I have a question on how to specify a GLMM. I made an experiment with two treatments (control and treated) to test the effect of a water contaminant on reproductive cells of tadpoles. I have data on proportion of oocytes in a histological photo. I took several photos for each animal. My main interest is to test the effect of the treatment on the response variable. However, animals happen to be in different developmental stages. I have 5 stages in total. I tried to model these data using a glm including treatment and stage as fixed factor and the photos nested within an animal as random factors.
So first, I found out using:
that the response variable is better modelled by a negative binomial, so I went on and used the
lme4::glm.nb like this:
My question is: should I include the stage as fixed factor or a random factor to which Animal and Photo would be nested within? I'm only interested in the effect of the treatment, I only included the stage to control for this effect. The point is, a given animal will always have the same stage. Is my model above correct?