[R-sig-ME] Model fit with a Poisson, cross-validation?

Lindsay Reynolds lindsayr at warnercnr.colostate.edu
Thu May 28 20:41:02 CEST 2009

Hello List,

I am in the process of learning mixed models in R and have a basic 
question. I am currently working on a model selection analysis with a 
suite of mixed models and Poisson-distributed count data. After reading 
Bolker et al 2009 (Trends In Ecology & Evolution 24:127-135) and having 
a basic understanding of standard model selection analysis (Burnam & 
Anderson) I was convinced that I could use the AICc alone to determine 
the best models. However, it has been suggested to me that I also 
include some sort of "R^2" value in my analysis to measure absolute fit 
of the model to the data. Since this does not exist for mixed models 
with Poisson distributed data, is was further suggested that I try 
cross-validating my models by building a predicted data set that I could 
compare to my observed data set.Can anyone point me to references who 
have done this sort of thing with mixed models in R? I would be much 

More details on my analysis:
My data are counts of trees established per year within 'site'. I have 
built several models that include various combinations of climate 
variables as fixed explanatory variables and all models have 'site' as a 
random effect. In every model I include a continuous predictor variable 
called 'year' that accounts for the fact that we expect there to always 
be more young trees than older trees due to natural mortality. (year = 
1,2,3... n). I have tested for overdispersion using penalized, weighted 
residual sum of squares (pwrss) divided by the number of observations: 
pwrss/n. The values range between 0.9 and 2. I have interpreted this as 
my data are not too overdispersed so I have continued with using the 
Poisson distribution in my models. Also, I have run all my models with 
Poisson and with quasiPoisson and the results are very similar. My 
models look like this, with variations on the fixed effects:

rosite<-glmer(trees~wy+wy1+year+(1|site), family=poisson)

Many thanks,

Lindsay Reynolds
Ph.D. Candidate
Graduate Degree Program in Ecology
Office location: Forestry 208
Colorado State University
Campus Delivery 1472
Ft. Collins, CO 80523-1878

More information about the R-sig-mixed-models mailing list