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 Jyv�skyl� P.O. Box 35, 40351 JYV�SKYL�, Finland Phone +358 14 260 2339 Mobile +358 50 3721504 Fax +358 14 260 2321 mailto:[EMAIL PROTECTED] http://www.jyu.fi/~aphalo/ ,,,^..^,,,
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