survrm2py 0.1.0

Python translation of survRM2 for Restricted Mean Survival Time (RMST) analysis

survRM2py

survRM2py is a Python reimplementation of the popular R package survRM2 for Restricted Mean Survival Time (RMST) analysis. It is designed to achieve absolute mathematical parity with the R reference implementation.

RMST is a robust alternative to the hazard ratio for comparing survival curves, representing the average survival time up to a pre-specified time point (tau).

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Installation

Standard Python Environment

You can install the package directly from PyPI:

pip install survrm2py

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Quick Start Example

import numpy as np
import pandas as pd
from survrm2py import run_rmst

# 1. Create mock survival data
np.random.seed(42)
n = 200
data = pd.DataFrame({
    "time": np.random.exponential(scale=10, size=n),
    "event": np.random.binomial(n=1, p=0.7, size=n),
    "arm": np.random.binomial(n=1, p=0.5, size=n),
    "age": np.random.normal(loc=60, scale=10, size=n)
})

# 2. Run unadjusted and covariate-adjusted RMST at tau = 8.0
results = run_rmst(
    df=data,
    time_col="time",
    event_col="event",
    arm_col="arm",
    tau=8.0,
    covariates=["age"],
    method="ipcw_rmst2"
)

# 3. Print unadjusted differences
print(f"RMST Arm 1: {results['rmst_arm1']:.4f}")
print(f"RMST Arm 0: {results['rmst_arm0']:.4f}")
print(f"Unadjusted Diff: {results['rmst_diff_unadjusted']:.4f} (p={results['p_unadjusted']:.4f})")

# 4. View adjusted covariate summary table
print("\nAdjusted IPCW Regression Summary:")
print(results["adjusted_summary"])

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Developer Guide (Pixi)

This package uses a unified pyproject.toml with tool.pixi environment manager.

Prerequisites

Make sure you have Pixi installed:

curl -fsSL https://pixi.sh/install.sh | bash

Running Tests

The test environment automatically sets up Python, R, and installs the reference survRM2 package from CRAN.

pixi run -e test test

Building Package Distribution Files

To build the distribution packages (.whl and .tar.gz) locally in a clean sandboxed environment:

pixi run -e test build

Built files will be generated under the dist/ directory.

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License

This package is licensed under the GNU General Public License v3 or later (GPLv3+), which maintains consistency with CRAN's survRM2 licensing.

References

Uno H, Claggett B, Tian L, Inoue E, Gallo P, Miyata T, Schrag D, Takeuchi M, Uyama Y, Zhao L, Skali H, Solomon S, Jacobus S, HughesM, Packer M, Wei LJ. Moving beyond the hazard ratio in quantifying the between-group difference in survival analysis. Journal of clinical Oncology 2014, 32, 2380-2385. doi:10.1200/JCO.2014.55.2208.

Tian L, Zhao L, Wei LJ. Predicting the restricted mean event time with the subject's baseline covariates in survival analysis. Biostatistics 2014, 15, 222-233. doi:10.1093/biostatistics/kxt050.