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(searchterm, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, ask = TRUE, verbose = TRUE, rows = NA, rank = NULL, division = NULL, parent = NULL, ...)
as.boldid(x, check = TRUE)
"as.boldid"(x, check = TRUE)
"as.boldid"(x, check = TRUE)
"as.boldid"(x, check = TRUE)
"as.boldid"(x, check = TRUE)
"as.boldid"(x, check = TRUE)
"as.data.frame"(x, ...)
get_boldid_(searchterm, verbose = TRUE, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, rows = NA, ...)

Arguments

searchterm

character; A vector of common or scientific names.

fuzzy

(logical) Whether to use fuzzy search or not (default: FALSE).

dataTypes

(character) Specifies the datatypes that will be returned. See Details 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.

verbose

logical; should progress be printed?

rows

numeric; Any number from 1 to inifity. 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.

...

Curl options passed on to GET

Input to as.boldid

check

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

Value

A vector of BOLD ids. If a taxon is not found NA. If more than one BOLD ID is found the function asks for user input (if ask = TRUE), otherwise returns NA. Comes with an attribute match to investigate the reason for NA (either 'not found', 'found' or if ask = FALSE 'NA due to ask=FALSE')

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

## Not run: 
# get_boldid(searchterm = "Agapostemon")
# get_boldid(searchterm = "Chironomus riparius")
# get_boldid(c("Chironomus riparius","Quercus douglasii"))
# splist <- names_list('species')
# get_boldid(splist, verbose=FALSE)
# 
# # Fuzzy searching
# get_boldid(searchterm="Osmi", fuzzy=TRUE)
# 
# # Get back a subset
# get_boldid(searchterm="Osmi", fuzzy=TRUE, rows = 1)
# get_boldid(searchterm="Osmi", fuzzy=TRUE, rows = 1:10)
# get_boldid(searchterm=c("Osmi","Aga"), fuzzy=TRUE, rows = 1)
# get_boldid(searchterm=c("Osmi","Aga"), fuzzy=TRUE, rows = 1:3)
# 
# # When not found
# get_boldid("howdy")
# get_boldid(c("Chironomus riparius", "howdy"))
# get_boldid('Epicordulia princeps')
# get_boldid('Arigomphus furcifer')
# 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 = "Plants")
# get_boldid("Satyrium", division = "Animals")
# 
# ## 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)
# 
# # Curl options
# library("httr")
# get_boldid(searchterm = "Agapostemon", config=verbose())
# get_boldid(searchterm = "Agapostemon", config=progress())
# 
# # use curl options
# library("httr")
# get_boldid("Agapostemon", config=verbose())
# bb <- get_boldid("Agapostemon", config=progress())
# ## End(Not run)