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rgbif

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_notnull(key)

pred_or(..., .list = list())

pred_and(..., .list = list())

pred_in(key, value)

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 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

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). 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)

  • scientificName (SCIENTIFIC_NAME)

  • country (COUNTRY)

  • publishingCountry (PUBLISHING_COUNTRY)

  • hasCoordinate (HAS_COORDINATE)

  • hasGeospatialIssue (HAS_GEOSPATIAL_ISSUE)

  • typeStatus (TYPE_STATUS)

  • recordNumber (RECORD_NUMBER)

  • lastInterpreted (LAST_INTERPRETED)

  • continent (CONTINENT)

  • geometry (GEOMETRY)

  • basisOfRecord (BASIS_OF_RECORD)

  • datasetKey (DATASET_KEY)

  • eventDate (EVENT_DATE)

  • catalogNumber (CATALOG_NUMBER)

  • 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)

  • establishmentMeans (ESTABLISHMENT_MEANS)

  • coordinateUncertaintyInMeters (COORDINATE_UNCERTAINTY_IN_METERS)

References

See Also

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("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))
rgbif

Interface to the Global 'Biodiversity' Information Facility API

v3.5.2
MIT + file LICENSE
Authors
Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>), Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>), Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>), Laurens Geffert [ctb], Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>), Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>), rOpenSci [fnd] (https://ropensci.org/)
Initial release

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