ungulates {ade4}R Documentation

Phylogeny and quantitative traits of ungulates.

Description

This data set describes the phylogeny of 18 ungulates as reported by Pélabon et al. (1995). It also gives 4 traits corresponding to these 18 species.

Usage

data(ungulates)

Format

fission is a list containing the 2 following objects :

tre
is a character string giving the phylogenetic tree in Newick format.
tab
is a data frame with 18 species and 4 traits

Details

Variables of ungulates$tab are the following ones :
afbw: is a numeric vector that describes the adult female body weight (g)
mnw: is a numeric vector that describes the male neonatal weight (g)
fnw: is a numeric vector that describes the female neonatal weight (g)
ls: is a numeric vector that describes the litter size

Source

Data were obtained from Pélabon, C., Gaillard, J.M., Loison, A. and Portier, A. (1995) Is sex-biased maternal care limited by total maternal expenditure in polygynous ungulates? Behavioral Ecology and Sociobiology, 37, 311–319.

Examples

data(ungulates)
ung.phy <- newick2phylog(ungulates$tre)
plot.phylog(ung.phy,clabel.l=1.25,clabel.n=0.75)
ung.x <- log(ungulates$tab[,1])
ung.y <- log((ungulates$tab[,2]+ungulates$tab[,3])/2)
names(ung.x) <- names(ung.phy$leaves)
names(ung.y) <- names(ung.x)
plot(ung.x,ung.y)
abline(lm(ung.y~ung.x))
symbols.phylog(ung.phy,ung.x-mean(ung.x))
dotchart.phylog(ung.phy,ung.x,cle=1.5,cno=1.5,cdot=1)
orthogram(ung.x,ung.phy$Bscores,nrep=9999)
ung.z <- residuals(lm(ung.y~ung.x))
names(ung.z) <- names(ung.phy$leaves)
dotchart.phylog(ung.phy,ung.z,cle=1.5,cno=1.5,cdot=1,ceti=0.75)
orthogram(ung.z,ung.phy$Bscores,nrep=9999)

Worked out examples


> library(ade4)
> ### Name: ungulates
> ### Title: Phylogeny and quantitative traits of ungulates.
> ### Aliases: ungulates
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ungulates)
> ung.phy <- newick2phylog(ungulates$tre)
> plot.phylog(ung.phy,clabel.l=1.25,clabel.n=0.75)
> ung.x <- log(ungulates$tab[,1])
> ung.y <- log((ungulates$tab[,2]+ungulates$tab[,3])/2)
> names(ung.x) <- names(ung.phy$leaves)
> names(ung.y) <- names(ung.x)
> plot(ung.x,ung.y)
> abline(lm(ung.y~ung.x))
> symbols.phylog(ung.phy,ung.x-mean(ung.x))
> dotchart.phylog(ung.phy,ung.x,cle=1.5,cno=1.5,cdot=1)
> orthogram(ung.x,ung.phy$Bscores,nrep=9999)
class: krandtest 
Monte-Carlo tests
Call: orthogram(x = ung.x, orthobas = ung.phy$Bscores, nrepet = 9999)

Test number:   4 
Permutation number:   9999 
   Test       Obs    Std.Obs     Alter Pvalue
1 R2Max 0.4702619  3.5473870   greater 0.0093
2 SkR2k 7.2902944 -1.1263280      less 0.1327
3  Dmax 0.2473821  0.9308545 two-sided 0.3593
4   SCE 0.4154382  0.5872891   greater 0.1921

other elements: NULL
> ung.z <- residuals(lm(ung.y~ung.x))
> names(ung.z) <- names(ung.phy$leaves)
> dotchart.phylog(ung.phy,ung.z,cle=1.5,cno=1.5,cdot=1,ceti=0.75)
> orthogram(ung.z,ung.phy$Bscores,nrep=9999)
class: krandtest 
Monte-Carlo tests
Call: orthogram(x = ung.z, orthobas = ung.phy$Bscores, nrepet = 9999)

Test number:   4 
Permutation number:   9999 
   Test       Obs    Std.Obs     Alter Pvalue
1 R2Max 0.3566524  0.7452384   greater 0.2572
2 SkR2k 5.3204632 -2.2736636      less 0.0085
3  Dmax 0.4273104  2.5589386 two-sided 0.0118
4   SCE 1.0474954  2.8739955   greater 0.0229

other elements: NULL
> 
> 
> 
> 

[Package ade4 Index]