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EUBON taxonomy search

Source: R/eubon.R
eubon_search.Rd

EUBON taxonomy search

Usage

eubon_search(
  query,
  providers = "pesi",
  searchMode = "scientificNameExact",
  addSynonymy = FALSE,
  addParentTaxon = FALSE,
  timeout = 0,
  dedup = NULL,
  limit = 20,
  page = 1,
  ...
)

Arguments

query

(character) The scientific name to search for. For example: "Bellis perennis", "Prionus" or "Bolinus brandaris". This is an exact search so wildcard characters are not supported

providers

(character) A list of provider id strings concatenated by comma characters. The default : "pesi,bgbm-cdm-server[col]" will be used if this parameter is not set. A list of all available provider ids can be obtained from the '/capabilities' service end point. Providers can be nested, that is a parent provider can have sub providers. If the id of the parent provider is supplied all subproviders will be queried. The query can also be restricted to one or more subproviders by using the following syntax: parent-id[sub-id-1,sub-id2,...]

searchMode

(character) Specifies the searchMode. Possible search modes are: scientificNameExact, scientificNameLike (begins with), vernacularNameExact, vernacularNameLike (contains), findByIdentifier. If the a provider does not support the chosen searchMode it will be skipped and the status message in the tnrClientStatus will be set to 'unsupported search mode' in this case.

addSynonymy

(logical) Indicates whether the synonymy of the accepted taxon should be included into the response. Turning this option on may cause an increased response time. Default: FALSE

addParentTaxon

(logical) Indicates whether the the parent taxon of the accepted taxon should be included into the response. Turning this option on may cause a slightly increased response time. Default: FALSE

timeout

(numeric) The maximum of milliseconds to wait for responses from any of the providers. If the timeout is exceeded the service will just return the responses that have been received so far. The default timeout is 0 ms (wait for ever)

dedup

(character) Allows to deduplicate the results by making use of a deduplication strategy. The deduplication is done by comparing specific properties of the taxon:

  • id: compares 'taxon.identifier'

  • id_name: compares 'taxon.identifier' AND 'taxon.taxonName.scientificName'

  • name: compares 'taxon.taxonName.scientificName' Using the pure 'name' strategy is not recommended.

limit

(numeric/integer) number of records to retrieve. default: 20. This only affects the search mode scientificNameLike and vernacularNameLike; other search modes are expected to return only one record per check list

page

(numeric/integer) page to retrieve. default: 1. This only affects the search mode scientificNameLike and vernacularNameLike; other search modes are expected to return only one record per check list

...

Curl options passed on to crul::verb-GET

References

https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html

See also

Other eubon-methods: eubon_capabilities(), eubon_children(), eubon_hierarchy()

Examples

if (FALSE) { # \dontrun{
eubon_search("Prionus")
eubon_search("Salmo", "pesi")
eubon_search("Salmo", c("pesi", "worms"))
eubon_search("Salmo", "worms", "scientificNameLike")
eubon_search("Salmo", "worms", "scientificNameLike", limit = 3)
eubon_search("Salmo", "worms", "scientificNameLike", limit = 20, page = 2)
eubon_search("Salmo", "worms", addSynonymy = TRUE)
eubon_search("Salmo", "worms", addParentTaxon = TRUE)
} # }