procella: Phylogeny and quantitative traits of birds

Description Usage Format Details References Examples

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

1

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
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 documentation built on June 17, 2021, 5:14 p.m.

Related to procella in ade4...