Search datasets in GBIF.

This function does not search occurrence data, only metadata on the datasets that contain occurrence data.

Usage

dataset_search(
  query = NULL,
  country = NULL,
  type = NULL,
  keyword = NULL,
  publishingOrg = NULL,
  hostingOrg = NULL,
  publishingCountry = NULL,
  decade = NULL,
  facet = NULL,
  facetMincount = NULL,
  facetMultiselect = NULL,
  limit = 100,
  start = NULL,
  pretty = FALSE,
  return = NULL,
  curlopts = list()
)

Arguments

query

Query term(s) for full text search. The value for this parameter can be a simple word or a phrase. Wildcards can be added to the simple word parameters only, e.g. q=*puma*

country

NOT YET IMPLEMENTED. Filters by country as given in isocodes$gbif_name, e.g. country="CANADA"

type

Type of dataset, options include occurrene, metadata, checklist, sampling_event (http://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/DatasetType.html)

keyword

Keyword to search by. Datasets can be tagged by keywords, which you can search on. The search is done on the merged collection of tags, the dataset keywordCollections and temporalCoverages.

publishingOrg

Publishing organization. A uuid string. See organizations

hostingOrg

Hosting organization. A uuid string. See organizations

publishingCountry

Publishing country. See options at isocodes$gbif_name

decade

Decade, e.g., 1980. Filters datasets by their temporal coverage broken down to decades. Decades are given as a full year, e.g. 1880, 1960, 2000, etc, and will return datasets wholly contained in the decade as well as those that cover the entire decade or more. Facet by decade to get the break down, e.g. /search?facet=DECADE&facet_only=true (see example below)

facet

A list of facet names used to retrieve the 100 most frequent values for a field. Allowed facets are: datasetKey, highertaxonKey, rank, status, extinct, habitat, and nameType. Additionally threat and nomenclaturalStatus are legal values but not yet implemented, so data will not yet be returned for them.

facetMincount

Used in combination with the facet parameter. Set facetMincount={#} to exclude facets with a count less than #

facetMultiselect

Used in combination with the facet parameter. Set facetMultiselect=true to still return counts for values that are not currently filtered

limit

Number of records to return. Default: 100. Maximum: 1000.

start

Record number to start at. Default: 0. Use in combination with limit to page through results.

pretty

Print informative metadata using cat. Not easy to manipulate output though.

return

Defunct. All components are returned; index to the one(s) you want

curlopts

list of named curl options passed on to HttpClient. see curl::curl_options for curl options

Value

A data.frame, list, or message printed to console (using pretty=TRUE).

Repeat parmeter inputs

Some parameters can tak emany inputs, and treated as 'OR' (e.g., a or b or c). The following take many inputs:

• type

• keyword

• publishingOrg

• hostingOrg

• publishingCountry

• decade

References

https://www.gbif.org/developer/registry#datasetSearch

Examples

if (FALSE) {
# Gets all datasets of type "OCCURRENCE".
dataset_search(type="OCCURRENCE", limit = 10)

# Fulltext search for all datasets having the word "amsterdam" somewhere in
# its metadata (title, description, etc).
dataset_search(query="amsterdam", limit = 10)

# Limited search
dataset_search(type="OCCURRENCE", limit=2)
dataset_search(type="OCCURRENCE", limit=2, start=10)

# Return metadata in a more human readable way (hard to manipulate though)
dataset_search(type="OCCURRENCE", pretty=TRUE, limit = 10)

# Search by country code. Lookup isocodes first, and use US for United States
isocodes[agrep("UNITED", isocodes$gbif_name),]
dataset_search(country="US", limit = 10)

# Search by decade
dataset_search(decade=1980, limit = 10)

# Faceting
## just facets
dataset_search(facet="decade", facetMincount="10", limit=0)

## data and facets
dataset_search(facet="decade", facetMincount="10", limit=2)

# Some parameters accept many inputs, treated as OR
dataset_search(type = c("metadata", "checklist"))$data
dataset_search(keyword = c("fern", "algae"))$data
dataset_search(publishingOrg = c("e2e717bf-551a-4917-bdc9-4fa0f342c530",
  "90fd6680-349f-11d8-aa2d-b8a03c50a862"))$data
dataset_search(hostingOrg = c("c5f7ef70-e233-11d9-a4d6-b8a03c50a862",
  "c5e4331-7f2f-4a8d-aa56-81ece7014fc8"))$data
dataset_search(publishingCountry = c("DE", "NZ"))$data
dataset_search(decade = c(1910, 1930))$data

## curl options
dataset_search(facet="decade", facetMincount="10", limit=2,
  curlopts = list(verbose=TRUE))
}