VeraSuperHub Survival Outcome — Full Analysis & Manuscript Generation
Table of Contents
- Scope
- Workflow
- Additional Inputs
- Output Structure
- Key References (read before generation)
- Reporting Standards
- Cross-Skill Interface
Open-source skill. Read reference/specs/output-variation-protocol.md
before every generation — apply all variation layers.
Scope
Right-censored survival data only. Does not handle left-censoring, interval-censoring, or competing risks. Supports time-varying predictors (covariates that change during follow-up) and recurring/recurrent events (same subject experiences the event multiple times).
Workflow
Continues from where vera-data-survival-reviewing stopped (PART 0-2 done).
| Step | Responsibility | Executor | Document | Input | Output |
|---|---|---|---|---|---|
| Additional tests | Run Additional Tests | Main Agent | workflow/step04-run-additional-tests.md |
Prior step output | PART 3 code + prose |
| Subgroup | Analyze Subgroups | Main Agent | workflow/step05-analyze-subgroups.md |
Prior step output | PART 4 code + prose |
| Modeling | Fit Models | Main Agent | workflow/step06-fit-models.md |
Prior step output | PART 5 code + prose |
| Comparison | Compare Models | Main Agent | workflow/step07-compare-models.md |
Prior step output | PART 6 code + prose |
| Manuscript | Generate Manuscript | Main Agent | workflow/step08-generate-manuscript.md |
Prior step output | methods.md + results.md |
Additional Inputs
Collect if not already provided:
- Target discipline (for reporting conventions)
- Target journal or style (APA 7th, STROBE, CONSORT, 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-data-survival-reviewing, plus:
- HR: always with 95% CI, "HR = X.XX, 95% CI [X.XX, X.XX]"
- Time ratio (AFT): "TR = X.XX, 95% CI [X.XX, X.XX]" with direction interpretation
- Median survival: always with 95% CI
- Survival rates at landmarks: with 95% CI
- Censoring: always report % censored overall and by group
- Log-rank: chi-sq(df) = X.XX, p = .XXX
- Cox global test: LR chi-sq, Wald chi-sq, Score chi-sq
- Concordance: C = X.XX (note in-sample if no validation)
- PH assumption: report Schoenfeld test per predictor and globally
- Coefficients: HR with SE for Cox; TR with SE for AFT
- Tree-based with small N: frame as "exploratory"; never claim predictive validity
- p-value rules same as other skills
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-data-survival-reviewing or orchestrated by vera-data-application-pipelining.