[R] Multiple comparisons following nlme

[Lorenz.Gygax@fat.admin.ch]

> I need to do multiple comparisons following nlme analysis (Compare
> the effects of different treatments on a response measured 
> repeatedly over time;
> fixed = response ~ treat*time).

If you have an interaction it does not really make sense to conduct a
multiple comparison because the difference in treatment depends on time,
i.e. this presumed post-hoc test could only give you a correct result for
one of your points in time. Why not conduct this analysis and then interpret
the pattern based on the estimates of your parameters and/or on a graphical
display of your data?

If your interaction is non-significant and you drop it, you still have a
mulitvariate problem and I have never come across a multiple comparison test
for such multivariate problems (but perhaps someone else has a pointer). In
your case it might be enough to carefully decide on how the set contrasts.

Then, an additional issue would be what kind of multiple comparisons to
conduct (for univarite anova's there are at least a dozen methods). You can
always conduct several to see which of the comparisons are highly
significant and which ones might not be so strong. But usually you do not
learn more than what you get when you interpret your parameters and/or
graphs of your data.

... and by the way, I guess your model is using lme (linear mixed effects
model) in package nlme and not actually an nlme (non-linear mixed effects
model) itself.

Regards, Lorenz
- 
Lorenz Gygax, Dr. sc. nat.
Centre for proper housing of ruminants and pigs
Swiss Federal Veterinary Office, agroscope FAT Tänikon