iNEXT: estimateD – R documentation

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estimateD

Compute species diversity with a particular of sample size/coverage

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

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

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

Interpolation and Extrapolation for Species Diversity

v2.0.20

GPL (>= 3)

Authors

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

Initial release