Linda--> 
> 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)?

Ben-->  I agree with you and disagree with the reviewer (since the effect of
season could be expected to be similar in each year).  If you were
using lme4 you could considering making the year-by-season interaction
as a random effect (how many seasons are there?), e.g. (1|year:season)


Me--> What about a third interpretation that would accommodate a correlation structure across years and seasons?  I would think that the effect of season is going to potentially be different by year (hence the inclusion of an interaction term), but that the correlation from season to season may also depend upon the year.  This could be addressed with a slight redefinition that sampling was done by year-season, yielding 16 sampling times, where an appropriate error structure could be applied.  I suppose that this is closer to a "nested" approach, but I think this will be a lot more satisfactory when it comes to estimating errors.

Steve Denham
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