Flexibly specify and fit Bayesian, regression-oriented models for infectious diseases. The implemented models define a likelihood for all observed data while also explicitly modeling transmission dynamics: an approach often termed as semi-mechanistic. Multiple regions can be modeled simultaneously with multilevel models. Key epidemiological quantities, including reproduction numbers and latent infections, may be estimated within the framework. The models may be used to evaluate the determinants of changes in transmission rates, including the effects of control measures. Epidemic dynamics may be simulated either from a fitted model or a “prior” model; allowing for prior/posterior predictive checks, experimentation, and forecasting.

Getting Started

After installing the software, the best way to get started is to become familiar with the model and its implementation. Once familiar with the model, there are a few articles showcasing the main features of the package using real example data. The simplest such article is here.