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)