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Changelog

Source: NEWS.md

finbif 0.10.1

CRAN release: 2026-10-22

MINOR IMPROVEMENTS

  • Improvements have been made to the output of properties materialEntityType, informationWithheld, dataGeneralizations, eventDate, occurrenceStatus and modified.

DEPRECATION

  • The use of properties eventDateTime and samplingEffort has been deprecated in favour eventDate. The former will be unavailable in the next release. While eventDateTime uses as.POSIXct class data eventDate data are strings in ISO8601 format.

finbif 0.10.0

CRAN release: 2026-07-02

MINOR IMPROVEMENTS

  • New variable materialEntityType added.

BREAKING CHANGES

  • The default value of finbif_use_dwc is now TRUE. meaning that finbif_occurrence() expects and returns DwC style variable names unless otherwise specified by the user.

finbif 0.9.14

CRAN release: 2026-04-17

MINOR IMPROVEMENTS

  • DwC style field names can be set with a global option finbif_use_dwc.
  • finbif_taxa gains a locale argument.

DEPRECATION

  • The default value of finbif_use_dwc is FALSE. This is deprecated and will be set to TRUE in v0.10.0.

finbif 0.9.13

CRAN release: 2026-03-04

MINOR IMPROVEMENTS

  • Package now uses version 1 of upstream API.
  • A collection ID QName is used if there is no collection code.

BUG FIXES

  • Fixed an error in the formatting of iso8061 dates.
  • Fixed an error triggered if collection code is requested without institution code.

finbif 0.9.12

CRAN release: 2026-01-27

MINOR IMPROVEMENTS

  • Added a new function to renew access tokens.

BUG FIXES

  • Fixed issue with fetching collection metadata due to upstream API changes.

finbif 0.9.11

CRAN release: 2025-08-22

MINOR IMPROVEMENTS

  • Added capacity to import new DarwinCore archive formatted FinBIF download files.
  • Added new variables and filters from upstream API (undocumented).

finbif 0.9.10

CRAN release: 2025-04-15

MINOR IMPROVEMENTS

  • Improvements have been made to the way errors in parsing json are handled.

finbif 0.9.9

CRAN release: 2024-11-05

DEFUNCT

  • Importing .ods and .xlsx occurrence data files is now defunct. Users should use .tsv download files only.

MINOR IMPROVEMENTS

  • Occurrence download progress indicator has been simplified.
  • Location data parsing (country, region, municipality and local area) has been improved.

finbif 0.9.8

CRAN release: 2024-08-19

DEPRECATION

  • Importing .ods and .xlsx occurrence data files has been deprecated and will be defunct in a future release.

MINOR IMPROVEMENTS

  • Caching behaviour has been made more consistent.

finbif 0.9.7

CRAN release: 2024-07-23

NEW FEATURES

  • Record pagination has been simplified and improved so that it should not be possible to have duplicate records when using finbif_occurrence.

MINOR IMPROVEMENTS

  • finbif_last_mod can be used without a filter argument value.
  • Error handling for API requests has been improved.

BUG FIXES

  • Fixed an issue triggered when multi-filter set requests returned zero results.
  • Fixed bug triggered when dropping columns of all NA data.
  • Fixed an issue with file-based caches timing out correctly.
  • Fixed an issue triggered when selecting certain variables and zero records were returned.

finbif 0.9.6

CRAN release: 2024-04-25

MINOR IMPROVEMENTS

  • New undocumented variable and filter local added from upstream API.

BUG FIXES

  • Fixed an issue that caused more records than requested to be returned for certain values of n.

finbif 0.9.5

CRAN release: 2024-03-15

MINOR IMPROVEMENTS

  • A more informative error message is given when requesting an access token for an email address that has already been assigned one.

BUG FIXES

  • Fixed an issue with reading facts for FinBIF record download files.
  • Fixed an issue with reading column names using data.table package to ingest FinBIF record download files.

finbif 0.9.4

CRAN release: 2024-01-12

NEW FEATURES

  • New undocumented variable “source” can be selected with finbif_occurrence.

MINOR IMPROVEMENTS

  • Record pagination should now often require less queries of FinBIF server and should be faster.
  • FinBIF collections field names have been sanitised.
  • When filtering records by “collection_id” a full URL ID can be used or a QName.

BUG FIXES

  • Reading zero observation data downloads will now produce a zero row data.frame instead of triggering an error.

finbif 0.9.3

CRAN release: 2023-09-28

BUG FIXES

  • Fix a bug resulting in the incorrect region being assigned to occurrence records.

MINOR IMPROVEMENTS

  • New undocumented variables institution_code and collection_code can be selected when using functions finbif_collections and finbif_occurrence.

finbif 0.9.2

CRAN release: 2023-08-28

BUG FIXES

  • Fixed a bug triggered when localising some variables and multiple pages of data had been requested.

finbif 0.9.1

CRAN release: 2023-06-29

NEW FEATURES

  • New option finbif_use_cache_metadata to set caching for metadata only. Is ignored if finbif_use_cache is TRUE.

BUG FIXES

  • Fixed a bug triggered when trying to compute a variable from an identifier and data returned contained zero records.

finbif 0.9.0

CRAN release: 2023-05-23

NEW FEATURES

  • New function finbif_update_cache can 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 restricted_api argument to finbif_occurrence.
  • Cached data can use a database as a backend by passing a DBI database connection object to the package option finbif_cache_path.
  • Cached data can be assigned a timeout by using a number (hours) instead of a logical value for the cache argument to finbif_ functions or the package option finbif_use_cache.
  • Record aggregations with finbif_occurrence can now be combined with multi-filter requests. Removing duplicate records or aggregate record combinations can be controlled with the duplicates argument and adding a column indicating the filter sets can be added with the filter_col argument.
BUG FIXES
  • Fixed a bug causing an infinite recursion when determining page size during record download pagination.
  • Fix bug triggered when using aggregation with some selected variables.

DEFUNCT

  • Mapping utilities finland_map, breaks_xy, hist_xy and the plot method for finbif_occ objects are now defunct.
  • User access to finbif_records and its classes and methods is now defunct.

finbif 0.8.0

CRAN release: 2023-03-29

DEPRECATION

  • Mapping utilities finland_map, breaks_xy, hist_xy and the plot method for finbif_occ objects have been deprecated as they are out-of-scope.
  • User access to finbif_records and its classes and methods isdeprecated in favour of finbif_occurrence.

NEW FEATURES

  • Record aggregations with finbif_occurrence can now include “individual” and “pair” sums.

finbif 0.7.2

CRAN release: 2023-02-06

MINOR IMPROVEMENTS

  • Updated deprecated use of tidy::pivot_wider.
  • Added new filters and variables from upstream API.

finbif 0.7.1

CRAN release: 2022-11-24

NEW FEATURES

  • New function finbif_mod_date to get last modified date for FinBIF occurrence data.
  • Region is now a selectable variable for finbif_occurrence and can also be used to filter records.

MINOR IMPROVEMENTS

  • For the sake of clarity “province” is now referred to as “bio-province”.
  • Many variables, including sex, life_stage and record_quality are now localised.
  • The variable restriction_reasons is now referred to in the singular as restriction_reason.
  • For consistency, lang argument to finbif_collections has been changed to locale.

BUG FIXES

  • Fixed bug that caused locale to be set incorrectly for multipage requests.

finbif 0.7.0

CRAN release: 2022-09-13

NEW FEATURES

  • New function taxon_id that returns FinBIF taxon identifiers given a scientific name, vernacular name or other taxon identifier.
  • New filters complete_list_taxon_id and complete_list_type now available.
  • New global option finbif_hide_progress to 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.
  • Option unlist added to finbif_occurrence that casts list columns to strings. If a cell has multiple values the values are cast to a string separated by semi-colons.
  • New argument facts added to finbif_occurrence that can be used to automatically extract facts when downloading occurrence records.

BUG FIXES

  • Fixed bug triggered by incorrect data type applied to taxonomic_order.
  • Fixed bug preventing locale switching of vernacular name data.

finbif 0.6.6

CRAN release: 2022-08-08

NEW FEATURES

  • New option to exclude all records with any NA values for any of the selected variables added to finbif_occurrence.

MINOR IMPROVEMENTS

  • The warning/error message returned when an invalid taxon is requested with finbif_occurrence has been made more detailed, warning the user they may be using synonyms or other invalid taxon names.

BUG FIXES

  • Fix applied for a print method error triggered by clashing class names.
  • Fixed issue with ordering by some variables.

finbif 0.6.5

CRAN release: 2022-05-20

NEW FEATURES

  • New variables and filters (currently undocumented) have been added for the forthcoming Finnish atlas of breeding birds.
  • Skip rows argument added to finbif_occurrence_load so files can be read in chunks.

MINOR IMPROVEMENTS

  • For clarity, KKJ coordinate reference system is now referred to as YKJ.
  • When selecting all available variables for download file imports using finbif_occurrence_load “extra” variables will no longer be automatically added.

finbif 0.6.4

CRAN release: 2022-03-10

MINOR IMPROVEMENTS

  • 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.
  • New argument aggregate_counts (defaulting to TRUE) added to finbif_occurrence to 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.

BUG FIXES

  • Fix bug triggered when printing occurrence records where all records have no coordinate uncertainty.

finbif 0.6.3

CRAN release: 2022-01-03

MINOR IMPROVEMENTS

  • Argument drop_na_facts has been changed to drop_facts_na for function finbif_occurrence_load to avoid problems due to partial matching of argument drop_na.
  • Data quality description has been appended to description field in data.frame returned by finbif_collections().
  • Occurrence record filtering can now be done using open-ended date ranges.
  • New administrative statuses added.

BUG FIXES

  • Fix bug in importing of file downloads triggered by string quotation errors.

finbif 0.6.2

CRAN release: 2021-09-03

NEW FEATURES

  • New package option, finbif_allow_query, with default value, TRUE. If set to FALSE then 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.

MINOR IMPROVEMENTS

  • A client-side error will be triggered if an attempt is made to filter by taxon and aggregate data by event with finbif_occurrence.

BUG FIXES

  • Fix bug preventing loading of FinBIF archives that is triggered when all variables are selected with select = "all".
  • Fix bug preventing finbif_occ objects from printing when one or more columns contain missing data only.

finbif 0.6.1

CRAN release: 2021-07-26

BUG FIXES

  • Fixed a regression in the last release that prevented collection names being converted from their URIs.

finbif 0.6.0

CRAN release: 2021-07-22

NEW FEATURES

  • New variables lat_euref and lon_euref available 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_load from ZIP archive or online reference.
  • Option now available to extract “facts” when using finbif_occurrence_load to 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 finbif_occurrence_load.
  • New filters (currently undocumented) ely_center_id and region_id are available for finbif_occurrence.
  • New function, 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 finbif_occ objects.
  • New computed variable epsg (currently undocumented). If selected, the column will have the EPSG code of the first column that contains geographic data.

MINOR IMPROVEMENTS

  • Can now select all available variables when importing a FinBIF download request file using finbif_occurrence_load with select = "all".
  • New option, drop_na, to drop columns that only contain missing data added to finbif_occurrence and finbif_occurrence_load.
  • 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.
  • The variable taxon_rank is now converted to a string on the fly via taxon_rank_id.
  • Variables that are computed from their identifiers are now localised when multiple languages are available.

BUG FIXES

  • Fixed bug that prevented occurrence record counting when caching was not in use.
  • Fixed bug that triggered an error when selected a variable that had to be computed from its ID when using DwC style variable names.

finbif 0.5.0

CRAN release: 2021-03-27

NEW FEATURES

  • Getting records from FinBIF can now be speed up (~1.5x) with asynchronous processing. If the future package 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_load can load data from a local file or remotely using a persistent identifier URI (e.g., http://tun.fi/HBF.49381).
  • Aggregation of records can now be performed at the recording “event” level as well as the “record” level.

finbif 0.4.1

CRAN release: 2021-01-27

NEW FEATURES

  • New functions scientific_name and common_name are 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).

MINOR IMPROVEMENTS

  • Collection name can be selected as a variable for occurrence records. Previously it had to be manually translated from collection ID.
  • Variables restriction_reasons_conservation, restriction_reason_embargo and restriction_reason_custom are no longer in use upstream and can no longer be selected.

finbif 0.4.0

CRAN release: 2020-12-17

NEW FEATURES

  • 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.

MINOR IMPROVEMENTS

  • Error is triggered when attempting to request less than one record.
  • New content on requesting aggregated occurrence records added to vignette:
    1. Occurrence records from FinBIF.

BUG FIXES

  • 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).

finbif 0.3.1

CRAN release: 2020-11-24

NEW FEATURES

  • Occurrence records can be ordered by the total number of records or total number of Finnish records of the taxon (variables: n_total_records & n_total_finnish_records, currently undocumented).
  • New Finnish occurrence status, records_only, added.
  • New administrative statuses added to filters.

MINOR IMPROVEMENTS

  • Filtering vignette updated to reflect changes to data quality filters.

finbif 0.3.0

CRAN release: 2020-04-23

NEW FEATURES

  • All user facing functions with a finbif_ prefix can now also be used with the alternative shorter prefix fb_.
  • Crop Wild Relative, CWR, added to admin statuses.
  • There are two new utility functions, to_dwc and to_native for converting variable names to and from Darwin Core style.
  • Users can select and order by variables in Darwin Core style when using finbif_occurrence.
  • Some changes in variables and filters have flowed from upstream changes to “api.laji.fi”. The variables is_unidentifiable, record_reliable, collection_reliability, taxon_reliability, taxon_reliability_message and taxon_reliability_source have been deprecated and replaced with requires_verification, requires_identification, record_reliability and record_quality. The filters collection_reliability and taxon_reliability have been deprecated and replaced with requires_verification, collection_quality, record_reliability, record_quality, and expert_verified.
  • 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.

MINOR IMPROVEMENTS

  • 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 finbif_occurrence().
  • Improved error messages when taxa fail checking in finbif_occurrence().
  • 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 finbif_occurrence() is run.
  • 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 finbif_occ objects.
  • 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 select argument to finbif_occurrence by prepending the variable name with a “-”.
  • After some failures, API requests are now automatically retried up to three times.

BUG FIXES

  • 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_occ objects that caused error when trying to display a single column objects with a list-col only.

finbif 0.2.0

CRAN release: 2020-01-16

NEW FEATURES

  • Add capacity to request a random sample of FinBIF records.

MINOR IMPROVEMENTS

  • Add more content to vignettes.

finbif 0.1.0

CRAN release: 2019-11-19

  • Initial release.