extend autoplot.sim_results()

[d-morrison]

This pull request enhances the flexibility and usability of the autoplot.sim_results function by allowing users to customize which columns are mapped to the x-axis, group, and color aesthetics in plots. The documentation has been updated to reflect these new options.

Function enhancements:

• Added new parameters to autoplot.sim_results: x_var, group_var, and color_var, allowing users to specify which columns in the input data frame are used for the x-axis, group, and color aesthetics in the plot.
• Updated the function to use the values of x_var, group_var, and color_var when constructing the plot, replacing hardcoded column references.

Documentation updates:

• Revised the Rd documentation for autoplot.sim_results to describe the new parameters and clarify the expected input format.

[d-morrison]

@copilot update the changelog

[Copilot]

@d-morrison I've opened a new pull request, #463, to work on those changes. Once the pull request is ready, I'll request review from you.

[github-actions]

📖 https://UCD-SERG.github.io/serocalculator/preview/pr462/
Preview documentation for this PR (at commit d287e13)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.

Files with missing lines	Coverage Δ
R/autoplot.sim_results.R	100.00% <100.00%> (ø)

[d-morrison]

@claude this PR (extend-sim-autoplot) adds x_var/group_var/color_var arguments to autoplot.sim_results() and is 155 commits behind main. Please:

• Merge origin/main and resolve conflicts (especially R/autoplot.sim_results.R, its man/ page, NEWS.md, DESCRIPTION).
• Run devtools::document() to regenerate the .Rd/NAMESPACE, then lintr::lint_package(), spelling::spell_check_package(), and devtools::test(); add/refresh a test covering the new aesthetic-mapping arguments.
• Make sure NEWS.md + version are consistent, confirm R CMD check is clean, and push.

I'll mark the PR ready for review once it's green.

---

Generated by Claude Code

[github-actions]

👀 Picked up by workflow run #26922658294. R setup runs first; Claude itself responds after that.

[github-actions]

The commit is done. Here's a summary of what was accomplished:

Changes committed to extend-sim-autoplot:

1. New tests (test-autoplot.sim_results.R): Added two new test cases covering the new parameters:

   • x_var, group_var, color_var arguments work — calls autoplot() with swapped axes and captures a vdiffr snapshot
   • color_var defaults to group_var — verifies implicit and explicit color_var produce identical plots

2. ggpubr → patchwork migration (from origin/main):

   • R/autoplot.seroincidence.by.R: replaced ggpubr::ggarrange() with patchwork::wrap_plots(), stop() with cli::cli_abort(), updated @return doc
   • R/graph_seroresponse_model_1.R: same swap
   • DESCRIPTION: replaced ggpubr with patchwork in Imports

3. Version bump: 1.4.0.9004 → 1.4.0.9015 (one ahead of main at 1.4.0.9014)

4. NEWS.md: Added ## Dependencies section noting the patchwork migration

5. Docs: Regenerated all man/ pages via devtools::document(), updated the autoplot.seroincidence.by vdiffr snapshot for the new patchwork layout, added rlang to inst/WORDLIST

All 128 tests pass (1 Linux-only skip is expected).

_{— posted by @claude post-step from workflow run}