rao {BAT} | R Documentation |
Rao quadratic entropy for Phylogenetic or Functional richness.
rao(comm, tree, distance, raref = 0, runs = 100)
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. |
Rao quadratic entropy (Rao, 1982) measures diversity based on the abundance of species and the dissimilarity between them.
A matrix of sites x diversity values (either "Rao" OR "Mean, Median, Min, LowerCL, UpperCL and Max").
Rao, C.R. (1982). Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21: 24-43.
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)