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.

Installation

rtaxref is not yet on CRAN. However, you can install the development version of rtaxref from GitHub with:

Usage

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

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):

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:

rtaxref::rt_taxa_search(sciname = "Helianthus annuus")
#> # A tibble: 9 x 61
#>       id referenceId parentId scientificName authority fullName
#>    <int>       <int>    <int> <chr>          <chr>     <chr>   
#> 1 101027      101027   193133 Helianthus an… L., 1753  Heliant…
#> 2 135249      101027       NA Helianthus an… L., 1753  Heliant…
#> 3 773544      101027       NA Helianthus an… (Heiser)… Heliant…
#> 4 773545      101027       NA Helianthus an… (Douglas… Heliant…
#> 5 773546      101027       NA Helianthus an… Heiser, … Heliant…
#> 6 772409      101027       NA Helianthus an… (Douglas… Heliant…
#> 7 613531      613531   101027 Helianthus an… L., 1753  Heliant…
#> 8 613530      613530   101027 Helianthus an… (DC.) Co… Heliant…
#> 9 621487      613530       NA Helianthus an… Thell.    Heliant…
#> # … with 55 more variables: fullNameHtml <chr>, rankId <chr>,
#> #   rankName <lgl>, 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>, vernacularGroup1 <lgl>,
#> #   vernacularGroup2 <lgl>, habitat <chr>, fr <chr>, gf <lgl>, mar <chr>,
#> #   gua <chr>, sm <chr>, sb <chr>, spm <chr>, may <chr>, epa <lgl>,
#> #   reu <chr>, sa <lgl>, ta <lgl>, nc <chr>, wf <lgl>, pf <chr>,
#> #   cli <lgl>, taxrefVersion <chr>, self.href <chr>, reference.href <chr>,
#> #   parent.href <chr>, classification.href <chr>, synonyms.href <chr>,
#> #   children.href <chr>, vernacularNames.href <chr>, media.href <chr>,
#> #   status.href <chr>, interactions.href <chr>, taxrefHistory.href <chr>,
#> #   externalIds.href <chr>, taxonomicRank.href <chr>, habitat.href <chr>,
#> #   taxrefUri.href <chr>, inpnWebpage.href <chr>

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

Dependency network (Imports only)

Dependency network (Imports and Suggests)

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.