Building an SLR with Claude Code

This is a systematic literature review project. Create the following directory structure:

- 01_search_and_screening/
- 02_data_extraction/
- 03_synthesis_and_writing/
- 04_manuscript_drafts/
- 00_literature_files/

Then populate CLAUDE.md with this SLR protocol:

# Systematic Literature Review Protocol

## Core Task
Systematic review to understand [YOUR RESEARCH QUESTION]

## File Structure
- /01_search_and_screening/ - Search strings, screening logs
- /02_data_extraction/ - Extraction tables (CSV/Markdown)
- /03_synthesis_and_writing/ - Theme analysis, drafts
- /04_manuscript_drafts/ - Final paper sections
- /00_literature_files/ - Full-text papers (markdown)

## Inclusion Criteria
- [YOUR CRITERIA - e.g., Peer-reviewed, 2020-2025, empirical]
- [Geographic/industry scope]
- [Methodology requirements]

## Exclusion Criteria
- [YOUR CRITERIA - e.g., Non-English, opinion pieces, duplicates]

## Citation Style
APA 7th Edition

## Custom Commands
- /screen: Evaluate abstract against inclusion criteria
- /extract: Extract data from full-text paper
- /critique: Review writing for quality and style

smith2024a.md
jones2024b.md
lee2023.md

"Analyze @/00_literature_files/smith2024a.md"
"Compare @/00_literature_files/smith2024a.md and @/00_literature_files/jones2024b.md"

"Apply the /screen command to every abstract in
@/01_search_and_screening/database_export_abstracts.txt
and output results to screening_results.csv"

"Scan @/04_manuscript_drafts/full_draft.docx and generate
a complete, alphabetized bibliography in APA 7th edition"

"Search all files in @/02_data_extraction/ and count
occurrences of: 'scalability', 'scaling', 'growth'"

"Run /extract on @/00_literature_files/smith2024a.md
and append results to @/02_data_extraction/extraction_table.md"

"Using data in @/02_data_extraction/extraction_table.md,
draft a 'Emerging Themes' section. Synthesize findings across
studies and identify patterns."

"Based on logs in @/01_search_and_screening/, create a PRISMA
flowchart showing: records identified, screened, included, excluded."

"Create a todo list for synthesizing these 5 papers on organizational learning:
- Identify common themes
- Extract methodological approaches
- Map theoretical frameworks
- Identify research gaps
- Draft synthesis section"

"Based on all papers in @/02_data_extraction/extraction_table.md,
what are the three most significant theoretical gaps? For each gap,
explain why it's important."

"My main argument is [YOUR ARGUMENT]. Act as a skeptical reviewer
from [TARGET JOURNAL]. Formulate three powerful critiques based on
the evidence I've synthesized."

"Based on limitations across all papers, propose a research agenda
with three novel questions that address these gaps. Justify why each
represents a meaningful contribution."

Evaluate this abstract against the inclusion criteria in @CLAUDE.md.

Abstract: $ARGUMENTS

## Screening Decision

**Decision:** [INCLUDE | EXCLUDE]

**Reason:** [Specific criterion met/failed]

**Confidence:** [High | Medium | Low]

**Notes:** [Any boundary cases or uncertainties]

Format as CSV row: decision, reason, confidence

/screen This paper examines organizational scaling in tech startups
using survey data from 500 companies across Europe and Asia between
2020-2023...

Extract structured data from this paper:

Paper: $ARGUMENTS

## Extraction Template

| Field | Content |
|-------|---------|
| Authors & Year | |
| Research Question | |
| Methodology | [Qual/Quant/Mixed] |
| Sample | [n=?, context] |
| Data Collection | |
| Analysis Approach | |
| Key Findings | [3-5 bullets] |
| Theoretical Contribution | |
| Limitations | |
| Future Research | |

Append this table to @/02_data_extraction/master_table.md

/extract @/00_literature_files/smith2024a.md

Review this writing section for quality:

Section: $ARGUMENTS

## Quality Checklist

1. **Logical Flow:** Are arguments well-structured?
2. **Evidence Strength:** Are claims supported by citations?
3. **APA 7th Compliance:** Citations formatted correctly?
4. **Clarity:** Is language precise and academic?
5. **Coherence:** Do paragraphs connect logically?

Provide specific feedback with line references.

"Create a search log in @/01_search_and_screening/search_log.md
documenting:
- Databases used: Web of Science, Scopus, etc.
- Search strings and boolean operators
- Date ranges
- Total hits per database"

"Apply /screen to each abstract in
@/01_search_and_screening/abstracts.txt
Output to screening_results.csv with columns: ID, Decision, Reason"

"Analyze screening_results.csv and generate PRISMA flowchart numbers:
- Records identified
- Records after deduplication
- Records screened
- Records excluded (with reasons)
- Full-text articles assessed
- Studies included in synthesis"

For each file in @/00_literature_files/:
/extract @/00_literature_files/[filename]

"Combine all extraction outputs into a single master table
at @/02_data_extraction/master_extraction_table.md"

"Review @/02_data_extraction/master_extraction_table.md
for missing data, inconsistencies, or errors. Flag any papers
needing manual review."

"Analyze @/02_data_extraction/master_extraction_table.md
and identify 5-7 major themes. For each theme, list:
- Papers that discuss it
- Key arguments/findings
- Points of agreement/disagreement"

"Create a methods summary table showing distribution of:
- Qualitative vs quantitative approaches
- Sample sizes and contexts
- Data collection methods
- Analysis techniques"

"Based on all papers, identify:
- Methodological gaps
- Theoretical gaps
- Empirical/contextual gaps
- Temporal gaps

For each gap, explain significance and future research implications."

"Using themes from @/03_synthesis_and_writing/themes.md,
draft a literature review section. Structure:
- Introduction to theme
- Discussion of each paper's contribution
- Synthesis of consensus and contradictions
- Implications for research"

/critique @/04_manuscript_drafts/literature_section_v1.md

"Extract all citations from @/04_manuscript_drafts/full_draft.md
and generate an APA 7th formatted bibliography"

/screen [abstract]
Decision: UNCERTAIN
→ Add to manual review queue

"Compare papers in @/00_literature_files/ with the citation network
exported from Research Rabbit. Identify:
- Highly cited papers we might have missed
- Citation clusters suggesting themes
- Outlier papers worth investigating"

"From all papers in @/00_literature_files/ with quantitative results,
extract effect sizes, sample sizes, and statistical significance.
Format as CSV for meta-analysis."

"Use 3 parallel agents to evaluate @/00_literature_files/smith2024a.md:
- Agent 1: Assess methodology rigor
- Agent 2: Evaluate theoretical contribution
- Agent 3: Identify practical implications

Synthesize their assessments into a comprehensive review."

"Split the abstracts in @/01_search_and_screening/batch1.txt
into 3 groups. Use parallel agents to screen each group
with /screen command. Compile results when complete."

"Generate a complete PRISMA 2020 flowchart based on:
- Search log: @/01_search_and_screening/search_log.md
- Screening results: @/01_search_and_screening/screening_results.csv
- Inclusion log: @/01_search_and_screening/included_papers.md

Output as markdown table and mermaid diagram."

"Convert @/02_data_extraction/master_extraction_table.md
to CSV format for:
1. Import into Excel/R for analysis
2. Appendix for manuscript submission
3. Supplementary materials"

"Compile these sections into a complete draft:
- @/04_manuscript_drafts/01_introduction.md
- @/04_manuscript_drafts/02_methods.md
- @/04_manuscript_drafts/03_results.md
- @/04_manuscript_drafts/04_discussion.md

Add section numbers, format headers, generate bibliography."

### AI-Assisted Analysis

Screening and data extraction were assisted by Claude Code (Anthropic, 2025)
using standardized prompts defined in the review protocol. All decisions were
verified by [AUTHOR NAME]. AI outputs were subject to human review and
quality control checkpoints. The complete protocol and prompts are available
in the supplementary materials.

# Export from database to text file
# Format: One abstract per line, with ID prefix

"Process @/01_search_and_screening/web_of_science_export.txt:

For each abstract:
1. Apply /screen command
2. Log decision with ID
3. Track exclusion reasons
4. Flag uncertain cases for manual review

Output to screening_results.csv with columns:
ID, Title, Authors, Year, Decision, Reason, Confidence"

"Show me all abstracts marked 'UNCERTAIN' in screening_results.csv
for manual review"

"Analyze screening_results.csv:
- Total abstracts screened
- Inclusion rate (%)
- Top 3 exclusion reasons
- Uncertain cases requiring manual review

Format as summary table."

"This SLR examines organizational scaling and scalability.
Inclusion: Peer-reviewed, 2020-2025, empirical studies on
business scaling. Exclusion: Non-English, opinion pieces,
case studies <3 companies."

/screen @Coviello et al. 2024. This paper distinguishes
organizational scaling (growth in size) from scalability
(capacity to grow) using multi-method approach with
50 high-growth firms...

→ INCLUDE (meets all criteria, novel conceptual distinction)

/extract @/00_literature_files/coviello2024.md

→ Generated structured table with RQ, methods, findings, contribution

"Analyze all papers with 'scalability' construct.
Compare definitions across studies. Identify conceptual confusion
vs. conceptual clarity. Draft 1-page synthesis."