Hi all,
I'm having problems calculating the the phylogenetic covariance matrix
of simulated trees.
tree1 <- birthdeath.tree(b=1, d=0, taxa.stop=8) # creates an
ultrametric tree with 8 species
plot(tree1)
vcv.phylo(tree1, cor=F) #phylogenetic covariance matrix
vcv.phylo(tree1, cor=T) #phylogenetic correlation matrix?
In most cases, the resultant matrix does not make sense: some closely
related species have zero covariance, and some off diagonal elements
are higher than the diagonal elements. Also, what's the meaning of the
correlation matrix in vcv.phylo()? Is it the covariance matrix divided
by the total time?
I'll appreciate any help with this.
Santiago
Santiago Claramunt
Museum of Natural Science,
119 Foster Hall,
Louisiana State University,
Baton Rouge, LA70803
scla...@lsu.edu
http://www.museum.lsu.edu/Claramunt/Home.html
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