[R] Odd diagnostic plots in mixed-effects models

[Andrew Robinson]

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
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