taxize (version 0.6.0)

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

Arguments

...

Further args passed on to itis_downstream or col_downstream

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', 'Infraorder','Sup

intermediate

(logical) If TRUE, return a list of length two with target taxon rank names, with additional list of data.frame's of intermediate taxonomic groups. Default: FALSE

rows

(numeric) Any number from 1 to inifity. 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 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')
downstream("Apis", db = 'itis', downto = 'Species')
downstream(c("Apis","Epeoloides"), db = 'itis', downto = 'Species')
downstream(c("Apis","Epeoloides"), 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')

# Collect intermediate names
## itis
downstream('Bangiophyceae', db="itis", downto="Genus")
downstream('Bangiophyceae', db="itis", downto="Genus", intermediate=TRUE)
downstream(get_tsn('Bangiophyceae'), downto="Genus")
downstream(get_tsn('Bangiophyceae'), downto="Genus", intermediate=TRUE)
## col
downstream(get_colid("Animalia"), downto="Class")
downstream(get_colid("Animalia"), downto="Class", intermediate=TRUE)

# Use the rows parameter
## note how in the second function call you don't get the prompt
downstream("Poa", db = 'col', downto="Species")
downstream("Poa", db = 'col', downto="Species", rows=1)

# use curl options
res <- downstream("Apis", db = 'col', downto = 'Species', config=verbose())
res <- downstream("Apis", db = 'itis', downto = 'Species', config=verbose())