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Search BOLD for specimens.

Source: R/bold_specimens.R
bold_specimens.Rd

Search BOLD for specimens.

Usage

bold_specimens(
  taxon = NULL,
  ids = NULL,
  bin = NULL,
  container = NULL,
  institutions = NULL,
  researchers = NULL,
  geo = NULL,
  response = FALSE,
  format = "tsv",
  cleanData = FALSE,
  ...
)

Arguments

taxon

(character) One or more taxonomic name. Optional.

ids

(character|integer|numeric) One or more IDs. Optional. IDs include Sample IDs, Process IDs, Museum IDs and Field IDs.

bin

(character) One or more Barcode Index Number URI. Optional.

container

(character) One or more project codes or dataset codes. Optional.

institutions

(character) One or more institution's name. Optional. Institutions are the Specimen Storing Site.

researchers

(character) One or more researcher names. Optional. Include collectors and specimen identifiers.

geo

(character) One or more geographic sites. Includes countries and province/states.

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.

format

(character) One of xml, json, tsv (default). tsv format gives back a data.frame object. xml gives back parsed XML as xml_document object. 'json' (JavaScript Object Notation) and 'dwc' (Darwin Core Archive) are supported in theory, but the JSON can be malformed, so we don't support that here, and the DWC option actually returns TSV.

cleanData

(logical) If TRUE, the cell values containing only duplicated values (ex : "COI-5P|COI-5P|COI-5P") will be reduce to one value ("COI-5P") and empty string will be change to NA. Default: FALSE

...

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

Note

If using the taxon parameter with another parameter, if the taxon isn't found in the public database, it will act as if no taxon was specified and try to return all the data for the other specified parameter. You can make sure that the taxon you're looking up has public records with bold_stats.

References

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

Examples

if (FALSE) { # \dontrun{
bold_specimens(taxon='Osmia')
bold_specimens(taxon='Osmia', format='xml')
bold_specimens(taxon='Osmia', response=TRUE)
res <- bold_specimens(taxon='Osmia', format='xml', response=TRUE)
res$url
res$status_code
res$response_headers

# More than 1 can be given for all search parameters
bold_specimens(taxon=c('Coelioxys','Osmia'))

## curl debugging
### These examples below take a long time, so you can set a timeout so that
### it stops by X sec
head(bold_specimens(taxon='Osmia', verbose = TRUE))
# head(bold_specimens(geo='Costa Rica', timeout_ms = 6))
} # }