Remove DiagrammeR in favour of mermaid

[avallecam]

Summary

• Remove dead library(DiagrammeR), library(webshot), and webshot::install_phantomjs() setup chunks from episodes/contact-matrices.Rmd and episodes/simulating-transmission.Rmd — all diagrams already used native mermaid flowchart syntax
• Update CONTRIBUTING.md to point new contributors to mermaid instead of DiagrammeR
• Remove DiagrammeR from renv/profiles/lesson-requirements/renv.lock via renv::remove() + renv::snapshot()

Closes #162

Test plan

• Verify mermaid diagrams still render in both episodes (SIR in contact-matrices, SEIR in simulating-transmission)
• Confirm no build errors from missing DiagrammeR/webshot

🤖 Generated with Claude Code

[github-actions]

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🤖 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:

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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-late/compare/md-outputs..md-outputs-PR-163

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)         |   84 -
 contact-matrices.md        |    2 -
 md5sum.txt                 |   36 +-
 renv.lock (gone)           | 5579 --------------------------------------------
 simulating-transmission.md |    2 -
 5 files changed, 18 insertions(+), 5685 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 2026-06-12 11:27:25 +0000