# audit-reproducibility

Checks numerical statements in research manuscripts against R, Stata, and Python results. Useful for catching mismatches before submission or a replication-package release.

- skill · `type=skill` · Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, OpenCode · ★ 1671
- Author: pedrohcgs
- License: MIT · policy=mirror · the beginning of the file is at the end of this page
- Source: https://github.com/pedrohcgs/claude-code-my-workflow/tree/HEAD/.claude/skills/audit-reproducibility/SKILL.md
- Updated: 2026-09-27
- HTML: https://affpapa.org/en/nevibecode/skills/audit-reproducibility

## What it does

The skill audits figures reported in a paper, including effect estimates, standard errors, p-values, and sample counts. It compares them with the outputs generated by the analysis pipeline, then assigns PASS or FAIL using the thresholds in `.claude/rules/replication-protocol.md`.

It checks consistency in two directions. Each manuscript claim is matched to its underlying result, then the same value is checked across other declared materials, such as supplements, slides, and posters listed in `appears_in`. The extracted claims are written to `quality_reports/reproducibility_claims_[manuscript-name].json` for review. Result lookup can use `.rds`, `.tex`, `.csv`, `.out`, `.log`, and `.json` files.

Before auditing, the skill reads the current tolerance rules, checks that the output directory contains results, and looks for `sessionInfo.txt` or an equivalent environment record. An empty or outdated output directory triggers a request to rerun the analysis pipeline. You need a manuscript in `.tex`, `.qmd`, `.md`, or `.pdf` format alongside the analysis outputs; stale results can undermine the audit.

## Install

### Claude Code (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add pedrohcgs/claude-code-my-workflow --skill audit-reproducibility -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/audit-reproducibility/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/audit-reproducibility/

### Codex

1. **Skills CLI (Vercel)**
```bash
npx skills add pedrohcgs/claude-code-my-workflow --skill audit-reproducibility -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/audit-reproducibility/SKILL.md` — For all projects use ~/.agents/skills/

### Cursor

1. **Skills CLI (Vercel)**
```bash
npx skills add pedrohcgs/claude-code-my-workflow --skill audit-reproducibility -a cursor
```

2. **Manually: put the files in place**
- File: `.cursor/skills/audit-reproducibility/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install pedrohcgs/claude-code-my-workflow audit-reproducibility
```

2. **Manually: put the files in place**
- File: `.github/skills/audit-reproducibility/SKILL.md`

### Gemini CLI

1. **Skills CLI (Vercel)**
```bash
npx skills add pedrohcgs/claude-code-my-workflow --skill audit-reproducibility -a gemini-cli
```

2. **Platform CLI**
```bash
gemini skills install https://github.com/pedrohcgs/claude-code-my-workflow --path .claude/skills/audit-reproducibility
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/audit-reproducibility/SKILL.md` — The legacy .windsurf/skills/ path still works

### OpenCode

**Skills CLI (Vercel)**
```bash
npx skills add pedrohcgs/claude-code-my-workflow --skill audit-reproducibility -a opencode
```

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/pedrohcgs/claude-code-my-workflow/tree/HEAD/.claude/skills/audit-reproducibility/SKILL.md

## When to use it
- Compare reported effect estimates with computed results
- Catch outdated figures in tables, slides, and supplements
- Check sample counts and p-values against tolerance rules
- Extract manuscript claims for manual review
- Verify that a replication package matches the paper

## Example prompts
- Audit `paper.tex` against the results in `output/` and report numerical mismatches.
- Compare the figures in `manuscript.qmd` with the latest analysis outputs and check related slides for stale values.
- Check reproducibility for `article.pdf` using the results stored in `_targets/objects/`.

## Source text · SKILL.md · MIT

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BEGIN THIRD-PARTY FILE 0876e46ce337fe29
```text
---
name: audit-reproducibility
description: Enforce the replication-protocol.md rule by cross-checking numeric claims in a manuscript against the actual R / Stata / Python outputs. Report PASS/FAIL per claim against tolerance thresholds. Use before submission and before releasing a replication package.
argument-hint: "[manuscript path] [outputs-dir] (outputs-dir defaults to output/)"
allowed-tools: ["Read", "Grep", "Glob", "Write", "Bash", "Agent", "Task", "Monitor"]
effort: high
---

# Audit Reproducibility

Compare numeric claims in a manuscript (point estimates, standard errors, p-values, counts) against the actual outputs produced by the analysis pipeline. Report PASS / FAIL per claim against the tolerance thresholds defined in [`.claude/rules/replication-protocol.md`](../../rules/replication-protocol.md).

**Core principle:** If the paper says `ATT = -1.632 (0.584)` and the code produces `-1.628 (0.591)`, we verify — **numerically** — that the difference is within the documented tolerance. No more "looks close enough" eyeballing.

**Two directions, not one.** *Vertically*, each claim is checked against the output that produced it. *Horizontally*, it is checked against every **other** artifact that displays the same number — the supplement table, the slide deck, the poster. The vertical check passes contentedly while a deck quotes last month's value; only the horizontal one catches that. Declared displays live in the passport's `appears_in` list — see [`replication-protocol.md` → The horizontal check](../../rules/replication-protocol.md#the-horizontal-check).

## When to use

- **Before submission.** Catches the "I updated the analysis but forgot to update Table 2" bug.
- **Before presenting or teaching from the same numbers.** Catches the deck, the poster, or the supplement that was never regenerated after the last rerun.
- **Before releasing a replication package.** Verifies the code actually reproduces the paper.
- **After a major revision.** Ensures the paper still matches the latest code.
- **Quality-gate in `/commit`.** Pair with a pre-commit invocation on manuscript + analysis changes.

## Inputs

- `$0` — path to the manuscript (`.tex`, `.qmd`, `.md`, `.pdf`). Required.
```
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