I am trying to analyse the effect of a treatment on the abundance of three response variables (either as absolute values, in which case they are counts with some zeros, or as relative proportions). Plots are stratified across 5 sites, each with 2 or 3 replicates of each of the 5 treatment levels. Each plot was sampled 3 times.
Because of the structure of my response variable I think I should use a generalised linear model, and was planning to analyse each of my three response variables separately. To take into account the repeated measures on the same individual, I suspect a generalised linear mixed effects model is likely to be the only way to proceed. The treatment would be my fixed effect, and site/block/season the random effects.
Can anyone suggest whether a more simple analysis might be possible? More specifically, is it possible to take into account repeated measures (at three distinct time points) within a generalised linear model?
Thanks in advance for any feedback, and apologies if this is too vague.