I have fitted an lme model using a factor variable studytreat. It appears in the model in two places, as a fixed effect, and also to model heterogeneity in the residual variance so that each level of studytreat has its own variance. This is the model:
modelLME <- lme(logkp ~ studytreat,
random = ~ -1 + STUDY | ptno,
weights = varIdent(form = ~1 | studytreat))
I have a problem which doesn't fill me with confidence in lme! If I label the levels in studytreat as 11, 12, 21, 24 (in that order) then the function works fine. However, if I switch the numbers around to get 11, 21, 12, 42 then when I call summary(modelLME)$apVar I get the error message:
[1] "Non-positive definite approximate variance-covariance"
Does anyone have any idea why this should make a difference?