https://github.com/rekyt/rtaxref
:package: R client to the API of French Taxonomical Reference (TAXREF)
https://github.com/rekyt/rtaxref
api api-client api-wrapper biodiversity r r-package rstats taxonomy
Last synced: about 2 months ago
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:package: R client to the API of French Taxonomical Reference (TAXREF)
- Host: GitHub
- URL: https://github.com/rekyt/rtaxref
- Owner: Rekyt
- License: gpl-3.0
- Created: 2019-03-02T09:01:53.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2022-07-21T15:11:03.000Z (almost 3 years ago)
- Last Synced: 2025-04-10T05:05:20.045Z (about 2 months ago)
- Topics: api, api-client, api-wrapper, biodiversity, r, r-package, rstats, taxonomy
- Language: R
- Homepage: https://rekyt.github.io/rtaxref/
- Size: 3.76 MB
- Stars: 5
- Watchers: 1
- Forks: 1
- Open Issues: 18
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
---
output: github_document
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%",
eval = TRUE
)
```
# rtaxref – an R client to the French Taxonomical Reference
[](https://www.repostatus.org/#active)
[](https://codecov.io/gh/Rekyt/rtaxref)
[](https://github.com/Rekyt/rtaxref/actions/workflows/R-CMD-check.yaml)
The goal of rtaxref is to provide an R client to TAXREF API,
the French Taxonomical Reference and associated database on species.
The API provides nomenclature, taxonomy, biogeographic repartition, statuses
and interactions of species. See the API documentation
[here](https://taxref.mnhn.fr/taxref-web/api/doc).
This project is still under development (especially the documentation) but most
functions should work out of the box. Please do use the
[issue tracker](https://github.com/Rekyt/rtaxref/issues) for any bug report,
suggestion, or idea.
## Installation
`rtaxref` is not yet on CRAN. However, you can install the development version of `rtaxref` from GitHub with:
```{r, eval=FALSE}
# install.packages("remotes")
remotes::install_github("Rekyt/rtaxref")
```
## Citation
`rtaxref` contains functions to retrieve data from TAXREF-Hub. The access data is released under the [Creative Commons Attribution-ShareAlike 3.0 (CC BY-SA 3.0) license](https://creativecommons.org/licenses/by-sa/3.0/). A suggestion of citation is included in `rtaxref` via `citation("rtaxref")`.
```{r citation}
citation("rtaxref")
```
## Usage
To avoid collisions with other packages all `rtaxref` functions are prefixed with `rt_*()`, for example `rt_taxa_id()` lets you access to the information about a taxon using its unique id (also called `cdNom` in TAXREF):
```{r rt_taxa_id}
library("rtaxref")
rt_taxa_id(id = 101027)
```
You get information about the taxon related to taxonomy, the referance name, vernacular names as well as distribution information.
`rt_taxa_search()` let's you search a taxon with different criteria:
```{r rt_taxa_search}
rt_taxa_search(sciname = "Helianthus annuus")
```
You a full list of functions included in `rtaxref` by going to the [`rtaxref` website](https://rekyt.github.io/rtaxref).
## Code of Conduct
Please note that the 'rtaxref' project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
## Related projects
Other packages lets you work with taxonomical information from relevant databases:
- [`taxize`](https://github.com/ropensci/taxize) let's you work with many databases as well as clean a list of taxon names,
- [`ritis`](https://github.com/ropensci/ritis) a client for another taxonomic database,
- [`taxa`](https://github.com/ropensci/taxa) a package that proposes a reference class for taxonomic information (maybe used by `rtaxref` in the future),
- [CRAN taxonomy Task View](https://github.com/ropensci/taxonomy) references many related packages that are used to work with taxonomic information.