adiv (version 2.0.1)

distinctTree: Tree-based Species' Originality

Description

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

Usage

distinctTree(phyl, method = c("ED", "ES"), standardized = FALSE)

Arguments

phyl

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

method

a string or a vector of strings. Possible values are "ED" and "ES". "ED" is for the evolutionary distinctiveness, also named fair-proportion, index (Redding 2003; Isaac et al. 2007); "ES" is for the Equal-Splits index (Redding and Mooers 2006).

standardized

a logical. If TRUE, the vector of originalities is divided by its sum (transforming absolute originalities into relative originalities).

Value

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

References

Redding, D.W. (2003) Incorporating genetic distinctness and reserve occupancy into a conservation priorisation approach. Master thesis: University of East Anglia, Norwich.

Redding, D.W., Mooers, A.O. (2006) Incorporating evolutionary measures into conservation prioritization. Conservation Biology, 20, 1670--1678.

Isaac, N.J., Turvey, S.T., Collen, B., Waterman, C., Baillie, J.E. (2007) Mammals on the EDGE: conservation priorities based on threat and phylogeny. PloS ONE, 2, e296.

See Also

distinctDis, distinctTopo, distinctUltra

Examples

# NOT RUN {
if(require(ape) && require(adephylo) && require(phylobase)){
data(carni70, package = "adephylo")
tre <- read.tree(text=carni70$tre)
U <- distinctTree(tre, standardize = TRUE)
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)
}
# }