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Changelog

Source: NEWS.md

ggRandomForests v2.7.2

  • Address CRAN reviewer (Benjamin Altmann) feedback on the v2.7.1 resubmission:
    • Add methods references to DESCRIPTION (Breiman 2001 and Ishwaran et al. 2008, with <doi:...> auto-links) per CRAN cookbook.
    • Drop the man/shift.Rd Rd file: shift() is an internal utility and the example used ggRandomForests:::shift(...). Marked the function @noRd so it no longer generates a help page.
    • Replace cat() in surv_partial.rfsrc() with message() so progress output is suppressible (suppressMessages()) and plays nicely inside notebooks / Shiny / quarto.
    • Restore the user’s par() settings in the surv_partial.rfsrc() example via oldpar <- par(no.readonly = TRUE); on.exit(par(oldpar)).

ggRandomForests v2.7.1

  • Fix gg_partial_rfsrc() for survival forests: partial.rfsrc() was being called without partial.type, causing a zero-length comparison (if (partial.type == "rel.freq") ...) inside the C-level prediction routine and aborting the call. Survival forests now pass partial.type = "surv" (default; configurable via the new partial.type argument accepting "surv", "chf", or "mort"). This unblocks the partial-dep chunk in the survival vignette.
  • Fix gg_partial_rfsrc() for survival forests with multiple partial.time values: get.partial.plot.data() returns yhat as an [length(partial.values) x length(partial.time)] matrix, but the previous code assumed a vector and crashed on column-mismatch when assigning time. The result is now reshaped to long form so each (x, time) pair is a single row.
  • Improve plot.gg_partial_rfsrc() survival layout: predictor value is now on the x-axis with one curve per (rounded) time point coloured by Time, faceted by variable name. The previous default put time on the x-axis and one curve per predictor value, producing a saturated legend with dozens of nearly-identical lines.
  • Add tests/testthat/test_plot_layer_data.R: regression suite that uses ggplot2::layer_data() to verify each plot.gg_*() method renders non-empty layers for every supported forest family. Catches the empty-figure class of bug (transform/plot column-name mismatch) without requiring visual inspection.
  • ggrandomforests.news() now reads NEWS.md (the canonical change log R also surfaces via utils::news()). The legacy hand-maintained inst/NEWS has been removed — it had silently drifted to v2.4.0 (June 2025) across three releases, so users running the helper saw stale version info. One source of truth, no more drift window.
  • Fix plot.gg_vimp() legend duplication: the bar geom mapped both fill and color to the positive column, but only the fill legend was titled “VIMP > 0”, leaving a redundant second legend titled “positive”. Both aesthetics now share the “VIMP > 0” title so ggplot merges them into a single legend by default.
  • Fix plot.gg_vimp() for forests with all-positive VIMP: the bar geom previously mapped only color (no fill), producing hollow / outline- only bars and an “Ignoring unknown labels: fill” warning whenever labs(fill = ...) was applied. Both fill and color are now mapped unconditionally, so bars render filled in every case.
  • Add @examples blocks to plot.gg_partial_rfsrc() and plot.gg_partialpro(). The latter uses a self-contained mock of the varpro::partialpro() output structure so the example runs without pulling in varpro as a dependency.

ggRandomForests v2.7.0

  • S3 design overhaul: gg_partial(), gg_partialpro(), and gg_partial_rfsrc() now stamp their return values with S3 classes (gg_partial, gg_partialpro, gg_partial_rfsrc respectively), enabling plot() dispatch without any boilerplate.
  • Add plot.gg_partial(), plot.gg_partial_rfsrc(), and plot.gg_partialpro() S3 methods; continuous predictors render as line plots, categorical as bar charts, faceted by variable name. Survival forests produce curves over time; two-variable surface plots group by xvar2.name.
  • Convert gg_survival() to an S3 generic dispatching on the class of its first argument. New gg_survival.rfsrc() method extracts the survival response directly from the fitted forest (no separate data argument needed); gg_survival.default() preserves the existing interface.
  • Fix plot.gg_survival() auto-coercion: previously called gg_survival(rfsrc_obj) treating the forest as the interval string argument, causing a latent crash; replaced with inherits() guard.
  • Deprecate surv_partial.rfsrc() via .Deprecated() with a pointer to gg_partial_rfsrc(); all package tests updated to suppress the warning.
  • Fix gg_partial_rfsrc() — make_eval_grid() used unlist(dplyr::select()) which coerced factor columns to integer codes; now uses newx[[xname]] to preserve column class. Categorical detection extended to cover is.factor() and is.character() in addition to the cardinality check.
  • Add guards to gg_partial_rfsrc(): all-NA xval after NA removal now emits a warning and skips the variable; all-NA grouping variable (xvar2) calls stop(); n_eval and cat_limit are validated as single integers >= 2 near function entry.
  • Fix cyclomatic complexity across gg_partial_rfsrc.R: refactored into eight top-level unexported helpers (validate_scalar_int, validate_partial_args, snap_partial_time, make_eval_grid, call_partial_rfsrc, partial_one_var, partial_no_group, partial_with_group, split_partial_result); all functions now score below the cyclocomp_linter limit of 20.
  • Fix @param partial.time documentation: “see the section above” corrected to “see the section below”.
  • Replace deprecated tidyr::gather() with tidyr::pivot_longer() in plot.gg_vimp() and plot.gg_partialpro().
  • Add gg_survival.rfsrc, gg_survival.default, plot.gg_partial, plot.gg_partial_rfsrc, and plot.gg_partialpro to NAMESPACE; add corresponding @rdname / @export roxygen tags.
  • Update tests: add expect_s3_class() checks for all new classes; add plot() smoke tests for gg_partial, gg_partial_rfsrc, gg_partialpro; add gg_survival.rfsrc tests for KM extraction, by stratification, and error on non-survival forest.
  • Add plot.gg_partial, plot.gg_partial_rfsrc, and plot.gg_partialpro to _pkgdown.yml reference index.

ggRandomForests v2.7.0

  • Fix critical visual bug in plot.gg_rfsrc: all aes() calls used bare string literals instead of .data[[col]], causing every aesthetic to map to a constant string rather than the underlying data column. All plot types (regression, classification, survival) were affected.
  • Fix aes() bare-string literals in plot.gg_roc multi-class branch; remove unreachable if (crv < 2) dead-code branch.
  • Fix bootstrap_survival CI-band indexing in gg_rfsrc: negative index computed via colnames() was a no-op on large datasets and a latent crash for data with ≤ 2 unique event times.
  • Fix gg_rfsrc.rfsrc: is.null(df[, col]) does not detect missing columns; replaced with !col %in% colnames() guard.
  • Fix gg_rfsrc.randomForest: method used non-existent object$xvar; now recovers the training frame via .rf_recover_model_frame().
  • Fix legend suppression in plot.gg_error for single-outcome forests where the data frame has no variable column.
  • Fix gg_vimp and plot.gg_vimp: 1:nvar replaced with seq_len(nvar) in both S3 methods; 1:0 silently returned c(1, 0) instead of integer(0) when nvar == 0.
  • Migrate full test suite to testthat 3.x API: expect_is → expect_s3_class / expect_type / expect_true(is.*()); expect_equivalent → expect_equal(ignore_attr = TRUE); all context() calls removed; testthat 1.x expect_that / is_identical_to removed.
  • Add .lintr package-level linter configuration; fix lintr spacing in gg_partial.
  • Improve GitHub Actions: lint.yaml now fails CI on any lint issue; R-CMD-check.yaml treats warnings as errors and uses Rtools 44; test-coverage.yaml duplicate codecov upload removed.
  • Add covr and vdiffr to Suggests.

ggRandomForests v2.6.1

  • Fix model-label assignment in gg_partial for categorical variable data
  • Refactor gg_partial and gg_partial_rfsrc to improve factor-level normalisation and categorical data handling

ggRandomForests v2.6.0

  • Add and export new plotting functions; update existing plot documentation
  • Improve unit and integration tests; overall coverage raised to 83%
  • Remove hvtiRutilities internal dependency; clean up associated imports
  • Refactor gg_partial_rfsrc to use .data pronoun for all dplyr calls

ggRandomForests v2.5.0

  • Initial gg_partial_rfsrc function: computes partial dependence data directly from an rfsrc model via randomForestSRC::partial.rfsrc, without requiring a separate plot.variable call
  • Add support for a grouping variable (xvar2.name) in gg_partial_rfsrc
  • Improved vignette formatting and namespace usage

ggRandomForests v2.4.0

  • Updating to latest ggplot2 functions
  • Utilize some namespace referencing
  • Added pkgdown documentation
  • Minor testing improvements

ggRandomForests v2.3.0

  • Knocking the dust off this.
  • Fix the ROC curves
  • Fix the colors on VIMP plot

ggRandomForests v2.2.1

CRAN release: 2022-09-01

  • Fix docs for HTML5/Roxygen update

ggRandomForests v2.2.0

CRAN release: 2022-05-09

  • Bring back the regression vignette
  • Improve package tests and code coverage
  • Clean up code with lintr

ggRandomForests v2.1.0

CRAN release: 2022-04-26

To pull this out of archive on randomForestSRC 3.1 build release. Fixed a plot bug for gg_error to show the actual curve (issue 35)

ggRandomForests v2.0.1

CRAN release: 2016-09-07

ggRandomForests v2.0.0

CRAN release: 2016-06-11

  • Added initial support for the randomForest package
  • Updated cache files for randomForestSRC 2.2.0 release.
  • Remove regression vignettes to meet CRAN size limits. These remain available at the package source https://github.com/ehrlinger/ggRandomForests
  • Minor bug and documentation fixes.

ggRandomForests v1.2.1

CRAN release: 2015-12-12

  • Update cached datasets for randomForestSRC 2.0.0 release.
  • Correct some vignette formatting errors (thanks Joe Smith)

ggRandomForests v1.2.0

CRAN release: 2015-11-15

  • Convert to semantic versioning http://semver.org/
  • Updates for release of ggplot2 2.0.0
  • Change from reshape2::melt dependence to tidyr::gather
  • Optimize tests for CRAN to optimize R CMD CHECK times.

ggRandomForests v1.1.4

CRAN release: 2015-03-29

  • combine.gg_partial bug when giving a single variable plot.variable object.

  • Remove dplyr depends to transitions from “Imports” to “Suggests”.

  • Argument for single outcome gg_vimp plot for classification forests.

  • Improvements to gg_vimp arguments for consistency.

  • Add bootstrap confidence intervals to gg_rfsrc function.

  • Initial partial.rfsrc function to replace the randomForestSRC::plot.variable function.

  • Move cache data to randomForestSRC v1.6.1 to take advantage of rfsrc version checking between function calls.

  • Vignette updates for JSS submission of “ggRandomForests: Exploring Random Forest Survival”.

  • Vignette updates for arXiv submission of ggRandomForests: Random Forests for Regression

  • Some optimizations to reduce package size.

  • Remove all tests from CRAN build to optimise R CMD CHECK times.

  • Remove pdf vignette figure from CRAN build.

  • Return S3method calls to NAMESPACE for “S3 methods exported but not registered” for R V3.2+.

  • Misc Bug Fixes.

ggRandomForests v1.1.3

CRAN release: 2015-01-08

  • Update “ggRandomForests: Visually Exploring a Random Forest for Regression” vignette.
  • Further development of draft package vignette “Survival with Random Forests”.
  • Rename vignettes to align with randomForestSRC package usage.
  • Add more tests and example functions.
  • Refactor gg_ functions into S3 methods to allow future implementation for other random forest packages.
  • Improved help files.
  • Updated DESCRIPTION file to remove redundant parts.
  • Misc Bug Fixes.

ggRandomForests v1.1.2

CRAN release: 2014-12-25

  • Add package vignette “ggRandomForests: Visually Exploring a Random Forest for Regression”
  • Add gg_partial_coplot, quantile_cuts and surface_matrix functions
  • export the calc_roc and calc_auc functions.
  • replace tidyr function dependency with reshape2 (melt instead of gather) due to lazy eval issues.
  • reduce dplyr dependencies (remove select and %>% usage for base equivalents, I still use tbl_df for printing)
  • Further development of package vignette “Survival with Random Forests”
  • Refactor cached example datasets for better documentation, estimates and examples.
  • Improved help files.
  • Updated DESCRIPTION file to remove redundant parts.
  • Misc Bug Fixes.

ggRandomForests v1.1.1

CRAN release: 2014-12-13

Maintenance release, mostly to fix gg_survival and gg_partial plots. * Fix the gg_survival functions to plot kaplan-meier estimates. * Fix the gg_partial functions for categorical variables. * Add some more S3 print functions. * Try to make gg_functions more consistent. * Further development of package vignette “Survival with Random Forests” * Modify the example cached datasets for better estimates and examples. * Improve help files. * Misc Bug Fixes.

ggRandomForests v1.1.0

CRAN release: 2014-12-05

  • Add panel option for gg_variable and gg_partial
  • Rework interactions plot
  • add gg_coplot functions
  • Imports instead of depends
  • Add version dependencies for randomForestSRC
  • Include package vignette “Random Forests for Survival”
  • Misc Bug Fixes

ggRandomForests v1.0.0

CRAN release: 2014-10-15

  • First CRAN release.

ggRandomForests v0.2

  • Initial useR!2014 release.