estimateD: Compute species diversity with a particular of sample...

Description Usage Arguments Value Examples

View source: R/invChat.R

Description

estimateD: computes species diversity (Hill numbers with q = 0, 1 and 2) with a particular user-specified level of sample size or sample coverage.

Usage

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estimateD(x, datatype = "abundance", base = "size", level = NULL,
  conf = 0.95)

Arguments

x

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

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").

base

comparison base: sample-size-based (base="size") or coverage-based
(base="coverage").

level

an value specifying a particular sample size or a number (between 0 and 1) specifying a particular value of sample coverage. If base="size" and level=NULL, then this function computes the diversity estimates for the minimum sample size among all sites. If base="coverage" and level=NULL, then this function computes the diversity estimates for the minimum sample coverage among all sites.

conf

a positive number < 1 specifying the level of confidence interval, default is 0.95. Remove C.I. by setting conf=NULL.

Value

a data.frame of species diversity table including the sample size, sample coverage, method (rarefaction or extrapolation), and diversity estimates with q = 0, 1, and 2 for the user-specified sample size or sample coverage.

Examples

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data(spider)
estimateD(spider, "abundance", base="size", level=NULL, conf=0.95)
estimateD(spider, "abundance", base="coverage", level=NULL, conf=0.95)

data(ant)
estimateD(ant, "incidence_freq", base="coverage", level=0.985, conf=NULL)

iNEXT documentation built on May 29, 2017, 2:48 p.m.