Get the OTT id for a search term
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 class 'tolid' as.tolid(x, check = TRUE) ## S3 method for class 'character' as.tolid(x, check = TRUE) ## S3 method for class 'list' as.tolid(x, check = TRUE) ## S3 method for class 'numeric' as.tolid(x, check = TRUE) ## S3 method for class 'data.frame' as.tolid(x, check = TRUE) ## S3 method for class 'tolid' as.data.frame(x, ...) get_tolid_(sci, messages = TRUE, rows = NA, sciname = NULL)
sci |
character; one or more scientific names. Or, a |
ask |
logical; should |
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 tol
class object with one to many identifiers. See |
sciname |
Deprecated, see |
... |
Ignored |
x |
Input to |
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_tpsid(),
get_tsn(),
get_uid(),
get_wiki(),
get_wormsid()
## Not run:
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"))
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.