Leakage-Safe Modeling and Auditing for Genomic and Clinical Data

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Documentation for package ‘bioLeak’ version 0.2.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

.guard_fit	Fit leakage-safe preprocessing pipeline
as_rsample	Convert LeakSplits to an rsample resample set
audit_leakage	Audit leakage and confounding
audit_leakage_by_learner	Audit leakage per learner
audit_report	Render an HTML audit report
calibration_summary	Calibration diagnostics for binomial predictions
confounder_sensitivity	Confounder sensitivity summaries
fit_resample	Fit and evaluate with leakage guards over predefined splits
impute_guarded	Leakage-safe data imputation via guarded preprocessing
LeakAudit-class	S4 Classes for bioLeak Pipeline
LeakFit-class	S4 Classes for bioLeak Pipeline
LeakSplits-class	S4 Classes for bioLeak Pipeline
make_split_plan	Create leakage-resistant splits
plot_calibration	Plot calibration curve for binomial predictions
plot_confounder_sensitivity	Plot confounder sensitivity
plot_fold_balance	Plot fold balance of class counts per fold
plot_overlap_checks	Plot overlap diagnostics between train/test groups
plot_perm_distribution	Plot permutation distribution for a LeakAudit object
plot_time_acf	Plot ACF of test predictions for time-series leakage checks
predict_guard	Apply a fitted GuardFit transformer to new data
show-method	Display summary for LeakSplits objects
simulate_leakage_suite	Simulate leakage scenarios and audit results
summary.LeakAudit	Summarize a leakage audit
summary.LeakFit	Summarize a LeakFit object
summary.LeakTune	Summarize a nested tuning result
tune_resample	Leakage-aware nested tuning with tidymodels