Ben Bolker has an interesting paper (outline of a paper) comparing different approaches to estimate GLMM in R environment, which is very helpful to what I am doing right now.
The paper pointed out the following options to fit GLMM using R:
- glmm (from the repeated package)
- BUGS (through R2WinBUGS)
I am not aware of the glmmAK package before. From the first glance, it seems to be very promising in the sense that it seems to allow non-Gaussian random effect in a Bayesian framework, something similar to what npmlreg does with ML method.
============== edited on March 3 ====================
DPpackage is another package that can estimate GLMM in a Bayesian framework.
============== edited on March 5 ====================
ASReml/ASReml-R is another choice. It is not free software, but it does seem to have some unique strengths. Maybe I should download a demo copy and try it myself.
============== edited on March 29 ===================
hglm is another possibility.