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.

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.

When to use

• Before submission. Catches the "I updated the analysis but forgot to update Table 2" bug.
• 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.
• $1 — path to the outputs directory. Defaults to scripts/R/_outputs/. Recognised alternatives: scripts/stata/_outputs/ (Stata pipelines built by /stata-replication), _targets/objects/ (R targets workflows), any directory the user-specified outputs live in.

Workflow