Public transit mobility as a leading indicator of COVID-19 transmission in 40 cities during the first wave of the pandemic
This repository contains code and data to reproduce the analyses presented in the manuscript "Public transit mobility as a leading indicator of COVID-19 transmission in 40 cities during the first wave of the pandemic" by Soucy et al. (doi: 10.7717/peerj.17455). This includes every table and figure with the exception of tables S1 and S2. This repository has also been mirrored on Zenodo.
Code and data for the previous version of this manuscript, entitled "Estimating effects of physical distancing on the COVID-19 pandemic using an urban mobility index" and available on medRxiv, may be found here.
All code is written in the programming language R. The easiest way to run it is to use the RStudio IDE. An .Rproj file is included with this repository for ease of use with RStudio. The scripts should run with any modern version of R.
The R packages required to reproduce the tables and figures at listed at the top of their respective scripts. They must be installed using install.packages or similar functionality within RStudio prior to running the script.
Run 3_analysis.R and 4_extra.R to create the output tables and figures.
There is no reason to run 1_download-data.R or 2_clean-data.R unless you wish to refresh the data used in the analysis (which is already available in the data directory). Note that rerunning these scripts may cause the analysis script to break if there are changes to the underlying datasets.
