lizards {adephylo} | R Documentation |
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.
data(lizards)
lizards
is a list containing the 3 following objects :
Variables of lizards$traits
are the following ones :
mean.L (mean length (mm)), matur.L (length at maturity (mm)),
max.L (maximum length (mm)), hatch.L (hatchling length (mm)),
hatch.m (hatchling mass (g)), clutch.S (Clutch size),
age.mat (age at maturity (number of months of activity)),
clutch.F (clutch frequency).
This dataset replaces the former version in ade4.
Bauwens, D., and D'iaz-Uriarte, R. (1997) Covariation of life-history traits in lacertid lizards: a comparative study. American Naturalist, 149, 91–111.
See a data description at http://pbil.univ-lyon1.fr/R/pps/pps063.pdf (in French).
## see data data(lizards) liz.tr <- read.tree(tex=lizards$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) }