[R-sig-phylo] Use of OUCH package

Carl Boettiger cboettig at gmail.com
Tue Jan 19 18:09:02 CET 2010


Hi Alejandro,

Yes, the data format would be my guess too.  If X is the data for the
traits in geiger, then this should work:

ouchdata = data.frame( as.numeric(c( rep('NA',length(X)-1)  , X)) )


I.e. if you call fitContinuous(apetree, X)

then running:

ouchtree = ape2ouch(apetree)
ouchdata = data.frame( as.numeric(c( rep('NA',length(X)-1)  , X)) )

brown(ouchdata, ouchtree)


should work.  Note that OUCH normalizes the tree to unit length in the
example above, so the parameters aren't immediately comparable (just
multiply sigma^2 by tree length to compare, or I believe you can tell
ouch not to normalize).

-Carl



On Tue, Jan 19, 2010 at 4:35 AM, Alejandro Gonzalez V
<alejandro.gonzalez at ebd.csic.es> wrote:
> Hello,
>
> I am interested in using the package OUCH to estimate parameters of an OU model of evolution for a suite of traits. I've been able to run the fitContinuous function in geiger without problems, but have hit an obstacle when it comes to OUCH. I think it probably has to do with how the data need to be organized in OUCH. I would greatly appreciate any tips to run the hansen function in OUCH, especially regarding data organization.
>
> Cheers
>
> Alejandro
>
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-- 
Carl Boettiger
Population Biology, UC Davis
http://two.ucdavis.edu/~cboettig



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