comm2sci function

Get scientific names from common names.

Get scientific names from common names.

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()

Returns

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

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.

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.

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)

See Also

sci2comm()

Author(s)

Scott Chamberlain