p-robot / Elicitation-1

MMODS Elicitation 1: COVID-19 reopening strategies at the county level in the face of uncertainty

MMODS Elicitation 1

Data and code used within the MMODS-1 elicitation of multiple modelling groups for supporting county reopening decisions during the COVID-19 pandemic in the US.

Software requirements

This repository uses both R and Python.

• R scripts within this repository require the following R packages: tidyverse, ggplot2, RColorBrewer, gridExtra.
• Python scripts within this repository require the following Python modules (Python >3.6): numpy, pandas, matplotlib. These requirements are listed under requirements.txt and can be installed using, for instance, pip install -r requirements.txt.

Usage

• Once data has been downloaded, the following command will create an Rdata file including various metadata used in visualization, make data_round2

• Individual figures can then be generated using, for instance: make fig2

Additional commands and notes

• make fig4_panels will generate subpanels for Figure 4, the multi-panel figure.
• see Makefile for all commands.

Output

Output figures are saved in output/figures.

For additional detail, see:

Shea, K., Borchering, R.K., Probert, W.J., Howerton, E., Bogich, T.L., Li, S., van Panhuis, W.G., Viboud, C., ... and Runge, M.C. (2020) COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support. medRxiv. https://www.medrxiv.org/content/10.1101/2020.11.03.20225409v1.full