Approaches for missing covariate data in logistic regression with MNAR sensitivity analyses

Data with missing covariate values but fully observed binary outcomes are an important subset of the missing data challenge. Common approaches are complete case analysis (CCA) and multiple imputation (MI). While CCA relies on missing completely at random (MCAR), MI usually relies on a missing at random (MAR) assumption to produce unbiased results. For MI involving logistic regression models, it is also important to consider several missing not at random (MNAR) conditions under which CCA is asymptotically unbiased and, as we show, MI is also valid in some cases. We use a data application and simulation study to compare the performance of several machine learning and parametric MI methods under a fully conditional specification framework (MI‐FCS). Our simulation includes five scenarios involving MCAR, MAR, and MNAR under predictable and nonpredictable conditions, where “predictable” indicates missingness is not associated with the outcome. We build on previous results in the literature to show MI and CCA can both produce unbiased results under more conditions than some analysts may realize. When both approaches were valid, we found that MI‐FCS was at least as good as CCA in terms of estimated bias and coverage, and was superior when missingness involved a categorical covariate. We also demonstrate how MNAR sensitivity analysis can build confidence that unbiased results were obtained, including under MNAR‐predictable, when CCA and MI are both valid. Since the missingness mechanism cannot be identified from observed data, investigators should compare results from MI and CCA when both are plausibly valid, followed by MNAR sensitivity analysis.