maples: Phylogeny and quantitative traits of flowers

In adephylo: Exploratory Analyses for the Phylogenetic Comparative Method

Phylogeny and quantitative traits of flowers

Description

This data set describes the phylogeny of 17 flowers as reported by Ackerly and Donoghue (1998). It also gives 31 traits corresponding to these 17 species.

Format

tithonia is a list containing the 2 following objects : - tre: a character string giving the phylogenetic tree in Newick format.
- tab: a data frame with 17 species and 31 traits.

Note

This dataset replaces the former version in ade4.

References

Ackerly, D. D. and Donoghue, M.J. (1998) Leaf size, sappling allometry, and Corner's rules: phylogeny and correlated evolution in Maples (Acer). American Naturalist, 152, 767–791.

Examples

if(require(ape) && require(phylobase)){

data(maples)

## see the tree
tre <- read.tree(text=maples$tre)
plot(tre)
axisPhylo()

## look at two variables
dom <- maples$tab$Dom
bif <- maples$tab$Bif
plot(bif,dom,pch = 20)
abline(lm(dom~bif)) # a strong negative correlation ?
summary(lm(dom~bif))
cor.test(bif,dom)

## look at the two variables onto the phylogeny
temp <- phylo4d(tre, data.frame(dom,bif, row.names=tre$tip.label))
table.phylo4d(temp) # correlation is strongly linked to phylogeny

## use ape's PIC (phylogenetic independent contrasts)
pic.bif <- pic(bif, tre)
pic.dom <- pic(dom, tre)
cor.test(pic.bif, pic.dom) # correlation is no longer significant
}

adephylo documentation built on Oct. 6, 2023, 5:07 p.m.