Cohort state transition models (cSTM), often called Markov models, are frequently used to inform policy makers about how to allocate healthcare resources under constrained budgets. In thiscourse we will teach participants how to integrate different components of a cSTM within a single framework using R. We will first give a conceptual overview of cSTMs and the general structure for their implementation in a programming language. This will be followed by a brief review of good coding practices and how to structure your code in an efficient, transparent and reproducible way. We will demonstrate a cSTM in R, followed by hands-on exercises that will help participants implement a cSTM in R. We will also demonstrate how to conduct a cost-effectiveness analysis(CEA)and how to calculate and visually present epidemiological and health economic outcomes using the cSTM. We will shortly cover the implementation of probabilistic sensitivity analysis (PSA)of a cSTM in R.