Hi Kyle,
Tomlinson, Kyle wrote on 08/07/2011 02:30:
Dear Dr Paradis
I trust that I am allowed to contact you directly like this? If not,
my sincere apologies.
I have constructed the covariance matrix for a phylogenetic tree
(using the vcv() command), which i would like to use directly in a gls()
procedure, instead of using the tree directly as appears to be done in
ape (because I only use a very small part of the tree i have constructed..).
You should be able do drop the species absent from this "small part of
the tree" using drop.tip(), then use the resulting tree in the usual way.
Best,
Emmanuel
{I am doing this in order to check my own gls procedure and the gls
procedure of PHYLOGr which I dont trust.}
Do you know if this can be done? I have tried to figure it out by
considering the corStruct class options in nlme, but none of these
options seems to allow one to directly input an existing covariance
matrix, and I simply dont understand the object construction methods of
R well enough to build a suitable corStruct object myself.
I hope you can help.
sincerely
Kyle Tomlinson
Resource Ecology Group
Centre for Ecosystem Studies
Wageningen University
Droevendaalsesteeg 3a
6708 PB Wageningen
The Netherlands
Phone: +31 317 485314
Fax: +31 317 484845
email: kyle.tomlin...@wur.nl
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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