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Estimating effects of physical distancing on the COVID-19 pandemic using an urban mobility index

Code and data to support "Estimating effects of physical distancing on the COVID-19 pandemic using an urban mobility index" by Soucy et al. The preprint is currently available on medRxiv.

Scripts

1_download-data.R

This script download mobility data from Citymapper and cumultive case data from many sources. Unless one desires to update the data, there is no reason to run this script. Data are already available in the directory data.

2_clean-data.R

This script processes the downloaded mobility data (data/cmi) and cumulative case data (data/cases) into two files placed in the main data directory: cmi_clean.csv and cases_clean.csv. Again, there is no reason to run this script unless one desires to update the data. These files are already available in the directory data.

3_analysis.R

This script runs all of the analyses and produces all of the results and figures used in the manuscript.

theme.R

This script defines a ggplot theme and colour palette used to generate the figures.

Contents

In addition to the scripts contained within the primary directory, this repository contains the following directories:

data

This folder contains mobility and case data downloaded using 1_download-data.R, raw case data downloaded manually rather than via the aforementioned script (data/cases/raw), and built-in datasets (such as locations.csv, which contain additional information about cities includes in the mobility dataset).

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Estimating effects of physical distancing on the COVID-19 pandemic using an urban mobility index

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