[R-sig-ME] AIC in nlmer

Helen Sofaer helen at lamar.colostate.edu
Tue Apr 12 23:41:44 CEST 2011

 Hi Ben,
 Thanks for taking a look at what I found. I’ll certainly use nlme for 
 now, and I’ll look forward to seeing the issues in lme4 get resolved. I 
 hadn’t realized that only the Laplace transformation was supposed to be 
 functional in nlmer.

 I was also wondering if there is any documentation about what constants 
 are dropped in calculating the likelihoods in the different packages 
 and/or using different approximation methods. As you mentioned, it’s 
 often hard to tell if the likelihoods from different packages are 
 comparable, and among other things, I’d like to compare the mixed models 
 I’m building to a model with only fixed effects. The paper you 
 suggested, which notes that the marginal AIC favors models without 
 random effects, made me more curious to do this. My experience is that 
 there’s no way to run a model without random effects in lme4, but I 
 wasn’t sure about nlme. More broadly, can a marginal AIC given by 
 nlme/lme4, based on the likelihood after integrating over the random 
 effect parameters, be compared to an AIC value based on a likelihood for 
 a fixed-effect model (e.g. from nls), as long as the dropped constants 
 don’t differ?

 Thanks again,

 Helen Sofaer
 PhD Candidate in Ecology
 Colorado State University

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