adiv (version 1.2)

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.

Usage

distinctUltra(phyl, method = 1:2)

Arguments

phyl

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

method

a numeric or a vector of numerics. Possible values are 1, and 2. 1 is for the Pavoine et al. QE-based (also named Qb) index (Pavoine et al. 2005); 2 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).

Value

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

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

See Also distinctDis, distinctTopo, distinctTree

Examples

# NOT RUN {
data(carni70, package = "adephylo")
tre <- read.tree(text=carni70$tre)
U <- distinctUltra(tre)
U.4d <- phylo4d(tre, as.matrix(U))
parmar <- par()$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)

# }
# NOT RUN {
if(requireNamespace("phylosignal", quietly = TRUE)) {
dotplot.phylo4d(U.4d, center = FALSE, scale = FALSE)
}
# }