1. Ecological data sets often use clustered measurements or use repeated sampling in a longitudinal design. Choosing the correct covariance structure is an important step in the analysis of such data, as the covariance describes the degree of similarity among the repeated observations.
2. Three methods for choosing the covariance are: the Akaike information criterion (AIC), the quasi-information criterion (QIC) and the deviance information criterion (DIC). We compared the methods using a simulation study and using a data set that explored effects of forest fragmentation on avian species richness over 15 years.
3. The overall success was 80·6% for the AIC, 29·4% for the QIC and 81·6% for the DIC. For the forest fragmentation study the AIC and DIC selected the unstructured covariance, whereas the QIC selected the simpler autoregressive covariance. Graphical diagnostics suggested that the unstructured covariance was probably correct.
4. We recommend using DIC for selecting the correct covariance structure.