Phylogeny and quantitative traits of carnivora
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.
carni70 is a list containing the 2 following objects:
is a character string giving the phylogenetic tree in Newick format. Branch lengths are expressed as divergence times (millions of years)
is a data frame with 70 species and two traits: size (body size (kg)) ; range (geographic range size (km)).
This dataset replaces the former version in ade4.
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.
## Not run:
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)
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)
}
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