Get the UK National Biodiversity Network ID from taxonomic names.

Get the UK National Biodiversity Network ID from taxonomic names.

Usage

get_nbnid(
  sci_com,
  ask = TRUE,
  messages = TRUE,
  rec_only = FALSE,
  rank = NULL,
  rows = NA,
  name = NULL,
  ...
)

as.nbnid(x, check = TRUE)

# S3 method for class 'nbnid'
as.nbnid(x, check = TRUE)

# S3 method for class 'character'
as.nbnid(x, check = TRUE)

# S3 method for class 'list'
as.nbnid(x, check = TRUE)

# S3 method for class 'data.frame'
as.nbnid(x, check = TRUE)

# S3 method for class 'nbnid'
as.data.frame(x, ...)

get_nbnid_(
  sci_com,
  messages = TRUE,
  rec_only = FALSE,
  rank = NULL,
  rows = NA,
  name = NULL,
  ...
)

Arguments

sci_com

character; a vector of common or scientific names. Or, a taxon_state object (see taxon-state)

ask

logical; should get_nbnid be run in interactive mode? If TRUE and more than one ID is found for the species, the user is asked for input. If FALSE NA is returned for multiple matches.

messages

logical; If TRUE the actual taxon queried is printed on the console.

rec_only

(logical) If TRUE ids of recommended names are returned (i.e. synonyms are removed). Defaults to FALSE. Remember, the id of a synonym is a taxa with 'recommended' name status.

rank

(character) If given, we attempt to limit the results to those taxa with the matching rank.

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 nbnid class object with one to many identifiers. See get_nbnid_() to get back all, or a subset, of the raw data that you are presented during the ask process.

name

Deprecated, see sci_com

...

Further args passed on to nbn_search

x

Input to as.nbnid()

check

logical; Check if ID matches any existing on the DB, only used in as.nbnid()

Value

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

an object of class nbnid, a light wrapper around a character string that is the taxonomic ID - includes attributes with relavant metadata

References

https://api.nbnatlas.org/

See also

classification()

Other taxonomic-ids: get_boldid(), get_eolid(), get_gbifid(), get_ids(), get_iucn(), get_natservid(), get_pow(), get_tolid(), get_tpsid(), get_tsn(), get_uid(), get_wiki(), get_wormsid()

Other nbn: nbn_classification(), nbn_search(), nbn_synonyms()

Author

Scott Chamberlain,

Examples

if (FALSE) { # \dontrun{
get_nbnid(sci_com='Poa annua')
get_nbnid(sci_com='Poa annua', rec_only=TRUE)
get_nbnid(sci_com='Poa annua', rank='Species')
get_nbnid(sci_com='Poa annua', rec_only=TRUE, rank='Species')
get_nbnid(sci_com='Pinus contorta')

# The NBN service handles common names too
get_nbnid(sci_com='red-winged blackbird')

# specify rows to limit choices available
get_nbnid('Poa ann')
get_nbnid('Poa ann', rows=1)
get_nbnid('Poa ann', rows=25)
get_nbnid('Poa ann', rows=1:2)

# When not found
get_nbnid(sci_com="uaudnadndj")
get_nbnid(c("Zootoca vivipara", "uaudnadndj"))
get_nbnid(c("Zootoca vivipara","Chironomus riparius", "uaudnadndj"))

# Convert an nbnid without class information to a nbnid class
as.nbnid(get_nbnid("Zootoca vivipara")) # already a nbnid, returns the same
as.nbnid(get_nbnid(c("Zootoca vivipara","Pinus contorta"))) # same
as.nbnid('NHMSYS0001706186') # character
# character vector, length > 1
as.nbnid(c("NHMSYS0001706186","NHMSYS0000494848","NBNSYS0000010867"))
# list
as.nbnid(list("NHMSYS0001706186","NHMSYS0000494848","NBNSYS0000010867"))
## dont check, much faster
as.nbnid('NHMSYS0001706186', check=FALSE)
as.nbnid(list("NHMSYS0001706186","NHMSYS0000494848","NBNSYS0000010867"),
  check=FALSE)

(out <- as.nbnid(c("NHMSYS0001706186","NHMSYS0000494848",
  "NBNSYS0000010867")))
data.frame(out)
as.nbnid( data.frame(out) )

# Get all data back
get_nbnid_("Zootoca vivipara")
get_nbnid_("Poa annua", rows=2)
get_nbnid_("Poa annua", rows=1:2)
get_nbnid_(c("asdfadfasd","Pinus contorta"), rows=1:5)

# use curl options
invisible(get_nbnid("Quercus douglasii", verbose = TRUE))
} # }