rao {BAT}

Rao quadratic entropy.

Description

Rao quadratic entropy for Phylogenetic or Functional richness.

Usage

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

Arguments

comm

A sites x species matrix, with abundance data.

tree

A phylo or hclust object (used only for PD or FD).

distance

A dist object representing the phylogenetic or functional distance between species or alternatively a species x traits matrix or data.frame to calculate distances.

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.

Details

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

Value

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

References

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

Examples

comm <- matrix(c(1,1,1,1,1,0,100,1,2,0), nrow = 2, ncol = 5, byrow = TRUE)
distance = dist(1:5)
rao(comm)
rao(comm, , distance)
rao(comm, hclust(distance), raref = 1)