randEH: Amount of Evolutionary History Preserved when Random Species...

In adiv: Analysis of Diversity

Amount of Evolutionary History Preserved when Random Species are Saved

Description

When branch lengths in an ultrametric phylogenetic tree are expressed as divergence times, the total sum of branch lengths in that tree expresses the amount of evolutionary history. The function randEH calculates the amount of evolutionary history preserved when k random species out of n original species are saved.

Usage

randEH(phyl, nbofsp, nrep = 10)

Arguments

phyl	an object inheriting the class phylo (see package ape), phylo4 (see package phylobase) or hclust.
nbofsp	an integer indicating the number of species saved (k).
nrep	an integer indicating the number of random sampling.

Value

Function randEH returns a numeric vector with the amount of evolutionary history preserved by each random drawing of the k species to be saved.

Author(s)

Sandrine Pavoine [e-mail] with contributions of Stephane Dray

References

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

Pavoine, S., Ollier, S. and Dufour, A.-B. (2005) Is the originality of a species measurable? Ecology Letters, 8, 579–586.

See Also

optimEH

Examples

## Not run: 
if(require(ape) && require(adephylo)){

data(carni70, package = "adephylo")
tre <- read.tree(text=carni70$tre)
adiv:::EH(tre)
R <- adiv:::randEH(tre, 10, nrep=1000)
hist(R)

}

## End(Not run)

adiv documentation built on May 29, 2024, 7:11 a.m.