your functions. For more on TSE, see: Weisberg, Herbert (2005, ISBN:0-
226-89128-3); Biemer, Paul (2010) <doi:10.1093/poq/nfq058>; Biemer, Paul
et.al. (2017, ISBN:9781119041672); etc. / GPL-2
r-tsgsis 0.1 To provide a high dimensional grouped variable selection approach for detec- noarch
tion of whole-genome SNP effects and SNP-SNP interactions, as described in
Fang et al. (2017, under review). / GPL-2
r-tshrc 0.1_6 Two-stage procedure compares hazard rate functions, which may or may not linux-
cross each other. / MIT 64,
osx-
64,
win-
64
r-tsmn 1.0.0 Return the first four moments of the SMN distributions (Normal, Student-t, noarch
Pearson VII, Slash or Contaminated Normal). / GPL (>= 3.0)
r-tsmodel 0.6 Tools for specifying time series regression models / GPL-2 noarch
r-tsne 0.1_3 A pure R implementation of the t-SNE algorithm. / GPL-3 noarch


Name Version
r-tsp 1.1_7 Basic infrastructure and some algorithms for the traveling salesperson problem linux-
(also traveling salesman problem; TSP). The package provides some simple 64,
algorithms and an interface to the Concorde TSP solver and its implementation osx-
of the Chained-Lin-Kernighan heuristic. The code for Concorde itself is not 64,
included in the package and has to be obtained separately. / GPL-3 win-
64
r-tsqn 1.0.0 Time Series Qn is a package with applications of the Qn estimator of noarch
Rousseeuw and Croux (1993) <doi:10.1080/01621459.1993.10476408> to
univariate and multivariate Time Series in time and frequency domains.
More specifically, the robust estimation of autocorrelation or autocovariance
matrix functions from Ma and Genton (2000, 2001) <doi:10.1111/1467-
9892.00203>, <doi:10.1006/jmva.2000.1942> and Cotta (2017)
<doi:10.13140/RG.2.2.14092.10883> are provided. The robust pseudo-
periodogram of Molinares et. al. (2009) <doi:10.1016/j.jspi.2008.12.014> is
also given. This packages also provides the M-estimator of the long-memory
parameter d based on the robustification of the GPH estimator proposed by
Reisen et al. (2017) <doi:10.1016/j.jspi.2017.02.008>. / GPL-2
r-tsss 1.2.4 Functions for statistical analysis, modeling and simulation of time series with linux-
state space model, based on the methodology in Kitagawa (1993, ISBN: 4-00- 64,
007703-1 and 2005, ISBN: 4-00-005455-4). / GPL-2 osx-
64,
win-
64
r-tstools 0.3.8 Plot official statistics’ time series conveniently: automatic legends, highlight noarch
windows, stacked bar chars with positive and negative contributions, sum-as-
line option, two y-axes with automatic horizontal grids that fit both axes and
other popular chart types. ‘tstools’ comes with a plethora of defaults to let
you plot without setting an abundance of parameters first, but gives you the
flexibility to tweak the defaults. In addition to charts, ‘tstools’ provides a
super fast, ‘data.table’ backed time series I/O that allows the user to export /
import long format, wide format and transposed wide format data to various
file types. / GPL-2
r-tstr 1.2 A ternary search tree is a type of prefix tree with up to three children and the noarch
ability for incremental string search. The package uses this ability for word
auto-completion and spell checking. Includes a dataset with the 10001 most
frequent English words. / GPL-2
r-tstutorial 1.2.3 Interactive laboratory of Time Series based in Box-Jenkins methodology. / noarch
GPL (>= 2.0)
r-tsvr 1.0.0 Tools for timescale decomposition of the classic variance ratio of community noarch
ecology. Tools are as described in Zhao et al (in prep), extending commonly
used methods introduced by Peterson et al (1975) <doi: 10.2307/1936306>. /
GPL-3
r-ttbbeer 1.1.0 U.S. Department of the Treasury, Alcohol and Tobacco Tax and Trade Bureau noarch
(TTB) collects data and reports on monthly beer industry production and oper-
ations. This data package includes a collection of 10 years (2006 - 2015) worth
of data on materials used at U.S. breweries in pounds reported by the Brewer’s
Report of Operations and the Quarterly Brewer’s Report of Operations forms,
ready for data analysis. This package also includes historical tax rates on dis-
tilled spirits, wine, beer, champagne, and tobacco products as individual data
sets. / CC0


Name Version
r-tth 4.3_2_1
C source code and R wrappers for the tth/ttm TeX to HTML/MathML transla- linux-
tors. / GPL-2 64,
osx-
64,
win-
64
r-ttmoment 1.0 Computing the first two moments of the truncated multivariate t (TMVT) dis- noarch
tribution under the double truncation. Appling the slice sampling algorithm to
generate random variates from the TMVT distribution. / GPL-2
r-ttr 0.23_4Functions and data to construct technical trading rules with R. / GPL-2 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-tts 1.0 Time-Temperature Superposition analysis is often applied to frequency modu- noarch
lated data obtained by Dynamic Mechanic Analysis (DMA) and Rheometry in
the analytical chemistry and physics areas. These techniques provide estimates
of material mechanical properties (such as moduli) at different temperatures in
a wider range of time. This package provides the Time-Temperature super-
position Master Curve at a referred temperature by the three methods: the
two wider used methods, Arrhenius based methods and WLF, and the newer
methodology based on derivatives procedure. The Master Curve is smoothed
by B-splines basis. The package output is composed of plots of experimen-
tal data, horizontal and vertical shifts, TTS data, and TTS data fitted using
B-splines with bootstrap confidence intervals. / GPL-2
r-tttplot 1.1.1 Implementation of Time to Target plot based on the work of Ribeiro and noarch
Rosseti (2015) <DOI:10.1007/s11590-014-0760-8>, that describe a numeri-
cal method that gives the probability of an algorithm A finds a solution at least
as good as a given target value in smaller computation time than algorithm B.
/ GPL-2
r-ttutils 1.0_1 Contains some auxiliary functions. / GPL-2 noarch
r-ttwa 0.8.5.1This package makes Travel To Work Area from a commuting flow data frame. noarch
/ GPL (>= 2.0)
r-tubern 0.1.0 Get statistics and reports from YouTube. To learn more about the YouTube noarch
Analytics and Reporting API, see <https://developers.google.com/youtube/
reporting/>. / MIT
r-tuckerr.mmgg 1.5.1 Performs Three-Mode Principal Components Analysis, which carries out noarch
Tucker Models. / GPL-3
r-tufte 0.5 Provides R Markdown output formats to use Tufte styles for PDF and HTML noarch
output. / GPL-3
r-tufterhandout 1.2.1 Custom template and output formats for use with rmarkdown. Produce Edward noarch
Tufte-style handouts in html formats with full support for rmarkdown features
/ MIT
r-tukeytrend 0.6 Provides wrapper functions to the multiple marginal model function mmm() of noarch
package ‘multcomp’ to implement the trend test of Tukey, Ciminera and Heyse
(1985) <DOI:10.2307/2530666> for general parametric models. / GPL-2


Name Version
r-tumblr 1.1 Provides an R-interface to the Tumblr web API (see Tumblr v2 API on https: noarch
//www.tumblr.com/docs/en/api/v2). Tumblr is a microblogging platform and
social networking website (https://www.tumblr.com). / Artistic-2.0
r-tunepareto 2.5 Generic methods for parameter tuning of classification algorithms using mul- linux-
tiple scoring functions. / GPL-2 64,
osx-
64,
win-
64
r-tuple 0.4_02Functions to find all matches or non-matches, orphans, and duplicate or other noarch
replicated elements. / LGPL-3
r-turboem 2018.1Algorithms for accelerating the convergence of slow, monotone sequences noarch
from smooth, contraction mapping such as the EM and MM algorithms. It can
be used to accelerate any smooth, linearly convergent acceleration scheme.
A tutorial style introduction to this package is available in a vignette on the
CRAN download page or, when the package is loaded in an R session, with
vignette(turboEM). / GPL-2
r-turtlegraphics 1.0_8 An implementation of turtle graphics <http://en.wikipedia.org/wiki/Turtle_ noarch
graphics>. Turtle graphics comes from Papert’s language Logo and has been
used to teach concepts of computer programming. / GPL-3
r-tutorial 0.4.3 DataCamp Light (<https://github.com/datacamp/datacamp-light>) is a light- noarch
weight implementation of the DataCamp UI, that allows you to embed inter-
active exercises inside HTML documents. The tutorial package makes it easy
to create these HTML files from R Markdown files. An extension to knitr,
tutorial detects appropriately formatted code chunks and replaces them with
DataCamp Light readable chunks in the resulting HTML file. / MIT
r-tuwmodel 1.0_2 The model, developed at the Vienna University of Technology, is a lumped linux-
conceptual rainfall-runoff model, following the structure of the HBV model. 64,
The model can also be run in a semi-distributed fashion. The model runs on a osx-
daily or shorter time step and consists of a snow routine, a soil moisture rou- 64,
tine and a flow routing routine. See Parajka, J., R. Merz, G. Bloeschl (2007) win-
<DOI:10.1002/hyp.6253> Uncertainty and multiple objective calibration in re- 64
gional water balance modelling: case study in 320 Austrian catchments, Hy-
drological Processes, 21, 435-446. / GPL-2
r-tvd 0.1.0 Total Variation Denoising is a regularized denoising method which effectively linux-
removes noise from piecewise constant signals whilst preserving edges. This 64,
package contains a C implementation of Condat’s very fast 1D squared error osx-
loss TVD algorithm. Additional methods and loss functions may be added in 64,
future versions. / EPL (>= 1.0) win-
64
r-tvsmiss 0.1.1 Use a regularization likelihood method to achieve variable selection purpose. linux-
Likelihood can be worked with penalty lasso, smoothly clipped absolute devia- 64,
tions (SCAD), and minimax concave penalty (MCP). Tuning parameter selec- osx-
tion techniques include cross validation (CV), Bayesian information criterion 64,
(BIC) (low and high), stability of variable selection (sVS), stability of BIC win-
(sBIC), and stability of estimation (sEST). More details see Jiwei Zhao, Yang 64
Yang, and Yang Ning (2018) <arXiv:1703.06379> Penalized pairwise pseudo
likelihood for variable selection with nonignorable missing data. Statistica
Sinica. / GPL-2


Name Version
r-tweedie 2.3.2 Maximum likelihood computations for Tweedie families, including the se- linux-
ries expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) 64,
and the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007- osx-
9039-6>), and related methods. / GPL-2 64,
win-
64
r-twfy 0.1.0 An R wrapper around the API of TheyWorkForYou, a parliamentary monitor- noarch
ing site that scrapes and repackages Hansard (the UK’s parliamentary record)
and augments it with information from the Register of Members’ Interests,
election results, and voting records to provide a unified source of information
about UK legislators and their activities. See <http://www.theyworkforyou.
com> for details. / GPL-3
r-twiddler 0.5_0 Twiddler is an interactive tool that automatically creates a Tcl/Tk GUI for noarch
manipulating variables in any R expression. See the documentation of the
function twiddle to get started. / GPL-2
r-twilio 0.1.0 The Twilio web service provides an API for computer programs to interact noarch
with telephony. The included functions wrap the SMS and MMS portions of
Twilio’s API, allowing users to send and receive text messages from R. See
<https://www.twilio.com/docs/> for more information. / MIT
r-twitter 1.1.9 Provides an interface to the Twitter web API. / Artistic-2.0 noarch
r-twitterwidget 0.1.1 Include the Twitter status widgets in HTML pages created using R markdown. noarch
The package uses the Twitter javascript APIs to embed in your document Twit-
ter cards associated to specific statuses. The main targets are regular HTML
pages or dashboards. / MIT
r-twocop 1.0 This package implements the nonparametric test of equality between two cop- linux-
ulas proposed by Remillard and Scaillet in their 2009 JMVA paper. / GPL-2 64,
osx-
64,
win-
64
r-twophaseind 1.1.1 Estimation of gene-treatment interactions in randomized clinical trials exploit- linux-
ing gene-treatment independence. / GPL-2 64,
osx-
64,
win-
64
r-twosamples 1.0.0 Fast randomization based two sample tests. Testing the hypothesis that two linux-
samples come from the same distribution using randomization to create p- 64,
values. Included tests are: Kolmogorov-Smirnov, Kuiper, Cramer-von Mises, osx-
and Anderson-Darling. There is also a very efficient test based on the Wasser- 64,
stein Distance. The default test ‘two_sample’ builds on the Wasserstein dis- win-
tance by using a weighting scheme like that of Anderson-Darling. We also 64
include the permutation scheme to make test building simple for others. /
GPL-2


Name Version
r- 1.0 For high-dimensional data whose main feature is a large number, p, of vari- noarch
twosampletest.hd ables but a small sample size, the null hypothesis that the marginal distribu-
tions of p variables are the same for two groups is tested. We propose a test
statistic motivated by the simple idea of comparing, for each of the p variables,
the empirical characteristic functions computed from the two samples. If one
rejects this global null hypothesis of no differences in distributions between
the two groups, a set of permutation p-values is reported to identify which
variables are not equally distributed in both groups. / GPL-2
r-twostepclogit 1.2.5 Conditional logistic regression with longitudinal follow up and individual- noarch
level random coefficients: A stable and efficient two-step estimation method.
/ GPL-2
r-twoway 0.6.2 Carries out analyses of two-way tables with one observation per cell, together noarch
with graphical displays for an additive fit and a diagnostic plot for removable
‘non-additivity’ via a power transformation of the response. It implements
Tukey’s Exploratory Data Analysis methods, including a 1-degree-of-freedom
test for row*column ‘non-additivity’, linear in the row and column effects. /
GPL-3
r-txtplot 1.0_3 Provides functions to produce rudimentary ascii graphics directly in the ter- noarch
minal window. Provides a basic plotting function (and equivalents of curve,
density, acf and barplot) as well as a boxplot function. / LGPL-3
r-types 1.0.0 Provides a simple type annotation for R that is usable in scripts, in the R con- noarch
sole and in packages. It is intended as a convention to allow other packages to
use the type information to provide error checking, automatic documentation
or optimizations. / MIT
r-ubcrm 1.0.1 Two Phase I designs are implemented in the package: the classical 33 and the noarch
Continual Reassessment Method. Simulations tools are also available to esti-
mate the operating characteristics of the methods with several user-dependent
options. / GPL-2
r-ucbthesis 1.0 This package contains latex, knitr and R Markdown templates that adhere to noarch
the UC Berkeley Graduate Division’s thesis guidelines. The templates are
located in the inst/ directory. / GPL-2
r-ucminf 1.1_4 An algorithm for general-purpose unconstrained non-linear optimization. The linux-
algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian 64,
and soft line search with a trust region type monitoring of the input to the line osx-
search algorithm. The interface of ‘ucminf’ is designed for easy interchange 64,
with ‘optim’. / GPL-2 win-
64
r- 0.1.0 Changes the column names of the inputted dataset to the correct names from noarch
ucr.columnnames the Uniform Crime Report codebook for the Offenses Known and Clearance
by Arrest datasets from 1998-2014. / GPL-3
r-udapi 0.1.3 A client for the Urban Dictionary <http://www.urbandictionary.com/> API. / noarch
MIT


Name Version
r- 1.0.0 The udder quarter infection data set contains infection times of individ- noarch
udderquarterinfectiondata ual cow udder quarters with Corynebacterium bovis (Laevens et al. 1997
<DOI:10.3168/jds.S0022-0302(97)76295-7>). Obviously, the four udder
quarters are clustered within a cow, and udder quarters are sampled only ap-
proximately monthly, generating interval-censored data. The data set contains
both covariates that change within a cow (e.g., front and rear udder quarters)
and covariates that change between cows (e.g., parity [the number of previous
calvings]). The correlation between udder infection times within a cow also is
of interest, because this is a measure of the infectivity of the agent causing the
disease. Various models have been applied to address the problem of interde-
pendence for right-censored event times. These models, as applied to this data
set, can be found back in the publications found in the reference list. / GPL-3
r-udpipe 0.8.3 This natural language processing toolkit provides language-agnostic ‘tok- linux-
enization’, ‘parts of speech tagging’, ‘lemmatization’ and ‘dependency pars- 64,
ing’ of raw text. Next to text parsing, the package also allows you to train osx-
annotation models based on data of ‘treebanks’ in ‘CoNLL-U’ format as pro- 64,
vided at <http://universaldependencies.org/format.html>. The techniques are win-
explained in detail in the paper: ‘Tokenizing, POS Tagging, Lemmatizing and 64
Parsing UD 2.0 with UDPipe’, available at <doi:10.18653/v1/K17-3009>. /
MPL-2.0
r-udunits2 0.13 Provides simple bindings to Unidata’s udunits library. / GPL-2 linux-
32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-ui 0.1.0 Implements functions to derive uncertainty intervals for (i) regression (linear noarch
and probit) parameters when outcome is missing not at random (non-ignorable
missingness) introduced in Genbaeck, M., Stanghellini, E., de Luna, X. (2015)
<doi:10.1007/s00362-014-0610-x> and Genbaeck, M., Ng, N., Stanghellini,
E., de Luna, X. (2018) <doi:10.1007/s10433-017-0448-x>; and (ii) double
robust and outcome regression estimators of average causal effects (on the
treated) with possibly unobserved confounding introduced in Genbaeck, M.,
de Luna, X. (2018) <doi:10.1111/biom.13001>. / GPL-2
r-uiucthemes 0.2.1 A set of custom ‘R’ ‘Markdown’ templates for documents and presentations noarch
with the University of Illinois at Urbana-Champaign (UIUC) color scheme and
identity standards. / MIT
r-ukbabynames 0.1.1 Full listing of UK baby names occurring more than three times per year be- noarch
tween 1996 and 2015, and rankings of baby name popularity by decade from
1904 to 1994. / CC0
r-ukgasapi 0.16 Allows users to access live UK gas market information via National Grid’s noarch
API. / GPL-2


Name Version
r-ulid 0.3.0 Universally unique identifiers (‘UUIDs’) can be suboptimal for many uses- linux-
cases because they aren’t the most character efficient way of encoding 128 64,
bits of randomness; v1/v2 versions are impractical in many environments, as osx-
they require access to a unique, stable MAC address; v3/v5 versions require a 64,
unique seed and produce randomly distributed IDs, which can cause fragmen- win-
tation in many data structures; v4 provides no other information than random- 64
ness which can cause fragmentation in many data structures. ‘ULIDs’ (<https:
//github.com/ulid/spec>) have 128-bit compatibility with ‘UUID’, 1.21e24
unique ‘ULIDs’ per millisecond, are lexicographically sortable, canonically
encoded as a 26 character string, as opposed to the 36 character ‘UUID’, use
Crockford’s ‘base32’ for better efficiency and readability (5 bits per character),
are case insensitive, have no special characters (i.e. are ‘URL’ safe) and have
a onotonic sort order (correctly detects and handles the same millisecond). /
MIT
r-ultimixt 2.1 A generic reference Bayesian analysis of unidimensional mixture distribu- noarch
tions obtained by a location-scale parameterisation of the model is imple-
mented. The including functions simulate and summarize posterior samples
for location-scale mixture models using a weakly informative prior. There is
no need to define priors for scale-location parameters except two hyperparam-
eters in which are associated with a Dirichlet prior for weights and a simplex.
/ GPL (>= 2.0)
r-umoments 0.1.0 Calculates one-sample unbiased central moment estimates and two-sample noarch
pooled estimates up to 6th order, including unbiased estimates of powers and
products of central moments. Provides the machinery for obtaining unbiased
central moment estimators beyond 6th order. / GPL-2
r-ump 0.5_8 Does uniformly most powerful (UMP) and uniformly most powerful unbiased linux-
(UMPU) tests. At present only distribution implemented is binomial distri- 64,
bution. Also does fuzzy tests and confidence intervals (following Geyer and osx-
Meeden, 2005, <doi:10.1214/088342305000000340>) for the binomial distri- 64,
bution (one-tailed procedures based on UMP test and two-tailed procedures win-
based on UMPU test). / MIT 64
r-umpire 1.3.7 The Ultimate Microrray Prediction, Reality and Inference Engine (UM- noarch
PIRE) is a package to facilitate the simulation of realistic microarray data
sets with link to associate outcomes. See Zhang and Coombes (2012)
<doi:10.1186/1471-2105-13-S13-S1>. / Apache License (== 2.0)
r-unbalhaar 2.0 The package implements top-down and bottom-up algorithms for nonparamet- noarch
ric function estimation in Gaussian noise using Unbalanced Haar wavelets. /
GPL-2
r-uncdecomp 0.0.4 If a procedure consists of several stages and there are several scenarios that can noarch
be selected for each stage, uncertainty of the procedure can be decomposed by
stages or scenarios. cum_uncertainty() is used to decompose uncertainty based
on the cumulative uncertainty. stage_uncertainty() and scenario_uncertainty()
is used to decompose uncertainty based on the second order interaction
ANOVA model. In stage_uncertainty() and scenario_uncertainty(), the un-
certainty from interaction effect from two stages is distributed equally to each
stage. / GPL-2
r-unf 2.0.6 Computes a universal numeric fingerprint (UNF) for an R data object. UNF noarch
is a cryptographic hash or signature that can be used to uniquely identify (a
version of) a rectangular dataset, or a subset thereof. UNF can be used, in
tandem with a DOI, to form a persistent citation to a versioned dataset. / GPL-
2


Name Version
r-unfoldr 0.7 Stereological unfolding of the joint size-shape-orientation distribution of linux-
spheroidal shaped particles. / GPL-3 64,
osx-
64,
win-
64
r-unicode 12.0.0_1
Data from Unicode 12.0.0 and related utilities. / GPL-2 noarch
r-unidoe 1.0.2 Efficient procedures for constructing uniform design of experiments under var- linux-
ious space-filling criteria. It is based on a stochastic and adaptive threshold ac- 64,
cepting algorithm with flexible initialization, adaptive threshold, and stochas- osx-
tic evolution. The package may also construct the augmented uniform designs 64,
in a sequential manner. / GPL-3 win-
64
r-unifed 1.1.1 Probability functions and family for glm() of the unifed distribution (Quijano linux-
Xacur, 2018; <arXiv:1812.00251>). / GPL-3 64,
osx-
64,
win-
64
r- 0.0_0 Perform L1 or L2 isotonic and unimodal regression on 1D weighted or un- linux-
uniisoregression weighted input vector and isotonic regression on 2D weighted or unweighted 64,
input vector. It also performs L infinity isotonic and unimodal regres- osx-
sion on 1D unweighted input vector. Reference: Quentin F. Stout (2008) 64,
<doi:10.1016/j.csda.2008.08.005>. Spouge, J., Wan, H. & Wilbur, W.(2003) win-
<doi:10.1023/A:1023901806339>. Q.F. Stout (2013) <doi:10.1007/s00453- 64
012-9628-4>. / GPL-2
r-unikn 0.1.0 Define and use graphical elements of corporate design manuals in R. The noarch
‘unikn’ package provides color functions (by defining dedicated colors and
color palettes, and commands for changing, viewing, and using them) and
styled text elements (e.g., for marking, underlining, or plotting colored titles).
The pre-defined range of colors and text functions is based on the corporate
design of the University of Konstanz <https://www.uni-konstanz.de/>, but can
be adapted and extended for other institutions and purposes. / CC BY-SA 4.0
r-unine 0.2.0 Implementation of light stemmers for French, German, Italian, Spanish, linux-
Portuguese, Finnish, Swedish. They are based on the same work as the 64,
light stemmers found in ‘SolR’ <https://lucene.apache.org/solr/> or ‘Elas- osx-
ticSearch’ <https://www.elastic.co/fr/products/elasticsearch>. A light stem- 64,
mer consists in removing inflections only for noun and adjectives. Index- win-
ing verbs for these languages is not of primary importance compared to 64
nouns and adjectives. The stemming procedure for French is described
in (Savoy, 1999) <doi:10.1002/(SICI)1097-4571(1999)50:10%3C944::AID-
ASI9%3E3.3.CO;2-H>. / MIT
r-uniqtag 1.0 For each string in a set of strings, determine a unique tag that is a substring noarch
of fixed size k unique to that string, if it has one. If no such unique substring
exists, the least frequent substring is used. If multiple unique substrings exist,
the lexicographically smallest substring is used. This lexicographically small-
est substring of size k is called the UniqTag of that string. / MIT
r-unitcircle 0.1.3 The uc.check() function checks whether the roots of a given polynomial lie noarch
outside the Unit circle. You can also easily draw an unit circle. / GPL-3


Name Version
r-unitedr 0.3.1 United is a software tool which can be downloaded at the following web- noarch
site <http://www.schroepl.net/pbm/software/united/>. In general, it is a virtual
manager game for football teams. This package contains helpful functions for
determining an optimal formation for a virtual match in United. E.g. knowing
that the opponent has a strong defensive it is advisable to beat him in the mid-
field. Furthermore, this package contains functions for computing the optimal
usage of hardness in a game. / GPL-2
r-unitizer 1.4.8 Simplifies regression tests by comparing objects produced by test code with noarch
earlier versions of those same objects. If objects are unchanged the tests pass,
otherwise execution stops with error details. If in interactive mode, tests can
be reviewed through the provided interactive environment. / GPL-2
r-units 0.6_2 Support for measurement units in R vectors, matrices and arrays: automatic linux-
propagation, conversion, derivation and simplification of units; raising errors 32,
in case of unit incompatibility. Compatible with the POSIXct, Date and diff- linux-
time classes. Uses the UNIDATA udunits library and unit database for unit 64,
compatibility checking and conversion. / GPL-2 osx-
64,
win-
32,
win-
64
r-unittest 1.3_0 Concise TAP <http://testanything.org/> compliant unit testing package. Au- noarch
thored tests can be run using CMD check with minimal implementation over-
head. / GPL-3
r-univrng 1.2 Pseudo-random number generation of 17 univariate distributions. / GPL-2 | noarch
GPL-3
r-unix 1.5 Bindings to system utilities found in most Unix systems such as POSIX func- linux-
tions which are not part of the Standard C Library. / MIT 64,
osx-64
r-unmarked 0.12_3Fits hierarchical models of animal abundance and occurrence to data collected linux-
using survey methods such as point counts, site occupancy sampling, distance 64,
sampling, removal sampling, and double observer sampling. Parameters gov- osx-
erning the state and observation processes can be modeled as functions of co- 64,
variates. / GPL-3 win-
64
r-unrepx 1.0 Provides half-normal plots, reference plots, and Pareto plots of effects from an noarch
unreplicated experiment, along with various pseudo-standard-error measures,
simulated reference distributions, and other tools. Many of these methods
are described in Daniel C. (1959) <doi:10.1080/00401706.1959.10489866>
and/or Lenth R.V. (1989) <doi:10.1080/00401706.1989.10488595>, but some
new approaches are added and integrated in one package. / GPL-2
r-unsystation 0.2.0 Performs a test for second-order stationarity of time series based on unsystem- linux-
atic sub-samples. / GPL-2 64,
osx-
64,
win-
64
r-unvotes 0.2.0 Historical voting data of the United Nations General Assembly. This includes noarch
votes for each country in each roll call, as well as descriptions and topic clas-
sifications for each vote. / MIT


Name Version
r-upsvarapprox 0.1.1 Variance approximations for the Horvitz-Thompson total estimator in Unequal noarch
Probability Sampling using only first-order inclusion probabilities. See Matei
and TillÃ© (2005) and Haziza, Mecatti and Rao (2008) for details. / GPL-3
r-uptimerobot 1.0.0 Provide a set of wrappers to call all the endpoints of UptimeRobot API noarch
which includes various kind of ping, keep-alive and speed tests. See <https:
//uptimerobot.com/> for more information. / MIT
r-urbin 0.1_8 Calculate unified measures that quantify the effect of a covariate on a binary noarch
dependent variable (e.g., for meta-analyses). This can be particularly im-
portant if the estimation results are obtained with different models/estimators
(e.g., linear probability model, logit, probit, . . . ) and/or with different transfor-
mations of the explanatory variable of interest (e.g., linear, quadratic, interval-
coded, . . . ). The calculated unified measures are: (a) semi-elasticities of lin-
ear, quadratic, or interval-coded covariates and (b) effects of linear, quadratic,
interval-coded, or categorical covariates when a linear or quadratic covariate
changes between distinct intervals, the reference category of a categorical vari-
able or the reference interval of an interval-coded variable needs to be changed,
or some categories of a categorical covariate or some intervals of an interval-
coded covariate need to be grouped together. Approximate standard errors of
the unified measures are also calculated. All methods that are implemented
in this package are described in the ‘vignette’ Extracting and Unifying Semi-
Elasticities and Effect Sizes from Studies with Binary Dependent Variables
that is included in this package. / GPL-2
r-urca 1.3_0 Unit root and cointegration tests encountered in applied econometric analysis linux-
are implemented. / GPL (>= 2) 32,
linux-
64,
osx-
64,
win-
32,
win-
64
r-uroot 2.0_9.1
Seasonal unit roots and seasonal stability tests. P-values based on response linux-
surface regressions are available for both tests. P-values based on bootstrap 32,
are available for seasonal unit root tests. A parallel implementation of the linux-
bootstrap method requires a CUDA capable GPU with compute capability >= 64,
3.0, otherwise a debugging version fully coded in R is used. / GPL-2 osx-
64,
win-
32,
win-
64
r-usaboundaries 0.3.1 The boundaries for geographical units in the United States of America con- noarch
tained in this package include state, county, congressional district, and zip
code tabulation area. Contemporary boundaries are provided by the U.S. Cen-
sus Bureau (public domain). Historical boundaries for the years from 1629
to 2000 are provided form the Newberry Library’s ‘Atlas of Historical County
Boundaries’ (licensed CC BY-NC-SA). Additional data is provided in the ‘US-
AboundariesData’ package; this package provides an interface to access that
data. / MIT


Name Version
r- 0.03 US Census 2000 Designated Places shapefiles and additional demographic noarch
uscensus2000cdp data from the SF1 100 percent files. This data set contains polygon files in
lat/lon coordinates and the corresponding demographic data for a number of
different variables. / GPL-2
r- 0.03 US 2000 Census Tract shapefiles and additional demographic data from the noarch
uscensus2000tract SF1 100 percent files. This data set contains polygon files in lat/lon coordinates
and the corresponding demographic data for a number of different variables. /
GPL-2
r-uscensus2010 0.11 US Census 2010 shape files and additional demographic data from the SF1 100 noarch
percent files. This package contains a number of helper functions for the US-
census2010blk, UScensus2010blkgrp, UScensus2010tract, UScensus2010cdp
packages. / GPL-2
r-usdm 1.1_18This is a framework that aims to provide methods and tools for assessing the noarch
impact of different sources of uncertainties (e.g.positional uncertainty) on per-
formance of species distribution models (SDMs).) / GPL-3
r-usedist 0.1.0 Functions to re-arrange, extract, and work with distances. / GPL-3 noarch
r-usethis 1.5.0 Automate package and project setup tasks that are otherwise performed man- noarch
ually. This includes setting up unit testing, test coverage, continuous integra-
tion, Git, ‘GitHub’, licenses, ‘Rcpp’, ‘RStudio’ projects, and more. / GPL-3
r-usgsstates2k 1.0.1 A map of the USA from the United States Geological Survey (USGS). Irucka noarch
worked with this data set while a Cherokee Nation Technology Solutions
(CNTS) USGS Contractor and/or USGS employee. It is replaced by ‘states2k’.
/ CC0
r-usmap 0.4.0 Obtain United States map data frames of varying region types (e.g. county, noarch
state). The map data frames include Alaska and Hawaii conveniently placed to
the bottom left, as they appear in most maps of the US. Convenience functions
for plotting choropleths and working with FIPS codes are also provided. /
GPL-3
r-ustatbookabsc 1.0.0 A set of functions leading to multivariate response L1 regression. This in- noarch
cludes functions on computing Euclidean inner products and norms, weighted
least squares estimates on multivariate responses, function to compute fitted
values and residuals. This package is a companion to the book U-Statistics,
M-estimation and Resampling, by Arup Bose and Snigdhansu Chatterjee, to
appear in 2017 as part of the Texts and Readings in Mathematics (TRIM) series
of Hindustan Book Agency and Springer-Verlag. / GPL-3
r-ustyc 1.0.0 Forms a query to submit for US Treasury yield curve data, posting this query noarch
to the US Treasury web site’s data feed service. By default the download
includes data yield data for 12 products from January 1, 1990, some of which
are NA during this span. The caller can pass parameters to limit the query to
a certain year or year and month, but the full download is not especially large.
The download data from the service is in XML format. The package’s main
function transforms that XML data into a numeric data frame with treasury
product items (constant maturity yields for 12 kinds of bills, notes, and bonds)
as columns and dates as row names. The function returns a list which includes
an item for this data frame as well as query-related values for reference and
the update date from the service. / MIT
r-utc 0.1.5 Three functions are provided: first function changes time from local to UTC, noarch
other changes from UTC to local and third returns difference between local
and UTC. %h% operator is also provided it adds hours to a time. / GPL-2


Name Version
r-utf8 1.1.4 Process and print ‘UTF-8’ encoded international text (Unicode). Input, vali- linux-
date, normalize, encode, format, and display. / Apache License (== 2.0) | file 32,
LICENSE linux-
64,
osx-
64,
win-
32,
win-
64
r-utility 1.4.3 Construct and plot objective hierarchies and associated value and utility func- noarch
tions. Evaluate the values and utilities and visualize the results as colored
objective hierarchies or tables. Visualize uncertainty by plotting median and
quantile intervals within the nodes of objective hierarchies. Get numerical
results of the evaluations in standard R data types for further processing. /
GPL-3
r-uuid 0.1_2 Tools for generating and handling of UUIDs (Universally Unique Identifiers). linux-
linux-
64,
osx-
64,
win-
32,
win-
64
r-v8 2.3 An R interface to Google’s open source JavaScript engine. This package can win-
now be compiled either with V8 version 6 or 7 (LTS) from nodejs or with the 64
legacy 3.14/3.15 branch of V8. / MIT
r-vaersndvax 1.0.4 Non-Domestic VAERS vaccine data for 01/01/2016 - 06/14/2016. If you noarch
want to explore the full VAERS data for 1990 - Present (data, symptoms,
and vaccines), then check out the ‘vaersND’ package from the URL below.
The URL and BugReports below correspond to the ‘vaersND’ package,
of which ‘vaersNDvax’ is a small subset (2016 only). ‘vaersND’ is not
hosted on CRAN due to the large size of the data set. To install the
Suggested ‘vaers’ and ‘vaersND’ packages, use the following R code:
‘devtools::install_git(https://gitlab.com/iembry/vaers.git, build_vignettes =
TRUE)’ and ‘devtools::install_git(https://gitlab.com/iembry/vaersND.git,
build_vignettes = TRUE)’. VAERS is a national vaccine safety surveil-
lance program co-sponsored by the US Centers for Disease Control and
Prevention (CDC) and the US Food and Drug Administration (FDA).
VAERS is a post-marketing safety surveillance program, collecting in-
formation about adverse events (possible side effects) that occur after
the administration of vaccines licensed for use in the United States. For
more information about the data, visit <https://vaers.hhs.gov/index>.
For information about vaccination/immunization hazards, visit
<http://www.questionuniverse.com/rethink.html/#vaccine>. / CC0


Name Version
r-vaersvax 1.0.5 US VAERS vaccine data for 01/01/2018 - 06/14/2018. If you want to explore noarch
the full VAERS data for 1990 - Present (data, symptoms, and vaccines), then
check out the ‘vaers’ package from the URL below. The URL and BugRe-
ports below correspond to the ‘vaers’ package, of which ‘vaersvax’ is a small
subset (2018 only). ‘vaers’ is not hosted on CRAN due to the large size of
the data set. To install the Suggested ‘vaers’ and ‘vaersND’ packages, use
the following R code: ‘devtools::install_git(<https://gitlab.com/iembry/vaers.
git>, build_vignettes = TRUE)’ and ‘devtools::install_git(<https://gitlab.com/
iembry/vaersND.git>, build_vignettes = TRUE)’. The Vaccine Adverse Event
Reporting System (VAERS) is a national early warning system to detect pos-
sible safety problems in U.S.-licensed vaccines. VAERS is co-managed by
the Centers for Disease Control and Prevention (CDC) and the U.S. Food and
Drug Administration (FDA). For more information about the data, visit <https:
//vaers.hhs.gov/>. For information about vaccination/immunization hazards,
visit <http://www.questionuniverse.com/rethink.html#vaccine>. / CC0
r-valaddin 1.0.0 A set of basic tools to transform functions into functions with input validation noarch
checks, in a manner suitable for both programmatic and interactive use. / MIT
r-valection 1.0.0 A binding for the ‘valection’ program which offers various ways to sample the noarch
outputs of competing algorithms or parameterizations, and fairly assess their
performance against each other. The ‘valection’ C library is required to use
this package and can be downloaded from: <http://labs.oicr.on.ca/boutros-lab/
software/valection>. Cooper CI, et al; Valection: Design Optimization for
Validation and Verification Studies; Biorxiv 2018; <doi:10.1101/254839>. /
GPL-3
r-valetr 0.1.0 Interface to Bank of Canada’s ‘Valet’ API (<https://www.bankofcanada.ca/ noarch
valet/docs>). Please read the API terms and conditions: <https://www.
bankofcanada.ca/terms/>. / GPL-3
r-validatejsonr 1.0.4 The current implementation uses the C library ‘RapidJSON’ to supply the linux-
schema functionality, it supports JSON Schema Draft v4. As of 2016-09-09, 64,
‘RapidJSON’ passed 262 out of 263 tests in JSON Schema Test Suite (JSON osx-
Schema draft 4). / BSD_2_clause 64,
win-
64
r-valorate 1.0_1 The algorithm implemented in this package was designed to quickly esti- linux-
mates the distribution of the log-rank especially for heavy unbalanced groups. 64,
VALORATE estimates the null distribution and the p-value of the log-rank osx-
test based on a recent formulation. For a given number of alterations that 64,
define the size of survival groups, the estimation involves a weighted sum win-
of distributions that are conditional on a co-occurrence term where muta- 64
tions and events are both present. The estimation of conditional distribu-
tions is quite fast allowing the analysis of large datasets in few minutes
<http://bioinformatica.mty.itesm.mx/valorate>. / GPL-2
r-valottery 0.0.1 Historical results for the state of Virginia lottery draw games. Data were down- noarch
loaded from https://www.valottery.com/. / CC0
r-var.etp 0.7 Estimation, Hypothesis Testing, Prediction for Stationary Vector Autoregres- noarch
sive Models / GPL-2


Name Version
r-varband 0.9.0 Implementation of the variable banding procedure for modeling local depen- linux-
dence and estimating precision matrices that is introduced in Yu & Bien (2016) 64,
and is available at <https://arxiv.org/abs/1604.07451>. / GPL-3 osx-
64,
win-
64
r-varbin 0.2.1 Tool for easy and efficient discretization of continuous and categorical data. noarch
The package calculates the most optimal binning of a given explanatory vari-
able with respect to a user-specified target variable. The purpose is to assign a
unique Weight-of-Evidence value to each of the calculated binpoints in order
to recode the original variable. The package allows users to impose certain
restrictions on the functional form on the resulting binning while maximizing
the overall information value in the original data. The package is well suited
for logistic scoring models where input variables may be subject to restrictions
such as linearity by e.g. regulatory authorities. An excellent source describing
in detail the development of scorecards, and the role of Weight-of-Evidence
coding in credit scoring is (Siddiqi 2006, ISBN: 978–0-471–75451–0). The
package utilizes the discrete nature of decision trees and Isotonic Regression
to accommodate the trade-off between flexible functional forms and maximum
information value. / GPL-2
r-vardiag 0.2_1 Interactive variogram diagnostics. / GPL-2 noarch
r-vared 1.0.0 Generating functions for both optimal and ordinary difference sequences, and noarch
the difference-based estimation functions. / GPL-2
r-vares 1.0 Computes Value at risk and expected shortfall, two most popular measures of noarch
financial risk, for over one hundred parametric distributions, including all com-
monly known distributions. Also computed are the corresponding probability
density function and cumulative distribution function. / GPL-2
r-varhandle 2.0.3 Variables are the fundamental parts of each programming language but han- noarch
dling them might be frustrating for programmers from time to time. This
package contains some functions to help user (especially data explorers) to
make more sense of their variables and take the most out of variables and
hardware resources. These functions are written, collected and crafted over 5
years of experience in statistical data analysis on high-dimensional data and
for each of them there was a need. Functions in this package are suppose to be
efficient and easy to use, hence they will be frequently updated to make them
more convenient. / GPL-2
r-variables 1.0_2 Abstract descriptions of (yet) unobserved variables. / GPL-2 noarch
r-vars 1.5_3 Estimation, lag selection, diagnostic testing, forecasting, causality analysis, linux-
forecast error variance decomposition and impulse response functions of VAR 32,
models and estimation of SVAR and SVEC models. / GPL (>= 2) linux-
64,
noarch,
osx-
64,
win-
32,
win-
64


Name Version
r-varsedig 1.9 An algorithm which identifies the morphometric features that significantly dis- noarch
criminate two taxa and validates the morphological distinctness between them
via a Monte-Carlo test, polar coordinates and overlap of the area under the
density curve. / GPL-2
r-varsel 0.1 Feature selection using Sequential Forward Floating feature Selection and noarch
Jeffries-Matusita distance. It returns a suboptimal set of features to use for
image classification. Reference: Dalponte, M., Oerka, H.O., Gobakken, T.,
Gianelle, D. & Naesset, E. (2013). Tree Species Classification in Boreal
Forests With Hyperspectral Data. IEEE Transactions on Geoscience and Re-
mote Sensing, 51, 2632-2645, <DOI:10.1109/TGRS.2012.2216272>. / GPL-3
r-varselrf 0.7_8 Variable selection from random forests using both backwards variable elimina- noarch
tion (for the selection of small sets of non-redundant variables) and selection
based on the importance spectrum (somewhat similar to scree plots; for the
selection of large, potentially highly-correlated variables). Main applications
in high-dimensional data (e.g., microarray data, and other genomics and pro-
teomics applications). / GPL-2
r-varswapprice 1.0 Computes a portfolio of European options that replicates the cost of capturing noarch
the realised variance of an equity index. / GPL-3
r-vbdm 0.0.4 Efficient algorithm for solving discrete mixture regression model for rare vari- linux-
ant association analysis. Uses variational Bayes algorithm to efficiently search 64,
over model space. Outputs an approximate likelihood ratio test as well as vari- osx-
ant level posterior probabilities of association. / GPL-2 64,
win-
64
r-vbsr 0.0.5 Efficient algorithm for solving ultra-sparse regularized regression models us- linux-
ing a variational Bayes algorithm with a spike (l0) prior. Algorithm is solved 64,
on a path, with coordinate updates, and is capable of generating very sparse osx-
models. There are very general model diagnostics for controling type-1 error 64,
included in this package. / GPL-2 win-
64
r-vca 1.4.0 ANOVA and REML estimation of linear mixed models is implemented, once linux-
following Searle et al. (1991, ANOVA for unbalanced data), once making use 64,
of the ‘lme4’ package. The primary objective of this package is to perform osx-
a variance component analysis (VCA) according to CLSI EP05-A3 guide- 64,
line Evaluation of Precision of Quantitative Measurement Procedures (2014). win-
There are plotting methods for visualization of an experimental design, plot- 64
ting random effects and residuals. For ANOVA type estimation two methods
for computing ANOVA mean squares are implemented (SWEEP and quadratic
forms). The covariance matrix of variance components can be derived, which
is used in estimating confidence intervals. Linear hypotheses of fixed effects
and LS means can be computed. LS means can be computed at specific values
of covariables and with custom weighting schemes for factor variables. See
?VCA for a more comprehensive description of the features. / GPL-3
r-vcd 1.4_4 Visualization techniques, data sets, summary and inference procedures aimed noarch
particularly at categorical data. Special emphasis is given to highly extensible
grid graphics. The package was package was originally inspired by the book
Visualizing Categorical Data by Michael Friendly and is now the main support
package for a new book, Discrete Data Analysis with R by Michael Friendly
and David Meyer (2015). / GPL-2


Name Version
r-vcov 0.0.1 Methods for faster extraction (about 5x faster in a few test cases) of variance- noarch
covariance matrices and standard errors from models. Methods in the ‘stats’
package tend to rely on the summary method, which may waste time comput-
ing other summary statistics which are summarily ignored. / GPL-2
r-vcvcomp 1.0.1 Comparison of variance - covariance patterns using relative principal com- noarch
ponent analysis (relative eigenanalysis). Also provides functions to compute
group covariance matrices, distance matrices, and perform proportionality
tests. A working sample on the body shape of cichlid fishes is included. /
GPL-3
r-vdgraph 2.2_2 Uses a modification of the published FORTRAN code in A Computer Program linux-
for Generating Variance Dispersion Graphs by G. Vining, Journal of Qual- 64,
ity Technology, Vol. 25 No. 1 January 1993, to produce variance dispersion osx-
graphs. Also produces fraction of design space plots, and contains data frames 64,
for several minimal run response surface designs. / GPL-2 win-
64
r-vdjgermlines 0.1 Contains variable, diversity, and joining sequences and accompanying func- noarch
tions that enable both the extraction of and comparison between immune V-
D-J genomic segments from a variety of species. Sources include IMGT from
MP Lefranc (2009) <doi:10.1093/nar/gkn838> and Vgenerepertoire from pub-
lication DN Olivieri (2014) <doi:10.1007/s00251-014-0784-3>. / GPL-2
r-vdspcalibration 1.0 Provides statistical methods for the design and analysis of a calibration noarch
study, which aims for calibrating measurements using two different meth-
ods. The package includes sample size calculation, sample selection, re-
gression analysis with error-in measurements and change-point regression.
The method is described in Tian, Durazo-Arvizu, Myers, et al. (2014)
<DOI:10.1002/sim.6235>. / GPL-3
r-vec2dtransf 1.1 A package for applying affine and similarity transformations on vector spatial noarch
data (sp objects). Transformations can be defined from control points or di-
rectly from parameters. If redundant control points are provided Least Squares
is applied allowing to obtain residuals and RMSE. / GPL-2
r-vecsets 1.2.1 The base ‘sets’ tools follow the algebraic definition that each element of a set noarch
must be unique. Since it’s often helpful to compare all elements of two vectors,
this toolset treats every element as unique for counting purposes. For ease of
use, all functions in vecsets have an argument ‘multiple’ which, when set to
FALSE, reverts them to the base::set tools functionality. / LGPL-3
r- 1.8 A 2D statistical analysis is performed, both numerical and graphical, of a set noarch
vecstatgraphs2d of vectors. Since a vector has two components (module and azimuth) vector
analysis is performed in three stages: modules are analyzed by means of linear
statistics, azimuths are analyzed by circular statistics, and the joint analysis of
modules and azimuths is done using density maps that allow detecting another
distribution properties (i.e. anisotropy) and outliers. Tests and circular statis-
tic parameters have associated a full range of graphing: histograms, maps of
distributions, point maps, vector maps, density maps, distribution modules and
azimuths. / GPL-3
r-vegalite 0.6.1 The ‘Vega-Lite’ ‘JavaScript’ framework provides a higher-level grammar for noarch
visual analysis, akin to ‘ggplot’ or ‘Tableau’, that generates complete ‘Vega’
specifications. Functions exist which enable building a valid ‘spec’ from
scratch or importing a previously created ‘spec’ file. Functions also exist to
export ‘spec’ files and to generate code which will enable plots to be embed-
ded in properly configured web pages. The default behavior is to generate an
‘htmlwidget’. / AGPL-3


Name Version
r-vegawidget 0.2.1 ‘Vega’ and ‘Vega-Lite’ parse text in ‘JSON’ notation to render chart- noarch
specifications into ‘HTML’. This package is used to facilitate the rendering. It
also provides a means to interact with signals, events, and datasets in a ‘Vega’
chart using ‘JavaScript’ or ‘Shiny’. / MIT
r-vegdata 0.9.5 Handling of vegetation data from different sources ( Turboveg <http://www. noarch
synbiosys.alterra.nl/turboveg/>; the German national repository <http://www.
vegetweb.de> and others. Taxonomic harmonization (given appropriate tax-
onomic lists, e.g. the German taxonomic standard list GermanSL, <http:
//germansl.infinitenature.org>). / GPL-2
r-vegetarian 1.2 This package computes diversity for community data sets using the methods noarch
outlined by Jost (2006, 2007). While there are differing opinions on the ideal
way to calculate diversity (e.g. Magurran 2004), this method offers the advan-
tage of providing diversity numbers equivalents, independent alpha and beta
diversities, and the ability to incorporate ‘order’ (q) as a continuous measure
of the importance of rare species in the metrics. The functions provided in
this package largely correspond with the equations offered by Jost in the cited
papers. The package computes alpha diversities, beta diversities, gamma di-
versities, and similarity indices. Confidence intervals for diversity measures
are calculated using a bootstrap method described by Chao et al. (2008).
For datasets with many samples (sites, plots), sim.table creates tables of all
pairwise comparisons possible, and for grouped samples sim.groups calculates
pairwise combinations of within- and between-group comparisons. / GPL-2
r-vegperiod 0.2.6 Collection of common methods to determine growing season length in a simple noarch
manner. Start and end dates of the vegetation periods are calculated solely
based on daily mean temperatures and the day of the year. / GPL-3
r-vembedr 0.1.3 A set of functions for generating HTML to embed hosted video in your R noarch
Markdown documents or Shiny applications. / MIT
r-venn 1.7 Draws and displays Venn diagrams up to 7 sets, and any Boolean union of set noarch
intersections. / GPL-2
r-venneuler 1.1_0 Calculates and displays Venn and Euler Diagrams / MPL-1.1 noarch
r-versions 0.3 Installs specified versions of R packages hosted on CRAN and provides noarch
functions to list available versions and the versions of currently installed
packages. These tools can be used to help make R projects and pack-
ages more reproducible. ‘versions’ fits in the narrow gap between the
‘devtools’ install_version() function and the ‘checkpoint’ package. dev-
tools::install_version() installs a stated package version from source files
stored on the CRAN archives. However CRAN does not store binary versions
of packages so Windows users need to have RTools installed and Windows
and OSX users get longer installation times. ‘checkpoint’ uses the Revolution
Analytics MRAN server to install packages (from source or binary) as they
were available on a given date. It also provides a helpful interface to detect the
packages in use in a directory and install all of those packages for a given date.
‘checkpoint’ doesn’t provide install.packages-like functionality however, and
that’s what ‘versions’ aims to do, by querying MRAN. As MRAN only goes
back to 2014-09-17, ‘versions’ can’t install packages archived before this date.
/ BSD_3_clause
r- 0.1 Creates Vertex Similarity matrix of an undirected graph based on the method noarch
vertexsimilarity stated by E. A. Leicht, Petter Holme, AND M. E. J. Newman in their paper
<DOI:10.1103/PhysRevE.73.026120>. / GPL-2


Name Version
r- 0.1.6 Multi-precission library that allows to store and operate with arbitrarily big linux-
verylargeintegers integers without loss of precision. It includes a large list of tools to work with 64,
them, like: - Arithmetic and logic operators - Modular-arithmetic operators - osx-
Computer Number Theory utilities - Probabilistic primality tests - Factoriza- 64,
tion algorithms - Random generators of diferent types of integers. / GPL-3 win-
64
r-vetr 0.2.7 Declarative template-based framework for verifying that objects meet struc- linux-
tural requirements, and auto-composing error messages when they do not. / 64,
GPL-2 osx-
64,
win-
64
r-vfprogression 0.7.1 Realization of published methods to analyze visual field (VF) progres- noarch
sion. Introduction to the plotting methods (designed by author TE)
for VF output visualization. A sample dataset for two eyes, each
with 10 follow-ups is included. The VF analysis methods could be
found in – Musch et al. (1999) <doi:10.1016/S0161-6420(99)90147-
1>, Nouri-Mahdavi et at. (2012) <doi:10.1167/iovs.11-9021>, Schell
et at. (2014) <doi:10.1016/j.ophtha.2014.02.021>, Aptel et al. (2015)
<doi:10.1111/aos.12788>. / GPL-2
r-vgam 1.1_1 An implementation of about 6 major classes of statistical regression mod- linux-
els. At the heart of it are the vector generalized linear and additive model 32,
(VGLM/VGAM) classes, and the book Vector Generalized Linear and Addi- linux-
tive Models: With an Implementation in R (Yee, 2015) <DOI:10.1007/978-1- 64,
4939-2818-7> gives details of the statistical framework and VGAM package. osx-
Currently only fixed-effects models are implemented, i.e., no random-effects 64,
models. Many (150) models and distributions are estimated by maximum like- win-
lihood estimation (MLE) or penalized MLE, using Fisher scoring. VGLMs 32,
can be loosely thought of as multivariate GLMs. VGAMs are data-driven win-
VGLMs (i.e., with smoothing). The other classes are RR-VGLMs (reduced- 64
rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-
column interaction models)—these classes perform constrained and uncon-
strained quadratic ordination (CQO/UQO) models in ecology, as well as con-
strained additive ordination (CAO). Note that these functions are subject to
change; see the NEWS and ChangeLog files for latest changes. / GPL-3
r-vgamdata 1.0_3 Data sets to accompany the VGAM package and the book Vector General- noarch
ized Linear and Additive Models: With an Implementation in R (Yee, 2015)
<DOI:10.1007/978-1-4939-2818-7>. These are used to illustrate vector gen-
eralized linear and additive models (VGLMs/VGAMs), and associated mod-
els (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction
Models, and constrained and unconstrained ordination models in ecology). /
GPL-2


Name Version
r-vgamextra 0.0_1 Extending the functionalities of the ‘VGAM’ package with additional func- linux-
tions and datasets. At present, ‘VGAMextra’ comprises new family func- 64,
tions (ffs) to estimate several time series models by maximum likelihood using osx-
Fisher scoring, unlike popular packages in CRAN relying on optim(), includ- 64,
ing ARMA-GARCH-like models, the Order-(p, d, q) ARIMAX model (non- win-
seasonal), the Order-(p) VAR model, error correction models for cointegrated 64
time series, and ARMA-structures with Student-t errors. For independent data,
new ffs to estimate the inverse- Weibull, the inverse-gamma, the generalized
beta of the second kind and the general multivariate normal distributions are
available. In addition, ‘VGAMextra’ incorporates new VGLM-links for the
mean-function, and the quantile-function (as an alternative to ordinary quan-
tile modelling) of several 1-parameter distributions, that are compatible with
the class of VGLM/VGAM family functions. Currently, only fixed-effects
models are implemented. All functions are subject to change; see the NEWS
for further details on the latest changes. / GPL-2
r- 0.3 This package provides an implementation of Linear discriminant analysis and noarch
vhdclassification quadratic discriminant analysis that works fine in very high dimension (when
there are many more variables than observations). / GPL-2
r-vhica 0.2.4 The Vertical and Horizontal Inheritance Consistence Analysis method is noarch
described in the following publication: VHICA: a new method to dis-
criminate between vertical and horizontal transposon transfer: application
to the mariner family within Drosophila by G. Wallau. et al. (2016)
<DOI:10.1093/molbev/msv341>. The purpose of the method is to detect hor-
izontal transfers of transposable elements, by contrasting the divergence of
transposable element sequences with that of regular genes. / GPL-2
r-vicmodel 0.1.2 The Variable Infiltration Capacity (VIC) model is a macroscale hydrologic linux-
model that solves full water and energy balances, originally developed by 64,
Xu Liang at the University of Washington (UW). The version of VIC source osx-
code used is of 5.0.1 on <https://github.com/UW-Hydro/VIC/>, see Hamman 64,
et al. (2018). Development and maintenance of the current official version win-
of the VIC model at present is led by the UW Hydro (Computational Hy- 64
drology group) in the Department of Civil and Environmental Engineering
at UW. VIC is a research model and in its various forms it has been ap-
plied to most of the major river basins around the world, as well as glob-
ally. If you make use of this model, please acknowledge the appropriate
references listed in the help page of this package or on the references page
<http://vic.readthedocs.io/en/master/Documentation/References/> of the VIC
official documentation website. These should include Liang et al. (1994) plus
any references relevant to the features you are using Reference: Liang, X., D.
P. Lettenmaier, E. F. Wood, and S. J. Burges (1994), A simple hydrologically
based model of land surface water and energy fluxes for general circulation
models, J. Geophys. Res., 99(D7), 14415-14428, <doi:10.1029/94JD00483>.
Hamman et al. (2018) about VIC 5.0.1 also can be considered: Hamman, J.
J., Nijssen, B., Bohn, T. J., Gergel, D. R., and Mao, Y. (2018), The Variable
Infiltration Capacity model version 5 (VIC-5): infrastructure improvements
for new applications and reproducibility, Geosci. Model Dev., 11, 3481-3496,
<doi:10.5194/gmd-11-3481-2018>. / GPL-3
r-vietnamcode 0.1.1 Converts Vietnam’s provinces’ names and ID across different formats. Han- noarch
dles diacritics and different spellings. / GPL-3


Name Version
r-vif 1.0 This package implements a fast regression algorithm for building linear model noarch
for large data as defined in the paper VIF-Regression: A Fast Regression Algo-
rithm for Large Data (2011), Journal of the American Statistical Association,
Vol. 106, No. 493: 232-247 by Dongyu Lin, Dean P. Foster, and Lyle H.
Ungar. / GPL-2
r-vifcp 1.2 Contains a function to support the following paper: Xiaoping Shi, Xiang- linux-
Sheng Wang, Dongwei Wei, Yuehua Wu (2016), <DOI:10.1007/s00180-015- 64,
0587-5>, A sequential multiple change-point detection procedure via VIF re- osx-
gression, Computational Statistics, 31(2): 671-691. / LGPL-3 64,
win-
64
r-vigor 1.0 Conducts linear regression using variational Bayesian inference, particularly linux-
optimized for genome-wide association mapping and whole-genome predic- 64,
tion which use a number of DNA markers as the explanatory variables. Pro- osx-
vides seven regression models which select the important variables (i.e., the 64,
variables related to response variables) among the given explanatory variables win-
in different ways (i.e., model structures). / MIT 64
r-violinmplot 0.2.1 A lattice violin-plot is overlayed with the arithmetic mean and standard devia- noarch
tion. / GPL-2
r-viopoints 0.2_1 viopoints draws one dimensional scatter plots with jitter using kernel density noarch
estimates in a similar way to violin plots. / GPL-2
r-vipor 0.4.5 Generate a violin point plot, a combination of a violin/histogram plot and a noarch
scatter plot by offsetting points within a category based on their density using
quasirandom noise. / GPL-2
r-viridis 0.5.1 Implementation of the ‘viridis’ - the default -, ‘magma’, ‘plasma’, ‘inferno’, linux-
and ‘cividis’ color maps for ‘R’. ‘viridis’, ‘magma’, ‘plasma’, and ‘inferno’ 32,
are ported from ‘matplotlib’ <http://matplotlib.org/>, a popular plotting library linux-
for ‘python’. ‘cividis’, was developed by Jamie R. Nuñez and Sean M. Colby. 64,
These color maps are designed in such a way that they will analytically be noarch,
perfectly perceptually-uniform, both in regular form and also when converted osx-
to black-and-white. They are also designed to be perceived by readers with 64,
the most common form of color blindness (all color maps in this package) and win-
color vision deficiency (‘cividis’ only). / MIT file LICENSE 32,
win-
64
r-viridislite 0.3.0 Implementation of the ‘viridis’ - the default -, ‘magma’, ‘plasma’, ‘inferno’, linux-
and ‘cividis’ color maps for ‘R’. ‘viridis’, ‘magma’, ‘plasma’, and ‘inferno’ 32,
are ported from ‘matplotlib’ <http://matplotlib.org/>, a popular plotting library linux-
for ‘python’. ‘cividis’, was developed by Jamie R. Nuñez and Sean M. Colby. 64,
These color maps are designed in such a way that they will analytically be noarch,
perfectly perceptually-uniform, both in regular form and also when converted osx-
to black-and-white. They are also designed to be perceived by readers with 64,
the most common form of color blindness (all color maps in this package) win-
and color vision deficiency (‘cividis’ only). This is the ‘lite’ version of the 32,
more complete ‘viridis’ package that can be found at <https://cran.r-project. win-
org/package=viridis>. / MIT file LICENSE 64
r-virustotal 0.2.1 Use VirusTotal, a Google service that analyzes files and URLs for viruses, noarch
worms, trojans etc., provides category of the content hosted by a domain from
a variety of prominent services, provides passive DNS information, among
other things. See <http://www.virustotal.com> for more information. / MIT


Name Version
r-visielse 1.2.1 A graphical tool designed to visualize and to give an overview of behavioral noarch
observations realized on individuals or groups. Visualization of raw data dur-
ing experimental observations of the realization of a procedure. It graphically
presents an overview of individuals and group actions usually acquired from
timestamps during video recorded sessions. Options of the package allow
adding graphical information as statistical indicators (mean, standard devia-
tion, quantile or statistical test) but also for each action green or black zones
providing visual information about the accuracy of the realized actions. /
AGPL-3
r-visnetwork 2.0.6 Provides an R interface to the ‘vis.js’ JavaScript charting library. It allows an linux-
interactive visualization of networks. / MIT file LICENSE 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-visreg 2.5_1 Provides a convenient interface for constructing plots to visualize the fit of noarch
regression models arising from a wide variety of models in R (‘lm’, ‘glm’,
‘coxph’, ‘rlm’, ‘gam’, ‘locfit’, ‘lmer’, ‘randomForest’, etc.) / GPL-3
r-visualize 4.3.0 Graphs the pdf or pmf and highlights what area or probability is present in noarch
user defined locations. Visualize is able to provide lower tail, bounded, upper
tail, and two tail calculations. Supports strict and equal to inequalities. Also
provided on the graph is the mean and variance of the distribution. / MIT
r-vita 1.0.0 Implements the novel testing approach by Janitza et al.(2015) <http:// linux-
nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19-epub-25587-4> for the 64,
permutation variable importance measure in a random forest and the PIMP- osx-
algorithm by Altmann et al.(2010) <doi:10.1093/bioinformatics/btq134>. Jan- 64,
itza et al.(2015) <http://nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19- win-
epub-25587-4> do not use the standard permutation variable importance but 64
the cross-validated permutation variable importance for the novel test ap-
proach. The cross-validated permutation variable importance is not based on
the out-of-bag observations but uses a similar strategy which is inspired by the
cross-validation procedure. The novel test approach can be applied for clas-
sification trees as well as for regression trees. However, the use of the novel
testing approach has not been tested for regression trees so far, so this routine
is meant for the expert user only and its current state is rather experimental. /
GPL-2
r-vitality 1.3 Provides fitting routines for four versions of the Vitality family of mortality noarch
models. / GPL-2
r-vkr 0.1 Provides an interface to the VK API <https://vk.com/dev/methods>. VK noarch
<https://vk.com/> is the largest European online social networking service,
based in Russia. / GPL-3


Name Version
r-vlad 0.2.0 Contains functions to set up risk-adjusted quality control charts in health care. linux-
For the variable life adjusted display (VLAD) proposed by Lovegrove et al. 64,
(1997) <doi:10.1016/S0140-6736(97)06507-0> signaling rules derived in Wit- osx-
tenberg et al. (2018) <doi: 10.1002/sim.7647> are implemented. Additionally, 64,
for the risk-adjusted cumulative sum chart based on log-likelihood ratio statis- win-
tic introduced by Steiner et al. (2000) <doi:10.1093/biostatistics/1.4.441> av- 64
erage run length and control limits can be computed. / GPL-2
r-vlf 1.0 Using frequency matrices, very low frequency variants (VLFs) are assessed for noarch
amino acid and nucleotide sequences. The VLFs are then compared to see if
they occur in only one member of a species, singleton VLFs, or if they occur in
multiple members of a species, shared VLFs. The amino acid and nucleotide
VLFs are then compared to see if they are concordant with one another. Amino
acid VLFs are also assessed to determine if they lead to a change in amino acid
residue type, and potential changes to protein structures. / GPL-3
r-vlmc 1.4_3_1
Functions, Classes & Methods for estimation, prediction, and simulation linux-
(bootstrap) of Variable Length Markov Chain (‘VLMC’) Models. / GPL-2 64,
osx-
64,
win-
64
r-vmask 1.0 The cumulative sum (CUSUM) control chart is considered to be an alterna- noarch
tive or complementary to Shewhart control charts in statistical process con-
trol (SPC) applications, owing to its higher sensitivity to small shifts in the
process mean. It utilizes all the available data rather than the last few ones
used in Shewhart control charts for quick decision making. V-mask is a tradi-
tional technique for separating meaningful data from unusual circumstances in
a Cumulative Sum (CUSUM) control chart; for see details about v-mask see
Montgomery (1985, ISBN:978-0471656319). The mask is a V-shaped overlay
placed on the CUSUM chart so that one arm of the V lines up with the slope
of data points, making it easy to see data points that lie outside the slope and
to determine whether these points should be discarded as random events, or
treated as a performance trend that should be addressed. But, complex compu-
tations is one disadvantage V-mask method for detect small changes in mean
using CUSUM control chart. Package ‘vMask’ can help to the applied users
to overcome this challenge by considering six different methods which each
of them are based on different information. / LGPL-3
r-vnm 7.1 Provide tools for finding multiple-objective optimal designs for estimating the linux-
shape of dose-response, the ED50 (the dose producing an effect midway be- 64,
tween the expected responses at the extreme doses) and the MED (the mini- osx-
mum effective dose level) for the 2,3,4-parameter logistic models and for eval- 64,
uating its efficiencies for the three objectives. The acronym VNM stands for win-
V-algorithm using Newton Raphson method to search multiple-objective opti- 64
mal design. / GPL-2


Name Version
r-vocaldia 0.8.2 Create adjacency matrices of vocalisation graphs from dataframes containing noarch
sequences of speech and silence intervals, transforming these matrices into
Markov diagrams, and generating datasets for classification of these diagrams
by ‘flattening’ them and adding global properties (functionals) etc. Vocalisa-
tion diagrams date back to early work in psychiatry (Jaffe and Feldstein, 1970)
and social psychology (Dabbs and Ruback, 1987) but have only recently been
employed as a data representation method for machine learning tasks includ-
ing meeting segmentation (Luz, 2012) <doi:10.1145/2328967.2328970> and
classification (Luz, 2013) <doi:10.1145/2522848.2533788>. / GPL-3
r-volesti 1.0.3 Provides an R interface for ‘volesti’ C package. ‘volesti’ computes estima- linux-
tions of volume of polytopes given by a set of points or linear inequalities or 64,
Minkowski sum of segments (zonotopes). There are two algorithms for vol- osx-
ume estimation (I.Z. Emiris and V. Fisikopoulos (2014) <arXiv:1312.2873> 64,
and B. Cousins, S. Vempala (2016) <arXiv:1409.6011>) as well as algo- win-
rithms for sampling, rounding and rotating polytopes. Moreover, ‘volesti’ pro- 64
vides algorithms for estimating copulas (L. Cales, A. Chalkis, I.Z. Emiris, V.
Fisikopoulos (2018) <arXiv:1803.05861>). / LGPL-3
r-volleystat 0.2.0 Volleyball match statistics of the German volleyball first division league (sea- noarch
sons 2013/2014 to 2018/2019). The data has been collected from the offi-
cial volleyball first division homepage (<www.volleyball-bundesliga.de>) and
contains information on teams, staff, sets, matches, and player-in-match statis-
tics (extracted automatically from the official match reports). / CC0
r-vortexrdata 1.0.5 Contains selected data from two publications, Campbell ‘et’ ‘al’. (2016) noarch
<DOI:10.1080/14486563.2015.1028486> and ‘Pacioni’ ‘et’ ‘al’. (2017)
<DOI:10.1071/PC17002>. The data is provided both as raw outputs from the
population viability analysis software ‘Vortex’ and packaged as R objects. The
R package ‘vortexR’ uses the raw data provided here to illustrate its function-
ality of parsing raw ‘Vortex’ output into R objects. / GPL-3
r-vote 1.1_0 Counting election votes and determining election results by different methods, noarch
including the single transferable vote, approval, score and plurality methods. /
GPL-2
r-votesys 0.1.1 Various methods to count ballots in voting systems are provided. Functions to noarch
check validity of ballots are also provided to ensure flexibility. / GPL-3
r-vottrans 1.0 Calculates voter transitions comparing two elections, using the function noarch
solve.QP() in package ‘quadprog’. / GPL-3
r-vowels 1.2_2 Procedures for the manipulation, normalization, and plotting of phonetic and noarch
sociophonetic vowel formant data. vowels is the backend for the NORM web-
site. / GPL-3
r-voxr 0.5.1 Tools for tree crown structure description based on T-LiDAR data voxelisation noarch
/ GPL (>= 2.0)
r-vrmlgen 1.4.9 vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes, para- noarch
metric functions and height maps in web-formats like the Virtual Reality
Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format. /
GPL-2
r-vrtest 0.97 A collection of statistical tests for martingale difference hypothesis / GPL-2 noarch
r-vstsr 1.0.0 Implementation of Visual Studio Team Services <https://www.visualstudio. noarch
com/team-services/> API calls. It enables the extraction of information about
repositories, build and release definitions and individual releases. It also helps
create repositories and work items within a project without logging into Vi-
sual Studio. There is the ability to use any API service with a shell for any
non-predefined call. / GPL-2


Name Version
r-vudc 1.1 Contains functions for visualization univariate data: ccdplot and qddplot. / noarch
GPL-2
r-vwr 0.3.0 Functions and data for use in visual word recognition research: Computa- noarch
tion of neighbors (Hamming and Levenshtein distances), average distances to
neighbors (e.g., OLD20), and Coltheart’s N. Also includes the LD1NN algo-
rithm to detect bias in the composition of a lexical decision task. Most of the
functions support parallel execution. Supplies wordlists for several languages.
Uses the string distance functions from the stringdist package by Mark van der
Loo. / GPL-3
r- 0.1_6 R interface to a W3C Markup Validation service. See <http://validator.w3. noarch
w3cmarkupvalidator org/> for more information. / GPL-2
r-waffect 1.2 waffect (pronounced ‘double-u affect’ for ‘weighted affectation’) is a package linux-
to simulate phenotypic (case or control) datasets under a disease model H1 64,
such that the total number of cases is constant across all the simulations (the osx-
constrain in the title). The package also makes it possible to generate pheno- 64,
types in the case of more than two classes, so that the number of phenotypes win-
belonging to each class is constant across all the simulations. waffect is used to 64
assess empirically the statistical power of Genome Wide Association studies.
/ GPL-3
r-wahc 1.0 Fit the fixed effect panel data model with heteroskedasticity and autocorrela- noarch
tion correction. / GPL-3
r-waiter 0.0.1 Full screen splash loading screens for ‘Shiny’. / MIT noarch
r-walkscoreapi 1.2 A collection of functions to perform the Application Programming Interface noarch
(API) calls associated with the Walk Score website (www.walkscore.com)
within the R environment. These functions can be used to query the Walk
Score and Transit Score database for a wide variety of information using R
scripts. This package includes the simple Walk Score and Transit Score API
calls, which return the scores associated with an input location, as well as calls
which return some data used to calculate the scores. These functions are es-
pecially useful for mass data collection and gathering Walk Score and Transit
Score values for large lists of locations. / GPL-2
r-wamasim 1.0.0 The outcome of various rehabilitation strategies for water distribution systems noarch
can be modeled with the Water Management Simulator (WaMaSim). Pipe
breaks and the corresponding damage and rehabilitation costs are simulated.
It is mainly intended to be used as educational tool for the Water Infrastructure
Experimental and Computer Laboratory at ETH Zurich, Switzerland. / GPL-3
r-wand 0.5.0 ‘MIME’ types are shorthand descriptors for file contents and can be deter- noarch
mined from magic bytes in file headers, file contents or intuited from file ex-
tensions. Tools are provided to perform curated magic tests as well as mapping
‘MIME’ types from a database of over 1,500 extension mappings. / MIT
r-warn 1.2_3 This estimates precise weaning ages for a given skeletal population by analyz- noarch
ing the stable nitrogen isotope ratios of them. Bone collagen turnover rates es-
timated anew and the approximate Bayesian computation (ABC) were adopted
in this package. / GPL-3


Name Version
r-washdata 0.1.2 Urban water and sanitation survey dataset collected by Water and Sanitation noarch
for the Urban Poor (WSUP) with technical support from Valid International.
These citywide surveys have been collecting data allowing water and sanitation
service levels across the entire city to be characterised, while also allowing
more detailed data to be collected in areas of the city of particular interest.
These surveys are intended to generate useful information for others working
in the water and sanitation sector. Current release version includes datasets
collected from a survey conducted in Dhaka, Bangladesh in March 2017. This
survey in Dhaka is one of a series of surveys to be conducted by WSUP in
various cities in which they operate including Accra, Ghana; Nakuru, Kenya;
Antananarivo, Madagascar; Maputo, Mozambique; and, Lusaka, Zambia. This
package will be updated once the surveys in other cities are completed and
datasets have been made available. / CC0
r-washer 0.1.2 Time series outlier detection by mean of non parametric test. Outlier detec- noarch
tion regarding two methodologies: single time series variability (a vector) and
grouped similar time series (a data frame). Andrea Venturini(2011) Statistica-
Universita’ Bologna, Vol.71, pp.329-344. / GPL-2
r-waterfall 1.0.2 Provides support for creating waterfall charts in R using both traditional base noarch
and lattice graphics. / BSD_2_clause
r-wateryeartype 1.0.1 Provides Water Year Hydrologic Classification Indices based on measured noarch
unimpaired runoff (in million acre-feet). Data is provided by California De-
partment of Water Resources and subject to revision. / MIT
r-waved 1.2 Makes available code necessary to reproduce figures and tables in papers on noarch
the WaveD method for wavelet deconvolution of noisy signals as presented in
The WaveD Transform in R, Journal of Statistical Software Volume 21, No. 3,
2007. / GPL-3
r-wavefunction 1.0.0 Real probability distributions can be represented as the square of an orthogonal noarch
sum in the Hermite basis. This representation is formally similar to the rep-
resentation of quantum mechanical states as wave functions, whose squared
modulus is a probability density. This is described in more detail in Wave
function representation of probability distributions, by Madeleine B. Thomp-
son <arXiv:1712.07764>. This package provides a reference implementation
of the technique. / Apache License (== 2.0)
r-waveletcomp 1.1 Wavelet analysis and reconstruction of time series, cross-wavelets and phase- noarch
difference (with filtering options), significance with simulation algorithms. /
GPL-2
r-wavelets 0.3_0.1
Contains functions for computing and plotting discrete wavelet transforms linux-
(DWT) and maximal overlap discrete wavelet transforms (MODWT), as well 64,
as their inverses. Additionally, it contains functionality for computing and osx-
plotting wavelet transform filters that are used in the above decompositions as 64,
well as multiresolution analyses. / GPL-2 win-
64
r-waveslim 1.7.5.1Basic wavelet routines for time series (1D), image (2D) and array (3D) anal- linux-
ysis. The code provided here is based on wavelet methodology developed in 64,
Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual- osx-
tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as 64,
implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002). win-
All figures in chapters 4-7 of GSW (2001) are reproducible using this package 64
and R code available at the book website(s) below. / BSD_3_clause


Name Version
r-wavethresh 4.6.8 Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondec- linux-
imated transforms, wavelet packet transforms, nondecimated wavelet packet 64,
transforms, multiple wavelet transforms, complex-valued wavelet transforms, osx-
wavelet shrinkage for various kinds of data, locally stationary wavelet time se- 64,
ries, nonstationary multiscale transfer function modeling, density estimation. win-
/ GPL-2 64
r-wbs 1.4 Provides efficient implementation of the Wild Binary Segmentation and Bi- linux-
nary Segmentation algorithms for estimation of the number and locations of 64,
multiple change-points in the piecewise constant function plus Gaussian noise osx-
model. / GPL-2 64,
win-
64
r-wce 1.0.2 A flexible method for modeling cumulative effects of time-varying exposures, noarch
weighted according to their relative proximity in time, and represented by
time-dependent covariates. The current implementation estimates the weight
function in the Cox proportional hazards model. The function that assigns
weights to doses taken in the past is estimated using cubic regression splines.
/ GPL-2
r-wcorr 1.9.1 Calculates Pearson, Spearman, polychoric, and polyserial correlation coeffi- linux-
cients, in weighted or unweighted form. The package implements tetrachoric 64,
correlation as a special case of the polychoric and biserial correlation as a spe- osx-
cific case of the polyserial. / GPL-2 64,
win-
64
r-wcq 0.2 The package contains the WCQ method for detection of QTL effects in a small noarch
mapping population. It also contains implementation of the Chen-Qin two-
sample and one-sample test of means. / GPL-3
r-wdi 2.6.0 Search, extract and format data from the World Bank’s World Development noarch
Indicators. / GPL-3
r-wdm 0.2.1 Provides efficient implementations of weighted dependence measures and re- linux-
lated asymptotic tests for independence. Implemented measures are the Pear- 64,
son correlation, Spearman’s rho, Kendall’s tau, Blomqvist’s beta, and Hoeffd- osx-
ing’s D; see, e.g., Nelsen (2006) <doi:10.1007/0-387-28678-0> and Hollander 64,
et al. (2015, ISBN:9780470387375). / MIT win-
64
r-weatherdata 0.5.0 Functions that help in fetching weather data from websites. Given a location linux-
and a date range, these functions help fetch weather data (temperature, pres- 32,
sure etc.) for any weather related analysis. / GPL linux-
64,
osx-
64,
win-
32,
win-
64
r-weathermetrics 1.2.2 Functions to convert between weather metrics, including conversions for met- noarch
rics of temperature, air moisture, wind speed, and precipitation. This package
also includes functions to calculate the heat index from air temperature and air
moisture. / GPL-2
r-webchem 0.4.0 Chemical information from around the web. This package interacts with a noarch
suite of web APIs for chemical information. / MIT


Name Version
r-webddx 0.1.0 Freely available online differential-diagnosis generating tools are changing noarch
clinical medicine and biomedical research. With webddx, useRs can gener-
ate differential diagnosis lists given a set of symptoms. The web tools would
likely be directly used in clinical practice, but programmatic interaction and
data manipulation can sharply increase efficiency and reproducibility of re-
search in clinical informatics. Relevant visualizations can also be created with
webddx. / GPL-3
r-webex 0.9.1 Functions for easily creating interactive web pages using ‘R Markdown’ that noarch
students can use in self-guided learning. / CC BY-SA 4.0
r-webp 1.0 Lossless webp images are 26% smaller in size compared to PNG. Lossy webp linux-
images are 25-34% smaller in size compared to JPEG. This package reads 64,
and writes webp images into a 3 (rgb) or 4 (rgba) channel bitmap array using osx-
conventions from the ‘jpeg’ and ‘png’ packages. / MIT 64,
win-
64
r-websearchr 0.0.3 Functions that allow for accessing domains and a number of search engines. / noarch
MIT
r-webshot 0.5.1 Takes screenshots of web pages, including Shiny applications and R Mark- linux-
down documents. / GPL-2 64,
noarch,
osx-
64,
win-
32,
win-
64
r-websocket 1.1.0 Provides a ‘WebSocket’ client interface for R. ‘WebSocket’ is a protocol linux-
for low-overhead real-time communication: <https://en.wikipedia.org/wiki/ 64,
WebSocket>. / GPL-2 osx-
64,
win-
64
r-webutils 1.0 Parses http request data in application/json, multipart/form-data, or linux-
application/x-www-form-urlencoded format. Includes example of hosting and 64,
parsing html form data in R using either ‘httpuv’ or ‘Rhttpd’. / MIT osx-
64,
win-
64
r-weco 1.2 Western Electric Company Rules (WECO) have been widely used for She- linux-
whart control charts in order to increase the sensitivity of detecting assignable 64,
causes of process change. This package implements eight commonly used osx-
WECO rules and allow to apply the combination of these individual rules for 64,
detecting the deviation from a stable process. The package also provides a win-
web-based graphical user interface to help users conduct the analysis. / GPL-3 64
r-wee 1.0 Secondary analysis of case-control studies using a weighted estimating equa- noarch
tion (WEE) approach: logistic regression for binary secondary outcomes, lin-
ear regression and quantile regression for continuous secondary outcomes. /
GPL-2


Name Version
r-weibullness 1.19.8Performs a goodness-of-fit test of Weibull distribution (weibullness test) and noarch
provides the maximum likelihood estimates of the three-parameter Weibull
distribution. Note that the threshold parameter is estimated based on the
correlation from the Weibull plot. For more details, see Park (2018)
<doi:10.1155/2018/6056975>. This work was supported by the National Re-
search Foundation of Korea (NRF) grant funded by the Korea government (No.
NRF-2017R1A2B4004169). / GPL-2 | GPL-3
r-weibullr 1.0.10Life data analysis in the graphical tradition of Waloddi Weibull. Methods linux-
derived from Robert B. Abernethy (2008, ISBN 0-965306-3-2), Wayne Nel- 64,
son (1982, ISBN: 9780471094586) <DOI:10.1002/0471725234>, William Q. osx-
Meeker and Lois A. Escobar (1998, ISBN: 1-471-14328-6), John I. McCool, 64,
(2012, ISBN: 9781118217986) <DOI:10.1002/9781118351994>. / GPL-3 win-
64
r- 1.0 Weighted descriptive statistics is the discipline of quantitatively describing the
noarch
weighted.desc.stat main features of real-valued fuzzy data which usually given from a fuzzy pop-
ulation. One can summarize this special kind of fuzzy data numerically or
graphically using this package. To interpret some of the properties of one or
several sets of real-valued fuzzy data, numerically summarize is possible by
some weighted statistics which are designed in this package such as mean,
variance, covariance and correlation coefficent. Also, graphically interpreta-
tion can be given by weighted histogram and weighted scatter plot using this
package to describe properties of real-valued fuzzy data set. / LGPL-3
r- 1.0 This packages contains the Weighted Portmanteau Tests as described in New noarch
weightedporttest Weighted Portmanteau Statistics for Time Series Goodness-of-Fit Testing’ ac-
cepted for publication by the Journal of the American Statistical Association.
/ GPL-3
r-weightedroc 2018.10.1
Fast computation of Receiver Operating Characteristic (ROC) curves and Area noarch
Under the Curve (AUC) for weighted binary classification problems (weights
are example-specific cost values). / GPL-3
r-weightquant 1.0 Estimation of observation-specific weights for incomplete longitudinal data noarch
and bootstrap procedure for weighted quantile regressions. / GPL (>= 2.0)
r-weirs 0.25 Provides computational support for flow over weirs, such as sharp-crested, noarch
broad-crested, and embankments. Initially, the package supports broad- and
sharp-crested weirs. / GPL-2
r-welchadf 0.3.2 Implementation of Johansen’s general formulation of Welch-James’s statistic noarch
with Approximate Degrees of Freedom, which makes it suitable for testing any
linear hypothesis concerning cell means in univariate and multivariate mixed
model designs when the data pose non-normality and non-homogeneous vari-
ance. Some improvements, namely trimmed means and Winsorized variances,
and bootstrapping for calculating an empirical critical value, have been added
to the classical formulation. The code departs from a previous SAS imple-
mentation by L.M. Lix and H.J. Keselman, available at <http://supp.apa.org/
psycarticles/supplemental/met_13_2_110/SAS_Program.pdf> and published
in Keselman, H.J., Wilcox, R.R., and Lix, L.M. (2003) <DOI:10.1111/1469-
8986.00060>. / LGPL-3
r-wesanderson 0.3.6 Palettes generated mostly from ‘Wes Anderson’ movies. / MIT noarch


r-wfe 1.9.1 Provides a computationally efficient way of fitting weighted linear fixed effects linux-
estimators for causal inference with various weighting schemes. Weighted lin- 64,
ear fixed effects estimators can be used to estimate the average treatment ef- osx-
fects under different identification strategies. This includes stratified random- 64,
ized experiments, matching and stratification for observational studies, first win-
differencing, and difference-in-differences. The package implements methods 64
described in Imai and Kim (2017) When should We Use Linear Fixed Effects
Regression Models for Causal Inference with Longitudinal Data?, available at
<https://imai.fas.harvard.edu/research/FEmatch.html>. / GPL-2
r-wfg 0.1 Implementation of Weighted Fast Greedy algorithm for community detection noarch
in networks with mixed types of attributes. / GPL-2
r-wgteff 0.1.2 Functions for determining the effect of data weights on the variance of survey noarch
data: users will load a data set which has a weights column, and the pack-
age will calculate the design effect (DEFF), weighting loss, root design effect
(DEFT), effective sample size (ESS), and/or weighted margin of error. / GPL-2
r-wheatmap 0.1.0 Builds complex plots, heatmaps in particular, using natural semantics. Bigger noarch
plots can be assembled using directives such as ‘LeftOf’, ‘RightOf’, ‘TopOf’,
and ‘Beneath’ and more. Other features include clustering, dendrograms and
integration with ‘ggplot2’ generated grid objects. This package is particularly
designed for bioinformaticians to assemble complex plots for publication. /
GPL-3
r-whereami 0.1.8.1Robust and reliable functions to return informative outputs to console with the noarch
run or source location of a command. This can be from the ‘RScript’/R ter-
minal commands or ‘RStudio’ console, source editor, ‘Rmarkdown’ document
and a Shiny application. / MIT
r- 0.1.2 White Box Cluster Algorithm Design allows you to create Representative noarch
whiboclustering based cluster algorithm by using reusable components. This way one can
recreate already available cluster algorithms (i.e. K-Means, K-Means, PAM)
but also create new cluster algorithms not available in the literature or any other
software. For more information see papers <doi:10.1007/s10462-009-9133-6>
and <doi:10.1016/j.datak.2012.03.005>. / GPL-3
r-whisker 0.3_2 logicless templating, reuse templates in many programming languages includ- linux-
ing R / GPL-3 32,
linux-
64,
noarch,
osx-
64,
win-
32,
win-
64
r-whitechapelr 0.3.0 Provides a set of functions to make tracking the hidden movements of the noarch
‘Jack’ player easier. By tracking every possible path Jack might have trav-
eled from the point of the initial murder including special movement such as
through alleyways and via carriages, the police can more accurately narrow
the field of their search. Additionally, by tracking all possible hideouts from
round to round, rounds 3 and 4 should have a vastly reduced field of search. /
MIT


Name Version
r-whitening 1.1.1 Implements the whitening methods (ZCA, PCA, Cholesky, ZCA-cor, and noarch
PCA-cor) discussed in Kessy, Lewin, and Strimmer (2018) Optimal whiten-
ing and decorrelation, <doi:10.1080/00031305.2016.1277159>, as well as the
whitening approach to canonical correlation analysis allowing negative canon-
ical correlations described in Jendoubi and Strimmer (2019) A whitening ap-
proach to probabilistic canonical correlation analysis for omics data integra-
tion, <doi:10.1186/s12859-018-2572-9>. / GPL-3
r-whoami 1.3.0 Look up the username and full name of the current user, the current user’s noarch
email address and ‘GitHub’ username, using various sources of system and
configuration information. / MIT
r-whoapi 0.1.2 Retrieve data from the ‘Whoapi’ (https://whoapi.com) store of domain in- noarch
formation, including a domain’s geographic location, registration status and
search prominence. / MIT
r-whopgenome 0.9.7 Provides very fast access to whole genome, population scale variation data linux-
from VCF files and sequence data from FASTA-formatted files. It also reads 64,
in alignments from FASTA, Phylip, MAF and other file formats. Provides osx-
easy-to-use interfaces to genome annotation from UCSC and Bioconductor 64,
and gene ontology data from AmiGO and is capable to read, modify and write win-
PLINK .PED-format pedigree files. / GPL-2 64
r-wicket 0.4.0 Utilities to generate bounding boxes from ‘WKT’ (Well-Known Text) objects linux-
and R data types, validate ‘WKT’ objects and convert object types from the 64,
‘sp’ package into ‘WKT’ representations. / MIT osx-
64,
win-
64
r-widgetframe 0.3.1 Provides two functions ‘frameableWidget()’, and ‘frameWidget()’. The noarch
‘frameableWidget()’ is used to add extra code to a ‘htmlwidget’ which allows
is to be rendered correctly inside a responsive ‘iframe’. The ‘frameWidget()’
is a ‘htmlwidget’ which displays content of another ‘htmlwidget’ inside a re-
sponsive ‘iframe’. These functions allow for easier embedding of ‘htmlwid-
gets’ in content management systems such as ‘wordpress’, ‘blogger’ etc. They
also allow for separation of widget content from main HTML content where
CSS of the main HTML could interfere with the widget. / MIT
r-wikibooks 0.2 The german Wikibook GNU R introduces R to new users. This package is noarch
a collection of functions and datas used in the german WikiBook GNU R /
GPL-2
r-wikifacts 0.1.0 Creates messages containing random facts from the Wikipedia homepage. In- noarch
tended to keep users interested during long waiting periods. / CC0
r-wikipediar 1.1 Provides an interface to the Wikipedia web application programming inter- noarch
face (API), using internet connexion.Three functions provide details for a spe-
cific Wikipedia page : all links that are present, all pages that link to, all the
contributions (revisions for main pages, and discussions for talk pages). Two
functions provide details for a specific user : all contributions, and general
information (as name, gender, rights or groups). It provides additional in-
formation compared to others packages, as WikipediR. It does not need login.
The multiplex network that can be constructed from the results of the functions
of WikipediaR can be modeled as Stochastic Block Model as in Barbillon P.,
Donnet, S., Lazega E., and Bar-Hen A. : Stochastic Block Models for Multi-
plex networks: an application to networks of researchers, ArXiv 1501.06444,
http://arxiv.org/abs/1501.06444. / GPL (> 2)


Name Version
r-wikipedir 1.5.0 A wrapper for the MediaWiki API, aimed particularly at the Wikimedia ‘pro- noarch
duction’ wikis, such as Wikipedia. It can be used to retrieve page text, infor-
mation about users or the history of pages, and elements of the category tree. /
MIT
r-wilcoxcv 1.0_2 This package provides functions to perform fast variable selection based on noarch
the Wilcoxon rank sum test in the cross-validation or Monte-Carlo cross-
validation settings, for use in microarray-based binary classification. / GPL-2
r-wildcard 1.1.0 Generate data frames from templates. / GPL-3 noarch
r-wildpoker 1.1 Provides insight into how the best hand for a poker game changes based on noarch
the game dealt, players who stay in until the showdown and wildcards added
to the base game. At this time the package does not support player tactics, so
draw poker variants are not included. / GPL-3
r-wingui 0.2 Helps for interfacing with the operating system particularly for Windows. / linux-
GPL-2 | GPL-3 | MIT 64,
osx-
64,
win-
64
r-wisam 0.2.8 In the course of a genome-wide association study, the situation often arises noarch
that some phenotypes are known with greater precision than others. It could
be that some individuals are known to harbor more micro-environmental vari-
ance than others. In the case of inbred strains of model organisms, it could
be the case that more organisms were observed from some strains than oth-
ers, so the strains with more organisms have better-estimated means. Package
‘wISAM’ handles this situation by allowing for weighting of each observa-
tion according to residual variance. Specifically, the ‘weight’ parameter to the
function conduct_scan() takes the precision of each observation (one over the
variance). / GPL-3
r-withr 2.1.2 A set of functions to run code ‘with’ safely and temporarily modified global linux-
state. Many of these functions were originally a part of the ‘devtools’ package, 32,
this provides a simple package with limited dependencies to provide access to linux-
these functions. / GPL (>= 2) 64,
noarch,
osx-
64,
win-
32,
win-
64
r-wkb 0.3_0 Utility functions to convert between the ‘Spatial’ classes specified by the noarch
package ‘sp’, and the well-known binary ‘(WKB)’ representation for geom-
etry specified by the Open Geospatial Consortium. Supports ‘Spatial’ objects
of class ‘SpatialPoints’, ‘SpatialPointsDataFrame’, ‘SpatialLines’, ‘SpatialLi-
nesDataFrame’, ‘SpatialPolygons’, and ‘SpatialPolygonsDataFrame’. Sup-
ports ‘WKB’ geometry types ‘Point’, ‘LineString’, ‘Polygon’, ‘MultiPoint’,
‘MultiLineString’, and ‘MultiPolygon’. Includes extensions to enable creation
of maps with ‘TIBCO Spotfire’. / BSD_3_clause
r-wktmo 1.0.5 Converts weekly data to monthly data. Users can use three types of week noarch
formats: ISO week, epidemiology week (epi week) and calendar date. / GPL-
2


Name Version
r-wlreg 1.0.0 Use various regression models for the analysis of win loss endpoints adjusting linux-
for non-binary and multivariate covariates. / GPL-2 64,
osx-
64,
win-
64
r-wmdb 1.0 Distance discriminant analysis method is one of classification methods ac- noarch
cording to multiindex performance parameters.However,the traditional Maha-
lanobis distance discriminant method treats with the importance of all param-
eters equally,and exaggerates the role of parameters which changes a little.The
weighted Mahalanobis distance is used in discriminant analysis method to dis-
tinguish the importance of each parameter.In the concrete application,firstly
based on the principal component analysis scheme,a new group of parameters
and their corresponding percent contributions of the parameters are calculated
,and the weighted matrix is regarded as the diagonal matrix of the contribu-
tions rates.Setting data to standardization,then the weighted Mahalanobis dis-
tance can be calculated.Besides the methods metioned above,bayes method is
also given. / GPL-2
r-wmwssp 0.4.0 Calculates the minimal sample size for the Wilcoxon-Mann-Whitney test that noarch
is needed for a given power and two sided type I error rate. The method works
for metric data with and without ties, count data, ordered categorical data,
and even dichotomous data. But data is needed for the reference group to
generate synthetic data for the treatment group based on a relevant effect. For
details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-
Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to
appear. / GPL-3
r-wnl 0.5.1 This is a set of minimization tools (maximum likelihood estimation and least noarch
square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner’s
book Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and
Applications 5th ed. (ISBN:9198299107). Examples include linear and non-
linear compartmental model, turn-over model, single or multiple dosing bo-
lus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-
vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling,
Emax model, inhibitory model, tolerance model, oscillating response model,
enantiomer interaction model, effect compartment model, drug-drug interac-
tion model, receptor occupancy model, and rebound phenomena model. /
GPL-3
r-wnnsel 0.1 New tools for the imputation of missing values in high-dimensional data are noarch
introduced using the non-parametric nearest neighbor methods. It includes
weighted nearest neighbor imputation methods that use specific distances for
selected variables. It includes an automatic procedure of cross validation and
does not require prespecified values of the tuning parameters. It can be used
to impute missing values in high-dimensional data when the s

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Anaconda Documentation

Jun 09, 2021

1 Anaconda Individual Edition 1

2 Anaconda Commercial Edition 3

3 Anaconda Team Edition 5

4 Anaconda Enterprise Edition 7

Anaconda Individual Edition

2 Chapter 1. Anaconda Individual Edition

Anaconda Commercial Edition

4 Chapter 2. Anaconda Commercial Edition

Anaconda Team Edition

6 Chapter 3. Anaconda Team Edition

Anaconda Enterprise Edition

8 Chapter 4. Anaconda Enterprise Edition

5.1 Anaconda Individual Edition

The Most Trusted Distribution for Data Science

Anaconda Navigator or conda?

Packages available in Anaconda

Tip: Looking for Python 3.5 or 3.6? See our FAQ.

1. Download the Anaconda installer.

Note: Do not install as Administrator unless admin privileges are required.

5.1. Anaconda Individual Edition 11

Or to install Anaconda without PyCharm, click the Next button.

5.1. Anaconda Individual Edition 13

macOS graphical install

1. Download the graphical macOS installer for your version of Python.

7. Click the continue button.

Or to install Anaconda without PyCharm, click the Continue button.

10. Verify your installation.

5.1. Anaconda Individual Edition 15

Using the command-line install

Use this method if you prefer to use a terminal window.

shasum -a 256 /path/filename

Note: Replace /path/filename with your installation’s path and filename.

3. Install for Python 3.7 or 2.7:

Note: Replace ~/Downloads with your actual path and Anaconda3-2020.02-MacOSX-x86_64.sh

Installation may take a few minutes to complete.

8. The installer displays “Thank you for installing Anaconda!”

Note: conda init is available in conda versions 4.6.12 and later.

12. Verify your installation.

5.1. Anaconda Individual Edition 17

De- apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2

For x86 systems.

3. Enter the following to install Anaconda for Python 3.7:

OR Enter the following to install Anaconda for Python 2.7:

Note: conda init is available in conda versions 4.6.12 and later.

12. Verify your installation.

5.1. Anaconda Individual Edition 19

Installing on Linux-aarch64 (arm64)

1. In your browser, download the Anaconda installer for Linux-aarch64.

Note: conda init is available in conda versions 4.6.12 and later.

11. Verify your installation.

Installing on AWS Graviton2 (arm64)

5.1. Anaconda Individual Edition 21

Note: conda init is available in conda versions 4.6.12 and later.

12. Verify your installation.

Installing on Linux-s390x (IBM Z)

1. In your browser, download the Anaconda installer for Linux-s390x.

5.1. Anaconda Individual Edition 23

Note: conda init is available in conda versions 4.6.12 and later.

11. Verify your installation.

Installing on Linux POWER

Red- yum install libXcomposite libXcursor libXi libXtst libXrandr alsa-lib

3. Enter the following to install Anaconda for Python 3.7: