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Changelog

Source: NEWS.md

OptSurvCutR 0.1.9.3 (2026-03-15)

DOCUMENTATION & STANDARDS

Graphical Abstract: Added the new graphical abstract to the image/ folder for inclusion in the README.md. OptSurvCutR Graphical Abstract ## COMMUNITY & OUTREACH

Presentations: Presented at FOSDEM 2026 in the Bioinformatics & Computational Biology DevRoom in Brussels, Belgium. View lightning talk details

Presentations: Presented at R!SK 2026 (February 18–19, 2026). This 100% online conference focuses on evaluating, measuring, and mitigating risk across diverse industries including healthcare, finance, and insurance. The event featured deep content sessions and live Q&A interactions. View presentation abstract

OptSurvCutR 0.1.9.2 (2025-11-25)

ROPENSCI REVIEW UPDATES (ITERATION 2)

BREAKING CHANGES

  • Renamed Functions: plot_optimization_curve() →\toplot_optimisation_curve() (British English) and plot_schoenfeld() →\toplot_cutpoint_residuals() (Namespace conflict).
  • Renamed Argument: maxiter is now max.generations in genetic algorithm functions to match rgenoud.

IMPROVEMENTS

  • Explicit Parameters: Exposed pop.size and max.generations as explicit arguments in find_cutpoint() and find_cutpoint_number().
  • Consistent Logic: All functions now use floor() for nmin calculation to ensure identical sample size handling.
  • Better Validation: validate_cutpoint() now accepts nmin as a proportion and issues an informative message when using the default 90% buffer (Standard G2.10).
  • Internal Cleanup: Removed export of helper operator %||%.

DOCUMENTATION & STANDARDS

  • British English: Standardised all functions and documentation (e.g., “optimise”, “summarise”).
  • Standards Compliance: Audited and updated all @srrstats tags; moved non-applicable standards to R/OptSurvCutR-package.R.
  • Testing: Added tests for new genetic parameters and updated snapshot tests for S3 methods.

OptSurvCutR 0.1.9.1 (2025-11-20)

POST-ROPENSCI INITIAL SUBMISSION

  • Renamed plot_diagnostics() → plot_schoenfeld() to avoid name clash with another package.
  • Stabilised and accepted all snapshot tests for pathological find_cutpoint_number_result S3 methods (now use real criterion "BIC").
  • Cleaned DESCRIPTION: removed unused Suggests (coxphf, patchwork, pROC, tibble, srr) and Remotes (ropensci-review-tools/srr).
  • Test suite now passes with zero failures/warnings on R CMD check.

OptSurvCutR 0.1.9

REFACTORING & MAINTENANCE

  • Simplified Parallel Interface: The use_parallel argument was removed from validate_cutpoint(). Parallel execution is now controlled exclusively by the n_cores argument (n_cores = 1 for sequential, n_cores > 1 for parallel).
  • Consolidated Validation Logic: A new internal helper .validate_event_column() was created in R/utils-helpers.R to centralise the logic for checking that an event column is numeric and contains only 0s and 1s. Both find_cutpoint_number() and the internal helper .validate_data_conditions() (also in R/utils-helpers.R) were updated to call this function, eliminating duplicated code.
  • Simplified Parallel Code: In validate_cutpoint(), the brittle functions_to_export block was removed. The function now correctly relies on the .packages = "OptSurvCutR" argument in the foreach loop, making it easier to maintain.

BUG FIXES

  • Fixed Parallel Reproducibility: A bug in validate_cutpoint() that prevented true reproducibility for parallel runs (n_cores > 1) was fixed. The function now checks for and registers the doRNG package when a seed is provided, ensuring results are identical regardless of the number of cores used. The incorrect set.seed(i) call inside the foreach loop was removed.
  • Improved S3 Method Robustness: The summary.find_cutpoint_number_result() S3 method was updated to robustly handle NULL values in the object$parameters list (e.g., method = NULL). This prevents potential errors if a result object is created manually or improperly and aligns its behaviour with the print() method.

DOCUMENTATION

  • Clarified Log-Rank Test: The documentation for find_cutpoint() was updated to clarify that when covariates are provided, the "logrank" criterion is automatically generalized to the more appropriate Cox score test.

IMPROVEMENTS

  • Test Coverage: Increased test coverage to 88.5% with new unit tests for parallel reproducibility, S3 method edge cases, and internal validation helpers.
  • Planned: A ROpenSci submission is planned for review.
  • Planned: A JOSS submission is planned post-rOpenSci review.

OptSurvCutR 0.1.8

CRITICAL BUG FIXES

  • Parallel Validation: Fixed a critical bug where validate_cutpoint(use_parallel = TRUE) would fail. This was caused by helper functions not being exported to the parallel workers.
  • Event Column Validation: Fixed a major bug where non-numeric outcome_event data (e.g., "0:LIVING") caused silent failures. The functions now “fail-fast” with an error, validating the column is numeric with only 0s and 1s.
  • Genetic Algorithm Reporting: Fixed a bug where method = "genetic" would report a failure (-Inf) as a successful result. The functions now correctly check for the failure signal and return NA.

NEW FEATURES

  • G3.1a Compliance — Schoenfeld Residual Diagnostics: Added plot_diagnostics() to generate publication-ready Schoenfeld residual plots, assessing the proportional hazards (PH) assumption.

IMPROVEMENTS

  • Code Quality (Refactoring): Refactored find_cutpoint() to resolve “high cyclomatic complexity” NOTEs by moving validation logic to internal helper functions.
  • Test Coverage: Increased test coverage by adding new unit tests for error conditions, edge cases, and validation logic.
  • rOpenSci/pkgcheck Compliance:
    • Added examples to all exported functions.
    • Added @srrstats tags to satisfy multi-directory requirements.
  • R CMD check Compliance: Addressed all ERRORs, WARNINGs, and NOTEs:
    • Added inst/WORDLIST, _PACKAGE documentation, and fixed empty Rd sections.
    • Added codemeta.json to .Rbuildignore.
  • Code Style:
    • Reformatted code to follow Tidyverse Style Guide principles (e.g., <- for assignment, " for strings, consistent spacing around operators).
    • Strictly enforced an 80-character maximum line length for all code, comments, and documentation.
    • Made Roxygen documentation, inline comments, and user-facing messages more concise.
    • Replaced sapply() with type-safe vapply() in S3 methods to prevent potential bugs.
  • Internal Data: The crc_virome dataset’s status column was corrected to be numeric 0/1 to match documentation and new validation rules.

OptSurvCutR 0.1.7

NEW FEATURES

  • Covariate Adjustment Added: Both find_cutpoint() (for method = "systematic" and method = "genetic") and find_cutpoint_number() now support covariate adjustment via the covariates argument. This allows finding optimal cut-points and determining the optimal number of groups while accounting for potential confounders, providing a more robust assessment of a biomarker’s independent prognostic value.

IMPROVEMENTS

  • Major Performance Optimisation: Significantly optimised performance in find_cutpoint() for criterion = "hazard_ratio" and criterion = "p_value" (both systematic and genetic methods). This was achieved by removing computationally expensive summary() calls, extracting coefficients and statistics directly from model objects, and using a fast, manual Likelihood Ratio Test for p-value calculation.
  • Simplified Parallelism: Removed internal parallel processing (use_parallel argument) from find_cutpoint and find_cutpoint_number systematic search. This prevents potential issues with nested parallel calls and relies on standard external parallelisation approaches, such as the explicit parallel loop within validate_cutpoint.
  • Test Suite Overhaul: Revamped the entire testthat suite for improved reliability and robustness. Replaced brittle expect_snapshot() tests with more stable checks like expect_output(), expect_s3_class(), and specific value comparisons. Corrected logic for error and warning expectations and improved mocking for dependency checks. Code coverage increased significantly (for example, to ~86%).
  • User-Friendly rgenoud Check: Added clear, informative error messages using cli in find_cutpoint() and find_cutpoint_number() that trigger immediately if method = "genetic" is requested but the suggested rgenoud package is not installed, guiding the user on how to install it.
  • Dependency Management: Moved optional dependencies broom (for plotting) and withr (for testing) from Imports to Suggests in the DESCRIPTION file, making the core package installation lighter. Removed unused magrittr import.
  • Simplified Evidence Labels: Renamed evidence labels in find_cutpoint_number() results for brevity (for example, “Substantial support” -> “Substantial”).
  • Code Maintainability: Centralised all utils::globalVariables definitions into globals.R to resolve R CMD check NOTEs and improve clarity. Removed redundant code.

BUG FIXES

  • quiet = TRUE Message Fix: Fixed a critical bug where find_cutpoint() and find_cutpoint_number() would fail silently (no console message) when quiet = TRUE was set. Failure messages are now always printed to the console via internal helpers, regardless of the quiet setting, improving user feedback on errors.
  • Genetic Algorithm Edge Cases: Added more robust input validation and handling within the internal .run_genetic_search() function to gracefully manage edge cases like insufficient data variability or non-finite predictor ranges, preventing downstream errors and cryptic warnings.
  • Genetic Algorithm Monitor: Fixed the internal monitoring function used by the genetic algorithm (rgenoud::genoud) to correctly respect the print.level argument (controlled indirectly via user functions), ensuring progress updates are displayed or suppressed as intended.
  • NAMESPACE Fix (stats::): Resolved NAMESPACE errors and related test failures by adding explicit stats:: calls where needed (for example, for stats::quantile, stats::sd, stats::pchisq) and ensuring correct regeneration of the NAMESPACE file via devtools::document().
  • foreach NOTE Fix: Resolved R CMD check NOTE regarding “no visible binding for global”.

IMPROVEMENTS

  • Planned: A ROpenSci submission is planned for review.
  • Planned: A JOSS submission is planned post-rOpenSci review.

OptSurvCutR 0.1.6

NEW FEATURES

IMPROVEMENTS

BUG FIXES

OptSurvCutR 0.1.5

IMPROVEMENTS

BUG FIXES

OptSurvCutR 0.1.0

NEW FEATURES

  • Initial release of OptSurvCutR for optimising cut-points in survival analysis.
  • Added find_cutpoint() to identify optimal cut-points for continuous predictors using systematic or genetic algorithms (via rgenoud) with log-rank, p-value, or hazard-ratio criteria.
  • Added find_cutpoint_number() to select the optimal number of cut-points using AIC, AICc, or BIC.
  • Added validate_cutpoint() for bootstrap-based stability assessment of cut-points.
  • Supports survival models via survival::coxph and survival::survdiff.
  • Includes example usage with simulated churn data, adaptable to TCGA virome datasets (for example, Alphapapillomavirus).

BUG FIXES

  • None (initial release).

IMPROVEMENTS

  • None (initial release).

DEPRECATIONS

  • None (initial release).