[R-sig-ME] Mixed model and negative binomial distribution

David Atkins datkins at u.washington.edu
Thu Oct 4 07:20:59 CEST 2012


You might take a look at a paper we wrote that is a tutorial on mixed 
model "count regression" -- including negative binomial and various 
zero-altered models.  It also has a fairly extensive R code "appendix". 
  The draft / data / R code can be found:


It's the following paper:

Atkins, D. C., Baldwin, S., Zheng, C., Gallop, R. J., & Neighbors, C. 
(in press). A tutorial on count regression and zero-altered count models 
for longitudinal addictions data.

Finally, you can fit a type of over-dispersed Poisson model using 
glmer() in lme4, or a true negative binomial mixed model using glmmADMB 
package.  (I *think* an example of the latter is in the R code, though 
we focused mostly on lme4 and MCMCglmm.)

Hope that helps.

cheers, Dave

Dave Atkins, PhD
University of Washington
datkins at u.washington.edu

August 1 - October 30:

Universitat Zurich
Psychologisches Institut
Klinische Psychologie
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+41 44 635 71 75

Dear mixed-model brain trust:

I am comparing snag (dead tree) densities 1 year and 5 years after
silvicultural treatment in forest plots to densities prior to treatment. In
nlme, my model is

lme(snagnum~treatment, random=(~1|plot), correlation=corExp(form=~year)).

{Treatment is a factor with values of Pre/1-year post/5-year post}. This
gives reasonable output, but I'm having a niggling doubt that I should be
using something akin to a negative binomial distribution, since about half
of the values are zeros (i.e., many plots had no snags prior to treatment,
and did not gain additional snags as a result of treatment). Can anyone
suggest an appropriate package and associated syntax for doing this mixed
model based on an alternative probability density function?

--Seth W. Bigelow

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