Hello
I have been using numeric vectors to perform phylogenetic independent contrasts
of several ecological variables for the cat phylogeny, using the ape package in
r, and I was wondering how this can be done using categorical values?
Example of how I have been using numeric values:
tree <- read.newick("phylogeny.txt")
tree <- as.phylo(tree)
tree <- root(tree,1)
x<-c() # x would vectors, for instance rainfall. One value for each operational
taxonomic unit on the tree, and the same order as they appear in the newick
file.
pic.rain <- pic(x, tree, scaled = T, var.contrasts = F, rescaled.tree = F) # To
generate the phylogenetic independent contrasts
cor.test(pic.rain,pic.rain) # To test for a correlation, obviously for rain and
rain it would be 1.
How can this be done using data such as habitat, i.e grassland/forest/desert,
or activity, i.e. nocturnal, diurnal etc?
I would be very grateful for any suggestions.
Kate.
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