High-Performance Open-Source Archive
finbif_use_dwc.finbif_taxa gains a locale argument.finbif_use_dwc is
FALSE. This is deprecated and will be set to
TRUE in v0.9.15..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.
Error handling for API requests has been improved.
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.
Fixed an issue with reading column names using
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no longer valid.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.
User access to 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.
User access to 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.
Added new filters and variables from upstream API.
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.
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.
Fixed bug preventing locale switching of vernacular name data.
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.
Fixed issue with ordering by some variables.
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.
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.
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.
Records can now be aggregated by document.
finbif_occurrence.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.
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.
Fixed bug that triggered an error when selected a variable that had to be computed from its ID when using DWC style variable names.
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.
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.
Variables 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.
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).
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.
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