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This article introduces epidemia, an R package for Bayesian,regression-oriented modeling of infectious diseases. The implemented modelsdefine a likelihood for all observed data while also explicitly modelingtransmission dynamics: an approach often termed as semi-mechanistic. Infectionsare propagated over time using renewal equations. This approach is inspired byself-exciting, continuous-time point processes such as the Hawkes process. Avariety of inferential tasks can be performed using the package. Keyepidemiological quantities, including reproduction numbers and latentinfections, may be estimated within the framework. The models may be used toevaluate the determinants of changes in transmission rates, including theeffects of control measures. Epidemic dynamics may be simulated either from afitted model or a prior model; allowing for prior/posterior predictive checks,experimentation, and forecasting.

Epidemia: An R Package for Semi-Mechanistic Bayesian Modelling of Infectious Diseases using Point Processes