Dear Simon,
Simon Maccracken Stump wrote on 09/04/2011 00:37:
Dear everyone,
Good morning. I have been trying to run a phylogenetic independent
contrast in R using Phylocom, using a tree from Phylomatic. I am
having some difficulty, and was wondering if anyone could help.
Here is what I have done:
library(picante)
mytree <-read.tree('phylo')
mytraits<-read.table('traits_means.txt', skip=1, header=TRUE, row.names=1)
traits2 <- mytraits[mytree$tip.label, ]
multiPhylosignal(traits2, mytree)
When I do this, I get the error message:
Error in vcv.phylo(phy, cor = TRUE) : the tree has no branch lengths
Is it clear what I’ve done wrong? Do I need to input branch lengths,
and if so, what is the best way to go about doing that, or even
finding the branch lengths (if it makes a difference, I am working
with annual plants)?
Maybe you should get a tree with branch lengths from phylomatic?
Also, I’ve tried just assigning everything a branch length of 1, and
it seems to not like the fact that my tree has ploytomies. What can I
do about that?
I guess you didn't use something like compute.brlen(tr, 1).
Last, I actually have data from several individuals of each species.
Is there some way to incorporate that, or do I just need to use the
averages?
I don't think there's an established method to deal with intraspecific
variation to calculate phylogenetic signal. For contrasts, see:
?pic.ortho
?varCompPhylip
HTH
Emmanuel
Thanks,
Simon
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--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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