rworkflows: automating reproducible practices for the R community
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Published version
Author(s)
Schilder, Brian
Murphy, Alan
Skene, Nathan
Type
Journal Article
Abstract
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.
Date Issued
2024-01-02
Date Acceptance
2023-12-14
Citation
Nature Communications, 2024, 15
ISSN
2041-1723
Publisher
Nature Portfolio
Journal / Book Title
Nature Communications
Volume
15
Copyright Statement
© The Author(s) 2024. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
License URL
Publication Status
Published
Article Number
ARTN 149