pammtools: Piece-wise exponential Additive Mixed Modeling tools

Abstract

This article introduces the pammtools package, which facilitates data transformation, estimation and interpretation of Piece-wise exponential Additive Mixed Models. A special focus is on time-varying effects and cumulative effects of time-dependent covariates, where multiple past observations of a covariate can cumulatively affect the hazard, possibly weighted by a non-linear function. The package provides functions for convenient simulation and visualization of such effects as well as a robust and versatile function to transform time-to-event data from standard formats to a format suitable for their estimation. The models can be represented as Generalized Additive Mixed Models and estimated using the R package mgcv. Many examples on real and simulated data as well as the respective R code are provided throughout the article.