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]

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-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.

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

[adamkucharski]

Thanks for putting together, some nice examples here. Have added review to content in superspreading-estimate.Rmd and will revisit superspreading-simulate.Rmd when more added.

[adamkucharski]

Nice work putting this together – lots of great content for learners. Have added few comments on the superspreading-simulate episode, mostly around consistency and clarity

[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.

[avallecam]

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

• assess for homogeneous ggplot2 format across episodes #63
• evaluate to use as.function() to <epidist> objects for cfr and epichains #64
• evaluate to create an isolated episode on contact data using {epicontacts} #65
• evaluate extreme dispersion parameter for MERS #66

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