STA 106 Fall 2021

Applied Statistical Methods: Analysis of Variance

University of California, Davis

Instructor and TA information

Instructor: Dr. Shizhe Chen TA: Ms. Yuanyuan Li
Email: szdchen@ucdavis.edu Email: yynli@ucdavis.edu
OH: MSB 1143, M 4:00 to 5:00 pm OH: Zoom W 10 am to 12 pm
Zoom T 4:00 to 5:00 pm
Basic information
Topics: Experimental design, causal inference, one-way and two-way fixed
and random effects analysis of variance, multiple comparisons, etc.
Objectives: Students will learn the basic concepts and methods related to the
aforementioned topics. Students will also practice data analysis using
a professional level software/language such as Python or R.
Prerequisites: C- or better in STA 13, STA 13Y, STA 32, STA 100
Lecture: In-person 2:10 - 3:00 pm, WMF (Wellman 234)
Discussion: In-person 8:00 - 8:50 am, R (Olson 147), 9:00-9:50 am, R (Art 217)
Recording: Canvas (to be posted within a week of lectures/discussion sessions)
Course website: Canvas (check regularly!)
Course note: static view on nbviewer, interactive notes on mybinder or using
jupyterhub (with some setup) , and source code on Github
Course schedule: link
References: Applied Regression Analysis and other Multivariable Methods, by
Kleinbaum, et al.
ANOVA: A Short Intro Using R, by Lukas Meier (link)
An Introduction to Statistical Learning, by James, et al.
Software: R 4.1.1 (available at http://www.r-project.org/)
Rstudio 1.4.1717 (available at https://www.rstudio.com/)
Zoom (see the UCD Zoom Guide for Students)

Grading

Homework: 35 points
A B C D F
Quiz & exam: 50 points
≥ 90 89-80 79-70 69-60 <60
Participation: 15 points
Note: +/− will be added as appropriate.
Bonus: 3 points

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Communication

Administrative questions: Come to office hour or send emails to the instructor and
copy the TA(s). Improper emails will not be replied (email etiquette). Please also
include the course name in the email title (e.g. [STA106] Questions regarding Canvas).
Other questions: Come to office hours, or post on Piazza. Do not ask the instruc-
tor or TA(s) to help you debug (...because we might not know how!). Do not expect
responses to last minute questions on homework assignments.
Weekly surveys: Feedbacks are collected every week via the weekly survey on Canvas.
See details in Page 4.

Public Health Expectations and Best Practices

Read the policies and requirements by UC Davis. Per the interim UC Davis student
conduct policy, “reports of students or student organizations who allegedly violate
campus policy, even when on private property, can be made to OSSJA for investigation.
If a student is found responsible, students can face consequences including, but not
limited to, censure, probation up to suspension or dismissal". The instructors will
strictly follow the university’s instructions to ensure the safety of everyone in this
class. In particular, in this class,

• Wear a proper face covering that covers your nose and mouth at all time. Excep-
tions need to be approved by the student disability center, and acknowledged by
the instructors before lectures.

• Follow the instructor and TA(s) instructions in class and during office hours. In
particular, the instructor and TA(s) may ask to see your Daily Symptom Survey
survey result in class or during office hours.

• Maintain physical distance when feasible. In particular, do not approach the

instructor and TA(s) before lectures or without explicit verbal consent, the in-
structor and TA(s) may ask you to leave the office hours if you linger on with no
particular questions or the room is over-crowded.

Collaboration and academic integrity

You are encouraged to study in groups, but you should write up the submissions in-
dependently. Academic misconduct includes copying from, or referencing without
proper acknowledgment, external sources or your peers, etc. Students must abide
by the UC Davis Code of Academic Conduct. All teaching faculty at UC Davis are
instructed to report all suspected cases of cheating and other misconduct to the Office
of Student Support and Judicial Affairs (http://ossja.ucdavis.edu), whether the student
admits to it or not.
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Campus support

Students can find support from Aggie Info and Help Line, Student Disability Center,
and other supporting resources listed in campus resources and campus ready.

Classroom policy

In addition to the public health policies, student behavior should fit the UC Davis
policy on student conduct and discipline. Please respect your fellow students, teach-
ing assistants, and the instructor in virtual lectures, discussion sessions, office hours,
and on the discussion board. Please refrain from any other activity that disrupts the
course of the lecture. Derogatory or inflammatory comments about other individuals,
cultures, groups, or viewpoints are not tolerated. As per UC Davis policy, instruc-
tors and teaching assistants may direct a student to leave a class immediately if the
student’s behavior is disruptive.

Homework

Overview: Assignments may include data analysis with R, interpretation of analysis

results, and rigorous derivations.
Submission: Assignments should be submitted electronically on Canvas by 5 pm
on the due date. Late submissions are not accepted. Submissions should be PDF
files. You can compile your submissions using Word, Latex, R Markdown, or any other
software of your choice. For instance, you can write your solutions on a piece of paper,
scan or take a picture of it, and turn it into a PDF file using Word.
Grading: Each assignment is worth 7 points. The lowest grade will be dropped when
calculating the final grade. To receive full credits, detailed steps of derivation are
required, and raw R output must be properly summarized.

Quiz

Overview: There are three quizzes on Canvas scheduled on Oct 22nd, Nov 12th, and
Dec 3rd, respectively. The format of the quiz can be found in the sample quiz. Each
quiz is worth 5 points.
Time and location: The quiz will be available on Canvas on the scheduled date
during regular class time. There is a 50-minute time limit to finish each quiz.

Final Exam

Overview: The final exam will be a comprehensive test for all materials covered in the
course. The final exam is closed-book but two sheets of handwritten notes (no larger
than letter size, two-sided) are allowed. Calculators can be used during the exam, but

STA 106 Syllabus 3 September 27th 2021

no cell phones or computers. Answers written with pencils or erasable pens will not
be accepted. A practice exam will be posted after Quiz III.
Time and location: The final exam is in-person at 1-3 pm Dec 10th in Wellman 234
(tentative).

Participation

Weekly survey
Weekly surveys are due every Monday at 11 am, starting from the second week. You
will earn one point for every survey so long as you complete the survey with honesty.
The survey contain a few questions mainly about your progress and experience in the
course so far. The instructor, TA(s), and reader(s) will use the survey results to adjust
the course materials, lecturing styles, grading schemes, etc.
Online discussion
Students are expected to participate in discussion on Piazza. The main purpose for
using a discussion board is to provide community support among students in this class.
The instructor and TA will monitor the discussion board, but will try to minimize their
influences on the process. In other words, you are expected to help other students and
seek for help among your fellow students. You can access Piazza in the navigation
tab on Canvas. Detailed rules for the 4 participation points will remain unspecified to
avoid exploitation. The sign-up code for Piazza is 2021.
Bonus points (up to 3): Individuals who receive high votes in the final survey (most
helpful classmates) will be rewarded with up to 3 bonus points.
Note: If you see Piazza in the contribution-mode, you do not need to pay in order to
participate in the online discussion.

Other policies on grading

There will be no extension without a documented, legitimate reason that is outside

of your control. Social conflicts or a heavy workload are unacceptable excuses. It is
required to contact the instructor no less than 14 days before the due date for any
submissions, except for emergencies. No exception can be guaranteed and decisions
will be made on a case-by-case basis.
Any grading dispute must be submitted in writing to the instructor within 24 hours
after the final grade is available on Canvas. No change will be made before the grade
is posted or after this deadline. Reasons irrelevant to your academic performances will
not be considered or responded. These reasons include but not limited to “I need to
pass this class to graduate", “I will be in academic probation if I failed this class", “It’s
not uncommon that professors would consider this situation when assigning grades",
etc.

STA 106 Syllabus 4 September 27th 2021

All submissions should be reproducible for receiving grades. Files for generating the
report or presentation should be ready upon submission, and made available to the
instructors within 24 hours upon requests. If your submissions cannot be reproduced
or have crucial discrepancies, you will be asked to reproduce your submission in a
recorded Zoom session with the instructors. Any suspicious records will be reported
to Office of Student Support and Judicial Affairs for their final verdict.

Recommendation letter policy

As a general policy, the instructor does not write recommendation letters for any
students who are currently enrolled in his course(s). Once you have completed the
instructor’s course (and your final grade is available), it is acceptable to ask for a rec-
ommendation letter. However, it is best to obtain recommendation letters from faculty
members that you have worked with outside of a classroom setting, e.g., as a research
assistant. If you do not have any non-classroom interaction with the instructor and/or
have not been an active participant in this course, the instructor will not be able to
write you a strong recommendation letter.

Auditing policy

The course is open for auditing as long as the auditors do not impede registered
students’ access to limited teaching resources. The auditor can choose to work with
any team on the course project, but the auditor’s contribution needs to be clearly
acknowledged. There can be at most one auditor on each team. Exemption is granted
on a case-by-case basis. The instructor reserves the right to grant assess to Canvas or
other course materials to auditors.

Academic (and legal) misconduct: Course materials

Lectures and course materials, including presentations, tests, outlines, and similar
materials, are protected by U.S. copyright law and by University policy. The instructor
is the exclusive owner of the copyright in those materials. You may take notes and
make copies of course materials for your own use. You may also share those mate-
rials with another student who is enrolled in or auditing this course. You may not
reproduce, distribute or display (post/upload) lecture notes or recordings or course
materials in any other way — whether or not a fee is charged — without my express
prior written consent. You also may not allow others to do so. If you do so, you
may be subject to student conduct proceedings under the UC Davis Code of Academic
Conduct.

STA 106 Syllabus 5 September 27th 2021