An Introductory Tutorial on Cohort State-Transition Models in R Using a Cost-Effectiveness Analysis Example

Fernando Alarid Escudero; Eline Krijkamp; Eva A. Enns; Alan Yang; M. G.Myriam Hunink; Petros Pechlivanoglou; Hawre Jalal

doi:10.1177/0272989X221103163

An Introductory Tutorial on Cohort State-Transition Models in R Using a Cost-Effectiveness Analysis Example

Fernando Alarid Escudero, Eline Krijkamp, Eva A. Enns, Alan Yang, M. G.Myriam Hunink, Petros Pechlivanoglou, Hawre Jalal

Health Policy and Management

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Abstract

Decision models can combine information from different sources to simulate the long-term consequences of alternative strategies in the presence of uncertainty. A cohort state-transition model (cSTM) is a decision model commonly used in medical decision making to simulate the transitions of a hypothetical cohort among various health states over time. This tutorial focuses on time-independent cSTM, in which transition probabilities among health states remain constant over time. We implement time-independent cSTM in R, an open-source mathematical and statistical programming language. We illustrate time-independent cSTMs using a previously published decision model, calculate costs and effectiveness outcomes, and conduct a cost-effectiveness analysis of multiple strategies, including a probabilistic sensitivity analysis. We provide open-source code in R to facilitate wider adoption. In a second, more advanced tutorial, we illustrate time-dependent cSTMs.

Original language	English (US)
Pages (from-to)	3-20
Number of pages	18
Journal	Medical Decision Making
Volume	43
Issue number	1
DOIs	https://doi.org/10.1177/0272989X221103163
State	Published - Jan 2023

Bibliographical note

Funding Information:
The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article. The authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: Dr. Alarid-Escudero was supported by grants U01-CA199335 and U01-CA253913 from the National Cancer Institute (NCI) as part of the Cancer Intervention and Surveillance Modeling Network (CISNET), and a grant by the Gordon and Betty Moore Foundation. Miss Krijkamp was supported by the Society for Medical Decision Making (SMDM) fellowship through a grant by the Gordon and Betty Moore Foundation (GBMF7853). Dr. Enns was supported by a grant from the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award no. K25AI118476. Dr. Hunink received research funding from the American Diabetes Association, the Netherlands Organization for Health Research and Development, the German Innovation Fund, Netherlands Educational Grant (“Studie Voorschot Middelen”), and the Gordon and Betty Moore Foundation. Dr. Jalal was supported by a grant from the National Institute on Drug Abuse of the National Institute of Health under award no. K01DA048985. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funding agencies had no role in the design of the study, interpretation of results, or writing of the manuscript. The funding agreement ensured the authors’ independence in designing the study, interpreting the data, writing, and publishing the report.

Publisher Copyright:
© The Author(s) 2022.

Keywords

Markov models
R software
cohort state-transition models
cost-effectiveness analysis
tutorial

PubMed: MeSH publication types

Journal Article

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abstract = "Decision models can combine information from different sources to simulate the long-term consequences of alternative strategies in the presence of uncertainty. A cohort state-transition model (cSTM) is a decision model commonly used in medical decision making to simulate the transitions of a hypothetical cohort among various health states over time. This tutorial focuses on time-independent cSTM, in which transition probabilities among health states remain constant over time. We implement time-independent cSTM in R, an open-source mathematical and statistical programming language. We illustrate time-independent cSTMs using a previously published decision model, calculate costs and effectiveness outcomes, and conduct a cost-effectiveness analysis of multiple strategies, including a probabilistic sensitivity analysis. We provide open-source code in R to facilitate wider adoption. In a second, more advanced tutorial, we illustrate time-dependent cSTMs.",

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An Introductory Tutorial on Cohort State-Transition Models in R Using a Cost-Effectiveness Analysis Example

Abstract

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