taxize (version 0.9.4)

eubon: EUBON taxonomy search

Description

EUBON taxonomy search

Usage

eubon(query, providers = "pesi", searchMode = "scientificNameExact",
  addSynonymy = FALSE, addParentTaxon = FALSE, timeout = 0,
  dedup = NULL, ...)
eubon_search(query, providers = "pesi", searchMode = "scientificNameExact",
  addSynonymy = FALSE, addParentTaxon = FALSE, timeout = 0,
  dedup = NULL, ...)

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.

...

Curl options passed on to GET

Details

Note that paging is not yet implemented, so you only get the first chunk of up to 50 results for methods that require paging. We will implement paging here when it is available in the EU BON API.

References

http://cybertaxonomy.eu/eu-bon/utis/1.2/doc.html

See Also

Other eubon-methods: eubon_capabilities, eubon_children, eubon_hierarchy

Examples

# NOT RUN {
eubon_search("Prionus")
eubon_search("Salmo", 'pesi')
eubon_search("Salmo", c('pesi', 'worms'))
eubon_search("Salmo", 'worms', 'scientificNameLike')
eubon_search("Salmo", 'worms', addSynonymy = TRUE)
eubon_search("Salmo", 'worms', addParentTaxon = TRUE)
# }