I have an experimental design measuring germination of a single species of tree under different treatments. The treatments include; cattle grazing and no cattle grazing and rodents and no rodents. The cattle grazing treatments are a paired design with a subplot with cattle fencing directly adjacent to a subplot without cattle fencing. There are 16 plots (32 sub plots) in all.
Unfortunately, the rodent cages we used would be completely destroyed by cattle had we put them in grazing subplots, so they were only installed in the no-grazed plots (fenced enclosure) over half the planted tree seeds. I was going to use GLMM in R to model the binary germination yes/no response.
If I am trying to determine the effects of grazing and no grazing how would I account for the treatment of rodent cages within the no-grazing treatment? Would I treat it as a random effect or just add it into the model as another fixed effect?