Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Conversation

avallecam
Copy link
Member

@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.

Copy link

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

github-actions bot pushed a commit that referenced this pull request Nov 4, 2024
github-actions bot pushed a commit that referenced this pull request Nov 4, 2024
github-actions bot pushed a commit that referenced this pull request Nov 5, 2024
github-actions bot pushed a commit that referenced this pull request Nov 5, 2024
github-actions bot pushed a commit that referenced this pull request Nov 7, 2024
github-actions bot pushed a commit that referenced this pull request Nov 7, 2024
github-actions bot pushed a commit that referenced this pull request Nov 7, 2024
github-actions bot pushed a commit that referenced this pull request Nov 7, 2024
github-actions bot pushed a commit that referenced this pull request Nov 7, 2024
@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
github-actions bot pushed a commit that referenced this pull request Nov 7, 2024
Copy link
Contributor

@Degoot-AM Degoot-AM left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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**!
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

add the link of this episode.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

github-actions bot pushed a commit that referenced this pull request Nov 8, 2024
github-actions bot pushed a commit that referenced this pull request Nov 12, 2024
@avallecam
Copy link
Member Author

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
4 checks passed
@avallecam avallecam deleted the add-refresher-delays branch November 12, 2024 21:11
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
Status: Done
Development

Successfully merging this pull request may close these issues.

2 participants