lifelines-kaplan-meier-starter

Name: lifelines-kaplan-meier-starter
Author: ma-compbio-lab

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How to install lifelines-kaplan-meier-starter?

ma-compbio-lab/skillfoundry/lifelines-kaplan-meier-starter

$npx -y skills add ma-compbio-lab/SkillFoundry --skill lifelines-kaplan-meier-starter

Installs into the current project.

Summary

Use this skill to run a deterministic Kaplan-Meier survival analysis over a toy cohort and summarize per-group survival curves.

Files · 1

SKILL.md

1	# Lifelines Kaplan Meier Starter
2
3	Use this skill to run a deterministic Kaplan-Meier survival analysis over a toy cohort and summarize per-group survival curves.
4
5	## What it does
6
7	- Loads a tiny cohort table with durations, events, and group labels.
8	- Fits one Kaplan-Meier curve per group with `lifelines`.
9	- Returns compact JSON with median survival times and survival probabilities at fixed time points.
10	- Optionally renders a PNG survival plot.
11
12	## When to use it
13
14	- You need a local starter for survival-analysis workflows.
15	- You want a verified template for grouped time-to-event data in Python.
16
17	## Example
18
19	```bash
20	slurm/envs/statistics/bin/python skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/scripts/run_lifelines_kaplan_meier.py \
21	--input skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/examples/toy_survival_cohort.tsv \
22	--summary-out scratch/lifelines/kaplan_meier_summary.json \
23	--png-out scratch/lifelines/kaplan_meier_plot.png
24	```
25
26	## Verification
27
28	- Skill-local tests: `python3 -m unittest discover -s skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/tests -p 'test_*.py'`
29	- Repository smoke: `python3 -m unittest tests.smoke.test_phase25_agent_and_clinical_skills -v`

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