Dear All,

I have two quick questions about my study design. For 4 years, once every season, we destructively sampled larvae on bushes (the same bushes every time) and measured parasitism on these larvae. We had 10 bushes per location and two locations. 
We are interested in whether parasitism changed over the years and varied with season. With repeated measures on bushes, and bushes nested in location, my model looks like this:

model<-glmmPQL(parasitism ~ year:season + year + season, random=~1|location/bush, family=binomial)

Question 1: A reviewer of our paper suggested that seasons are nested 
within years and that we should include this in the model. However, I 
think seasons are crossed with years, not nested. If that's the case, 
can I leave the model as is (as far as season and years are concerned)?

Question 2: I know it is ridiculous to have location as a random factor since it only has two levels. Could I alternatively just include it as a fixed factor like this: glmmPQL(parasitism ~ year:season + year + season + location, random=~1|bush, family=binomial)? Totally leaving it out is not an option because levels of parasitism vary significantly with location (but that is of no interest to us, hence not really a fixed factor, just a covariate?).

Thank you already for any answers and suggestions!

PS. I used glmmPQL instead of lmer because without the over-/underdispersion function in lmer everything was highly significant, whereas with glmmPQL it is not.


 		 	   		  
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