R: Get common names from scientific names.

sci2comm {taxize} | R Documentation

## Get common names from scientific names.

### Description

Get common names from scientific names.

### Usage

    sci2comm(...)

    ## Default S3 method:
    sci2comm(scinames, db = "eol", simplify = TRUE, ...)

    ## S3 method for class 'uid'
    sci2comm(id, ...)

    ## S3 method for class 'tsn'
    sci2comm(id, simplify = TRUE, ...)

    ## S3 method for class 'wormsid'
    sci2comm(id, simplify = TRUE, ...)

    ## S3 method for class 'iucn'
    sci2comm(id, simplify = TRUE, ...)

### Arguments

`...` | Further arguments passed on to functions `get_uid`, `get_tsn`.
`scinames` | character; One or more scientific names or partial names.
`db` | character; Data source, one of "eol" (default), "itis" "ncbi", "worms", or "iucn". 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).
`simplify` | (logical) If TRUE, simplify output to a vector of names. If FALSE, return variable formats from different sources, usually a data.frame. Only applies to eol and itis. Specify `FALSE` to obtain the language of each vernacular in the output for eol and itis.
`id` | character; identifiers, as returned by `get_tsn`, `get_uid`.

### Details

Note that EOL requires an API key. You can pass in your EOL api key in the function call like `sci2comm('Helianthus annuus', key="<your eol api key>")`. You can also store your EOL API key in your .Rprofile file as `options(eolApiKey = "<your eol api key>")`, or just for the current session by running `options(eolApiKey = "<your eol api key>")` in the console.

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

### Value

List of character vectors, named by input taxon name, or taxon ID

### Author(s)

Scott Chamberlain (myrmecocystus@gmail.com)

### See Also

`comm2sci`

### Examples

    ## Not run:
    sci2comm(scinames='Helianthus annuus', db='eol')
    sci2comm(scinames='Helianthus annuus', db='itis')
    sci2comm(scinames=c('Helianthus annuus', 'Poa annua'))
    sci2comm(scinames='Puma concolor', db='ncbi')
    sci2comm('Gadus morhua', db='worms')
    sci2comm('Pomatomus saltatrix', db='worms')
    sci2comm('Loxodonta africana', db='iucn')

    # Passing id in, works for sources: itis and ncbi, not eol
    sci2comm(get_tsn('Helianthus annuus'))
    sci2comm(get_uid('Helianthus annuus'))
    sci2comm(get_wormsid('Gadus morhua'))
    sci2comm(get_iucn('Loxodonta africana'))

    # Don't simplify returned
    sci2comm(get_tsn('Helianthus annuus'), simplify=FALSE)
    sci2comm(get_iucn('Loxodonta africana'), simplify=FALSE)

    # Use curl options
    library("httr")
    sci2comm('Helianthus annuus', db="ncbi", config=verbose())

    ## End(Not run)

[Package taxize version 0.9.0 Index]