Adding new occ_search terms

R/occ_count.r

@@ -212,6 +212,61 @@ occ_count <- function(...,occurrenceStatus="PRESENT", curlopts = list()) {
  lifeStage = args$lifeStage,
  isInCluster = args$isInCluster,
  distanceFromCentroidInMeters = args$distanceFromCentroidInMeters,
+ geoDistance = args$geoDistance,
+ sex = args$sex,
+ dwcaExtension = args$dwcaExtension,
+ gbifId = args$gbifId,
+ gbifRegion = args$gbifRegion,
+ projectId = args$projectId,
+ programme = args$programme,
+ preparations = args$preparations,
+ datasetId = args$datsetId,
+ datasetName = args$datasetName,
+ publishedByGbifRegion = args$publishedByGbifRegion,
+ island = args$island,
+ islandGroup = args$islandGroup,
+ taxonId = args$taxonId,
+ taxonConceptId = args$taxonConceptId,
+ taxonomicStatus = args$taxonomicStatus,
+ acceptedTaxonKey = args$acceptedTaxonKey,
+ collectionKey = args$collectionsKey,
+ institutionKey = args$institutionKey,
+ otherCatalogNumbers = args$otherCatalogNumbers,
+ georeferencedBy = args$georeferencedBy,
+ installationKey = args$installationKey,
+ hostingOrganizationKey = args$hostingOrganizationKey,
+ crawlId = args$crawlId,
+ modified = args$modified,
+ higherGeography = args$higherGeography,
+ fieldNumber = args$fieldNumber,
+ parentEventId = args$parentEventId,
+ samplingProtocol = args$samplingProtocol,
+ sampleSizeUnit = args$sampleSizeUnit,
+ pathway = args$pathway,
+ gadmLevel0Gid = args$gadmLevel0Gid,
+ gadmLevel1Gid = args$gadmLevel1Gid,
+ gadmLevel2Gid = args$gadmLevel2Gid,
+ gadmLevel3Gid = args$gadmLevel3Gid,
+ earliestEonOrLowestEonothem = args$earliestEonOrLowestEonothem,
+ latestEonOrHighestEonothem = args$latestEonOrHighestEonothem,
+ earliestEraOrLowestErathem = args$earliestEraOrLowestErathem,
+ latestEraOrHighestErathem = args$latestEraOrHighestErathem,
+ earliestPeriodOrLowestSystem = args$earliestPeriodOrLowestSystem,
+ latestPeriodOrHighestSystem = args$latestPeriodOrHighestSystem,
+ earliestEpochOrLowestSeries = args$earliestEpochOrLowestSeries,
+ latestEpochOrHighestSeries = args$latestEpochOrHighestSeries,
+ earliestAgeOrLowestStage = args$earliestAgeOrLowestStage,
+ latestAgeOrHighestStage = args$latestAgeOrHighestStage,
+ lowestBiostratigraphicZone = args$lowestBiostratigraphicZone,
+ highestBiostratigraphicZone = args$highestBiostratigraphicZone,
+ group = args$group,
+ formation = args$formation,
+ member = args$member,
+ bed = args$bed,
+ associatedSequences = args$aassociatedSequences,
+ isSequenced = args$isSequenced,
+ startDayOfYear = args$startDayOfYear,
+ endDayOfYear = args$endDayOfYear,
  limit=0,
  start=0,
  fields = 'all',
@@ -224,10 +279,23 @@ occ_count <- function(...,occurrenceStatus="PRESENT", curlopts = list()) {
  facetLimit = args$facetLimit)
 
  if("facet" %in% arg_names) {
- not_facet_arg <- c("skip_validate","...","curlopts","facetMultiselect",
- "facetMincount", "facet","return","fields","start",
- "limit","verbatimTaxonId","geometry", "geom_big",
- "geom_size","geom_n","search")
+ not_facet_arg <- c("skip_validate",
+ "...",
+ "curlopts",
+ "facetMultiselect",
+ "facetMincount", 
+ "facet",
+ "return",
+ "fields",
+ "start",
+ "limit",
+ "verbatimTaxonId",
+ "geometry",
+ "geom_big",
+ "geom_size",
+ "geom_n",
+ "search",
+ "geoDistance")
  acc_facet_arg <- formal_args[!formal_args %in% not_facet_arg]
  if(!args$facet %in% acc_facet_arg) stop("Bad facet arg.")
  count <- stats::setNames(res$facet[[1]],c(args$facet,"count"))

R/occ_data.R

@@ -1,45 +1,242 @@
-#' Search for GBIF occurrences - simplified for speed
+#' Legacy alternative to occ_search 
 #'
-#' @export
-#' @template occsearch
-#' @template oslimstart
-#' @template occ
-#' @template occ_data_egs
-#' @seealso [downloads()], [occ_search()]
-#' @section occ_data vs. occ_search:
-#' This does nearly the same thing as [occ_search()], but
-#' is simplified for speed, and is for the most common use case where
-#' user just wants occurrence data, and not other information like taxon
-#' hierarchies and media (e.g., images). Alot of time in [occ_search()]
-#' is used parsing data to be more useable downstream. We do less of that
-#' in this function. 
+#' @param 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 \code{occ_search(taxonKey=c(1,212))}.
+#' @param scientificName A scientific name from the GBIF backbone. All included
+#' and synonym taxa are included in the search.
+#' @param country (character) The 2-letter country code (ISO-3166-1) 
+#' in which the occurrence was recorded. \code{enumeration_country()}.
+#' @param 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](https://www.gbif.org/dataset/7e380070-f762-11e1-a439-00145eb45e9a).
+#' @param 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).
+#' @param 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.
+#' @param recordedBy (character) The person who recorded the occurrence.
+#' @param recordedByID (character) Identifier (e.g. ORCID) for the person who
+#' recorded the occurrence
+#' @param identifiedByID (character) Identifier (e.g. ORCID) for the person who
+#' provided the taxonomic identification of the occurrence.
+#' @param 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.
+#' @param institutionCode An identifier of any form assigned by the source to 
+#' identify the institution the record belongs to.
+#' @param basisOfRecord (character) The specific nature of the data record. See 
+#' [here](https://gbif.github.io/parsers/apidocs/org/gbif/api/vocabulary/BasisOfRecord.html).
+#' 
+#' \itemize{
+#' \item "FOSSIL_SPECIMEN" 
+#' \item "HUMAN_OBSERVATION" 
+#' \item "MATERIAL_CITATION" 
+#' \item "MATERIAL_SAMPLE" 
+#' \item "LIVING_SPECIMEN" 
+#' \item "MACHINE_OBSERVATION" 
+#' \item "OBSERVATION" 
+#' \item "PRESERVED_SPECIMEN" 
+#' \item "OCCURRENCE" 
+#' }
+#' @param 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).
+#' @param 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).
+#' @param search (character) Query terms. The value for this parameter can be a 
+#' simple word or a phrase. For example, [search="puma"](https://www.gbif.org/occurrence/search?q=puma)
+#' @param 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).
+#' @param 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).
+#' @param publishingCountry The 2-letter country code (as per ISO-3166-1) of 
+#' the country in which the occurrence was recorded. See 
+#' \code{enumeration_country()}. 
+#' @param elevation Elevation in meters above sea level. Supports range 
+#' queries, 'smaller,larger' (e.g., '5,30', whereas '30,5' wouldn't work).
+#' @param 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). 
+#' @param geometry (character) Searches for occurrences inside a polygon in 
+#' Well Known Text (WKT) format. A WKT shape written as either 
+#' 
+#' \itemize{
+#' \item "POINT"
+#' \item "LINESTRING" 
+#' \item "LINEARRING"
+#' \item "POLYGON"
+#' \item "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.
+#' @param geom_big (character) One"bbox" or "asis" (default). 
+#' @param geom_size (integer) An integer indicating size of the cell. Default: 
+#' 40.
+#' @param geom_n (integer) An integer indicating number of cells in each 
+#' dimension. Default: 10.
+#' @param hasGeospatialIssue (logical) Includes/excludes occurrence records 
+#' which contain spatial issues (as determined in our record interpretation), 
+#' i.e. \code{hasGeospatialIssue=TRUE} returns only those records with spatial 
+#' issues while \code{hasGeospatialIssue=FALSE} includes only records without 
+#' spatial issues. The absence of this parameter returns any record with or 
+#' without spatial issues.
+#' @param 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](https://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/OccurrenceIssue.html). 
+#' See [here](https://data-blog.gbif.org/post/issues-and-flags/) for definitions.
+#' @param hasCoordinate (logical) Return only occurrence records with lat/long 
+#' data (\code{TRUE}) or all records (\code{FALSE}, default).
+#' @param typeStatus Type status of the specimen. One of many 
+#' [options](https://www.gbif.org/occurrence/search?type_status=PARATYPE). 
+#' @param recordNumber Number recorded by collector of the data, different from 
+#' GBIF record number. 
+#' @param 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).
+#' @param continent The source supplied continent. 
+#'
+#' \itemize{
+#' \item "africa" 
+#' \item "antarctica" 
+#' \item "asia" 
+#' \item "europe" 
+#' \item "north_america"
+#' \item "oceania"
+#' \item "south_america"
+#' }
+#' 
+#' Continent is not inferred but only populated if provided by the 
+#' dataset publisher. Applying this filter may exclude many relevant records.
+#' @param mediaType (character) Media type of "MovingImage", "Sound", or 
+#' "StillImage".
+#' @param repatriated (character) Searches for records whose publishing country
+#' is different to the country where the record was recorded in.
+#' @param kingdomKey (numeric) Kingdom classification key.
+#' @param phylumKey (numeric) Phylum classification key.
+#' @param classKey (numeric) Class classification key.
+#' @param orderKey (numeric) Order classification key.
+#' @param familyKey (numeric) Family classification key.
+#' @param genusKey (numeric) Genus classification key.
+#' @param speciesKey (numeric) Species classification key.
+#' @param subgenusKey (numeric) Subgenus classification key.
+#' @param 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.
 #' 
-#' There are a number of data fields GBIF returns that we drop to speed up
-#' processing time within R. These fields take extra time to process
-#' because they are deeply nested and so take extra time to check if
-#' they are empty or not, and if not, figure out how to parse them 
-#' into a data.frame. The fields are:
+#' \itemize{
+#' \item "Introduced"
+#' \item "Native"
+#' \item "NativeReintroduced"
+#' \item "Vagrant"
+#' \item "Uncertain"
+#' \item "IntroducedAssistedColonisation"
+#' }
+#' 
+#' @param 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](https://www.gbif.org/occurrence/search?advanced=1&degree_of_establishment=Managed).
+#' @param protocol (character) Protocol or mechanism used to provide the
+#' occurrence record. One of many [options](https://www.gbif.org/occurrence/search?protocol=DWC_ARCHIVE&advanced=1).
+#' @param license (character) The type license applied to the dataset or record.
 #' 
-#' - `gadm`
-#' - `media`
-#' - `facts`
-#' - `relations`
-#' - `extensions`
-#' - `identifiers`
-#' - `recordedByIDs`
-#' - `identifiedByIDs`
+#' \itemize{
+#' \item "CC0_1_0"
+#' \item "CC_BY_4_0"
+#' \item "CC_BY_NC_4_0"
+#' }
+#' 
+#' @param 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.
+#' @param publishingOrg (character) The publishing organization key (a UUID).
+#' @param stateProvince (character) The name of the next smaller administrative
+#' region than country (state, province, canton, department, region, etc.) in
+#' which the Location occurs.
+#' @param waterBody (character) The name of the water body in which the
+#' locations occur
+#' @param locality (character) The specific description of the place.
+#' @param occurrenceStatus (character) Default is "PRESENT". Specify whether 
+#' search should return "PRESENT" or "ABSENT" data.
+#' @param gadmGid (character) The gadm id of the area occurrences are desired 
+#' from. https://gadm.org/.
+#' @param 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).
+#' @param verbatimScientificName (character) Scientific name as provided by the 
+#' source.
+#' @param verbatimTaxonId (character) The taxon identifier provided to GBIF by 
+#' the data publisher.
+#' @param eventId (character) identifier(s) for a sampling event.
+#' @param identifiedBy (character) names of people, groups, or organizations.
+#' @param networkKey (character) The occurrence network key (a uuid) 
+#' who assigned the Taxon to the subject.
+#' @param occurrenceId (character) occurrence id from source. 
+#' @param 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). 
+#' @param organismQuantityType (character) The type of quantification system 
+#' used for the quantity of organisms. For example, "individuals" or "biomass".
+#' @param 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).
+#' @param iucnRedListCategory (character) The IUCN threat status category. 
+#' 
+#' \itemize{
+#' \item "NE" (Not Evaluated) 
+#' \item "DD" (Data Deficient)
+#' \item "LC" (Least Concern)
+#' \item "NT" (Near Threatened)
+#' \item "VU" (Vulnerable)
+#' \item "EN" (Endangered)
+#' \item "CR" (Critically Endangered) 
+#' \item "EX" (Extinct)
+#' \item "EW" (Extinct in the Wild)
+#' }
+#' @param lifeStage (character) the life stage of the occurrence. One of many 
+#' [options](https://www.gbif.org/occurrence/search?advanced=1&life_stage=Tadpole).
+#' @param isInCluster (logical) identify potentially related records on GBIF.
+#' @param 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.
+#' @param skip_validate (logical) whether to skip wellknown::validate_wkt call 
+#' or not. passed down to check_wkt(). Default: TRUE
+#' @param 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
+#' \code{limit+start}, so \code{start=99,000} and \code{limit=2000} won't work
+#' @param 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 \code{start} parameter
+#' @param curlopts (list) 
+#' 
+#' @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. 
 #' 
-#' To get these fields use [occ_search()] instead.
-#' @note Maximum number of records you can get with this function is 100,000.
-#' See https://www.gbif.org/developer/occurrence
 #' @return 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)
-
+#' @export
+#'
 occ_data <- function(taxonKey=NULL,
  scientificName=NULL, 
  country=NULL,
@@ -90,9 +287,6 @@ occ_data <- function(taxonKey=NULL,
  stateProvince = NULL,
  waterBody = NULL,
  locality = NULL,
- limit=500,
- start=0,
- skip_validate = TRUE,
  occurrenceStatus = 'PRESENT',
  gadmGid = NULL,
  coordinateUncertaintyInMeters = NULL,
@@ -109,6 +303,9 @@ occ_data <- function(taxonKey=NULL,
  lifeStage = NULL,
  isInCluster = NULL,
  distanceFromCentroidInMeters = NULL,
+ skip_validate = TRUE,
+ limit=500,
+ start=0,
  curlopts = list(http_version=2)) {
 
  geometry <- geometry_handler(geometry, geom_big, geom_size, geom_n)