Phylogenetic diversity

PD calculates Faith's (1992) phylogenetic diversity and relative phylogenetic diversity.

PD(x, phy)

RPD(x, phy)

Arguments

x

a community matrix, i.e. an object of class matrix or Matrix or an object of class phyloseq.

phy

a phylogenetic tree (object of class phylo).

Value

a vector with the PD for all samples.

References

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

See also

read.community read.tree phylobeta_core

Examples

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)
#> g1 g2 g3 g4 g5 g6 
#>  5  2  5  6  4  3 
# Relative phylogenetic diversity
RPD(com, tree)
#> g1 g2 g3 g4 g5 g6 
#>  1  1  1  1  1  1