worms | R Documentation |
Paging in worms_*
functions: Where available, you an use the offset
parameter to
give the first record to return. The max records to return is 50, which you can not change.
If there are more than 50 records, you can do the same request, but set offset=51
,
for example.
WORMS has a SOAP API. We store the machine generated API specification in the package as the
object worms_iface
. However, you can update the spec if you want using
worms_gen_iface
, then pass the output of that fxn to the iface
parameter of
worms_*
functions.
The following functions are available to interact with WoRMS:
worms_gen_iface Generate new WoRMS SOAP API interface.
worms_children Get immediate children from a WoRMS ID.
worms_common Get common (vernacular) names from a WoRMS ID.
worms_extid Get external IDs from a WoRMS ID, E.g., get an NCBI identifier.
worms_hierarchy Get complete taxonomic hierarchy from a WoRMS ID.
worms_name Get scientific name from a WoRMS ID.
worms_records Get WoRMS records from a WoRMS ID, an external ID, a scientific name, a common name, or a start- or end-date.
worms_sources Get sources (references) for taxa from a WoRMS ID.
worms_synonyms Get scientific name synonyms from a WoRMS ID.
Each WoRMS record (row in the output of most worms_
functions) has the same
output columns:
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 as a label for a taxon. Requires taxonomic opinion to define the scope of a taxon
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
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