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 tsn as.tsn(x, check = TRUE) # S3 method for character as.tsn(x, check = TRUE) # S3 method for list as.tsn(x, check = TRUE) # S3 method for numeric as.tsn(x, check = TRUE) # S3 method for data.frame as.tsn(x, check = TRUE) # S3 method for 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()
if (FALSE) { 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) }