filters {finbif}

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 functions finbif_check_taxa() and finbif_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 the specified taxa are not found in the FinBIF taxonomy then matches are attempted with the occurrence record names as originally supplied verbatim.

• quality_controlled_det Logical. If TRUE (default) use quality controlled taxonomic determinations. Or, if FALSE use the originally recorded taxonomic determinations.

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

• invalid_taxa Logical. If TRUE (default) return records for taxa not found in the FinBIF taxonomic database as well as taxa that are in the FinBIF database. Or, if FALSE 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 linked to the recorded taxa in the FinBIF database. Use the function finbif_informal_groups() to see the informal taxonomic groups available in FinBIF.

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

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

• red_list_status Character vector. Filter by IUCN red list status code. Use the function finbif_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 function finbif_metadata() to see habitat (sub)types and codes for taxa in the FinBIF database. Habitat type/subtypes can be refined further by indicating habitat qualifiers with a named list of character vectors where the names are habitat (sub)type codes and the elements of the character vector are the habitat qualifier codes. Use the function finbif_metadata() to see habitat qualifiers and codes. The records returned will be of taxa whose primary habitat is considered to be the (sub)habitat/habitat qualifier combination supplied.

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

• finnish_occurrence_status Character vector. Filter by Finnish occurrence status of taxa. Use finbif_metadata() to see the possible occurrence statuses of taxa.

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

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

• invasive Logical. If TRUE, limit records to invasive taxa. Or if FALSE limit to non-invasive taxa. If unspecified (default) return records of invasive and non-invasive taxa.

• taxon_rank Character vector. Filter by taxonomic rank. Use finbif_metadata() to see the taxonomic ranks available. Records returned will be limited to the specified ranks and 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 the countries, bio-provinces, and municipalities (see below) in FinBIF, if none of these locality types match exactly then will return records with verbatim locality matches in the original records.

• country Character vector. Filter by country. Use finbif_metadata() to see country names and ISO codes (2 and 3 character) used in FinBIF.

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

• bio_province Character vector. Filter by bio-province. Use finbif_metadata() to see bio-province names and codes.

• municipality Character vector. Filter by municipality. Use finbif_metadata() to see municipality names.

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

• bird_assoc_area Character vector. Filter by BirdLife Finland association area. Use finbif_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 minimum and maximum longitude (or can be minimums only). The third element is the coordinate system; either one of "wgs84", "euref" or "ykj". The optional fourth element is a positive value less than 1. When 1, the coverage area of the returned records will be completely within the box bound by the coordinates values. Values less than 1 requires the returned record's coverage to overlap with the bounding box in that proportion. When using the system "ykj" the coordinates will be coerced to integers with units inferred from the number of integer digits (7 digits equals km's, 6 equals 10km's, etc.,). If coordinate maximums are not specified they will be assumed to be one unit above the minimums (e.g., c(666, 333, "ykj") is equivalent to list(c(6660000, 6670000), c(3330000, 3340000), "ykj")).

• coordinates_center Coordinates. A character vector or list of coordinate data. Must be of length 3. The first two elements are latitude and longitude and third is the coordinate system (currently only "wgs84" is implemented). Records returned will be those 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 corner of 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 only recorded municipality).

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

Time

Filters related to time of record include:

• date_range_ymd Dates. A vector of one to two Date objects (begin and end dates) or objects that are coercible to the Date. When supplying 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 in two-digit/leading zero form. If the begin or end dates are partial date strings they will be interpreted as the first or last day of the month or year (e.g., c(2001, 2003) is equivalent to c("2001-01-01", "2003-12-12")). If a single date is supplied as a partial date string then all records that fall within that month or year will be returned (e.g., c("2001-01") is equivalent to c("2001-01-01", "2001-01-31")). Use empty strings for the begin or end date to specify open-ended date ranges (e.g., c("2000-01-01", "") for all dates 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 to 366). If begin or end date is omitted 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"). If begin or end date is omitted then it is interpreted as the first or last day of the year.

• ⁠{first|last}_import_date_{min|max}⁠ Date. Filter by date record was imported/modified. Either a Date object or object that is coercible to the Date class, or the number of seconds since 1970-01-01 00:00.00 UTC (the so-called UNIX epoch). Note that this means that specifying a year, such as 2019, without a month and day will be interpreted as 2019 seconds after midnight on Jan 1, 1970 and not the year 2019.

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 the record, the event, or the document. The default is "without_issues" unless filtering by record, event or document ID or record annotation status.

• requires_verification Logical. Show only records requiring verification (TRUE) or not requiring verification (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 is c("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 or finbif_collections() data.frame. Filter by collection. If a character vector can refer to collection ID, collection name (in English) or abbreviated name. Use finbif_collections() to see list of collections and metadata. Can also use the results of a call to finbif_collections() directly to filter records.

• subcollections Logical. If TRUE (default) include the subcollections of the collections specified. If FALSE do not include subcollections.

• not_collection Character vector or finbif_collections() data.frame. As for collection, but result will be the negation of the specified collections.

• source Character vector. Filter by information system data source. Use finbif_metadata() to see data source IDs names and descriptions.

• record_basis Character vector. Filter by basis of record. Use finbif_metadata() to see list of record 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. Use finbif_metadata() to see list of organism life stages.

• sex Character vector. Filter by organism sex and sex-related category name or code. Use finbif_metadata() to see list of organism sexes and sex-related categories and codes. If "male" or "female" is specified then records returned will be those with sex specified as male or female respectively and 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 is c("wild", "unknown").

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

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

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

• has_record_media Logical. Filter by whether there is media (images, video, audio, etc.) associated with 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. See finbif_metadata() for a list of reasons data may have security restrictions.

• restriction_level Character vector. Filter by data restriction level. See finbif_metadata() for a list of the levels of data restrictions.

• restricted Logical. Filter records by whether any data restrictions are in place (TRUE) or not (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 and linked to the FinBIF taxon database (FALSE) or has not been identified to species level reliably and linked to the taxon database (TRUE).

• taxon_census Character vector. Return records belonging to surveys or censuses of a given taxon or taxonomic group. Specify the taxonomic group with a FinBIF taxon ID. Use finbif_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 the form "<fact>=<value>". Value can be omitted in which case all records with 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 during monitoring that produces taxon lists for a given group of taxa (e.g., birds) can include all species observed with breeding status recorded for each observed species (all_species_and_breeding), all species observed without breeding status recorded for all species observed, all species observed 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.