comm2sci: Get scientific names from common names.

In ropensci/taxize: Taxonomic Information from Around the Web

Get scientific names from common names.

Description

Get scientific names from common names.

Usage

comm2sci(...)

## Default S3 method:
comm2sci(
  com,
  db = "ncbi",
  itisby = "search",
  simplify = TRUE,
  commnames = NULL,
  ...
)

## S3 method for class 'tsn'
comm2sci(id, db = "ncbi", itisby = "search", simplify = TRUE, ...)

## S3 method for class 'uid'
comm2sci(id, db = "ncbi", itisby = "search", simplify = TRUE, ...)

Arguments

...	Further arguments passed on to internal methods.
com	One or more common names or partial names.
db	Data source, one of "ncbi" (default), "itis", "tropicos", "eol", or "worms". If using ncbi, we recommend getting an API key; see taxize-authentication
itisby	Search for common names across entire names (search, default), at beginning of names (begin), or at end of names (end).
simplify	(logical) If TRUE, simplify output to a vector of names. If FALSE, return variable formats from different sources, usually a data.frame.
commnames	Deprecated, see com
id	taxon identifiers, as returned by get_tsn() or get_uid()

Details

For data sources ITIS and NCBI you can pass in common names directly, and use get_uid() or get_tsn() to get ids first, then pass in to this fxn.

For the other data sources, you can only pass in common names directly.

Value

If simplify=TRUE, a list of scientific names, with list labeled by your input names. If simplify=FALSE, a data.frame with columns that vary by data source. 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')

Rate limits

In case you run into errors due to your rate limit being exceeded, see taxize_options(), where you can set ncbi_sleep.

Author(s)

Scott Chamberlain

See Also

sci2comm()

Examples

## Not run: 
comm2sci(com='american black bear')
comm2sci(com='american black bear', simplify = FALSE)
comm2sci(com='black bear', db='itis')
comm2sci(com='american black bear', db='itis')
comm2sci(com='annual blue grass', db='tropicos')
comm2sci(com=c('annual blue grass','tree of heaven'), db='tropicos')
comm2sci('blue whale', db = "worms")
comm2sci(c('blue whale', 'dwarf surfclam'), db = "worms")

# ncbi: pass in uid's from get_uid() directly
x <- get_uid("western capercaillie", modifier = "Common Name")
comm2sci(x)
# itis: pass in tsn's from get_tsn() directly
x <- get_tsn(c("Louisiana black bear", "american crow"),
  searchtype = "common")
comm2sci(x)

## End(Not run)

ropensci/taxize documentation built on Jan. 25, 2024, 6:49 p.m.