BAT (version 2.5.1)

rao.alpha: Rao quadratic entropy.

Description

Rao quadratic entropy for Phylogenetic or Functional richness.

Usage

rao.alpha(comm, tree, distance, raref = 0, runs = 100)

Arguments

comm

A sites x species matrix, with abundance data.

tree

An hclust or phylo object representing a phylogenetic or functional tree. One of tree or distance must be provided.

distance

A dist object representing the phylogenetic or functional distance between species.

raref

An integer specifying the number of individuals for rarefaction (individual based). If raref < 1 no rarefaction is made. If raref = 1 rarefaction is made by the minimum abundance among all sites. If raref > 1 rarefaction is made by the abundance indicated. If not specified, default is 0.

runs

Number of resampling runs for rarefaction. If not specified, default is 100.

Value

A matrix of sites x diversity values (either "Rao" OR "Mean, Median, Min, LowerCL, UpperCL and Max").

Details

Rao quadratic entropy (Rao, 1982) measures diversity based on the abundance of species and the dissimilarity between them.

References

Rao, C.R. (1982). Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21: 24-43.

Examples

# NOT RUN {
comm <- matrix(c(0,0,1,1,0,0,100,1,2,0), nrow = 2, ncol = 5, byrow = TRUE)
distance = dist(1:5)
rao.alpha(comm)
rao.alpha(comm, , distance)
rao.alpha(comm, hclust(distance), raref = 1)
# }