I have recently run some analyses which were:-
individual animal model
mean + animal + group effects (group fixed)
I then added in a permanent environmental effect
due to dams. For a number of the traits, the ide(dam)
effect went to zero. However, the LogL was slightly
lower than for the initial analysis, and the animal
genetic variance increased. I tried running the analyses
further with !continue, but nothing changed.
I presume this is a result of fixing the variance at
the parameter boundary. Should I be concerned? If I
saw these results in a paper I would wonder about them.