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()

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

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.

Author

Scott Chamberlain

Examples

if (FALSE) { # \dontrun{
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)
} # }