Package: rtaxref 0.1.0

rtaxref: An R client for TaxRef the French Taxonomical Database

Provides an R client to the TaxRef API <https://taxref.mnhn.fr/taxref-web/api/doc>, the French Taxonomical Reference Database which indexes names of species with unique identifiers as well as conservation statuses, biological interactions and taxonomic relationships.

Authors:Matthias Grenié [aut, cre], Hugo Gruson [aut]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rtaxref/json (API)

# Install 'rtaxref' in R:

install.packages('rtaxref', repos = c('https://rekyt.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rekyt/rtaxref/issues

On CRAN:

api api-client api-wrapper biodiversity taxonomy

3.54 score 7 stars 4 scripts 36 exports 18 dependencies

Last updated from:40e7cf676e. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	114
source / vignettes	OK	197
linux-release-x86_64	OK	136
macos-release-arm64	OK	87
macos-oldrel-arm64	OK	83
windows-devel	OK	105
windows-release	OK	77
windows-oldrel	OK	81
wasm-release	OK	105

Exports:rt_biogeo_status rt_external_db rt_habitats rt_interactions_find_type rt_interactions_opgroup rt_interactions_search rt_interactions_type rt_languages rt_operational_groups rt_source_uses rt_sources_find_term rt_sources_id rt_sources_match rt_status_find_type rt_status_opgroup rt_status_search rt_status_type rt_taxa_autocomplete rt_taxa_children rt_taxa_externalids rt_taxa_factsheet rt_taxa_from_externalids rt_taxa_fuzzymatch rt_taxa_id rt_taxa_interactions rt_taxa_media rt_taxa_parent rt_taxa_search rt_taxa_sources rt_taxa_status rt_taxa_synonyms rt_taxa_taxrefhistory rt_taxa_vernacular rt_taxo_ranks rt_taxref_versions rt_vernacular_groups

Dependencies:askpass cli curl glue httr jsonlite lifecycle magrittr mime openssl pillar pkgconfig R6 rlang sys tibble utf8 vctrs

Introduction to rtaxref

Searching for a taxon name | Retrieving the status of species | Additional info | Getting interaction data | Linking this information to other databases

Rendered fromrtaxref.Rmdusingknitr::rmarkdown

Last update: 2022-06-04
Started: 2022-06-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Retrieve biogeographic statuses used in TAXREF	rt_biogeo_status
Retrieve external DBs referenced in TAXREF	rt_external_db
Retrieve habitats used in TAXREF	rt_habitats
Retrieve the status of all Taxa according to a Status Type	rt_interactions_find_type
Retrieve the interactions of all Taxa in an Operational Group	rt_interactions_opgroup
Search Interactions based on a list of criteria	rt_interactions_search
Retrieve Interactions Types used in TAXREF	rt_interactions_type
Retrieve the languages used in TAXREF	rt_languages
Retrieve operational groups used in TAXREF	rt_operational_groups
Retrieve the list of source uses in TAXREF	rt_source_uses
Search a source from a term	rt_sources_find_term
Retrieve a source of taxonomic information using its id	rt_sources_id
Search a source from a citation by fuzzy matching	rt_sources_match
Retrieve the status of all Taxa according to a Status Type	rt_status_find_type
Retrieve the status of all Taxa in an Operational Group	rt_status_opgroup
Search statuses based on a list of criteria	rt_status_search
Retrieve Status Types Used in TAXREF	rt_status_type
Retrieve Taxon ID from partially matching its Name	rt_taxa_autocomplete
Retrieve a taxon children	rt_taxa_children
Retrieve IDs of the taxon in external databases	rt_taxa_externalids
Get factsheet for taxa	rt_taxa_factsheet
Retrieve Taxon using the ids from external databases	rt_taxa_from_externalids
Find taxa by fuzzy matching their scientific Name	rt_taxa_fuzzymatch
Retrieve a taxon information using its id	rt_taxa_id
Retrieve Interactions of taxon with other taxa	rt_taxa_interactions
Retrieve Media (photos & others) Associated with a Taxon	rt_taxa_media
Retrieve classification above the taxon	rt_taxa_parent
Search for a taxon information	rt_taxa_search
Retrieve Sources Associated with a Taxon	rt_taxa_sources
Retrieve Taxon Conservation Status	rt_taxa_status
Retrieve Synonyms associated with a Taxon	rt_taxa_synonyms
Retrieve history of a taxon through TAXREF versions	rt_taxa_taxrefhistory
Retrieve VernacularNames associated with a Taxon	rt_taxa_vernacular
Retrieve taxonomic ranks in TAXREF	rt_taxo_ranks
Retrieve the list of existing TAXREF versions	rt_taxref_versions
Retrieve the list of vernacular groups in TAXREF	rt_vernacular_groups