iNEXT: iNterpolation and EXTrapolation of Hill numbers

In JohnsonHsieh/iNEXT: Interpolation and Extrapolation for Species Diversity

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
)

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.

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.

Examples

## Not run: 
## 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.

## End(Not run)
## example for abundance based data (data.frame)
data(bird)
out2 <- iNEXT(bird, q=0, datatype="abundance")
out2

## Not run: 
## 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

## End(Not run)

JohnsonHsieh/iNEXT documentation built on March 26, 2024, 5:19 a.m.