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Get BOLD stats

Source: R/bold_stats.R
bold_stats.Rd

Get BOLD stats

Usage

bold_stats(
  taxon = NULL,
  ids = NULL,
  bin = NULL,
  container = NULL,
  institutions = NULL,
  researchers = NULL,
  geo = NULL,
  dataType = "drill_down",
  response = FALSE,
  simplify = 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.

dataType

(character) one of "drill_down"(default) or "overview". "drill_down": a detailed summary of information which provides record counts by BINs, Countries, Storing Institutions, Orders, Families, Genus, Species. "overview": the total record counts of BINs, Countries, Storing Institutions, Orders, Families, Genus, Species. The record counts include all gene markers, not only COI. To see the drill down of markers use bold_tax_id2 with "stats" as dataTypes.

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.

simplify

(logical) whether the returned list should be simplified to a data.frame. See Details.

...

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

Value

By default, returns a nested list with the number of total records, the number of records with a species name, then for each of bins, countries, depositories, order, family, genus and species, the total count and the drill down of the records by up to 10 entities of that category. If simplify is set to TRUE, returns a list of length 2 : the overview data (number of total records, the number of records with a species name, and the total counts) simplified as a data.frame of 1 row and 9 columns and the drill_down data simplified to a one level list of data.frame. When dataType is set to "overview", returns a nested list with the number of total records, the number of records with a species name, and the total count for each of bins, countries, depositories, order, family, genus and species. If simplify is set to TRUE, returns a data.frame of 1 row and 9 columns.

References

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

Examples

if (FALSE) { # \dontrun{
x <- bold_stats(taxon='Osmia')
x$total_records
x$records_with_species_name
x$bins
x$countries
x$depositories
x$order
x$family
x$genus
x$species

# just get all counts
lapply(Filter(is.list, x), `[[`, "count")

bold_stats(taxon='Osmia', dataType = "overview", simplified = TRUE)

x <- bold_stats(taxon='Osmia', simplified = TRUE)
x$overview
x$drill_down

res <- bold_stats(taxon='Osmia', response=TRUE)
res$url
res$status_code
res$response_headers

# More than 1 can be given for all search parameters

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