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Bayesian workflow for disease transmission modeling in Stan
Author(s) -
Grinsztajn Léo,
Semenova Elizaveta,
Margossian Charles C.,
Riou Julien
Publication year - 2021
Publication title -
statistics in medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.996
H-Index - 183
eISSN - 1097-0258
pISSN - 0277-6715
DOI - 10.1002/sim.9164
Subject(s) - computer science , inference , bayesian inference , workflow , markov chain monte carlo , prior probability , frequentist inference , bayesian probability , machine learning , uncertainty quantification , python (programming language) , inference engine , artificial intelligence , data mining , programming language , database
This tutorial shows how to build, fit, and criticize disease transmission models in Stan, and should be useful to researchers interested in modeling the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic and other infectious diseases in a Bayesian framework. Bayesian modeling provides a principled way to quantify uncertainty and incorporate both data and prior knowledge into the model estimates. Stan is an expressive probabilistic programming language that abstracts the inference and allows users to focus on the modeling. As a result, Stan code is readable and easily extensible, which makes the modeler's work more transparent. Furthermore, Stan's main inference engine, Hamiltonian Monte Carlo sampling, is amiable to diagnostics, which means the user can verify whether the obtained inference is reliable. In this tutorial, we demonstrate how to formulate, fit, and diagnose a compartmental transmission model in Stan, first with a simple susceptible‐infected‐recovered model, then with a more elaborate transmission model used during the SARS‐CoV‐2 pandemic. We also cover advanced topics which can further help practitioners fit sophisticated models; notably, how to use simulations to probe the model and priors, and computational techniques to scale‐up models based on ordinary differential equations.