get_worms_record: Get a record from WoRMS for a given species id

In einarhjorleifsson/fishvice: A collection of various personal functions used in my work on fish stock assessment

Get a record from WoRMS for a given species id

Description

xxx

Connection to WoRMS webservice getAphiaRecordByID.

Usage

get_worms_record(aphiaID = 126436, long = TRUE)

Arguments

aphiaID	An integer value
long	A boolean, if TRUE (default) a long table (21 rows and 2 rows). If FALSE returns a wide table (21 columns and 1 row). The latter form is useful when doing a for-loop.

Value

The returned AphiaRecord has this format:

• AphiaID: unique and persistent identifier within WoRMS. Primary key in the database.

• url: HTTP URL to the AphiaRecord

• scientificname: the full scientific name without authorship

• authority: the authorship information for the scientificname formatted according to the conventions of the applicable nomenclaturalCode

• rank: the taxonomic rank of the most specific name in the scientificname

• status: the status of the use of the scientificname (usually a taxonomic opinion). Additional technical statuses are (1) quarantined: hidden from public interface after decision from an editor and (2) deleted: AphiaID should NOT be used anymore, please replace it by the valid_AphiaID

• unacceptreason: the reason why a scientificname is unaccepted

• valid_AphiaID: the AphiaID (for the scientificname) of the currently accepted taxon

• valid_name: the scientificname of the currently accepted taxon

• valid_authority: the authorship information for the scientificname of the currently accepted taxon

• kingdom: the full scientific name of the kingdom in which the taxon is classified

• phylum: the full scientific name of the phylum or division in which the taxon is classified

• class: the full scientific name of the class in which the taxon is classified

• order: the full scientific name of the order in which the taxon is classified

• family: the full scientific name of the family in which the taxon is classified

• genus: the full scientific name of the genus in which the taxon is classified

• citation: a bibliographic reference for the resource as a statement indicating how this record should be cited (attributed) when used

• lsid: LifeScience Identifier. Persistent GUID for an AphiaID

• isMarine: a boolean flag indicating whether the taxon is a marine organism, i.e. can be found in/above sea water. Possible values: 0/1/NULL

• isBrackish: a boolean flag indicating whether the taxon occurrs in brackish habitats. Possible values: 0/1/NULL

• isFreshwater: a boolean flag indicating whether the taxon occurrs in freshwater habitats, i.e. can be found in/above rivers or lakes. Possible values: 0/1/NULL

• isTerrestrial: a boolean flag indicating the taxon is a terrestial organism, i.e. occurrs on land as opposed to the sea. Possible values: 0/1/NULL

• isExtinct: a flag indicating an extinct organism. Possible values: 0/1/NUL

• match_type: Type of match. Possible values: exact/like/phonetic/near_1/near_2

• modified: The most recent date-time in GMT on which the resource was changed

einarhjorleifsson/fishvice documentation built on Jan. 4, 2024, 8:43 p.m.