ChaoShannon: Estimation of Shannon entropy/diversity

Description

ChaoShannon: estimation of Shannon entropy or transformed Shannon diversity based on the method proposed by Chao et al. (2013)

Usage

ChaoShannon(x, datatype = "abundance", transform = FALSE, conf = 0.95,
  B = 200)
ChaoEntropy(x, datatype = "abundance", transform = FALSE, conf = 0.95,
  B = 200)

Arguments

a vector 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.

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 = "inci

transform

a logical constant to compute traditional Shannon entropy index (transform=FALSE) or the transformed Shannon diversity (transform=TRUE).

conf

a positive number $\le$ 1 specifying the level of confidence interval.

an integer specifying the number of bootstrap replications.

Value

A vector of observed Shannon entropy/diversity, estimate of entropy/diversity, s.e. and the associated confidence interval.

References

Chao, A., Wang, Y.T. & Jost, L. (2013) Entropy and the species accumulation curve: a novel entropy estimator via discovery rates of new species. Methods in Ecology and Evolution, 4, 1091-1100.

Examples

Run this code

data(spider)
ChaoShannon(spider$Girdled, datatype="abundance")