FAIRification of pharmacoepidemiological research using Git

Transparency and reproducibility in conducting healthcare database studies in pharmacoepidemiology are critical scientific requirements for meaningful research. To increase the adoption of transparent and reproducible workflows in real-world evidence (RWE) studies using the version control systems (VCS), this tutorial aims to give a practical introduction tailored for pharmacoepidemiologists on how to set up, structure, and implement workflows using Git, the most frequently used VCS to date.

About

This repository hosts all documents and files for the manuscript project on...

The FAIRification of pharmacoepidemiological research: A practical introduction to reproducible analytical workflows using git and R

This manuscript was published in the journal Pharmacoepidemiology and Drug Safety (PDS) special issue focusing on Pharmacoepidemiology Research Reproducibility

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Advanced readings on Git and other resources

• Main Git website to download and learn more about Git: https://git-scm.com

• Pro Git by Scott Chacon and Ben Straub.

• Comprehensive guide on the use of Git in combination with R: https://happygitwithr.com/

• Cheatsheet on most important Git commands: https://education.github.com/git-cheat-sheet-education.pdf

• GitHub Desktop App: https://desktop.github.com/

• Git manual by Atlassian (provider of the Bitbucket platform): https://www.atlassian.com/git

• Coursera courses:

  • Introduction to Git and GitHub (Google)

  • Version Control with Git (Atlassian)

  • Getting Started with Git and GitHub (IBM)

  • Making Data Science Work for Clinical Reporting (Genentech)

• Quarto (open-source scientific and technical publishing system for reproducible research): https://quarto.org

• Choosing a suitable license for a remote repository: Public repositories need to be licensed to be truly open source. If no license is provided, the work is by default under exclusive copyright. The website https://choosealicense.com provides an excellent overview of the different types of licenses.

• Useful Git repositories for observational healthcare research:

  • Division of Pharmacoepidemiology and Pharmacoeconomics: https://gitlab-scm.partners.org/drugepi

  • Observational Health Data Sciences and Informatics (OHDSI): https://github.com/OHDSI

  • Darwin EU® Private Development Repository: https://github.com/darwin-eu-dev

  • Pharmaverse (Network of developers of curated open source R packages for clinical reporting): https://pharmaverse.org & https://github.com/pharmaverse/

Repository details

This repository contains the following sub-directories/-files:

• README.md: Short description and information about the project.

• manuscript: Sub-directory where manuscript and supplementary material are stored.

• renv: Project-specific R package library. Fore more information, please visit the renv website.

• renv.lock: renv lockfile that keeps track of all R packages and version.

• .gitignore: File to specify which files should not be tracked via git.

• .Rprofile: Environment file for R projects to store things like paths or keys (you can also setup an .Renviron)

• .git: Sub-directory where all Git changes are tracked

Dependencies

To reproduce R scripts and Quarto files in this repository, git clone or fork it and run renv::restore().