| name | vera-stat-binary-analyzing |
| description | Server-side extension that completes the full analysis pipeline for binary outcome variables after vera-stat-binary-testing has run. Adds remaining association tests (chi-square/Fisher's for additional predictors, point-biserial for continuous predictors), stratified odds ratio analysis with Breslow-Day test and forest plot, full modeling (logistic regression with OR and 95% CI, Hosmer-Lemeshow GOF, pseudo-R2, ROC curve with AUC, classification table, tree-based classification with CART/RF/GBM), and cross-method variable importance comparison on a 0-100 unified scale. Generates manuscript-ready methods.md and results.md with formatted tables, publication-quality figures, and references.bib. Applies output variation and code style variation for natural, non-repetitive output. Triggered after vera-stat-binary-testing completes, or direct request with a binary outcome variable. |
| user-invocable | true |
| allowed-tools | Read, Bash, Write, Edit, Grep, Glob |
Binary Outcome --- Full Analysis & Manuscript Generation
Open-source skill. Read reference/specs/output-variation-protocol.md
before every generation --- apply all variation layers.
Workflow
Continues from where vera-stat-binary-testing stopped (PART 0-2 done).
| Step | File | Executor | Output |
|---|
| Additional tests | workflow/04-run-additional-tests.md | Main Agent | PART 3 code + prose |
| Subgroup | workflow/05-analyze-subgroups.md | Main Agent | PART 4 code + prose |
| Modeling | workflow/06-fit-models.md | Main Agent | PART 5 code + prose |
| Comparison | workflow/07-compare-models.md | Main Agent | PART 6 code + prose |
| Manuscript | workflow/08-generate-manuscript.md | Main Agent | methods.md + results.md |
Additional Inputs
Collect if not already provided:
- Target discipline (for reporting conventions)
- Target journal or style (APA 7th, STROBE, etc.)
- Research question / hypothesis
- Subgroup variable (if subgroup analysis desired)
Output Structure
output/
├── methods.md
├── results.md
├── tables/ ← Markdown + CSV per table
├── figures/ ← PNGs, 300 DPI
├── references.bib
├── code.R ← Style-varied
└── code.py ← Style-varied
Key References (read before generation)
| File | Purpose |
|---|
reference/specs/output-variation-protocol.md | Output quality variation layers |
reference/specs/code-style-variation.md | Seven-dimension code style diversity |
reference/patterns/sentence-bank.md | 4-6 phrasings per result type |
reference/rules/reporting-standards.md | Hard rules for statistical reporting |
Reporting Standards
Same as vera-stat-binary-testing, plus:
- Logistic coefficients: report OR (not raw B) in results text; raw B with SE in supplementary table
- Pseudo-R2: report McFadden and Nagelkerke; say "the model accounted for" --- never "explained"
- AUC: report with 95% CI; note "in-sample" if no cross-validation performed
- Classification: report sensitivity, specificity, and threshold used
- Tree-based with small N: frame as "exploratory"; never claim predictive validity
- Hosmer-Lemeshow: report chi-sq, df, p; non-significant = adequate fit
Cross-Skill Interface
Method Unit Contract:
├── code_r → .R script (style-varied)
├── code_python → .py script (style-varied)
├── methods_md → methods.md (varied structure)
├── results_md → results.md (varied phrasing)
├── tables/ → Markdown + CSV
├── figures/ → PNGs 300 DPI (varied layout)
├── references_bib → .bib with cited references
└── comparison → cross-method narrative (in results.md)
Invoked directly after vera-stat-binary-testing or orchestrated by vera-stat-application-pipeline.
