Description Usage Format Note Source References Examples
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.
1 |
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.
This dataset replaces the former version in ade4.
Data were obtained from the URL http://www.stanford.edu/~dackerly/acerdata.html (no longer maintained).
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ## 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)
|
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.