https://github.com/LimaRAF/plantR
An R Package for Managing Species Records from Biological Collections
https://github.com/LimaRAF/plantR
biodiversity biological-data data-cleaning data-downloader data-mining gbif herbarium r r-package
Last synced: about 1 month ago
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An R Package for Managing Species Records from Biological Collections
- Host: GitHub
- URL: https://github.com/LimaRAF/plantR
- Owner: LimaRAF
- License: gpl-3.0
- Created: 2019-06-16T11:10:59.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2026-04-02T18:25:59.000Z (3 months ago)
- Last Synced: 2026-05-13T22:03:41.180Z (about 2 months ago)
- Topics: biodiversity, biological-data, data-cleaning, data-downloader, data-mining, gbif, herbarium, r, r-package
- Language: R
- Homepage:
- Size: 596 MB
- Stars: 20
- Watchers: 2
- Forks: 7
- Open Issues: 14
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
- open-sustainable-technology - plantR - An R Package for Managing Species Records from Biological Collections. (Biosphere / Plants and Vegetation)
README
---
output: github_document
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# plantR
[](https://github.com/LimaRAF/plantR/actions/workflows/R-CMD-check.yaml)
[](https://github.com/LimaRAF/plantR/actions/workflows/test-coverage.yaml)
An R Package for Managing Species Records from Biological Collections
### Description
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](https://github.com/LimaRAF/plantR/blob/dev/vignettes/plantR.pdf)
and detailed [Tutorial](https://github.com/LimaRAF/plantR/blob/dev/vignettes/articles/plantR_tutorial.pdf) for more details.
#### Installation
The package can be installed in R from [github](https://github.com/) with:
``` {r, eval = FALSE}
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:
```{r, eval = FALSE}
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.
##### Bug report and suggestions
The plantR project is hosted on [GitHub](https://github.com/LimaRAF/plantR/).
Please report any bugs and suggestions of improvements for the package
[here](https://github.com/LimaRAF/plantR/issues).
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.
### Authors and contributors
Renato A. F. de Lima, Sara R. Mortara, Andrea Sánchez-Tapia, Guilherme
S. Grittz, Mali Oz Salles, Hans ter Steege & Marinez F. de Siqueira
### Citation
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
### Funding
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). The improvement of the package internal
dictionaries was supported by the INCT Synthesis for Biodiversity in
Amazonia (CNPq/MCTIC/INCT-2022, process No 406767/2022-0).
### Acknowledgements
We thank Sidnei Souza from CRIA/speciesLink for his help with the web
API. We also thank the [CNCFlora](http://cncflora.jbrj.gov.br) and the
[TreeCo database](http://labtrop.ib.usp.br/doku.php?id=projetos:treeco:start)
for providing many of the localities used to construct the package
gazetteer. We thank the Harvard University Herbarium, Brazilian
Herbaria Network, American Society of Plant Taxonomists and the
Taxonomic Catalogue of the Fauna of Brazil, 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. We are
greatly in debt to Eduardo Pinto and André Montanari, who greatly
improved the quantity and quality of the dictionaries available in the
package.