Get the TSN code for a search term.
Retrieve the taxonomic serial numbers (TSN) of a taxon from ITIS.
get_tsn( sci_com, searchtype = "scientific", accepted = FALSE, ask = TRUE, messages = TRUE, rows = NA, searchterm = NULL, ... ) as.tsn(x, check = TRUE) ## S3 method for class 'tsn' as.tsn(x, check = TRUE) ## S3 method for class 'character' as.tsn(x, check = TRUE) ## S3 method for class 'list' as.tsn(x, check = TRUE) ## S3 method for class 'numeric' as.tsn(x, check = TRUE) ## S3 method for class 'data.frame' as.tsn(x, check = TRUE) ## S3 method for class 'tsn' as.data.frame(x, ...) get_tsn_( sci_com, messages = TRUE, searchtype = "scientific", accepted = TRUE, rows = NA, searchterm = NULL, ... )
sci_com |
character; A vector of common or scientific names.
Or, a |
searchtype |
character; One of 'scientific' or 'common', or any unique abbreviation |
accepted |
logical; If TRUE, removes names that are not accepted valid
names by ITIS. Set to |
ask |
logical; should get_tsn be run in interactive mode?
If |
messages |
logical; should progress be printed? |
rows |
numeric; Any number from 1 to infinity. If the default NA, all
rows are considered. Note that this function still only gives back a tsn
class object with one to many identifiers. See
|
searchterm |
Deprecated, see |
... |
Ignored |
x |
Input to as.tsn |
check |
logical; Check if ID matches any existing on the DB, only
used in |
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA is given. If more than one identifier
is found the function asks for user input if ask = TRUE, otherwise
returns NA. If ask=FALSE and rows does not equal
NA, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details for further details including
attributes and exceptions
Other taxonomic-ids:
get_boldid(),
get_eolid(),
get_gbifid(),
get_ids(),
get_iucn(),
get_natservid(),
get_nbnid(),
get_pow(),
get_tolid(),
get_tpsid(),
get_uid(),
get_wiki(),
get_wormsid()
## Not run:
get_tsn("Quercus douglasii")
get_tsn("Chironomus riparius")
get_tsn(c("Chironomus riparius","Quercus douglasii"))
splist <- c("annona cherimola", 'annona muricata', "quercus robur",
"shorea robusta", "pandanus patina", "oryza sativa", "durio zibethinus")
get_tsn(splist, messages=FALSE)
# specify rows to limit choices available
get_tsn('Arni')
get_tsn('Arni', rows=1)
get_tsn('Arni', rows=1:2)
# When not found
get_tsn("howdy")
get_tsn(c("Chironomus riparius", "howdy"))
# Using common names
get_tsn("black bear", searchtype="common")
# Convert a tsn without class information to a tsn class
as.tsn(get_tsn("Quercus douglasii")) # already a tsn, returns the same
as.tsn(get_tsn(c("Chironomus riparius","Pinus contorta"))) # same
as.tsn(19322) # numeric
as.tsn(c(19322,129313,506198)) # numeric vector, length > 1
as.tsn("19322") # character
as.tsn(c("19322","129313","506198")) # character vector, length > 1
as.tsn(list("19322","129313","506198")) # list, either numeric or character
## dont check, much faster
as.tsn("19322", check=FALSE)
as.tsn(19322, check=FALSE)
as.tsn(c("19322","129313","506198"), check=FALSE)
as.tsn(list("19322","129313","506198"), check=FALSE)
(out <- as.tsn(c(19322,129313,506198)))
data.frame(out)
as.tsn( data.frame(out) )
# Get all data back
get_tsn_("Arni")
get_tsn_("Arni", rows=1)
get_tsn_("Arni", rows=1:2)
get_tsn_(c("asdfadfasd","Pinus contorta"), rows=1:5)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.