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Validation of prediction models in presence of competing risks: a guide through modern methods

R Code repository for the manuscript 'Validation of prediction models in presence of competing risks: a guide through modern methods' published in BMJ.

The repository contains the following code:

  • Prediction_CSC_minimal.R : the companion R script for the manuscript. This script reproduces all main tables and figures of the manuscript. The file evaluates the performance of a cause specific hazards prediction model. Data are available here.

  • Prediction_CSC.md : a markdown document containing a more in-depth version of the script, with details on model development, descriptive tables and supplementary plots. This document requires installing several add-on packages that are not needed to run the minimal script. The RMarkdown source code (.Rmd) is here. Additional functions useful for this script are available here.

  • Additional code to alternatively develop a competing risk prediction model using the subdistribution hazard approach (Fine & Gray) is here. The Rmarkdown source code (.Rmd) is here. A more concise R source code (.R) is here.

  • sharing_CSC_model.R : example/template of how to share a cause-specific hazards prediction model for external validation, without having to share the original development data.

Usage

If you are git user, you can clone the directory by using

git clone https://github.com/survival-lumc/ValidationCompRisks.git

Otherwise, you can simply download a zip file containing the directory by clicking Code -> Download ZIP at the top-right of this Github page. Extract the zipped files to a directory of your choice.

Afterwards, you can double-click the ValidationCompRisks.Rproj file to open an Rstudio session in the directory you have just downloaded. This will ensure all file-paths called in the files are maintained. The minimal script and the .Rmd files can now be executed.

Contributions

Name Affiliation Role
Daniele Giardiello University of Milan-Bicocca (IT) Author .Rmd files/maintainer
Edouard Bonneville Leiden University Medical Center (NL) Author minimal .R and CSC sharing scripts/review of .Rmd scripts
Nan van Geloven Leiden University Medical Center (NL) Review of both .R and .Rmd scripts
Maarten van Smeden University Medical Centre Utrecht (NL) Review of .Rmd script