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COVID-19 Scenario Hub website: guide to code

https://covid19scenariohub.eu/

Contents:

Analysis and reporting

Analysis

Scenario analyses hinge on the file scenarios.R which provides meta-data for each scenario round.

Analysis functions are in sub-folders of code, as follows:

Load

  • scenarios.R: Create scenario metadata
  • load_local_results.R: load files from a local clone of the main scenario hub
  • download_results.R: fetch a parquet file stored on github
  • plot_palettes: Get colour palettes for plotting
  • plot_scenarios: Plot the four scenarios side by side

Report

  • prep.R: load and prepare data using functions in load
  • results-multi-country.Rmd: create results comparing scenarios for countries with multiple models

Summarise

  • cumulative.R: summarise cumulative outcomes
  • peaks.R: find and summarise outcomes at projected peaks

Reporting

Reports can be run via the script create-report.R, or separately by interactively knitting each report's Rmd file. Reports use the following Rmd chunks of common code:

  • _model_feature.Rmd: number of models etc.
  • _cumulative_plots.Rmd: create cumulative plots
  • _peaks.Rmd: create plots of peaks
  • _by_scenario.Rmd: plot by scenario

Website pages

The website updates (builds and deploys) automatically after each push to the main branch, using a Github action.