review-pap

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). Also exclude previous review reports and AI-generated commentary: PAP_REVIEW_*.md, PRE_SUBMISSION_REVIEW_*.md, QUICK_REVIEW_*.md, GRANT_PROPOSAL_REVIEW_*.md, code_review_report*.md, and anything inside a reviews/ folder. These are outputs of earlier review runs, not PAP materials.
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.