Quantifying the spatiotemporal dynamics of the first two epidemic waves of SARS-CoV-2 infections in the United States

This repo stores code and data to reproduce the analysis in the manuscript, "Quantifying the spatiotemporal dynamics of the first two epidemic waves of SARS-CoV-2 infections in the United States", currently under review at PLOS Computational Biology.

Project description

We developed tools to produce high-resolution visualizations and to quantify the complex patterns of spatial and temporal spread of SARS-CoV-2 during first two major waves of infections in the contiguous United States.

Repository folder structure

/data

All the data used and generated by the model

/data-products

All the data generated from the model, such as final runs for the CAR model

/data-sources

All the source data used by the model, such as Meta30m population estimates and covidestim model observations coded to FIPS.

/scripts

Scripts numbered to run the whole analysis, some of the data is not the complete dataset due to a limit on storing files in git.

/1_create-hexgrid.R

Script to create the hexgrid used in the analysis

/2_pull-covidestim-data.R

Pull county-level covidestim infection estimates to estimate SARS-CoV-2 burden.

/3_allocate-infections-hexgrid.R

Distribute the county-level covidestim infection estimates to the hexgrid using population weighting based on a hexgrid distributed 30m population estimates.

/4_run-CAR-models.R

Run a conditional autoregressive model on the hexgrid infections.

/5_identify-wavefronts.R

Identifies and visualizes the boundary between the

/6_compute-wavefront-speed.R

Uses the wavefront results and calculates speed using the distance between the line-segments at time t and the nearest point on the wavefront at time t+1.

/7_CAR-model-gif.R

Creates gifs of the CAR model results

/8_create-figures.R

Script to create all figures in the manuscript and supplement

/figures

Folder holding .pdf and .png figures for the manuscript

/extra_figures

Supplemental figures and extra created figures.

/img

Folder containing .gif and .mov files of the movies of the wavefront expansion and wavefront speed computation

/wavefronts

Folder to store the individual pngs to make the gifs of wavefronts and wavefront speed. As these files are large, we provide only one example figure in each directory. It can be filled by the user using 6_compute-wavefront-speed.R.