[R] post hoc tests two way repeated measures anova

[Frank E Harrell Jr]

Dieter Menne wrote:
> Jean-Pierre Bresciani <bresciani <at> tuebingen.mpg.de> writes:
> 
>> is there a specific/appropriate function/package to perform post hoc tests
>> when running a two way repeated measures anova? I'm looking for something
>> that will be equivalent to the 'TukeyHSD()' for between subjects anova (with
>> 'aov()'). For one way repeated measures anova, the 'pairwise.t.test()'
>> function seems to work correctly but the results are questionable for two+
>> way anovas, as if the adjustment of the p values for multiple comparisons
>> was not correct.
> 
> Classical repeated measurement has fallen a bit out of favor, because mixed
> models as in lme (package nlme) and lmer(package lme4) are MUCH more flexible
> and in general more stable when data are missing.

And don't forget generalized least squares (gls in nlme) which has the 
same advantages using only fixed effects.

Frank

> 
> So I recommend to switch to lme (better documented, currently), and use
> 
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/20725.html
> 
> as a starter when trying to do multiple comparisons.
> 
> Dieter Menne (Tübingen)
> 

-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University