adiv (version 1.2)

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.

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. Polytomies are allowed.

method

a character a vector of characters. 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

See Also distinctDis, distinctTopo, distinctUltra

Examples

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