Phylogeny and quantitative traits of lizards
This data set describes the phylogeny of 18 lizards as reported by Bauwens and D\'iaz-Uriarte (1997). It also gives life-history traits corresponding to these 18 species.
lizards is a list containing the 3 following objects :
is a data frame with 18 species and 8 traits.
is a character string giving the phylogenetic tree (hypothesized phylogenetic relationships based on immunological distances) in Newick format.
is a character string giving the phylogenetic tree (hypothesized phylogenetic relationships based on morphological characteristics) in Newick format.
Variables of lizards$traits are the following ones : mean.L (mean
length (mm)), matur.L (length at maturity (mm)), max.L (maximum length
(mm)), hatch.L (hatchling length (mm)), hatch.m (hatchling mass (g)),
clutch.S (Clutch size), age.mat (age at maturity (number of months of
activity)), clutch.F (clutch frequency).
This dataset replaces the former version in ade4.
Bauwens, D., and D\'iaz-Uriarte, R. (1997) Covariation of life-history traits in lacertid lizards: a comparative study. American Naturalist, 149, 91–111.
See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps063.pdf (in French).
## Not run:
if(require(ape) && require(phylobase)){
## see data
data(lizards)
liz.tr <- read.tree(tex=lizards$hprA) # make a tree
liz <- phylo4d(liz.tr, lizards$traits) # make a phylo4d object
table.phylo4d(liz)
## compute and plot principal components
if(require(ade4)){
liz.pca1 <- dudi.pca(lizards$traits, cent=TRUE,
scale=TRUE, scannf=FALSE, nf=2) # PCA of traits
myPC <- phylo4d(liz.tr, liz.pca1$li) # store PC in a phylo4d object
varlab <- paste("Principal \ncomponent", 1:2) # make labels for PCs
table.phylo4d(myPC, ratio=.8, var.lab=varlab) # plot the PCs
add.scatter.eig(liz.pca1$eig,2,1,2,posi="topleft", inset=c(0,.15))
title("Phylogeny and the principal components")
## compute a pPCA ##
## remove size effect
temp <- lapply(liz.pca1$tab, function(e) residuals(lm(e~-1+liz.pca1$li[,1])) )
temp <- data.frame(temp)
row.names(temp) <- tipLabels(liz)
## build corresponding phylo4d object
liz.noSize <- phylo4d(liz.tr, temp)
ppca1 <- ppca(liz.noSize, method="Abouheif", scale=FALSE, scannf=FALSE)
plot(ppca1)
}
}
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