adapt website to overview format linking to all tutorial URLs

[avallecam]

REMINDER: this is a Partial review. Before merging, redirect this to main

---

Fix #132
Fix #69

Please check if the PR fulfills these requirements

• I have read the CONTRIBUTING guidelines

What kind of change does this PR introduce?

• Update summary page on the "Workshop overview" linking all tutorials.
• Simplify software setup instructions.
• Add an introduction episode to the Outbreak Analytics Pipeline on the vision, strategy, and plan for the workshop

What is the current behavior? (You can also link to an open issue here)

The website contains all the episodes before the repo split.

What is the new behavior (if this is a feature change)?

• Summary page on the Workshop overview
• Software Setup section with all the packages for all the three tutorial pages
• Introductory episode on the Outbreak analytics pipeline

Further details

How to review?

• follow the steps in the reviewer role section of the contributing.md file
• if local rendering doesn't work, please, report them in Issues.
• you can read online the knitted content of this PR in branch md-output-PR-137 (drawback, figure captions not visible)
  • index.md
  • setup.md
  • introduction.md

[avallecam]

@CarmenTamayo could we have your review for the introduction episode and the updated outlook of the website when building this locally?

[github-actions]

Thank you!

Thank you for your pull request 😃

🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

• 🎯 correct output
• 🖼️ correct figures
• ❓ new warnings
• ‼️ new errors

Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials/compare/md-outputs..md-outputs-PR-137

The following changes were observed in the rendered markdown documents:

 compare-interventions.md (gone)                    |  258 ---
 config.yaml (gone)                                 |   87 -
 create-forecast.md (gone)                          |  391 ----
 ...rventions-rendered-unnamed-chunk-1-1.png (gone) |  Bin 65010 -> 0 bytes
 ...forecast-rendered-unnamed-chunk-11-1.png (gone) |  Bin 8647 -> 0 bytes
 ...-forecast-rendered-unnamed-chunk-3-1.png (gone) |  Bin 50344 -> 0 bytes
 ...-forecast-rendered-unnamed-chunk-9-1.png (gone) |  Bin 10331 -> 0 bytes
 fig/distribution-zoo.png (new)                     |  Bin 0 -> 23148 bytes
 fig/generation-time-gr2_lrg.jpg (new)              |  Bin 0 -> 354591 bytes
 ...roduction-rendered-unnamed-chunk-5-1.png (gone) |  Bin 50909 -> 0 bytes
 fig/model-choices-rendered-diagram-1.png (gone)    |  Bin 18643 -> 0 bytes
 ...l-choices-rendered-unnamed-chunk-1-1.png (gone) |  Bin 27875 -> 0 bytes
 ...l-choices-rendered-unnamed-chunk-3-1.png (gone) |  Bin 13663 -> 0 bytes
 ...l-choices-rendered-unnamed-chunk-4-1.png (gone) |  Bin 9082 -> 0 bytes
 ...ng-interventions-rendered-baseline-1.png (gone) |  Bin 33760 -> 0 bytes
 ...terventions-rendered-diagram_SEIRV-1.png (gone) |  Bin 23029 -> 0 bytes
 ...-interventions-rendered-plot_masks-1.png (gone) |  Bin 34141 -> 0 bytes
 ...erventions-rendered-plot_vaccinate-1.png (gone) |  Bin 39125 -> 0 bytes
 fig/pkgs-hexlogos-2.png (new)                      |  Bin 0 -> 622072 bytes
 ...sibility-rendered-unnamed-chunk-15-1.png (gone) |  Bin 31186 -> 0 bytes
 ...sibility-rendered-unnamed-chunk-16-1.png (gone) |  Bin 30121 -> 0 bytes
 ...sibility-rendered-unnamed-chunk-19-1.png (gone) |  Bin 84682 -> 0 bytes
 ...ssibility-rendered-unnamed-chunk-4-1.png (gone) |  Bin 5925 -> 0 bytes
 ...ssibility-rendered-unnamed-chunk-7-1.png (gone) |  Bin 10256 -> 0 bytes
 ...d-delays-rendered-unnamed-chunk-20-1.png (gone) |  Bin 11595 -> 0 bytes
 ...ting-transmission-rendered-diagram-1.png (gone) |  Bin 18643 -> 0 bytes
 ...ulating-transmission-rendered-plot-1.png (gone) |  Bin 16307 -> 0 bytes
 ...ulating-transmission-rendered-traj-1.png (gone) |  Bin 51739 -> 0 bytes
 ...ng-transmission-rendered-visualise-1.png (gone) |  Bin 51739 -> 0 bytes
 index.md                                           |   36 +-
 introduction.md                                    |   91 +-
 md5sum.txt                                         |   29 +-
 model-choices.md (gone)                            |  354 ---
 modelling-interventions.md (gone)                  |  430 ----
 quantify-transmissibility.md (gone)                |  539 -----
 read-delays.md (gone)                              | 1675 --------------
 reference.md                                       |   13 +-
 renv.lock (gone)                                   | 2279 --------------------
 setup.md                                           |  302 ++-
 simulating-transmission.md (gone)                  |  464 ----
 40 files changed, 368 insertions(+), 6580 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2024-10-29 18:57:51 +0000