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.
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 underrequirements.txt
and can be installed using, for instance,pip install -r requirements.txt
.
-
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
make fig4_panels
will generate subpanels for Figure 4, the multi-panel figure.- see
Makefile
for all commands.
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