Search Barcode of Life for taxonomic IDs
Search Barcode of Life for taxonomic IDs
bold_search( sci = NULL, id = NULL, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, response = FALSE, name = NULL, ... )
sci |
(character) One or more scientific names. |
id |
(integer) One or more BOLD taxonomic identifiers. |
fuzzy |
(logical) Whether to use fuzzy search or not (default: |
dataTypes |
(character) Specifies the datatypes that will be returned.
See Details for options. This variable is ignored if |
includeTree |
(logical) If TRUE (default: FALSE), returns a list containing
information for parent taxa as well as the specified taxon. Only used if |
response |
(logical) Note that response is the object that returns from the curl call, useful for debugging, and getting detailed info on the API call. |
name |
Deprecated, see |
... |
named curl options passed on to crul::verb-GET |
You must provide one of sci or id to this function. The other
parameters are optional. Note that when passing in sci, fuzzy can be used
as well, while if id is passed, then fuzzy is ignored, and dataTypes
includeTree can be used.
Options for dataTypes parameter:
all returns all data
basic returns basic taxon information
images returns specimen image. Includes copyright information, image URL, image metadata.
stats Returns specimen and sequence statistics. Includes public species count, public BIN count, public marker counts, public record count, specimen count, sequenced specimen count, barcode specimen count, species count, barcode species count.
geo Returns collection site information. Includes country, collection site map.
sequencinglabs Returns sequencing labs. Includes lab name, record count.
depository Returns specimen depositories. Includes depository name, record count.
thirdparty Returns information from third parties. Includes wikipedia summary, wikipedia URL, GBIF map.
A list of data.frame's.
http://www.boldsystems.org/index.php/resources/api
## Not run:
# A basic example
bold_search(sci="Apis")
bold_search(sci="Agapostemon")
bold_search(sci="Poa")
# Fuzzy search
head(bold_search(sci="Po", fuzzy=TRUE))
head(bold_search(sci="Aga", fuzzy=TRUE))
# Many names
bold_search(sci=c("Apis","Puma concolor"))
nms <- names_list('species')
bold_search(sci=nms)
# Searching by ID - dataTypes can be used, and includeTree can be used
bold_search(id=88899)
bold_search(id=88899, dataTypes="stats")
bold_search(id=88899, dataTypes="geo")
bold_search(id=88899, dataTypes="basic")
bold_search(id=88899, includeTree=TRUE)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.