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Background  Multiple imputation by chained equations (MICE) requires specifying a suitable conditional imputation model for each incomplete variable and then iteratively imputes the missing values. In the presence of missing not at random (MNAR) outcomes, valid statistical inference often requires joint models for missing observations and their indicators of missingness. In this study, we derived an imputation model for missing binary data with MNAR mechanism from Heckman’s model using a one-step maximum likelihood estimator. We applied this approach to improve a previously developed approach for MNAR continuous outcomes using Heckman’s model and a two-step estimator. These models allow us to use a MICE process and can thus also handle missing at random (MAR) predictors in the same MICE process.    Methods  We simulated 1000 datasets of 500 cases. We generated the following missing data mechanisms on 30% of the outcomes: MAR mechanism, weak MNAR mechanism, and strong MNAR mechanism. We then resimulated the first three cases and added an additional 30% of MAR data on a predictor, resulting in 50% of complete cases. We evaluated and compared the performance of the developed approach to that of a complete case approach and classical Heckman’s model estimates.    Results  With MNAR outcomes, only methods using Heckman’s model were unbiased, and with a MAR predictor, the developed imputation approach outperformed all the other approaches.    Conclusions  In the presence of MAR predictors, we proposed a simple approach to address MNAR binary or continuous outcomes under a Heckman assumption in a MICE procedure.    Electronic supplementary material  The online version of this article (10.1186/s12874-018-0547-1) contains supplementary material, which is available to authorized users.

Heckman imputation models for binary or continuous MNAR outcomes and MAR predictors