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Phylogeny and quantitative traits of birds

procella.Rd

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$Amat,wt,9999)
#> class: krandtest lightkrandtest 
#> Monte-Carlo tests
#> Call: as.krandtest(sim = matrix(res$result, ncol = nvar, byrow = TRUE), 
#>     obs = res$obs, alter = alter, names = test.names)
#> 
#> Number of tests:   5 
#> 
#> Adjustment method for multiple comparisons:   none 
#> Permutation number:   9999 
#>       Test          Obs      Std.Obs   Alter Pvalue
#> 1 site.fid 0.0999203829  0.718413734 greater 0.2250
#> 2 mate.fid 0.1775615101  1.239682018 greater 0.1168
#> 3     mass 0.5446640572  3.836265591 greater 0.0005
#> 4      ALE 0.0009167618 -0.004577594 greater 0.4754
#> 5       BF 0.1972100051  1.395279370 greater 0.0925
#>