filters | R Documentation |
Filters available for FinBIF records and occurrence data.
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.
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 kms, 6
equals 10kms, 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).
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.
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"
.
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.
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