procella {ade4} | R Documentation |
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.
data(procella)
procella
is a list containing the 2 following objects:
is a character string giving the phylogenetic tree in Newick format.
is a data frame with 19 species and 6 traits
Variables of procella$traits
are the following ones:
site.fid: a numeric vector that describes the percentage of site fidelity
mate.fid: a numeric vector that describes the percentage of mate fidelity
mass: an integer vector that describes the adult body weight (g)
ALE: a numeric vector that describes the adult life expectancy (years)
BF: a numeric vector that describes the breeding frequencies
col.size: an integer vector that describes the colony size (no nests monitored)
Bried, J., Pontier, D. and Jouventin, P. (2002) Mate fidelity in monogamus birds: a re-examination of the Procellariiformes. Animal Behaviour, 65, 235–246.
See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps037.pdf (in French).
data(procella) pro.phy <- newick2phylog(procella$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)