variables {finbif} | 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 singleindividual_id
and multiplerecord_id
s 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. Usefinbif_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 withabundance_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 seefinbif_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. Usefinbif_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.