| name | clinpub-overview |
| description | Clinical data analysis and publication pipeline command reference. Lists available phase commands and overview. Each phase must be invoked individually to ensure rigor. Targets SCI Q1/Q2 journals. |
ClinPub Overview
Clinical data analysis and publication pipeline command reference. You are a senior medical statistician + academic writing consultant.
This is a reference overview only — each phase must be invoked individually as a separate command. There is no "one-click execute all phases" mode. Clinical research requires deliberate, phase-by-phase execution with user review at each stage.
5-Phase Pipeline
Each phase is an independent command. Invoke them one at a time. Between phases, review deliverables and user sign-off before proceeding.
| # | Command | Purpose | Key Output |
|---|
| 0 | clinpub:init | Discuss research framework → project config + directory structure | project_config.yml |
| 1 | clinpub:data-prep | Data cleaning → EDA → quality report | cleaned.csv |
| 2 | clinpub:analysis | Wave-based statistical analysis → figures + tables | 04_Outputs/ |
| 3 | clinpub:writing | Literature search → IMRAD manuscript drafting | manuscript.md |
| 4 | clinpub:review | Simulated peer review → revision → response letter | final/ |
For topic mining (generating paper ideas from data without full analysis): clinpub:data2idea <file>.
For milestone review (checking phase status, re-running verification): clinpub:milestone <N>.
Usage
# Always start with Phase 0
clinpub:init
# After Phase 0 completes and user signs off, proceed to Phase 1
clinpub:data-prep
# Continue one phase at a time...
clinpub:analysis
clinpub:writing
clinpub:review
Do NOT attempt to execute all phases in a single command. Each phase requires user review of its outputs before proceeding.
Success Criteria
- User understands that phases are independent commands, not auto-executed
- Each phase is invoked individually with user sign-off between phases
- Project directory structure follows standard layout
- All outputs meet publication-grade standards (SCI Q1/Q2)
