R: Phylogeny and quantitative traits of birds

procella {ade4} | R Documentation

## Phylogeny and quantitative traits of birds

### Description

This data set describes the phylogeny of 19 birds as reported by Bried et al. (2002). It also gives 6 traits corresponding to these 19 species.

### Usage

    data(procella)

### Format

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

tre

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

traits

  is a data frame with 19 species and 6 traits

### Details

Variables of `procella$traits` are the following ones:
site.fid: a numeric vector that describes the percentage of site fidelity
mate.fid: a numeric vector that describes the percentage of mate fidelity
mass: an integer vector that describes the adult body weight (g)
ALE: a numeric vector that describes the adult life expectancy (years)
BF: a numeric vector that describes the breeding frequencies
col.size: an integer vector that describes the colony size (no nests monitored)

### References

Bried, J., Pontier, D. and Jouventin, P. (2002) Mate fidelity in monogamus birds: a re-examination of the Procellariiformes. Animal Behaviour, 65, 235–246.

See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps037.pdf (in French).

### Examples

    data(procella)
    pro.phy <- newick2phylog(procella$tre)
    plot(pro.phy,clabel.n = 1, clabel.l = 1)
    wt <- procella$traits
    wt$site.fid[is.na(wt$site.fid)] <- mean(wt$site.fid[!is.na(wt$site.fid)])
    wt$site.fid <- asin(sqrt(wt$site.fid/100))
    wt$ALE[is.na(wt$ALE)] <- mean(wt$ALE[!is.na(wt$ALE)])
    wt$ALE <- sqrt(wt$ALE)
    wt$BF[is.na(wt$BF)] <- mean(wt$BF[!is.na(wt$BF)])
    wt$mass <- log(wt$mass)
    wt <- wt[, -6]
    table.phylog(scalewt(wt), pro.phy, csi = 2)
    gearymoran(pro.phy$Amat,wt,9999)

[Package ade4 version 1.7-19 Index]