distinctTree {adiv}

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)

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).

Value

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

Author(s)

Sandrine Pavoine [e-mail]

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. 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

## 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)
}

## End(Not run)