The epidemia package allows researchers to flexibly specify and fit Bayesian epidemiological models in the style of Flaxman et al. (2020). The package leverages R’s formula interface to parameterize the time-varying reproduction rate as a function of covariates. Multiple populations can be modeled simultaneously with hierarchical models. The design of the package has been inspired by, and has borrowed from, rstanarm (Goodrich et al. 2020). epidemia uses rstan (Stan Development Team 2020) as the backend for fitting models.


This is an early beta release of the package. As a beta release, there will be regular updates with additional features and more extensive testing. Any feedback is greatly appreciated - in particular if you find bugs, find the documentation unclear, or have feature requests, please report them here.

Package Website

To get started, please see the package website, where you can find installation instructions, function documentation, and vignettes.