[R-sig-phylo] tests of correlated evolution

Emmanuel Paradis Emmanuel.Paradis at mpl.ird.fr
Mon Apr 14 10:35:18 CEST 2008


Katie Wagner a écrit :
> Hi Emmanuel,
> 
> Thanks for these thoughts -- this is a really interesting issue.
> 
>> In R, when you print the results of gls() with summary() you have both
>> the AIC and log-likelihood printed at once. If you use the corMartins
>> function from ape to specify an OU type correlation structure, then  
>> gls will estimate the 'alpha' parameter of the OU process and adjust  
>> the number of estimated parameters accordingly.
> 
> Yes, I used corMartins for the OU -- so that AIC should be ok.
> 
>> How did you specify the correlation structure for the 'lambda BM'  
>> model? We don't have one in ape at the moment.
> 
> Perhaps this is incorrect, but I simply transformed my phylogeny  
> according the the estimated lambda using lambdaTree() in geiger, and  
> used this transformed tree and corBrownian() to generate a correlation  
> structure to give to gls(). I think by using the transformed tree, I  
> should be generating the appropriately modified BM correlation  
> structure. But perhaps I'm misunderstanding how the lambda-modified  
> correlation structure is generated. Please correct me if I am wrong  
> here!

At least you should add 2 to the AIC returned by gls. But this won't 
solve the problem pointed out by Simon.

I shall try to implement this correlation structure in ape. Does anybody 
know where to find the formulae for this? They don't seem to be in 
Pagel's paper in Nature (1999)...

Emmanuel

> Cheers,
> Katie
> 
> _______________________________________
> 
> Katie Wagner
> Ph.D. Candidate
> Department of Ecology & Evolutionary Biology
> Corson Hall
> Cornell University
> Ithaca NY 14853
> 
> Ph: (607)254-4240	email: cew35 at cornell.edu
> 
> 
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-- 
Emmanuel Paradis
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