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intercept value in lme

Dear Victor:

Firstly, why do you think something is wrong? Ignoring the fact that
your DV is not continuous for a moment and your distributional
assumptions assume it is, could it not be the case that conditional on
your covariates the changes in the intercept are correct?

I might be missing something, but to me it seems that you are concluding
that something is wrong because of the vast changes in the intercept. As
far as I can see in this thread so far we still do not know anything
about the covariates that could help diagnose the issue.

Syntactically, your lme model is correct (although you should switch to
lmer which is more supported), but you might consider a transformation
of you DV (e.g., log) to better coincide with your distributional
assumptions.