add episodes on estimate superspreading and simulate chains (trial 04)

[avallecam]

Fix #20

PR is now ready to review

I'll appreciate your specific feedback providing a clear next step to remove, change or add content.

how to review?

• follow the steps in the reviewer role section of the contributing.md file

• Before running sandpaper::build_lesson(), in the config.yaml file deactivate these episodes:

episodes:
# - quantify-transmissibility.Rmd
# - create-forecast.Rmd
# - severity-static.Rmd

• if local rendering doesn't work, please, report them in Issues.

• preliminary deployment to review: md-outputs-PR-29

[github-actions[bot]]

Thank you!

Thank you for your pull request :smiley:

:robot: 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:

• :dart: correct output
• :framed_picture: correct figures
• :question: new warnings
• :bangbang: new errors

Rendered Changes

:mag: Inspect the changes: https://github.com/epiverse-trace/tutorials-middle/compare/md-outputs..md-outputs-PR-29

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)                                 |   82 -
 create-forecast.md                                 |   36 +-
 fig/SEE-dist.png (new)                             |  Bin 0 -> 35883 bytes
 ...-individual-reproductive-number-fig-b.png (new) |  Bin 0 -> 42785 bytes
 ...-individual-reproductive-number-fig-c.png (new) |  Bin 0 -> 41607 bytes
 ...-individual-reproductive-number-fig-d.png (new) |  Bin 0 -> 32479 bytes
 fig/SEE-individual-reproductive-number.png (new)   |  Bin 0 -> 149897 bytes
 fig/SEE-params.png (new)                           |  Bin 0 -> 41828 bytes
 fig/contact-tracing-backward-time.png (new)        |  Bin 0 -> 32611 bytes
 fig/contact-tracing-serial-interval.png (new)      |  Bin 0 -> 270280 bytes
 fig/contact-tracing-strategies.png (new)           |  Bin 0 -> 147619 bytes
 ...create-forecast-rendered-unnamed-chunk-11-1.png |  Bin 8289 -> 8330 bytes
 fig/create-forecast-rendered-unnamed-chunk-4-1.png |  Bin 50555 -> 50093 bytes
 fig/create-forecast-rendered-unnamed-chunk-9-1.png |  Bin 10170 -> 10162 bytes
 fig/see-intro-secondary-cases-fig-b.png (new)      |  Bin 0 -> 84087 bytes
 fig/see-intro-secondary-cases.png (new)            |  Bin 0 -> 169707 bytes
 fig/see-intro-superspreading.png (new)             |  Bin 0 -> 629581 bytes
 fig/see-nature04153_Fig2-c.jpg (new)               |  Bin 0 -> 7325 bytes
 fig/see-nature04153_Fig2.jpg (new)                 |  Bin 0 -> 21641 bytes
 ...-estimate-rendered-unnamed-chunk-10-1.png (new) |  Bin 0 -> 15447 bytes
 ...-estimate-rendered-unnamed-chunk-11-1.png (new) |  Bin 0 -> 4831 bytes
 ...-estimate-rendered-unnamed-chunk-14-1.png (new) |  Bin 0 -> 16689 bytes
 ...-estimate-rendered-unnamed-chunk-17-1.png (new) |  Bin 0 -> 38476 bytes
 ...g-estimate-rendered-unnamed-chunk-4-1.png (new) |  Bin 0 -> 6057874 bytes
 ...g-estimate-rendered-unnamed-chunk-9-1.png (new) |  Bin 0 -> 4745 bytes
 ...g-simulate-rendered-unnamed-chunk-1-1.png (new) |  Bin 0 -> 39727 bytes
 ...-simulate-rendered-unnamed-chunk-15-1.png (new) |  Bin 0 -> 37532 bytes
 ...-simulate-rendered-unnamed-chunk-18-1.png (new) |  Bin 0 -> 4596 bytes
 ...-simulate-rendered-unnamed-chunk-19-1.png (new) |  Bin 0 -> 39727 bytes
 ...-simulate-rendered-unnamed-chunk-21-1.png (new) |  Bin 0 -> 11576 bytes
 ...-simulate-rendered-unnamed-chunk-24-1.png (new) |  Bin 0 -> 4052 bytes
 ...-simulate-rendered-unnamed-chunk-25-1.png (new) |  Bin 0 -> 8636 bytes
 ...g-simulate-rendered-unnamed-chunk-4-1.png (new) |  Bin 0 -> 10931 bytes
 md5sum.txt                                         |   26 +-
 network.html (new)                                 | 5319 ++++++++++++++++++++
 renv.lock (gone)                                   | 2174 --------
 setup.md                                           |    1 -
 superspreading-estimate.md (new)                   |  718 +++
 superspreading-simulate.md (new)                   |  886 ++++
 webshot.png (new)                                  |  Bin 0 -> 6057874 bytes
 40 files changed, 6955 insertions(+), 2287 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.

:stopwatch: Updated at 2024-05-01 00:05:34 +0000

[avallecam]

@adamkucharski major comments collected. I'll leave the others for next week.

Regarding the extreme k = 0.02. We can try to look for studies that estimated and published this from the MERS data. This k value is the one estimated in the superspreading-estimate episode. Should we add some additional context as papers on MERS with complementary estimates in a callout?

[avallecam]

@joshwlambert @jamesmbaazam could we have your review during the coming week? We expect to merge this on Thursday 25th April.

[jamesmbaazam]

Hi @avallecam, unfortunately, I'm sorry I have not been able to review this before your deadline today. I am at a full-day workshop tomorrow and can't take a look but I could do that by the close of Monday if that is fine.

[avallecam]

Hi @avallecam, unfortunately, I'm sorry I have not been able to review this before your deadline today. I am at a full-day workshop tomorrow and can't take a look but I could do that by the close of Monday if that is fine.

thank you @jamesmbaazam for sharing your availability. Monday also works for me. In the meantime, I'll incorporate all the current feedback.

Given the time to event, for your feedback on Monday, we'll prioritize key edits. After trial 04, we'll open a new full-review PR to collect any major edits required.

[jamesmbaazam]

Given the time to event, for your feedback on Monday, we'll prioritize key edits. After trial 04, we'll open a new full-review PR to collect any major edits required.

Agreed.

[joshwlambert]

@avallecam nice work on building these tutorials. I have a read through the "Account for superspreading" and "Simulate transmission chains" sections and it looks good. I'll wait until after the tutorial is delivered to the students for the first time before recommending any substantial changes, but nothing required immediately, and we can see if any parts need restructuring if the students struggle at certain points.

[avallecam]

Thanks for your reviews! I moved the larger ones to issues for further inspection and evaluation:

• 63

• 64

• 65

• 66

I plan to merge this after the checks pass. Then I'll open a post-trial branch to collect more feedback