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Development Notes

2025-12-30 — Commit 95afbf8: Add coverage test for rate_limits validation (Codecov patch fix)

Files touched

  • tests/testthat/test-plot_ic_acceptance_matrix.R
  • dev-notes.md

Summary

  • Added a targeted unit test exercising plot_ic_acceptance_matrix() input validation for rate_limits when plot_rate_of_improvement = TRUE.
  • Covers the new error path (stop(...)) introduced with rate_limits, restoring Codecov patch coverage for the plotting changes.

Intent

  • Keep coverage stable while preserving strict argument validation for the new rate_limits option.

2025-12-30 — Commit 96028bb: Restore plotting par; add rate-limits control; vignette print fix

Files touched

  • R/plot_ic_acceptance_matrix.R
  • man/plot_ic_acceptance_matrix.Rd
  • vignettes/jaw-shape-vignette.Rmd
  • dev-notes.md

Summary

  • plot_ic_acceptance_matrix() plotting robustness + configurability:
    • Restores user graphical parameters on exit (par(no.readonly=TRUE) + on.exit(par(oldpar))) to avoid leaking par() settings across calls (addresses CRAN-style note).
    • Added rate_limits argument (default c(-400, 150)) to control the secondary y-axis limits for the rate-of-improvement overlay.
    • Added input validation for rate_limits (numeric length-2, finite; sorted internally).
  • Documentation:
    • Regenerated Rd; updated details to reflect restored par() behavior and the new rate_limits argument.
  • Vignette:
    • Print ic_weights as a matrix inside the chunk to avoid RStudio rendering issues (paged/Unicode table display).

Intent

  • Make the IC acceptance plot function safe to call inside packages/vignettes (no persistent par() side effects) and provide user control over the diff(IC) axis scale.

2025-12-27 — Commit 380134c: Linting cleanup + CRAN compliance fixes (no behavior change)

Files touched

  • R/plot_ic_acceptance_matrix.R
  • R/searchOptimalConfiguration.R
  • R/utils.R
  • tests/testthat/test-addShiftToModel.R
  • tests/testthat/test-fitMvglsAndExtractBIC.formula.R
  • tests/testthat/test-fitMvglsAndExtractGIC.formula.r
  • tests/testthat/test-plot_ic_acceptance_matrix.R
  • .Rbuildignore
  • .gitignore

Summary

  • Performed a focused linting and style cleanup across core R files and tests:
    • Standardized spacing, argument formatting, and quoting (no functional changes).
    • Improved readability and consistency with tidyverse / CRAN style expectations.
  • Minor test refactors to make on.exit() usage explicit and robust in plotting tests.
  • No changes to model logic, algorithms, or numerical behavior.
  • This commit intentionally does not address the outstanding CRAN note about restoring graphical parameters; that fix will be handled in a subsequent commit.

Intent

  • Reduce diff noise and improve maintainability before implementing CRAN-requested fixes.
  • Ensure future functional changes are isolated from formatting-only edits.

2025-12-26 — Commit 2ca1922: Update print output, citation hint, and vignette demo

Files touched

  • R/bifrost_search-methods.R
  • inst/CITATION
  • vignettes/jaw-shape-vignette.Rmd
  • dev-notes.md

Summary

  • Print method: reorganized output blocks for readability, added versioned header underline, and added a one-line citation hint (citation("bifrost")) at the end of the printout.
  • Citation: updated inst/CITATION entries to reflect current package metadata.
  • Vignette: added a small snippet demonstrating that bifrost_search has a custom print method.

2025-12-26 — Commit 96c9941: Refactor print helpers; expand/clean test suite; minor CI + vignette updates

Files touched

  • .Rbuildignore
  • .gitignore
  • .github/workflows/R-CMD-check.yaml
  • R/bifrost_search-methods.R
  • dev-notes.md
  • tests/testthat/test-addShiftToModel.R
  • tests/testthat/test-addShiftToModel_alt.R
  • tests/testthat/test-extractRegimeVCVs.R
  • tests/testthat/test-fitMvglsAndExtractBIC.formula.R
  • tests/testthat/test-fitMvglsAndExtractGIC.formula.r
  • tests/testthat/test-generatePaintedTrees.R
  • tests/testthat/test-generateViridisColorScale.R
  • tests/testthat/test-getDescendants.R
  • tests/testthat/test-mvgls-functions.R
  • tests/testthat/test-paintSubTree_mod.R
  • tests/testthat/test-paintSubTree_removeShift.R
  • tests/testthat/test-plot_ic_acceptance_matrix.R
  • tests/testthat/test-print-bifrost_search.R
  • tests/testthat/test-removeShiftFromTree.R
  • tests/testthat/test-searchOptimalConfiguration.R
  • tests/testthat/test-whichShifts.R
  • vignettes/jaw-shape-vignette.Rmd

Summary

  • Refactored print.bifrost_search into internal helper functions (behavior/output preserved) to reduce complexity and improve maintainability.
  • Continued improving test coverage and stability:
    • Added/updated targeted tests across core helpers (addShiftToModel*, fitMvglsAndExtract*, generatePaintedTrees, plotting helpers, shift utilities, and whichShifts).
    • Consolidated/cleaned print-method tests in test-print-bifrost_search.R.
    • Added additional coverage-oriented assertions while keeping tests deterministic.
  • Minor repository/CI housekeeping:
    • Updated ignore rules and the R-CMD-check workflow.
    • Updated jaw-shape vignette content as part of ongoing documentation refinement.

2025-12-20 — Commit 108b19e: Add bifrost_search print method with IC-history plot; reorganize tests

Files touched

  • DESCRIPTION
  • NAMESPACE
  • R/searchOptimalConfiguration.R
  • R/bifrost_search-methods.R
  • man/print.bifrost_search.Rd
  • R/utils.R
  • tests/testthat/test-searchOptimalConfiguration.R
  • tests/testthat/test-print-bifrost_search.R
  • tests/testthat/test-extractRegimeVCVs.R

Summary

  • Added an S3 class (bifrost_search) for searchOptimalConfiguration() results and a new print.bifrost_search() method:
    • Prints a compact console summary (IC baseline/optimal/ΔIC, search settings, mvgls fit info, shift nodes).
    • Optionally prints an ASCII IC-history plot using txtplot when store_model_fit_history=TRUE.
    • Prints IC weights (support table) when present.
  • Added txtplot to Imports to support the IC-history console plot.
  • Reorganized tests to keep core search tests focused:
    • Moved print-method tests into a dedicated file (test-print-bifrost_search.R) and expanded branch coverage.
  • Cleaned up extractRegimeVCVs by removing/commenting unreachable error code and added tests for missing-component behavior and scaling logic.
  • Added Config/testthat/parallel: false to stabilize test execution behavior in CI.

2025-12-19 — Commit 1e3af6d: Improve IC-weights output consistency and expand tests

Files touched

  • R/searchOptimalConfiguration.R
  • README.md
  • tests/testthat/test-searchOptimalConfiguration.R
  • vignettes/jaw-shape-vignette.Rmd

Summary

  • Standardized ic_weights output across serial (uncertaintyweights) and parallel (uncertaintyweights_par) modes:
    • Always returns a data.frame with columns: node, ic_with_shift, ic_without_shift, delta_ic, ic_weight_withshift, ic_weight_withoutshift, evidence_ratio
    • When no shifts are detected, returns an empty data.frame with the same schema (instead of NA).
  • Improved no-shifts behavior: model_no_uncertainty now returns the baseline mvgls model rather than NULL.