Improving the correlation structure selection approach for generalized estimating equations and balanced longitudinal data

Generalized estimating equations are commonly used to analyze correlated data. Choosing an appropriate working correlation structure for the data is important, as the efficiency of generalized estimating equations depends on how closely this structure approximates the true structure. Therefore, most studies have proposed multiple criteria to select the working correlation structure, although some of these criteria have neither been compared nor extensively studied. To ease the correlation selection process, we propose a criterion that utilizes the trace of the empirical covariance matrix. Furthermore, use of the unstructured working correlation can potentially improve estimation precision and therefore should be considered when data arise from a balanced longitudinal study. However, most previous studies have not allowed the unstructured working correlation to be selected as it estimates more nuisance correlation parameters than other structures such as AR‐1 or exchangeable. Therefore, we propose appropriate penalties for the selection criteria that can be imposed upon the unstructured working correlation. Via simulation in multiple scenarios and in application to a longitudinal study, we show that the trace of the empirical covariance matrix works very well relative to existing criteria. We further show that allowing criteria to select the unstructured working correlation when utilizing the penalties can substantially improve parameter estimation. Copyright © 2014 John Wiley & Sons, Ltd.