I set up a study using a BACI design testing for the impacts of a restoration treatment on several species of wildlife. I conducted mark-recapture on small mammals in trapping grids. I had planned to analyze these data using closed capture models to estimate abundance on each grid by year, then use those abundance estimates as response variables in the BACI model. Then I became aware of random effects and zero-inflated models and planned to incorporate those.
This is what I imagine is a common problem in our world. Does anyone have thoughts integrating closed capture abundance estimates with generalized linear mixed models?