p3state.msm: Analyzing survival data from an illness-death model

Abstract

In longitudinal studies of disease, patients can experience several events across a follow-up period. Analysis of such studies can be successfully performed by multi-state models. In the multi-state framework, issues of interest include the study of the relationship between covariates and disease evolution, estimation of transition probabilities, and survival rates. This paper introduces p3state.msm, a software application for R which performs inference in an illness-death model. It describes the capabilities of the program for estimating semi-parametric regression models and for implementing nonparametric estimators for several quantities. The main feature of the package is its ability for obtaining non-Markov estimates for the transition probabilities. Moreover, the methods can also be used in progressive three-state models. In such a model, estimators for other quantities, such as the bivariate distribution function (for sequentially ordered events), are also given. The software is illustrated using data from the Stanford Heart Transplant Study.