covid-vaccine-impact-orderly

This is an orderly project. The directories are:

src: tasks used to generate the reports

vignettes: guidance on running the tasks

data: Contains the following data:

• excess_mortality: Fitted nimue models and pre-generated simulations, along with vaccine allocation information, for the fits to excess mortality.
• reported_deaths: Fitted nimue models and pre-generated simulations, along with vaccine allocation information, for the fits to reported COVID deaths.
• raw: Raw data used in modelling:
  • owid.rds: Our World In Data dataset used for vaccine allocation, downloaded 13-02-2022
  • excess_deaths.rds: Excess death estimates from the Economist, downloaded 13-02-2022
  • combined_data.Rds: Reported COVID deaths dataset, downloaded 13-02-2022
  • vaccine_agreements.rds, vaccine_doses_by_manufacturer.rds, who_vacc.rds, who_vacc_meta.rds: Other vaccination datasets, downloaded 13-02-2022
  • worldsf.Rds: World map sf used in the plotting, downloaded 20-04-2022 from https://datahub.io/core/geo-countries/r/countries.geojson
  • generate_counterfactuals.R: R code used to generate the simulations from the model fits

The purpose of this repository is to estimate the number of deaths averted by COVID-19 vaccinations to date. This utilises the nimue fits generated in global-lmic-reports-orderly, which are also used to produce the reports here.

Installation

git clone https://github.com/mrc-ide/covid-vaccine-impact-orderly.git
cd covid-vaccine-impact-orderly
open covid-vaccine-impact-orderly.Rproj

Usage

A vignette that briefly runs through the tasks used in this repo can be found here, and also in the vignettes folder.

Interactive Map

This repo also generates an interactive map of the estimated deaths averted. This can be found here.