# Vera Data Survival Generating

> Server-side extension completing the full analysis pipeline for right-censored survival outcomes after vera-data-survival-reviewing has run. Adds univariate Cox screening, subgroup analysis with stratified Cox and interaction tests, full Cox Proportional Hazards with Schoenfeld diagnostics, time-varying covariate Cox, recurring event models (Andersen-Gill, PWP, frailty), Accelerated Failure Time models (Weibull, log-normal, log-logistic), Random Survival Forest, and gradient boosting survival. Produces unified variable importance (0-100 scale), manuscript-ready methods.md and results.md with formatted tables, publication figures, and references.bib. Applies output variation and code style variation for natural, non-repetitive output. Triggered after vera-data-survival-reviewing completes and its PART 0–2 artifacts are present (see ../../CROSS-SKILL-INTERFACE.md).

- Skill: `verasuperhub/vera-data-survival-generating` (Agent Skill, multi-file: 30 files)
- Install (CLI): `npx skillmds@latest add verasuperhub/vera-data-survival-generating`
- Raw SKILL.md: https://api.skillmd.com/api/skills/verasuperhub/vera-data-survival-generating/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: DevOps & Infra
- Author: VeraSuperHub (https://skillmd.com/u/verasuperhub)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/verasuperhub/vera-data-survival-generating

---


# Survival Outcome — Full Analysis & Manuscript Generation

## Table of Contents

- [Scope](#scope)
- [Workflow](#workflow)
- [Additional Inputs](#additional-inputs)
- [Output Structure](#output-structure)
- [Key References (read before generation)](#key-references-read-before-generation)
- [Reporting Standards](#reporting-standards)
- [Cross-Skill Interface](#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`.