R: Phylogeny and quantitative traits of carnivora

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 1.7-19 Index]