adiv (version 2.2.1)

distinctTree: Tree-based Species' Originality

Description

The function calculates 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", "Delta*"), palpha = 0, standardized = FALSE)

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.

method

a string or a vector of strings. Possible values are "ED", "ES", and "Delta*". "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); "Delta*" is for the parametric \(^{\alpha}\Delta\) index of Pavoine and Ricotta (2021).

palpha

a numeric value or a numeric vector of values for parameter \(\alpha\) of \(^{\alpha}\Delta\) index by Pavoine and Ricotta (2021).

standardized

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

Author

Sandrine Pavoine

References

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.

Pavoine, S., Ricotta, C. (2021) On the relationships between rarity, uniqueness, distinctiveness, originality and functional/phylogenetic diversity. BiorXiv. tools:::Rd_expr_doi("10.1101/2021.08.09.455640")

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.

See Also

distinctDis, distinctTopo, distinctUltra

Examples

if (FALSE) {
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)
}
}