Skip to main content

Table 1 Sample principle of a workflow for RR with a standardized folder structure

From: Teaching reproducible research for medical students and postgraduate pharmaceutical scientists

Main folder

Contents

Comment on item

Project name

 

Naming according to recurring pattern, which may include initials of the researcher and the date

 └

Readme

Mandatory (text) file with important project information on prerequisites, scientific and technical background, and an instruction how to run the project code. Can also include a list of necessary software (package) versions, if not supplied as a separate file

 └

Folder “data”

Folder with (raw) data or preprocessed data

 └

Folder “lib”

Folder for storing literature or cross-project scripts (e.g., R functions, R packages, …)

 └

Folder “results”

Folder for saving results of any kind (tables, figures, R-images, …)

 └

Folder “src”

Folder with all executable [“source()”] files

 └

Folder “paper”

Folder for storing publication drafts of any kind (e.g., Word documents, Markdown results, Shiny apps, …)

 └

Folder “old”

Optional collection folder for old version of scripts or similar

 └

Make

Central executable files for reproduction of the project