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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