The default example in the MixedLM notebook example does not work for the profile likelihood. It will be merged in #2097 mainly because the steps are instructive I guess. I don't know if it's just a hard problem, there's a bug, or if there's anything that can be done in the algorithm to restrict the covariance to be positive-(semi?)definite or to fix the likelihood calculation to account for this.
I also don't know why it works in this notebook other than the usual version/system differences.
Fix bug in profile_re, closes #2102
Thanks for catching this. I think it is fixed now.
Backport PR #2111: Mixed profile
This should close #2102. I did not correctly update the profile likelihood code after creating a class for managing the model parameters.
I also updated the notebook at: