Before revision: This paper is concerned with the application of recently developed statistical methods for inference in infectious disease models. We use hierarchical models as well as deterministic and stochastic epidemic processes based upon systems of ordinary differential equations. We illustrate the application of Hamiltonian Monte Carlo and Variational Inference using the freely available software Stan .
After revision: This paper is concerned with the application of recent statistical advances to inference of infectious disease dynamics. We describe the fitting of a class of epidemic models using Hamiltonian Monte Carlo and Variational Inference using the freely available software Stan .