[R] Re peated Measure ANOVA-Old question

[Gavin Simpson]

On Wed, 2008-07-30 at 00:49 -0700, Mark Difford wrote:
> Hi Chunhao,
> 
> If you carefully read the posting that was referred to you will see that
> lme() and not lmer() was used as an example (for using with the multcomp
> package). lmer() was only mentioned as an aside... lmer() is S4 and doesn't
> work with multcomp, which is S3.

That is not true (but it may once have been?). multcomp ``suggests''
lme4 and is distributed with a vignette that has a lmer example with the
same random effect expression as the R-Help thread you directed the OP
to read.

The OP's example works for me with latest CRAN versions of multcomp,
lme4 and Matrix installed (well, with a warning about false convergence
from nlminb in the lmer call and a warning from the call to glht about
the covariate interaction and questioning if the default contrasts are
appropriate - all things for Chunhao to consider himself me thinks...).

Chunhoa, I'm not familiar enough with lme4 to know what is the correct
way to specify the random effects you want. You could consider moving
this onto the R-mixed-models SIG:

https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

or search the archives of that list as lmer/lm4 are discussed there
quite a lot.

HTH

G

> 
> Apropos of specifying random effects: an example was given in the posting
> showing that aov(... +Error(...)) and lme(..., random =...) give the same
> result. Use that as your guideline.
> 
> HTH, Mark.
> 
> 
> ctu wrote:
> > 
> > Tank you (Anna & Mark) very much for this super information
> > Let me confirm that IF I want to perform the RM-ANOVA
> > I should use "lmer" and perform the post-hoc test by using "glht", right?
> > 
> > Because I am not so familiar with "lmer" so I have two more questions.
> > Let me use that following example again,
> > 1. Is the random effect statement correct? if no what will be?
> > 2. What did I do wrong in glht?
> > 
> > 
> > require(lme4);require(nlme)
> > group <-rep(rep(1:2, c(5,5)), 3);time <-rep(1:3, rep(10,3));subject <-  
> > rep(1:10,3)
> > p.pa <- c(92, 44, 49, 52, 41, 34, 32, 65, 47, 58, 94, 82, 48, 60, 47,
> > 46, 41, 73, 60, 69, 95, 53, 44, 66, 62, 46, 53, 73, 84, 79)
> > P.PA <- data.frame(subject, group, time, p.pa)
> > P.PA$group=factor(P.PA$group);P.PA$time=factor(P.PA$time)
> > P.PA$subject=factor(P.PA$subject)
> > 
> > tlmer<-lmer (p.pa ~ time * group + (time*group | subject), data=P.PA )
> > 
> >> summary(glht(tlmer,linfct=mcp(group="Tukey")))
> > Error in UseMethod("fixef") : no applicable method for "fixef"
> > In addition: Warning message
> > 
> > Thank you very much
> > Chunhao
> > 
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> > 
> > 
> 
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