[R] autocorrelation in count data

[dave fournier]

You can fit this model with AD Model Builder's random effects module.
there is an example fitting a Poisson and negative binomial to the 
venerable
polio data set with ar(1) random effects at

        
http://admb-project.org/examples/count-data/negative-binomial-serially-correlated-counts

A big advantage of ADMB is flexible modeling of both the mean and 
overdispersion.