COVID-19 Scenario Hub website: guide to code

https://covid19scenariohub.eu/

Contents:

• Code for analysis and reporting
• Editing specific website pages

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.

• Home
• About
• Scenarios
  • Overview
  • Report 1
  • Report 2
• Models
• Community
• Contact
• Website header
• Website footer