ungulates: Phylogeny and quantitative traits of ungulates.

In adephylo: adephylo: exploratory analyses for the phylogenetic comparative method.

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

Note

This dataset replaces the former version in ade4.

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

## Not run: 
if(require(ape) && require(phylobase)){
## load data
data(ungulates)
tre <- read.tree(text=ungulates$tre)
plot(tre)

## look at two traits
afbw <- log(ungulates$tab[,1])
neonatw <- log((ungulates$tab[,2]+ungulates$tab[,3])/2)
names(afbw) <- tre$tip.label
names(neonatw) <- tre$tip.label
plot(afbw, neonatw) # relationship between traits
lm1 <- lm(neonatw~afbw)
abline(lm1)
x <- phylo4d(tre, cbind.data.frame(afbw, neonatw)) # traits on the phylogeny

## test phylogenetic inertia in residuals
orthogram(residuals(lm1), x) 
}

## End(Not run)

Example output

Loading required package: ade4
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges

class: krandtest lightkrandtest 
Monte-Carlo tests
Call: orthogram(x = residuals(lm1), tre = x)

Number of tests:   4 

Adjustment method for multiple comparisons:   none 
Permutation number:   999 
   Test       Obs    Std.Obs   Alter Pvalue
1 R2Max 0.3566524  0.7054886 greater  0.269
2 SkR2k 5.1897459 -2.3175072 greater  0.991
3  Dmax 0.4273104  2.4612224 greater  0.018
4   SCE 1.1067580  3.0578316 greater  0.016

adephylo documentation built on May 2, 2019, 4:54 p.m.