CRAN release: 2023-05-23
finbif_update_cachecan be used to update all the cached objects that have reached their expiration and are no longer valid.
A restricted data API token can be explicitly declared via the
Cached data can use a database as a backend by passing a
DBIdatabase connection object to the package option
Cached data can be assigned a timeout by using a number (hours) instead of a logical value for the
finbif_functions or the package option
Record aggregations with
finbif_occurrencecan now be combined with multi-filter requests. Removing duplicate records or aggregate record combinations can be controlled with the
duplicatesargument and adding a column indicating the filter sets can be added with the
CRAN release: 2023-03-29
hist_xyand the plot method for
finbif_occobjects have been deprecated as they are out-of-scope.
User access to
finbif_recordsand its classes and methods is deprecated in favour of
CRAN release: 2023-02-06
CRAN release: 2022-11-24
finbif_mod_dateto get last modified date for FinBIF occurrence data.
Region is now a selectable variable for
finbif_occurrenceand can also be used to filter records.
For the sake of clarity “province” is now referred to as “bio-province”.
Many variables, including
record_qualityare now localised.
restriction_reasonsis now referred to in the singular as
finbif_collectionshas been changed to
CRAN release: 2022-09-13
taxon_idthat returns FinBIF taxon identifiers given a scientific name, vernacular name or other taxon identifier.
New global option
finbif_hide_progressto suppress progress bars when downloading, importing or processing FinBIF records.
For the sake of clarity and consistency the term “administrative status” is now referred to as “regulatory status” throughout.
Regulatory status, informal taxonomic group and habitat data are now localised.
finbif_occurrencethat casts list columns to strings. If a cell has multiple values the values are cast to a string separated by semi-colons.
finbif_occurrencethat can be used to automatically extract facts when downloading occurrence records.
CRAN release: 2022-08-08
- New option to exclude all records with any NA values for any of the selected variables added to
- The warning/error message returned when an invalid taxon is requested with
finbif_occurrencehas been made more detailed, warning the user they may be using synonyms or other invalid taxon names.
CRAN release: 2022-05-20
New variables and filters (currently undocumented) have been added for the forthcoming Finnish atlas of breeding birds.
Skip rows argument added to
finbif_occurrence_loadso files can be read in chunks.
CRAN release: 2022-03-10
New administrative statuses added.
The number of (and interval between) api request retries can be configured (currently undocumented).
For some museum collections scientific names have been added for non-Finnish species.
New fields have been added to citable download imports.
TRUE) added to
finbif_occurrenceto toggle the inclusion of aggregation count fields on and off.
New bird association area, occurrence types and location tag metadata added.
New filters and variables (currently undocumented) added from upstream API.
CRAN release: 2022-01-03
drop_na_factshas been changed to
finbif_occurrence_loadto avoid problems due to partial matching of argument
Data quality description has been appended to description field in
Occurrence record filtering can now be done using open-ended date ranges.
New administrative statuses added.
CRAN release: 2021-09-03
New package option,
finbif_allow_query, with default value,
TRUE. If set to
FALSEthen remote API queries will trigger an error meaning only cached requests will run if a cache is found.
Records can now be aggregated by document.
- A client-side error will be triggered if an attempt is made to filter by taxon and aggregate data by event with
CRAN release: 2021-07-26
CRAN release: 2021-07-22
lon_eurefavailable for occurrence record downloads. These new variables represent the central point of a bounding box encompassing a record’s geographic coverage in the EUREF (ETRS89/ETRS-TM35FIN) coordinate system.
Option now available to retain the TSV data file when loading FinBIF occurrence data with
finbif_occurrence_loadfrom ZIP archive or online reference.
Option now available to extract “facts” when using
finbif_occurrence_loadto import records from a ZIP archive. The user must supply a named list, where the names refer to one or more fact types: “record”, “event” and/or “document”, and the list elements are character vectors indicating which “facts” to extract.
“Lite” download files (occurrence record datasets of less than 10,000 records downloaded directly from laji.fi) can now be imported using
New filters (currently undocumented)
region_idare available for
from_schema, to convert variable names from FinBIF schema to other styles.
New computed variable
date_time_ISO8601(currently undocumented) can be selected when creating
New computed variable
epsg(currently undocumented). If selected, the column will have the EPSG code of the first column that contains geographic data.
Can now select all available variables when importing a FinBIF download request file using
select = "all".
drop_na, to drop columns that only contain missing data added to
User can now select columns multiple times and rename them on the fly by using a named character vector as the value of the ‘select’ argument.
taxon_rankis now converted to a string on the fly via
Variables that are computed from their identifiers are now localised when multiple languages are available.
CRAN release: 2021-03-27
Getting records from FinBIF can now be speed up (~1.5x) with asynchronous processing. If the
futurepackage is available and an asynchronous strategy (e.g.,
plan(multisession, workers = 2)) is selected then downloading records and processing them will occur simultaneously in separate threads, often leading to a significant speed up over sequential processing.
Occurrence records can now be requested using multiple sets of filters at the same time. If a list of filters (with unnamed elements) is supplied then a record request will be made for each set of filters and the results of all requests combined and all duplicate records removed.
Occurrence records can now be read directly from FinBIF download request files. The function
finbif_occurrence_loadcan load data from a local file or remotely using a persistent identifier URI (e.g.,
Aggregation of records can now be performed at the recording “event” level as well as the “record” level.
CRAN release: 2021-01-27
common_nameare now available to get scientific and common names for taxa (given a taxon name or FinBIF ID code) or extract names from a
finbif_taxa- class object.
Add ability to extract complex record variables such as those associated with record media (currently undocumented).
Collection name can be selected as a variable for occurrence records. Previously it had to be manually translated from collection ID.
restriction_reason_customare no longer in use upstream and can no longer be selected.
CRAN release: 2020-12-17
- Occurrence record requests can now be made with aggregation,
aggregate = c("records", "species", "taxa"). This returns the number of records, and/or species or taxa for each combination of the selected variables instead of the occurrence records themselves.
Error is triggered when attempting to request less than one record.
New content on requesting aggregated occurrence records added to vignette: 2. Occurrence records from FinBIF.
Fixed two bugs in print method for FinBIF occurrence records that were triggered when attempting to print only one row of data.
Fixed bug triggering error when attempting to print occurrence record objects with zero rows.
Fixed bug triggered when trying to print occurrence record data with NA values.
Fixed bug causing incorrect subsetting of occurrence records when using logical vectors to subset rows.
Fixed bug that printed occurrence records with multi-element data incorrectly when there was a single element.
Fixed bug triggered by some system locales (#1).
CRAN release: 2020-11-24
Occurrence records can be ordered by the total number of records or total number of Finnish records of the taxon (variables:
n_total_finnish_records, currently undocumented).
New Finnish occurrence status,
New administrative statuses added to filters.
CRAN release: 2020-04-23
All user facing functions with a
finbif_prefix can now also be used with the alternative shorter prefix
Crop Wild Relative, CWR, added to admin statuses.
There are two new utility functions,
to_nativefor converting variable names to and from Darwin Core style.
Users can select and order by variables in Darwin Core style when using
Some changes in variables and filters have flowed from upstream changes to “api.laji.fi”. The variables
taxon_reliability_sourcehave been deprecated and replaced with
record_quality. The filters
taxon_reliabilityhave been deprecated and replaced with
Vernacular names are now localised. Users can select a language to use for taxon vernacular names. Missing names will fallback gracefully to other languages. A package-wide locale can be set and is by default set to the system locale (if not set or can’t be determined it will default to English).
New vignettes on getting occurrence records, selecting and ordering variables, metadata and plotting have been added.
Caching defaults to in memory caching instead of relying on the temporary directory.
Front matter of vignettes is now visible when using the R help browser.
Retired “quiet” option for “on_check_fail” argument in function
Improved error messages when taxa fail checking in
Global option to set timezone, “finbif_tz”, as default value for “tzone” argument to
finbif_occurrence(). Avoids having to set system environment variable TZ or specify “tzone” every time
Now when a record has no time information the start time is assumed to be midday. Previous behaviour was to assume start time was midnight, making errors potentially biased.
Package options are now documented in the package level man page.
News file is now accessible via R internal help system.
The number of default variables selected when accessing occurrence records has been reduced to speed up downloads and improve the display of
The print method for occurrence record objects has been updated. It is now aware of console width and when truncating variable values is more considerate of the context.
Variables can now be “deselected” when using the
finbif_occurrenceby prepending the variable name with a “
After some failures, API requests are now automatically retried up to three times.
Ordering by descending variables did not work when ordering by both ascending and descending variables.
Fixed bug in handling of duplicates that could result in an infinite recursion.
Fixed bug that (when “on_check_fail” = “warn”) all taxa failed checks ‘finbif_occurrence()’ would proceed as if no taxa had been selected.
Fixed bug in print method for
finbif_occobjects that caused error when trying to display a single column objects with a list-col only.
CRAN release: 2020-01-16