[R] nlme and multiple comparisons

Pedro J. Aphalo pedro.aphalo at cc.jyu.fi
Fri Feb 20 12:38:55 CET 2004

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 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/                       ,,,^..^,,,

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