PD: Phylogenetic diversity
In phyloregion: Biogeographic Regionalization and Macroecology

Description Usage Arguments Value References See Also Examples

PD calculates Faith's (1992) 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.

Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation 61: 1–10.

read.community read.tree phylobeta_core

library(ape)
library(Matrix)
tree <- read.tree(text ="((t1:1,t2:1)N2:1,(t3:1,t4:1)N3:1)N1;")
com <- sparseMatrix(c(1,3,4,1,4,5,1,2,3,4,5,6,3,4,6),
  c(1,1,1,2,2,2,3,3,3,3,3,3,4,4,4),x=1,
  dimnames = list(paste0("g", 1:6), tree$tip.label))

PD(com, tree)