Review of Account for superspreading and Simulate transmission chains episodes

[joshwlambert]

This PR makes several minor updates the the Account for superspreading (episodes/superspreading-estimate.Rmd) and Simulate transmission chains (episodes/superspreading-simulate.Rmd) episodes.

This PR is part of the review of Epiverse tutorials for the upcoming Outbreak Analytics and Applied Modelling in R short course (Week 3).

Please see commit messages for descriptions of specific changes. Please feel free to revert any changes in this PR that you disagree with. There are quite a few commits for relatively few changes in this PR so it may be preferable to squash merge.

• Please check if the PR fulfills these requirements

• I have read the CONTRIBUTING guidelines
• A new item has been added to NEWS.md
• Tests for the changes have been added (for bug fixes / features)
• Docs have been added / updated (for bug fixes / features)
• Checks have been run locally and pass

• What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)

Minor textual changes.

• What is the current behavior? (You can also link to an open issue here)

N/A

• What is the new behavior (if this is a feature change)?

No new behaviour.

• Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)

No.

• Other information:

[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
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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-middle/compare/md-outputs..md-outputs-PR-260

The following changes were observed in the rendered markdown documents:

 config.yaml (new)                                  |   92 +
 ...reading-estimate-rendered-unnamed-chunk-5-1.png |  Bin 6411784 -> 6855165 bytes
 md5sum.txt                                         |    4 +-
 network.html                                       |    6 +-
 renv.lock (new)                                    | 6683 ++++++++++++++++++++
 superspreading-estimate.md                         |   22 +-
 superspreading-simulate.md                         |   10 +-
 webshot.png                                        |  Bin 6411784 -> 6855165 bytes
 8 files changed, 6796 insertions(+), 21 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 2026-03-23 16:47:48 +0000

[avallecam]

thanks @joshwlambert ! just added two optional edit suggestions.

• express that both mean and dispersion determine the variance of the NB distribution.
• preferring a writing style using commas instead of an em dash.