The Impact of COVID-19 and Strategies for Mitigation and Suppression in Low- and Middle-Income Countries

This repository contains the code used to generate the analyses contained within the paper "The Impact of COVID-19 and Strategies for Mitigation and Suppression in Low- and Middle-Income Countries", - Walker et al, 2020.

It is divided into 7 subfolders, each containing all the relevant data and R scripts required to generate a set of analyses contained in the paper.

• 1_Demographic_mixing_spread_severity - contains the code used to generate Figure 1, Supplementary Figures 5 & 6
• 2_Determining_Healthcare_Capacity - contains the code used to generate Figure 2.
• 3_Comorbidity_Exploration - contains the code used to generate Figure 3.
• 4_Control_and_Disease_Burden - contains the code used to generate Figure 4, Supplementary Figure 4.
• 5_Suppression_Triggering_and_Exploration - contains the code used to generate Figure 5.
• Table_1_Government_Measures - contains the code used to generate Table 1.
• S1_optimal_mitigation_example - contains the code used to generate Supplementary Figure 1.

In addition to this code, running these analyses also requires downloading and installing an R package developed specifically for these analyses and that allows simulation of COVID-19 epidemics using an age-structured SEIR model (with explicit healthcare representation). The package is called squire and is available here: https://github.com/mrc-ide/squire. For the paper concerned, squire version 0.4.14 was used and can be installed with:

devtools::install_github("mrc-ide/squire@v0.4.14")

For all other packages used in this repository, the version can be found within 'installed_packages.rds'