Fitting a Basic SIR Model in Stan

Today, it seems like everyone is an epidemiologist. I am definitely not an epidemiologist but I did want to learn the basics of the popular SIR (Susceptible, Infected, Recovered) models. My guide is “Contemporary statistical inference for infectious disease models using Stan” by Chatzilena et al. [1], which does a great job at describing the model and in the spirit of reproducibility provides both Stan and R code. In this blog post, I will test a slightly modified version of the model on a simulated dataset and implement out-of-sample prediction logic in Stan.

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