[R] moving from aov() to lmer()

Adam D. I. Kramer adik at ilovebacon.org
Sun Sep 14 23:22:10 CEST 2008

On Sat, 13 Sep 2008, roberto toro wrote:

> Hello,
> I've used this command to analyse changes in brain volume:
> mod1<-aov(Volume~Sex*Lobe*Tissue+Error(Subject/(Lobe*Tissue)),data.vslt)
> I'm comparing males/females. For every subject I have 8 volume measurements
> (4 different brain lobes and 2 different tissues (grey/white matter)).
> As aov() provides only type I anovas, I would like to use lmer() with type
> II, however, I have struggled to find the right syntaxis.
> How should I write the model I use with aov() using lmer()??
> Specifying Subject as a random effect is straightforward
> mod2<-lmer(Volume~Sex*Lobe*Tissue+(1|Subject),data.vslt)
> but I can't figure out the /(Lobe*Tissue) part...

You're trying to model a separate effect of lobe, of tissue, and of the
interaction between lobe and tissue for each subject, so you want


...the resulting fixed effect for Lobe, Tissue, and L:T in the summary()
then corresponds to the within-subjects effect aggregated (but not exactly
AVERAGED) across subjects. So, it's not exactly providing you a Type II
ANOVA...it's doing a mixed-effects model (or HLM, if you prefer), which as
you've written it is a Type III analysis (though once again, not an ANOVA in
the classical sense).

To get something more akin to type II using the lmer function (and I trust
someone will pipe up if there is a better way), you could first fit


...and interpret the coefficients and effects provided by it, then fit the
crossed model to get the coefficients and effects for the higher-order

I hope this made sense and that I have understood you correctly.


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