[R] post hoc test for lme using glht ?
David Winsemius
dwinsemius at comcast.net
Thu Jul 22 00:53:24 CEST 2010
On Jul 21, 2010, at 6:36 PM, SNAFU1 wrote:
>
> Hi,
>
> I have a fairly simple repeated measures-type data set I've been
> attempting
> to analyze using the lme function in the nlme package. Repeated
> searches
> here and other places lead me to believe I have specified my model
> correctly.
>
> However, I am having trouble with post-hoc tests. From what I
> gather, other
> people are successfully using the glht function from the multcomp
> package to
> perform post-hoc tests. I've tried multiple iterations, but can't
> seem to
> get it to work. Here is (a subset of) what I have been trying. Any
> help
> would be greatly appreciated:
>
>> model.3<-lme(fixed=Totnum~Wk*Pop, random=~1|nUID, data=nona)
> #Wk has 6 levels, 0-5; Pop has 2 levels; nUID is a unique ID given
> to each
> individual (multiple individuals from each population were re-
> measured each
> week)
>> anova(model.3)
> numDF denDF F-value p-value
> (Intercept) 1 592 649.7753 <.0001
> Week 5 592 302.9706 <.0001
> Pop 1 222 70.7268 <.0001
> Week:Pop 5 592 36.8576 <.0001
Come on... are you cutting and pasting fro disjoint sections of your
console? The formula says Wk and the parameter name in the anova
result is Week. What gives?
>> summary(glht(model.3, linfct=mcp(Wk = "Tukey")))
> Error in mcp2matrix(model, linfct = linfct) :
> Variable(s) ‘Wk’ of class ‘integer’ is/are not contained as a
> factor in
> ‘model’.
>> is.factor(Wk)
Well, this object should not even exist at the top level environment
unless you attached it and didn't tell us about it.
Try:
Wk <- NULL
nona$Wk <- factor(nona$Wk)
Then re-run your code.
> [1] FALSE
>> Week<-factor(Wk)
>> is.factor(Week)
> [1] TRUE
>> model.3<-lme(fixed=Totnum~Week*Pop, random=~1|nUID)
>> summary(glht(model.3, linfct=mcp(Week = "Tukey")))
> Error in contrMat(table(mf[[nm]]), type = types[pm]) :
> less than two groups
>
> Thanks,
>
> Rob
--
David Winsemius, MD
West Hartford, CT
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