.ods and .xlsx occurrence data files is now defunct users
should use .tsv download files only..ods and .xlsx occurrence data files has been
deprecated and will be defunct in a future release.finbif_occurrence.finbif_last_mod can be used without a filter argument value.
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.
local added from upstream
API.n.Fixed an issue with reading facts for FinBIF record download files.
data.table package
to ingest FinBIF record download files.finbif_occurrence.Record pagination should now often require less queries of FinBIF server and be 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.
data.frame instead of triggering an error.institution_code and collection_code
can be selected when using functions finbif_collections and
finbif_occurrence.finbif_use_cache_metadata to set caching for metadata
only. Is ignored if finbif_use_cache is TRUE.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cached objects that have reached their expiration and are no longer
valid.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.
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.
Mapping utilities finland_map, breaks_xy, hist_xy and the plot
method for finbif_occ objects are now defunct.
finbif_records and its classes and methods is now
defunct.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.
finbif_records and its classes and methods is
deprecated in favour of finbif_occurrence.finbif_occurrence can now include
"individual" and "pair" sums.Updated deprecated use of tidy::pivot_wider.
New function finbif_mod_date to get last modified date for FinBIF
occurrence data.
finbif_occurrence and can
also be used to filter records.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.
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.
Fixed bug triggered by incorrect data type applied to
taxonomic_order.
finbif_occurrence.finbif_occurrence has been made more detailed,
warning the user they may be using synonyms or other invalid taxon
names.Fix applied for a print method error triggered by clashing class names.
New variables and filters (currently undocumented) have been added for the forthcoming Finnish atlas of breeding birds.
finbif_occurrence_load so files can be
read in chunks.For clarity, KKJ coordinate reference system is now referred to as YKJ.
finbif_occurrence_load "extra" variables will no longer be
automatically added.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.
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.
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.
finbif_occurrence.Fix bug preventing loading of FinBIF archives that is triggered when
all variables are selected with select = "all".
finbif_occ objects from printing when one or
more columns contain missing data only.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.
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.
Fixed bug that prevented occurrence record counting when caching was not in use.
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.
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.
Collection name can be selected as a variable for occurrence records. Previously it had to be manually translated from collection ID.
restriction_reasons_conservation,
restriction_reason_embargo and restriction_reason_custom are no
longer in use upstream and can no longer be selected.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.
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).
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.
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.
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.
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.