Get common names from scientific names.

Get common names from scientific names.

Usage

sci2comm(...)

# Default S3 method
sci2comm(sci, db = "ncbi", simplify = TRUE, scinames = NULL, ...)

# 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().

sci

character; One or more scientific names or partial names.

db

character; Data source, one of "ncbi" (default), "itis" "eol", "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). If using ncbi or iucn we recommend getting an API key; see taxize-authentication

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.

scinames

Deprecated, see sci

id

character; identifiers, as returned by get_tsn(), get_uid().

Value

List of character vectors, named by input taxon name, or taxon ID. character(0) on no match

Authentication

See taxize-authentication for help on authentication

HTTP version for NCBI requests

We hard code http_version = 2L to use HTTP/1.1 in HTTP requests to the Entrez API. See curl::curl_symbols('CURL_HTTP_VERSION')

See also

comm2sci()

Author

Scott Chamberlain

Examples

if (FALSE) { # \dontrun{
sci2comm(sci='Helianthus annuus')
sci2comm(sci='Helianthus annuus', db='eol')
sci2comm(sci=c('Helianthus annuus', 'Poa annua'))
sci2comm(sci='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_uid('Helianthus annuus'))
sci2comm(get_wormsid('Gadus morhua'))
sci2comm(get_iucn('Loxodonta africana'))

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

# Use curl options
sci2comm('Helianthus annuus', db="ncbi", verbose = TRUE)
} # }