PStrata: An R Package for Principal Stratification

Abstract: Post-treatment confounding is a common problem in causal inference, including special cases of noncompliance, truncation by death, surrogate endpoint, etc. Principal stratification (Frangakis and Rubin 2002) is a general framework for defining and estimating causal effects in the presence of post-treatment confounding. A prominent special case is the instrumental variable approach to noncompliance in randomized experiments (Angrist, Imbens, and Rubin 1996). Despite its versatility, principal stratification is not accessible to the vast majority of applied researchers because its inherent latent mixture structure requires complex inference tools and highly customized programming. We develop the R package PStrata to automatize statistical analysis of principal stratification for several common scenarios. PStrata supports both Bayesian and frequentist paradigms. For the Bayesian paradigm, the computing architecture combines R, C++, Stan, where R provides user-interface, Stan automatizes posterior sampling, and C++ bridges the two by automatically generating Stan code. For the Frequentist paradigm, PStrata implements a triply-robust weighting estimator. PStrata accommodates regular outcomes and time-to-event outcomes with both unstructured and clustered data.