| name | clinpub-analysis |
| description | Phase 2: Adaptive statistical analysis. Claude diagnoses data structure (groups, timepoints, outcome types), proposes a customized analysis plan, discusses with user, and executes in dependency order. Each method outputs figure + table + README with publication-grade standards. |
ClinPub Analysis
Phase 2: Statistical analysis. Execute selected analysis methods in wave order, each producing publication-grade figures (≥300 DPI), formatted tables, and method documentation.
A shared figure configuration script (_figure_config.R) is generated at the start of Phase 2 to ensure all method figures share consistent theme, color palette, and DPI. Every method R script must source("04_Outputs/_figure_config.R") after library() calls.
Wave 1 → Wave 2 → Wave 3 → Wave 4 with dependency tracking. Only execute user-confirmed methods.
Execution Context
- Workflow:
pipeline/workflows/analysis.md
- References:
pipeline/references/analysis_methods.md, r_patterns.md
Process
Execute the analysis workflow from pipeline/workflows/analysis.md end-to-end.
Success Criteria
- Shared figure config script (
_figure_config.R) exists in 04_Outputs/ and is sourced by all method R scripts
- Each confirmed method has figure + table + README in 04_Outputs/
- Figures at ≥300 DPI, English labels, publication-grade theme
- All method figures share consistent style (theme, color palette, DPI) via
_figure_config.R
- Statistical reports include effect size + 95%CI + exact p-value
- Code reads from cleaned.csv, independently runnable
- R version and key package versions documented
