download_predicate_dsl {rgbif} | R Documentation |
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 |
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)
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))