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Search BOLD for taxonomy data by BOLD ID.

Source: R/bold_tax_id2.R
bold_tax_id2.Rd

Search BOLD for taxonomy data by BOLD ID.

Usage

bold_tax_id2(
  id,
  dataTypes = "basic",
  includeTree = FALSE,
  response = FALSE,
  ...
)

Arguments

id

(integer|numeric|character) One or more BOLD taxonomic identifiers. required.

dataTypes

(character) One or more BOLD data types: 'basic', 'stats', 'geo', 'images'/'img', 'sequencinglabs'/'labs', 'depository'/'depo', 'thirdparty'/'wiki' or 'all' (default: 'basic'). Specifies the information that will be returned, see details.

includeTree

(logical) If TRUE (default: FALSE), returns the information for parent taxa as well as the specified taxon, see details.

response

(logical) Default : FALSE. If TRUE, returns the object from the Curl call. Useful for debugging and getting more detailed info on the API call.

...

Further args passed on to crul::verb-GET, main purpose being curl debugging

dataTypes

"basic" returns basic taxonomy info: includes taxid, taxon name, tax rank, tax division, parent taxid, parent taxon name. "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. "images" returns specimen images: includes copyright information, image URL, image metadata. "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 summary, wikipedia_summary URL. "all" returns all information: identical to specifying all data types at once.

includeTree

When includeTree is set to true, for the dataTypes other than 'basic' the information of the parent taxa are identified by their taxonomic id only. To get their ranks and names too, make sure 'basic' is in dataTypes.

References

http://v4.boldsystems.org/index.php/resources/api?type=taxonomy

See also

bold_tax_name, bold_get_attr, bold_get_errors, bold_get_params

Examples

if (FALSE) { # \dontrun{
bold_tax_id2(id = 88899)
bold_tax_id2(id = 88899, includeTree = TRUE)
bold_tax_id2(id = 88899, includeTree = TRUE, dataTypes = "stats")
bold_tax_id2(id = c(88899, 125295))

## dataTypes parameter
bold_tax_id2(id = 88899, dataTypes = "basic")
bold_tax_id2(id = 88899, dataTypes = "stats")
bold_tax_id2(id = 88899, dataTypes = "images")
bold_tax_id2(id = 88899, dataTypes = "geo")
bold_tax_id2(id = 88899, dataTypes = "sequencinglabs")
bold_tax_id2(id = 88899, dataTypes = "depository")
bold_tax_id2(id = 88899, dataTypes = "thirdparty")
bold_tax_id2(id = 88899, dataTypes = "all")
bold_tax_id2(id = c(88899, 125295), dataTypes = c("basic", "geo"))
bold_tax_id2(id = c(88899, 125295), dataTypes = c("basic", "stats", "images"))

## Passing in NA
bold_tax_id2(id = NA)
bold_tax_id2(id = c(88899, 125295, NA))

## get http response object only
bold_tax_id2(id = 88899, response = TRUE)
bold_tax_id2(id = c(88899, 125295), response = TRUE)

## curl debugging
bold_tax_id2(id = 88899, verbose = TRUE)
} # }