A joint Bayesian hierarchical model for estimating SARS-CoV-2 genomic and subgenomic RNA viral dynamics and seroconversion

Here are some example R code and JAGS code for the model implementation in "A joint Bayesian hierarchical model for estimating SARS-CoV-2 genomic and subgenomic RNA viral dynamics and seroconversion" by Dong and Brown (2023).

• joint_vl_sero_r.R: R code for fitting the joint Bayesian model.

• joint_vl_sero_jags.txt: JAGS code for fitting the joint Bayesian model.

• dummy_dataset.rds: A dummy dataset for test-running the R script and JAGS script.

• model_par_diag_primary.pdf: Full model diagnostic report for the primary model fitted to the COVID-19 PEP study data, as described in Section 4.1 of the main manuscript and Section S1.3 of the Supplement.