materialEntityType added.finbif_use_dwc is now
TRUE. meaning that finbif_collections()
expects and returns DwC style variable names unless otherwise specified
by the user.finbif_use_dwc.finbif_taxa gains a locale argument.finbif_use_dwc is
FALSE. This is deprecated and will be set to
TRUE in v0.10.0..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.local added from
upstream API.n.data.table package to ingest FinBIF record download
files.finbif_occurrence.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.finbif_update_cache can be used to update
all the cached objects that have reached their expiration and are no
longer valid.restricted_api argument to
finbif_occurrence.DBI database connection object to the package option
finbif_cache_path.cache argument to
finbif_ functions or the package option
finbif_use_cache.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.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.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 isdeprecated in favour of finbif_occurrence.finbif_occurrence can now
include “individual” and “pair” sums.tidy::pivot_wider.finbif_mod_date to get last modified date
for FinBIF occurrence data.finbif_occurrence and can also be used to filter
records.sex, life_stage
and record_quality are now localised.restriction_reasons is now referred to in
the singular as restriction_reason.lang argument to
finbif_collections has been changed to
locale.taxon_id that returns FinBIF taxon
identifiers given a scientific name, vernacular name or other taxon
identifier.complete_list_taxon_id and
complete_list_type now available.finbif_hide_progress to suppress
progress bars when downloading, importing or processing FinBIF
records.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.facts added to
finbif_occurrence that can be used to automatically extract
facts when downloading occurrence records.taxonomic_order.finbif_occurrence.finbif_occurrence has been made more
detailed, warning the user they may be using synonyms or other invalid
taxon names.finbif_occurrence_load so
files can be read in chunks.finbif_occurrence_load “extra” variables will no
longer be automatically added.aggregate_counts (defaulting to
TRUE) added to finbif_occurrence to toggle the
inclusion of aggregation count fields on and off.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.frame returned by
finbif_collections().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.select = "all".finbif_occ objects from printing
when one or more columns contain missing data only.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.finbif_occurrence_load from ZIP
archive or online reference.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.finbif_occurrence_load.ely_center_id and
region_id are available for
finbif_occurrence.from_schema, to convert variable names
from FinBIF schema to other styles.date_time_ISO8601 (currently
undocumented) can be selected when creating finbif_occ
objects.epsg (currently undocumented). If
selected, the column will have the EPSG code of the first column that
contains geographic data.finbif_occurrence_load with
select = "all".drop_na, to drop columns that only contain
missing data added to finbif_occurrence and
finbif_occurrence_load.taxon_rank is now converted to a string on
the fly via taxon_rank_id.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.finbif_occurrence_load can load
data from a local file or remotely using a persistent identifier URI
(e.g., http://tun.fi/HBF.49381).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.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.n_total_records & n_total_finnish_records,
currently undocumented).records_only,
added.finbif_ prefix can now
also be used with the alternative shorter prefix fb_.to_dwc and
to_native for converting variable names to and from Darwin
Core style.finbif_occurrence.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.on_check_fail argument in
function finbif_occurrence().finbif_occurrence().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.finbif_occ objects.select
argument to finbif_occurrence by prepending the variable
name with a “-”.on_check_fail = "warn") all taxa
failed checks finbif_occurrence() would proceed as if no
taxa had been selected.finbif_occ objects that
caused error when trying to display a single column objects with a
list-col only.
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