Analysis of COVID-19 transmission in Vietnam

This repository contains the code and data for the manuscript "Lessons learned from Vietnam's COVID-19 response: the role of adaptive behaviour change in epidemic control". Manuscript: https://doi.org/10.1101/2020.12.18.20248454

Installation

1. Clone this repository (https://github.com/optimamodel/covid_vietnam) into one folder.
2. Clone Covasim (https://github.com/institutefordiseasemodeling/covasim) into another folder. (Note: because the scripts require a particular version, you cannot use Covasim as installed by pip.)
3. Change to the vietnam_lancetgh tag: git checkout vietnam_lancetgh. If this command succeeded, you should see HEAD is now at e9afde91 fix intervention conflicts.
4. Install Covasim with pip install -e ..
5. You should now be ready to run the scripts in this repository.

Usage

1. The files for generating Figure 1 are in the fig1 folder. Figure 1 can be created by running fig1-epi-stats.R. This will save a file called output/fig1.png.
2. The file run_vietnam_central.py can be configured to (1) calibrate the model, and (2) run scenarios. Choose which of these you want to do by setting whattorun. If you set save_sim = True, the simulations will be saved as *.obj to the results folder.
3. Run plot_vietnam_calibration.py, plot_vietnam_scenarios.py, and plot_vietnam_multiscens.py to load the *.obj files generated by the previous step and generate Figures 2-4 respectively.