get_boldid: Get the BOLD (Barcode of Life) code for a search term.

Description

Get the BOLD (Barcode of Life) code for a search term.

Usage

get_boldid(
  sci,
  fuzzy = FALSE,
  dataTypes = "basic",
  includeTree = FALSE,
  ask = TRUE,
  messages = TRUE,
  rows = NA,
  rank = NULL,
  division = NULL,
  parent = NULL,
  searchterm = NULL,
  ...
)
as.boldid(x, check = TRUE)
# S3 method for boldid
as.boldid(x, check = TRUE)
# S3 method for character
as.boldid(x, check = TRUE)
# S3 method for list
as.boldid(x, check = TRUE)
# S3 method for numeric
as.boldid(x, check = TRUE)
# S3 method for data.frame
as.boldid(x, check = TRUE)
# S3 method for boldid
as.data.frame(x, ...)
get_boldid_(
  sci,
  messages = TRUE,
  fuzzy = FALSE,
  dataTypes = "basic",
  includeTree = FALSE,
  rows = NA,
  searchterm = NULL,
  ...
)

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

Arguments

sci: character; A vector of scientific names. Or, a taxon_state object (see taxon-state)
fuzzy: (logical) Whether to use fuzzy search or not (default: FALSE).
dataTypes: (character) Specifies the datatypes that will be returned. See bold_search() for options.
includeTree: (logical) If TRUE (default: FALSE), returns a list containing information for parent taxa as well as the specified taxon.
ask: logical; should get_tsn be run in interactive mode? If TRUE and more than one TSN is found for teh species, the user is asked for input. If FALSE NA is returned for multiple matches.
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 boldid class object with one to many identifiers. See get_boldid_() to get back all, or a subset, of the raw data that you are presented during the ask process.
rank: (character) A taxonomic rank name. See rank_ref for possible options. Though note that some data sources use atypical ranks, so inspect the data itself for options. Optional. See Filtering below.
division: (character) A division (aka phylum) name. Optional. See Filtering below.
parent: (character) A parent name (i.e., the parent of the target search taxon). Optional. See Filtering below.
searchterm: Deprecated, see sci
...: Curl options passed on to crul::verb-GET
x: Input to as.boldid()
check: logical; Check if ID matches any existing on the DB, only used in as.boldid()

Filtering

The parameters division, parent, and rank are not used in the search to the data provider, but are used in filtering the data down to a subset that is closer to the target you want. For all these parameters, you can use regex strings since we use grep() internally to match. Filtering narrows down to the set that matches your query, and removes the rest.

Examples

Run this code

if (FALSE) {
get_boldid(sci = "Agapostemon")
get_boldid(sci = "Chironomus riparius")
get_boldid(c("Chironomus riparius","Quercus douglasii"))
splist <- names_list('species')
get_boldid(splist, messages=FALSE)

# Fuzzy searching
get_boldid(sci="Osmi", fuzzy=TRUE)

# Get back a subset
get_boldid(sci="Osmi", fuzzy=TRUE, rows = 1)
get_boldid(sci="Osmi", fuzzy=TRUE, rows = 1:10)
get_boldid(sci=c("Osmi","Aga"), fuzzy=TRUE, rows = 1)
get_boldid(sci=c("Osmi","Aga"), fuzzy=TRUE, rows = 1:3)

# found
get_boldid('Epicordulia princeps')
get_boldid('Arigomphus furcifer')

# When not found
get_boldid("howdy")
get_boldid(c("Chironomus riparius", "howdy"))
get_boldid("Cordulegaster erronea")
get_boldid("Nasiaeshna pentacantha")

# Narrow down results to a division or rank, or both
## Satyrium example
### Results w/o narrowing
get_boldid("Satyrium")
### w/ phylum
get_boldid("Satyrium", division = "Plantae")
get_boldid("Satyrium", division = "Animalia")

## Rank example
get_boldid("Osmia", fuzzy = TRUE)
get_boldid("Osmia", fuzzy = TRUE, rank = "genus")

# Fuzzy filter on any filtering fields
## uses grep on the inside
get_boldid("Satyrium", division = "anim")
get_boldid("Aga", fuzzy = TRUE, parent = "*idae")

# Convert a boldid without class information to a boldid class
as.boldid(get_boldid("Agapostemon")) # already a boldid, returns the same
as.boldid(get_boldid(c("Agapostemon","Quercus douglasii"))) # same
as.boldid(1973) # numeric
as.boldid(c(1973,101009,98597)) # numeric vector, length > 1
as.boldid("1973") # character
as.boldid(c("1973","101009","98597")) # character vector, length > 1
as.boldid(list("1973","101009","98597")) # list, either numeric or character
## dont check, much faster
as.boldid("1973", check=FALSE)
as.boldid(1973, check=FALSE)
as.boldid(c("1973","101009","98597"), check=FALSE)
as.boldid(list("1973","101009","98597"), check=FALSE)

(out <- as.boldid(c(1973,101009,98597)))
data.frame(out)
as.boldid( data.frame(out) )

# Get all data back
get_boldid_("Osmia", fuzzy=TRUE, rows=1:5)
get_boldid_("Osmia", fuzzy=TRUE, rows=1)
get_boldid_(c("Osmi","Aga"), fuzzy=TRUE, rows = 1:3)
}