bold_search: Search Barcode of Life for taxonomic IDs

In ropensci/taxize: Taxonomic Information from Around the Web

Search Barcode of Life for taxonomic IDs

Description

Search Barcode of Life for taxonomic IDs

Usage

bold_search(
  sci = NULL,
  id = NULL,
  fuzzy = FALSE,
  dataTypes = "basic",
  includeTree = FALSE,
  response = FALSE,
  name = NULL,
  ...
)

Arguments

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: FALSE). Only used if name passed.
dataTypes	(character) Specifies the datatypes that will be returned. See Details for options. This variable is ignored if name parameter is passed, but is used if the id parameter is passed.
includeTree	(logical) If TRUE (default: FALSE), returns a list containing information for parent taxa as well as the specified taxon. Only used if id passed.
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 sci
...	named curl options passed on to crul::verb-GET

Details

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.

Value

A list of data.frame's.

References

http://www.boldsystems.org/index.php/resources/api

Examples

## 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)

ropensci/taxize documentation built on Jan. 25, 2024, 6:49 p.m.