In Rekyt/rtaxref: An R client for TaxRef the French Taxonomical Database

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rtaxref – an R client to the French Taxonomical Reference

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.

This project is still under development (especially the documentation) but most functions should work out of the box. Please do use the issue tracker 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:

# 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. A suggestion of citation is included in rtaxref via citation("rtaxref").

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):

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:

rt_taxa_search(sciname = "Helianthus annuus")

You a full list of functions included in rtaxref by going to the rtaxref website.

Code of Conduct

Please note that the 'rtaxref' project is released with a Contributor Code of Conduct. 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 let's you work with many databases as well as clean a list of taxon names,
ritis a client for another taxonomic database,
taxa a package that proposes a reference class for taxonomic information (maybe used by rtaxref in the future),
CRAN taxonomy Task View references many related packages that are used to work with taxonomic information.