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.

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.