A Quick Introduction to iNextPD

via Examples
T. C. Hsieh

2017-03-11

iNextPD (iNterpolation and extrapolation for Phylogenetic Diversity) is an R package provides the

rarefaction and extrapolation framework to making fair comparison of abundance-sensitive
phylogenetic diversity among multiple assemblages (Hsieh and Chao, Systematic Biology, 2016). In
this document, we provide a quick introduction demonstrating how to run iNextPD. Detailed
information about iNextPD functions is provided in the iNextPD Manual, also available in CRAN.
See Chao et al. (2015) and Hsieh and Chao (2016) for methodologies. An online version
ofPhDOnline (https://chao.shinyapps.io/PhDOnline/) is also available for users without an R
background. A neutral theory of species diversity is included in Chao et al. (2014); and a brief
description of methods and R package (iNEXT) are included in an application paper by Hsieh, Ma &
Chao (2016).
iNextPD is an extension for iNEXT, which extending trdional rarefaction and extrapoltion framework
for species diversity to abundance-sensitive phylogenetic diversity. iNextPD focuses on three
measures of Hill numbers of order q: Faith’s PD (q = 0), a simple transformation of phylogenetic
entropy (q = 1) and and a simple transformation of Rao’s quadratic entropy (q = 2). For each
diversity measure, iNextPD uses the observed sample of abundance or incidence data (called the
“reference sample”) to compute diversity estimates and the associated 95% confidence intervals for
the following two types of rarefaction and extrapolation (R/E):

1. Sample‐size‐based R/E sampling curves: iNextPD computes diversity estimates for rarefied

and extrapolated samples up to an appropriate size. This type of sampling curve plots the
diversity estimates with respect to sample size (tyep=1).
2. Coverage‐based R/E sampling curves: iNextPD computes diversity estimates for rarefied
and extrapolated samples with sample completeness (as measured by sample coverage)
up to an appropriate coverage. This type of sampling curve plots the diversity estimates
with respect to sample coverage (type=3).

iNextPD also plots the above two types of sampling curves and a sample completeness curve. The
sample completeness curve provides a bridge between these two types of curves (type=2).

SOFTWARE NEEDED TO RUN INEXTPD IN R

o Required: R
o Suggested: RStudio IDE

HOW TO RUN INEXTPD:

The iNextPD package is available on CRAN and can be downloaded with a standard R installation

procedure using the following commands. For a first‐time installation, the additional visualization
extension packages (ade4, ggplot2, iNEXT, Rcpp) must be loaded.
## install iNEXT package from CRAN

install.packages("iNextPD")

## install the latest version from github

install.packages('devtools')

library(devtools)

install_github('JohnsonHsieh/iNextPD')

## import packages

library(iNextPD)

library(ggplot2)

library(ade4)

Remark: In order to install devtools package, you should update R to the latest version. Also, to
get install_github to work, you should install the httr package.

MAIN FUNCTION: iNextPD()

We first describe the main function iNextPD() with default arguments:

iNextPD(x, labels, phy, q=0, datatype="abundance", size=NULL, endpoint=NULL, knots=40,
se=FALSE, conf=0.95, nboot=50)

The arguments of this function are briefly described below, and will be explained in more details by
illustrative examples in later text. This main function computes diversity estimates of order q = 0, 1,
2, the sample coverage estimates and related statistics for K (if knots=K) evenly‐spaced knots
(sample sizes) between size 1 and the endpoint, where the endpoint is described below. Each knot
represents a particular sample size for which diversity estimates will be calculated. By default,
endpoint = double the reference sample size (total sample size for abundance data; total sampling
units for incidence data). For example, if endpoint = 10, knot = 4, diversity estimates will be
computed for a sequence of samples with sizes (1, 4, 7, 10).

Argumen
Description
t

x a matrix, data.frame, lists of species abundances or incidence data.

labels species names for object x.

Argumen
Description
t

phy a phylog objcet for input phylo-tree.

q a number or vector specifying the diversity order(s) of Hill numbers.

data type of input data: individual-based abundance data (datatype = "abundance"), or

datatype
species by sampling-units incidence matrix (datatype = "incidence_raw").

an integer vector of sample sizes for which diversity estimates will be computed. If NULL,
size then diversity estimates will be calculated for those sample sizes determined by the
specified/default endpoint and knots.

an integer specifying the sample size that is the endpoint for R/E calculation; If NULL,
endpoint
then endpoint=double the reference sample size.

an integer specifying the number of equally-spaced knots (say K, default is 40) between

size 1 and the endpoint; each knot represents a particular sample size for which diversity
estimate will be calculated. If the endpoint is smaller than the reference sample size,
theniNextPD() computes only the rarefaction esimates for approximately K evenly spaced
knots
knots. If the endpoint is larger than the reference sample size, then iNextPD() computes
rarefaction estimates for approximately K/2 evenly spaced knots between sample size 1
and the reference sample size, and computes extrapolation estimates for approximately
K/2 evenly spaced knots between the reference sample size and the endpoint.

se a logical variable to calculate the bootstrap standard error and conf confidence interval.

conf a positive number < 1 specifying the level of confidence interval, default is 0.95.

nboot an integer specifying the number of bootstrap replications.

This function returns an "iNextPD" object which can be further used to make plots using the
function ggiNEXT() to be described below.

DATA FORMAT/INFORMATION

Three types of data are supported:

1. Individual‐based abundance data (datatype="abundance"): Input data for each
assemblage/site include samples species abundances in an empirical sample of n
individuals (“reference sample”). When there are N assemblages, input data consist of an S
by N abundance matrix, or N lists of species abundances.
2. Sampling‐unit‐based incidence data: Incidence‐raw data (datatype="incidence_raw"): for
each assemblage, input data for a reference sample consist of a species‐by‐sampling‐unit
matrix; when there are N assemblages, input data consist of N lists of matrices, and each
matrix is a species‐by‐sampling‐unit matrix.

RAREFACTION/EXTRAPOLATION VIA EXAMPLES

Bird phylogeny and survey dataset is included in iNextPD package. This data set describes the
phylogeny ($tre) of 41 birds as reported by Jetz et al. (2012). It also gives the two sites of species
abundance ($abun) and incidence ($inci) data to these 41 species in November 2012 at Barrington
Tops National Park, Australia. For this data, the following commands display basic data
visualization:
data(bird)

str(bird)

List of 3

$ tre : chr
"(((((Alisterus_scapularis:31.96595541,Platycercus_elegans:31.96595545):13.04819101,
(Cacatua_galerita:32.14669035,Calyptorhynchu"| __truncated__

$ abun:'data.frame': 41 obs. of 2 variables:

..$ North.site: int [1:41] 0 0 41 0 3 1 5 4 4 11 ...

..$ South.site: int [1:41] 3 18 31 2 1 2 5 1 6 32 ...

$ inci:List of 2

..$ North.site: num [1:41, 1:12] 0 0 1 0 0 0 0 0 1 1 ...

.. ..- attr(*, "dimnames")=List of 2

.. .. ..$ : chr [1:41] "Acanthiza_lineata" "Acanthiza_nana" "Acanthiza_pusilla"

"Acanthorhynchus_tenuirostris" ...

.. .. ..$ : chr [1:12] "F1O" "F2A" "F3A" "F3O" ...

..$ South.site: num [1:41, 1:17] 1 0 0 0 0 0 0 0 0 1 ...

.. ..- attr(*, "dimnames")=List of 2

 .. .. ..$ : chr [1:41] "Acanthiza_lineata" "Acanthiza_nana" "Acanthiza_pusilla"
"Acanthorhynchus_tenuirostris" ...

.. .. ..$ : chr [1:17] "G.beech" "G1A" "G1C" "G2A" ...

bird.lab <- rownames(bird$abun)

bird.phy <- ade4::newick2phylog(bird$tre)

# plot(bird.phy)

table.phylog(bird$abun, bird.phy, csize=4, f.phylog=0.7)

For is data, the following commands display basic data information and run the iNextPD() function
for q = 0.
iNextPD(x=bird$abun, labels=bird.lab, phy=bird.phy, q=0, datatype="abundance")

The iNextPD() function returns the "iNextPD" object including three data frames: $DataInfo for

summarizing data information; $iNextPDEst for showing phylogenetic diversity estimates along with
related statistics for a series of rarefied and extrapolated samples; and $AsyPDEst for showing
asymptotic phylogenetic diversity estimates along with related statistics. $DataInfo, as shown
below, returns basic data information including the reference sample size (n), observed species
richness (S.obs), a sample coverage estimate (SC), and the first ten frequency counts (f1‐f10). This
part of output can also be computed by the function iNEXT::DataInfo()
$DataInfo: basic data information

site n S.obs SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10

1 North.site 202 27 0.9705 6 4 2 2 2 0 1 1 1 0

2 South.site 307 38 0.9838 5 6 3 2 3 4 2 0 2 2

For incidence data, the list $DataInfo includes the reference sample size (T), observed species
richness (S.obs), total number of incidences (U), a sample coverage estimate (SC), and the first ten
incidence frequency counts (Q1‐Q10).
In the North.site, by default, 40 equally spaced knots (samples sizes) between 1 and 404 (= 2 x
202, double reference sample size) are selected. Diversity estimates and related statistics are
computed for these 40 knots(corresponding to sample sizes m = 1, 12, 23, … 202, …, 404), which
locates the reference sample at the mid‐point of the selected knots. By default we only show five
estimates on the screen, user should call iNextPD.object$iNextPDEst to show complete output. If
the argument se=TRUE, then the bootstrap method is applied to obtain the conf (by
default conf=0.95) confidence intervals for each diversity and sample coverage estimates.
For the sample size corresponding to each knot, the list $iNextPDEst (as shown below for
the North.site) includes the sample size (m, i.e., each of the 40 knots), the method
(interpolated, observed, or extrapolated, depending on whether the size m is less than, equal to,
or greater than the reference sample size), the diversity order, the diversity estimate of order q
(qPD), the 95% lower and upper confidence limits of diversity (qD.95.LCL, qD.95.UCL), and the
sample coverage estimate (SC) along with the 95% lower and upper confidence limits of sample
coverage (SC.95.LCL, SC.95.UCL). These sample coverage estimates with conf% confidence
intervals are used for plotting the sample completeness curve and coverage-based R/E curves.
$iNextPDEst: phylogenetic diversity estimates with rarefied and extrapolated samples.

$North.site
 m method order qPD qPD.95.LCL qPD.95.UCL SC SC.95.LCL SC.95.UCL

1 1 interpolated 0 82.858 75.467 90.248 0.080 0.059 0.100

10 101 interpolated 0 1043.756 961.640 1125.873 0.935 0.915 0.954

20 202 observed 0 1222.098 1091.198 1352.998 0.970 0.952 0.989

30 298 extrapolated 0 1299.178 1125.847 1472.508 0.984 0.967 1.000

40 404 extrapolated 0 1337.896 1122.961 1552.832 0.992 0.978 1.000

NOTE1: Only show five estimates, call iNextPD.object$iNextPDEst to show complete output.

$AsyPDEst lists the observed diversity, asymptotic estimates, estimated bootstrap s.e. and 95%
confidence intervals for Hill numbers with q = 0, 1, and 2. See Hsieh and Chao (2016) for
asymptotic estimators. The output for the bird data is shown below. All row and column variables
are self‐explanatory.
$AsyPDEst: asymptotic phylogenetic diversity estimates along with related statistics.

Observed Estimator Est_s.e. 95% Lower 95% Upper

North.site q = 0 1222.098 1367.729 139.957 1222.098 1642.039

q = 1 437.248 456.014 23.520 437.248 502.113

q = 2 212.398 214.063 10.678 212.398 234.992

South.site q = 0 1416.719 1561.469 87.287 1416.719 1732.548

q = 1 455.438 469.981 20.677 455.438 510.508

q = 2 205.894 206.898 8.704 205.894 223.958

To show the completed branch abundance/incience and branch length (Ui, Li), i = 1, 2, …, B, user
could call iNextPD.object$ExpandData.
In practice, the user may specify an integer sample size for the argument endpoint to designate the
maximum sample size of R/E calculation. For Faith’s PD, the extrapolation method is reliable up to
the double reference sample size; beyond that, the prediction bias may be large. However, for
measures of q = 1 and 2, the extrapolation can usually be safely extended to the asymptote if data
are not sparse; thus there is no limit for the value of endpoint for these two measures.
The user may also specify the number of knots in the range of sample size between 1 and the
endpoint. If you choose a large number of knots, then it may take a long time to obtain the output
due to the time‐consuming bootstrap method. Alternatively, the user may specify a series of sample
sizes for R/E computation, as in the following example:
# set a series of sample sizes (m) for R/E computation

m <- c(1, 5, 20, 50, 100, 200, 400)

iNextPD(x=bird$abun, labels=bird.lab, phy=bird.phy,

q=0, datatype="abundance", size=m)

Further, iNextPD can simultaneously run R/E computation for Hill numbers with q = 0, 1, and 2 by
specifying a vector for the argument q as follows:
out <- iNextPD(x=bird$abun, labels=bird.lab, phy=bird.phy,

q=c(0,1,2), datatype="abundance", size=m)

POINT ESTIMATION FUNCTION: estimatePD()

We also supply the function

estimatePD(x, labels, phy, datatype="abundance", base="size",

level=NULL, conf=0.95, digits=4)

to compute diversity estimates with q = 0, 1, 2 for any particular level of sample size (base="size")
or any specified level of sample coverage (base="coverage") for either abundance data
(datatype="abundance") or incidence data ("incidence_raw"). If level=NULL, this function computes
the diversity estimates for the minimum sample size/coverage among all sites.
For example, the following command returns the species diversity with a specified level of sample
coverage of 97.5% for the bird abundance-based data. For some sites, this coverage value
corresponds to the rarefaction part whereas the others correspond to extrapolation, as indicated in
the method of the output.
estimatePD(bird$abun, bird.lab, bird.phy, "abundance",

base="coverage", level=0.975, conf=0.95)

site m method order SC qPD qPD.95.LCL qPD.95.UCL

1 North.site 227.0711 extrapolated 0 0.975 1248.1118 1128.6005 1367.6232

3 North.site 227.0711 extrapolated 1 0.975 439.4657 386.8856 492.0458

5 North.site 227.0711 extrapolated 2 0.975 212.5806 179.6321 245.5291

8 South.site 247.8890 interpolated 0 0.975 1367.1348 1288.1097 1446.1600

10 South.site 247.8890 interpolated 1 0.975 451.9783 412.1321 491.8246

12 South.site 247.8890 interpolated 2 0.975 205.6565 176.3483 234.9647

GRAPHIC DISPLAYS: FUNCTION ggiNEXT()

The function ggiNEXT(), which extends ggplot2 to the "iNextPD" object with default arguments, is

described as follows:
ggiNEXT(x, type=1, se=TRUE, facet.var="none", color.var="site", grey=FALSE)

Here x is an "iNextPD" object. Three types of curves are allowed:

1. Sample-size-based R/E curve (type=1): this curve plots diversity estimates with confidence
intervals (if se=TRUE) as a function of sample size up to double the reference sample size,
by default, or a user‐specified endpoint.
2. Sample completeness curve (type=2) with confidence intervals (if se=TRUE): this curve plots
the sample coverage with respect to sample size for the same range described in (1).
3. Coverage-based R/E curve (type=3): this curve plots the diversity estimates with confidence
intervals (if se=TRUE) as a function of sample coverage up to the maximum coverage
obtained from the maximum size described in (1).
The argument facet.var=("none", "order", "site" or "both")  is used to create a separate plot
for each value of the specified variable. For example, the following code displays a separate plot for
each value of the diversity order q. The user may also use the argument grey=TRUE to plot
black/white figures. The usage of color.var is illustrated in the incidence data example described in
later text. The ggiNEXT() function is a wrapper around ggplot2 package to create a R/E curve using
a single line of code. The resulting object is of class "ggplot", so can be manipulated using
the ggplot2 tools.
out <- iNextPD(bird$abun, bird.lab, bird.phy,

q=c(0, 1, 2), datatype="abundance", endpoint=400)

# Sample‐size‐based R/E curves, separating by "site""

ggiNEXT(out, type=1, facet.var="site")

## Not run:

# Sample‐size‐based R/E curves, separating by "order"

ggiNEXT(out, type=1, facet.var="order")

# display black‐white theme

ggiNEXT(out, type=1, facet.var="order", grey=TRUE)

## End(Not run)

The argument facet.var="site" in ggiNEXT function creates a separate plot for each site as shown

below:
# Sample‐size‐based R/E curves, separating by "site""

ggiNEXT(out, type=1, facet.var="site")

The argument facet.var="order" and color.var="site" creates a separate plot for each diversity

order site, and within each plot, different colors are used for two sites.
ggiNEXT(out, type=1, facet.var="order", color.var="site")

The following commands return the sample completeness curve in which different colors are used
for the two sites:
ggiNEXT(out, type=2, facet.var="none", color.var="site")

The following commands return the coverage‐based R/E sampling curves in which different colors
are used for the two sites (facet.var="site") and for three orders (facet.var="order")
ggiNEXT(out, type=3, facet.var="site")

ggiNEXT(out, type=3, facet.var="order", color.var="site")

The argument color.var = ("none", "order", "site" or "both")  is used to display curves in
different colors for values of the specified variable. For example, the following code using the
argument color.var="site" displays the sampling curves in different colors for the five sites. Note
that theme_bw() is a ggplot2 function to modify display setting from grey background to black‐and‐
white. The following commands return three types R/E sampling curves for ant data.

Example for incidence data

out.inc <- iNextPD(bird$inci, bird.lab, bird.phy,

q=0, datatype="incidence_raw",

endpoint = 25, se=TRUE)

# Sample‐size‐based R/E curves

ggiNEXT(out.inc, type=1, color.var="site") +

theme_bw(base_size = 18) +

theme(legend.position="none")

# Sample completeness curves

ggiNEXT(out.inc, type=2, color.var="site") +

xlim(c(5,25)) + ylim(c(0.7,1)) +

theme_bw(base_size = 18) +

theme(legend.position="none")

# Coverage‐based R/E curves

ggiNEXT(out.inc, type=3, color.var ="site") +

xlim(c(0.7,1)) +

theme_bw(base_size = 18) +

theme(legend.position="bottom",

legend.title=element_blank())

Hacking ggiNEXT()

The ggiNEXT() function is a wrapper around ggplot2 package to create a R/E curve using a single

line of code. The resulting object is of class "ggplot", so can be manipulated using
the ggplot2 tools. The following are some useful examples for customizing graphs.

Remove legend
out2 <- iNextPD(bird$abun, bird.lab, bird.phy,

q=c(0, 1, 2), datatype="abundance",

endpoint=400, se=TRUE)

ggiNEXT(out2, type=3, facet.var="site") +

theme(legend.position="none")

Change to theme and legend.position

ggiNEXT(out2, type=1, facet.var="site") +

theme_bw(base_size = 18) +

theme(legend.position="right")

Display black‐white theme

ggiNEXT(out2, type=1, facet.var="order", grey=TRUE)

Free the scale of axis

ggiNEXT(out2, type=1, facet.var="order") +

facet_wrap(~order, scales="free")

Change the shape of reference sample size

ggiNEXT(out2, type=1, facet.var="site") +

scale_shape_manual(values=c(19,19,19))

General customization

The data visualization package ggplot2 provides scale_ function to customize data which is

mapped into an aesthetic property of a geom_. The following functions would help user to
customize ggiNEXT output.

o change point shape: scale_shape_manual

o change line type : scale_linetype_manual
o change line color: scale_colour_manual
 o change band color: scale_fill_manual
see quick reference for style setting.

Example: bird data

To show how to custmized ggiNEXT output, we use abundance-based data spider as an example.

library(iNextPD)

library(ggplot2)

library(gridExtra)

data(bird)

bird.lab <- rownames(bird$abun)

bird.phy <- ade4::newick2phylog(bird$tre)

out <- iNextPD(bird$abun, bird.lab, bird.phy, q=0,

datatype="abundance", se=TRUE)

g <- ggiNEXT(out, type=1, color.var = "site")

Change shapes, line types and colors

g1 <- g + scale_shape_manual(values=c(11, 12)) +

scale_linetype_manual(values=c(1,2))

g2 <- g + scale_colour_manual(values=c("red", "blue")) +

scale_fill_manual(values=c("red", "blue"))

# Draw multiple graphical objec on a page

# library(gridExtra)

grid.arrange(g1, g2, ncol=2)

Customize point/line size by hacking

In order to chage the size of reference sample point or rarefaction/extrapolation curve, user need
modify ggplotobject.

o change point size:

the reference sample size point is drawn on the first layer by ggiNEXT. Hacking point size by
the following

# point is drawn on the 1st layer, default size is 5

gb3 <- ggplot_build(g)

gb3$data[[1]]$size <- 10

gt3 <- ggplot_gtable(gb3)

# use grid.draw to draw the graphical object

# library(grid)

# grid.draw(gt3)

o change line width (size):

the reference sample size point is drawn on the second layer by ggiNEXT. Hacking point
size by the following

# line is drawn on the 2nd layer, default size is 1.5

gb4 <- ggplot_build(g)

gb4$data[[2]]$size <- 3

gt4 <- ggplot_gtable(gb4)

# grid.draw(gt4)

grid.arrange(gt3, gt4, ncol=2)

Customize theme

A ggplot object can be themed by adding a theme. User could run help(theme_grey) to show the
default themes inggplot2. Further, some extra themes provided by ggthemes package. Examples
shown in the following:
g5 <- g + theme_bw() +

theme(legend.position = "bottom", legend.box = "vertical")

g6 <- g + theme_classic() +

theme(legend.position = "bottom", legend.box = "vertical")

grid.arrange(g5, g6, ncol=2)

library(ggthemes)

g7 <- g + theme_hc(bgcolor = "darkunica") +

theme(legend.box = "vertical") +

scale_colour_hc("darkunica")

g8 <- g + theme_economist() +
 theme(legend.box = "vertical") +

scale_colour_economist()

grid.arrange(g7, g8, ncol=2)

Black-White theme

The following are custmized themes for black-white figure. To modifiy legend, see Cookbook for
R for more details.
g9 <- g + theme_bw(base_size = 18) +

scale_fill_grey(start = 0, end = .4) +

scale_colour_grey(start = .2, end = .2) +

theme(legend.position="bottom",

legend.title=element_blank(),

legend.box = "vertical")

g10 <- g + theme_tufte(base_size = 12) +

scale_fill_grey(start = 0, end = .4) +

scale_colour_grey(start = .2, end = .2) +

theme(legend.position="bottom",

legend.title=element_blank(),

legend.box = "vertical")

grid.arrange(g9, g10, ncol=2)

Draw R/E curves by yourself

In iNextPD, we provide a S3 ggplot2::fortify method for class iNextPD. The

function fortify offers a single plotting interface for rarefaction/extrapolation curves. Set
argument type = 1, 2, 3 to plot the corresponding rarefaction/extrapolation curves.
df <- fortify(out, type=1)

head(df)

datatype plottype site method order x y y.lwr y.upr

1 abundance 1 North.site interpolated 0 1 82.858 77.745 87.970

2 abundance 1 North.site interpolated 0 12 428.313 393.623 463.002

3 abundance 1 North.site interpolated 0 23 607.781 562.347 653.216

4 abundance 1 North.site interpolated 0 34 726.034 674.556 777.511

5 abundance 1 North.site interpolated 0 45 811.060 754.022 868.098

6 abundance 1 North.site interpolated 0 56 876.145 813.297 938.994

df.point <- df[which(df$method=="observed"),]

df.line <- df[which(df$method!="observed"),]

df.line$method <- factor(df.line$method,

c("interpolated", "extrapolated"),

c("interpolation", "extrapolation"))

ggplot(df, aes(x=x, y=y, colour=site)) +

geom_point(aes(shape=site), size=5, data=df.point) +

geom_line(aes(linetype=method), lwd=1.5, data=df.line) +

geom_ribbon(aes(ymin=y.lwr, ymax=y.upr,

fill=site, colour=NULL), alpha=0.2) +

labs(x="Number of individuals", y="Phylogenetic diversity") +

theme(legend.position = "bottom",

legend.title=element_blank(),

text=element_text(size=18),

legend.box = "vertical")

License

The iNextPD package is licensed under the GPLv3. To help refine iNextPD, your comments or
feedbacks would be welcome (please send them to T. C. Hsieh or report an issue on iNextPD
github reop).

How to cite

If you publish your work based on results from iNextPD (R package), please make reference to
Hsieh and Chao (2016) and Chao et al. (2015) given in the following list.

References
o Chao, A., Gotelli, N.J., Hsieh, T.C., Sander, E.L., Ma, K.H., Colwell, R.K. & Ellison, A.M.
(2014) Rarefaction and extrapolation with Hill numbers: a framework for sampling and
estimation in species diversity studies. Ecological Monographs, 84, 45–67.
o Chao A., Chiu C.H., Hsieh T.C., Davis T., Nipperess D.A. & Faith D.P. (2015) Rarefaction
and extrapolation of phylogenetic diversity.Method Ecol. Evol. 6:380–388.
o Hsieh, T.C., Ma, K.H. and Chao, A. (2016) iNEXT: an R package for rarefaction and
extrapolation of species diversity (Hill numbers). Methods Ecol Evol.
o Jetz, W., Thomas, G.H., Joy, J.B., Hartmann, K. & Mooers A.O. (2012) The global diversity
of birds in space and time. Nature, 491, 444-448.