Delphi Analysis Notebooks

This repository contains parameterizable notebooks for analyzing and tracking epidemiological indicators in the Delphi data pipeline.

Existing Notebooks

• indicator_analysis/indicator_evaluation.qmd. A notebook designed to evaluate a candidate indicator against a guiding indicator.
• revision_analysis/revision_analysis.qmd. A notebook for tracking indicator revisions over time to analyze their stabilization properties. It tracks how quickly initial daily/weekly estimates converge to their final values over time.

Generating and Publishing Examples

The notebooks act as parameterized templates. To generate local examples and publish them as a website to GitHub Pages, the repository relies on Quarto's publishing mechanism and a pre-render hook.

Some relevant files are:

• _quarto.yml. Contains the rules for the website structure, navigation menu, and specifies the pre-render script.
• scripts/pre_render.R. Automatically executes the .qmd notebooks with pre-defined parameters to generate static HTML examples before the website is built.
• index.qmd. The main page of the website. It is used to make the rendered html files visible in the website.

Including a New Example

To add a new analysis example to the website:

1. Add a new block of code in scripts/pre_render.R that calls quarto::quarto_render() with your desired execute_params.
2. To make the rendered html visible on the website, update _quarto.yml and/or index.qmd to include a link to your newly generated HTML file.
3. Preview or Publish:
   • To view the changes locally, run:

     quarto preview

   • To publish the updated examples directly to the gh-pages branch, run:

     quarto publish gh-pages