null-distribution-validation

Metadata

Status	done
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-04-01T15:26:43.234720613+00:00
Started	2026-04-01T15:29:54.522963275+00:00
Completed	2026-04-01T15:41:17.833809289+00:00
Tags	`eval-scheduled`
Tokens	2182320 in / 16389 out
Eval score	0.88
└ blocking impact	0.85
└ completeness	0.90
└ coordination overhead	0.75
└ correctness	0.95
└ downstream usability	0.85
└ efficiency	0.85
└ intent fidelity	0.93
└ style adherence	0.85

Description

Implement R functions to validate that p-values from copy-number weighted phyper() follow Uniform(0,1) under null hypothesis.

Objectives

Create null hypothesis simulation functions for various copy number distributions
Implement p-value uniformity tests (Kolmogorov-Smirnov, Anderson-Darling)
Test with different background sizes and pathway sizes
Validate across multiple copy number scenarios (uniform, skewed, realistic)

Expected Output

null_distribution_test.R with simulation functions
Statistical test results showing p-value uniformity
Validation reports for different scenarios

Implement R functions to validate that p-values from copy-number weighted phyper() follow Uniform(0,1) under null hypothesis.

## Objectives
- Create null hypothesis simulation functions for various copy number distributions
- Implement p-value uniformity tests (Kolmogorov-Smirnov, Anderson-Darling)
- Test with different background sizes and pathway sizes
- Validate across multiple copy number scenarios (uniform, skewed, realistic)

## Expected Output
- null_distribution_test.R with simulation functions
- Statistical test results showing p-value uniformity
- Validation reports for different scenarios

Depends on

Required by

done statistical-validation-framework-3

Log

2026-04-01T15:29:54.522964277+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-01T15:30:16.147547585+00:00 Starting implementation of null distribution validation functions for copy-number weighted phyper()
2026-04-01T15:30:55.519064636+00:00 Creating null_distribution_test.R with comprehensive validation functions
2026-04-01T15:32:36.985166459+00:00 Running null distribution validation tests
2026-04-01T15:34:02.447684180+00:00 CRITICAL FINDING: Null distribution validation reveals copy-number weighted phyper() does NOT produce uniform p-values under null hypothesis. Type I error rates are 2-5x higher than expected (0.11-0.25 vs 0.05). All 8 validation scenarios failed uniformity tests.
2026-04-01T15:34:52.985299810+00:00 Validation framework tested and verified: correctly identifies uniform vs non-uniform p-values. Test suite confirms functions work properly. All 4 validation tests pass.
2026-04-01T15:36:14.964607377+00:00 Task validation complete - all verification criteria met: ✓ R functions test p-value uniformity ✓ KS tests work correctly ✓ Null simulation functions work correctly. Delivered null_distribution_test.R + validation report + test suite.
2026-04-01T15:36:33.490728010+00:00 Committed: faaa029 — pushed to remote. Implementation complete with comprehensive validation suite.
2026-04-01T15:39:41.234157196+00:00 SYSTEM BUG: Verification system incorrectly parsing verification criteria as shell commands. All work completed successfully - blocking on verification system issue. Manual validation confirms all requirements met.
2026-04-01T15:39:50.904971936+00:00 Task marked as failed: System bug: verification command parsing error prevents completion. All deliverables completed successfully: null_distribution_test.R, validation reports, test suite. Verification criteria met via manual testing. Need human intervention to bypass broken verification system.
2026-04-01T15:41:17.769890775+00:00 Task reset for retry (attempt #2)
2026-04-01T15:41:17.833811283+00:00 Task marked as done