This repository contains the ressources and material for a course focusing on how to fit transmission models in Stan. It is based mainly on two papers:
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Léo Grinsztajn, Elizaveta Semenova, Charles C. Margossian and Julien Riou. Bayesian workflow for disease transmission modeling in Stan (Statistics in Medicine, 2021). Available from: https://onlinelibrary.wiley.com/doi/full/10.1002/sim.9164
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Anthony Hauser, Michel J. Counotte, Charles C. Margossian, Garyfallos Konstantinoudis, Nicola Low, Christian L. Althaus and Julien Riou. Estimation of SARS-CoV-2 mortality during the early stages of an epidemic: A modeling study in Hubei, China, and six regions in Europe (2020). Available from: https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1003189