brycewang-stanford/audit-replication

Audit Replication Package

Run end-to-end validation of the replication package for the sewage-house-prices project.

Input: $ARGUMENTS — directory containing the replication package (Replication/ by default), or here for the current project root.

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Project-Specific Context

Expected Structure

• Pipeline scripts: scripts/R/01_data_ingestion/ through scripts/R/06_analysis_datasets/
• Analysis scripts: scripts/R/09_analysis/
• Utilities: scripts/R/utils/
• Python: scripts/python/
• Data: data/raw/, data/processed/, data/final/
• Output: output/tables/, output/figures/
• Manuscript: docs/overleaf/
• R packages: renv.lock

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Workflow

Step 1: Locate Package

• If $ARGUMENTS is a directory path: use it
• If $ARGUMENTS is here or empty: use Replication/ if it exists, otherwise project root
• Verify the directory exists and contains scripts

Step 2: Run 10 Verification Checks

Standard Checks (1-4)

1. Script syntax — All .R files parse without syntax errors
2. File references — All read_parquet(), readRDS(), read.csv() targets exist or are documented as inputs
3. File integrity — No orphaned scripts (referenced but missing), no orphaned outputs (generated but unreferenced)
4. Output freshness — Output files are newer than their source scripts (no stale outputs)

Submission Checks (5-10)

5. Package inventory — Scripts are logically ordered, master script exists
6. Dependency verification — renv.lock present, R version documented, Python deps documented
7. Data provenance — Every dataset has documented source, access date, and restrictions
8. Path hygiene — No hardcoded absolute paths, all paths use here::here()
9. Output cross-reference — Every table/figure in the manuscript traces to a specific script
10. README completeness — AEA format: data availability, computational requirements, program descriptions, instructions

Step 3: Handle Failures

If failures found:

1. Display specific error with file and line number
2. Suggest concrete fix
3. Ask user if they want to fix and re-audit (max 3 iterations)

Step 4: Present Results

# Replication Audit Report
**Date:** YYYY-MM-DD
**Directory:** [path]

## Check Results
| # | Check | Status | Details |
|---|-------|--------|---------|
| 1 | Script syntax | PASS/FAIL | |
| 2 | File references | PASS/FAIL | |
| 3 | File integrity | PASS/FAIL | |
| 4 | Output freshness | PASS/FAIL | |
| 5 | Package inventory | PASS/FAIL | |
| 6 | Dependencies | PASS/FAIL | |
| 7 | Data provenance | PASS/FAIL | |
| 8 | Path hygiene | PASS/FAIL | |
| 9 | Output cross-reference | PASS/FAIL | |
| 10 | README completeness | PASS/FAIL | |

## Summary
- Checks passed: N / 10
- **Overall: PASS / FAIL**
- Blocking issues: [list]
- Positive findings: [list]

Save to output/log/replication_audit_[date].md.

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Principles

• Read and analyse only. Do not modify the package during audit.
• Specific errors. "Script 03_robustness.R references data/final/panel.parquet which does not exist" beats "file reference error."
• AEA Data Editor standards. The target is full compliance.
• Path checking is critical. Any setwd() or absolute path is a FAIL for Check 8.
• Restricted data awareness. Land Registry and Zoopla data may have access restrictions — document, don't block.