This repository contains code used in the manuscript Semi-parametric modeling of SARS-CoV-2 transmission using tests, cases, deaths, and seroprevalence data by Damon Bayer (@damonbayer), Jon Fintzi (@fintzij), Isaac Goldstein (@igoldsteinh), Volodymyr Minin (@vnminin), et al.
This model is able to account for time-varying testing policy, infection-fatality ratio, and reproduction number. Additionally, we are able to use data from seroprevalence studies.
The main model code is available in src/bayes_seird.jl.
The workflow for fitting and evaluating models is available in the slurm_submissions directory.
In order, we run