This repository contains code to reproduce results as given in the paper "Data-Adaptive Automatic Threshold Calibration for Stability Selection" (Huang et al. 2026). For any questions please email martin.huang@sydney.edu.au.
We provide all simulation results.
- For artificial simulations, the code is located under "Artificial-Simulations.R", "Artificial-Simulations-Unif", and "Artificial-Simulations-t".
- For applied simulations, the code is located under "Proteomics-Simulations.R" and "Diabetes-Simulations.R".
We also provide the distribution analysis of the exclusion probability threshold under "Eta-Proteomics-Diabetes.R and "Artificial-Simulations.R" for the respective datasets. FDR analysis is found under "FDR-Simulations.R".
To reproduce the figures, we provide RData files in the "Data" folder, and also provide code in their respective scripts. I.e. to reproduce figures in the Proteomics simulations, the code are found at the end of "Proteomics-Simulation.R".
All of these scripts require the use of user-defined functions given in "Functions.R".
Please note that we are aware of an issue whereby the stabsel function does not work in Positron. To avoid this issue, we recommend executing the code in RStudio.
We provide the plasma proteomics dataset as "Proteomics.csv" in the folder "Data", and was sourced from Rumer et al. (2022). The diabetes dataset can be accessed through the R-package lars and data(diabetes). The artificial data generation process can be located in "Functions.R"
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