FastJM: An R Package for Efficient Implementation of Semiparametric Joint Models for Longitudinal and Survival Data

Abstract

Joint models provide a flexible framework for characterizing the association between longitudinal and time-to-event processes and have been widely applied in biomedical research. However, fitting joint models can be computationally challenging for large-scale and complex biomedical data. This paper introduces the \proglang{R} package \pkg{FastJM}, which provides computationally efficient frequentist estimation for three classes of semiparametric joint models: joint models with a single longitudinal biomarker, joint models with multiple longitudinal biomarkers, and joint models with a single longitudinal biomarker with heterogeneous within-subject (WS) variability. Within an expectation--maximization framework, \pkg{FastJM} employs customized linear-scan algorithms to efficiently update the nonparametric baseline hazards, thereby addressing a major computational bottleneck in semiparametric joint modeling. The package also supports commonly used time-dependent latent association structures by integrating these algorithms with a landmark multivariate joint modeling framework. \pkg{FastJM} provides a unified interface for model specification, estimation, inference, visualization, dynamic prediction, and prediction performance assessment, including cross-validated time-dependent accuracy measures and time-independent concordance statistics. We describe the underlying methodology and software implementation and demonstrate the main functionality of \pkg{FastJM} through reproducible examples.