adiv (version 2.2.1)

EH: Faith Phylogenetic Diversity

Description

Function EH computes the sum of branch lengths on a phylogenetic tree.

Usage

EH(phyl, select = NULL)

Value

Function EH returns a real value

Arguments

phyl

an object inheriting the class phylo (see package ape), phylo4 (see package phylobase) or hclust.

select

a vector containing the numbers of the leaves (species) which must be considered in the computation of Phylogenetic Diversity (PD) (or merely sum of branch lengths on the tree). This argument allows the calculation of PD for a subset of species (including the branch between the subtree and the most ancient node of the full tree).

Author

Sandrine Pavoine with contributions of Stephane Dray

References

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

Nee, S. and May, R.M. (1997) Extinction and the loss of evolutionary history. Science, 278, 692--694.

See Also

optimEH, randEH

Examples

if (FALSE) {
if(require(ape) && require(adephylo)){
data(carni70, package = "adephylo")
tre <- read.tree(text = carni70$tre)
adiv:::EH(tre)
adiv:::EH(tre, select=c("Mustela.nigripes", "Mustela.frenata", "Puma.concolor"))
adiv:::EH(tre, select=c(1,68,70))
}
}