Hi all,
As a side note to this discussion: ape has now the function
compute.brtime (though it considers only node ages), available on ape's
SVN in R/compute.brtime.R.
Cheers,
Emmanuel
Scott Chamberlain wrote on 14/07/2011 11:15:
Hi Roger,
Can you provide a reproducible example (perhaps a subset of your tree
and their tip and node ages if the tree is very large)? I don't know
what the problem could be without the data, but perhaps Gene knows?
Scott
On Wednesday, July 13, 2011 at 10:57 PM, Roger Close wrote:
Hello all,
I wish to transform branch lengths on a tree according to ages of
terminal taxa and internal node ages; to this end I have tried to
implement the script written by Gene Hunt mentioned in a recent post
to this list
(http://www.mail-archive.com/r-sig-phylo@r-project.org/msg01005.html;
script available at https://gist.github.com/938313).
However, when attempting to run the command scalePhylo(tr, tip.ages,
node.mins), it crunches away for hours on my computer (a 2010 MacBook
Pro Core i7, which is quite fast). Clearly there's something wrong.
I'm afraid I don't know enough about R to debug a script.
I thought I'd send this to the list in case someone other than Gene
Hunt or Scott Chamberlain has had a go at using this script.
Thanks in advance,
Roger
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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