taxize (version 0.6.6)

synonyms: Retrieve synonyms from various sources given input taxonomic names or identifiers.

Description

Retrieve synonyms from various sources given input taxonomic names or identifiers.

Usage

synonyms(...)
## S3 method for class 'default':
synonyms(x, db = NULL, rows = NA, ...)
## S3 method for class 'tsn':
synonyms(id, ...)
## S3 method for class 'colid':
synonyms(id, ...)
## S3 method for class 'tpsid':
synonyms(id, ...)
## S3 method for class 'nbnid':
synonyms(id, ...)
## S3 method for class 'ids':
synonyms(id, ...)

Arguments

...

Other passed arguments to internal functions get_*() and functions to gather synonyms.

x

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

db

character; database to query. either itis, tropicos, col, or nbn.

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, tpsid, nbnid, ids.

id

character; identifiers, returned by get_tsn, get_tpsid, or get_nbnid

Value

• A named list of data.frames with the synonyms of every supplied taxa.

Details

If IDs are supplied directly (not from the get_* functions) you must specify the type of ID.

For db = "itis" you can pass in a parameter accepted to toggle whether only accepted names are used accepted = TRUE, or if all are used accepted = FALSE. The default is accepted = FALSE.

See Also

get_tsn, get_tpsid, get_nbnid

Examples

# Plug in taxon IDs
synonyms("183327", db="itis")
synonyms("25509881", db="tropicos")
synonyms("NBNSYS0000004629", db='nbn')
synonyms("87e986b0873f648711900866fa8abde7", db='col')

# Plug in taxon names directly
synonyms("Pinus contorta", db="itis")
synonyms("Puma concolor", db="itis")
synonyms(c("Poa annua",'Pinus contorta','Puma concolor'), db="itis")
synonyms("Poa annua", db="tropicos")
synonyms("Pinus contorta", db="tropicos")
synonyms(c("Poa annua",'Pinus contorta'), db="tropicos")
synonyms("Pinus sylvestris", db='nbn')
synonyms("Puma concolor", db='col')
synonyms("Ursus americanus", db='col')
synonyms("Amblyomma rotundatum", db='col')

# not accepted names, with ITIS
## looks for whether the name given is an accepted name,
## and if not, uses the accepted name to look for synonyms
synonyms("Acer drummondii", db="itis")
synonyms("Spinus pinus", db="itis")

# Use get_* methods
synonyms(get_tsn("Poa annua"))
synonyms(get_tpsid("Poa annua"))
synonyms(get_nbnid("Carcharodon carcharias"))
synonyms(get_colid("Ornithodoros lagophilus"))

# Pass many ids from class "ids"
out <- get_ids(names="Poa annua", db = c('itis','tropicos'))
synonyms(out)

# Use the rows parameter to select certain rows
synonyms("Poa annua", db='tropicos', rows=1)
synonyms("Poa annua", db='tropicos', rows=1:3)
synonyms("Pinus sylvestris", db='nbn', rows=1:3)
synonyms("Amblyomma rotundatum", db='col', rows=2)
synonyms("Amblyomma rotundatum", db='col', rows=2:3)

# Use curl options
synonyms("Poa annua", db='tropicos', rows=1, config=verbose())
synonyms("Poa annua", db='itis', rows=1, config=verbose())
synonyms("Poa annua", db='col', rows=1, config=verbose())