Changelog

Source: NEWS.md

bregr 1.5.0

• Added br_seed(), br_seed_screen(), br_seed_select(), and br_seed_model() implementing the SEED (Selection of Essential prognostic genes from Expression Data) pipeline for identifying cancer prognosis target genes without control samples (#57). Based on Yang et al. (2025) Cancer Letters, DOI: 10.1016/j.canlet.2025.217960. The four-step pipeline includes:
  • Step 1 (br_seed_screen): Univariate screening via Cox/logistic regression or Spearman correlation against one or more clinical indicators, with p-value threshold filtering and significance intersection across indicators.
  • Step 2 (optional enrichment): GO/KEGG pathway enrichment via clusterProfiler to refine gene sets (gated by enrich argument).
  • Step 3 (br_seed_select): Sequential gene selection through Lasso regularization (glmnet), multivariate regression, and stepwise selection with reproducibility via seed.
  • Step 4 (br_seed_model): Risk score model construction with coefficient extraction and optional z-score expression scaling. All functions return S3 list objects with cli-based print methods, reuse the existing br_pipeline() engine for batch regression, and support mirai parallelization via n_workers.
• Added br_get_model_stats() returning a tidy data.frame of per-model summary statistics (N, events, C-index, AIC, LR test p, PH test p for Cox; N, AIC, deviance for GLM; N, R-squared for LM), eliminating the need for manual supplementary model fitting to obtain diagnostic metrics (#68).
• Added AIC to Cox model diagnostics in br_diagnose().
• Systematically support non-standard variable names: FGFR3::TACC3, EGFR-AS1, 1p/2q, gene name, R reserved words (if, TRUE, NA), and backtick-quoted user input in x, x2, and y variables (#69). Refactored repair_names() with remove_backticks() for robust quoting, and applied quoting to response variables in br_set_y().
• Added biocViews field to DESCRIPTION for Bioconductor Suggests compatibility.

bregr 1.4.0

CRAN release: 2026-01-18

• Added br_compare_models() and br_show_forest_comparison() (#54).
• Replaced the deprecated package qs with qs2.
• Updated br_show_fitted_line() and br_show_fitted_line_2d() documentation for compatibility with visreg 3.0, which removes the gg argument and renames line.par, fill.par, points.par to line, fill, points (#65).

bregr 1.3.2

• Checked with devtools::check(env_vars = c('_R_CHECK_DEPENDS_ONLY_' = "true")) and fixed reported check issues.

bregr 1.3.1

CRAN release: 2025-12-17

• Fixed typo in class construction.

bregr 1.3.0

CRAN release: 2025-09-22

• Updated paper citation.
• Updated tests in br_pipeline() to reduce running time.
• Fixed CRAN check issue in br_show_coxph_diagnostics().

bregr 1.2.0

CRAN release: 2025-08-19

Enhancements & New Features:

• Introduced br_show_forest_circle()for circular forest plots.
• Added diagnostic visualization for Cox PH models via br_show_coxph_diagnostics().
• Implemented br_show_nomogram()for clinical prediction modeling.
• Added dry_runoption to br_pipeline()for pipeline validation.

Fixes & Improvements:

• Resolved interaction term display and factor scaling in br_show_nomogram().

bregr 1.1.0

• Improved factor handling and warnings in polar plot and risk network functions.
• Added br_show_residuals() to show residuals vs fitted plot for regression models.
• Updated br_set_x() and br_set_x2() to properly handle different input types, including valid column names (in R), invalid column names, and model formula terms.
• Supported error handling when model construction failed.
• Added br_get_model_names() and br_rename_models() to get and set model names.
• Soft-deprecated run_parallel in br_run().
• Soft-deprecated br_get_model() by merging it with br_get_models().
• Introduced global options “bregr.save_model” and “bregr.path”, configurable via options().
• Enabled cross-platform parallel computation.
• Addressed lifecycle deprecation warnings in functions from ggplot2.
• Set the default exponentiate option appropriately in br_run().
• Expanded br_avail_methods_use_exp() to include c("poisson", "quasipoisson").
• Added a log_first option to br_show_forest().
• Enhanced compatibility with multiple models from broom.helpers.
• Implemented the use of : for interaction term combinations throughout the package.
• Created several new vignettes to introduce the capabilities of bregr.
• Fixed a bug where dropping multiple columns failed in br_show_forest().
• Resolved an issue where br_get_model() couldn’t properly process multiple string inputs for the idx parameter.

bregr 1.0.0

CRAN release: 2025-06-28

• The first experimental version submitted to CRAN.