VasGBIF

• **The buffered logical column has been removed.** It was fully implied by native_status_source == "buffered", and was always FALSE in the country-code result, so it carried no information of its own. Both results now append exactly three classification columns: LEVEL3_COD, native_status, native_status_source.

Other signature changes

• **customized_filter() no longer takes gbif_issue.** The argument had to be filled with the output of extract_gbif_issues(), which is now called internally, so the signature drops to customized_filter(occ_import, taxa_checked, filter_countryCode = TRUE, filter_coordinateUncertainty = 10000, filter_date = FALSE, filter_identifiedBy = FALSE, filter_recordedBy = FALSE, filter_gbif_issues_max = 5).
• **export_records() gains a native_detected_country argument and renames its output files.** The signature becomes export_records(native_detected_coord = NA, native_detected_country = NA, export_path = NA). Each classification supplied is written as its own pair - all_records_coord.csv.gz / native_records_coord.csv.gz and all_records_country.csv.gz / native_records_country.csv.gz - replacing all_records.csv.gz / native_records.csv.gz. The two sets are never bound into a combined table.
• **map_records() gains a species argument.** The signature becomes map_records(native_detected_coord = NA, species = "all", precision = 3, cex = 3), so a single species can be mapped without subsetting the table by hand. A name that selects nothing stops with an error rather than rendering an empty map.
• **import_records() accepts an already-extracted occurrence table, and remove_tempfile defaults to TRUE.** The default was NULL, which resolved to TRUE for an auto-created directory but FALSE for a user-supplied one; it is now a plain TRUE. The extension check on path is gone: a non-ZIP file is no longer rejected on its suffix but probed for a gbifID first column, which rejects non-GBIF files including comma-separated ones whose header would otherwise arrive as a single column.

Dependency and documentation

• **The rnaturalearthdata dependency has been removed.** The seas test is evaluated against the bundled WorldLandMap object, which is passed explicitly as seas_ref, so the package was never imported at run time.
• **The documented workflow is now seven steps:** import_records() -\> check_taxon() -\> customized_filter() -\> par_clean_coordinates() -\> detect_native_coord() / detect_native_country() -\> map_records() -\> export_records(). Every step number was decremented after the removal of the issue-extraction step.

Bug Fixes

• **par_clean_coordinates() returned different results for a data.table and a data.frame.** CoordinateCleaner::clean_coordinates() behaves differently on the two: inside cc_outl() it subsets with k[, c(species, lon, lat)], which on a data.table returns a three-element character vector rather than the columns, silently changing which records are flagged as outliers. The table is now converted with as.data.frame() before it is handed over, so the same input always yields the same output. This was a reproducibility defect: the result depended on the class of the caller's object rather than on its contents.
• **import_records() could delete a directory the caller supplied.** Cleanup ran unlink(ex_path, recursive = TRUE) unconditionally when tempdir was given, so a user-supplied directory was removed in full even though it may have held unrelated files. An auto-created directory is still removed whole, but a caller-supplied one now has only the extracted members unlinked.
• **set_threads() stopped with "illegal !!!".** A non-positive x now stops with ` x must be a single positive number. ` instead of an unexplained exclamation.
• **par_clean_coordinates() rejects a whole customFiltered object with a usable message.** Passing the object rather than the table it contains previously failed deep inside the coordinate tests; it now stops with ` input is a customFiltered object, not a table. Pass the table it contains, for example par_clean_coordinates(filtered$occ_filtered). The guard tests for the class, so an ordinary list or data.frame` input is unaffected.

Improvements

• **par_clean_coordinates() names its columns and chunks by species.** The species, longitude and latitude arguments free the input from GBIF field names, and the parallel split runs per species so a chunk never straddles a taxon boundary. The seas test is evaluated against the bundled WorldLandMap land polygons buffered by 5 km.
• **customized_filter() reports per-rule verdicts.** Each rule now evaluates the whole table and stores a logical filter_* column, so one record can be audited against several rules at once. occ_filtered carries no verdict columns; the verdicts are returned separately in occ_marked, one column per applied rule. summary gains failed (records the rule rejects on its own terms) and only_failed_here (records it rejects and no other rule does) alongside the existing sequential dropped / remaining, whose sums differ on overlapping rules.
• **extract_issues() returns one tidy table.** The previous "issue" object bundled a wide logical matrix with a per-code summary; the internal function returns a single data.table of gbifID and a numeric issue_count, which is all the gbif_issues_max rule needs.
• **export_records() validates and documents both channels.** The coordinate channel requires gbifID, native_status, decimalLongitude and decimalLatitude, and rejects a record with a missing coordinate; the country-code channel requires only gbifID and native_status. Supplying one argument leaves the files of the other untouched.
• **The country-code stage keeps every record.** A countryCode that is blank, NA, or maps to no WGSRPD Level 3 area is retained as unknown / unmatched rather than dropped, and a country that maps but has no distribution entry for the taxon is unknown / no_entry. The two are distinct in native_status_source, so a genuinely absent country is never confused with a taxon that has no record there.

Documentation

• Package-level documentation, README, Example.Rmd, and Application.Rmd rewritten for the seven-step workflow, the renamed functions, and the new column contracts.
• Every clean_coordinates(), refine_coordinates(), custom_filter() and extract_gbif_issues() reference has been updated across R/, README, and the vignettes. References to the internal extract_gbif_issues() are cross-links to the unexported extract_issues().
• _pkgdown.yml step headings renumbered to match, and the removed print.issue method dropped from the reference index.
• Rd files regenerated for the renamed and updated functions.

Testing

• test-custom_filter.R rewritten for the verdict-column contract: the gbif_issue argument is gone, raw pipe-separated issue strings are built in the fixtures, and the failed / only_failed_here semantics are pinned against overlapping and disjoint rules.
• test-detect_native_coord.R and test-detect_native_country.R rewritten for the table input, the auto-generated gbifID, and the renamed classification values; both add a regression test that a column named species does not shadow the species argument.
• test-par_clean_coordinates.R added, replacing test-refine_coordinates.R. It covers the renamed argument, table-like inputs, the customFiltered guard, and a thread-independence check that threads = 1 and threads = 2 return identical() results.
• test-extract_issues.R added, replacing test-extract_gbif_issues.R. It asserts the new return contract and that the function stays internal with no print.issue method.
• test-export_records.R extended to the country-code channel and the renamed files; the fixtures now create their own temporary directories.
• test-import_records.R, test-map_records.R, and test-set_threads.R updated for the new tempdir semantics, the header probe error, the species argument, and the reworded thread error. The set_threads snapshot was re-recorded.