upstream {taxize}R Documentation

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(...)

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

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

## S3 method for class 'colid'
upstream(x, db = NULL, upto = NULL, ...)

## S3 method for class 'ids'
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
### get all genera at one level up
upstream("Pinus contorta", db = 'col', upto = 'genus')
### goes to same level, Abies is a genus
upstream("Abies", db = 'col', upto = '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', verbose = TRUE)

## End(Not run)
[Package taxize version 0.9.3 Index]