This is a research pipeline example. Think of it as a one-stop-shop which allows you to run the entire process from data preparation to a ready-to-submit manuscript with references in the required journal citation style. It allows us to do this entire process without ever switching software. Its major advantage lies in the reproducibility of projects and that it allows us to easily explore alternative cut-offs, definitions, or subsets of our study population. The setup is perfectly suited to be run in batch-mode server settings - settings where we send files away to high performance computing environments and recieve the result of the process later.
Download this folder and close your R session. Open the R-project file - this will trigger RStudio to open in RProject mode. Now open the main control file "00_main.R", select all code and run it. The final output will be created and stored in the "ROutput" folder.