Saturday, February 27, 2010

An interesting paper

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:
  1. glmer
  2. glmmML
  3. glmm (from the repeated package)
  4. glmmADMB
  5. MCMCglmm
  6. glmmBUGS
  7. glmmPQL
  8. BUGS (through R2WinBUGS)
  9. glmmAK
And I would like to add one more, npmlreg.

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. 


Eric said...

So, based on your experience, which package would you suggest using?

Shige said...

They each has unique advantages and weaknesses. In my work, I use glmer ("lme4" package) and allvc ("npmlreg" package) a lot; and I am starting to get in the world of Bayesian analysis, and MCMCglmm is a real life saver.