Simulation studies accompanying the paper 'All that glitters is not gold: Type-I error controlled variable selection from clinical trial data' (CPT 2024)
This repository contains example code to run simulation studies like the ones in Zimmermann et al. (2024). Due to confidentiality and privacy concerns, the data or code from the real case studies presented in the same paper cannot be shared publicly.
To install this repository from GitHub, use:
if(!require(devtools)) install.packages("devtools")
devtools::install_github("Novartis/knockoffs-cpt2024paper-simulations")To use this repository, ensure that the following packages are installed (e.g. from CRAN): bnlearn, caret, clustermq, dplyr, ggtext, ggthemes, grid, gridExtra, gtools, latex2exp, lemon, recipes, tictoc, and tidyverse
In addition, the knockofftools repository should be installed.
To do this, use:
if(!require(devtools)) install.packages("devtools")
devtools::install_github("Novartis/knockofftools")This repository is intended to be used in a high performance computing environment as it uses clustermq to run simulations in parallel.
The folder simulation_studies contains one subfolder for each simulation-based Figure in Zimmermann et al. (2024). To run the simulations and produce summary plots, run the R-Script(s) within the respective subfolder. This will also generate an .RDS file with the results in the output folder. Note that the working directory is intended to be the folder of this repository.
This repository accompanies the following publication: Zimmermann et al. (2024). The R implementation of the sequential knockoff algorithm was introduced in Kormaksson et al. (2021)
The following authors contributed to this repository:
- Matthias Kormaksson, [email protected]
- Konstantinos (Kostas) Sechidis, [email protected]
- Manuela Zimmermann, [email protected]
Please note that the content of this repository is provided for informational purposes only. The authors or Novartis make no representations or warranties of any kind, expressed or implied. Furthermore, the authors or Novartis shall not be held responsible or liable for any errors, omissions, or delays in this information or any losses, injuries, or damages arising from its display, download or use. All information is provided on an as-is basis.