Phylogenetic diversity calculator for community matrix

Phylogenetic diversity calculator for community matrix

Here is a function that calculates phylogenetic diversity (i.e. Faith's) for a set of community samples. It takes a community matrix (could be species inventories from field plots or map grid cells) and an associated tree with branch lengths.

phylogenetic.diversity.sites.R [https://raw.githubusercontent.com/GregGuerin/biomap/master/phylogenetic.diversity.sites.R]

Although coded differently, this is more or less equivalent to the 'pd' function in the picante package. I have pulled it out as a stand-alone function for a community matrix from the unweighted (pd) case of this phylogenetic endemism function, which has point record inputs and gridded map outputs. It returns a list with a vector of phylogenetic diversity scores (site names as labels). The example:

library(vegan)
data(mite)
library(ape)
mite.tree <- rtree(n=ncol(mite), tip.label=colnames(mite))

source(“phylogenetic.diversity.sites.R”)
mite.PD <- phylogenetic.diversity.sites(mite, phylo.tree=mite.tree)

mite.PD