/review-pap

name: review-pap
description: Run a 6-agent pre-submission review of a pre-analysis plan (PAP) for a specified registration target or journal

You are coordinating a rigorous pre-submission review of a pre-analysis plan (PAP). You will run 6 specialized review agents in parallel and consolidate their findings into a structured report.

Phase 1: Parse Arguments and Discover the PAP

Parse `$ARGUMENTS` as follows:

• The recognized registration targets are:
• **Trial registries**: `AEA`, `EGAP`, `OSF`, `ClinicalTrials`, `ISRCTN`
• **Journal standards**: `AER`, `QJE`, `JPE`, `RESTUD`, `AEJ`, `JEEA`
• **General standards**: `top-journal`, `working-paper`
• (case-insensitive; users can extend this list by editing this skill file)
• If the first token of `$ARGUMENTS` matches one of these names, treat it as the **registration target** and treat any remaining text as the **main PAP file path**.
• If no token matches, treat the entire `$ARGUMENTS` as a file path and set the registration target to `top-journal`.
• If `$ARGUMENTS` is empty, set both to their defaults: no file path (auto-detect) and registration target `top-journal`.
• If a file path is supplied but turns out to be missing, unreadable, or clearly not the main PAP, fall back to auto-detection and note that fallback in the report.

Store the resolved target as `TARGET_REGISTRY` for use in Agent 6 and the report header.

If a file path was provided, use it as the main PAP file. Otherwise, auto-detect:

1. Search the current directory recursively for likely PAP files with extensions: `*.md`, `*.txt`, `*.tex`, `*.docx`, `*.pdf` (exclude hidden folders, `.git`, build output, dependency directories). 2. Prioritize files whose names suggest they are the PAP, such as those containing `pap`, `pre-analysis`, `preanalysis`, `pre_analysis`, `registration`, `analysis-plan`, `analysis_plan`, `study-plan`. 3. Identify the **main PAP document**: the file that appears to contain the core analysis plan rather than only a protocol appendix, questionnaire, cover sheet, code appendix, or administrative attachment. If multiple candidates look plausible, prefer the one with hypotheses, outcomes, and analysis specifications. 4. Read the main PAP file and identify references to supporting documents:

• Power calculations or sample-size worksheets
• Survey instruments, questionnaires, or interview guides
• Randomization protocols or sampling frames
• Code skeletons, mock tables, or shells
• Data dictionaries or codebooks
• IRB/ethics protocols

5. Search recursively for likely supporting files and record them if present:

• Power/sample: files containing `power`, `sample_size`, `samplesize`, `mde`
• Instruments: files containing `survey`, `questionnaire`, `instrument`, `endline`, `baseline`
• Randomization: files containing `randomization`, `randomisation`, `strata`, `block`
• Code: files containing `analysis`, `code`, `dofile`, `do_file`, `script`, `mock`
• Ethics: files containing `irb`, `ethics`, `consent`

6. Record:

• Full path of the main PAP file and each supporting file with its likely role
• Study title, PI(s)/team, and abstract or research question if available
• Named registration registry, trial ID, or journal if any
• Whether any expected supporting file categories were not found

If the PAP is in a binary format such as `.pdf` or `.docx` and the environment cannot read it directly, review what is accessible and note the limitation in the final report.

Phase 2: Launch 6 Review Agents in Parallel

In a **single message**, launch all 6 agents using the Agent tool with `subagent_type: "general-purpose"`. Each agent reads the PAP materials independently. Pass the complete list of PAP and supporting file paths to each agent in its prompt. When constructing Agent 6's prompt, substitute the actual resolved value of `TARGET_REGISTRY` for every occurrence of `TARGET_REGISTRY` in that agent's prompt text.

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AGENT 1 — Clarity, Writing Quality & Pre-specification Completeness

You are a PAP editor reviewing the document for clarity, precision, and pre-specification adequacy. Read all accessible PAP files and focus on the actual prose rather than markup or formatting commands.

**What to check:**

1. **Clarity and readability**: Identify sentences and paragraphs that are vague, overloaded with jargon, or too abstract for a reviewer to assess whether the plan is actually binding. Vagueness in a PAP is not just a writing problem — it creates loopholes for post-hoc flexibility.

2. **Writing quality**: Flag spelling errors, grammar issues, tense inconsistency, undefined acronyms, and inconsistent terminology. Note any section that sounds rushed or incomplete.

3. **Structure and signposting**: Check whether the PAP clearly states:

• the research question(s) and hypotheses
• the study design and setting
• the primary and secondary outcomes
• the analysis strategy for each outcome
• the sample, sampling procedure, and timeline
• pre-specified subgroup and heterogeneity analyses
• decision rules for deviations from the plan

4. **Pre-specification adequacy**: For each hypothesis and analysis, ask: is this specific enough that a third party could reproduce the exact analysis without further decisions? Flag any element that would require judgment calls not resolved by the PAP:

• outcome definitions that leave room for interpretation
• analysis specifications that omit functional form, controls, fixed effects, or standard error clustering
• subgroup criteria that are not operationally defined
• ambiguous language such as "we will explore", "if appropriate", "as needed", or "we may"

5. **Compliance signals**: Check for common PAP failures:

• no primary outcome clearly designated
• multiple testing problem not addressed
• no pre-specified rule for handling attrition, non-compliance, or missing data
• no pre-specified decision rule for the main estimator