search_taxonomy: Query taxonomy

In mangal-wg/rmangal: 'Mangal' Client

Query taxonomy

Description

Search network by taxon names and unique taxonomic identifiers. This function offers the opportunity to retrieve taxon based on (i) known identifier such as the taxonomic serial number (TSN), GBIF ID etc. or (ii) text search using partial match. Have a look at the list of arguments to see the complete list of identifiers accessible. If any unique identifier argument is used (i.e. tsn etc.), then query is ignored. Moreover, if several taxonomic identifiers are specified, then only the first one is considered.

Usage

search_taxonomy(
  query,
  tsn = NULL,
  gbif = NULL,
  eol = NULL,
  col = NULL,
  bold = NULL,
  ncbi = NULL,
  verbose = TRUE,
  ...
)

Arguments

query	a character string including a single keyword. Note that if an empty character string is passed, then all datasets available are returned.
tsn	a numeric. Unique taxonomic identifier from Integrated Taxonomic Information System (https://www.itis.gov).
gbif	a numeric. Unique taxonomic identifier from Global Biodiversity Information Facility (https://www.gbif.org).
eol	a numeric. Unique taxonomic identifier from Encyclopedia of Life (https://eol.org).
col	a numeric. Unique taxonomic identifier from Catalogue of Life (https://www.catalogueoflife.org).
bold	a numeric. Unique taxonomic identifier from Barcode of Life (http://www.boldsystems.org).
ncbi	a numeric. Unique taxonomic identifier from National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov).
verbose	a logical. Should extra information be reported on progress?
...	further arguments to be passed to httr::GET().

Details

Taxon names of the taxonomy table were validated with TNRS (see https://tnrs.biendata.org and/or GNR might not be the taxon name documented in the original publication. In order to identify relevant networks with the original name, use search_nodes().

The validation of taxon names was performed by an automated procedure and if there is any doubt, the original names recorded by authors should be regarded as the most reliable information. Please report any issue related to taxonomy at https://github.com/mangal-interactions/contribute/issues/new/choose/.

Value

An object of class mgSearchTaxonomy, which is a data.frame including all taxa matching the query.

References

• https://mangal.io/#/

• https://mangal-interactions.github.io/mangal-api/#taxonomy

See Also

search_nodes()

Examples

 search_taxonomy("Acer")
 # Retrieve higher classification
 tsn_acer <- search_taxonomy("Acer")$taxonomy.tsn

mangal-wg/rmangal documentation built on Jan. 15, 2024, 10:23 p.m.