taxize (version 0.7.9)

upstream: Retrieve the upstream taxa for a given taxon name or ID.

Description

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) or Catalogue of Life (col). There is no method exposed by itis or col for getting taxa at a specific taxonomic rank, so we do it ourselves inside the function.

Usage

upstream(...)
"upstream"(x, db = NULL, upto = NULL, rows = NA, ...)
"upstream"(x, db = NULL, upto = NULL, ...)
"upstream"(x, db = NULL, upto = NULL, ...)
"upstream"(x, db = NULL, upto = NULL, ...)

Arguments

...

Further args passed on to itis_downstream or col_downstream

x

Vector of taxa names (character) or IDs (character or numeric) to query.

db

character; database to query. One or both of itis, col. 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).

upto

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'

rows

(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, colid.

Value

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.

Examples

## Not run: 
# ## col
# upstream("Pinus contorta", db = 'col', upto = 'genus') # get all genera at one level up
# upstream("Abies", db = 'col', upto = 'genus') # goes to same level, Abies is a genus
# upstream('Pinus contorta', db = 'col', upto = 'family')
# upstream('Poa annua', db = 'col', upto = 'family')
# upstream('Poa annua', db = 'col', upto = 'order')
# 
# ## itis
# upstream(x='Pinus contorta', db = 'itis', upto = 'genus')
# 
# ## both
# upstream(get_ids('Pinus contorta', db = c('col','itis')), upto = 'genus')
# 
# # Use rows parameter to select certain
# upstream('Poa annua', db = 'col', upto = 'genus')
# upstream('Poa annua', db = 'col', upto = 'genus', rows=1)
# 
# # use curl options
# res <- upstream('Poa annua', db = 'col', upto = 'genus', config=verbose())
# ## End(Not run)