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