carni70 {ade4} | R Documentation |
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.
Usage
data(carni70)
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)).
Source
Diniz-Filho, J. A. F., and N. M. Tôrres. (2002) Phylogenetic comparative methods and the geographic range size-body size relationship in new world terrestrial carnivora. Evolutionary Ecology, 16, 351–367.
Examples
## Not run:
if (requireNamespace("adephylo", quietly = TRUE) & requireNamespace("ape", quietly = TRUE)) {
data(carni70)
carni70.phy <- newick2phylog(carni70$tre)
plot(carni70.phy)
size <- scalewt(log(carni70$tab))[,1]
names(size) <- row.names(carni70$tab)
symbols.phylog(carni70.phy,size)
tre <- ape::read.tree(text = carni70$tre)
adephylo::orthogram(size, tre = tre)
yrange <- scalewt(carni70$tab[,2])
names(yrange) <- row.names(carni70$tab)
symbols.phylog(carni70.phy,yrange)
adephylo::orthogram(as.vector(yrange), tre = tre)
if(adegraphicsLoaded()) {
g1 <- s.label(cbind.data.frame(size, yrange), plabel.cex = 0)
g2 <- addhist(g1)
} else {
s.hist(cbind.data.frame(size, yrange), clabel = 0)
}
}
## End(Not run)
[Package ade4 version 1.7-22 Index]