Survival Outcome — Diagnostics & Hypothesis Testing
Table of Contents
Open-source skill.
Scope Boundary
Use this skill when:
- The endpoint is standard right-censored time-to-event data and the first need is KM plus log-rank style inference.
- A univariate or simple grouped survival baseline is appropriate before multivariable hazard modeling.
Do not use this skill when:
- The data involve left/interval censoring, competing risks, or multi-state structures.
- The primary question already depends on recurrent-event or time-varying-covariate modeling.
Workflow
Read each step file in workflow/ before executing that step.
| Step |
Responsibility |
Executor |
Document |
Input |
Output |
| Collect |
Collect Inputs |
Main Agent |
workflow/step01-collect-inputs.md |
User input |
Structured input summary |
| Diagnose |
Check Distribution |
Main Agent |
workflow/step02-check-distribution.md |
Prior step output |
PART 1 code block |
| Test |
Run Primary Test |
Main Agent |
workflow/step03-run-primary-test.md |
Prior step output |
PART 2-3 code blocks |
Decision Tree
1. CHECK FOLLOW-UP & CENSORING
├── Censoring rate > 80% → Warning: limited events, wide CIs expected
├── Censoring rate < 5% → Note: standard regression may suffice
└── Otherwise → proceed normally
2. GROUP COMPARISON
├── 2 groups → Log-rank test + HR from univariate Cox
└── 3+ groups → Log-rank test + pairwise log-rank (Bonferroni)
Required Inputs
| Role |
What to collect |
| Time variable |
Continuous, ≥0, follow-up/survival time |
| Event indicator |
Which value = event occurred, which = censored |
| Group variable |
What defines groups, how many levels |
| Predictors |
For recommendation block (not executed) |
Code Structure
PART 0: Setup & Data Loading
PART 1: Follow-Up & Censoring Diagnostics → plot_01_km_overall.png, plot_01b_event_histogram.png
PART 2: Primary Hypothesis Test → plot_02_km_groups.png
PART 3: Recommendation Block → text listing additional analyses available
Reporting Standards
- p-values: "< .001" not "0.000"; exact to 3 decimals otherwise
- Hazard ratio: HR with 95% CI, "HR = X.XX, 95% CI [X.XX, X.XX]"
- 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
- Decimal places: 2 for median survival, 3 for p and HR
- Non-significance: "not statistically significant at alpha = .05" — never "no effect"
- Cox regression: when reported, include Schoenfeld-residual test for proportional hazards (global p-value + per-covariate). Flag any PH violation explicitly.
Hypothesis Tests
| Scenario |
Test |
| 2 independent groups |
Log-rank + univariate Cox HR |
| 3+ independent groups |
Log-rank + pairwise log-rank (Bonferroni) |
Paired/clustered designs are out of scope for this version.
Example Dataset
R built-in survival::lung: outcome = time (survival time), status (1=censored, 2=dead).
Predictors: age, sex, ph.ecog, ph.karno, pat.karno, meal.cal, wt.loss.
Python: from lifelines.datasets import load_lung or reconstruct from R.
Method Status
| Status |
Methods |
| Implemented in this skill |
Kaplan-Meier summaries, log-rank tests, median survival, landmark survival rates, univariate Cox preview |
Implemented downstream in vera-data-survival-generating |
Multivariable Cox, AFT, recurrent-event models, random survival forest, boosting survival methods |
| Out of scope in this open-source baseline |
Competing-risks, multi-state, left-censored, and interval-censored survival families |
Minimal Smoke Test
- Smoke-test prompt: "Run
vera-data-survival-reviewing on survival::lung, using time as follow-up, status as the event indicator, and sex as the grouping variable. Produce the standard baseline artifacts."
Cross-Skill Interface
Output:
├── code_r → .R script
├── code_python → .py script
├── figures/ → 2 PNGs (KM overall + KM groups)
└── recommendations → text block (additional analyses available)
Next step: Invoke vera-data-survival-generating from this skillset to run the full pipeline (additional tests, subgroup analysis, modeling, manuscript generation). See ../../CROSS-SKILL-INTERFACE.md for the shared handoff contract.
1---2name: vera-data-survival-reviewing3description: Runs survival diagnostics and primary hypothesis tests for right-censored time-to-event outcomes. Produces Kaplan-Meier curves with number-at-risk tables, log-rank test for group comparison, median survival, landmark survival rates, and HR preview from univariate Cox regression. Outputs .R and .py scripts with publication-quality plots. Triggered when user has a time-to-event outcome and says "survival outcome," "time to event," "Kaplan-Meier," "hazard," "OS/PFS/DFS." Right-censored data only. Competing risks, recurrent events, and multi-state models are out of scope. Does not handle binary, count, continuous, ordinal, repeated measures, or SEM outcomes.4---56# Survival Outcome — Diagnostics & Hypothesis Testing78## Table of Contents910- [Scope Boundary](#scope-boundary)11- [Workflow](#workflow)12- [Decision Tree](#decision-tree)13- [Required Inputs](#required-inputs)14- [Code Structure](#code-structure)15- [Reporting Standards](#reporting-standards)16- [Hypothesis Tests](#hypothesis-tests)17- [Example Dataset](#example-dataset)18- [Method Status](#method-status)19- [Minimal Smoke Test](#minimal-smoke-test)20- [Cross-Skill Interface](#cross-skill-interface)212223Open-source skill.2425## Scope Boundary2627Use this skill when:28- The endpoint is standard right-censored time-to-event data and the first need is KM plus log-rank style inference.29- A univariate or simple grouped survival baseline is appropriate before multivariable hazard modeling.3031Do not use this skill when:32- The data involve left/interval censoring, competing risks, or multi-state structures.33- The primary question already depends on recurrent-event or time-varying-covariate modeling.3435## Workflow3637Read each step file in `workflow/` before executing that step.3839| Step | Responsibility | Executor | Document | Input | Output |40|---|---|---|---|---|---|41| Collect | Collect Inputs | Main Agent | `workflow/step01-collect-inputs.md` | User input | Structured input summary |42| Diagnose | Check Distribution | Main Agent | `workflow/step02-check-distribution.md` | Prior step output | PART 1 code block |43| Test | Run Primary Test | Main Agent | `workflow/step03-run-primary-test.md` | Prior step output | PART 2-3 code blocks |4445## Decision Tree4647```481. CHECK FOLLOW-UP & CENSORING49 ├── Censoring rate > 80% → Warning: limited events, wide CIs expected50 ├── Censoring rate < 5% → Note: standard regression may suffice51 └── Otherwise → proceed normally52532. GROUP COMPARISON54 ├── 2 groups → Log-rank test + HR from univariate Cox55 └── 3+ groups → Log-rank test + pairwise log-rank (Bonferroni)56```5758## Required Inputs5960| Role | What to collect |61|---|---|62| **Time variable** | Continuous, ≥0, follow-up/survival time |63| **Event indicator** | Which value = event occurred, which = censored |64| **Group variable** | What defines groups, how many levels |65| **Predictors** | For recommendation block (not executed) |6667## Code Structure6869```70PART 0: Setup & Data Loading71PART 1: Follow-Up & Censoring Diagnostics → plot_01_km_overall.png, plot_01b_event_histogram.png72PART 2: Primary Hypothesis Test → plot_02_km_groups.png73PART 3: Recommendation Block → text listing additional analyses available74```7576## Reporting Standards77781. p-values: "< .001" not "0.000"; exact to 3 decimals otherwise792. Hazard ratio: HR with 95% CI, "HR = X.XX, 95% CI [X.XX, X.XX]"803. Median survival: always with 95% CI814. Survival rates at landmarks: with 95% CI825. Censoring: always report % censored overall and by group836. Log-rank: chi-sq(df) = X.XX, p = .XXX847. Decimal places: 2 for median survival, 3 for p and HR858. Non-significance: "not statistically significant at alpha = .05" — never "no effect"869. Cox regression: when reported, include Schoenfeld-residual test for proportional hazards (global p-value + per-covariate). Flag any PH violation explicitly.8788## Hypothesis Tests8990| Scenario | Test |91|---|---|92| 2 independent groups | Log-rank + univariate Cox HR |93| 3+ independent groups | Log-rank + pairwise log-rank (Bonferroni) |9495Paired/clustered designs are out of scope for this version.9697## Example Dataset9899R built-in `survival::lung`: outcome = time (survival time), status (1=censored, 2=dead).100Predictors: age, sex, ph.ecog, ph.karno, pat.karno, meal.cal, wt.loss.101Python: `from lifelines.datasets import load_lung` or reconstruct from R.102103## Method Status104105| Status | Methods |106|---|---|107| Implemented in this skill | Kaplan-Meier summaries, log-rank tests, median survival, landmark survival rates, univariate Cox preview |108| Implemented downstream in `vera-data-survival-generating` | Multivariable Cox, AFT, recurrent-event models, random survival forest, boosting survival methods |109| Out of scope in this open-source baseline | Competing-risks, multi-state, left-censored, and interval-censored survival families |110111## Minimal Smoke Test112113- Smoke-test prompt: "Run `vera-data-survival-reviewing` on `survival::lung`, using `time` as follow-up, `status` as the event indicator, and `sex` as the grouping variable. Produce the standard baseline artifacts."114115## Cross-Skill Interface116117```118Output:119├── code_r → .R script120├── code_python → .py script121├── figures/ → 2 PNGs (KM overall + KM groups)122└── recommendations → text block (additional analyses available)123```124125Next step: Invoke `vera-data-survival-generating` from this skillset to run the full pipeline (additional tests, subgroup analysis, modeling, manuscript generation). See `../../CROSS-SKILL-INTERFACE.md` for the shared handoff contract.
VeraSuperHub