ma-peer-review

name	ma-peer-review
description	Act as Reviewer 1 and Reviewer 2 for a meta-analysis manuscript, checking rigor, reproducibility, and reporting compliance. Use when validating the final paper before submission.

Ma Peer Review

Overview

Perform structured peer review and produce actionable feedback and validation checks.

Inputs

• 07_manuscript/ rendered outputs
• 06_analysis/validation.md
• 01_protocol/ and 03_screening/ artifacts

Outputs

• 08_reviews/reviewer1.md
• 08_reviews/reviewer2.md
• 08_reviews/action-items.md
• 08_reviews/grade_summary.csv
• 08_reviews/grade_summary.md
• 08_reviews/analysis_stats.json (collected from Stage 06)
• 08_reviews/grade_suggestions.csv (semi-automated)
• 08_reviews/grade_suggestions.md (semi-automated)
• 08_reviews/grade_detailed.md (per-domain reviewer decision format)
• 03_screening/round-01/quality_rob2.csv (RoB 2 for RCTs)
• 03_screening/round-01/rob2_assessment.md (RoB 2 narrative)
• 03_screening/round-01/quality_robins_i.csv (ROBINS-I for observational)
• 03_screening/round-01/robins_i_assessment.md (ROBINS-I narrative)

Workflow

1. Reviewer 1 focuses on methodology, inclusion criteria, and statistical validity.
   • Review 01_protocol/pico.yaml, 03_screening/round-01/agreement.md, 06_analysis/validation.md
   • Write to 08_reviews/reviewer1.md
2. Reviewer 2 focuses on clarity, reporting completeness, and reproducibility.
   • Review 07_manuscript/index.pdf, 07_manuscript/prisma_checklist.md
   • Write to 08_reviews/reviewer2.md
3. Record issues with severity, location, and recommended fixes.
   • Write to 08_reviews/action-items.md (columns: issue_id, severity, location, recommendation, status)
4. Create a consolidated action list with owners and status.
   • Update 08_reviews/action-items.md
5. Initialize GRADE summary tables with scripts/init_grade_summary.py via uv run.
   • Use scripts/init_grade_summary.py
   • Read from 05_extraction/extraction.csv (outcomes)
   • Write to 08_reviews/grade_summary.csv (columns: outcome, n_studies, n_participants, effect_estimate, certainty, reasons)
   • Write to 08_reviews/grade_summary.md
6. Collect analysis statistics from Stage 06 outputs with scripts/collect_analysis_stats.py.
   • Parses markdown reports and CSV tables for I², Egger's test, CI bounds, total events
   • Optionally includes RoB 2 assessment summary via --rob-csv
   • Write to 08_reviews/analysis_stats.json
7. Generate semi-automated GRADE suggestions with scripts/auto_grade_suggestion.py.
   • Use --stats 08_reviews/analysis_stats.json to enable computed suggestions
   • Use --out-detailed-md for per-domain reviewer decision format
   • Write to 08_reviews/grade_suggestions.csv, grade_suggestions.md, grade_detailed.md

Resources

• references/reporting-checks.md for PRISMA-style reporting checks.
• references/grade-template.md for GRADE evidence profiling.
• references/grade-summary-schema.md for GRADE summary columns.
• references/rob2-template.md for RoB 2 per-study assessment (RCTs).
• references/robins-i-template.md for ROBINS-I per-study assessment (observational).
• scripts/init_grade_summary.py for generating GRADE summary tables.
• scripts/collect_analysis_stats.py for extracting statistics from Stage 06 outputs.
• scripts/auto_grade_suggestion.py for semi-automated certainty suggestions with computed rationale.
• scripts/init_rob2_assessment.py for initializing RoB 2 assessment tables.
• scripts/init_robins_i_assessment.py for initializing ROBINS-I assessment tables.

Validation

• Verify that methods and results are consistent with the protocol.
• Confirm that all outputs are reproducible from the stored data and scripts.

Pipeline Navigation

Step	Skill	Stage
Prev	/ma-manuscript-quarto	07 Manuscript Drafting
Next	/ma-publication-quality	09 Publication Quality
All	/ma-end-to-end	Full pipeline orchestration