paper-reviewer

name	paper-reviewer
description	Comprehensive pre-submission review orchestrator. Coordinates methodology checks, bias detection, AI text detection, statistical validation, and reporting guideline compliance for journal submissions.
version	1.0.0
author	Aaron Storey

Paper Reviewer

Comprehensive pre-submission review for journal manuscripts. Orchestrates multiple specialized skills from research-assistant to ensure publication readiness.

When to Use

• Before submitting papers to journals
• After completing systematic reviews
• When preparing dissertation chapters for committee
• For quality assurance on research manuscripts

Features

1. AI Text Detection - Identify LLM-generated patterns
2. Methodology Assessment - Verify research design rigor
3. Bias Detection - Apply RoB 2, ROBINS-I, QUADAS-2 frameworks
4. Statistical Validation - Check assumptions, effect sizes, power analysis
5. Reporting Compliance - Validate CONSORT, PRISMA, STROBE guidelines
6. Citation Integrity - Verify references, check for retractions
7. Reproducibility Audit - Assess code/data availability

Usage

Review the manuscript at ~/Documents/submissions/AffectivePrompting/ for journal submission.
This is a systematic review targeting IEEE Transactions.

Review Pipeline

Phase 1: Triage

• Classify paper type (RCT, systematic review, observational, etc.)
• Identify target journal requirements
• List available files

Phase 2: AI Detection

• Run ai-check skill
• Flag sections with AI patterns >30%
• Generate authenticity report

Phase 3: Methodology

• Assess study design appropriateness
• Verify protocol adherence
• Check randomization/blinding (if applicable)

Phase 4: Risk of Bias

• Apply appropriate RoB tool
• Document domain-by-domain assessment
• Generate traffic light visualization

Phase 5: Statistical Validation

• Verify assumption testing
• Check effect size reporting
• Validate power analysis

Phase 6: Reporting Compliance

• Apply appropriate checklist (CONSORT/PRISMA/STROBE)
• Calculate compliance percentage
• List missing items

Phase 7: Citation Audit

• Verify all references
• Check for retractions
• Validate DOIs

Phase 8: Reproducibility

• Check code availability
• Verify data accessibility
• Assess documentation completeness

Output

Generates comprehensive review report:

• Executive summary with overall assessment
• Section-by-section findings
• Priority-ranked revision checklist
• Detailed appendices

Paper Type-Specific Workflows

Systematic Reviews

• PRISMA 2020 compliance
• AMSTAR 2 quality assessment
• Meta-analysis validation

RCTs

• CONSORT compliance
• RoB 2 bias assessment
• ITT/per-protocol analysis check

Observational Studies

• STROBE compliance
• ROBINS-I bias assessment
• Confounding control verification

Integration

Uses research-assistant skills:

• ai-check
• risk-of-bias
• hypothesis-test
• effect-size
• power-analysis
• publication-prep
• citation-format
• prisma-diagram

Configuration

Default thresholds (can override):

• AI detection: 30% (flag if higher)
• Reporting compliance: 85% minimum
• All 8 phases enabled by default

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Part of ai_scientist research workflow automation