Retrieve the Open Tree of Life Taxonomy (OTT) id of a taxon from OpenTreeOfLife
get_tolid(sci, ask = TRUE, messages = TRUE, rows = NA, sciname = NULL, ...)
as.tolid(x, check = TRUE)
# S3 method for tolid
as.tolid(x, check = TRUE)
# S3 method for character
as.tolid(x, check = TRUE)
# S3 method for list
as.tolid(x, check = TRUE)
# S3 method for numeric
as.tolid(x, check = TRUE)
# S3 method for data.frame
as.tolid(x, check = TRUE)
# S3 method for tolid
as.data.frame(x, ...)
get_tolid_(sci, messages = TRUE, rows = NA, sciname = NULL)character; one or more scientific names. Or, a taxon_state
object (see taxon-state)
logical; should get_tolid be run in interactive mode?
If TRUE and more than one TOL is found for the species, the user is
asked for input. If FALSE NA is returned for multiple matches.
logical; should progress be printed?
numeric; Any number from 1 to infinity. If the default NA, all
rows are considered. Note that this function still only gives back a tol
class object with one to many identifiers. See get_tolid_()
to get back all, or a subset, of the raw data that you are presented during
the ask process.
Deprecated, see sci
Ignored
Input to as.tolid
logical; Check if ID matches any existing on the DB, only
used in as.tolid()
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_tpsid(),
get_tsn(),
get_uid(),
get_wiki(),
get_wormsid()
if (FALSE) {
get_tolid(sci = "Quercus douglasii")
get_tolid(sci = "Chironomus riparius")
get_tolid(c("Chironomus riparius","Quercus douglasii"))
splist <- c("annona cherimola", 'annona muricata', "quercus robur",
"shorea robusta", "pandanus patina", "oryza sativa", "durio zibethinus")
get_tolid(splist, messages=FALSE)
# specify rows to limit choices available
get_tolid('Arni')
get_tolid('Arni', rows=1)
get_tolid('Arni', rows=1:2)
# When not found
get_tolid("howdy")
get_tolid(c("Chironomus riparius", "howdy"))
# Convert a tol without class information to a tol class
as.tolid(get_tolid("Quercus douglasii")) # already a tol, returns the same
as.tolid(get_tolid(c("Chironomus riparius","Pinus contorta"))) # same
as.tolid(5907893) # numeric
as.tolid(c(3930798,515712,872577)) # numeric vector, length > 1
as.tolid("3930798") # character
as.tolid(c("3930798","515712","872577")) # character vector, length > 1
as.tolid(list("3930798","515712","872577")) # list, either numeric or character
## dont check, much faster
as.tolid("3930798", check=FALSE)
as.tolid(3930798, check=FALSE)
as.tolid(c("3930798","515712","872577"), check=FALSE)
as.tolid(list("3930798","515712","872577"), check=FALSE)
(out <- as.tolid(c(3930798,515712,872577)))
data.frame(out)
as.tolid( data.frame(out) )
# Get all data back
get_tolid_("Arni")
get_tolid_("Arni", rows=1)
get_tolid_("Arni", rows=1:2)
get_tolid_(c("asdfadfasd","Pinus contorta"))
}