Retrieve synonyms from various sources given input taxonomic names or identifiers
Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms(...) ## Default S3 method: synonyms(sci_id, db = NULL, rows = NA, x = NULL, ...) ## S3 method for class 'tsn' synonyms(id, ...) ## S3 method for class 'tpsid' synonyms(id, ...) ## S3 method for class 'nbnid' synonyms(id, ...) ## S3 method for class 'wormsid' synonyms(id, ...) ## S3 method for class 'iucn' synonyms(id, ...) ## S3 method for class 'pow' synonyms(id, ...) ## S3 method for class 'ids' synonyms(id, ...) synonyms_df(x)
... |
Other passed arguments to internal functions |
sci_id |
Vector of taxa names (character) or IDs (character or numeric) |
db |
character; database to query. either |
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, tpsid, nbnid, ids. |
x |
For |
id |
character; identifiers, returned by |
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
Note that IUCN requires an API key. See rredlist::rredlist-package for help on authentiating with IUCN Redlist
A named list of results with three types of output in each slot:
if the name was not found: NA_character_
if the name was found but no synonyms found, an empty data.frame (0 rows)
if the name was found, and synonyms found, a data.frames with the synonyms - the column names vary by data source
## Not run:
# Plug in taxon IDs
synonyms(183327, db="itis")
synonyms("25509881", db="tropicos")
synonyms("NBNSYS0000004629", db='nbn')
synonyms(105706, db='worms')
synonyms(12392, db='iucn')
synonyms('urn:lsid:ipni.org:names:358881-1', db='pow')
# 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('Pomatomus', db='worms')
synonyms('Pomatomus saltatrix', db='worms')
synonyms('Lithocarpus mindanaensis', db='pow')
synonyms('Poa annua', db='pow')
synonyms(c('Poa annua', 'Pinus contorta', 'foo bar'), db='pow')
# 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_iucn('Loxodonta africana'))
synonyms(get_pow('Lithocarpus mindanaensis'))
# 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)
# Use curl options
synonyms("Poa annua", db='tropicos', rows=1, verbose = TRUE)
synonyms("Poa annua", db='itis', rows=1, verbose = TRUE)
# combine many outputs together
x <- synonyms(c("Osmia bicornis", "Osmia rufa", "Osmia"), db = "itis")
synonyms_df(x)
## note here how Pinus contorta is dropped due to no synonyms found
synonyms_df(x)
## note here that ids are taxon identifiers b/c you start with them
x <- synonyms(c(25509881, 13100094), db="tropicos")
synonyms_df(x)
## NBN
x <- synonyms(c('Aglais io', 'Usnea hirta', 'Arctostaphylos uva-ursi'),
db="nbn")
synonyms_df(x)
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