I am trying to do post-hoc tests associated with a repeated measures
analysis with on factor nested within respondents.
The factor (SOI) has 17 levels. The overall testing is working fine, but I
can't seem to get the multiple comparisons to work.
The first step is to "stack" the data.
Then I used "lme" to specify and test the overall model.
Finally I'm trying to use "glht" to do multiple comparisons.
Here's my code and the resulting output.
> ImpSoi<-ImpData[,c("iobs", soi)]
> ImpSoi[1:5,]
iobs soi1 soi2 soi3 soi4 soi5 soi6 soi7 soi8 soi9 soi10 soi11 soi12 soi13
soi14 soi15 soi16
1 32 7.00 7.00 7.00 7.00 7.00 6.00 7.0 7.00 5.00 7.00 7.00 7.00 7.00
5.00 7.00 6.00
2 70 5.95 4.95 7.00 4.95 5.20 5.40 4.2 3.95 4.15 4.95 4.85 4.95 6.75
5.95 5.20 5.10
3 78 3.00 1.00 4.75 2.75 3.00 4.50 4.0 4.00 1.50 4.00 4.00 4.50 2.50
3.00 3.75 4.00
4 104 3.75 3.50 6.25 5.25 4.25 3.75 4.0 5.25 4.75 4.75 5.00 5.75 6.00
4.00 4.75 3.75
5 117 5.00 5.00 4.00 5.00 2.00 4.62 5.0 4.00 4.00 4.00 5.00 4.00 4.70
4.70 5.00 2.00
soi17
1 7.00
2 5.15
3 4.00
4 5.50
5 4.00
> stack <-
reshape(ImpSoi,varying=soi,timevar="solution",idvar="iobs",sep="",
dir="long")
> solution <- factor(solution,levels(1:17),)
> stack[1:5,]
iobs solution soi
32.1 32 1 7.00
70.1 70 1 5.95
78.1 78 1 3.00
104.1 104 1 3.75
117.1 117 1 5.00
> Lmes.mod <- lme(soi ~ solution + iobs, random = ~1 | iobs/solution, data =
stack)
> anova(Lmes.mod)
numDF denDF F-value p-value
(Intercept) 1 2383 2894.8342 <.0001
solution 1 2383 0.0003 0.9870
iobs 1 147 0.0126 0.9109
> summary(glht(Lmes.mod, linfct=mcp(solution="Tukey")))
Error in mcp2matrix(model, linfct = linfct) :
Variable(s) 'solution' of class 'numeric' is/are not contained as a factor
in 'model'.
>
I don't understand the error since "solution" is clearly a factor in the
model.
Any suggestions would be welcome.
Bruce
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