cgpt-stats-audit

name	cgpt-stats-audit
description	Compact Codex skill for report-only statistical audits of manuscripts against source data, extracted numerals, sample labels, figures, and cross-references.

CGPT Stats Audit

Use this skill when the user asks for a stats audit, statistical verification, manuscript number check, pre-submission stats gate, or consistency check between a manuscript and source data.

Default Behavior

• Report only by default. Do not edit manuscripts, supplements, data, figures, or project state.
• Write audit artifacts only when the user asks for a file-based audit or when the project already uses quality_reports/.
• Do not declare a manuscript "submission-ready" unless the statistical audit passes and any existing render/citation checks also pass.
• If the user asks for fixes, first report the exact mismatches and ask which files to edit unless the requested edit scope is already explicit.

Pipeline

Run in this order:

1. Compute ground truth from source data.
2. Extract all manuscript numerals.
3. Match extracted values against ground truth and lint supporting evidence.

Do not skip a phase unless the user asks for a narrow spot check.

Phase 1: Compute Ground Truth

Inputs:

• source data paths from MEMORY.md, CLAUDE.md, PROJECT_STATE.json, or user instructions
• CSV/XLSX data files in project data or results directories

Expected artifact:

• quality_reports/ground_truth.json

Rules:

• Compute values from source data, not from manuscript prose.
• Include explicit sample labels in keys when possible, for example sample=restricted_N57.
• Mark uncomputable values as UNVERIFIABLE with a note explaining what data is missing.
• Preserve or create a reproducible script when doing a full audit, commonly quality_reports/stats_audit_compute.py.

Phase 2: Extract Numerals

Inputs:

• manuscript .qmd, .md, .docx, supplement, tables, captions, footnotes, and appendices

Expected artifact:

• quality_reports/extracted_numbers.csv

Extract every numeral and classify it as one of:

• structural
• N
• rank
• correlation
• p_value
• test_statistic
• coefficient
• R_squared
• percentage
• descriptive
• unknown

Capture document, section, line number if available, sentence or table-row context, raw value, normalized value, type, and sample label.

Phase 3: Match and Lint

Expected artifact:

• quality_reports/audit_report.md

Checks:

• strict deterministic rounding against ground truth
• sample-label consistency
• impossible values such as correlations outside [-1, 1], p-values outside [0, 1], negative SDs, rank values greater than sample size, or invalid HHI/Gini ranges
• stale figures by comparing figure timestamps to source data timestamps when possible
• banned terms and project-specific conventions from CLAUDE.md
• stale sample or tier references from MEMORY.md
• broken Quarto references such as missing @tbl-, @fig-, @sec-, or @eq- targets

PASS Criteria

Report PASS only when all must-fix categories are zero:

• critical mismatches
• sample label issues
• impossible values
• stale figures
• banned word or convention violations that the project treats as blockers
• stale tier or sample references
• cross-reference failures

Orphan numbers and unmatched ground-truth keys are warnings unless project instructions make them blockers.

Report Format

Use this structure for a full audit:

# Stats Audit Report
**Date:**
**Manuscript:**
**Ground truth:**
**Extracted numerals:**

## Critical Mismatches
| Location | Manuscript value | Expected | Ground-truth key | Issue |
|---|---:|---:|---|---|

## Sample Label Issues
| Location | Value | Matched key | Issue |
|---|---:|---|---|

## Impossible Values
| Location | Value | Type | Rule violated |
|---|---:|---|---|

## Stale Figures
| Figure | Figure date | Source data date | Issue |
|---|---|---|---|

## Convention and Cross-Reference Checks
| Location | Pattern | Issue |
|---|---|---|

## Orphan Numbers
| Location | Value | Type | Context |
|---|---:|---|---|

## Unmatched Ground Truth
| Key | Value | Note |
|---|---:|---|

## Summary
- Critical mismatches:
- Sample label issues:
- Impossible values:
- Stale figures:
- Convention violations:
- Cross-reference failures:
- Orphan numbers:
- Unmatched ground-truth keys:

## Verdict
**Audit status:** PASS / FAIL

For a spot check, keep the same severity logic but report only the requested values.

Source Material

This Codex skill is a compact workflow derived from the local manuscript development kit:

• MANUSCRIPT-DEV-KIT/protocols/stats-audit-protocol.md
• MANUSCRIPT-DEV-KIT/agents/stats-calculator.md
• MANUSCRIPT-DEV-KIT/agents/stats-extractor.md
• MANUSCRIPT-DEV-KIT/agents/stats-matcher.md