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Title:	Interface for the 'Finnish Biodiversity Information Facility'API
Version:	0.9.11
Description:	A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (https://api.laji.fi). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.
License:	MIT + file LICENSE
URL:	https://github.com/luomus/finbif,https://luomus.github.io/finbif/
BugReports:	https://github.com/luomus/finbif/issues
VignetteBuilder:	knitr
Encoding:	UTF-8
Language:	en-US
Depends:	R (≥ 3.5.0)
Imports:	digest, httr, jsonlite, lutz, utils
RoxygenNote:	7.3.2
Suggests:	callr, data.table, DBI, future, knitr, rmarkdown, RSQLite,testthat (≥ 3.0.0), vcr (≥ 0.6.0), webfakes
Config/testthat/edition:	3
X-schema.org-applicationCategory:	Biodiversity
X-schema.org-keywords:	api, biodiversity, biodiversity-informatics,biodiversity-information, finbif, finbif-access, occurrences,r-package, r-programming, rstats, species, specimens, taxon,taxonomy, web-services
X-schema.org-isPartOf:	https://species.fi
NeedsCompilation:	no
Packaged:	2025-08-22 09:14:26 UTC; atlanci
Author:	Finnish Museum of Natural History - Luomus [cph], Finnish Biodiversity Information Facility [cph], William K. Morris [aut, cre]
Maintainer:	William K. Morris <willi@mmorris.email>
Repository:	CRAN
Date/Publication:	2025-08-22 09:30:16 UTC

finbif: Interface for the 'Finnish Biodiversity Information Facility' API

Description

A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (https://api.laji.fi). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.

Package options

finbif_api_url

Character. The base url of the API to query. Default:"https://api.laji.fi"

finbif_api_version

Character. The API version to use. Default:"v0"

finbif_allow_query

Logical. Should remote API queries by allowed.Default:TRUE

finbif_use_cache

Logical or Integer. IfTRUE or a number greaterthan zero, then data-caching will be used. If not logical then cache willbe invalidated after the number of hours indicated by the value. Default:TRUE

finbif_use_cache_metadata

Logical or Integer. IfTRUE or a numbergreater than zero, then metadata-caching will be used. If not logical thencache will be invalidated after the number of hours indicated by the value.Default:TRUE

finbif_cache_path

Character. The path to the directory where tostore cached API queries. If unset (the default) in memory caching isused.

finbif_tz

Character. The timezone used byfinbif functions thatcompute dates and times. Default:Sys.timezone()

finbif_locale

Character. One of the supported two-letter ISO 639-1language codes. Current supported languages are English, Finnish andSwedish. By default, the system settings are used to set this option ifthey are set to one of the supported languages, otherwise English is used.

finbif_hide_progress

Logical. Global option to suppress progressindicators for downloading, importing and processing FinBIF records.Default:FALSE

Author(s)

Maintainer: William K. Morriswilli@mmorris.email (ORCID)

Other contributors:

• Finnish Museum of Natural History - Luomus (03tcx6c30) [copyright holder]

• Finnish Biodiversity Information Facility (01c0yey93) [copyright holder]

See Also

Useful links:

• https://github.com/luomus/finbif

• https://luomus.github.io/finbif/

• Report bugs athttps://github.com/luomus/finbif/issues

Caching FinBIF downloads

Description

Working with cached data from FinBIF.

Turning caching off

By default, local caching of most FinBIF API requests is turned on. Anyrequest made using the same arguments will only request data from FinBIF inthe first instance and subsequent requests will use the local cache while itexists. This will increase the speed of repeated requests and save bandwidthand computation for the FinBIF server. Caching can be turned off temporarilyby settingcache = c(FALSE, FALSE) in the requesting function.

Settingoptions(finbif_use_cache = FALSE, finbif_use_cache_metadata = FALSE) willturn off caching for the current session.

Using filesystem caching

By default cached requests are stored in memory. This can be changed bysetting the file path for the current session withoptions(finbif_cache_path = "path/to/cache").

Using database caching

Caching can also be done using a database. Using a database for cachingrequires theDBI package and a database backend package such asRSQLiteto be installed. To use the database for caching simply pass the connectionobjected created withDBI::dbConnect to thefinbif_cache_path option(e.g.,db <- DBI::dbConnect(RSQLite::SQLite(), "my-db.sqlite");options(finbif_cache_path = db)).

Timeouts

A cache timeout can be set by using an integer (number of hours until cacheis considered invalid and is cleared) instead of a logical value for thefinbif_use_cache andfinbif_use_cache_metadata options or thecachefunction arguments.

Clearing the cache

The cache can be resetfinbif_clear_cache().

Updating the cache

The cache can be updated usingfinbif_update_cache().

Filtering FinBIF records

Description

Filters available for FinBIF records and occurrence data.

Taxa

Filters related to taxa include:

• taxon_id Character vector.FinBIF taxon IDs. The functionsfinbif_check_taxa() andfinbif_taxa()can be used to search for taxon IDs.

• taxon_name Character vector.Filter based on taxon names (scientific or common) rather than IDs. If thespecified taxa are not found in the FinBIF taxonomy then matches areattempted with the occurrence record names as originally supplied verbatim.

• quality_controlled_det Logical.IfTRUE (default) use quality controlled taxonomic determinations. Or, ifFALSE use the originally recorded taxonomic determinations.

• subtaxa Logical.IfTRUE (default) return records of all taxa belonging to specified taxa.Or, ifFALSE only return records for exact matches to the specified taxa(e.g., if a genus is specified, do not return records of the speciesbelonging to the genus, return records of individuals identified as thatgenus only and not identified to a lower taxonomic level).

• invalid_taxa Logical.IfTRUE (default) return records for taxa not found in the FinBIFtaxonomic database as well as taxa that are in the FinBIF database. Or, ifFALSE limit records to only those of taxa found in the FinBIF database.

• informal_groups Character vector.Filter by informal taxonomic groups. Only including informal groups linkedto the recorded taxa in the FinBIF database. Use the functionfinbif_informal_groups() to see the informal taxonomic groups availablein FinBIF.

• informal_groups_reported Character vector.Filter by informal taxonomic groups including groups reported directly withthe record and those linked to the recorded taxa in the FinBIF database.Use the functionfinbif_informal_groups() to see the informal taxonomicgroups available in FinBIF.

• regulatory_status Character vector.Filter by regulatory status code. Use the functionfinbif_metadata() to see regulatory statuses and codes.

• red_list_status Character vector.Filter by IUCN red list status code. Use the functionfinbif_metadata()to see red list statuses and codes.

• primary_habitat Character vector or named list of character vectors.Filter by primary habitat code. Use the functionfinbif_metadata()to see habitat (sub)types and codes for taxa in the FinBIF database.Habitat type/subtypes can be refined further by indicating habitatqualifiers with a named list of character vectors where the names arehabitat (sub)type codes and the elements of the character vector are thehabitat qualifier codes. Use the functionfinbif_metadata() tosee habitat qualifiers and codes. The records returned will be of taxawhose primary habitat is considered to be the (sub)habitat/habitatqualifier combination supplied.

• primary_secondary_habitat Character or named list of character vectors.As above, except the records returned will be of taxa whose primary orsecondary habitat is considered to be the combination supplied.

• finnish_occurrence_status Character vector.Filter by Finnish occurrence status of taxa. Usefinbif_metadata() to see the possible occurrencestatuses of taxa.

• finnish_occurrence_status_neg Character vector.Negation of the above. Selecting a status will filter out rather thaninclude records with the selected status.

• finnish Logical.IfTRUE, limit records to taxa thought to occur in Finland. Or ifFALSElimit to taxa not thought to occur in Finland. If unspecified (default)return records of all taxa.

• invasive Logical.IfTRUE, limit records to invasive taxa. Or ifFALSE limit tonon-invasive taxa. If unspecified (default) return records of invasive andnon-invasive taxa.

• taxon_rank Character vector.Filter by taxonomic rank. Usefinbif_metadata() to see the taxonomicranks available. Records returned will be limited to the specified ranksand not include records of lower taxonomic levels.

Location

Filters related to location of record include:

• locality Character vector.Filter by name of locality. Will first try to match strings to thecountries, bio-provinces, and municipalities (see below) in FinBIF, if noneof these locality types match exactly then will return records withverbatim locality matches in the original records.

• country Character vector.Filter by country. Usefinbif_metadata() to see country names and ISOcodes (2 and 3 character) used in FinBIF.

• region Character vector.Filter by region. Usefinbif_metadata() to see region names and codes.

• bio_province Character vector.Filter by bio-province. Usefinbif_metadata() to see bio-province namesand codes.

• finnish_municipality Character vector.Filter by municipality. Usefinbif_metadata() to see Finnish municipalitynames.

• location_tag Character vectorFilter by tags associated with a location (e.g.,"farmland").

• bird_assoc_area Character vector.Filter by BirdLife Finland association area. Usefinbif_metadata()to see association names and codes.

• coordinates Coordinates.A character vector or list of coordinate data. Must be length 3 to 4 (e.g.,list(lat = c(60.4, 61), lon = c(22, 22.5), system = "wgs84", ratio = 1).The first element is minimum and maximum latitude and the second minimumand maximum longitude (or can be minimums only). The third element is thecoordinate system; either one of"wgs84","euref" or"ykj". Theoptional fourth element is a positive value less than1. When1, thecoverage area of the returned records will be completely within the boxbound by the coordinates values. Values less than1 requires the returnedrecord's coverage to overlap with the bounding box in that proportion. Whenusing the system "ykj" the coordinates will be coerced to integers withunits inferred from the number of integer digits (7 digits equals kms, 6equals 10kms, etc.,). If coordinate maximums are not specified they willbe assumed to be one unit above the minimums (e.g.,c(666, 333, "ykj") isequivalent tolist(c(6660000, 6670000), c(3330000, 3340000), "ykj")).

• coordinates_center Coordinates.A character vector or list of coordinate data. Must be of length 3. Thefirst two elements are latitude and longitude and third is the coordinatesystem (currently only"wgs84" is implemented). Records returned will bethose for which the center point exactly matches that which is specified.

• ⁠coordinates_cell_{1k|10k|50k|100k}⁠ Coordinates.A vector of coordinate data (lat, lon). Filter by grid cell at scale*.Where* is 1, 10, 50 or 100. The coordinates specify the southeast cornerof the cell. Coordinates system is"ykj".

• ⁠coordinates_cell_{1k|10k|50k|100k}_center⁠ Coordinates.As above, except coordinates indicate center of grid cell.

• coordinates_source Character.Filter by source of coordinates. Currently accepted values are"reported_value" (coordinates were recorded at time of observation) and"finnish_municipality" (coordinates were derived and observer onlyrecorded Finnish municipality).

• coordinates_uncertainty_max Integer.Filter by maximum uncertainty of coordinates (i.e.,coordinates_uncertainty_max = 100 will return records that are accurateto 100m).

Time

Filters related to time of record include:

• date_range_ymd Dates.A vector of one to twoDate objects (begin and enddates) or objects that are coercible to theDate. Whensupplying dates as strings, the day or month-and-day can be omitted (e.g.,"2001-04" or"2001"). Note however, that when omitting day, only "-"is allowed to separate year and month, and months must be intwo-digit/leading zero form. If the begin or end dates are partial datestrings they will be interpreted as the first or last day of the month oryear (e.g.,c(2001, 2003) is equivalent toc("2001-01-01", "2003-12-12")). If a single date is supplied as a partialdate string then all records that fall within that month or year will bereturned (e.g.,c("2001-01") is equivalent toc("2001-01-01", "2001-01-31")). Use empty strings for the begin or enddate to specify open-ended date ranges (e.g.,c("2000-01-01", "") for alldates from the turn of the century).

• date_range_ym Dates.As above, but days (if supplied) will be ignored.

• date_range_d Integer vector.Filter by day of the year (e.g.,1 to366). If begin or end date isomitted then it is interpreted as the first or last day of the year.

• date_range_md Character vector.Filter by month and day of the year (e.g.,"01-01" to"12-31"). Ifbegin or end date is omitted then it is interpreted as the first or lastday of the year.

• ⁠{first|last}_import_date_{min|max}⁠ Date.Filter by date record was imported/modified. Either aDate object or object that is coercible to theDate class, or the number of seconds since 1970-01-0100:00.00 UTC (the so-called UNIX epoch). Note that this means thatspecifying a year, such as 2019, without a month and day will beinterpreted as 2019 seconds after midnight on Jan 1, 1970 and not the year2019.

Quality

Filters related to quality of record:

• quality_issues. Character.Filter by the presence of record quality issues. One of"without_issues","with_issues" or"both". Issues include any quality issues with therecord, the event, or the document. The default is"without_issues"unless filtering by record, event or document ID or record annotationstatus.

• requires_verification Logical.Show only records requiring verification (TRUE) or not requiringverification (FALSE).

• collection_quality Character vector.Filter by one or more collection quality types. Must be one of"professional","hobbyist" or"amateur".

• record_reliability Character vector.Filter by the reliability of the record. Must be one or more of"reliable",⁠"unassessed⁠ or"unreliable". Default isc("reliable", "unassessed").

• record_quality Character vector.Filter by the quality of the record. Must be one or more of"expert_verified","community_verified","unassessed","uncertain",or"erroneous".

Misc

Other filters:

• keywords Character vector.Filter by keywords.

• collection Character vector orfinbif_collections() data.frame.Filter by collection. If a character vector can refer to collection ID,collection name (in English) or abbreviated name.Usefinbif_collections() to see list of collections and metadata. Canalso use the results of a call tofinbif_collections() directly tofilter records.

• subcollections Logical.IfTRUE (default) include the subcollections of the collectionsspecified. IfFALSE do not include subcollections.

• not_collection Character vector orfinbif_collections() data.frame.As forcollection, but result will be the negation of the specifiedcollections.

• source Character vector.Filter by information system data source. Usefinbif_metadata() to seedata source IDs names and descriptions.

• record_basis Character vector.Filter by basis of record. Usefinbif_metadata() to see list ofrecord bases.

• superrecord_basis Character vector.Filter by superset of record basis. One or more of"human_observation","machine_observation", or"specimen".

• life_stage Character vector.Filter by organism life stage. Usefinbif_metadata() to see list oforganism life stages.

• sex Character vector.Filter by organism sex and sex-related category name or code. Usefinbif_metadata() to see list of organism sexes and sex-relatedcategories and codes. If"male" or"female" is specified then recordsreturned will be those with sex specified as male or female respectivelyand those records where the corresponding⁠{male|female}_abundance > 1⁠.

• event_id Character.Filter by event (list of records, etc.) ID.

• document_id Character.Filter by the document (collection of events) ID of occurrences.

• record_id Character.

• individual_id Character.Filter by individual (an individual organism) ID.

• abundance_min Integer.Filter by the minimum number of individual organisms in the record.

• abundance_max Integer.Filter by the maximum number of individual organisms in the record.

• type_specimen Logical.Filter by whether or not the record is a type specimen.

• wild_status Character.Filter by "wildness" status of records. One or more of"wild","non_wild" or"unknown". Default isc("wild", "unknown").

• is_breeding_location Logical.Filter by whether or not the occurrence is recorded at a known breedinglocation.

• has_document_media Logical.Filter by whether there is media (images, video, audio, etc.) associatedwith the records' document.

• has_event_media Logical.Filter by whether there is media (images, video, audio, etc.) associatedwith the records' event.

• has_record_media Logical.Filter by whether there is media (images, video, audio, etc.) associatedwith the record.

• has_media Logical.Filter by whether there is any media (images, video, audio, etc.)associated with the record, its document or its event.

• event_observer_name Character.Filter by observer name.

• event_observer_id Integer.Filter by observer ID.

• restriction_reason Character vector.Filter by reason data has security restrictions. Seefinbif_metadata() for a list of reasons data may have securityrestrictions.

• restriction_level Character vector.Filter by data restriction level. Seefinbif_metadata() for a list of the levels of datarestrictions.

• restricted Logical.Filter records by whether any data restrictions are in place (TRUE) ornot (FALSE).

• annotated Logical.Filter records that do (TRUE) or do not (FALSE) have annotations.

• unidentified Logical.Filter by whether the record has been identified to species level andlinked to the FinBIF taxon database (FALSE) or has not been identified tospecies level reliably and linked to the taxon database (TRUE).

• taxon_census Character vector.Return records belonging to surveys or censuses of a given taxon ortaxonomic group. Specify the taxonomic group with a FinBIF taxon ID. Usefinbif_check_taxa() to find taxon IDs.

• ⁠{record|event|document}_fact⁠ Character vector.Filter by record, event or document facts. Facts are key-value pairs of theform"<fact>=<value>". Value can be omitted in which case all recordswith any value recorded for the specified fact will be returned.

• has_sample Logical.Record includes a sample or samples (e.g., a DNA sample or preparation).

• complete_list_type Filter by complete list type. Records made duringmonitoring that produces taxon lists for a given group of taxa (e.g.,birds) can include all species observed with breeding status recorded foreach observed species (all_species_and_breeding), all species observedwithout breeding status recorded for all species observed, all speciesobserved with or without breeding status recorded for all observed species(all_species), or only some of the species observed (incomplete).

• complete_list_taxon_id Filter by the taxon ID of the target group (e.g.,birds) for a complete list.

Check FinBIF taxa

Description

Check that taxa are in the FinBIF database.

Usage

finbif_check_taxa(taxa, cache = getOption("finbif_use_cache"))

Arguments

Value

An object of classfinbif_taxa. A list with the same form astaxa.

Examples

## Not run: # Check a scientific namefinbif_check_taxa("Cygnus cygnus")# Check a common namefinbif_check_taxa("Whooper swan")# Check a genusfinbif_check_taxa("Cygnus")# Check a list of taxafinbif_check_taxa(  list(    species = c("Cygnus cygnus", "Ursus arctos"),    genus   = "Betula"  ))## End(Not run)

Clear cache

Description

Remove cached FinBIF API requests.

Usage

finbif_clear_cache()

Examples

## Not run: finbif_clear_cache()## End(Not run)

FinBIF collections

Description

Get information on collections in the FinBIF database.

Usage

finbif_collections(  filter,  select,  subcollections = TRUE,  supercollections = FALSE,  locale = getOption("finbif_locale"),  nmin = 0,  cache = getOption("finbif_use_cache_metadata"))

Arguments

Value

A data.frame.

Examples

## Not run: # Get collection metadatacollections <- finbif_collections()## End(Not run)

FinBIF informal groups

Description

Display the informal taxonomic groups used in the FinBIF database.

Usage

finbif_informal_groups(  group,  limit = 5,  quiet = FALSE,  locale = getOption("finbif_locale"),  cache = getOption("finbif_use_cache_metadata"))

Arguments

Value

A character vector (invisibly).

Examples

## Not run: # Display the informal taxonomic groups used by FinBIFfinbif_informal_groups()## End(Not run)

Get last modified date for FinBIF occurrence records

Description

Get last modified date for filtered occurrence data from FinBIF.

Usage

finbif_last_mod(..., filter)

Arguments

Value

ADate object

Examples

## Not run: # Get last modified date for Whooper Swan occurrence records from Finlandfinbif_last_mod("Cygnus cygnus", filter = c(country = "Finland"))## End(Not run)

FinBIF metadata

Description

Display metadata from the FinBIF database.

Usage

finbif_metadata(  which,  locale = getOption("finbif_locale"),  cache = getOption("finbif_use_cache_metadata"))

Arguments

Value

A data.frame.

Examples

## Not run: finbif_metadata("red_list")## End(Not run)

Download FinBIF occurrence records

Description

Download filtered occurrence data from FinBIF as adata.frame.

Usage

finbif_occurrence(  ...,  filter = NULL,  select = NULL,  order_by = NULL,  aggregate = "none",  sample = FALSE,  n = 10,  page = 1,  count_only = FALSE,  quiet = getOption("finbif_hide_progress"),  cache = getOption("finbif_use_cache"),  dwc = FALSE,  date_time_method = NULL,  check_taxa = TRUE,  on_check_fail = c("warn", "error"),  tzone = getOption("finbif_tz"),  locale = getOption("finbif_locale"),  seed = NULL,  drop_na = FALSE,  aggregate_counts = TRUE,  exclude_na = FALSE,  unlist = FALSE,  facts = NULL,  duplicates = FALSE,  filter_col = NULL,  restricted_api = NULL)

Arguments

Value

Adata.frame. Ifcount_only = TRUE an integer.

Examples

## Not run: # Get recent occurrence data for taxonfinbif_occurrence("Cygnus cygnus")# Specify the number of recordsfinbif_occurrence("Cygnus cygnus", n = 100)# Get multiple taxafinbif_occurrence("Cygnus cygnus", "Ursus arctos")# Filter the recordsfinbif_occurrence(  species = "Cygnus cygnus",  filter = list(coordinate_accuracy_max = 100))## End(Not run)

Load FinBIF occurrence records from a file

Description

Load occurrence data from a file as adata.frame.

Usage

finbif_occurrence_load(  file,  select = NULL,  n = -1,  count_only = FALSE,  quiet = getOption("finbif_hide_progress"),  cache = getOption("finbif_use_cache"),  dwc = FALSE,  date_time_method = NULL,  tzone = getOption("finbif_tz"),  write_file = tempfile(),  dt = NA,  keep_tsv = FALSE,  facts = list(),  type_convert_facts = TRUE,  drop_na = FALSE,  drop_facts_na = drop_na,  locale = getOption("finbif_locale"),  skip = 0)

Arguments

Value

Adata.frame, or ifcount_only = TRUE an integer.

Examples

## Not run: # Get occurrence datafinbif_occurrence_load(49381)## End(Not run)

Get a FinBIF personal access token

Description

Have a personal access token for use with the FinBIF API sent to a specifiedemail address.

Usage

finbif_request_token(email, quiet = FALSE)

Arguments

Value

If an access token has already been set thenNULL (invisibly) ifnot then, invisibly, afinbif_api object containing the response fromthe FinBIF server.

Examples

## Not run: # Request a token for example@email.comfinbif_request_token("example@email.com")## End(Not run)

Search the FinBIF taxa

Description

Search the FinBIF database for taxon.

Usage

finbif_taxa(  name,  n = 1,  type = c("exact", "partial", "likely"),  cache = getOption("finbif_use_cache"))common_name(name, locale = getOption("finbif_locale"))scientific_name(name)taxon_id(name)

Arguments

Value

Forfinbif_taxa afinbif_taxa object. Otherwise, a charactervector.

Examples

## Not run: # Search for a taxonfinbif_taxa("Ursus arctos")# Use partial matchingfinbif_taxa("Ursus", n = 10, "partial")# Get Swedish name of Eurasian Eagle-owlcommon_name("Bubo bubo", "sv")# Get scientific name of "Otter"scientific_name("Otter")# Get taxon identifier of "Otter"taxon_id("Otter")## End(Not run)

Update cache

Description

Update all cached FinBIF API requests.

Usage

finbif_update_cache()

Examples

## Not run: finbif_update_cache()## End(Not run)

Convert variable names

Description

Convert variable names to Darwin Core or FinBIF R package native style.

Usage

to_dwc(...)to_native(...)from_schema(..., to = c("native", "dwc"), file = c("none", "citable", "lite"))

Arguments

Value

Character vector.

Examples

to_dwc("record_id", "date_time", "scientific_name")

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 capturedmultiple times will have a singleindividual_id and multiplerecord_idscorresponding to each capture).

• event_id Character.Event ID. An event can contain one or more records (e.g., a survey ofplants 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 specificinstitution). Collections themselves can be part of a larger(super)collection (e.g., all the collections at a specific museum). Onlythe 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 onlywill be formatted asGenus 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 rankgenus 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) inthe 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 therecord 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 differsby 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 manyrecords withabundance_interpreted == 1L only indicate the record is ofone individual and may not necessarily imply that this was the abundance atthat specified place and time (e.g., a preserved museum specimen consistingof 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 (inEUREF orWGS84 coordinate system)of the central point of a bounding box encompassing the record's geographiccoverage.

• ⁠{lat|lon}_{min|max}_{euref|ykj|wgs84}⁠. Numeric.Vertices of a bounding box encompassing the record's geographic coverage.Coordinates are available inEUREF,YKJ, orWGS84.

• coordinates_uncertainty Integer.The horizontal distance (in meters) from the record's given coordinatesdescribing the smallest circle containing the whole of the record'slocation.

• coordinates_source Character.Source of coordinates.

• ⁠footprint_{euref|ykj|wgs84}⁠ Character.Well-Known Text (WKT) representation of the geographic shape defining thelocation 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 ofBiogeographical Province. See link fordetails.

• 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 specificpart 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 afterrecords are downloaded from FinBIF. Its timezone and accuracy can becontrolled seefinbif_occurrence() for details.

• duration Duration.The duration of the recording event. This variable is computed afterrecords 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 numberindicating 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 numberindicating the day of the year in MMDD (%m%d) format.

• century Integer.The century during which the recording event occurred (NA if the eventspans multiple centuries).

• decade Integer.The decade during which the recording event occurred (NA if the eventspans multiple decades).

• year Integer.The year during which the recording event occurred (NA if the event spansmultiple years).

• month Integer.The month of the year during which the recording event occurred (NA ifthe event spans multiple months).

• day Integer.The day of the month during which the recording event occurred (NA if theevent 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 ordocument.

• reported_taxon_confidenceReliability of the record's taxonomic identification as reported by theoriginal data author.

• ⁠{document|time|location|event|record}_issue⁠ Character.Issues with record associated with its document, time, location, event, orthe 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 specificinstitution). Collections themselves can be part of a larger(super)collection (e.g., all the collections at a specific museum). Onlythe 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 withthe record.

• ⁠{document|event|record}_media_count⁠ Integer.How many media items (images, audio, video, etc., ...) are associated withthe record's document, event or the record itself.