mstate: An R Package for the Analysis of Competing Risks and Multi-State Models

The sixth paper in the special issue of Journal of Statistical Software is by Liesbeth de Wreede, Marta Fiocco and Hein Putter and is about the R package mstate. A journal article on the package already exists in Computer Methods and Programs in Biomedicine. However, while that paper primarily dealt with theoretical aspects, the current paper is largely a case-study example based on a 6 state model for leukemia patients after bone marrow transplantation.

mstate uses the existing survival package to fit the Cox proportional hazards models. Much of the infrastructure of mstate is in functions for preparing data to be in the correct form. To use mstate for a Cox-Markov or Cox-semi-Markov model, a single coxph() object is required. This results in somewhat messy commands being required because separate strata are required and the same covariate needs to appear multiple times to allow it to have different effects for each transition intensity. For instance the call to coxph in the paper requires 16 lines. While there is perhaps some pedagogical advantage to this complication, in ensuring the user really understands what they are fitting, there is surely scope to allow some automation to this process so that the user only need specify which covariates are required for each transition intensity and this could be passed to coxph behind the scenes.

Finally, as has been noted elsewhere, mstate currently does virtually all calculations within R itself. As a result computation times are sometimes disappointing, especially for models on large datasets.