e2tree 1.2.0

Robustness fixes (2026-05)

• CatBoost multi-class leaf extraction: for multi-class
  objectives (MultiClass, MultiClassOneVsAll)
  catboost.predict(..., prediction_type = "RawFormulaVal", ntree_start, ntree_end) returns an n_obs x n_classes matrix rather than a
  scalar vector, which broke the leaf-proxy assignment with
  Error in leaf_mat[, t] <- as.integer(factor(round(raw, digits = 10L))) : number of items to replace is not a multiple of replacement length.
  The CatBoost adapter now collapses the per-tree raw-score matrix into a
  single key per observation (concatenation of the rounded class scores)
  before discretising into a leaf proxy. The single-output regression
  case is unchanged.
• CatBoost loss-function parsing: in some catboost releases the
  loss_function returned by catboost.get_model_params() is a
  list (e.g. list(type = "MultiClass", border = 0.5)) instead of a
  bare character scalar. The previous detection code piped this
  list directly into startsWith() and failed with
  Error: non-character object(s). The new
  .catboost_extract_loss() canonicalises any of the documented
  shapes (plain character, list-with-type, list-with-name, list
  whose first element holds the name) to a length-one character
  string before classification/regression dispatch and falls back to
  attr(ensemble, "params") when catboost.get_model_params() does
  not expose the loss.
• CatBoost 1.2.x compatibility: starting from catboost 1.2 the
  R objects returned by catboost.train() carry the class
  catboost.Model instead of the previous catboost.CatBoost.
  All three S3 generics in the adapter layer (get_ensemble_type,
  extract_terminal_nodes, get_ensemble_predictions) now register
  methods for both class names, sharing a single internal worker, so
  models trained with either version are accepted out of the box.
  ensemble_backend() and .SUPPORTED_BACKENDS recognise both class
  names. createDisMatrix() now sets the e2tree_label attribute on
  CatBoost ensembles automatically when the user passes label,
  eliminating the previously required manual
  attr(ensemble, "e2tree_label") <- ... step.
• moda() accepts non-factor responses: classification ensembles
  trained on integer 0/1 responses (typical of gbm with the
  bernoulli distribution) no longer trigger
  Error in res[1] <- as.character(levels(x)[res[1]]) : replacement has length zero. The internal moda() helper now coerces the
  modal value to character independently of whether the response is
  a factor, an integer, a character or a numeric vector. Affected
  call sites: eStoppingRules(), e2tree(), vimp().
• Vignette models.Rmd corrected: the regression examples now
  pass the response column through data together with
  label = "<response_name>", as required by createDisMatrix() for
  regression backends; the gbm regression example sets
  n.minobsinnode = 2 and bag.fraction = 0.8 so it does not fail
  the gbm internal sample-size check on the small mtcars training
  set; the lightgbm regression example uses num_leaves = 8 and
  min_data_in_leaf = 2, which prevents the small-sample degenerate
  case caught by validate_terminal_nodes(). The classification
  example based on the binary is_setosa indicator now passes a
  factor copy of the response to e2tree() while leaving the
  numeric copy to gbm.

Multi-backend hardening (2026-04)

• Adapter contract validation: createDisMatrix() now calls
  validate_terminal_nodes() immediately after extract_terminal_nodes().
  Malformed adapter output (wrong row count, non-numeric leaf columns, or
  the all-same-leaf degenerate case that previously made GBM silently
  produce an all-zero D) is now rejected with an informative error.
• Backend tagging: dissimilarity matrices returned by createDisMatrix()
  carry a new ensemble_backend attribute identifying the backend used.
  e2tree() and as.rpart() warn when the supplied ensemble does not match
  this tag, catching the common "stale D reused with a different model"
  mistake.
• xgboost 3.x compatibility: models built via the high-level
  xgboost::xgboost() wrapper (which adds an xgboost class on top of
  xgb.Booster) are now handled correctly; previously the wrapper's
  predict.xgboost method rejected xgb.DMatrix input and broke leaf
  extraction.
• Chunked dissimilarity path wired in: when chunk_size < n_obs the
  function now actually uses compute_dissimilarity_chunked() (previously
  the parameter was accepted but ignored). Optional use_disk = TRUE
  persists the result via saveRDS().
• C++ type checks: compute_cooccurrences_cpp(),
  compute_cooccurrences_sparse_cpp() and compute_all_cooccurrences_cpp()
  now validate that Tree* and resp columns are integer/double, raising
  a clear error rather than silently coercing factors/characters to zeros.
• Adapter de-duplication: the three S3 generics share a single
  .unsupported_backend() helper and a single supported-classes list;
  the xgboost adapters share a .xgb_dmatrix() builder.
• Documentation: ?createDisMatrix now contains an "Interpretation
  note (RF vs boosting)" section explaining why the dissimilarity scale
  differs systematically between bagging and boosting backends.
• Tests: new tests/testthat/test-multi-backend.R exercises the D
  invariants (square, zero diagonal, symmetric, non-degenerate, correctly
  tagged) for each available backend, and covers the validator and the
  default-method failure paths.

S3 class system overhaul

• e2tree class now properly listed as first in the class vector (c("e2tree", "list")).
• New S3 methods for e2tree: predict(), fitted(), residuals().
• predict.e2tree() replaces ePredTree() as the standard prediction interface.
  For regression, returns a data frame with fit and sd (node-level standard deviation).
  For classification, returns a data frame with fit, accuracy, and score.
• fitted.e2tree() returns fitted values for training data.
• residuals.e2tree() returns residuals for regression E2Trees.
• methods(class = "e2tree") now shows: as.rpart, e2splits, fitted, nodes, plot, predict, print, residuals, summary.
• methods(class = "eValidation") now shows: measures, plot, print, proximity, summary.

Accessor functions (new)

• nodes(): Extract tree node data frame from an e2tree object, with optional terminal filter.
• e2splits(): Extract split and categorical split information.
• measures(): Extract validation measures from an eValidation object.
• proximity(): Extract proximity matrices (ensemble, e2tree, or both) from an eValidation object.

Coercion methods (new)

• as.rpart(): Generic and method for converting e2tree to rpart format.
• as.party(): Method for converting e2tree to partykit's constparty format (registered conditionally when partykit is installed). Produces proper bar plots in terminal nodes for classification trees.
• rpart2Tree() retained for backward compatibility with a deprecation note.

Validation framework improvements

• eValidation() gains a test argument: "mantel" (Mantel test only), "measures" (divergence/similarity measures only), or "both" (default). This allows choosing between association testing and agreement testing.
• print.eValidation(), summary.eValidation(), and plot.eValidation() updated to handle all three test modes gracefully.

Variable importance improvements

• vimp(): Auto-detects classification/regression from the e2tree object; type argument now optional.
• Fixed incorrect y-axis label ("Variance" instead of "Variable") in variable importance plots.
• Regression variable importance bars now sorted by importance (previously unsorted).
• Consistent column naming (Variable, MeanImpurityDecrease) across classification and regression.
• Internal logic refactored into .vimp_classification() and .vimp_regression().

Documentation

• All man page titles standardized to Title Case.
• \dontrun{} replaced with \donttest{} in all examples; interactive-only examples wrapped in if (interactive()).
• Examples updated to use accessor functions and predict() instead of direct $ access.
• New vignette e2tree-introduction covering classification, regression, validation (Mantel test, divergence measures, LoI decomposition), and comparison with partykit/stablelearner.
• ePredTree() documentation updated with deprecation note pointing to predict.e2tree().

Package infrastructure

• Added partykit, knitr, rmarkdown to Suggests.
• Added VignetteBuilder: knitr to DESCRIPTION.
• e2tree object now stores fitted.values, y, and data for S3 method support.
• Conditional .onLoad hook for registering as.party.e2tree when partykit is loaded.

e2tree 1.0.0

New functions

• goi(): Goodness of Interpretability (GoI) index measuring how well the E2Tree-estimated proximity matrix reconstructs the original ensemble proximity matrix.
• goi_perm(): Permutation test for the GoI index to assess statistical significance.
• goi_analysis(): Combined GoI analysis returning both the observed statistic and permutation results.
• plot.goi_perm(): Plot method for goi_perm objects displaying the permutation distribution.
• plot_e2tree_vis(): Interactive E2Tree visualization using visNetwork with draggable nodes, zoom/pan, and multiple layout options.
• plot_e2tree_click(): Interactive E2Tree plot in the R graphics device with click-to-inspect node details.
• save_e2tree_html(): Save an interactive visNetwork tree plot as a standalone HTML file.
• print_e2tree_summary(): Print a formatted summary of an e2tree object.

Performance improvements

• createDisMatrix: C++ backend (CoOccurrences.cpp) with OpenMP thread-level parallelism replaces the R-level foreach/doParallel loop; co-occurrence normalization also moved to C++.
• e2tree: vectorized Wt computation using vapply; simplified internal get_classes helper.
• ePredTree: split rules are now pre-parsed once (parse_all_splits + apply_split_rule), eliminating repeated regex/eval(parse()) calls during prediction.
• vimp: three group_by operations consolidated into one; eval/parse removed.
• split: ordSplit and catSplit vectorized with outer().
• eImpurity: single-step integer matrix conversion.

Bug fixes

• Fixed Rcpp type conversion (NumericVector + static_cast<int>) for ranger compatibility (ranger returns double columns for tree node assignments).
• Fixed ePredTree returning character instead of double for regression trees.
• Fixed bare filter() call in proximity_longer.R causing namespace conflict with dplyr.
• Added missing NAMESPACE imports for graphics, grDevices, and utils.

Internal changes

• New aaa_utils.R with shared internal helpers: e2_variance(), get_ensemble_type(), check_package().
• Refactored eValidation, eImpurity, and eStoppingRules for consistency and performance.

e2tree 0.2.0

• Added support for 'ranger' models
• Several improvements in e2tree plots