plantR

An R Package for Managing Species Records from Biological Collections.
https://github.com/limaraf/plantr

Category: Biosphere
Sub Category: Plants and Vegetation

Keywords

biodiversity biological-data data-cleaning data-downloader data-mining gbif herbarium r r-package

Last synced: about 9 hours ago
JSON representation

Repository metadata

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 (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2026-04-02T18:25:59.000Z (about 1 month ago)
• Last Synced: 2026-05-05T18:04:06.953Z (9 days 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: 13
• Releases: 2
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • License: LICENSE

README.Rmd

          ---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```


# plantR



[![R-CMD-check: master](https://github.com/LimaRAF/plantR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/LimaRAF/plantR/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://github.com/LimaRAF/plantR/actions/workflows/test-coverage.yaml/badge.svg)](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.

        

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Owner metadata

• Name: Renato Lima
• Login: LimaRAF
• Email:
• Kind: user
• Description:
• Website: https://renatodelima.com/
• Location: Piracicaba, Brazil
• Twitter: treeco_db
• Company: Universidade de São Paulo
• Icon url: https://avatars.githubusercontent.com/u/15707374?u=2f28ad9bd995cea43c1e4bb85bb82edce59dbd6b&v=4
• Repositories: 4
• Last ynced at: 2024-04-23T11:36:56.103Z
• Profile URL: https://github.com/LimaRAF

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GitHub Events

Total

• Delete event: 2
• Pull request event: 34
• Fork event: 4
• Issues event: 119
• Watch event: 3
• Issue comment event: 107
• Push event: 56

Last Year

• Pull request event: 12
• Issues event: 37
• Watch event: 1
• Issue comment event: 46
• Push event: 26

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Committers metadata

Last synced: 2 days ago

Name	Email	Commits
raflima1981	r****a@u****r	429
Andrea Sánchez Tapia	k****i@g****m	90
saramortara	s****a@g****m	39
Mali Oz	m****s@g****m	12
Guilherme S. Grittz	g****z@o****m	11

Committer domains:

• usp.br: 1

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Issue and Pull Request metadata

Last synced: 2 days ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/limaraf/plantr

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Dependencies

Score: 5.10594547390058