v3.4.0: port uvarpro figures (gg_beta_uvarpro + gg_sdependent) to the V3 CRAN line

[ehrlinger]

⚠️ DO NOT SUBMIT TO CRAN YET. Holding for the frequency window (3.2.0 shipped 2026-06-23). This + 3.3.0 (already on main, unreleased) ship together in the next submission.

Summary

Ports the two uvarpro visualization wrappers from the dev_rhf line down to a V3 3.4.0 CRAN minor, per the V3 = varPro / V4 = randomForestRHF boundary (recorded in the branch-strategy memory). Both wrap varPro:: only — no randomForestRHF dependency.

• gg_beta_uvarpro() / plot — entropy-ranking bar chart from varPro::get.beta.entropy(); the unsupervised analogue of gg_beta_varpro(). print/summary/autoplot companions.
• gg_sdependent() / plot — signal-variable lollipop from varPro::sdependent(); complements gg_udependent() (structure) with a signal-vs-noise ranking.

What's in the port

• 6 new files (4 R + 2 tests) from dev_rhf; print/summary/autoplot are self-contained in the gg_*.R files. man/ (4 pages) + NAMESPACE regenerated.
• No new dependency (varPro already in Imports).
• Tests carry skip_on_cran for the upstream uvarpro-grow gcc-UBSAN issue.
• _pkgdown.yml entries added.
• Vignette: two subsections in the existing "Cross-variable dependency" section, run live on the cached u_boston fit (same treatment as gg_udependent).
• Version 3.3.0 → 3.4.0.

Verification

• New tests pass; full suite + news + lint clean
• R CMD check --as-cran with manual: clean (only env NOTEs — days-since-update, local HTML-tidy); vignette rebuilds with the new chunks; ~3.5 min

Note on dev_rhf

dev_rhf already has these files (PR #121). After 3.4.0 is accepted, the main→dev_rhf forward-merge reconciles them to V3's version (take main's side if diverged).

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 97.36842% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.06%. Comparing base (253155d) to head (a9984d9).

Files with missing lines	Patch %	Lines
R/gg_beta_uvarpro.R	95.41%	5 Missing ⚠️
R/gg_sdependent.R	98.73%	1 Missing ⚠️
R/plot.gg_beta_uvarpro.R	97.61%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #130      +/-   ##
==========================================
+ Coverage   87.45%   88.06%   +0.60%     
==========================================
  Files          44       48       +4     
  Lines        4090     4356     +266     
==========================================
+ Hits         3577     3836     +259     
- Misses        513      520       +7     

Files with missing lines	Coverage Δ
R/plot.gg_sdependent.R	100.00% <100.00%> (ø)
R/gg_sdependent.R	98.73% <98.73%> (ø)
R/plot.gg_beta_uvarpro.R	97.61% <97.61%> (ø)
R/gg_beta_uvarpro.R	95.41% <95.41%> (ø)

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[Copilot]

Pull request overview

Ports the unsupervised uvarpro visualization wrappers into the V3/CRAN line, adding tidy data wrappers plus plot/print/summary/autoplot companions for entropy-based importance and signal-variable detection from varPro::uvarpro() fits.

Changes:

• Added new exported wrappers gg_beta_uvarpro() and gg_sdependent() with corresponding S3 plot, print, summary, and autoplot methods.
• Added test coverage for both wrappers (including a CRAN-skipped live integration check).
• Updated documentation and site/vignette surfaces (Rd pages, vignette sections, pkgdown reference), and bumped version to 3.4.0.

Reviewed changes

Copilot reviewed 11 out of 17 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
R/gg_beta_uvarpro.R	New tidy wrapper around varPro::get.beta.entropy() including print/summary/autoplot and validation helpers.
R/plot.gg_beta_uvarpro.R	New bar-chart plot method for gg_beta_uvarpro.
R/gg_sdependent.R	New tidy wrapper around varPro::sdependent() including print/summary/autoplot.
R/plot.gg_sdependent.R	New lollipop plot method for gg_sdependent.
tests/testthat/test_gg_beta_uvarpro.R	Unit tests for shape/ranking/cutoff/provenance + CRAN-skipped live integration.
tests/testthat/test_gg_sdependent.R	Unit tests for shape/ranking/signal flag/provenance + CRAN-skipped live integration.
vignettes/varpro.qmd	Adds vignette sections demonstrating both new wrappers.
man/gg_beta_uvarpro.Rd	New Rd page for gg_beta_uvarpro().
man/plot.gg_beta_uvarpro.Rd	New Rd page for plot.gg_beta_uvarpro().
man/gg_sdependent.Rd	New Rd page for gg_sdependent().
man/plot.gg_sdependent.Rd	New Rd page for plot.gg_sdependent().
man/print.gg.Rd	Regenerated to include the new print methods.
man/summary.gg.Rd	Regenerated to include the new summary methods.
NAMESPACE	Registers new S3 methods / exports and ggplot2 import for geom_segment.
_pkgdown.yml	Adds the new topics to the pkgdown reference index.
NEWS.md	Adds the v3.4.0 release notes for the new wrappers.
DESCRIPTION	Bumps version from 3.3.0 to 3.4.0.

Files not reviewed (6)

• man/gg_beta_uvarpro.Rd: Generated file
• man/gg_sdependent.Rd: Generated file
• man/plot.gg_beta_uvarpro.Rd: Generated file
• man/plot.gg_sdependent.Rd: Generated file
• man/print.gg.Rd: Generated file
• man/summary.gg.Rd: Generated file

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