Cohort state-transition models in R: From conceptualization to implementation

This GitHub repository provides the code of the three different implementations of cohort state-transition model (cSTM), explained in the following manuscript:

• Alarid-Escudero F, Krijkamp EM, Enns EA, Hunink MGM, Pechlivanoglou P, Jalal H. Cohort state-transition models in R: From conceptualization to implementation. arXiv:200107824v1. 2020:1-31.

We recommend to first read the manuscript before using the code. Understanding of the use of the multidimensional dynamics array described in

• Krijkamp EM, Alarid-Escudero F, Enns EA, Pechlivanoglou P, Hunink MGM, Yang A, Jalal HJ. A multidimensional array representation of state-transition model dynamics. Medical Decision Making, 2020 (Forthcoming)

is recommended.

The R folder includes three different scripts corresponding to the different implementations of the cSTM:

• STM_01.R: time-independent cSTM
• STM_02.R: age-dependent cSTM with calculations of epidemiological outcomes
• STM_03.R: age- and history-dependent cSTM

In addition we include the data folder with age-specific mortality for the age-dependent and age- and history-dependent cSTM.

To run the cost-effectiveness analysis, you require The Decision Analytic Modeling Package (dampack), an R package for analyzing and visualizing the health economic outputs of decision models.

Full list of Contributors:

• Fernando Alarid-Escudero

• Eline Krijkamp

• Eva Enns

• Myriam Hunink

• Petros Pechlivanoglou

• Hawre Jalal