PD: Phylogenetic diversity
In darunabas/bioregion: an R package for mapping biodiversity and conservation

Description Usage Arguments Value See Also Examples

PD calculates Faith's phylogenetic diversity.

1	PD(x, phy)

`x`	a community matrix, i.e. an object of class matrix or Matrix.
`phy`	a phylogenetic tree (object of class phylo).

a vector with the PD for all samples.

read.community read.tree phylobeta_core

library(ape)
tree <- read.tree(text ="((t1:1,t2:1)N2:1,(t3:1,t4:1)N3:1)N1;")
com <- matrix(c(1,0,1,1,0,0,
                1,0,0,1,1,0,
                1,1,1,1,1,1,
                0,0,1,1,0,1), 6, 4,
              dimnames=list(paste0("g",1:6), tree$tip.label))
PD(com, tree)