[R] Is using glht with "Tukey" for lme post-hoc comparisons an appropriate substitute to TukeyHSD?

[Anne Aubut]

Hello,

I am trying to determine the most appropriate way to run post-hoc  
comparisons on my lme model.  I had originally planned to use Tukey  
HSD method as I am interested in all possible comparisons between my  
treatment levels.  TukeyHSD, however, does not work with lme.  The  
only other code that I was able to find, and which also seems to be  
widely used, is glht specified with Tukey:

summary(glht(model, linfct=mcp(Treatment="Tukey")))

Out of curiosity, I ran TukeyHSD and the glht code for a simple ANOVA  
and found that they had quite different p-values.  If the glht code is  
not running TukeyHSD, what does the "Tukey" in the code specify?  Is  
using glht code appropriate if I am interested in a substitute for  
TukeyHSD?  Are there any other options for multiple comparisons for  
lme models?  I am really interested in knowing if the Tukey contrasts  
generated from the glht code is providing me with appropriate p-values  
for my post-hoc comparisons.

I feel like I have reached a dead end and am not sure where else to  
look for information on this issue. I would be grateful for any  
feedback on this matter.


Anne Cheverie
M.Sc. Candidate
Dalhousie University