Leakage-Safe Modeling and Auditing for Genomic and Clinical Data

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Documentation for package ‘bioLeak’ version 0.3.7

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

Help Pages

as_leaksplits	Convert a splitGraph split_spec into bioLeak splits
as_rsample	Convert LeakSplits to an rsample resample set
audit_batch_assoc	Batch / study association results from a LeakAudit
audit_duplicates	Near-duplicate sample pairs from a LeakAudit
audit_info	Auxiliary information list from a LeakAudit
audit_leakage	Audit leakage and confounding
audit_leakage_by_learner	Audit leakage per learner
audit_perm_gap	Permutation-gap test results from a LeakAudit
audit_report	Render an HTML audit report
audit_target_assoc	Target leakage scan results from a LeakAudit
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)
dlsi_ci	BCa confidence interval from a LeakDeltaLSI
dlsi_metric	Raw delta-metric estimate from a LeakDeltaLSI
dlsi_p_value	Sign-flip p-value from a LeakDeltaLSI
dlsi_repeats	Per-repeat metric data frames from a LeakDeltaLSI
dlsi_robust	Huber-robust delta_lsi point estimate from a LeakDeltaLSI
dlsi_R_eff	Effective number of paired repeats from a LeakDeltaLSI
dlsi_tier	Inference tier from a LeakDeltaLSI
fit_metrics	Per-fold metric data frame from a LeakFit
fit_resample	Fit and evaluate with leakage guards over predefined splits
guard_ensure_levels	Ensure consistent categorical levels for guarded preprocessing
guard_fit	Fit leakage-safe preprocessing pipeline
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.GuardFit	Apply a fitted GuardFit transformer to new data
predict_guard	Apply a fitted GuardFit transformer to new data
print.LeakTune	Print a LeakTune object
show-method	S4 Classes for bioLeak Pipeline
show-method	Display summary for LeakAudit objects
show-method	Display summary for LeakFit objects
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