Stan for epidemiology

Stan for epidemiology

The Stan epidemiology page is meant to serve as a centralized location for all types of work in epidemiology that use the software Stan for Bayesian inference. Anyone can contribute helpful resources, papers, posters or anything else epidemiology-related that makes use of Stan, regardless of the level, through the Stan epidemiology GitHub page.

To ask Stan-related questions, please go to the Stan forum. More specifically, you can use the epidemiology or covid-19 tags to ensure that posts are seen by anyone interested in epidemiology problems as well.

Tutorials and case studies

Bayesian workflow for disease transmission modeling in Stan

Contemporary statistical inference for infectious disease models using Stan

Spatial Models in Stan: Intrinsic Auto-Regressive Models for Areal Data

Experience of using the Stan software for Bayesian inference in HIV epidemiology

Estimating transmission by fitting mechanistric models in Stan

Estimating Joint Models for Longitudinal and Time-to-Event Data with rstanarm

Bayesian Survival Analysis 1: Weibull Model with Stan

Epidemiology papers

For a list of epidemiology papers using Stan, see here. You can also find here an updated list of papers specifically on Covid-19.

We need your help!

If you’re working in epidemiology and want to help to maintain this page, please send an email to leo.grinsztajn@polytechnique.edu to be added to the Github repo.