Simulation Code and Results

This repository contains the simulation code and results for the following paper: "Evaluating diagnostic accuracy of binary medical tests in multi-reader multi-case study."

The materials are organized to reproduce the simulation results in Sections 2.3 and 5 of the manuscript.

There are two main folders in this repository, as follows:

• Simulation in Sec 2.3: Contains simulation code and results related to Section 2.3 of the manuscript.
• Simulation in Sec 5: Contains simulation code and results related to Section 5 of the manuscript.

For details on each folder and the files within it, please refer to the descriptions below.

Simulation in Sec 2.3

This folder contains R scripts, RData, and result (Table and Figure) files used to reproduce simulation results for Section 2.3 in the main manuscript.

Below is a brief description of each file in this folder:

📁 Folder Contents

File	Description
Simulation in Sec 2.3.R	R code to perform simulation
Simulation in Sec 2.3.RData	Output files (.RData) from Simulation in Sec 2.3.R
Simulation in Sec 2.3.xlsx	Tables S4 and S5 in the Supporting Information
Simulation in Sec 2.3_n100_b2.pdf	Figure S1 in the Supporting Information
Simulation in Sec 2.3_n100_b3.pdf	Figure S2 in the Supporting Information
Simulation in Sec 2.3_n500_b2.pdf	Figure S3 in the Supporting Information
Simulation in Sec 2.3_n500_b3.pdf	Figure S4 in the Supporting Information
Summary and plot for simulation in Sec 2.3.R	R code to output all simulation results

🔍 Additional Notes

• For detailed simulation settings, please refer to Section S2.2 of the Supporting Information.
• Make sure to specify an appropriate working directory before running the code.
• All simulation studies were conducted on the x86_64-pc-linux-gnu (64-bit) platform, running under Ubuntu 22.04.3 LTS, utilizing 100 CPU cores through parallel processing, and took approximately 13 minutes to complete (for a total of 6 combinations).

Simulation in Sec 5

This folder contains R scripts, RData, and result (Table and Figure) files used to reproduce simulation results for Section 5 of the manuscript.

Below is a brief description of each file in this folder:

📁 Folder Contents

File	Description
Simulation in Sec 5.R	R code to perform simulation
Simulation in Sec 5.xlsx	Tables S6 and S7 in the Supporting Information
Simulation in Sec 5_b0(2.5)_b2(1)_b3(1)_n100_b2.pdf	Figure 1 in the main manuscript
Simulation in Sec 5_b0(2.5)_b2(1)_b3(1)_n100_b3.pdf	Figure S5 in the Supporting Information
Simulation in Sec 5_b0(2.5)_b2(1)_b3(1)_n500_b2.pdf	Figure S6 in the Supporting Information
Simulation in Sec 5_b0(2.5)_b2(1)_b3(1)_n500_b3.pdf	Figure S7 in the Supporting Information
Summary and plot for simulation in Sec 5.R	R code to output all simulation results

📥 Download RData file

• The RData file size is too large to be uploaded directly to this repository (about 895MB).
• Therefore, you can download the Simulation.in.Sec.5.RData file (output files (.RData) from Simulation in Sec 5.R) from the latest release.
• Before loading the downloaded file in R, you must change the file name from Simulation.in.Sec.5.RData to Simulation in Sec 5.RData.

🔍 Additional Notes

• For detailed simulation settings, please refer to Section 5 in the main manuscript.
• Make sure to specify an appropriate working directory before running the code.
• The currently uploaded results are for the only combination reported in the paper.
• To see results for other combinations, see the results after modifying "beta_0_v", "beta_2k_v", and "beta_3k_v" values ​​in lines 42–44 of Summary and plot for simulation in Sec 5.R.
• All simulation studies were conducted on the x86_64-pc-linux-gnu (64-bit) platform, running under Ubuntu 22.04.3 LTS, utilizing 100 CPU cores through parallel processing, and took approximately 12 hours to complete (for a total of 288 combinations).