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")
#> 
#> To cite this package in publications, please use:
#> 
#>   Grenié M, Gruson H (2022). _rtaxref: An R Client for TAXREF the
#>   French Taxonomical Reference API_. R package version 0.1.0,
#>   <https://github.com/Rekyt/rtaxref>.
#> 
#> Please also cite the data provider:
#> 
#>   TAXTREF (2022). Data released under the Creative Commons
#>   Attribution-ShareAlike 3.0 (CC BY-SA 3.0) license,
#>   <https://taxref.mnhn.fr/taxref-web/accueil>.
#> 
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.

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)
#> # A tibble: 1 × 46
#>       id referenceId parentId scientificName    authority fullName  fullNameHtml
#>    <int>       <int>    <int> <chr>             <chr>     <chr>     <chr>       
#> 1 101027      101027   193133 Helianthus annuus L., 1753  Helianth… <i>Helianth…
#> # … with 39 more variables: rankId <chr>, rankName <chr>, referenceName <chr>,
#> #   referenceNameHtml <chr>, frenchVernacularName <chr>,
#> #   englishVernacularName <chr>, genusName <chr>, familyName <chr>,
#> #   orderName <chr>, className <chr>, phylumName <lgl>, kingdomName <chr>,
#> #   vernacularGenusName <lgl>, vernacularFamilyName <lgl>,
#> #   vernacularOrderName <lgl>, vernacularClassName <chr>,
#> #   vernacularPhylumName <lgl>, vernacularKingdomName <chr>, …

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")
#> # A tibble: 9 × 62
#>       id referenceId parentId scientificName     authority fullName fullNameHtml
#>    <int>       <int>    <int> <chr>              <chr>     <chr>    <chr>       
#> 1 773546      101027       NA Helianthus annuus… Heiser, … Heliant… <i>Helianth…
#> 2 772409      101027       NA Helianthus annuus… (Douglas… Heliant… <i>Helianth…
#> 3 613531      613531   101027 Helianthus annuus… L., 1753  Heliant… <i>Helianth…
#> 4 613530      613530   101027 Helianthus annuus… (DC.) Co… Heliant… <i>Helianth…
#> 5 101027      101027   193133 Helianthus annuus  L., 1753  Heliant… <i>Helianth…
#> 6 135249      101027       NA Helianthus annuus… L., 1753  Heliant… <i>Helianth…
#> 7 773544      101027       NA Helianthus annuus… (Heiser)… Heliant… <i>Helianth…
#> 8 773545      101027       NA Helianthus annuus… (Douglas… Heliant… <i>Helianth…
#> 9 621487      613530       NA Helianthus annuus… Thell.    Heliant… <i>Helianth…
#> # … with 55 more variables: rankId <chr>, rankName <chr>, referenceName <chr>,
#> #   referenceNameHtml <chr>, frenchVernacularName <chr>,
#> #   englishVernacularName <chr>, genusName <chr>, familyName <chr>,
#> #   orderName <chr>, className <chr>, phylumName <lgl>, kingdomName <chr>,
#> #   vernacularGenusName <lgl>, vernacularFamilyName <lgl>,
#> #   vernacularOrderName <lgl>, vernacularClassName <chr>,
#> #   vernacularPhylumName <lgl>, vernacularKingdomName <chr>, …

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.

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.