Estimating COVID-19 prevalence in Rio de Janeiro from the EPICOVID serological survey (and case data).

This repository contains code to reproduce the prevalence estimation analyses in Bastos, Carvalho & Gomes (2021).

The contents of data/ are an amalgamation of data from the EPICOVID and Brasil.io projects, for serological survey and case/death data, respectively. The stan folder contains Stan code for fitting (i) simple prevalence correction model where the true number of cases projected from the prevalence is a generated quantity and (ii) a slightly less simple model that takes case data and prior knowledge about underreporting to estimate prevalence and detection probability jointly from survey and case data.