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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

• 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

• Fixed typo in class construction.

bregr 1.3.0

• 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

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

• The first experimental version submitted to CRAN.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.