R: Search Barcode of Life for taxonomic IDs

bold_search {taxize} | R Documentation

## Search Barcode of Life for taxonomic IDs

### Description

Search Barcode of Life for taxonomic IDs

### Usage

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

### Arguments

`name` | (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.
`...` | Further args passed on to `GET`, main purpose being curl debugging

### Details

You must provide one of name or id to this function. The other parameters are optional. Note that when passing in `name`, `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(name="Apis")
    bold_search(name="Agapostemon")
    bold_search(name="Poa")

    # Fuzzy search
    head(bold_search(name="Po", fuzzy=TRUE))
    head(bold_search(name="Aga", fuzzy=TRUE))

    # Many names
    bold_search(name=c("Apis","Puma concolor"))
    nms <- names_list('species')
    bold_search(name=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)

[Package taxize version 0.9.0 Index]