A Quick Introduction to iNEXT via

Examples
T. C. Hsieh, K. H. Ma, and Anne Chao

Latest version 3.0.0 (July, 2022)

Latest Updates in July 2022: (1) We have modified (in the main function iNEXT) the bootstrap method
used to obtain confidence intervals for the coverage-based rarefaction and extrapolation curves. We have
expanded the iNEXT output ($iNextEst) to include two lists ($size_based and $coverage_based). (2) In the
function estimateD, for a given coverage value, we have refined our algorithm to find the corresponding
sample size (not necessarily restricted to integers) to obtain more accurate diversity estimates. (3) We
have changed some column names in the output in order to conform to our forthcoming iNEXT series
(iNEXT.3D, iNEXT.4steps, iNEXT.link). Please download the latest version of iNEXT available from CRAN or
from Anne Chao’s iNEXT_github, or use the latest version of iNEXT Online available from Shiny iNEXT-
Online.
iNEXT (iNterpolation and EXTrapolation) is an R package modified from the original version which was
supplied in the Supplement of Chao et al. (2014). In the latest updated version, we have added more user‐
friendly features, improved some algorithms, and refined the graphic displays. In this document, we
provide a quick introduction demonstrating how to run iNEXT. Detailed information about iNEXT functions is
provided in the iNEXT Manual, also available in CRAN. See Chao & Jost (2012), Colwell et al. (2012) and
Chao et al. (2014) for methodologies. A short review of the theoretical background and a brief description
of methods are included in an application paper by Hsieh, Ma & Chao (2016). An online version of iNEXT-
online is also available for users without an R background.
iNEXT focuses on three measures of Hill numbers of order q: species richness (q = 0), Shannon diversity (q
= 1, the exponential of Shannon entropy) and Simpson diversity (q = 2, the inverse of Simpson
concentration). For each diversity measure, iNEXT 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 (or size-based) R/E sampling curves: iNEXT 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.
2. Coverage‐based R/E sampling curves: iNEXT computes diversity estimates for rarefied and
extrapolated samples based on a standardized level of sample completeness (as measured by
sample coverage) up to an appropriate coverage value. This type of sampling curve plots the
diversity estimates with respect to sample coverage.

iNEXT also plots the above two types of sampling curves and a sample completeness curve (which depicts
how sample coverage varies with sample size). The sample completeness curve provides a bridge
between the size- and coverage-based R/E sampling curves.

HOW TO CITE iNEXT

If you publish your work based on the results from the iNEXT package, you should make references to the
following methodology paper (Chao et al. 2014) and the application paper (Hsieh, Ma & Chao, 2016):
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.
 Hsieh, T.C., Ma, K.H. & Chao, A. (2016) iNEXT: An R package for interpolation and extrapolation of
species diversity (Hill numbers). Methods in Ecology and Evolution, 7, 1451-1456.

SOFTWARE NEEDED TO RUN iNEXT IN R

Required: R
Suggested: RStudio IDE

HOW TO RUN iNEXT:

The iNEXT package is available from CRAN and can be downloaded with a standard R installation
procedure or can be downloaded from Anne Chao’s iNEXT_github using the following commands. For a
first‐time installation, an additional visualization extension package (ggplot2) must be installed and loaded.

## install iNEXT package from CRAN

install.packages("iNEXT")
## install the latest version from github
install.packages('devtools')
library(devtools)
install_github('AnneChao/iNEXT')
## import packages
library(iNEXT)
library(ggplot2)

MAIN FUNCTION: iNEXT()

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

iNEXT(x, q=0, datatype="abundance", size=NULL, endpoint=NULL, knots=40, se=TRUE, 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, 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 an example, if
endpoint = 10, knots = 4, diversity estimates will be computed for a sequence of samples with sizes (1, 4,
7, 10). In a later real-data example, we have endpoint = 336, knots = 40; diversity estimates will be
computed for a sequence of samples with sizes (1, 10,19, 28, …, 318, 327, 336).

Argument Description

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

x
frequencies (see data format/information below).

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

datatype type of input data, “abundance”, “incidence_raw” or “incidence_freq”.

 Argument Description

an integer vector of sample sizes for which diversity estimates will be computed. If
size NULL, 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
endpoint
NULL, then endpoint=double the reference sample size.

an integer specifying the number of equally‐spaced knots between size 1 and the
knots
endpoint; default is 40.

a logical variable to calculate the bootstrap standard error and conf confidence
se
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; default is 50.

This function returns an "iNEXT" 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 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: There are two kinds of input data.

a. Incidence-raw data (datatype="incidence_raw"): for each assemblage, input data for a reference
sample consisting of a species-by-sampling-unit matrix; each element in the raw matrix is 1 for a
detection, and 0 otherwise. When there are N assemblages, input data consist of N lists of raw
matrices, and each matrix is a species-by-sampling-unit matrix.
b. Incidence-frequency data (datatype="incidence_freq"): input data for each assemblage consist of
species sample incidence frequencies (i.e., row sums of the corresponding incidence raw matrix).
When there are N assemblages, input data consist of an (S+1) by N matrix, or N lists of species
incidence frequencies. The first entry of each column/list must be the total number of sampling units,
followed by the species incidence frequencies.

RAREFACTION/EXTRAPOLATION VIA EXAMPLES

Four data sets are included in the iNEXT package for illustration. There are two abundance data sets:
spider (list of two vectors) and bird (in data.frame format), and two incidence data sets: ant (list of 5
vectors) and ciliates (list of 3 matrices). The input datatypes are the same for the two abundance data
sets (datatype="abundance"), but the input datatypes are different for the ant data
(datatype="incidence_freq") and the ciliates data (datatype="incidence_raw"). We first use the spider
data for illustration; see Chao et al. (2014) for analysis details and data interpretations. The spider data
consist of abundance data from two canopy manipulation treatments (“Girdled” and “Logged”) of hemlock
trees (Ellison et al. 2010). For these data, the following commands run the iNEXT() function for q = 0.

data(spider)
str(spider)
 iNEXT(spider, q=0, datatype="abundance")

The iNEXT() function returns the "iNEXT" object including three output lists: $DataInfo for summarizing data
information; $iNextEst for showing size- and coverage-based diversity estimates along with related
statistics for a series of rarefied and extrapolated samples; and $AsyEst for showing asymptotic 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), sample coverage estimate for the
reference sample (SC), and the first ten frequency counts (f1‐f10). This part of output can also be
computed by the function DataInfo()

$DataInfo: basic data information

Assemblage n S.obs SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
1 Girdled 168 26 0.9289 12 4 0 1 0 2 0 1 1 0
2 Logged 252 37 0.9446 14 4 4 3 1 0 3 2 0 1

For incidence data, the list $DataInfo includes the reference sample size (T), observed species richness
(S.obs), total number of incidences (U), sample coverage estimate for the reference sample (SC), and the
first ten incidence frequency counts (Q1‐Q10).
In the Girdled treatment assemblage, by default, 40 equally spaced knots (samples sizes) between 1 and
336 (= 2 x 168, double the reference sample size, Chao et al. 2014) are selected. Diversity estimates and
related statistics are computed for these 40 knots (corresponding to sample sizes m = 1, 10, 19, …, 327,
336), which locates the reference sample at the mid-point of the selected knots. If the argument se=TRUE,
then the bootstrap method is applied to obtain the 95% confidence intervals for each diversity and sample
coverage estimate.
The list $iNextEst output includes two data frames: $size_based and $coverage_based. (Note the output in
the list $iNextEst is different from that obtained from earlier iNEXT versions < 3.0.0, due to a modification in
the bootstrap method.) For the sample size corresponding to each knot, the first data frame (as shown
under $size_based) includes the name of Assemblage, the sample size (m, i.e., each of the 40 knots), the
method (Rarefaction, Observed, or Extrapolation, depending on whether the size m is less than, equal to, or
greater than the reference sample size), the diversity order (order.q), the diversity estimate of order q (qD),
the 95% lower and upper confidence limits of diversity (qD.LCL, qD.UCL), and the sample coverage estimate
(SC) along with the 95% lower and upper confidence limits of sample coverage (SC.LCL, SC.UCL). These
sample coverage estimates with confidence intervals are used for plotting the sample completeness curve.

$iNextEst: diversity estimates with rarefied and extrapolated samples.

$size_based (LCL and UCL are obtained for fixed size.)

Assemblage m Method Order.q qD qD.LCL qD.UCL SC SC.LCL SC.UCL

1 Girdled 1 Rarefaction 0 1.000 1.000 1.000 0.122 0.089 0.156
10 Girdled 84 Rarefaction 0 18.912 15.902 21.923 0.900 0.872 0.927
20 Girdled 168 Observed 0 26.000 21.492 30.508 0.929 0.904 0.954
30 Girdled 248 Extrapolation 0 30.883 25.149 36.618 0.948 0.918 0.979
40 Girdled 336 Extrapolation 0 34.731 27.187 42.275 0.964 0.931 0.996
41 Logged 1 Rarefaction 0 1.000 1.000 1.000 0.145 0.109 0.180
50 Logged 126 Rarefaction 0 28.268 24.935 31.600 0.908 0.886 0.930
60 Logged 252 Observed 0 37.000 31.789 42.211 0.945 0.925 0.964
70 Logged 371 Extrapolation 0 42.786 35.844 49.727 0.958 0.935 0.980
80 Logged 504 Extrapolation 0 47.644 38.485 56.804 0.969 0.946 0.991

NOTE: The above output only shows five estimates for each assemblage; call
iNEXT.object$iNextEst$size_based to view complete output.

The second data frame (as shown under $coverage_based) includes the name of Assemblage, the
standardized sample coverage (SC), the corresponding sample size for the standardized coverage (m, i.e.,
each of the 40 knots), the method (Rarefaction, Observed, or Extrapolation, depending on whether the
sample coverage SC is less than, equal to, or greater than the reference sample coverage), the diversity
order (order.q), the diversity estimate of order q (qD), and the 95% lower and upper confidence limits of
diversity (qD.LCL, qD.UCL). These diversity estimates and confidence intervals are used for plotting the
coverage-based R/E curves.

$coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to
varying size in bootstraps.)

Assemblage SC m Method order.q qD qD.LCL qD.UCL

1 Girdled 0.122 1 Rarefaction 0 1.000 0.857 1.143
10 Girdled 0.900 84 Rarefaction 0 18.912 10.761 27.064
20 Girdled 0.929 168 Observed 0 26.000 13.239 38.761
30 Girdled 0.948 248 Extrapolation 0 30.883 12.129 49.638
40 Girdled 0.964 336 Extrapolation 0 34.731 9.788 59.673
41 Logged 0.145 1 Rarefaction 0 1.000 0.796 1.204
50 Logged 0.908 126 Rarefaction 0 28.268 20.192 36.343
60 Logged 0.945 252 Observed 0 37.000 20.209 53.791
70 Logged 0.958 371 Extrapolation 0 42.786 21.977 63.594
80 Logged 0.969 504 Extrapolation 0 47.644 23.357 71.932

NOTE: The above output only shows five estimates for each assemblage; call
iNEXT.object$iNextEst$coverage_based to view complete output.

In the above output ($size_based and $coverage_based), the confidence intervals of any standardized
diversity are obtained by a bootstrap method. In the size-based standardization, the sample size is fixed in
each regenerated bootstrap sample. In the coverage-based standardization, for a given standardized
coverage value, the corresponding size needed to attain the same level of coverage may vary with
regenerated bootstrap samples. Thus, the sampling uncertainty is greater in the coverage-based
standardization and the resulting confidence interval is wider than that in the corresponding size-based
standardization. For example, if the size for a future survey will be fixed at a sample size of 84, we can
obtain a 95% CI of (15.9, 21.9) for the expected diversity (q = 0) based on the first data frame ($size_based
output). However, if the coverage of a survey is fixed at the level of 0.9, the size needed for the current
data is 84, but the size needed for a regenerated bootstrap sample may be different from 84; the second
data frame ($coverage_based output) shows a CI of (10.8, 27.1), which is wider than the former one based
on a size of 84. Because we use a random bootstrapping/regeneration process, with 50 replications
(default), to obtain each CI, the output for qD.LCL and qD.UCL may vary slightly each time you enter the
same data.
$AsyEst lists the name of Assemblage, the Diversity (species richness for q = 0, Shannon diversity for q = 1,
and Simpson diversity for q = 2), the observed diversity (Observed), the asymptotic diversity estimate
(Estimator), the s.e. of the asymptotic estimator (s.e.) and the associated 95% lower and upper
confidence limits (LCL, UCL). The estimated asymptotes are calculated via the functions ChaoRichness() for q
= 0, ChaoShannon() for q = 1 and ChaoSimpson() for q = 2; see Chao et al. (2014) for the formulas of all
asymptotic estimators. The output for the spider data is shown below.

$AsyEst: asymptotic diversity estimates along with related statistics.

Assemblage Diversity Observed Estimator s.e. LCL UCL
1 Girdled Species richness 26.000 43.893 17.219 26.000 77.642
2 Girdled Shannon diversity 12.060 13.826 1.339 11.201 16.451
3 Girdled Simpson diversity 7.840 8.175 0.934 6.344 10.006
4 Logged Species richness 37.000 61.403 19.692 37.000 99.998
5 Logged Shannon diversity 14.421 16.337 1.864 12.684 19.990
6 Logged Simpson diversity 6.761 6.920 0.926 5.106 8.734
The user may specify an integer sample size for the argument endpoint to designate the maximum sample
size of R/E calculation. For species richness, the extrapolation method is reliable up to double the
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 the endpoint for these two measures.
The user may also specify the number of knots in the sample size range 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 nature of the 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)
iNEXT(spider, q=0, datatype="abundance", size=m)

Further, iNEXT 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 <- iNEXT(spider, q=c(0,1,2), datatype="abundance", size=m)

A data.frame input format for abundance-based analysis is also supported:

data(bird)
str(bird) # 41 obs. of 2 variables
iNEXT(bird, q=0, datatype="abundance")

GRAPHIC DISPLAYS: FUNCTION ggiNEXT()

The function ggiNEXT(), which extends ggplot2 to the "iNEXT" object with default arguments, is described
as follows:

ggiNEXT(x, type=1, se=TRUE, facet.var="None", color.var="Assemblage", grey=FALSE)

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

1. Sample-size-based R/E curve (type=1): see Figs. 1a and 2a in Hsieh et al. (2016). 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): see Figs. 1b and 2b in
Hsieh et al. (2016). 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): see Figs. 1c and 2c in Hsieh et al. (2016). 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 ggiNEXT() function is a wrapper around the ggplot2 package to create a R/E curve using a single line
of code. The resulting object is of class "ggplot", so it can be manipulated using the ggplot2 tools. The
argument facet.var=("None", "Order.q", "Assemblage" or "Both") can be used to create a separate plot
for each value of the specified variable. See the following examples.
The argument facet.var="Assemblage" in the ggiNEXT function creates a separate plot for each assemblage
as shown below:
 # Sample‐size‐based R/E curves, separating by "Assemblage""
out <- iNEXT(spider, q=c(0, 1, 2), datatype="abundance", endpoint=500)
ggiNEXT(out, type=1, facet.var="Assemblage")

The argument facet.var="Order.q" and color.var="Assemblage" creates a separate plot for each diversity
order assemblage, and within each plot, different colors are used for the two assemblages.

ggiNEXT(out, type=1, facet.var="Order.q", color.var="Assemblage")

The following commands return the sample completeness curve in which different colors are used for the
two assemblages:

ggiNEXT(out, type=2, facet.var="None", color.var="Assemblage")

The following commands return the coverage-based R/E sampling curves in which different colors are
used for the two assemblages (facet.var="Assemblage") and for three orders (facet.var="Order.q")

ggiNEXT(out, type=3, facet.var="Assemblage")

ggiNEXT(out, type=3, facet.var="Order.q", color.var="Assemblage")
INCIDENCE DATA with datatype=“incidence_freq”

For illustration, we use the tropical ant data (in the dataset ant included in the package) at five elevations
(50m, 500m, 1070m, 1500m, and 2000m) collected by Longino & Colwell (2011) from Costa Rica. The 5
lists of incidence frequencies are shown below. The first entry of each list must be the total number of
sampling units, followed by the species incidence frequencies.

data(ant)
str(ant)
List of 5
$ h50m : num [1:228] 599 330 263 236 222 195 186 183 182 129 ...
$ h500m : num [1:242] 230 133 131 123 78 73 65 60 60 56 ...
$ h1070m: num [1:123] 150 99 96 80 74 68 60 54 46 45 ...
$ h1500m: num [1:57] 200 144 113 79 76 74 73 53 50 43 ...
$ h2000m: num [1:15] 200 80 59 34 23 19 15 13 8 8 ...

The argument color.var = ("None", "Order.q", "Assemblage" 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="Assemblage" displays the sampling curves in different colors for the five assemblages. Note that
theme_bw() is a ggplot2 function to modify the display setting from a grey to a white background with black
gridlines. The following commands return three types of R/E sampling curves for the ant data.

t <- seq(1, 700, by=10)

out.inc <- iNEXT(ant, q=0, datatype="incidence_freq", size=t)

# Sample‐size‐based R/E curves

ggiNEXT(out.inc, type=1, color.var="Assemblage") +
theme_bw(base_size = 18) +
theme(legend.position="None")
# Sample completeness curves
ggiNEXT(out.inc, type=2, color.var="Assemblage") +
ylim(c(0.9,1)) +
theme_bw(base_size = 18) +
theme(legend.position="None")
# Coverage‐based R/E curves
ggiNEXT(out.inc, type=3, color.var ="Assemblage") +
xlim(c(0.9,1)) +
theme_bw(base_size = 18) +
theme(legend.position="bottom",
legend.title=element_blank(),
text=element_text(size=18),
legend.box = "vertical")
INCIDENCE DATA with datatype=“incidence_raw”

We use the ciliates data collected from three coastal dune habitats to demostrate the use of the input
datatype="incidence_raw". The data set (ciliates) included in the package is a list of three species-by-
plots matrices. Run the following commands to get the output as shown below.

data(ciliates)
str(ciliates)
List of 3
$ EtoshaPan : int [1:365, 1:19] 0 0 0 0 0 0 0 0 0 0 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:365] "Acaryophrya.collaris" "Actinobolina.multinucleata.n..sp."
"Afroamphisiella.multinucleata.n..sp." "Afrothrix.multinucleata.n..sp." ...
.. ..$ : chr [1:19] "x53" "x54" "x55" "x56" ...
$ CentralNamibDesert : int [1:365, 1:17] 0 0 0 0 0 1 0 0 0 0 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:365] "Acaryophrya.collaris" "Actinobolina.multinucleata.n..sp."
"Afroamphisiella.multinucleata.n..sp." "Afrothrix.multinucleata.n..sp." ...
.. ..$ : chr [1:17] "x31" "x32" "x34" "x35" ...
$ SouthernNamibDesert: int [1:365, 1:15] 0 0 0 0 0 0 0 0 0 0 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:365] "Acaryophrya.collaris" "Actinobolina.multinucleata.n..sp."
"Afroamphisiella.multinucleata.n..sp." "Afrothrix.multinucleata.n..sp." ...
.. ..$ : chr [1:15] "x9" "x17" "x19" "x20" ...

out.raw <- iNEXT(ciliates, q = 0, datatype="incidence_raw", endpoint=150)

out.raw
# ggiNEXT(out.raw)

Compare 3 assemblages with Hill number order q = 0.

$class: iNEXT

$DataInfo: basic data information

Assemblage T U S.obs SC Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10
1 EtoshaPan 19 516 216 0.8017 107 44 26 14 6 5 4 3 2 2
2 CentralNamibDesert 17 379 130 0.8425 63 28 13 4 3 7 1 2 1 0
3 SouthernNamibDesert 15 358 150 0.7816 82 28 14 8 6 1 1 2 2 1

$iNextEst: diversity estimates with rarefied and extrapolated samples.

$size_based (LCL and UCL are obtained for fixed size.)

Assemblage t Method Order.q qD qD.LCL qD.UCL SC SC.LCL SC.UCL

1 EtoshaPan 1 Rarefaction 0 27.158 24.893 29.423 0.190 0.164 0.216
10 EtoshaPan 10 Rarefaction 0 153.260 141.984 164.536 0.680 0.644 0.716
20 EtoshaPan 20 Extrapolation 0 221.386 203.508 239.263 0.810 0.778 0.843
30 EtoshaPan 88 Extrapolation 0 333.606 291.244 375.967 0.991 0.985 0.997
39 EtoshaPan 150 Extrapolation 0 338.901 293.346 384.456 0.999 0.999 1.000
40 CentralNamibDesert 1 Rarefaction 0 22.294 20.579 24.009 0.374 0.340 0.408
49 CentralNamibDesert 10 Rarefaction 0 98.993 90.442 107.545 0.764 0.736 0.791
58 CentralNamibDesert 24 Extrapolation 0 151.018 135.480 166.557 0.892 0.856 0.929
67 CentralNamibDesert 87 Extrapolation 0 195.191 156.456 233.925 0.996 0.990 1.000
76 CentralNamibDesert 150 Extrapolation 0 196.656 154.935 238.377 1.000 0.999 1.000
77 SouthernNamibDesert 1 Rarefaction 0 23.867 21.566 26.167 0.282 0.245 0.319
85 SouthernNamibDesert 9 Rarefaction 0 112.485 103.115 121.854 0.699 0.657 0.741
94 SouthernNamibDesert 30 Extrapolation 0 207.213 185.149 229.276 0.893 0.846 0.940
103 SouthernNamibDesert 93 Extrapolation 0 259.337 209.899 308.776 0.995 0.988 1.000
111 SouthernNamibDesert 150 Extrapolation 0 261.886 209.174 314.598 1.000 0.999 1.000

NOTE: The above output only shows five estimates for each assemblage; call
iNEXT.object$iNextEst$size_based to view complete output.

$coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to
varying size in bootstraps.)

Assemblage SC t Method Order.q qD qD.LCL qD.UCL

1 EtoshaPan 0.1901402 1 Rarefaction 0 27.158 24.894 29.422
10 EtoshaPan 0.6799226 10 Rarefaction 0 153.260 135.451 171.069
20 EtoshaPan 0.8103610 20 Extrapolation 0 221.386 194.992 247.779
30 EtoshaPan 0.9909111 88 Extrapolation 0 333.606 288.842 378.369
39 EtoshaPan 0.9994305 150 Extrapolation 0 338.901 293.087 384.715
40 CentralNamibDesert 0.3743404 1 Rarefaction 0 22.294 20.572 24.016
49 CentralNamibDesert 0.7635124 10 Rarefaction 0 98.993 86.617 111.369
58 CentralNamibDesert 0.8921419 24 Extrapolation 0 151.018 125.356 176.681
67 CentralNamibDesert 0.9964228 87 Extrapolation 0 195.191 153.805 236.576
76 CentralNamibDesert 0.9998814 150 Extrapolation 0 196.656 154.657 238.655
77 SouthernNamibDesert 0.2821229 1 Rarefaction 0 23.867 21.581 26.152
85 SouthernNamibDesert 0.6993084 9 Rarefaction 0 112.484 97.518 127.451
94 SouthernNamibDesert 0.8931001 30 Extrapolation 0 207.213 171.199 243.227
103 SouthernNamibDesert 0.9946808 93 Extrapolation 0 259.337 207.038 311.636
111 SouthernNamibDesert 0.9996478 150 Extrapolation 0 261.886 208.751 315.021
 NOTE: The above output only shows five estimates for each assemblage; call
iNEXT.object$iNextEst$coverage_based to view complete output.

$AsyEst: asymptotic diversity estimates along with related statistics.

Assemblage Diversity Observed Estimator s.e. LCL UCL
1 CentralNamibDesert Species richness 130.000 196.706 19.523 158.441 234.971
2 CentralNamibDesert Shannon diversity 81.812 106.480 5.291 96.110 116.850
3 CentralNamibDesert Simpson diversity 54.225 59.556 3.175 53.333 65.778
4 EtoshaPan Species richness 216.000 339.255 23.121 293.938 384.571
5 EtoshaPan Shannon diversity 158.367 222.936 11.125 201.130 244.741
6 EtoshaPan Simpson diversity 116.677 142.833 8.700 125.780 159.885
7 SouthernNamibDesert Species richness 150.000 262.067 30.638 202.018 322.115
8 SouthernNamibDesert Shannon diversity 103.705 149.910 9.301 131.681 168.139
9 SouthernNamibDesert Simpson diversity 72.327 84.597 5.276 74.255 94.938

POINT ESTIMATION FUNCTION: estimateD()

We also supply the following function

estimateD(x, datatype="abundance", base="size", level=NULL)

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 abundance data (datatype="abundance") or
incidence data (datatype="incidence_freq" or "incidence_raw"). If base="size" and level=NULL, then this
function computes the diversity estimates for the minimum among all doubled reference sample sizes. If
base="coverage" and level=NULL, then this function computes the diversity estimates for the minimum
among the coverage values for samples extrapolated to double the size of the reference sample.
The following command returns the species diversity with a specified level of sample coverage of 98.5%
for the ant data. For some assemblages, this coverage value corresponds to rarefaction (i.e., less than the
coverage of the reference sample), while for the others it corresponds to extrapolation (i.e., greater than
the coverage of the reference sample), as indicated under the method column of the output.

estimateD(ant, datatype="incidence_freq",
base="coverage", level=0.985, conf=0.95)

Assemblage t Method Order.q SC qD qD.LCL qD.UCL

1 h50m 327.165 Rarefaction 0 0.985 197.488 186.058 208.918
2 h50m 327.165 Rarefaction 1 0.985 78.053 75.389 80.717
3 h50m 327.165 Rarefaction 2 0.985 50.461 48.640 52.282
4 h500m 342.859 Extrapolation 0 0.985 268.726 242.802 294.650
5 h500m 342.859 Extrapolation 1 0.985 103.847 100.256 107.438
6 h500m 342.859 Extrapolation 2 0.985 64.758 61.983 67.534
7 h1070m 158.951 Extrapolation 0 0.985 123.609 113.000 134.218
8 h1070m 158.951 Extrapolation 1 0.985 59.592 56.903 62.280
9 h1070m 158.951 Extrapolation 2 0.985 41.775 39.465 44.085
10 h1500m 125.959 Rarefaction 0 0.985 50.479 41.666 59.291
11 h1500m 125.959 Rarefaction 1 0.985 26.249 24.575 27.923
12 h1500m 125.959 Rarefaction 2 0.985 18.649 17.446 19.852
13 h2000m 104.631 Rarefaction 0 0.985 12.910 11.002 14.817
14 h2000m 104.631 Rarefaction 1 0.985 7.711 6.915 8.506
15 h2000m 104.631 Rarefaction 2 0.985 5.795 5.079 6.510
Hacking ggiNEXT()

The ggiNEXT() function is a wrapper around the ggplot2 package to create a R/E curve using a single line
of code. The resulting object is of class "ggplot", so it can be manipulated using the ggplot2 tools. The
following are some useful examples for customizing graphs.

Remove legend

ggiNEXT(out, type=3, facet.var="Assemblage") +

theme(legend.position="None")

Change the theme and legend.position

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

theme_bw(base_size = 18) +
theme(legend.position="right")
Display black-white figures

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

Free the scales of the axis

ggiNEXT(out, type=1, facet.var="Order.q") +

facet_wrap(~Order.q, scales="free")
change the shape of the reference sample point

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

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

The data visualization package ggplot2 provides the 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.
change point shape: scale_shape_manual
change line type : scale_linetype_manual
change line color: scale_colour_manual
change band color: scale_fill_manual
see quick reference for style setting.

Example: spider data

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

library(iNEXT)
library(ggplot2)
library(gridExtra)
library(grid)
data("spider")
out <- iNEXT(spider, q=0, datatype="abundance")
g <- ggiNEXT(out, type=1, color.var = "Assemblage")
g
Change shapes, line types and colors

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

scale_linetype_manual(values=c(1,2)) +
theme(legend.text = element_text(size = 9.5))
g2 <- g + scale_colour_manual(values=c("red", "blue")) +
scale_fill_manual(values=c("red", "blue")) +
theme(legend.text = element_text(size = 9.5))
# Draw multiple graphical object on a page
# library(gridExtra)
grid.arrange(g1, g2, ncol=2)
Customize point/line size by hacking

In order to change the size of the reference sample point or rarefaction/extrapolation curve, the user need
to modify the ggplot object.
change point size:
the reference sample size point is drawn on the first layer by ggiNEXT. Hack the point size by the
following

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

gb3 <- ggplot_build(g + theme(legend.text = element_text(size = 9.5)))
gb3$data[[1]]$size <- 10
gt3 <- ggplot_gtable(gb3)
# use grid.draw to draw the graphical object
# library(grid)
# grid.draw(gt3)

change line width (size):

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

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

gb4 <- ggplot_build(g + theme(legend.text = element_text(size = 9.5)))
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. The User could run help(theme_grey) to show the
default themes in ggplot2. Further, some extra themes are provided by the ggthemes package. Examples
are 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",
legend.text = element_text(size = 12)) +
scale_colour_hc("darkunica")
g8 <- g + theme_economist() +
theme(legend.position="bottom",
legend.box = "vertical",
legend.text = element_text(size = 13)) +
scale_colour_economist()
grid.arrange(g7, g8, ncol=2)
Black-White figures

The following are custmized themes for black-white figures. To modifiy the 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 iNEXT, we provide a S3 ggplot2::fortify method for class iNEXT. 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 Assemblage Method Order.q x y y.lwr y.upr
1 abundance 1 Girdled Rarefaction 0 1 1.000000 1.000000 1.00000
2 abundance 1 Girdled Rarefaction 0 10 6.478617 5.983295 6.97394
3 abundance 1 Girdled Rarefaction 0 19 9.450323 8.530705 10.36994
4 abundance 1 Girdled Rarefaction 0 28 11.514220 10.253775 12.77466
5 abundance 1 Girdled Rarefaction 0 37 13.126817 11.575192 14.67844
6 abundance 1 Girdled Rarefaction 0 47 14.622424 12.778255 16.46659
df.point <- df[which(df$Method=="Observed"),]
df.line <- df[which(df$Method!="Observed"),]
df.line$Method <- factor(df.line$Method,
c("Rarefaction", "Extrapolation"),
c("Rarefaction", "Extrapolation"))

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

geom_point(aes(shape=Assemblage), 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=Assemblage, colour=NULL), alpha=0.2) +
labs(x="Number of individuals", y="Species diversity") +
 theme(legend.position = "bottom",
legend.title=element_blank(),
text=element_text(size=18),
legend.box = "vertical")

License

The iNEXT package is licensed under the GPLv3. To help refine iNEXT, your comments or feedback would
be welcome (please send them to Anne Chao or report an issue on the iNEXT github iNEXT_github.

References

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.
Chao, A. & Jost, L. (2012) Coverage‐based rarefaction and extrapolation: standardizing samples by
completeness rather than size. Ecology, 93, 2533–2547.
Colwell, R.K., Chao, A., Gotelli, N.J., Lin, S.‐Y., Mao, C.X., Chazdon, R.L. & Longino, J.T. (2012)
Models and estimators linking individual-based and sample-based rarefaction, extrapolation and
comparison of assemblages. Journal of Plant Ecology, 5, 3–21.
Ellison, A.M., Barker-Plotkin, A.A., Foster, D.R. & Orwig, D.A. (2010) Experimentally testing the role
of foundation species in forests: the Harvard Forest Hemlock Removal Experiment. Methods in
Ecology and Evolution, 1, 168–179.
Hsieh, T.C., Ma, K.H. & Chao, A. (2016) iNEXT: An R package for interpolation and extrapolation of
species diversity (Hill numbers). Methods in Ecology and Evolution, 7, 1451-1456.
Longino, J.T. & Colwell, R.K. (2011) Density compensation, species composition, and richness of
ants on a neotropical elevational gradient. Ecosphere, 2:art29.