This repo stores code and data to partially reproduce the analysis done in the title paper.

The repo folder structure is:

• 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.
  • 00-manuscript_figures_new.R ## Script to generate all the figures
  • 01-hexAllocation_Infections_Meta30m.R ## Population and Infections allocation to the hexgrid
  • 02-CAR_models_meta30m.R ## CAR models running
  • 03-CAR_meta30m_gif.R ## Wave recruting and expansion .gif creation
  • 04-Compute_Speed.R ## Wavefront speed calculation and .gif creation
  • wavefronts.R ## Function to calculate wavefront speed
• 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
• Waves-Manuscript.Rproj ## Rproj
• README.md ## This file
• .gitignore ## To keep some of the data untracked and avoid issues with large files stored in git