taxize (version 0.2.2)

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

Description

This function uses a while loop to continually collect children taxa down to the taxonomic rank that you specify in the downto 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

downstream(...)
## S3 method for class 'default':
downstream(x, db = NULL, downto = NULL, ...)
## S3 method for class 'tsn':
downstream(x, db = NULL, ...)
## S3 method for class 'colid':
downstream(x, db = NULL, ...)
## S3 method for class 'ids':
downstream(x, db = NULL, downto, ...)

Arguments

x

character; taxons to query.

db

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

downto

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', 'Infraord

...

Further args passed on to itis_downstream or col_downstream

Value

• A named list of data.frames with the downstream names of every supplied taxa. You get an NA if there was no match in the database.

Examples

# Plug in taxon names
downstream("Insecta", db = 'col', downto = 'Order')
downstream("Apis", db = 'col', downto = 'Species')

# Plug in IDs
id <- get_colid("Apis")
downstream(id, downto = 'Species')

## Equivalently, plug in the call to get the id via e.g., get_colid into downstream
identical(downstream(id, downto = 'Species'),
         downstream(get_colid("Apis"), downto = 'Species'))

id <- get_colid("Apis")
downstream(id, downto = 'Species')
downstream(get_colid("Apis"), downto = 'Species')

# Many taxa
sp <- names_list("genus", 3)
downstream(sp, db = 'col', downto = 'Species')
downstream(sp, db = 'itis', downto = 'Species')

# Both data sources
ids <- get_ids("Apis", db = c('col','itis'))
downstream(ids, downto = 'Species')
## same result
downstream(get_ids("Apis", db = c('col','itis')), downto = 'Species')