edit tutorials with new socialmixr and contactsurveys interoperability

[avallecam]

Closes #140

Summary

• Fix deprecated age.limits → age_limits in compare-interventions.Rmd and template.Rmd
• Update contact-matrices.Rmd with the new loading pattern (contactsurveys::download_survey() + socialmixr::load_survey()), add return_demography = TRUE, new callouts for country name warning and demography requirement, and standardized object names
• Apply the same pattern uniformly to all downstream episodes: simulating-transmission.Rmd, modelling-interventions.Rmd, compare-interventions.Rmd, disease-burden.Rmd, vaccine-comparisons.Rmd, template.Rmd

Test plan

• Render contact-matrices.Rmd and verify the new callouts display correctly
• Verify contacts_byage$demography is populated (requires return_demography = TRUE)
• Render each downstream episode and confirm no broken object references
• Check that levels(survey_load$participants$country) output matches expected countries for POLYMOD and Zambia surveys

🤖 Generated with Claude Code

[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-late/compare/md-outputs..md-outputs-PR-145

The following changes were observed in the rendered markdown documents:

 compare-interventions.md   |  52 +++++++++++---------
 contact-matrices.md        | 119 +++++++++++++++++++++++++++------------------
 disease-burden.md          |  31 +++++++-----
 md5sum.txt                 |  36 +++++++-------
 model-choices.md           |  20 ++++----
 modelling-interventions.md |  34 +++++++------
 setup.md                   |  14 +++---
 simulating-transmission.md |  50 ++++++++++---------
 vaccine-comparisons.md     |  42 ++++++++--------
 9 files changed, 225 insertions(+), 173 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 18:36:34 +0000

[avallecam]

hi @Degoot-AM an experimental PR using Claude Code to edit all the calls for socialmixr in this repo.

Some thoughts:

• Nice case study to use for updating the practical files and how-to guides in a similar way.
• It even generated text updates in the tutorial steps (which I forgot and was not expecting).
• It needed minimal feedback from me after generating the plan detailed in the issue linked.
• Only the last commit was a required fix that came from my local review.

This should be ready to review after passing all checks.

[Degoot-AM]

Nicely done ! I have made a few edits.