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add refresher delays episode #154

Merged
merged 52 commits into from
Nov 12, 2024
Merged

add refresher delays episode #154

merged 52 commits into from
Nov 12, 2024

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avallecam
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@avallecam avallecam commented Nov 4, 2024

This PR replaces the currently visible episode with one on Introduction to Outbreak Analytics, focused on epidemiological delays while refreshing basic R functions that will be used downstream the tutorials.

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github-actions bot commented Nov 4, 2024

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-154

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)                                 |   81 --
 data/linelist.csv (new)                            |  167 +++
 data/linelist.rds (new)                            |  Bin 0 -> 13881 bytes
 data/linelist.xlsx (new)                           |  Bin 0 -> 18330 bytes
 delays-refresher.md (new)                          | 1056 +++++++++++++++
 fig/delays-adapted-es.png (new)                    |  Bin 0 -> 214631 bytes
 fig/delays-adapted.png (new)                       |  Bin 0 -> 196502 bytes
 ...refresher-rendered-unnamed-chunk-11-1.png (new) |  Bin 0 -> 28184 bytes
 ...refresher-rendered-unnamed-chunk-16-1.png (new) |  Bin 0 -> 4380 bytes
 ...refresher-rendered-unnamed-chunk-18-1.png (new) |  Bin 0 -> 5174 bytes
 ...refresher-rendered-unnamed-chunk-19-1.png (new) |  Bin 0 -> 5142 bytes
 ...refresher-rendered-unnamed-chunk-20-1.png (new) |  Bin 0 -> 15278 bytes
 ...refresher-rendered-unnamed-chunk-34-1.png (new) |  Bin 0 -> 4539 bytes
 ...-refresher-rendered-unnamed-chunk-5-1.png (new) |  Bin 0 -> 7433 bytes
 fig/fig5a-normaldistribution.png (new)             |  Bin 0 -> 111729 bytes
 ...roduction-rendered-unnamed-chunk-5-1.png (gone) |  Bin 50115 -> 0 bytes
 fig/seria-interval-fitted-distributions.jpg (new)  |  Bin 0 -> 200736 bytes
 fig/serial-interval-pairs.jpg (new)                |  Bin 0 -> 923818 bytes
 introduction.md (gone)                             |  239 ----
 md5sum.txt                                         |   22 +-
 renv.lock (gone)                                   | 1399 --------------------
 21 files changed, 1234 insertions(+), 1730 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 2024-11-12 20:48:37 +0000

@avallecam avallecam force-pushed the add-refresher-delays branch from 80d5074 to d739141 Compare November 4, 2024 21:12
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@avallecam avallecam requested a review from Degoot-AM November 7, 2024 23:42
@avallecam avallecam marked this pull request as ready for review November 7, 2024 23:42
github-actions bot pushed a commit that referenced this pull request Nov 7, 2024
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have made a few adjustments based on the remarks, with only a few remaining to be completed.

episodes/delays-refresher.Rmd Show resolved Hide resolved
dplyr::filter(delay_onset_death < 0)
```

More on estimating a _delay-adjusted_ CFR on the episode about **Estimating outbreak severity**!
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add the link of this episode.

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Agree. But I added links to all at the end, in this commit dc6dd0a

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github-actions bot pushed a commit that referenced this pull request Nov 12, 2024
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avallecam commented Nov 12, 2024

worked on some final edits and added helper visuals. now merging.

@avallecam avallecam merged commit afa88d1 into main Nov 12, 2024
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@avallecam avallecam deleted the add-refresher-delays branch November 12, 2024 21:11
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