Code for "Controlling COVID-19 via testing, tracing, and quarantine"

This repository includes the code for reproducing the results in the manuscript "Controlling COVID-19 via testing, tracing, and quarantine". The citation for the manuscript is:

Controlling COVID-19 via test-trace-quarantine. Kerr CC, Mistry D, Stuart RM, Rosenfeld R, Hart G, Núñez RC, Selvaraj P, Cohen JA, Abeysuriya RG, George L, Hagedorn B, Jastrzębski M, Fagalde M, Duchin J, Famulare M, Klein DJ. Nature Communications 2021 12:2993. doi: https://doi.org/10.1038/s41467-021-23276-9.

A webapp with an interactive version of the figures is available at http://ttq-app.covasim.org.

Organization

The repository is organized as follows:

• fig1_calibration through fig5_projections are the main folders containing the code for reproducing each figure of the manuscript. In each of these folders, there is a file called plot_figX.py that will generate the corresponding figure from the manuscript. These scripts can be run directly, without the need to re-run the scripts for generating the underlying data (some of which take considerable CPU time). These are the scripts that are being run by the webapp.
• inputs and outputs are folders containing the input data and the model-based outputs, respectively.
• webapp includes the code for serving the figures via the interactive webapp or a local Jupyter notebook.

Installation and usage

Use pip install -e . to install basic dependencies. This will install the latest version of each library (including Covasim). You can also install with pip install -e .[frozen] to use the versions of libraries (including Covasim) that were used for the paper. You can also install with pip install -e .[web], which will also let you run the notebook/webapp in the webapp folder.

Note: installation is intended for Ubuntu 18.04/20.04 using a Python 3.8 conda virtual environment. Other platforms or environments may work with minor modifications to the scripts, but they have not been extensively tested.

Usage

Run the scripts in the figure folders (see the readme in each folder for more information), or start the webapp and browse the figures there.

Further information

Further information on Covasim is available here. If you have further questions or would like technical assistance, please reach out to us at [email protected].