[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)...


> 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
Institut de Recherche pour le Développement
GAMET - BP 5095
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   mailto: Emmanuel.Paradis at mpl.ird.fr

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