survival-analysis-km

# Survival Analysis (Kaplan-Meier)

Kaplan-Meier survival analysis tool for clinical and biological research. Generates publication-ready survival curves with statistical tests.

## Features

- **Kaplan-Meier Curve Generation**: Publication-quality survival plots with confidence intervals
- **Statistical Tests**: Log-rank test, Wilcoxon test, Peto-Peto test
- **Hazard Ratios**: Cox proportional hazards regression with 95% CI
- **Summary Statistics**: Median survival time, restricted mean survival time (RMST)
- **Multi-group Analysis**: Supports 2+ comparison groups
- **Risk Tables**: Optional at-risk table below curves

## Usage

### Python Script

```bash
python scripts/main.py --input data.csv --time time_col --event event_col --group group_col --output results/
```

### Arguments

| 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 |

### Input Format

CSV with columns:
- **Time column**: Numeric, time to event or censoring
- **Event column**: Binary (1 = event occurred, 0 = censored/right-censored)
- **Group column**: Categorical variable for stratification

Example:
```csv
patient_id,time_months,death,treatment_group
P001,24.5,1,Drug_A
P002,36.2,0,Drug_A
P003,18.7,1,Placebo
```

### Output Files

- `km_curve.png`: Kaplan-Meier survival curve
- `km_curve.pdf`: Vector version for publications
- `survival_stats.csv`: Statistical summary (median survival, confidence intervals)
- `hazard_ratios.csv`: Cox regression results with HR and 95% CI
- `logrank_test.csv**: Pairwise comparison p-values
- `report.txt**: Human-readable summary report

## Tec...