An R Package for Managing Species Records from Biological Collections
The package plantR provides tools for downloading, processing, cleaning, validating, summarizing and exporting records of species occurrences from biological collections.
Please read the package Introduction and detailed Tutorial for more details.
The package can be installed in R from github with:
library("remotes")
install_github("LimaRAF/plantR")
library("plantR")You can also download the development (and probably most up-to-date) version of the package with:
install_github("LimaRAF/plantR", ref = "dev")
library("plantR")If you run into errors while installing the package, please check the detailed package introduction for alternatives.
The plantR project is hosted on GitHub. Please report any bugs and suggestions of improvements for the package here.
The package gazetteer and the list of taxonomists are constantly being improved. If you want to contribute with regional gazetteers or with missing names of taxonomists, please e-mail raflima@usp.br.
Renato A. F. de Lima, Sara R. Mortara, Andrea Sánchez-Tapia, Guilherme S. Grittz, Hans ter Steege & Marinez F. de Siqueira
Lima, R.A.F., Sánchez-Tapia, A., Mortara, S.R., ter Steege, H., Siqueira, M.F. (2023). plantR: An R package and workflow for managing species records from biological collections. Methods in Ecology and Evolution 14(2): 332-339. https://doi.org/10.1111/2041-210X.13779
The development of this package was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 795114, by the Coordination for the Improvement of Higher Education Personnel (CAPES, process 88887.145924/2017-00), and by the ‘Instituto Nacional da Mata Atlântica’ (INMA).
We thank Sidnei Souza from CRIA/speciesLink for his help with the web API. We also thank the CNCFlora and the TreeCo database for providing many of the localities used to construct the package gazetteer. We thank the Harvard University Herbarium, Brazilian Herbaria Network and the American Society of Plant Taxonomists, who were main sources to compile the current list of taxonomists. We also thank Vinícius C. Souza (ESALQ/USP), who helped to validate and improve the list of plant taxonomists used in the package, João Vieira for suggestions of code fixes and updates, and André L. de Gasper and Leila Meyer, for their valuable suggestions on how to make this package more useful and flexible for collection managers, taxonomists and ecologists.