R: Retrieve synonyms from various sources given input taxonomic...

synonyms {taxize} | R Documentation

## 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(...)

    ## Default S3 method:
    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 'wormsid'
    synonyms(id, ...)

    ## S3 method for class 'iucn'
    synonyms(id, ...)

    ## S3 method for class 'ids'
    synonyms(id, ...)

    synonyms_df(x)

### 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`, `nbn`, or `worms`. 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).
`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.
`id` | character; identifiers, returned by `get_tsn`, `get_tpsid`, `get_nbnid`, `get_colid`, `get_wormsid`

### 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`

Note that IUCN requires an API key. See `rredlist-package` for help on authentiating with IUCN Redlist

### Value

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

### See Also

`get_tsn`, `get_tpsid`, `get_nbnid`, `get_colid`, `get_wormsid`, `get_iucn`

### Examples

    ## Not run:
    # Plug in taxon IDs
    synonyms(183327, db="itis")
    synonyms("25509881", db="tropicos")
    synonyms("NBNSYS0000004629", db='nbn')
    # synonyms("87e986b0873f648711900866fa8abde7", db='col') # FIXME
    synonyms(105706, db='worms')
    synonyms(12392, db='iucn')

    # 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')
    synonyms('Pomatomus', db='worms')
    synonyms('Pomatomus saltatrix', db='worms')

    # 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"))
    synonyms(get_iucn('Loxodonta africana'))

    # 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())

    # 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
    x <- synonyms(c("Poa annua",'Pinus contorta','Puma concolor'), db="col")
    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)

    ## xxx
    x <- synonyms(c('Aglais io', 'Usnea hirta', 'Arctostaphylos uva-ursi'),
      db="nbn")
    synonyms_df(x)

    ## End(Not run)

[Package taxize version 0.9.0 Index]