I am struggling to choose the correct statistical test for my data. I want to know if species richness is statistically different between these three habitats. Im not interested in whether it has changed over time. Only whether, when you take account that it does vary over time, you consider it to be different or not between habitats.
I have considered repeated measures ANOVA but from what Ive read this is not applicable if you have more than one observation for each factor level (replication). Maybe MANOVA or mixed models are more applicable? but Im not certain and Ive played around with a mixed model in lme4 but wasn't sure what factor to put in the Error term. The data can be normalised and with equal variances when transformed, but I have a very unbalanced design. So for each of those error bars the data are from 2-12 sites (2 sites for mudflat, 2 for Fringe, and 12 sites for Mangrove).
Any help would be greatly appreciated!!