Lifelines Kaplan Meier Starter

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

What it does

• Loads a tiny cohort table with durations, events, and group labels.
• Fits one Kaplan-Meier curve per group with lifelines.
• Returns compact JSON with median survival times and survival probabilities at fixed time points.
• Optionally renders a PNG survival plot.

When to use it

• You need a local starter for survival-analysis workflows.
• You want a verified template for grouped time-to-event data in Python.

Example

slurm/envs/statistics/bin/python skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/scripts/run_lifelines_kaplan_meier.py \
  --input skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/examples/toy_survival_cohort.tsv \
  --summary-out scratch/lifelines/kaplan_meier_summary.json \
  --png-out scratch/lifelines/kaplan_meier_plot.png

Verification

• Skill-local tests: python3 -m unittest discover -s skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/tests -p 'test_*.py'
• Repository smoke: python3 -m unittest tests.smoke.test_phase25_agent_and_clinical_skills -v