I have data from 7 sites, which are under 3 types of AMD impairment (2 impaired, 3 recovered, 2 unimpaired); each site has 3 different treatments (Undisturbed Upstream, Disturbed, Undisturbed Downstream). Sites were sampled right before the treatment (day 0), and then 5, 10, 15, and 30 days after treatment.
I want to see if there are any significant differences in macro measurements (abundance, richness, feeding groups, etc.) over time across the AMD impairment types and the treatments.
My first thought is a repeated-measures ANOVA like:
Macro_abund ~ AMD_Impairment*Treatment*Day + Error(Site/Impairment*Section)
Using function aov in R, I get an error that the model is singular.
I'm beginning to wonder if repeated measures ANOVA is an inappropriate analysis, but I'm not sure what a better alternative would be.