Palaeoverse: A community-driven R package to support palaeobiological analysis

Jones, Lewis A.; Gearty, William; Allen, Bethany J.; Eichenseer, Kilian; Dean, Christopher D.; Galván, Sofía; Kouvari, Miranta; Godoy, Pedro L.; Nicholl, Cecily S. C.; Buffan, Lucas; Dillon, Erin M.; Flannery-Sutherland, Joseph T.; Chiarenza, Alfio Alessandro

Abstract

The open-source programming language ‘R' has become a standard tool in the palaeobiologist's toolkit. Its popularity within the palaeobiological community continues to grow, with published articles increasingly citing the usage of R and R packages. However, there are currently a lack of agreed standards for data preparation and available frameworks to support the implementation of such standards. Consequently, data preparation workflows are often unclear and not reproducible, even when code is provided. Moreover, due to a lack of code accessibility and documentation, palaeobiologists are often forced to ‘reinvent the wheel’ to find solutions to issues already solved by other members of the community. Here, we introduce palaeoverse, a community-driven R package to aid data preparation and exploration for quantitative palaeobiological research. The package is freely available and has three core principles: (1) streamline data preparation and analyses; (2) enhance code readability; and (3) improve reproducibility of results. To develop these aims, we assessed the analytical needs of the broader palaeobiological community using an online survey, in addition to incorporating our own experiences. In this work, we first report the findings of the survey, which shaped the development of the package. Subsequently, we describe and demonstrate the functionality available in palaeoverse and provide usage examples. Finally, we discuss the resources we have made available for the community and our future plans for the broader Palaeoverse project.
palaeoverse is a community-driven R package for palaeobiology, developed with the intention of bringing palaeobiologists together to establish agreed standards for high-quality quantitative research. The package provides a user-friendly platform for preparing data for analysis with well-documented open-source code to enhance transparency. The functionality available in palaeoverse improves code reproducibility and accessibility, which is beneficial for both the review process and future research.

Citation

Jones, L. A., Gearty, W., Allen, B. J., Eichenseer, K., Dean, C. D., Galván, S., …Chiarenza, A. A. (2023). Palaeoverse: A community-driven R package to support palaeobiological analysis. Methods in Ecology and Evolution, 14(9), 2189-2510. https://doi.org/10.1111/2041-210X.14099

• Journal Article Type: Article
• Acceptance Date: Mar 10, 2023
• Online Publication Date: Apr 13, 2023
• Publication Date: Apr 13, 2023
• Deposit Date: Feb 7, 2024
• Publicly Available Date: Feb 7, 2024
• Journal: Methods in Ecology and Evolution
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• Volume: 14
• Issue: 9
• Pages: 2189-2510
• DOI: https://doi.org/10.1111/2041-210X.14099
• Public URL: https://durham-repository.worktribe.com/output/2228756