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Phylogeny and quantitative traits of ungulates.

ungulates.Rd

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(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)

if (requireNamespace("adephylo", quietly = TRUE) & requireNamespace("ape", quietly = TRUE)) {
  tre <- ape::read.tree(text = ungulates$tre)
  adephylo::orthogram(ung.x, tre)
  ung.z <- residuals(lm(ung.y~ung.x))
  names(ung.z) <- names(ung.phy$leaves)
  dotchart.phylog(ung.phy,ung.z,cle=1.5,cno=1.5,cdot=1,ceti=0.75)
  adephylo::orthogram(ung.z, tre)
}



#> class: krandtest lightkrandtest 
#> Monte-Carlo tests
#> Call: adephylo::orthogram(x = ung.z, tre = tre)
#> 
#> Number of tests:   4 
#> 
#> Adjustment method for multiple comparisons:   none 
#> Permutation number:   999 
#>    Test       Obs    Std.Obs   Alter Pvalue
#> 1 R2Max 0.3566524  0.7448346 greater  0.237
#> 2 SkR2k 5.1897459 -2.3174353 greater  0.991
#> 3  Dmax 0.4273104  2.4519295 greater  0.015
#> 4   SCE 1.1067580  3.1277143 greater  0.014
#>