smdi: an R package to perform structural missing data investigations on partially observed confounders in real-world evidence studies
Janick Weberpals, Sudha R. Raman, Pamela A. Shaw, Hana Lee, Bradley G. Hammill, Sengwee Toh, John G. Connolly, Kimberly J. Dandreo, Fang Tian, Wei Liu, Jie Li, José J. Hernández‐Muñoz, Robert J. Glynn, Rishi Desai
Abstract
Objectives: Partially observed confounder data pose a major challenge in statistical analyses aimed to inform causal inference using electronic health records (EHRs). While analytic approaches such as imputation are available, assumptions on underlying missingness patterns and mechanisms must be verified. We aimed to develop a toolkit to streamline missing data diagnostics to guide choice of analytic approaches based on meeting necessary assumptions. Materials and methods: We developed the smdi (structural missing data investigations) R package based on results of a previous simulation study which considered structural assumptions of common missing data mechanisms in EHR. Results: smdi enables users to run principled missing data investigations on partially observed confounders and implement functions to visualize, describe, and infer potential missingness patterns and mechanisms based on observed data. Conclusions: The smdi R package is freely available on CRAN and can provide valuable insights into underlying missingness patterns and mechanisms and thereby help improve the robustness of real-world evidence studies.