The current tutorial demonstrates the Bayesian workflow to model shedding data using Rstan. We use the longitudinal SARS-CoV-2 fecal shedding data from Wölfel et al. (2020). The data includes observations of SARS-CoV-2 RNA concentration in 82 stool samples from 9 patients. As most samples collected in shedding studies are several days after symptom onset when the number of pathogens shed is decreasing. In this tutorial, we focus on modeling the decay phase of the shedding dynamics. We consider two classical models, exponential decay model and gamma model.

We develop a realistic model of the time course of virus shedding which includes an initial increase in virus concentration, followed by a decrease to undetectable levels. In this tutoiral, we apply the model to the longitudinal SARS-CoV-2 fecal shedding data from Wölfel et al. (2020) using JAGS. The data includes observations of SARS-CoV-2 RNA concentration in 82 stool samples from 9 patients.