Package 'finbif'

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

finbif_use_cache_metadata

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

finbif_cache_path

Character. The path to the directory where to store cached API queries. If unset (the default) in memory caching is used.

finbif_tz

Character. The timezone used by finbif functions that compute dates and times. Default: Sys.timezone()

finbif_locale

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

finbif_hide_progress

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

Author(s)

Maintainer: William K. Morris [email protected] (ORCID)

Other contributors:

• Finnish Museum of Natural History - Luomus [copyright holder]

See Also

Useful links:

• https://github.com/luomus/finbif

• https://finbif-docs-dev.netlify.app/

• Report bugs at https://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. Any request made using the same arguments will only request data from FinBIF in the first instance and subsequent requests will use the local cache while it exists. This will increase the speed of repeated requests and save bandwidth and computation for the FinBIF server. Caching can be turned off temporarily by setting cache = c(FALSE, FALSE) in the requesting function.

Setting options(finbif_use_cache = FALSE, finbif_use_cache_metadata = FALSE) will turn off caching for the current session.

Using filesystem caching

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

Using database caching

Caching can also be done using a database. Using a database for caching requires the DBI package and a database backend package such as RSQLite to be installed. To use the database for caching simply pass the connection objected created with DBI::dbConnect to the finbif_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 cache is considered invalid and is cleared) instead of a logical value for the finbif_use_cache and finbif_use_cache_metadata options or the cache function arguments.

Clearing the cache

The cache can be reset finbif_clear_cache().

Updating the cache

The cache can be updated using finbif_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 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 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).

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.

---

Check FinBIF taxa

Description

Check that taxa are in the FinBIF database.

Usage

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

Arguments

taxa	Character (or list of named character) vector(s). If a list each vector can have the name of a taxonomic rank (genus, species, etc.,). The elements of the vectors should be the taxa to check.
cache	Logical or Integer. If TRUE or a number greater than zero, then data-caching will be used. If not logical then cache will be invalidated after the number of hours indicated by the argument.

Value

An object of class finbif_taxa. A list with the same form as taxa.

Examples

## Not run: 

# Check a scientific name
finbif_check_taxa("Cygnus cygnus")

# Check a common name
finbif_check_taxa("Whooper swan")

# Check a genus
finbif_check_taxa("Cygnus")

# Check a list of taxa
finbif_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

filter	Logical. Expression indicating elements or rows to keep: missing values are taken as false.
select	Expression. Indicates columns to select from the data frame.
subcollections	Logical. Return subcollection metadata of higher level collections.
supercollections	Logical. Return lowest level collection metadata.
locale	Character. Language of data returned. One of "en", "fi", or "sv".
nmin	Integer. Filter collections by number of records. Only return information on collections with greater than value specified. If NA then return information on all collections.
cache	Logical or Integer. If TRUE or a number greater than zero, then data-caching will be used. If not logical then cache will be invalidated after the number of hours indicated by the argument.

Value

A data.frame.

Examples

## Not run: 

# Get collection metadata
collections <- 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

group	Character. Optional, if supplied only display this top-level group and its subgroups.
limit	Integer. The maximum number top-level informal groups (and their sub-groups) to display.
quiet	Logical. Return informal group names without displaying them.
locale	Character. One of the supported two-letter ISO 639-1 language codes. Current supported languages are English, Finnish and Swedish. For data where more than one language is available the language denoted by locale will be preferred while falling back to the other languages in the order indicated above.
cache	Logical or Integer. If TRUE or a number greater than zero, then data-caching will be used. If not logical then cache will be invalidated after the number of hours indicated by the argument.

Value

A character vector (invisibly).

Examples

## Not run: 

# Display the informal taxonomic groups used by FinBIF
finbif_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

...	Character vectors or list of character vectors. Taxa of records to download.
filter	List of named character vectors. Filters to apply to records.

Value

A Date object

Examples

## Not run: 

# Get last modified date for Whooper Swan occurrence records from Finland
finbif_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

which	Character. Which category of metadata to display. If unspecified, function returns the categories of metadata available.
locale	Character. One of the supported two-letter ISO 639-1 language codes. Current supported languages are English, Finnish and Swedish. For data where more than one language is available the language denoted by locale will be preferred while falling back to the other languages in the order indicated above.
cache	Logical or Integer. If TRUE or a number greater than zero, then data-caching will be used. If not logical then cache will be invalidated after the number of hours indicated by the argument.

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 a data.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

...	Character vectors or list of character vectors. Taxa of records to download.
filter	List of named character vectors. Filters to apply to records.
select	Character vector. Variables to return. If not specified, a default set of commonly used variables will be used. Use "default_vars" as a shortcut for this set. Variables can be deselected by prepending a - to the variable name. If only deselects are specified the default set of variables without the deselection will be returned.
order_by	Character vector. Variables to order records by before they are returned. Most, though not all, variables can be used to order records before they are returned. Ordering is ascending by default. To return in descending order append a - to the front of the variable (e.g., "-date_start"). Default order is "-date_start" > "-load_data" > "reported_name".
aggregate	Character. If "none" (default), returns full records. If one or more of "records", "species", "taxa", "individuals", "pairs", "events" or "documents"; aggregates combinations of the selected variables by counting records, species, taxa, individuals or events or documents. Aggregation by events or documents cannot be done in combination with any of the other aggregation types.
sample	Logical. If TRUE randomly sample the records from the FinBIF database.
n	Integer. How many records to download/import.
page	Integer. Which page of records to start downloading from.
count_only	Logical. Only return the number of records available.
quiet	Logical. Suppress the progress indicator for multipage downloads. Defaults to value of option finbif_hide_progress.
cache	Logical or Integer. If TRUE or a number greater than zero, then data-caching will be used. If not logical then the cache will be invalidated after the number of hours indicated by the argument. If a length one vector is used, its value will only apply to caching occurrence records. If the value is length two, then the second element will determine how metadata is cached.
dwc	Logical. Use Darwin Core (or Darwin Core style) variable names.
date_time_method	Character. Passed to lutz::tz_lookup_coords() when date_time and/or duration variables have been selected. Default is "fast" when less than 100,000 records are requested and "none" when more. Using method "none" assumes all records are in timezone "Europe/Helsinki", Use date_time_method = "accurate" (requires package sf) for greater accuracy at the cost of slower computation.
check_taxa	Logical. Check first that taxa are in the FinBIF database. If true only records that match known taxa (have a valid taxon ID) are returned.
on_check_fail	Character. What to do if a taxon is found not valid. One of "warn" (default) or "error".
tzone	Character. If date_time has been selected the timezone of the outputted date-time. Defaults to system timezone.
locale	Character. One of the supported two-letter ISO 639-1 language codes. Current supported languages are English, Finnish and Swedish. For data where more than one language is available the language denoted by locale will be preferred while falling back to the other languages in the order indicated above.
seed	Integer. Set a seed for randomly sampling records.
drop_na	Logical. A vector indicating which columns to check for missing data. Values recycled to the number of columns. Defaults to all columns.
aggregate_counts	Logical. Should count variables be returned when using aggregation.
exclude_na	Logical. Should records where all selected variables have non-NA values only be returned.
unlist	Logical. Should variables that contain non atomic data be concatenated into a string separated by ";"?
facts	Character vector. Extra variables to be extracted from record, event and document "facts".
duplicates	Logical. If TRUE, allow duplicate records/aggregated records when making multi-filter set requests. If FALSE (default) duplicate records are removed.
filter_col	Character. The name of a column, with values derived from the names of the filter sets used when using multiple filters, to include when using multiple filter sets. If NULL (default), no column is included.
restricted_api	Character. If using a restricted data API token in addition to a personal access token, a string indicating the name of an environment variable storing the restricted data API token.

Value

A data.frame. If count_only = TRUE an integer.

Examples

## Not run: 

# Get recent occurrence data for taxon
finbif_occurrence("Cygnus cygnus")

# Specify the number of records
finbif_occurrence("Cygnus cygnus", n = 100)

# Get multiple taxa
finbif_occurrence("Cygnus cygnus", "Ursus arctos")

# Filter the records
finbif_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 a data.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

file	Character or Integer. Either the path to a Zip archive or tabular data file that has been downloaded from "laji.fi", a URI linking to such a data file (e.g., https://tun.fi/HBF.49381) or an integer representing the URI (i.e., 49381).
select	Character vector. Variables to return. If not specified, a default set of commonly used variables will be used. Use "default_vars" as a shortcut for this set. Variables can be deselected by prepending a - to the variable name. If only deselects are specified the default set of variables without the deselection will be returned. Use "all" to select all available variables in the file.
n	Integer. How many records to import. Negative and other invalid values are ignored causing all records to be imported.
count_only	Logical. Only return the number of records available.
quiet	Logical. Suppress the progress indicator for multipage downloads. Defaults to value of option finbif_hide_progress.
cache	Logical or Integer. If TRUE or a number greater than zero, then data-caching will be used. If not logical then the cache will be invalidated after the number of hours indicated by the argument. If a length one vector is used, its value will only apply to caching occurrence records. If the value is length two, then the second element will determine how metadata is cached.
dwc	Logical. Use Darwin Core (or Darwin Core style) variable names.
date_time_method	Character. Passed to lutz::tz_lookup_coords() when date_time and/or duration variables have been selected. Default is "fast" when less than 100,000 records are requested and "none" when more. Using method "none" assumes all records are in timezone "Europe/Helsinki", Use date_time_method = "accurate" (requires package sf) for greater accuracy at the cost of slower computation.
tzone	Character. If date_time has been selected the timezone of the outputted date-time. Defaults to system timezone.
write_file	Character. Path to write downloaded zip file to if file refers to a URI. Will be ignored if getOption("finbif_cache_path") is not NULL and will use the cache path instead.
dt	Logical. If package, data.table, is available return a data.table object rather than a data.frame.
keep_tsv	Logical. Whether to keep the TSV file if file is a ZIP archive or represents a URI. Is ignored if file is already a TSV. If TRUE the tsv file will be kept in the same directory as the ZIP archive.
facts	List. A named list of "facts" to extract from supplementary "fact" files in a local or online FinBIF data archive. Names can include one or more of "record", "event" or "document". Elements of the list are character vectors of the "facts" to be extracted and then joined to the return value.
type_convert_facts	Logical. Should facts be converted from character to numeric or integer data where applicable?
drop_na	Logical. A vector indicating which columns to check for missing data. Values recycled to the number of columns. Defaults to all columns.
drop_facts_na	Logical. Should missing or "all NA" facts be dropped? Any value other than a length one logical vector with the value of TRUE will be interpreted as FALSE. Argument is ignored if drop_na is TRUE for all variables explicitly or via recycling. To only drop some missing/NA-data facts use drop_na argument.
locale	Character. One of the supported two-letter ISO 639-1 language codes. Current supported languages are English, Finnish and Swedish. For data where more than one language is available the language denoted by locale will be preferred while falling back to the other languages in the order indicated above.
skip	Integer. The number of lines of the data file to skip before beginning to read data (not including the header).

Value

A data.frame, or if count_only = TRUE an integer.

Examples

## Not run: 

# Get occurrence data
finbif_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 specified email address.

Usage

finbif_request_token(email, quiet = FALSE)

Arguments

email	Character. The email address to which to send the API access token.
quiet	Logical. Suppress messages.

Value

If an access token has already been set then NULL (invisibly) if not then, invisibly, a finbif_api object containing the response from the FinBIF server.

Examples

## Not run: 

# Request a token for [email protected]
finbif_request_token("[email protected]")


## 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

name	Character. The name or ID of a taxon. Or, for functions other than finbif_taxa a finbif_taxa object.
n	Integer. Maximum number of matches to return. For types "exact" and "likely" only one taxon will be returned.
type	Character. Type of match to make. Must be one of exact, partial or likely.
cache	Logical or Integer. If TRUE or a number greater than zero, then data-caching will be used. If not logical then cache will be invalidated after the number of hours indicated by the argument.
locale	Character. One of the supported two-letter ISO 639-1 language codes. Current supported languages are English, Finnish and Swedish. For data where more than one language is available the language denoted by locale will be preferred while falling back to the other languages in the order indicated above.

Value

For finbif_taxa a finbif_taxa object. Otherwise, a character vector.

Examples

## Not run: 

# Search for a taxon
finbif_taxa("Ursus arctos")

# Use partial matching
finbif_taxa("Ursus", n = 10, "partial")

# Get Swedish name of Eurasian Eagle-owl
common_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", "short"),
  file = c("none", "citable", "lite")
)

Arguments

...	Character. Variable names to convert. For to_dwc and to_native the names must be in the opposite format. For from_schema the names must be from the FinBIF schema (e.g., names returned by https://api.laji.fi) or a FinBIF download file (citable or lite).
to	Character. Type of variable names to convert to.
file	Character. For variable names that are derived from a FinBIF download file which type of file.

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 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.

---