This function uses a while loop to continually collect taxa up to the
taxonomic rank that you specify in the upto parameter. You can get data
from ITIS (itis) only currently. There is no method exposed by itis
for getting taxa at a specific taxonomic rank, so we do it ourselves inside
the function.
upstream(...)
# S3 method for default
upstream(sci_id, db = NULL, upto = NULL, rows = NA, x = NULL, ...)
# S3 method for tsn
upstream(sci_id, db = NULL, upto = NULL, ...)
# S3 method for ids
upstream(sci_id, db = NULL, upto = NULL, ...)Further args passed on to itis_downstream()
Vector of taxa names (character) or IDs (character or numeric) to query.
character; database to query. One or both of itis. Note
that each taxonomic data source has their own identifiers, so that if you
provide the wrong db value for the identifier you could get a result, but
it will likely be wrong (not what you were expecting).
What taxonomic rank to go down to. One of: 'superkingdom', 'kingdom', 'subkingdom','infrakingdom','phylum','division','subphylum', 'subdivision','infradivision', 'superclass','class','subclass','infraclass', 'superorder','order','suborder','infraorder','superfamily','family', 'subfamily','tribe','subtribe','genus','subgenus', 'section','subsection', 'species','subspecies','variety','form','subvariety','race', 'stirp', 'morph','aberration','subform', or 'unspecified'
(numeric) Any number from 1 to infinity. If the default NA, all rows are considered. Note that this parameter is ignored if you pass in a taxonomic id of any of the acceptable classes: tsn.
Deprecated, see sci_id
A named list of data.frames with the upstream names of every supplied taxa. You get an NA if there was no match in the database.
if (FALSE) {
upstream('Pinus contorta', db = 'itis', upto = 'genus')
}