# Leakage-Safe Modeling and Auditing for Genomic and Clinical Data

## Documentation for package ‘bioLeak’ version 0.3.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
benchmark_leakage_suite | Simulation benchmark matrix for leakage diagnostics
calibration_summary | Calibration diagnostics for binomial predictions
check_split_overlap | Check split overlap invariants
confounder_sensitivity | Confounder sensitivity summaries
cv_ci | Confidence intervals for cross-validated metrics
delta_lsi | Delta Leakage Sensitivity Index (Delta LSI)
fit_resample | Fit and evaluate with leakage guards over predefined splits
guard_to_recipe | Convert guard preprocessing steps to a recipes recipe
impute_guarded | Leakage-safe data imputation via guarded preprocessing
LeakAudit-class | S4 Classes for bioLeak Pipeline
LeakDeltaLSI-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 | S4 Classes for bioLeak Pipeline
show-method | Display summary for LeakSplits objects
simulate_leakage_suite | Simulate leakage scenarios and audit results
summary.LeakAudit | Summarize a leakage audit
summary.LeakDeltaLSI | Summarize a LeakDeltaLSI object
summary.LeakFit | Summarize a LeakFit object
summary.LeakTune | Summarize a nested tuning result
tune_resample | Leakage-aware nested tuning with tidymodels