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, ...)
... |
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 |
commnames |
Deprecated, see |
id |
For the other data sources, you can only pass in common names directly.
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
See taxize-authentication for help on authentication
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')
In case you run into errors due to your rate limit being exceeded, see
taxize_options(), where you can set ncbi_sleep.
Scott Chamberlain
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.