distinctUltra | R Documentation |
The function calculates two indices of species' originality that rely on the structure and branch lengths of ultrametric (phylogenetic) trees. Trees with polytomies are allowed.
distinctUltra(phyl, method = c("Qb","2Hb"))
phyl |
an object inheriting the class |
method |
a string or a vector of strings. Possible values are |
A data frame with species as rows and originality indices as columns.
Sandrine Pavoine sandrine.pavoine@mnhn.fr with contributions of Stephane Dray
Pavoine, S., Ollier, S., Dufour, A.B. (2005) Is the originality of a species measurable? Ecology Letters, 8, 579–586.
Pavoine, S. and Izsak, J. (2014) New biodiversity measure that includes consistent interspecific and intraspecific components. Methods in Ecology and Evolution, 5, 165–172.
distinctDis
, distinctTopo
, distinctTree
## Not run: if(require(ape) && require(adephylo) && require(phylobase)){ data(carni70, package = "adephylo") tre <- read.tree(text=carni70$tre) U <- distinctUltra(tre) U.4d <- phylo4d(tre, as.matrix(U)) dotp4d(U.4d, center = FALSE, scale = FALSE) barp4d(U.4d, center = FALSE, scale = FALSE) gridp4d(U.4d, center = FALSE, scale = FALSE) parmar <- par()$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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