Thanks, @jiltao. That is likely the case, especially as I left out a step. After calculating the sum of squared deviations and before taking a square root, there needs to be a division by an appropriate degrees of freedom value. So we would have the deviations of the values predicted by the model from the observed values, each then squared, summed over all observations, divided by an appropriate, model-based, degrees of freedom value. That looks, at least to me, a lot like a variance due to things not in the model like unmodeled fixed or random effects. If the model was as simple as a mean, it would be the variance, wouldn't it? Taking the square root gives a standard deviation, or in the case of a general linear model, the RMSE.
Since the predicted values are empirical BLUPs, this calculated value is a measure of how closely the empirical BLUPs represent the variability in the raw data. I really need my copy of Graybill's Theory and Application of the Linear Model to refresh my BLUP knowledge, but it is in a box in the basement somewhere...
SteveDenham
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