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Search for dataset metadata.

Source: R/dataset_export.R, R/dataset_search.r, R/dataset_suggest.r
dataset_search.Rd

Search for dataset metadata.

Usage

dataset_export(
  query = NULL,
  type = NULL,
  publishingCountry = NULL,
  subtype = NULL,
  license = NULL,
  keyword = NULL,
  publishingOrg = NULL,
  hostingOrg = NULL,
  endorsingNodeKey = NULL,
  decade = NULL,
  projectId = NULL,
  hostingCountry = NULL,
  networkKey = NULL,
  doi = NULL
)

dataset_search(
  query = NULL,
  type = NULL,
  publishingCountry = NULL,
  subtype = NULL,
  license = NULL,
  keyword = NULL,
  publishingOrg = NULL,
  hostingOrg = NULL,
  endorsingNodeKey = NULL,
  decade = NULL,
  projectId = NULL,
  hostingCountry = NULL,
  networkKey = NULL,
  doi = NULL,
  facet = NULL,
  facetLimit = NULL,
  facetOffset = NULL,
  facetMincount = NULL,
  facetMultiselect = NULL,
  limit = 100,
  start = NULL,
  description = FALSE,
  curlopts = list()
)

dataset_suggest(
  query = NULL,
  type = NULL,
  publishingCountry = NULL,
  subtype = NULL,
  license = NULL,
  keyword = NULL,
  publishingOrg = NULL,
  hostingOrg = NULL,
  endorsingNodeKey = NULL,
  decade = NULL,
  projectId = NULL,
  hostingCountry = NULL,
  networkKey = NULL,
  doi = NULL,
  limit = 100,
  start = NULL,
  description = FALSE,
  curlopts = list()
)

Arguments

query

Simple full text search parameter. The value for this parameter can be a simple word or a phrase. Wildcards are not supported.

type

The primary type of the dataset. Available values: "OCCURRENCE", "CHECKLIST", "METADATA", "SAMPLING_EVENT", "MATERIAL_ENTITY".

publishingCountry

Filters datasets by their owning organization's country given as a ISO 639-1 (2 letter) country code.

subtype

The sub-type of the dataset.The sub-type of the dataset. Available values: "TAXONOMIC_AUTHORITY", "NOMENCLATOR_AUTHORITY", "INVENTORY_THEMATIC", "INVENTORY_REGIONAL", "GLOBAL_SPECIES_DATASET", "DERIVED_FROM_OCCURRENCE", "SPECIMEN", "OBSERVATION".

license

The dataset's licence. Available values: "CC0_1_0", "CC_BY_4_0", "CC_BY_NC_4_0", "UNSPECIFIED", "UNSUPPORTED".

keyword

Filters datasets by a case insensitive plain text keyword. The search is done on the merged collection of tags, the dataset keywordCollections and temporalCoverages.

publishingOrg

Filters datasets by their publishing organization UUID key.

hostingOrg

Filters datasets by their hosting organization UUID key

endorsingNodeKey

Node UUID key that endorsed this dataset's publisher.

decade

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. Ranges can be used like this "1800,1900".

projectId

Filter or facet based on the project ID of a given dataset. A dataset can have a project id if it is the result of a project. Multiple datasets can have the same project id.

hostingCountry

Filters datasets by their hosting organization's country given as a ISO 639-1 (2 letter) country code.

networkKey

Filters network UUID associated to a dataset.

doi

DOI of the dataset.

facet

A facet name used to retrieve the most frequent values for a field.

facetLimit

Facet parameters allow paging requests using the parameters facetOffset and facetLimit.

facetOffset

Facet parameters allow paging requests using the parameters facetOffset and facetLimit

facetMincount

Used in combination with the facet parameter.

facetMultiselect

Used in combination with the facet parameter.

limit

Controls the number of results in the page. Using too high a value will be overwritten with the default maximum threshold, depending on the service. Sensible defaults are used so this may be omitted.

start

Determines the offset for the search results. A limit of 20 and offset of 40 will get the third page of 20 results. Some services have a maximum offset.

description

Logical whether to return descriptions.

curlopts

options passed on to crul::HttpClient.

Value

A list for dataset_search(). A tibble for dataset_export().

Details

dataset_search() searches and returns metadata on GBIF datasets from the registry. This function does not search occurrence data, only metadata on the datasets that contain may contain occurrence data. It also searches over other dataset types, such checklist and metadata datasets. Only a sample of results is returned.

dataset_export() function will download a tibble of the results of a dataset_search(). This function is primarily useful if you want the full results of a dataset_search().

Use dataset_search(facet="x",limit=0)$facets to get simple group by counts for different parameters.

References

https://techdocs.gbif.org/en/openapi/v1/registry#/Datasets/searchDatasets

Examples

if (FALSE) { # \dontrun{
# search metadata on all datasets and return a sample
dataset_search()
# dataset_export() # download info on all +90K datasets 

dataset_search(publishingCountry = "US")
dataset_search(type = "OCCURRENCE") 
dataset_search(keyword = "bird")
dataset_search(subtype = "TAXONOMIC_AUTHORITY") 
dataset_search(license = "CC0_1_0") 
dataset_search(query = "frog") 
dataset_search(publishingCountry = "UA") 
dataset_search(publishingOrg = "e2e717bf-551a-4917-bdc9-4fa0f342c530") 
dataset_search(hostingOrg = "7ce8aef0-9e92-11dc-8738-b8a03c50a862") 
dataset_search(decade="1890,1990",limit=5)
dataset_search(projectId = "GRIIS") 
dataset_search(hostingCountry = "NO") 
dataset_search(networkKey = "99d66b6c-9087-452f-a9d4-f15f2c2d0e7e") 
dataset_search(doi='10.15468/aomfnb') 

# search multiple values 
dataset_search(projectId = "GRIIS;BID-AF2020-140-REG") 
dataset_search(hostingCountry = "NO;SE")
dataset_search(doi="10.15468/aomfnb;10.15468/igasai")

# multiple filters
dataset_search(license = "CC0_1_0",subtype = "TAXONOMIC_AUTHORITY")
# dataset_export(license = "CC0_1_0",subtype = "TAXONOMIC_AUTHORITY")

# using dataset export to get all datasets 
dataset_export(decade="1800,1900")
dataset_export(projectId="GRIIS")

# get simple group by counts 
dataset_search(facet="type",limit=0,facetLimit=5)$facets 
dataset_search(facet="publishingCountry",limit=0,facetLimit=5)$facets
dataset_search(facet="license",limit=0,facetLimit=5, facetMincount=10000)

} # }