maples: Phylogeny and quantitative traits of flowers

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

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.

Usage

data(maples)

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.

Source

Data were obtained from the URL http://www.stanford.edu/~dackerly/acerdata.html (no longer maintained).

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

## Not run: 
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
}

## 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


	Pearson's product-moment correlation

data:  pic.bif and pic.dom
t = -1.5823, df = 14, p-value = 0.1359
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 -0.7419510  0.1316186
sample estimates:
       cor 
-0.3894993 

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