iNEXT (version 3.0.1)

iNEXT: iNterpolation and EXTrapolation of Hill numbers

Description

iNEXT: Interpolation and extrapolation of Hill number with order q

Usage

iNEXT(
  x,
  q = 0,
  datatype = "abundance",
  size = NULL,
  endpoint = NULL,
  knots = 40,
  se = TRUE,
  conf = 0.95,
  nboot = 50
)

Value

a list of three objects: $DataInfo for summarizing data information; $iNextEst for showing diversity estimates for rarefied and extrapolated samples along with related statistics; and $AsyEst for showing asymptotic diversity estimates along with related statistics.

NOTE: From version 3.0.0, $iNextEst has been expanded to include $size_based and

$coverage_based to provide two types of confidence intervals.

Arguments

x

a matrix, data.frame (species by sites), or list of species abundances or incidence frequencies. If datatype = "incidence_freq", then the first entry of the input data must be total number of sampling units in each column or list.

q

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

datatype

data type of input data: individual-based abundance data (datatype = "abundance"), sampling-unit-based incidence frequencies data (datatype = "incidence_freq") or species by sampling-units incidence matrix (datatype = "incidence_raw").

size

an integer vector of sample sizes (number of individuals or sampling units) for which diversity estimates will be computed. If NULL, then diversity estimates will be computed for those sample sizes determined by the specified/default endpoint and knots .

endpoint

an integer specifying the sample size that is the endpoint for rarefaction/extrapolation. If NULL, then endpoint = double the reference sample size.

knots

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, then iNEXT() computes only the rarefaction esimates for approximately K evenly spaced knots. If the endpoint is larger than the reference sample size, then iNEXT() 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 replications; default is 50.

Examples

if (FALSE) {
## example for abundance based data (list of vector)
data(spider)
out1 <- iNEXT(spider, q=c(0,1,2), datatype="abundance")
out1$DataInfo # showing basic data information.
out1$AsyEst # showing asymptotic diversity estimates.
out1$iNextEst$size_based 
# showing diversity estimates with rarefied and extrapolated samples; 
# confidence limits are obtained for fixed sample size.

out1$iNextEst$coverage_based 
# showing diversity estimates with rarefied and extrapolated samples;
# confidence limits are obtained for fixed sample coverage.
}
## example for abundance based data (data.frame)
data(bird)
out2 <- iNEXT(bird, q=0, datatype="abundance")
out2

if (FALSE) {
## example for incidence frequencies based data (list of data.frame)
data(ant)
t <- round(seq(10, 500, length.out=20))
out3 <- iNEXT(ant$h500m, q=1, datatype="incidence_freq", size=t, se=FALSE)
out3$iNextEst
}