rworkflows: automating reproducible practices for the R community

Despite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards sharing open-source software has been revolutionary, GitHub does not have a...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Nature communications 2024-01, Vol.15 (1), p.149-149, Article 149
Hauptverfasser: Schilder, Brian M., Murphy, Alan E., Skene, Nathan G.
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung:Despite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards sharing open-source software has been revolutionary, GitHub does not have any default built-in checks for minimal coding standards or software usability. This makes it difficult to assess the current quality R packages, or to consistently use them over time and across platforms. While GitHub-native solutions are technically possible, they require considerable time and expertise for each developer to write, implement, and maintain. To address this, we develop rworkflows ; a suite of tools to make robust continuous integration and deployment ( https://github.com/neurogenomics/rworkflows ). rworkflows can be implemented by developers of all skill levels using a one-time R function call which has both sensible defaults and extensive options for customisation. Once implemented, any updates to the GitHub repository automatically trigger parallel workflows that install all software dependencies, run code checks, generate a dedicated documentation website, and deploy a publicly accessible containerised environment. By making the rworkflows suite free, automated, and simple to use, we aim to promote widespread adoption of reproducible practices across a continually growing R community. Reproducibility is essential for the progress of research, yet achieving it remains elusive even in computational fields. Here, authors develop the rworkflows suite, making robust CI/CD workflows easy and freely accessible to all R package developers.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-023-44484-5