adiv (version 2.2.1)

distinctUltra: Ultrametric Tree-based Species' Originality

Description

The function calculates two indices of species' originality that rely on the structure and branch lengths of ultrametric (phylogenetic) trees. Trees with polytomies are allowed.

Usage

distinctUltra(phyl, method = c("Qb","2Hb"))

Value

A data frame with species as rows and originality indices as columns.

Arguments

phyl

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

method

a string or a vector of strings. Possible values are Qb and 2Hb. Qb is for the Pavoine et al. QE-based (also named Qb) index (Pavoine et al. 2005); 2Hb is for Pavoine et al. 2H-based index (which could also be named more shortly as 2Hb) (vector that maximizes index \(^2H\), Pavoine and Izsak 2014).

Author

Sandrine Pavoine with contributions of Stephane Dray

References

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

Pavoine, S. and Izsak, J. (2014) New biodiversity measure that includes consistent interspecific and intraspecific components. Methods in Ecology and Evolution, 5, 165--172.

See Also

distinctDis, distinctTopo, distinctTree

Examples

if (FALSE) {
if(require(ape) && require(adephylo) && require(phylobase)){
data(carni70, package = "adephylo")
tre <- read.tree(text=carni70$tre)
U <- distinctUltra(tre)
U.4d <- phylo4d(tre, as.matrix(U))

dotp4d(U.4d, center = FALSE, scale = FALSE)
barp4d(U.4d, center = FALSE, scale = FALSE)
gridp4d(U.4d, center = FALSE, scale = FALSE)

parmar <- par()$mar
par(mar=rep(.1,4))
table.phylo4d(U.4d, show.node=FALSE, symbol="squares", center=FALSE, scale=FALSE, cex.symbol=2)
par(mar=parmar)
}
}