survalis 1.0.0

• Added CoxBoost as a new survival learner: fit_coxboost(), predict_coxboost(), and tune_coxboost(), wrapping the CoxBoost package’s likelihood-based componentwise boosting for the Cox partial likelihood. Registered in list_survlearners() and usable directly through benchmark().
• Wrapped tune_glmnet()’s example in \donttest{} (per CRAN win-builder pretest feedback: it exceeded the 5s/10s example runtime limit on Debian/Windows).

survalis 0.9.0

• Added a title argument to every plotting function (plot_ale(), plot_pdp(), plot_shap(), plot_interactions(), plot_calibration(), plot_counterfactual(), plot_surrogate(), plot_tree_surrogate(), plot_varimp(), plot_survmat(), plot_survmetalearner_weights(), plot_benchmark(), cv_plot(), plot_survcurve()). If omitted, the previous automatically generated title is used (fully backward compatible); pass title = NULL to omit the title entirely, for journals that require caption-only figures.

survalis 0.8.9

• Added a dashed zero-reference line to every plot that can show both negative and positive values (previously only plot_shap()’s bar chart had one): plot_ale() (both per_time and integrated), plot_shap()’s time-dependent curve, plot_counterfactual(), plot_surrogate(), and plot_varimp().

survalis 0.8.8

• plot_varimp() now draws a boxplot of the full per-repetition permutation distribution for each feature instead of a single point estimate with no uncertainty shown. compute_varimp() retains the per-repetition values (previously discarded after computing summary stats) as a "raw_scores" attribute on its return value, used by plot_varimp(); falls back to the previous point-plot behavior for objects without that attribute (e.g. hand-built summary tables).

survalis 0.8.7

• Flipped the direction of plot_interactions(type = "heatmap")’s viridis scale so high interaction values are dark and low values are bright, matching the conventional reading of heatmap intensity.

survalis 0.8.6

• Fixed plot_interactions(type = "heatmap"), which was genuinely hard to read: the white -> steelblue gradient had too little contrast in the mid-range, and the diagonal (self-interaction, value 0) blended into the low end of the scale. Switched to scale_fill_viridis_c() (perceptually uniform, high contrast), added an explicit na.value for any genuinely missing cells, and fixed a squished legend by widening the colorbar guide.
• Unified color usage across all plotting functions: grouped plots (color/fill mapped to a variable) previously fell back to ggplot2’s default hue palette everywhere except plot_survcurve(); they now all use scale_color_survalis()/scale_fill_survalis(). Single-series hardcoded colors ("steelblue", "skyblue", "lightblue", "pink", "tomato", plain "blue", and ad-hoc green/red hex codes for positive/negative direction) now draw from the same shared Dark2-based palette instead of arbitrary named/hex colors. This was explicitly deferred in PR #22 and is now closed out.

survalis 0.8.5

• Fixed GitHub Actions CI, which had been failing since before this development cycle: man/compute_tree_surrogate.Rd, man/plot_tree_surrogate.Rd, and man/tune_survdnn.Rd were stale, hand-drifted copies using \donttest{} (which runs under R CMD check --run-donttest, as CI does) instead of the \dontrun{} already present in the roxygen source, causing plot_tree_surrogate(tree_ranger, ...) to fail on an undefined tree_ranger object. Regenerated all three from source via devtools::document(); verified locally with R CMD check --run-donttest (Status: OK), matching the CI configuration.

survalis 0.8.4

• summarise_benchmark() now rounds mean/sd/se/lower/upper to 3 decimals by default (digits = 3 argument), matching cv_summary()’s convention; it previously returned full-precision values (e.g. sd = 0.014142136).

survalis 0.8.3

• Normalized base_size to the shared theme_survalis() default (13) everywhere: compute_shap.R, fit_survmetalearner.R’s weights plot, and plot_benchmark() previously carried over a hardcoded base_size = 14 from before the theme retrofit (PR #22).

survalis 0.8.2

• Migrated compute_shap(), compute_shap_mean(), compute_calibration(), and plot_survmetalearner_weights() from dplyr/tidyr to data.table. This was the remaining unqualified (non-dplyr::-prefixed) dplyr/tidyr usage missed by the original file-by-file migration inventory.
• dplyr, tidyr, purrr, and tibble are now fully removed from Imports: the package no longer depends on any tidyverse package for its data-manipulation code; data.table is the sole engine throughout.

survalis 0.8.1

• Migrated the nested/tuned-CV half of benchmark_default_survlearners.R (benchmark_default_survlearners(), .nested_surv_* helpers, summarise_benchmark(), summarize_benchmark_results(), best_survlearner()) from dplyr/tidyr/tibble to data.table. This completes the file-by-file dplyr/tidyverse -> data.table migration across the package. Reuses the shared .score_metrics() helper in .nested_surv_score_predictions() instead of a fifth duplicated copy of the per-metric scoring switch() block.

survalis 0.8.0

• Migrated cv_survmetalearner() from dplyr/tidyr/purrr/tibble to data.table, reusing the shared .score_metrics() helper instead of a third duplicated copy of the per-metric scoring switch() block.

survalis 0.7.27

• Migrated list_survlearners(), list_interpretability_methods(), and list_metrics() from tibble::tibble() to data.table::data.table() (cosmetic descriptive tables, no behavior change).

survalis 0.7.26

• Migrated plot_survmat() from dplyr/tidyr to data.table (data.table::melt() for the wide-to-long reshape, [.data.table with by = for the group/time summaries).

survalis 0.7.25

• Migrated compute_varimp() from dplyr/purrr/tibble to data.table.

survalis 0.7.24

• Migrated tune_survdnn() from dplyr/tidyr/purrr/tibble to data.table, including the list-valued hidden architecture parameter (grid expansion built manually over unique levels per parameter, since data.table::CJ() doesn’t support list-valued columns).

survalis 0.7.23

• Migrated tune_survsvm() from dplyr/tidyr/purrr/tibble to data.table (grid expansion via data.table::CJ()); the CRAN-motivated refit-fallback behavior (PR #14) is unchanged and still verified passing.

survalis 0.7.22

• Migrated tune_glmnet() from dplyr/tidyr/purrr/tibble to data.table, including its tidyr::crossing() grid-expansion step (now data.table::CJ(), a sorted-unique cross join with matching semantics).

survalis 0.7.21

• Migrated tune_selectcox() from dplyr/tidyr/purrr/tibble to data.table.

survalis 0.7.20

• Migrated tune_flexsurvreg() from dplyr/tidyr/purrr/tibble to data.table. Added .map_rbind_dt() in R/dt-utils.R, a data.table replacement for purrr::map_dfr() over a plain vector (as opposed to .pmap_rbind_dt() for a parameter grid).

survalis 0.7.19

• Migrated tune_blackboost() from dplyr/tidyr/purrr/tibble to data.table.

survalis 0.7.18

• Migrated tune_bart() from dplyr/tidyr/purrr/tibble to data.table.

survalis 0.7.17

• Migrated tune_rsf() from dplyr/tidyr/purrr/tibble to data.table.

survalis 0.7.16

• Migrated tune_orsf() from dplyr/tidyr/purrr/tibble to data.table.

survalis 0.7.15

• Migrated tune_cforest() from dplyr/tidyr/purrr/tibble to data.table.

survalis 0.7.14

• Migrated tune_bnnsurv() from dplyr/tidyr/purrr/tibble to data.table.

survalis 0.7.13

• Migrated tune_xgboost() from dplyr/tidyr/purrr/tibble to data.table.

survalis 0.7.12

• Migrated tune_ranger() from dplyr/tidyr/purrr/tibble to data.table.

survalis 0.7.11

• Fixed benchmark_tuned_survlearners() silently dropping learners whose tune_*() has been migrated to data.table: tuning_results[1, cols, drop = FALSE] relies on data.frame [ semantics, but data.table’s [ does not select columns when cols is a variable (only a literal character vector triggers that); it was returning the raw column-name vector instead of a one-row parameter table, causing every fold to error and the learner to be dropped with a warning. Added .select_cols() in R/dt-utils.R that selects columns correctly for either a data.frame/tibble or a data.table, so the nested-tuning code stays agnostic to migration state.

survalis 0.7.10

• Retrofitted all existing plotting functions to use theme_survalis() instead of ad-hoc theme_minimal() calls with inconsistent base_size values, so package figures share one consistent visual style: plot_ale(), survmat plotting helpers, plot_surrogate()/plot_shap(), cv_plot(), plot_pdp(), plot_interactions(), plot_counterfactual(), plot_tree_surrogate(), plot_benchmark(), plot_varimp(), fit_survmetalearner()’s plotting path. Hardcoded per-plot colors are unchanged in this pass (follow-up).

survalis 0.7.9

• Added plot_survcurve(), a survminer-inspired Kaplan-Meier curve with confidence ribbon, log-rank p-value annotation, and an aligned number-at-risk table, built natively on theme_survalis() / scale_color_survalis() (no dependency on the survminer package). The risk table uses patchwork (added to Suggests).

survalis 0.7.8

• Added theme_survalis(), a shared ggplot2 theme, and scale_color_survalis()/scale_fill_survalis(), colorblind-friendly discrete scales (ColorBrewer “Dark2”-based, recycled/interpolated beyond 8 levels), for a consistent visual style across package figures. Not yet applied to existing plotting functions (follow-up).

survalis 0.7.7

• Migrated tune_rpart() from dplyr/tidyr/purrr/tibble to data.table. Added internal data.table helpers (R/dt-utils.R) shared by the ongoing file-by-file migration of the remaining tune_*()/fit_*() grid-search code (tracked in the project TODO).

survalis 0.7.6

• Added benchmark(), the single entry point for comparing survival learners: tune = FALSE (default) dispatches to benchmark_default_survlearners(), tune = TRUE dispatches to benchmark_tuned_survlearners() (nested CV with per-learner tuning). benchmark_default_survlearners() and benchmark_tuned_survlearners() remain available directly.

survalis 0.7.5

• Migrated the core CV/metrics engine (cv_survlearner(), cv_summary(), score_survmodel()) from dplyr/tidyr/tibble/purrr to data.table; data.table is now the main data-manipulation engine going forward, replacing the dplyr/tidyverse approach used previously. This is a first step; the remaining tuning/fitting code (tune_*()/fit_*()) still uses dplyr/purrr and will be migrated incrementally.
• cv_summary() and score_survmodel()/cv_survlearner() metric values now round to 3 decimals by default (digits = 3 argument on cv_summary()).
• These functions now return data.table objects instead of tibbles (is.data.frame() still holds; code relying on tibble-specific behavior should call tibble::as_tibble() explicitly).

survalis 0.7.4

• Added timeroc_survmat(), a vectorized cumulative/dynamic time-dependent AUC curve over a vector of evaluation times (Uno et al. 2007 / Heagerty and Zheng 2005 estimator), matching timeROC::timeROC(weighting = "marginal") to ~1e-3.
• Fixed auc_survmat() to define cases as events strictly before t_star (time < t_star) rather than time <= t_star, matching the canonical Uno/timeROC definition; this corrects the "auc" metric used throughout score_survmodel(), benchmark_*(), and fit_survmetalearner().
• Added timeROC to Suggests for numerical validation in tests.

survalis 0.7.3

• Fixed plot_pdp() per-time facets using free y-axis scales, which made survival probability panels visually incomparable across facets; now uses a fixed [0, 1] scale via coord_cartesian().

survalis 0.7.2

• Fixed tune_survsvm(refit_best = TRUE) crashing when the top-ranked grid candidate fails to refit on the full dataset (e.g., a quadprog QP infeasibility that only manifests on certain BLAS backends, as seen on CRAN’s OpenBLAS check machine); it now falls back to the next-best candidate and only errors if every candidate fails.

survalis 0.7.1

• Revised DESCRIPTION to include CRAN-compliant, family-level methodological references using validated DOI/URL anchors and representative (non-exhaustive) wording.
• Reworked examples across evaluation, benchmarking, interpretation, and meta-learner topics to remove commented code and provide executable minimal examples.
• Replaced unnecessary \\dontrun{} wrappers with \\donttest{} for executable-but-longer workflows and kept fast examples unwrapped where feasible.
• Fixed documentation/example mismatches (including variable-importance examples) and regenerated Rd files with devtools::document().
• Verified package checks including run_dont_test = TRUE for CRAN resubmission readiness.

survalis 0.7.0

• First CRAN submission candidate.
• Added a cumulative/dynamic time-dependent AUC metric to the evaluation layer.
• Added plot_counterfactual() for visualizing counterfactual recommendations.
• Added plot_survmat() for plotting predicted survival curves, including grouped summaries.
• Hardened documentation and examples for CRAN checks.
• Updated dependency declarations so exported learners and CV/tuning helpers work after installation.
• Added clearer runtime checks for survdnn when the LibTorch runtime is missing.