carni70: Phylogeny and quantitative traits of carnivora

In adephylo: Exploratory Analyses for the Phylogenetic Comparative Method

Phylogeny and quantitative traits of carnivora

Description

This data set describes the phylogeny of 70 carnivora as reported by Diniz-Filho and Torres (2002). It also gives the geographic range size and body size corresponding to these 70 species.

Format

carni70 is a list containing the 2 following objects:

tre

is a character string giving the phylogenetic tree in Newick format. Branch lengths are expressed as divergence times (millions of years)

tab

is a data frame with 70 species and two traits: size (body size (kg)) ; range (geographic range size (km)).

Note

This dataset replaces the former version in ade4.

Source

Diniz-Filho, J. A. F., and N. M. Torres. (2002) Phylogenetic comparative methods and the geographic range size-body size relationship in new world terrestrial carnivora. Evolutionary Ecology, 16, 351–367.

Examples

if(require(ape) && require(phylobase)){

data(carni70)
rownames(carni70$tab) <- gsub("_", ".", rownames(carni70$tab))
tre <- read.tree(text=carni70$tre)
x <- phylo4d(tre, carni70$tab)
table.phylo4d(x)

oldpar <- par(mar=rep(.1,4))
table.phylo4d(x,cex.lab=.5, show.n=FALSE, ratio=.5)


## transform size in log and test for a phylogenetic signal
size <- log(carni70$tab)[,1]
names(size) <- row.names(carni70$tab)
orthogram(size, tre)

## transform range and test for a phylogenetic signal
yrange <- scale(carni70$tab)[,2]
names(yrange) <- row.names(carni70$tab)
orthogram(yrange, tre)

par(oldpar)
}

adephylo documentation built on Oct. 6, 2023, 5:07 p.m.