taxize (version 0.6.0)

sci2comm: Get common names from scientific names.

Description

Get common names from scientific names.

Usage

sci2comm(...)
## S3 method for class 'default':
sci2comm(scinames, db = "eol", simplify = TRUE, ...)
## S3 method for class 'uid':
sci2comm(id, ...)
## S3 method for class 'tsn':
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" or "ncbi".

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.

id

character; identifiers, as returned by get_tsn, get_uid.

Value

• List of character vectors.

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=""). You can also store your EOL API key in your .Rprofile file as options(eolApiKey = ""), or just for the current session by running options(eolApiKey = "") in the console.

See Also

searchbycommonname, searchbycommonnamebeginswith, searchbycommonnameendswith, eol_search, tp_search, comm2sci

Examples

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')

# Passing id in, works for sources: itis and ncbi, not eol
sci2comm(get_tsn('Helianthus annuus'))
sci2comm(get_uid('Helianthus annuus'))

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

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