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Dear R People: Sorry for the off-topic. Could someone recommend a good reference for using the EM algorithm on mixed models, please? I've been looking and there are so many of them. Perhaps someone here can narrow things down a bit. Thanks in advance, Sincerely, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown

As I understand it lme (in R v1.9.x) estimates random effect variances on a log scale, constraining them to be positive. Whilst this seems sensible, it does lead to apparently biased estimates if the variance is actually zero - which makes our simulation results look strange. Whilst we need to think a bit deeper about it - I still haven't got my head around what a negative variance could