README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

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

<img src="https://raw.githubusercontent.com/liibre/plantR_logo/master/figs/plantR_logo.png?token=AA4OYDE3TMIXBWRYVMNCINC72PIUY" align="right" alt="" width="120" />

# plantR


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 plant species occurrences from
biological collections. Please read the Introduction and Tutorial of the package
for more details.
 
#### Installation

The package can be installed in R from [github](https://github.com/) with:

``` r
library("remotes")
install_github("LimaRAF/plantR")
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, Hans ter Steege &
Marinez F. de Siqueira

### Citation

Lima, R.A.F., Sánchez-Tapia, A., Mortara, S.R., ter Steege, H., Siqueira, M.F.
(2021). *plantR*: An R package and workflow for managing species records from
biological collections. Methods in Ecology and Evolution.
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).

### 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 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, 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 and taxonomists.