Theoretical_background

[Degoot-AM]

This PR adds a new episode to the mid-stage tutorial, explaining how delays are adjusted when estimating $R_t$ via the renewal equation.
​

It summarizes the approach we previously used to convey this content to synchronous participants during classes, but now documents it in written form for the benefit of a wider audience.

[github-actions]

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🤖 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:

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• 🖼️ correct figures
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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-middle/compare/md-outputs..md-outputs-PR-221

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)                                 |   86 -
 create-forecast.md                                 |   50 +-
 delays-functions.md                                |   16 +-
 ...create-forecast-rendered-unnamed-chunk-10-1.png |  Bin 9592 -> 9585 bytes
 ...create-forecast-rendered-unnamed-chunk-12-1.png |  Bin 8724 -> 8446 bytes
 fig/create-forecast-rendered-unnamed-chunk-4-1.png |  Bin 46536 -> 46414 bytes
 ...elays-functions-rendered-unnamed-chunk-16-1.png |  Bin 48844 -> 49174 bytes
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 ...elays-functions-rendered-unnamed-chunk-20-1.png |  Bin 51093 -> 49374 bytes
 ...elays-functions-rendered-unnamed-chunk-21-1.png |  Bin 29927 -> 29620 bytes
 ...l-equation-rendered-unnamed-chunk-1-1.png (new) |  Bin 0 -> 4866 bytes
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 ...l-equation-rendered-unnamed-chunk-5-1.png (new) |  Bin 0 -> 23822 bytes
 ...ransmissibility-rendered-unnamed-chunk-10-1.png |  Bin 72588 -> 63611 bytes
 ...ransmissibility-rendered-unnamed-chunk-17-1.png |  Bin 28973 -> 28900 bytes
 ...ransmissibility-rendered-unnamed-chunk-18-1.png |  Bin 31854 -> 32443 bytes
 fig/severity-static-rendered-unnamed-chunk-2-1.png |  Bin 6672 -> 6577 bytes
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 ...reading-estimate-rendered-unnamed-chunk-4-1.png |  Bin 6402587 -> 6533045 bytes
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 intro-renewal-equation.md (new)                    |  168 +
 md5sum.txt                                         |   35 +-
 network.html                                       |    6 +-
 quantify-transmissibility.md                       |   43 +-
 renv.lock (gone)                                   | 6154 --------------------
 webshot.png                                        |  Bin 6402587 -> 6533045 bytes
 32 files changed, 241 insertions(+), 6317 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 2025-09-25 12:43:22 +0000

[avallecam]

Hi @Degoot-AM thanks for contributing this episode. I just added some title rename, a solution and minor edit at the end. This contains the key messages we showed in deliveries, also some extra features from the comparison.

Please, double check the solution I drafted to the challenge you proposed.

Lastly, What do you think about moving this to the More Resources tab? As the Intro to Math Modelling of ID in tutorials-late? We can link this episode in the quantifying transmissibility episode as a callout: "How does {EpiNow2} work?" similar to what we have in cfr episode, and would also replace.

Happy to read your thoughts.

[Degoot-AM]

Hi @Degoot-AM thanks for contributing this episode. I just added some title rename, a solution and minor edit at the end. This contains the key messages we showed in deliveries, also some extra features from the comparison.

Please, double check the solution I drafted to the challenge you proposed.

Lastly, What do you think about moving this to the More Resources tab? As the Intro to Math Modelling of ID in tutorials-late? We can link this episode in the quantifying transmissibility episode as a callout: "How does {EpiNow2} work?" similar to what we have in cfr episode, and would also replace.

Happy to read your thoughts.

Thanks @avallecam for your suggestions — I’ve accepted them.
I’m happy to relocate the episode to another location, as long as it remains easily accessible to learners.

[avallecam]

I’m happy to relocate the episode to another location, as long as it remains easily accessible to learners.

Nice! I'll proceed with two steps locally:

• change location to More Resources
• add callout box to the quantify transmission

[avallecam]

now ready to merge 🚀 . any further improvements can be done in additional PRs