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:

record_id Character. The ID of a record of organism's occurrence at a time and place.
individual_id Character. ID of an individual organism (e.g., a ringed bird that has been captured multiple times will have a single individual_id and multiple record_ids corresponding to each capture).
event_id Character. Event ID. An event can contain one or more records (e.g., a survey of plants at a particular location and time.)
document_id Character. Document ID. A set of events that share common metadata.
form_id Character. Form ID. The form used to create the document, event, record data.
collection_id Character. Collection ID. All documents, events, and records belong to a collection (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 ID for a record is returned. Use finbif_collections() to explore the hierarchy of collections.
source_id Character. Source ID. The source of the collection's data.

Taxa

Variables related to taxonomy of records include:

taxon_id Character. The taxon ID in the form of a URI.
orig_taxon_id Character. The taxon ID before (if any) annotation.
annotated_taxon_id Character. The new taxon ID if the record has had it's taxonomy annotated.
reported_taxon_id Character. The taxon ID as originally reported by the record creator.
scientific_name Character. Scientific name of taxon.
orig_scientific_name Character. The scientific name before (if any) annotation.
scientific_display_name Character. Scientific name of taxon formatted for display (e.g., taxa with genus only will be formatted as Genus sp.).
orig_scientific_display_name Character. Scientific display name before (if any) annotation.
common_name Character. Common (vernacular) name of taxon.
orig_common_name Character. Common name before (if any) annotation.
reported_name Character. The name of the taxon as originally reported by the record creator.
scientific_name_italicised Logical. Is the scientific name normally italicised (i.e., is the taxonomic rank genus or below.)
orig_scientific_name_italicised Logical. Is the original scientific name normally italicised.
scientific_name_author Character. The authority for the taxon scientific name.
orig_scientific_name_author Character. The authority for the taxon scientific name before (if any) annotation.
reported_author Character. The authority of the taxon as originally reported by the record creator.
taxon_rank Character. The taxonomic rank of the taxon.
orig_taxon_rank Character. The taxonomic rank of the taxon before (if any) annotation.
informal_groups List. The informal taxonomic groups that the taxon belongs to (e.g., birds) in the form of URIs.
orig_informal_groups List. The informal taxonomic groups that the taxon belonged to before (if any) annotation.
reported_informal_groups List. The informal taxonomic groups that the taxon belongs to as reported by the record creator.
taxon_checklist Character. The checklist (as a URI) that that taxon is found in.
orig_taxon_checklist Character. The checklist (as a URI) that that taxon was found in before (if any) annotation.
taxon_finnish Logical. Is the taxon considered Finnish. The definition of a Finnish taxon differs by taxonomic group?
orig_taxon_finnish Logical. Was the taxon considered Finnish before (if any) annotation?

Abundance, sex & life history

Variables related to abundance, sex and life history include:

abundance Integer. Number of individuals recorded.
abundance_interpreted Integer. Number of individuals recorded or inferred from the record. Note that many records with abundance_interpreted == 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).
⁠{female|male}_abundance⁠ Integer. Number of female or male individuals recorded.
pair_abundance Integer. Number of mating pairs recorded.
abundance_verbatim Character. The abundance as reported by the record creator.
life_stage Character. Life stage of individual(s) recorded.
sex Character. Sex of individual(s) recorded.

Location

Variables related to the location of records include:

⁠{lat|lon}_{euref|wgs84}⁠ Numeric. Coordinates (in EUREF or WGS84 coordinate system) of the central point of a bounding box encompassing the record's geographic coverage.
⁠{lat|lon}_{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.
coordinates_uncertainty Integer. The horizontal distance (in meters) from the record's given coordinates describing the smallest circle containing the whole of the record's location.
coordinates_source Character. Source of coordinates.
⁠footprint_{euref|ykj|wgs84}⁠ Character. Well-Known Text (WKT) representation of the geographic shape defining the location of the record in either EUREF, YKJ or WGS84 coordinate systems.
country Character. The country of the record's location.
region Character. The administrative area directly below the level of country.
bio_province Character. For data from Finland FinBIF uses the concept of Biogeographical Province. See link for details.
municipality. Character. Administrative level below region
higher_geography Character. Geographic place name that is at higher level than country.
line_length_m Integer. The length of linear locations (e.g., line transect surveys).
area_m2 Integer. The size of record's location in meters squared.
is_breeding_location Logical. Whether or not the occurrence is recorded at a known breeding location.
location_id Character. A location ID in the form of a URI.
section 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:

date_time 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.
duration Duration. The duration of the recording event. This variable is computed after records are downloaded from FinBIF.
date_start Character. The date the recording event began.
date_end Character. The date the recording event ended.
hour_start Integer. The hour (24 hour time) of the day the recording event began.
hour_end Integer. The hour (24 hour time) of the day the recording event ended.
minute_start Integer. The minute of the hour the recording event began.
minute_end Integer. The minute of the hour the recording event started.
ordinal_day_start Integer. The ordinal day of the year the recording event began.
ordinal_day_end Integer. The ordinal day of the year the recording event ended
season_start 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.
season_end 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).
formatted_date_time Character. Date and time of the recording event formatted for display.
date_created Character. The date the original data was created.
first_load_date Character. The date the record was first loaded into the FinBIF database.
modified_date Character. The most recent date the original data was modified.
load_date Character. The most recent date the record was loaded into the FinBIF database.

Data restrictions

Variables related to restricted records include:

restriction Logical. Has the record been restricted in some way (e.g., geospatially aggregated).
restriction_level Character. What level of restriction has been applied to the record.
restriction_reason List. List of reasons restriction has been applied.

Data quality

Variables related to the quality of records include:

any_issues Logical. Are there any data quality issues associated with the record, its event or document.
reported_taxon_confidence Reliability of the record's taxonomic identification as reported by the original data author.
⁠{document|time|location|event|record}_issue⁠ Character. Issues with record associated with its document, time, location, event, or the record itself.
⁠{document|time|location|event|record}_issue_message⁠ Character. Details about the issue.
⁠{document|time|location|event|record}_issue_source⁠ Character. Source determining the issue.
requires_verification Logical. Has the record been flagged for expert verification?
requires_identification Logical. Has the record been flagged for expert identification?
record_reliability Character. Indication of the record's reliability.
record_quality Character. Indication of the record's quality.

Misc

Other variables:

collection Character. Collection name. All documents, events, and records belong to a collection (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.
observers_ids List. List of observer identifiers for the record.
determiner Character. Person who determined the taxonomic identification of the record.
record_basis Character. The type of or method used to obtain the record.
superrecord_basis Character. Higher level type of or method used to obtain the record.
type_specimen Logical. Whether or not the record is of a type specimen.
is_wild Logical. Whether or not the record is of a "wild" organism.
license Character. The license of the data associated with the record.
⁠{document|event|record}_notes⁠ Character. Notes associated with the document, event or record itself.
⁠{document|record}_keywords⁠ List. List of keywords associated with the document or record.
record_annotation_count Integer. How many annotations are associated with the record.
sample_count Integer. How many material samples (DNA extractions, etc., ...) are associated with the record.
⁠{document|event|record}_media_count⁠ Integer. How many media items (images, audio, video, etc., ...) are associated with the record's document, event or the record itself.