PH & RMST Efficiency

Overview

This repository contains the code needed to reproduce all outputs presented in the paper titled "Efficiency of Nonparametric Two-Sample Superiority Tests Based on Restricted Mean Survival Time versus The Log-Rank Test Under Proportional Hazards." The repository includes simulations, case studies, and supporting functions for data analysis.

Authors

• Dominic Magirr (Maintainer)
• Craig Wang
• Xinlei Deng
• Mark Baillie

Repository Structure

The repository is organized into the following main directories:

1. data/

This directory contains all datasets utilized in the analyses presented in the paper:

• CLEOPATRA_2a.rda: Data from the CLEOPATRA trial.
• leader_km.csv: Data for the LEADER case study.
• sustain_idp.csv: Data for the SUSTAIN case study.
• poplar.csv: Data for the POPLAR case study.

2. reproduce_results/

This directory includes all the scripts required to reproduce the results in the paper. It contains the following subfolders:

• case_studies/: Code for analyzing clinical trial data presented as case studies.
• censoring/: Code for illustrating the recruitment rate and censoring distributions.
• simulation/: Scripts to perform simulation studies discussed in the paper.
• weight_functions/: Code for applying the weight functions used in the analyses.

3. src/

This folder includes helper functions used across various parts of the analysis:

• sim_helper_fns.R: Contains helper functions for simulations.
• survRM2_fns.R: Functions for calculating Restricted Mean Survival Time (RMST) and related survival analyses.

Installation and Setup

To run the analysis, you need to have R installed, along with the necessary R packages. You can install the required packages and run the main analysis by executing the provided script:

source("00_install_required_packages.R")

This script will install all the dependencies automatically.

Reproducing the Results

To reproduce the results presented in the paper, follow these steps:

1. Clone the repository to your local machine:

   git clone https://github.com/yourusername/ph-rmst-efficiency.git
   cd ph-rmst-efficiency

2. Install the required R packages by running the following command within your R session:

   source("00_install_required_packages.R")

3. Run the main script to generate all figures and results. Note that for full simulation studies, you will need to toggle the relevant simulation flag:

   source("01_generate_figures.R")

   The script includes both figure generation and case study analyses. Make sure to configure the settings as needed before running simulations, as these can be computationally intensive.

Citation

If you use this code or data in your research, please cite the following paper:

Magirr, D., Wang, C., Deng, X., Morris, T., & Baillie, M. (2024). Efficiency of Nonparametric Two-Sample Superiority Tests Based on Restricted Mean Survival Time versus The Log-Rank Test Under Proportional Hazards. (Journal To Be Confirmed).

Notes and Considerations

• Computational Requirements: Some scripts, particularly the simulation scripts, may require significant computational resources. We recommend running these scripts on a machine with adequate memory and processing power.

Contact

For questions or issues related to this repository, please contact the maintainer.