And yet, you might still want to consider the two years as non-independent. To me, one of the really nice things about modeling the error structure is that you can accommodate even small correlations. With only two repeated observations, an unstructured covariance matrix is the most flexible statement of the situation. Yes, the two years may have only a small correlation, but if so, that will not greatly affect any standard errors of the difference of fixed effect means. And there may not be enough data to adequately estimate confidence bounds, so that 0 might be included, even if the covariance is substantially away from 0.
My mantra is: If you measure the same experimental unit for the same endpoint, you ought to assume that those points are likely to be more closely related than points from independent units.
Steve Denham
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