Generates Kaplan-Meier survival curves, calculates survival statistics (log-rank test, median survival time), and estimates hazard ratios for clinical and biological survival data analysis. Triggered when user requests survival analysis, Kaplan-Meier plots, time-to-event analysis, or asks about survival statistics in biomedical contexts.
Kaplan-Meier survival analysis tool for clinical and biological research. Generates publication-ready survival curves with statistical tests.
python scripts/main.py --input data.csv --time time_col --event event_col --group group_col --output results/
| Argument | Description | Required |
|---|---|---|
--input | Input CSV file path | Yes |
--time | Column name for survival time | Yes |
--event | Column name for event indicator (1=event, 0=censored) | Yes |
--group | Column name for grouping variable | Optional |
--output | Output directory for results | Yes |
--conf-level | Confidence level (default: 0.95) | Optional |
--risk-table | Include risk table in plot | Optional |
CSV with columns:
Example:
patient_id,time_months,death,treatment_group
P001,24.5,1,Drug_A
P002,36.2,0,Drug_A
P003,18.7,1,Placebo
km_curve.png: Kaplan-Meier survival curvekm_curve.pdf: Vector version for publicationssurvival_stats.csv: Statistical summary (median survival, confidence intervals)hazard_ratios.csv: Cox regression results with HR and 95% CIKaplan-Meier Estimator: Non-parametric maximum likelihood estimate of survival function
Log-Rank Test: Most widely used test for comparing survival curves
Cox Proportional Hazards: Semi-parametric regression model
lifelines: Core survival analysis librarymatplotlib, seaborn: Visualizationpandas, numpy: Data handlingscipy: Statistical testsThis skill involves advanced statistical modeling. Results should be reviewed by a biostatistician, especially for:
See references/ folder for:
| Parameter | Type | Default | Description |
|---|---|---|---|
--input | str | Required | Input CSV file path |
--time | str | Required | Column name for survival time |
--event | str | Required | |
--group | str | Required | |
--output | str | Required | Output directory for results |
--conf-level | float | 0.95 | |
--risk-table | str | Required | Include risk table in plot |
--figsize | str | '10 | |
--dpi | int | 300 |
# Basic survival curve
python scripts/main.py \
--input clinical_data.csv \
--time overall_survival_months \
--event death \
--group treatment_arm \
--output ./results/ \
--risk-table
Output includes:
| Risk Indicator | Assessment | Level |
|---|---|---|
| Code Execution | Python/R scripts executed locally | Medium |
| Network Access | No external API calls | Low |
| File System Access | Read input files, write output files | Medium |
| Instruction Tampering | Standard prompt guidelines | Low |
| Data Exposure | Output files saved to workspace | Low |
# Python dependencies
pip install -r requirements.txt