distinctTree | R Documentation |
The function calculates indices of species' originality that rely on the structure and branch lengths of (phylogenetic) trees. Trees with polytomies are allowed.
distinctTree(phyl, method = c("ED", "ES", "Delta*"), palpha = 0, standardized = FALSE)
phyl |
an object inheriting the class |
method |
a string or a vector of strings. Possible values are |
palpha |
a numeric value or a numeric vector of values for parameter α of ^{α}Δ index by Pavoine and Ricotta (2021). |
standardized |
a logical. If |
A data frame with species as rows and originality indices as columns.
Sandrine Pavoine sandrine.pavoine@mnhn.fr
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.
distinctDis
, distinctTopo
, distinctUltra
## 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)
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