[R] nlme and multiple comparisons

[Pedro J. Aphalo]

This is only partly a question about R, as I am not quite sure about the 
underlying statistical theory either.

I have fitted a non-linear mixed-effects model with nlme. In the fixed 
part of the model I have a factor with three levels as explanatory 
variable. I would like to use Tukey HSD or a similar test to test for 
differences between these three levels.

I have two grouping factors: 'plant' to which the treatments were 
assigned at random, and 'leaf' which are subsamples.

With summary, with the default setting for contrasts I get two of the 
possible three comparisons. One possibility that I can think of is to 
change the order of the levels in the factor, repeat the fit, use 
summary again, and finally use p.adjust. Would this be valid?

Is there a more elegant solution?

If it matters, the data are slightly unbalanced (missing observations).

Sorry that this message became so long... Thanks in advance for any 
suggestions, and I hope I haven't missed the answer when looking at the 
help pages, FAQ, MASS(3ed) and Pinheiro and Bates' book.

Pedro.

-- 
==================================================================
Pedro J. Aphalo
Department of Biological and Environmental Science
University of Jyväskylä
P.O. Box 35, 40351 JYVÄSKYLÄ, Finland
Phone  +358 14 260 2339
Mobile +358 50 3721504
Fax    +358 14 260 2321
mailto:pedro.aphalo at cc.jyu.fi
http://www.jyu.fi/~aphalo/                       ,,,^..^,,,