glht is probably what you should be using. Both TukeyHSD and glht give essesntially identical confidence intervals for the example in ?glht. What aren't you satisfied with?
amod <- aov(breaks ~ tension, data = warpbreaks) confint(glht(amod, linfct = mcp(tension = "Tukey"))) TukeyHSD(amod) On Mon, Jan 2, 2012 at 6:19 PM, Anne Aubut <an438...@dal.ca> wrote: > 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 > > ______________________________**________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide http://www.R-project.org/** > posting-guide.html <http://www.r-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
