DR-covid19

This repo contains code and data to model the COVID-19 pandemic in the Dominican Republic from 2020-2022. This analysis uses covidm, a model developed by Davies and colleagues to estimate the impact of NPIs on COVID-19 transmission in the UK. Model fitting requires installation of Rcpp, instructions for the installation of covidm can be found in R/covidm_for_fitting

Model set up and fitting is performed in the following scripts:

• R/00_load-data.R
• R/01_covidm-set-up.R
• R/02_burden-processes.R
• R/03_fit-covidm.R

Then, scenario analysis is performed in scripts:

• R/04_run-vaccine-counterfactuals.R
• R/05_run-counterfactual-trade-off.R

Figures included in the manuscript can be generated by knitting reports/manuscript-figures.Rmd. These can also be generated from model fits and scenario results used in the manuscript, which are saved in the output folder.

Data required for the analysis can be found in the data folder and includes:

• Serological data from Nilles et al, 2021
• COVID-19 death data from the Dominican Republic's COVID-19 dashboard
• COVID-19 case data from Johns Hopkins Coronavirus Resource Centre
• Hospital and ICU bed occupancy data, scraped from daily COVID-19 bulletins published by the Ministerio de Salud Pública y Asistencia Social
• Vaccinations from Oxford's Our World in Data
• Shape files for the Caribbean and the Dominican Republic
• GISAID sequence data for the Dominican Republic
• Age-dependent susceptibility and symptomatic rates from Davies et al 2020

Please note that data on the clusters shown in Figure 1 are not publicly available and are not included in this repo.