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Legacy alternative to occ_search

Source: R/occ_data.R
occ_data.Rd

Legacy alternative to occ_search

Usage

occ_data(
  taxonKey = NULL,
  scientificName = NULL,
  country = NULL,
  publishingCountry = NULL,
  hasCoordinate = NULL,
  typeStatus = NULL,
  recordNumber = NULL,
  lastInterpreted = NULL,
  continent = NULL,
  geometry = NULL,
  geom_big = "asis",
  geom_size = 40,
  geom_n = 10,
  recordedBy = NULL,
  recordedByID = NULL,
  identifiedByID = NULL,
  basisOfRecord = NULL,
  datasetKey = NULL,
  eventDate = NULL,
  catalogNumber = NULL,
  year = NULL,
  month = NULL,
  decimalLatitude = NULL,
  decimalLongitude = NULL,
  elevation = NULL,
  depth = NULL,
  institutionCode = NULL,
  collectionCode = NULL,
  hasGeospatialIssue = NULL,
  issue = NULL,
  search = NULL,
  mediaType = NULL,
  subgenusKey = NULL,
  repatriated = NULL,
  phylumKey = NULL,
  kingdomKey = NULL,
  classKey = NULL,
  orderKey = NULL,
  familyKey = NULL,
  genusKey = NULL,
  speciesKey = NULL,
  establishmentMeans = NULL,
  degreeOfEstablishment = NULL,
  protocol = NULL,
  license = NULL,
  organismId = NULL,
  publishingOrg = NULL,
  stateProvince = NULL,
  waterBody = NULL,
  locality = NULL,
  occurrenceStatus = "PRESENT",
  gadmGid = NULL,
  coordinateUncertaintyInMeters = NULL,
  verbatimScientificName = NULL,
  eventId = NULL,
  identifiedBy = NULL,
  networkKey = NULL,
  verbatimTaxonId = NULL,
  occurrenceId = NULL,
  organismQuantity = NULL,
  organismQuantityType = NULL,
  relativeOrganismQuantity = NULL,
  iucnRedListCategory = NULL,
  lifeStage = NULL,
  isInCluster = NULL,
  distanceFromCentroidInMeters = NULL,
  skip_validate = TRUE,
  limit = 500,
  start = 0,
  curlopts = list(http_version = 2)
)

Arguments

taxonKey

(numeric) A taxon key from the GBIF backbone. All included and synonym taxa are included in the search, so a search for aves with taxononKey=212 will match all birds, no matter which species. You can pass many keys to occ_search(taxonKey=c(1,212)).

scientificName

A scientific name from the GBIF backbone. All included and synonym taxa are included in the search.

country

(character) The 2-letter country code (ISO-3166-1) in which the occurrence was recorded. enumeration_country().

publishingCountry

The 2-letter country code (as per ISO-3166-1) of the country in which the occurrence was recorded. See enumeration_country().

hasCoordinate

(logical) Return only occurrence records with lat/long data (TRUE) or all records (FALSE, default).

typeStatus

Type status of the specimen. One of many options.

recordNumber

Number recorded by collector of the data, different from GBIF record number.

lastInterpreted

Date the record was last modified in GBIF, in ISO 8601 format: yyyy, yyyy-MM, yyyy-MM-dd, or MM-dd. Supports range queries, 'smaller,larger' (e.g., '1990,1991', whereas '1991,1990' wouldn't work).

continent

The source supplied continent.

  • "africa"

  • "antarctica"

  • "asia"

  • "europe"

  • "north_america"

  • "oceania"

  • "south_america"

Continent is not inferred but only populated if provided by the dataset publisher. Applying this filter may exclude many relevant records.

geometry

(character) Searches for occurrences inside a polygon in Well Known Text (WKT) format. A WKT shape written as either

  • "POINT"

  • "LINESTRING"

  • "LINEARRING"

  • "POLYGON"

  • "MULTIPOLYGON"

For Example, "POLYGON((37.08 46.86,38.06 46.86,38.06 47.28,37.08 47.28, 37.0 46.8))". See also the section WKT below.

geom_big

(character) One"bbox" or "asis" (default).

geom_size

(integer) An integer indicating size of the cell. Default: 40.

geom_n

(integer) An integer indicating number of cells in each dimension. Default: 10.

recordedBy

(character) The person who recorded the occurrence.

recordedByID

(character) Identifier (e.g. ORCID) for the person who recorded the occurrence

identifiedByID

(character) Identifier (e.g. ORCID) for the person who provided the taxonomic identification of the occurrence.

basisOfRecord

(character) The specific nature of the data record. See here.

  • "FOSSIL_SPECIMEN"

  • "HUMAN_OBSERVATION"

  • "MATERIAL_CITATION"

  • "MATERIAL_SAMPLE"

  • "LIVING_SPECIMEN"

  • "MACHINE_OBSERVATION"

  • "OBSERVATION"

  • "PRESERVED_SPECIMEN"

  • "OCCURRENCE"

datasetKey

(character) The occurrence dataset uuid key. That can be found in the dataset page url. For example, "7e380070-f762-11e1-a439-00145 eb45e9a" is the key for Natural History Museum (London) Collection Specimens.

eventDate

(character) Occurrence date in ISO 8601 format: yyyy, yyyy-MM, yyyy-MM-dd, or MM-dd. Supports range queries, 'smaller,larger' ('1990,1991', whereas '1991,1990' wouldn't work).

catalogNumber

(character) An identifier of any form assigned by the source within a physical collection or digital dataset for the record which may not unique, but should be fairly unique in combination with the institution and collection code.

year

The 4 digit year. A year of 98 will be interpreted as AD 98. Supports range queries, 'smaller,larger' (e.g., '1990,1991', whereas 1991, 1990' wouldn't work).

month

The month of the year, starting with 1 for January. Supports range queries, 'smaller,larger' (e.g., '1,2', whereas '2,1' wouldn't work).

decimalLatitude

Latitude in decimals between -90 and 90 based on WGS84. Supports range queries, 'smaller,larger' (e.g., '25,30', whereas '30,25' wouldn't work).

decimalLongitude

Longitude in decimals between -180 and 180 based on WGS84. Supports range queries (e.g., '-0.4,-0.2', whereas '-0.2,-0.4' wouldn't work).

elevation

Elevation in meters above sea level. Supports range queries, 'smaller,larger' (e.g., '5,30', whereas '30,5' wouldn't work).

depth

Depth in meters relative to elevation. For example 10 meters below a lake surface with given elevation. Supports range queries, 'smaller,larger' (e.g., '5,30', whereas '30,5' wouldn't work).

institutionCode

An identifier of any form assigned by the source to identify the institution the record belongs to.

collectionCode

(character) An identifier of any form assigned by the source to identify the physical collection or digital dataset uniquely within the text of an institution.

hasGeospatialIssue

(logical) Includes/excludes occurrence records which contain spatial issues (as determined in our record interpretation), i.e. hasGeospatialIssue=TRUE returns only those records with spatial issues while hasGeospatialIssue=FALSE includes only records without spatial issues. The absence of this parameter returns any record with or without spatial issues.

issue

(character) One or more of many possible issues with each occurrence record. Issues passed to this parameter filter results by the issue. One of many options. See here for definitions.

(character) Query terms. The value for this parameter can be a simple word or a phrase. For example, search="puma"

mediaType

(character) Media type of "MovingImage", "Sound", or "StillImage".

subgenusKey

(numeric) Subgenus classification key.

repatriated

(character) Searches for records whose publishing country is different to the country where the record was recorded in.

phylumKey

(numeric) Phylum classification key.

kingdomKey

(numeric) Kingdom classification key.

classKey

(numeric) Class classification key.

orderKey

(numeric) Order classification key.

familyKey

(numeric) Family classification key.

genusKey

(numeric) Genus classification key.

speciesKey

(numeric) Species classification key.

establishmentMeans

(character) provides information about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans.

  • "Introduced"

  • "Native"

  • "NativeReintroduced"

  • "Vagrant"

  • "Uncertain"

  • "IntroducedAssistedColonisation"

degreeOfEstablishment

(character) Provides information about degree to which an Organism survives, reproduces, and expands its range at the given place and time. One of many options.

protocol

(character) Protocol or mechanism used to provide the occurrence record. One of many options.

license

(character) The type license applied to the dataset or record.

  • "CC0_1_0"

  • "CC_BY_4_0"

  • "CC_BY_NC_4_0"

organismId

(numeric) An identifier for the Organism instance (as opposed to a particular digital record of the Organism). May be a globally unique identifier or an identifier specific to the data set.

publishingOrg

(character) The publishing organization key (a UUID).

stateProvince

(character) The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs.

waterBody

(character) The name of the water body in which the locations occur

locality

(character) The specific description of the place.

occurrenceStatus

(character) Default is "PRESENT". Specify whether search should return "PRESENT" or "ABSENT" data.

gadmGid

(character) The gadm id of the area occurrences are desired from. https://gadm.org/.

coordinateUncertaintyInMeters

A number or range between 0-1,000,000 which specifies the desired coordinate uncertainty. A coordinateUncertainty InMeters=1000 will be interpreted all records with exactly 1000m. Supports range queries, 'smaller,larger' (e.g., '1000,10000', whereas '10000,1000' wouldn't work).

verbatimScientificName

(character) Scientific name as provided by the source.

eventId

(character) identifier(s) for a sampling event.

identifiedBy

(character) names of people, groups, or organizations.

networkKey

(character) The occurrence network key (a uuid) who assigned the Taxon to the subject.

verbatimTaxonId

(character) The taxon identifier provided to GBIF by the data publisher.

occurrenceId

(character) occurrence id from source.

organismQuantity

A number or range which specifies the desired organism quantity. An organismQuantity=5 will be interpreted all records with exactly 5. Supports range queries, smaller,larger (e.g., '5,20', whereas '20,5' wouldn't work).

organismQuantityType

(character) The type of quantification system used for the quantity of organisms. For example, "individuals" or "biomass".

relativeOrganismQuantity

(numeric) A relativeOrganismQuantity=0.1 will be interpreted all records with exactly 0.1 The relative measurement of the quantity of the organism (a number between 0-1). Supports range queries, "smaller,larger" (e.g., '0.1,0.5', whereas '0.5,0.1' wouldn't work).

iucnRedListCategory

(character) The IUCN threat status category.

  • "NE" (Not Evaluated)

  • "DD" (Data Deficient)

  • "LC" (Least Concern)

  • "NT" (Near Threatened)

  • "VU" (Vulnerable)

  • "EN" (Endangered)

  • "CR" (Critically Endangered)

  • "EX" (Extinct)

  • "EW" (Extinct in the Wild)

lifeStage

(character) the life stage of the occurrence. One of many options.

isInCluster

(logical) identify potentially related records on GBIF.

distanceFromCentroidInMeters

A number or range. A value of "2000,*" means at least 2km from known centroids. A value of "0" would mean occurrences exactly on known centroids. A value of "0,2000" would mean within 2km of centroids. Max value is 5000.

skip_validate

(logical) whether to skip wellknown::validate_wkt call or not. passed down to check_wkt(). Default: TRUE

limit

Number of records to return. Default: 500. Note that the per request maximum is 300, but since we set it at 500 for the function, we do two requests to get you the 500 records (if there are that many). Note that there is a hard maximum of 100,000, which is calculated as the limit+start, so start=99,000 and limit=2000 won't work

start

Record number to start at. Use in combination with limit to page through results. Note that we do the paging internally for you, but you can manually set the start parameter

curlopts

(list)

Value

An object of class gbif_data, which is a S3 class list, with slots for metadata (meta) and the occurrence data itself (data), and with attributes listing the user supplied arguments and whether it was a "single" or "many" search; that is, if you supply two values of the datasetKey parameter to searches are done, and it's a "many". meta is a list of length four with offset, limit, endOfRecords and count fields. data is a tibble (aka data.frame)

Details

This function is a legacy alternative to occ_search(). It is not recommended to use occ_data() as it is not as flexible as occ_search(). New search terms will not be added to this function and it is only supported for legacy reasons.