variables: FinBIF record variables
In finbif: Interface for the 'Finnish Biodiversity Information Facility' API

variables

R Documentation

FinBIF record variables

Description

FinBIF record variables that can be selected in a finbif occurrence search.

Identifiers

All identifiers are returned in the form of a URI. Identifiers include:

occurrenceID Character. The ID of a record of organism's occurrence at a time and place.
organismID Character. ID of an individual organism (e.g., a ringed bird that has been captured multiple times will have a single organismID and multiple occurrenceIDs corresponding to each capture).
eventID Character. Event ID. An event can contain one or more records (e.g., a survey of plants at a particular location and time.)
catalogNumber Character. Document ID. A set of events that share common metadata.
formID Character. Form ID. The form used to create the document, event, record data.
datasetID Character. Dataset ID. All documents, events, and records belong to a collection/dataset (e.g., a museum collection, or the datasets collected by a specific institution). Collections themselves can be part of a larger (super)collection (e.g., all the collections at a specific museum). Only the lowest level dataset ID for a record is returned. Use finbif_collections() to explore the hierarchy of collections/datasets.
sourceID Character. Source ID. The source of the collection's data.

Taxa

Variables related to taxonomy of records include:

taxonConceptID Character. The taxon ID in the form of a URI.
originalTaxonConceptID Character. The taxon ID before (if any) annotation.
annotatedTaxonConceptID Character. The new taxon ID if the record has had it's taxonomy annotated.
verbatimTaxonConceptID Character. The taxon ID as originally reported by the record creator.
scientificName Character. Scientific name of taxon.
originalScientificName Character. The scientific name before (if any) annotation.
scientificNameDisplay Character. Scientific name of taxon formatted for display (e.g., taxa with genus only will be formatted as Genus sp.).
originalScientificNameDisplay Character. Scientific display name before (if any) annotation.
vernacularName Character. Common (vernacular) name of taxon.
originalVernacularName Character. Common name before (if any) annotation.
verbatimIdentification Character. The name of the taxon as originally reported by the record creator.
scientificNameItalicised Logical. Is the scientific name normally italicised (i.e., is the taxonomic rank genus or below.)
originalScientificNameItalicised Logical. Is the original scientific name normally italicised.
scientificNameAuthorship Character. The authority for the taxon scientific name.
originalScientificNameAuthorship Character. The authority for the taxon scientific name before (if any) annotation.
verbatimScientificNameAuthorship Character. The authority of the taxon as originally reported by the record creator.
taxonRank Character. The taxonomic rank of the taxon.
originalTaxonRank Character. The taxonomic rank of the taxon before (if any) annotation.
informalTaxonGroups List. The informal taxonomic groups that the taxon belongs to (e.g., birds) in the form of URIs.
originalInformalTaxonGroups List. The informal taxonomic groups that the taxon belonged to before (if any) annotation.
verbatimInformalTaxonGroups List. The informal taxonomic groups that the taxon belongs to as reported by the record creator.
taxonChecklist Character. The checklist (as a URI) that that taxon is found in.
originalTaxonChecklist Character. The checklist (as a URI) that that taxon was found in before (if any) annotation.
taxonFinnishStatus Logical. Is the taxon considered Finnish. The definition of a Finnish taxon differs by taxonomic group?
originalFinnishStatus Logical. Was the taxon considered Finnish before (if any) annotation?

Abundance, sex & life history

Variables related to abundance, sex and life history include:

individualCount Integer. Number of individuals recorded.
individualCountInterpreted Integer. Number of individuals recorded or inferred from the record. Note that many records with individualCount == 1L only indicate the record is of one individual and may not necessarily imply that this was the abundance at that specified place and time (e.g., a preserved museum specimen consisting of a single individual).
⁠individualCount{Female|Male}⁠ Integer. Number of female or male individuals recorded.
pairCount Integer. Number of mating pairs recorded.
organismQuantity Character. The abundance as reported by the record creator.
lifeStage Character. Life stage of individual(s) recorded.
sex Character. Sex of individual(s) recorded.

Location

Variables related to the location of records include:

⁠decimal{Latitude|Longitude}⁠ Numeric. Coordinates (in WGS84 coordinate system) of the central point of a bounding box encompassing the record's geographic coverage.
⁠decimal{Latitude|Longitude}EUREF⁠ Numeric. Coordinates (in EUREF coordinate system) of the central point of a bounding box encompassing the record's geographic coverage.
⁠decimal{Latitude|Longitude}{Min|Max}{EUREF|YKJ|WGS84}⁠. Numeric. Vertices of a bounding box encompassing the record's geographic coverage. Coordinates are available in EUREF, YKJ, or WGS84.
coordinateUncertaintyInMeters Integer. The horizontal distance (in meters) from the record's given coordinates describing the smallest circle containing the whole of the record's location.
georeferenceSources Character. Source of coordinates.
footprintWKT Character. Well-Known Text (WKT) representation of the geographic shape defining the location of the record in WGS84 coordinate systems.
⁠footprintWKT{_EUREF|_YKJ}⁠ Character. Well-Known Text (WKT) representation of the geographic shape defining the location of the record in either EUREF or YKJ coordinate systems.
country Character. The country of the record's location.
stateProvince Character. The administrative area directly below the level of country.
bioStateProvince Character. For data from Finland FinBIF uses the concept of Biogeographical Province. See link for details.
county. Character. Administrative level below region
higherGeography Character. Geographic place name that is at higher level than country.
lineLengthMeters Integer. The length of linear locations (e.g., line transect surveys).
areaMetersSquared Integer. The size of record's location in meters squared.
isBreedingSite Logical. Whether or not the occurrence is recorded at a known breeding location.
locationID Character. A location ID in the form of a URI.
eventSection Integer. A numeric identifier for a sub-location of a location (e.g., a specific part of a transect that undergoes repeated surveys.)

Time

Variables related to time of record include:

eventDateTime POSIXct. The date and time of the recording event. This variable is computed after records are downloaded from FinBIF. Its timezone and accuracy can be controlled see finbif_occurrence() for details.
samplingEffort Duration. The duration of the recording event. This variable is computed after records are downloaded from FinBIF.
eventDateStart Character. The date the recording event began.
eventDateEnd Character. The date the recording event ended.
hourStart Integer. The hour (24 hour time) of the day the recording event began.
hourEnd Integer. The hour (24 hour time) of the day the recording event ended.
minuteStart Integer. The minute of the hour the recording event began.
minuteEnd Integer. The minute of the hour the recording event started.
startDayOfYear Integer. The ordinal day of the year the recording event began.
endDayOfYear Integer. The ordinal day of the year the recording event ended
seasonStart Integer. The day of the year the recording event began. A four digit number indicating the day of the year in MMDD (%m%d) format.
seasonEnd Integer. The day of the year the recording event ended. A four digit number indicating the day of the year in MMDD (%m%d) format.
century Integer. The century during which the recording event occurred (NA if the event spans multiple centuries).
decade Integer. The decade during which the recording event occurred (NA if the event spans multiple decades).
year Integer. The year during which the recording event occurred (NA if the event spans multiple years).
month Integer. The month of the year during which the recording event occurred (NA if the event spans multiple months).
day Integer. The day of the month during which the recording event occurred (NA if the event spans multiple days).
eventDateTimeDisplay Character. Date and time of the recording event formatted for display.
documentCreatedDate Character. The date the original data was created.
available Character. The date the record was first loaded into the FinBIF database.
modified Character. The most recent date the original data was modified.
documentLoadedDate Character. The most recent date the record was loaded into the FinBIF database.

Data restrictions

Variables related to restricted records include:

informationRestricted Logical. Has the record been restricted in some way (e.g., geospatially aggregated).
dataGeneralizations Character. What level of restriction has been applied to the record.
informationWithheld Character. Description of information about a record that is not public available but may accessed on request.

Data quality

Variables related to the quality of records include:

hasIssues Logical. Are there any data quality issues associated with the record, its event or document.
identificationQualifer Reliability of the record's taxonomic identification as reported by the original data author.
⁠{document|time|location|event|occurrence}Issue⁠ Character. Issues with record associated with its document, time, location, event, or the record itself.
⁠{document|time|location|event|occurrence}IssueRemarks⁠ Character. Details about the issue.
⁠{document|time|location|event|occurrence}IssueSource⁠ Character. Source determining the issue.
requiresVerification Logical. Has the record been flagged for expert verification?
requiresIdentification Logical. Has the record been flagged for expert identification?
occurrenceReliability Character. Indication of the record's reliability.
identificationVerificationStatus Character. Indication of the record's quality.

Misc

Other variables:

datasetName Character. Dataset name. All documents, events, and records belong to a collection/dataset (e.g., a museum collection, or the datasets collected by a specific institution). Collections themselves can be part of a larger (super)collection (e.g., all the collections at a specific museum). Only the lowest level collection name for a record is returned. Use finbif_collections() to explore the hierarchy of collections/datasets.
recordedByIDs List. List of observer identifiers for the record.
identifiedBy Character. Person who determined the taxonomic identification of the record.
basisOfRecord Character. The type of or method used to obtain the record.
basisOfSuperRecord Character. Higher level type of or method used to obtain the record.
typeStatus Logical. Whether or not the record is of a type specimen.
occurrenceIsWild Logical. Whether or not the record is of a "wild" organism.
license Character. The license of the data associated with the record.
⁠{document|event|occurrence}Remarks⁠ Character. Notes associated with the document, event or record itself.
⁠{document|occurrence}Keywords⁠ List. List of keywords associated with the document or record.
occurrenceAnnotationCount Integer. How many annotations are associated with the record.
materialSampleCount Integer. How many material samples (DNA extractions, etc., ...) are associated with the record.
⁠{document|event|occurrence}AssociatedMediaCount⁠ Integer. How many media items (images, audio, video, etc., ...) are associated with the record's document, event or the record itself.