taxize (version 0.8.9)

sci2comm: Get common names from scientific names.

Description

Get common names from scientific names.

Usage

sci2comm(...)
# S3 method for default
sci2comm(scinames, db = "eol", simplify = TRUE, ...)
# S3 method for uid
sci2comm(id, ...)
# S3 method for tsn
sci2comm(id, simplify = TRUE, ...)
# S3 method for wormsid
sci2comm(id, simplify = TRUE, ...)
# S3 method for 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.

id

character; identifiers, as returned by get_tsn, get_uid.

Value

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

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

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())
# }