peer-review skill

---
name: peer-review
description: Systematic peer review and self-evaluation toolkit. Evaluate methodology, statistics, experimental design, reproducibility, ethics, and reporting standards. Use during the REVIEW phase to assess manuscript quality before submission, or when reviewing others' work.
---

# Scientific Peer Review

> Rigorously evaluate scientific work for quality, validity, and reproducibility.

## When to Use

- Self-reviewing manuscript before submission (REVIEW phase)
- Evaluating methodology and experimental design
- Checking statistical analyses and reporting
- Assessing reproducibility and data availability
- Reviewing others' manuscripts for journals
- Evaluating grant proposals
- Quality checking your own work during ANALYSIS phase

## Review Workflow

```
1. INITIAL SCAN      → Overall impression, scope, significance
2. SECTION REVIEW    → Detailed evaluation of each section
3. METHODOLOGY       → Rigor, assumptions, controls
4. STATISTICS        → Appropriate tests, effect sizes, reporting
5. REPRODUCIBILITY   → Data, code, materials availability
6. FIGURES/TABLES    → Clarity, integrity, accessibility
7. ETHICS            → Approvals, consent, conflicts
8. WRITING           → Clarity, organization, accuracy
9. SYNTHESIZE        → Major/minor issues, recommendation
```

---

## Stage 1: Initial Assessment

### Quick Questions (5 minutes)

1. **What is the central research question?**
2. **What are the main findings?**
3. **Is the work scientifically sound?**
4. **Are there any immediate major flaws?**
5. **Is it appropriate for the intended venue?**

### Initial Summary Template

```markdown
## Initial Assessment

**Research Question**: [One sentence summary]

**Main Findings**: [2-3 key results]

**Initial Impression**: [Sound/Concerning/Major issues]

**Significance**: [Novel contribution to field?]
```

---

## Stage 2: Section-by-Section Review

### Abstract & Title

| Check | Question | Status |
|-------|----------|--------|
| Accuracy | Does abstract reflect the actual study? | ☐ |
| Clarity | Is the title specific and informative? | ☐ |
| Completeness | Are key findings summarized? | ☐ |
| Accessibility | Understandable to broad audience? | ☐ |

### Introduction

| Check | Question | Status |
|-------|----------|--------|
| Context | Is background adequate and current? | ☐ |
| Rationale | Is the research question justified? | ☐ |
| Novelty | Is originality clearly stated? | ☐ |
| Literature | Are relevant papers cited? | ☐ |
| Objectives | Are aims/hypotheses clear? | ☐ |

### Methods

| Check | Question | Status |
|-------|----------|--------|
| Reproducibility | Can another researcher replicate this? | ☐ |
| Rigor | Are methods appropriate for the question? | ☐ |
| Detail | Protocols, reagents, parameters described? | ☐ |
| Ethics | Approvals and consent documented? | ☐ |
| Statistics | Methods described and justified? | ☐ |
| Controls | Appropriate controls included? | ☐ |

**Critical Details to Verify:**
- Sample sizes and power calculations
- Randomization and blinding
- Inclusion/exclusion criteria
- Software versions
- Statistical tests and corrections

### Results

| Check | Question | Status |
|-------|----------|--------|
| Presentation | Logical and clear? | ☐ |
| Figures | Appropriate, clear, labeled? | ☐ |
| Statistics | Effect sizes, CIs, p-values? | ☐ |
| Objectivity | Results without interpretation? | ☐ |
| Completeness | Negative results included? | ☐ |

**Common Issues:**
- Selective reporting
- Inappropriate statistical tests
- Missing error bars
- Over-fitting
- Batch effects or confounders
- Missing controls

### Discussion

| Check | Question | Status |
|-------|----------|--------|
| Interpretation | Conclusions supported by data? | ☐ |
| Limitations | Acknowledged and discussed? | ☐ |
| Context | Placed appropriately in literature? | ☐ |
| Speculation | Distinguished from data-supported claims? | ☐ |
| Significance | Implications clearly stated? | ☐ |

**Red Flags:**
- Overstated conclusions
- Ignoring contradictory evidence
- Causal claims from correlational data
- Mechanistic claims without evidence

---

## Stage 3: Methodological Rigor

### Statistical Assessment

| Check | Question | Status |
|-------|----------|--------|
| Assumptions | Are statistical assumptions met? | ☐ |
| Effect sizes | Reported alongside p-values? | ☐ |
| Multiple testing | Correction applied? | ☐ |
| Confidence intervals | Provided? | ☐ |
| Sample size | Justified with power analysis? | ☐ |
| Missing data | Handled appropriately? | ☐ |
| Exploratory vs confirmatory | Clearly distinguished? | ☐ |

### Experimental Design

| Check | Question | Status |
|-------|----------|--------|
| Controls | Appropriate and adequate? | ☐ |
| Replication | Biological and technical? | ☐ |
| Confounders | Identified and controlled? | ☐ |
| Randomization | Properly implemented? | ☐ |
| Blinding | Adequate for the study? | ☐ |

---

## Stage 4: Reproducibility Assessment

### Data Availability

| Check | Question | Status |
|-------|----------|--------|
| Raw data | Deposited in repository? | ☐ |
| Accession numbers | Provided for databases? | ☐ |
| Restrictions | Justified (e.g., privacy)? | ☐ |
| Formats | Standard and accessible? | ☐ |

### Code and Materials

| Check | Question | Status |
|-------|----------|--------|
| Analysis code | Available (GitHub, Zenodo)? | ☐ |
| Protocols | Detailed enough to reproduce? | ☐ |
| Materials | Available or recreatable? | ☐ |

### Reporting Standards

Check adherence to discipline-specific guidelines:

| Study Type | Guideline | Status |
|------------|-----------|--------|
| Randomized trial | CONSORT | ☐ |
| Observational | STROBE | ☐ |
| Systematic review | PRISMA | ☐ |
| Diagnostic study | STARD | ☐ |
| Animal research | ARRIVE | ☐ |
| Case report | CARE | ☐ |

---

## Stage 5: Figure and Table Review

### Quality Checks

| Check | Question | Status |
|-------|----------|--------|
| Resolution | High quality? | ☐ |
| Labels | All axes/columns labeled with units? | ☐ |
| Error bars | Defined (SD, SEM, CI)? | ☐ |
| Statistics | Significance markers explained? | ☐ |
| Color | Colorblind-friendly? | ☐ |
| Scale bars | Included for images? | ☐ |

### Integrity Checks

| Check | Question | Status |
|-------|----------|--------|
| Manipulation | Any signs of image manipulation? | ☐ |
| Splicing | Gels/blots appropriately presented? | ☐ |
| Representative | Images truly representative? | ☐ |
| Complete | All conditions shown? | ☐ |

---

## Stage 6: Writing Quality

### Structure and Organization

| Check | Question | Status |
|-------|----------|--------|
| Logic | Manuscript logically organized? | ☐ |
| Flow | Sections flow coherently? | ☐ |
| Transitions | Clear between ideas? | ☐ |
| Narrative | Compelling and clear? | ☐ |

### Writing Quality

| Check | Question | Status |
|-------|----------|--------|
| Clarity | Language clear and precise? | ☐ |
| Jargon | Minimized and defined? | ☐ |
| Grammar | Correct throughout? | ☐ |
| Concise | No unnecessary complexity? | ☐ |

---

## Structuring the Review Report

### Summary Statement (1-2 paragraphs)

```markdown
## Summary

[Brief synopsis of the research]

**Recommendation**: [Accept / Minor revisions / Major revisions / Reject]

**Key Strengths**:
1. [Strength 1]
2. [Strength 2]
3. [Strength 3]

**Key Weaknesses**:
1. [Weakness 1]
2. [Weakness 2]

**Bottom Line**: [Overall assessment of significance and soundness]
```

### Major Comments

Issues that significantly impact validity or interpretability:

```markdown
## Major Comments

1. **[Issue Title]**
   - *Problem*: [Clear statement of the issue]
   - *Why it matters*: [Impact on conclusions]
   - *Suggestion*: [How to address it]

2. **[Issue Title]**
   ...
```

**Major issues typically include:**
- Fundamental methodological flaws
- Inappropriate statistical analyses
- Unsupported conclusions
- Missing critical controls
- Reproducibility concerns

### Minor Comments

Less critical issues that would improve the manuscript:

```markdown
## Minor Comments

1. [Page/Figure X]: [Issue and suggestion]
2. [Methods section]: [Missing detail]
3. [Figure 2]: [Clarity improvement]
```

---

## Review Tone Guidelines

### Do ✓

- Be constructive and specific
- Acknowledge strengths
- Provide actionable suggestions
- Focus on the science
- Be thorough but proportionate

### Don't ✗

- Use dismissive language
- Make personal attacks
- Be vague or sarcastic
- Request unnecessary experiments
- Impose personal preferences as requirements

---

## Self-Review Checklist (Before Submission)

Use this during your REVIEW phase:

### Methodology
- [ ] Methods are reproducible
- [ ] Controls are appropriate and documented
- [ ] Statistical methods are justified
- [ ] Sample sizes are adequate

### Results
- [ ] All results support conclusions
- [ ] Effect sizes are reported
- [ ] Negative results are included
- [ ] Figures are clear and accessible

### Reproducibility
- [ ] Data will be available
- [ ] Code is documented and available
- [ ] Protocols are detailed
- [ ] Reporting guidelines followed

### Writing
- [ ] Abstract accurately summarizes the work
- [ ] Conclusions are supported by data
- [ ] Limitations are acknowledged
- [ ] References are current and complete

---

## Integration with RA Workflow

### REVIEW Phase Activities

1. Run self-review using this checklist
2. Document issues in `tasks.md`
3. Address each issue systematically
4. Re-review until checklist passes
5. Update `.research/logs/activity.md`

### Pre-Submission Verification

Before calling a manuscript complete:
- [ ] Self-review completed
- [ ] All major issues addressed
- [ ] Figures meet journal requirements
- [ ] Data/code deposited
- [ ] Reporting checklist complete
- [ ] Cover letter prepared