varPro Phase 3: gg_udependent — dependency graph for uvarpro fits

[ehrlinger]

Summary

• Adds gg_udependent(): tidy extractor wrapping varPro::get.beta.entropy() + varPro::sdependent() on a uvarpro fit. Returns \$edges, \$nodes, \$graph (igraph), and a provenance attribute.
• Adds plot.gg_udependent(): ggraph network renderer with edge width/opacity by dependency strength, node colour by signal status, configurable layout ("fr", "kk", "stress", etc.).
• Adds print, summary, autoplot S3 companions (in shared method files per project convention).
• Moves igraph from Suggests: to Imports: (required by importFrom in NAMESPACE).
• Adds ggraph to Suggests:.
• Bumps version to 2.7.3.9004.

Test plan

• All test_gg_udependent.R tests pass (806 pass, 11 skip — ggraph/vdiffr skips expected)
• devtools::check(args='--as-cran') returns 0 errors, 0 warnings, 0 notes
• CI passes on all platforms
• vdiffr snapshots recorded on platform with ggraph installed

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 83.07692% with 33 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.39%. Comparing base (6e64c20) to head (661a388).

Files with missing lines	Patch %	Lines
R/plot.gg_udependent.R	65.45%	19 Missing ⚠️
R/gg_udependent.R	88.79%	13 Missing ⚠️
R/print_methods.R	91.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #86      +/-   ##
==========================================
- Coverage   86.62%   86.39%   -0.23%     
==========================================
  Files          36       38       +2     
  Lines        2826     3021     +195     
==========================================
+ Hits         2448     2610     +162     
- Misses        378      411      +33     

Files with missing lines	Coverage Δ
R/autoplot_methods.R	85.71% <100.00%> (+1.09%)	⬆️
R/summary_methods.R	92.10% <100.00%> (+0.61%)	⬆️
R/print_methods.R	89.58% <91.66%> (+0.29%)	⬆️
R/gg_udependent.R	88.79% <88.79%> (ø)
R/plot.gg_udependent.R	65.45% <65.45%> (ø)

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[Copilot]

Pull request overview

Adds a new varPro Phase 3 feature to ggRandomForests for extracting and visualizing cross-variable dependency structure from varPro::uvarpro fits, including an igraph-backed data object, ggraph plotting, S3 companions, documentation, and tests.

Changes:

• Introduces gg_udependent() to compute a dependency graph ($edges, $nodes, $graph) plus a provenance attribute from a uvarpro fit.
• Adds plot.gg_udependent() (ggraph renderer) and S3 companions (print, summary, autoplot) + corresponding documentation/NAMESPACE updates.
• Updates dependencies/tests/metadata (Imports/Suggests, NEWS, pkgdown reference, snapshot tests).

Reviewed changes

Copilot reviewed 13 out of 48 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tests/testthat/test_snapshots.R	Adds vdiffr snapshot cases for gg_udependent (guarded by env var + ggraph).
tests/testthat/test_gg_udependent.R	New unit + smoke tests for gg_udependent structure, provenance, S3 methods, and plotting behavior.
tests/testthat/_snaps/snapshots/gg-vimp-survival-rfsrc.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-vimp-regression-rfsrc.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-vimp-regression-rf.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-vimp-classification-rfsrc.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-vimp-classification-rf.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-varpro-default.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-varpro-conditional.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-roc-classification-rfsrc.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-roc-classification-rf.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-rfsrc-regression-rf.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-partial-varpro-mortality.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-partial-varpro-continuous.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-partial-varpro-categorical.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-error-survival-rfsrc.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-error-regression-rfsrc.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-error-regression-rf.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-error-classification-rfsrc.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-brier-survival-overall.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-brier-survival-envelope.svg	Removes an existing vdiffr baseline snapshot (SVG).
tests/testthat/_snaps/snapshots/gg-brier-survival-crps.svg	Removes an existing vdiffr baseline snapshot (SVG).
R/summary_methods.R	Adds summary.gg_udependent() implementation.
R/print_methods.R	Adds print.gg_udependent() and print.summary.gg_udependent().
R/plot.gg_udependent.R	New ggraph-based plot method for gg_udependent.
R/gg_udependent.R	New extractor computing dependency adjacency, edges/nodes, and igraph object.
R/autoplot_methods.R	Adds autoplot.gg_udependent() delegating to plot().
NEWS.md	Documents the new gg_udependent() feature and dependency update.
NAMESPACE	Registers S3 methods and imports required functions (igraph, varPro, ggplot2).
man/summary.gg.Rd	Adds alias/usage entry for summary.gg_udependent.
man/print.gg.Rd	Adds aliases/usages for print.gg_udependent and print.summary.gg_udependent.
man/plot.gg_udependent.Rd	New Rd page for plot.gg_udependent.
man/gg_udependent.Rd	New Rd page for gg_udependent.
man/autoplot.gg.Rd	Adds alias/usage for autoplot.gg_udependent.
dev/plans/2026-05-20-varpro-phase3-gg-udependent-design.md	Adds design document for Phase 3 implementation.
DESCRIPTION	Bumps version, moves igraph to Imports, adds ggraph to Suggests.
_pkgdown.yml	Adds gg_udependent and plot.gg_udependent to reference index.

Files not reviewed (5)

• man/autoplot.gg.Rd: Language not supported
• man/gg_udependent.Rd: Language not supported
• man/plot.gg_udependent.Rd: Language not supported
• man/print.gg.Rd: Language not supported
• man/summary.gg.Rd: Language not supported

Comments suppressed due to low confidence (1)

R/gg_udependent.R:116

• Edge weights are currently assigned as imp_mat[i, j] using the (from, to) ordering returned by igraph. For directed = FALSE, this can produce weights that are below the threshold (or otherwise inconsistent) when the undirected edge exists due to the reverse direction. For undirected graphs, compute the edge weight from both directions (e.g., max/mean of I[i,j] and I[j,i]) so the reported/visualised strength matches the edge selection logic.

  ## ---- Build tidy edge data frame with raw weights -------------------------
  edge_df <- igraph::as_data_frame(g, what = "edges")
  if (nrow(edge_df) > 0L) {
    edge_df$weight <- mapply(
      function(i, j) imp_mat[i, j],
      edge_df[[1L]], edge_df[[2L]]
    )

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