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() directlyx <- get_uid("western capercaillie", modifier ="Common Name")comm2sci(x)# itis: pass in tsn's from get_tsn() directlyx <- get_tsn(c("Louisiana black bear","american crow"), searchtype ="common")comm2sci(x)## End(Not run)