histograms of phylogenetic similarity

phylosim

require(picante)

#function that maps dissimilarity to similarity & scales between 0 and 1
range01 <- function(x){exp((-1/max(x))*x)}

#Calculate branch lengths bewteen taxa
dist <- cophenetic(tree)

#calculate similarity between taxa from 0 to 1
Z <- range01(dist)
hist(Z)

#if you have a community matrix and want to do a site-by-site comparison of distances, you need to subset your matrix
#X = your site of interest (should be a row or set of rows in a community matrix)

site <- subset(names(samp[X,]),  samp[X,] > 0)
Z <- Z[site,site]
upper <- col(Z) <= row(Z)
Z <- Z[upper]
hist(Z)