[R] Odd diagnostic plots in mixed-effects models

From: Andrew Robinson <andrewr_at_uidaho.edu>
Date: Tue 19 Apr 2005 - 12:41:24 EST

Dear R community,

In the excellent nlme package the default diagnostic plot graphs the innermost residuals against innermost fitted values. I recently fit a mixed-effects model in which there was a very clear positive linear trend in this plot.

I inferred that this trend occurred because my fixed effect was a two-level factor, and my random effect was a 12-level factor. The negative residuals were associated with negative random effects (because of shrinkage, I assume), and the positive with positive. The fixed effects explained little varaition. Therefore plotting the innermost residuals against the innermost fitted values had the negative residuals to the left and the positive residuals to the right, occasioning a trend.

My questions are: is it (as I suspect) harmless, or does it suggest that the model is lacking? And, is this effect likely to compromise the interpretation of any of the other standard diagnostic plots (eg qqnorm)?

Thanks much for any thoughts,


Andrew Robinson                      Ph: 208 885 7115
Department of Forest Resources       Fa: 208 885 6226
University of Idaho                  E : andrewr@uidaho.edu
PO Box 441133                        W : http://www.uidaho.edu/~andrewr
Moscow ID 83843                      Or: http://www.biometrics.uidaho.edu
No statement above necessarily represents my employer's opinion.

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Received on Tue Apr 19 12:47:58 2005

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