A Bayesian Latent Variable Selection Model for Nonignorable Missingness

Missing data are exceedingly common across a variety of disciplines, such as educational, social, and behavioral science areas. Missing not at random (MNAR) mechanism where missingness is related to unobserved data is widespread in real data and has detrimental consequence. However, the existing MNAR-based methods have potential problems such as leaving the data incomplete and failing to accommodate incomplete covariates with interactions, non-linear terms, and random slopes. We propose a Bayesian latent variable imputation approach to impute missing data due to MNAR (and other missingness mechanisms) and estimate the model of substantive interest simultaneously. In addition, even when the incomplete covariates involves interactions, non-linear terms, and random slopes, the proposed method can handle missingness appropriately. Computer simulation results suggested that the proposed Bayesian latent variable selection model (BLVSM) was quite effective when the outcome and/or covariates were MNAR. Except when the sample size was small, estimates from the proposed BLVSM tracked closely with those from the complete data analysis. With a small sample size, when the outcome was less predictable from the covariates, the missingness proportions of the covariates and the outcome were larger, and the missingness selection processes of the covariates and the outcome were more MNAR and MAR, the performance of BLVSM was less satisfactory. When the sample size was large, BLVSM always performed well. In contrast, the method with an MAR assumption provided biased estimates and undercoverage confidence intervals when the missingness was MNAR. The robustness and the implementation of BLVSM in real data were also illustrated. The proposed method is available in the Blimp software application, and the paper includes a data analysis example illustrating its use.