[R-sig-ME] Likelihood Ratio tests and fixed effects with LMER

David Duffy David.Duffy at qimr.edu.au
Tue Dec 16 23:03:19 CET 2008

On Tue, 16 Dec 2008, David Grimardias wrote:

> So for each type of behaviour, I want to know if fixed effects (habitat, parr 
> and interaction) are significant or not. As previously requested, and 
> answered by Mister Bates 
> (https://stat.ethz.ch/pipermail/r-sig-mixed-models/2008q4/001458.html), I 
> tried to use Likelihood ratio tests to determine if these two factors are 
> significant or not. Here are an example about one type of behaviour (Fprob = 
> number of probings by female) :
>> Fprob.lmer.full<-lmer(Fprob ~habitat+parr+habitat:parr +(1|female),family=poisson)
>> Fprob.lmer.add<-lmer(Fprob ~habitat+ parr +(1|female),family=poisson)
>> Fprob.lmer.hab<-lmer(Fprob ~habitat+(1|female),family=poisson)
>> Fprob.lmer.parr<-lmer(Fprob ~ parr +(1|female),family=poisson)
>> Fprob.lmer.null<-lmer(Fprob ~1+(1|female),family=poisson)
> So, I considered as LR test for each effect :
> Habitat : Chi2 = 0.9866; df = 1; p = 0.3206
> Parr : Chi2 = 2.0372; df = 1; p = 0.1535
> Interaction Habitat :parr : Chi2 = 0.545; df = 1; p = 0.4604
> I first would like to know if I am wrong, or if I correctly analysed my data?

Yes, though there has been some discussion on this list about the adequacy of
the chi-square approximation for the LRTS in these models.

You should also compare the results to those from simple models ignoring
the fact that females may appear more than once.  They should be broadly
similar.  How large is the variance due to the random effects anyway?

> Second, I guess that LMER function is optimizing REML by default (if I 
> correctly read the help file), but I had understood that we need to optimize 
> ML to compare fixed effects (from  Pinheiro J C & Bates D M, "Mixed-effects 
> models in S and S-PLUS"). If right, what do I need to change to correctly 
> analyzed my data with Likelihood ratio tests ?

REML is not done for GLMMs IIRC.

David Duffy.

| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v

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