adiv (version 1.2)

distinctTopo: Topology-based Species' Originality

Description

The function calculates three indices of species' originality that rely on the topology of (phylogenetic) trees.

Usage

distinctTopo(phyl, method = 1:3, standardized = FALSE)

Arguments

phyl

an object inheriting the class phylo (see package ape), phylo4 (see package phylobase), or hclust.

method

a numeric or a vector of numerics. Possible values are 1, 2 and 3. 1 is for Vane-Wright et al. index (Vane-Wright et al. 1991) (noted VW); 2 is for May index (May 1990) (noted M); 3 is for Pavoine et al. index of originality derived from Abouheif (1999) (Pavoine et al. 2008) (noted A).

standardized

a logical. If FALSE, the minimum score is scaled to 1 as in May (1990). 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

May, R.M. (1990) Taxonomy as destiny. Nature, 347, 129--130.

Vane-Wright, R.I., Humphries, C.J., Williams, P.H. (1991) What to protect? Systematics and the agony of choice. Biological Conservation, 55, 235--254.

Abouheif, E. (1999) A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research, 1, 895--909.

Pavoine, S., Ollier, S., Pontier, D., Chessel, D. (2008) Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities. Theoretical Population Biology, 73, 79--91.

See Also

See Also distinctDis, distinctTree, distinctUltra

Examples

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