PD: Phylogenetic diversity

In darunabas/phyloregion: Biogeographic Regionalization and Macroecology

Phylogenetic diversity

Description

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

Usage

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)
# Relative phylogenetic diversity
RPD(com, tree)

darunabas/phyloregion documentation built on Oct. 27, 2024, 10:01 p.m.