Get the BOLD (Barcode of Life) code for a search term.
Get the BOLD (Barcode of Life) code for a search term.
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 class 'boldid' as.boldid(x, check = TRUE) ## S3 method for class 'character' as.boldid(x, check = TRUE) ## S3 method for class 'list' as.boldid(x, check = TRUE) ## S3 method for class 'numeric' as.boldid(x, check = TRUE) ## S3 method for class 'data.frame' as.boldid(x, check = TRUE) ## S3 method for class 'boldid' as.data.frame(x, ...) get_boldid_( sci, messages = TRUE, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, rows = NA, searchterm = NULL, ... )
sci |
character; A vector of scientific names. Or,
a |
fuzzy |
(logical) Whether to use fuzzy search or not (default: FALSE). |
dataTypes |
(character) Specifies the datatypes that will be returned.
See |
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 |
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 |
division |
(character) A division (aka phylum) name. Optional. See |
parent |
(character) A parent name (i.e., the parent of the target search
taxon). Optional. See |
searchterm |
Deprecated, see |
... |
Curl options passed on to |
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
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.
Other taxonomic-ids:
get_eolid(),
get_gbifid(),
get_ids(),
get_iucn(),
get_natservid(),
get_nbnid(),
get_pow(),
get_tolid(),
get_tpsid(),
get_tsn(),
get_uid(),
get_wiki(),
get_wormsid()
## Not run:
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)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.