Semi-parametric modeling of SARS-CoV-2 transmission using tests, cases, deaths, and seroprevalence data

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.

Name		Name	Last commit message	Last commit date
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.vscode		.vscode
archive		archive
data		data
illustrative_examples		illustrative_examples
renv		renv
scripts		scripts
slurm_submissions		slurm_submissions
src		src
.Rprofile		.Rprofile
.gitignore		.gitignore
LocalPreferences.toml		LocalPreferences.toml
Manifest.toml		Manifest.toml
Project.toml		Project.toml
README.md		README.md
model_table.csv		model_table.csv
renv.lock		renv.lock
semi_parametric_COVID_19_OC_model.Rproj		semi_parametric_COVID_19_OC_model.Rproj

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Semi-parametric modeling of SARS-CoV-2 transmission using tests, cases, deaths, and seroprevalence data

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