ade4: procella – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

procella

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)

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release