Load mlumr and ggplot2 once per vignette

[choxos]

Six vignettes loaded mlumr and ggplot2 twice: once in the setup chunk that also sets mc.cores, and again at the top of the worked example. The second copy is gone from both the precompile source (.Rmd.orig) and the knitted .Rmd; library() prints nothing, so the knitted output needs no rebuild.

No set.seed() was added: the sampler takes seed = 2026 in every mlumr() call, the integration points are an unscrambled Sobol sequence, the survival STC bootstrap is passed seed = 2026, and every chunk that draws random numbers in R already sets the seed directly above it.

Checks: one library(mlumr) per file in all twelve files; the repository checks on vignette currency pass (180 assertions); 28 deletions, no other change.

Summary by CodeRabbit

• Documentation
  • Simplified vignette setup by removing repeated package-loading statements.
  • All examples continue to use the required packages and datasets as before.
  • No changes to the documented analyses or user-facing functionality.

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📥 Commits

Reviewing files that changed from the base of the PR and between 006b604 and 4e9f105.

📒 Files selected for processing (12)

• vignettes/binary-outcomes.Rmd
• vignettes/binary-outcomes.Rmd.orig
• vignettes/choosing-a-method.Rmd
• vignettes/choosing-a-method.Rmd.orig
• vignettes/continuous-outcomes.Rmd
• vignettes/continuous-outcomes.Rmd.orig
• vignettes/count-outcomes.Rmd
• vignettes/count-outcomes.Rmd.orig
• vignettes/fitting-and-diagnostics.Rmd
• vignettes/fitting-and-diagnostics.Rmd.orig
• vignettes/survival-outcomes.Rmd
• vignettes/survival-outcomes.Rmd.orig

💤 Files with no reviewable changes (12)

• vignettes/count-outcomes.Rmd.orig
• vignettes/fitting-and-diagnostics.Rmd
• vignettes/binary-outcomes.Rmd.orig
• vignettes/continuous-outcomes.Rmd.orig
• vignettes/survival-outcomes.Rmd.orig
• vignettes/binary-outcomes.Rmd
• vignettes/continuous-outcomes.Rmd
• vignettes/count-outcomes.Rmd
• vignettes/fitting-and-diagnostics.Rmd.orig
• vignettes/choosing-a-method.Rmd
• vignettes/choosing-a-method.Rmd.orig
• vignettes/survival-outcomes.Rmd

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📝 Walkthrough

Walkthrough

The pull request removes redundant mlumr and ggplot2 library calls from six vignette files and their data-preparation chunks. Earlier package-loading code remains unchanged.

Changes

Vignette package-loading cleanup

Layer / File(s)	Summary
Remove redundant library calls vignettes/*.Rmd, vignettes/*.Rmd.orig	The vignettes no longer repeat package attachment calls in setup or data-preparation chunks. Existing earlier package initialization remains in place.

Priority: ⬇️ Low

Estimated code review effort: 1 (Trivial) | ~5 minutes

Change: Refactor

Merge Risk: ⚪ Minimal · up to 4e9f1

The cleanup preserves package availability and paired vignette-source behavior. No merge-blocking risk remains.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description check	⚠️ Warning	The description explains the change, reproducibility considerations, and verification results. It does not follow the required template because it omits the Type of Change, Statistical or User-Facing …	Add all required template sections. Select the applicable Type of Change options, state the user-facing and statistical impact, complete the Documentation and Checklist sections, and place the verification commands and results under a Verif…

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and concisely describes the main change: loading mlumr and ggplot2 once per vignette.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

Full details: Description check

Explanation

The description explains the change, reproducibility considerations, and verification results. It does not follow the required template because it omits the Type of Change, Statistical or User-Facing Impact, Documentation, and Checklist sections, and it does not use the required Verification heading or command-and-result block.

Resolution

Add all required template sections. Select the applicable Type of Change options, state the user-facing and statistical impact, complete the Documentation and Checklist sections, and place the verification commands and results under a Verification heading.

• Fix all pre-merge checks with AI

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Commit to this branch
• Create a new PR

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