palaeoverse: A community‐driven R package to support palaeobiological analysis

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.

Turtle body size evolution is determined by lineage‐specific specializations rather than global trends

“…The figures presented by this study were made using the R packages palaeoverse (Jones et al, 2023 ) and deeptime (Gearty, 2023 ).…”

Spatial standardization of taxon occurrence data—a call to action

“…Additionally, many spatial analysis scripts in paleobiology and ecology have used functions from the R packages sp and raster, which were recently deprecated, and the dependent packages maptools, rgdal, and rgeos, which were retired in 2023. There is a need for formal, actively maintained tool kits to perform common spatial analysis steps in paleobiology, similar to the divDyn and palaeoverse packages of tools to streamline common data manipulation tasks (e.g., time-binning) and perform common calculations (e.g., extinction and origination rates) in paleobiology (Kocsis et al 2019; Jones et al 2023).…”

Spatial standardization of taxon occurrence data—a call to action

“…Additionally, many spatial analysis scripts in paleobiology and ecology have used functions from the R packages sp and raster, which were recently deprecated, and the dependent packages maptools, rgdal, and rgeos, which were retired in 2023. There is a need for formal, actively maintained tool kits to perform common spatial analysis steps in paleobiology, similar to the divDyn and palaeoverse packages of tools to streamline common data manipulation tasks (e.g., time-binning) and perform common calculations (e.g., extinction and origination rates) in paleobiology (Kocsis et al 2019;Jones et al 2023).…”