NEWS

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OmicsBraid 0.2.2

Frozen manuscript release

• Frozen the covariance-aware v0.2.2 statistical core used for manuscript analyses.
• Provides subject-level permutation calibration for the cross-omic omnibus test.
• Provides null-shift matched-subject bootstrap calibration for Q_omics.
• Retains analytic confidence intervals as default reporting and BCa layer intervals as sensitivity analysis.
• Retains covariance-aware GLS trajectory inference and hierarchical confirmatory/suggestive braid classification.
• Includes Evidence Forest, Effect Braid, braid heatmap, concordance map, export helpers, and known-truth simulation.
• Adds public-facing GitHub/pkgdown/release documentation without altering the frozen R/ statistical source.

Development history

Robust empirical calibration

• Adds empirical_omics_tests() for resampling-calibrated cross-omic inference.
• Global omnibus evidence can be calibrated by matched-subject group-label permutation or by centered matched-subject bootstrap.
• Cross-omic heterogeneity can be calibrated by a raw-data null-shift matched-subject bootstrap (recommended) or an effect-level centered bootstrap under the fitted common-effect null; naive label permutation is deliberately not used for this composite null.
• The permutation omnibus uses a covariance-aware Mahalanobis/Wald statistic calibrated by the joint subject-level permutation distribution. Empirical heterogeneity uses a covariance-aware GLS residual quadratic statistic calibrated by matched-subject bootstrap nulls. Both avoid requiring a chi-square reference distribution under heavy tails.
• Asymptotic p-values are preserved alongside empirical p-values. run_omics_braid() reports empirical tests only when explicitly requested; empirical p-values are not made primary unless empirical_use_as_primary = TRUE.
• Layer CI workflow now also exposes the already-supported basic bootstrap interval.
• Adds a final targeted robust-calibration benchmark comparing asymptotic, permutation, centered-bootstrap, and null-shift-bootstrap Type-I error, inversion power, and analytic/basic/percentile/BCa interval coverage.
• Adds persistent internal-disk checkpointing for the final robust-calibration run (04_RUN_ROBUST_CALIBRATION.R).
• The validated v0.1.9/v0.2.1 braid classifier logic is otherwise unchanged.

OmicsBraid 0.2.1

• I/O-resilience patch for confirmatory validation; statistical algorithms and simulation design are unchanged from v0.2.0.
• Confirmatory checkpoints and high-frequency outputs are now written to persistent internal-disk storage under ~/OmicsBraid_ValidationCache/confirmatory_v020_design.
• Valid checkpoints from an interrupted v0.2.0 run are imported automatically; incomplete/corrupt RDS files are ignored.
• Checkpoints are validated before reuse and written atomically via temporary-file + rename.
• Final validation outputs are synchronized back to the package _CONFIRMATORY_VALIDATION_OUTPUT folder only after the local run completes.

OmicsBraid 0.2.0

• Froze the v0.1.9 omnibus/GLS/Q/equivalence/trend/classification definitions for confirmatory validation rather than continuing classifier redesign.
• Added bootstrap_effect_intervals() with subject-bootstrap percentile, basic, and BCa confidence intervals for layer-specific Hedges' g effects.
• Added bootstrap_consensus_intervals() with percentile/basic bootstrap confidence intervals for GLS consensus effects.
• Added end-to-end ci_method and integrated_ci_method options to run_omics_braid() while deliberately retaining analytic SEs and p-values as the inferential basis.
• Preserved analytic intervals alongside bootstrap intervals (conf_low_analytic, conf_high_analytic) so interval-method sensitivity is auditable.
• Added a targeted confirmatory simulation runner with n/group = 20/40/80/160/320, normal versus heavy-tailed residuals, Monte-Carlo calibration intervals, CI-method comparisons, trend-power curves, equivalence-power curves, covariance-assumption comparators, decisive-classification safety metrics, checkpoint/resume support, and validation figures.
• Added a focused BCa validation subset because BCa requires leave-one-subject-out acceleration and is substantially more computationally expensive.
• Added unit tests ensuring robust intervals are ordered/finite and that changing the displayed CI method does not change analytic p-values or omnibus inference.
• Version 0.2.0 is the confirmatory-validation build motivated by the completed v0.1.9 benchmark, which showed strong core calibration but mild heavy-tail undercoverage for analytic layer CIs.

OmicsBraid 0.1.9

• Added test_braid_trend(), a covariance-aware GLS trajectory test with a prespecified practical slope margin.
• Replaced raw observed-slope attenuation/amplification rules with inferential trajectory states.
• Added hierarchical braid status: confirmed subtype, direction-confirmed broader concordance, no-evidence, unresolved, and insufficient.
• Added no_detectable_effect to distinguish failure to reject the joint null from demonstrated practical equivalence (null_equivalent).
• Buffering/emergence remain confirmatory only when the required layers pass equivalence testing; a separate suggestive_pattern reports effect geometry when precision is insufficient.
• Expanded simulation validation with Monte-Carlo intervals, trend operating characteristics, exact versus hierarchical-family accuracy, null-compatible outcomes, independence-assumption comparators, scenario-failure reporting, and stratification by sample size/correlation/missingness/distribution.

OmicsBraid 0.1.0

• Initial research implementation.