full review post-trial 01 and new episodes in tutorials-early

[avallecam]

This PR aims to collect edit suggestions for the tutorials-early repository.

This includes any specific addition to:

• new episodes added on read, clean, validate, and aggregate data
• add content on epidemiological background or field applications
• add conceptual explanations of methods

All rendered content is in https://epiverse-trace.github.io/tutorials-early/

[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
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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-early/compare/md-outputs..md-outputs-PR-70

The following changes were observed in the rendered markdown documents:

 clean-data.md                                      | 129 +++++++++++++--------
 config.yaml                                        |   2 +-
 delays-functions.md                                |  28 ++---
 delays-reuse.md                                    |  21 +++-
 describe-cases.md                                  |  40 +++++--
 ...elays-functions-rendered-unnamed-chunk-16-1.png | Bin 50192 -> 50680 bytes
 ...elays-functions-rendered-unnamed-chunk-17-1.png | Bin 52012 -> 51545 bytes
 ...elays-functions-rendered-unnamed-chunk-20-1.png | Bin 51371 -> 51418 bytes
 ...elays-functions-rendered-unnamed-chunk-21-1.png | Bin 33484 -> 32932 bytes
 ...ransmissibility-rendered-unnamed-chunk-16-1.png | Bin 31542 -> 31716 bytes
 ...ransmissibility-rendered-unnamed-chunk-17-1.png | Bin 30825 -> 29949 bytes
 ...ransmissibility-rendered-unnamed-chunk-20-1.png | Bin 84470 -> 84466 bytes
 md5sum.txt                                         |  18 +--
 quantify-transmissibility.md                       | 121 ++++++++++---------
 read-cases.md                                      |  99 +++++++++++-----
 setup.md                                           |  33 ++++--
 simple-analysis.md                                 |  83 ++++++++++---
 17 files changed, 382 insertions(+), 192 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 2024-06-17 20:48:14 +0000

[Degoot-AM]

@avallecam, I have a few comments on this PR, please review the changes.

[avallecam]

@Degoot-AM I finally managed to go through all the first four episodes! thank you work on them!

I prioritized code flow, that everything is running with the recent package versions. I found some edits required for cleanepi code, and one that I reported as issue.

Then I suggested to add some space between code lines within long chunks.

I added namespace reminders and some callout box of prerequisites as reminders of the dataset that we need to download before going through the episode.

For the first episode on read case data, we may open it to four subtitles to add brief details on each step. Also I suggested a figure as a first intro to databases.

Regarding the setup page, better if we focus to update the download links and the packages required for the four episodes. We had mixed and overlapping suggestions here and in the PR #64 so better if we reconciliate them after merging these most recent edits.

Are you able to approve commits in this PR? If yes, please, go ahead!

[Degoot-AM]

Thank you @avallecam for you feedback.

[Degoot-AM]

Suggested change

	is stable. This is controlled by a single lockfile which documents the packages
	is stable. This is controlled by our (workflow) [https://github.com/epiverse-trace/tutorials-early/tree/main/.github/workflows] that can generate (PRs to update) [https://github.com/epiverse-trace/research-compendium/pull/38] package versions in the (lockfile) [https://github.com/epiverse-trace/tutorials-early/blob/main/renv/profiles/lesson-requirements/renv.lock].

[avallecam]

since this file is a workflow file from the workbench infrastructure, better to propose edits in the carpentries template file

[avallecam]

redirecting this PR to main now