rgbif (version 3.8.2)

download_predicate_dsl: Download predicate DSL (domain specific language)

Description

Download predicate DSL (domain specific language)

Usage

pred(key, value)
pred_gt(key, value)
pred_gte(key, value)
pred_lt(key, value)
pred_lte(key, value)
pred_not(...)
pred_like(key, value)
pred_within(value)
pred_isnull(key)
pred_notnull(key)
pred_or(..., .list = list())
pred_and(..., .list = list())
pred_in(key, value)
pred_default()

Arguments

key

(character) the key for the predicate. See "Keys" below

value

(various) the value for the predicate

..., .list

For pred_or() or pred_and(), one or more objects of class occ_predicate, created by any pred* function

predicate methods and their equivalent types

pred* functions are named for the 'type' of operation they do, following the terminology used by GBIF, see https://www.gbif.org/developer/occurrence#predicates

Function names are given, with the equivalent GBIF type value (e.g., pred_gt and greaterThan)

The following functions take one key and one value:

• pred: equals

• pred_lt: lessThan

• pred_lte: lessThanOrEquals

• pred_gt: greaterThan

• pred_gte: greaterThanOrEquals

• pred_like: like

The following function is only for geospatial queries, and only accepts a WKT string:

• pred_within: within

The following function is only for stating the you don't want a key to be null, so only accepts one key:

• pred_notnull: isNotNull

The following function is only for stating that you want a key to be null.

• pred_isnull : isNull

The following two functions accept multiple individual predicates, separating them by either "and" or "or":

• pred_and: and

• pred_or: or

The not predicate accepts one predicate; that is, this negates whatever predicate is passed in, e.g., not the taxonKey of 12345:

• pred_not: not

The following function is special in that it accepts a single key but many values; stating that you want to search for all the values:

• pred_in: in

The following function will apply commonly used defaults.

• pred_default

Using pred_default() is equivalent to running:

  pred_and(
   pred("HAS_GEOSPATIAL_ISSUE",FALSE),
   pred("HAS_COORDINATE",TRUE),
   pred("OCCURRENCE_STATUS","PRESENT"),
   pred_not(pred_in("BASIS_OF_RECORD",
    c("FOSSIL_SPECIMEN","LIVING_SPECIMEN")))
  )

What happens internally

Internally, the input to pred* functions turns into JSON to be sent to GBIF. For example ...

pred_in("taxonKey", c(2480946, 5229208)) gives:

{
   "type": "in",
   "key": "TAXON_KEY",
   "values": ["2480946", "5229208"]
 }

pred_gt("elevation", 5000) gives:

{
   "type": "greaterThan",
   "key": "ELEVATION",
   "value": "5000"
}

pred_or(pred("taxonKey", 2977832), pred("taxonKey", 2977901)) gives:

{
  "type": "or",
  "predicates": [
     {
       "type": "equals",
       "key": "TAXON_KEY",
       "value": "2977832"
     },
     {
       "type": "equals",
       "key": "TAXON_KEY",
       "value": "2977901"
     }
  ]
}

Keys

Acceptable arguments to the key parameter are (with the version of the key in parens that must be sent if you pass the query via the body parameter; see below for examples). You can also use the 'ALL_CAPS' version of a key if you prefer. Open an issue in the GitHub repository for this package if you know of a key that should be supported that is not yet.

• taxonKey (TAXON_KEY)

• acceptedTaxonKey (ACCEPTED_TAXON_KEY)

• kingdomKey (KINGDOM_KEY)

• phylumKey (PHYLUM_KEY)

• classKey (CLASS_KEY)

• orderKey (ORDER_KEY)

• familyKey (FAMILY_KEY)

• genusKey (GENUS_KEY)

• subgenusKey (SUBGENUS_KEY)

• speciesKey (SPECIES_KEY)

• scientificName (SCIENTIFIC_NAME)

• country (COUNTRY)

• publishingCountry (PUBLISHING_COUNTRY)

• hasCoordinate (HAS_COORDINATE)

• hasGeospatialIssue (HAS_GEOSPATIAL_ISSUE)

• typeStatus (TYPE_STATUS)

• recordNumber (RECORD_NUMBER)

• lastInterpreted (LAST_INTERPRETED)

• modified (MODIFIED)

• continent (CONTINENT)

• geometry (GEOMETRY)

• basisOfRecord (BASIS_OF_RECORD)

• datasetKey (DATASET_KEY)

• datasetID/datasetId (DATASET_ID)

• eventDate (EVENT_DATE)

• catalogNumber (CATALOG_NUMBER)

• otherCatalogNumbers (OTHER_CATALOG_NUMBERS)

• year (YEAR)

• month (MONTH)

• decimalLatitude (DECIMAL_LATITUDE)

• decimalLongitude (DECIMAL_LONGITUDE)

• elevation (ELEVATION)

• depth (DEPTH)

• institutionCode (INSTITUTION_CODE)

• collectionCode (COLLECTION_CODE)

• issue (ISSUE)

• mediatype (MEDIA_TYPE)

• recordedBy (RECORDED_BY)

• recordedById/recordedByID (RECORDED_BY_ID)

• establishmentMeans (ESTABLISHMENT_MEANS)

• coordinateUncertaintyInMeters (COORDINATE_UNCERTAINTY_IN_METERS)

• gadm (GADM_GID) (for the Database of Global Administrative Areas)

• level0Gid (GADM_LEVEL_0_GID)

• level1Gid (GADM_LEVEL_1_GID)

• level2Gid (GADM_LEVEL_2_GID)

• level3Gid (GADM_LEVEL_3_GID)

• stateProvince (STATE_PROVINCE)

• occurrenceStatus (OCCURRENCE_STATUS)

• publishingOrg (PUBLISHING_ORG)

• occurrenceId/occurrenceID (OCCURRENCE_ID)

• eventId/eventID (EVENT_ID)

• parentEventId/parentEventID (PARENT_EVENT_ID)

• identifiedBy (IDENTIFIED_BY)

• identifiedById/identifiedByID (IDENTIFIED_BY_ID)

• license (LICENSE)

• locality(LOCALITY)

• pathway (PATHWAY)

• preparations (PREPARATIONS)

• networkKey (NETWORK_KEY)

• organismId/organismID (ORGANISM_ID)

• organismQuantity (ORGANISM_QUANTITY)

• organismQuantityType (ORGANISM_QUANTITY_TYPE)

• protocol (PROTOCOL)

• relativeOrganismQuantity (RELATIVE_ORGANISM_QUANTITY)

• repatriated (REPATRIATED)

• sampleSizeUnit (SAMPLE_SIZE_UNIT)

• sampleSizeValue (SAMPLE_SIZE_VALUE)

• samplingProtocol (SAMPLING_PROTOCOL)

• verbatimScientificName (VERBATIM_SCIENTIFIC_NAME)

• taxonID/taxonId (TAXON_ID)

• taxonomicStatus (TAXONOMIC_STATUS)

• waterBody (WATER_BODY)

• iucnRedListCategory (IUCN_RED_LIST_CATEGORY)

• degreeOfEstablishment (DEGREE_OF_ESTABLISHMENT)

• isInCluster (IS_IN_CLUSTER)

• lifeStage (LIFE_STAGE)

• distanceFromCentroidInMeters (DISTANCE_FROM_CENTROID_IN_METERS)

• gbifId (GBIF_ID)

• institutionKey (INSTITUTION_KEY)

References

Download predicates docs: https://www.gbif.org/developer/occurrence#predicates

See Also

Other downloads: occ_download_cached(), occ_download_cancel(), occ_download_dataset_activity(), occ_download_datasets(), occ_download_get(), occ_download_import(), occ_download_list(), occ_download_meta(), occ_download_queue(), occ_download_wait(), occ_download()

Examples

pred("taxonKey", 3119195)
pred_gt("elevation", 5000)
pred_gte("elevation", 5000)
pred_lt("elevation", 1000)
pred_lte("elevation", 1000)
pred_within("POLYGON((-14 42, 9 38, -7 26, -14 42))")
pred_and(pred_within("POLYGON((-14 42, 9 38, -7 26, -14 42))"),
  pred_gte("elevation", 5000))
pred_or(pred_lte("year", 1989), pred("year", 2000))
pred_and(pred_lte("year", 1989), pred("year", 2000))
pred_in("taxonKey", c(2977832, 2977901, 2977966, 2977835))
pred_in("basisOfRecord", c("MACHINE_OBSERVATION", "HUMAN_OBSERVATION"))
pred_not(pred("taxonKey", 729))
pred_like("catalogNumber", "PAPS5-560%")
pred_notnull("issue")
pred("basisOfRecord", "LITERATURE")
pred("hasCoordinate", TRUE)
pred("stateProvince", "California")
pred("hasGeospatialIssue", FALSE)
pred_within("POLYGON((-14 42, 9 38, -7 26, -14 42))")
pred_or(pred("taxonKey", 2977832), pred("taxonKey", 2977901),
  pred("taxonKey", 2977966))
pred_in("taxonKey", c(2977832, 2977901, 2977966, 2977835))