Review tutorials late

[joshwlambert]

This PR makes several minor updates the the Contact matrices (episodes/contact-matrices.Rmd), Simulating transmission (episodes/simulating-transmission.Rmd) and Modelling interventions (episodes/modelling-interventions.Rmd) episodes.

There are also some small edits to compare-interventions.Rmd, vaccine-comparisons.Rmd and learners/setup.Rmd.

This PR is part of the review of Epiverse tutorials for the upcoming Outbreak Analytics and Applied Modelling in R short course (Week 4).

Please feel free to revert any changes in this PR that you disagree with.

• 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
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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-late/compare/md-outputs..md-outputs-PR-149

The following changes were observed in the rendered markdown documents:

 compare-interventions.md   |    2 +-
 config.yaml (new)          |   86 +
 contact-matrices.md        |   10 +-
 md5sum.txt                 |   12 +-
 modelling-interventions.md |    8 +-
 renv.lock (new)            | 5326 ++++++++++++++++++++++++++++++++++++++++++++
 setup.md                   |    6 +-
 simulating-transmission.md |   12 +-
 vaccine-comparisons.md     |    2 +-
 9 files changed, 5438 insertions(+), 26 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 2026-03-31 04:22:12 +0000