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lmer residual variance estimate with prior weights [SEC=UNCLASSIFIED]
2 messages · Steve Candy, Ben Bolker
1 day later
Steve Candy <Steve.Candy at ...> writes:
Hi mixed-modellers
I am fitting a simple linear mixed model to some abundance data which are mean densities on the log10 scale for a set of spatial cells with sample sizes used as prior weights. I define a random cell intercept model and fit a linear year trend. I get very similar estimates of the intercept and slope when using each of lmer(.) and asreml(.) but get much smaller estimates of the SEs of these parameters for lmer(.). This is due to a much smaller estimate of the residual standard error with estimate of 0.534 for lmer and 3.016 for asreml with corresponding estimates of the cell-level standard deviation of 0.0014 for lmer and 0.2151 (=0.04626^0.5) for asreml. Comparing these to a simple lm(.) fit gives a similar but slightly higher estimate of the residual standard error compared to the asreml estimate with the a value of 3.116. The lmer estimate appears to be orders of magnitude out. Am I interpreting these results correctly? Has it something to do with how the weighting is done!
[context snipped because gmane hates me] I have a sneaking suspicion that lmer doesn't scale the sum of the weights to 1 before doing calculations, as it arguably should. What happens if you manually scale the weights to 1 (which seems appropriate in this case)? Ben Bolker