R: Phylogeny and quantitative traits of ungulates.

ungulates {ade4} | R Documentation

## Phylogeny and quantitative traits of ungulates.

### Description

This data set describes the phylogeny of 18 ungulates as reported by Pélabon et al. (1995). It also gives 4 traits corresponding to these 18 species.

### Usage

    data(ungulates)

### Format

`fission` is a list containing the 2 following objects :

tre

  is a character string giving the phylogenetic tree in Newick format.

tab

  is a data frame with 18 species and 4 traits

### Details

Variables of `ungulates$tab` are the following ones :
afbw: is a numeric vector that describes the adult female body weight (g)
mnw: is a numeric vector that describes the male neonatal weight (g)
fnw: is a numeric vector that describes the female neonatal weight (g)
ls: is a numeric vector that describes the litter size

### Source

Data were obtained from Pélabon, C., Gaillard, J.M., Loison, A. and Portier, A. (1995) Is sex-biased maternal care limited by total maternal expenditure in polygynous ungulates? Behavioral Ecology and Sociobiology, 37, 311–319.

### Examples

    data(ungulates)
    ung.phy <- newick2phylog(ungulates$tre)
    plot(ung.phy,clabel.l=1.25,clabel.n=0.75)
    ung.x <- log(ungulates$tab[,1])
    ung.y <- log((ungulates$tab[,2]+ungulates$tab[,3])/2)
    names(ung.x) <- names(ung.phy$leaves)
    names(ung.y) <- names(ung.x)
    plot(ung.x,ung.y)
    abline(lm(ung.y~ung.x))
    symbols.phylog(ung.phy,ung.x-mean(ung.x))
    dotchart.phylog(ung.phy,ung.x,cle=1.5,cno=1.5,cdot=1)
    if (requireNamespace("adephylo", quietly = TRUE) & requireNamespace("ape", quietly = TRUE)) {
      tre <- ape::read.tree(text = ungulates$tre)
      adephylo::orthogram(ung.x, tre)
      ung.z <- residuals(lm(ung.y~ung.x))
      names(ung.z) <- names(ung.phy$leaves)
      dotchart.phylog(ung.phy,ung.z,cle=1.5,cno=1.5,cdot=1,ceti=0.75)
      adephylo::orthogram(ung.z, tre)
    }

[Package ade4 version 1.7-17 Index]