taxize: upstream – R documentation

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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) 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.

Usage

upstream(...)

## Default S3 method:
upstream(sci_id, db = NULL, upto = NULL, rows = NA, x = NULL, ...)

## S3 method for class 'tsn'
upstream(sci_id, db = NULL, upto = NULL, ...)

## S3 method for class 'ids'
upstream(sci_id, db = NULL, upto = NULL, ...)

Arguments

`...`	Further args passed on to `itis_downstream()`
`sci_id`	Vector of taxa names (character) or IDs (character or numeric) to query.
`db`	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).
`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.
`x`	Deprecated, see `sci_id`

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: 
upstream('Pinus contorta', db = 'itis', upto = 'genus')

## End(Not run)

taxize

Taxonomic Information from Around the Web

v0.9.100

MIT + file LICENSE

Authors

Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Eduard Szoecs [aut], Zachary Foster [aut, cre], Zebulun Arendsee [aut], Carl Boettiger [ctb], Karthik Ram [ctb], Ignasi Bartomeus [ctb], John Baumgartner [ctb], James O'Donnell [ctb], Jari Oksanen [ctb], Bastian Greshake Tzovaras [ctb], Philippe Marchand [ctb], Vinh Tran [ctb], Maëlle Salmon [ctb], Gaopeng Li [ctb], Matthias Grenié [ctb], rOpenSci [fnd] (https://ropensci.org/)

Initial release