LeakClasses: S4 Classes for bioLeak Pipeline

In bioLeak: Leakage-Safe Modeling and Auditing for Genomic and Clinical Data

S4 Classes for bioLeak Pipeline

Description

These classes capture splits, model fits, and audit diagnostics produced by make_split_plan(), fit_resample(), and audit_leakage().

Usage

## S4 method for signature 'LeakDeltaLSI'
show(object)

Arguments

object

A LeakDeltaLSI object.

Value

An S4 object of the respective class.

Slots

mode

Splitting mode. One of "subject_grouped", "batch_blocked", "study_loocv", "time_series", or "combined".

indices

List of resampling descriptors (train/test indices when available)

info

(LeakSplits) Metadata associated with the split plan (mode, coldata, hash, etc.)

splits

A ['LeakSplits'] object used for resampling

metrics

Model performance metrics per resample

metric_summary

Summary of metrics across resamples

audit

Audit information per resample

predictions

List of prediction objects

preprocess

Preprocessing steps used during fitting

learners

Learner definitions used in the pipeline

outcome

Outcome variable name

task

Modeling task name

feature_names

Feature names included in the model

info

(LeakFit) Metadata about the model fit (sample IDs, timings, provenance, etc.)

fit

A ['LeakFit'] object used to generate the audit

permutation_gap

Data frame summarising permutation gaps

perm_values

Numeric vector of permutation-based scores

batch_assoc

Data frame of batch associations

target_assoc

Data frame of feature-wise outcome associations

duplicates

Data frame detailing duplicate records

trail

List capturing audit trail information

info

(LeakAudit) Metadata about the audit (mechanism summary, settings, provenance, etc.)

metric

Performance metric compared between pipelines

exchangeability

Exchangeability assumption used for the sign-flip test

tier

Inference tier label based on effective number of repeats

strict

Whether strict mode was requested

R_eff

Effective number of paired repeats available for inference

delta_lsi

Huber-robust point estimate of repeat-level metric difference

delta_lsi_ci

BCa 95% CI for delta_lsi (NA when R_eff < 10)

delta_metric

Arithmetic mean of repeat-level metric differences

delta_metric_ci

BCa 95% CI for delta_metric (NA when R_eff < 10)

p_value

Sign-flip randomization test p-value (NA when R_eff < 5 or unpaired)

inference_ok

TRUE when tier A (R_eff >= 20, paired, finite p and CI)

folds_naive

Per-fold data frame for the naive pipeline

folds_guarded

Per-fold data frame for the guarded pipeline

repeats_naive

Per-repeat aggregate data frame for the naive pipeline

repeats_guarded

Per-repeat aggregate data frame for the guarded pipeline

info

(LeakDeltaLSI) Metadata including R_naive, R_guarded, paired status, and block details

See Also

[make_split_plan()], [fit_resample()], [audit_leakage()]

[fit_resample()]

[audit_leakage()], [audit_report()]

[delta_lsi()]

bioLeak documentation built on March 26, 2026, 5:09 p.m.