Analyzing educational datasets we have samples of children from samples of class in samples of schools - we have sampling weights, so I use the survey package e.g. to do a linear model. But this kind of design also requires looking at the mixed effects. But this isn’t possible using the survey package. I can do this in nlme – but then I don't know how to account for the weighting. I guess I could use the sample weights as predictors in nlme regressions but I don’t think that is correct.
It seems that this kind of design (in fact any stratified survey sample which includes nested levels) needs analysing from both perspectives – (survey weights and mixed effects) at once – but the packages of choice for each of these perspectives, survey and nlme, each don’t seem to have slots for the other perspective.
Can someone put me on the right track, or suggest another package which does both at the same time?