Step Function Package Brief description Citation
Pre-filtering bdc_scientificName_empty bdc Flag occurrences without a scientific name (Ribeiro et al. 2022)
bdc_coordinates_empty bdc Flag occurrences without latitude or longitude (Ribeiro et al. 2022)
bdc_coordinates_outOfRange bdc Flag occurrences that don’t map on Earth (Ribeiro et al. 2022)
bdc_basisOfRecords_notStandard bdc Flag occurrences based on ”basisOfRecord” (Ribeiro et al. 2022)
bdc_country_from_coordinates bdc Get country name using coordinates (where no country name is provided) (Ribeiro et al. 2022)
jbd_CfC_chunker BeeBDC A chunked and multi-threaded function similar to bdc_country_from_coordinates where datasets are otherwise too large (Dorey et al. In review)
bdc_country_standardized bdc Standardises country names and adds ISO2 codes, if needed (Ribeiro et al. 2022)
bdc_coordinates_transposed bdc Flags occurrences where latitude and longitude appear to be transposed (Ribeiro et al. 2022)
jbd_Ctrans_chunker BeeBDC A chunked and multi-threaded function similar to bdc_coordinates_transposed where datasets are otherwise too large (Dorey et al. In review)
bdc_coordinates_country_inconsistent & jbd_coordCountryInconsistent bdc and BeeBDC Flag occurrences where the country name does not match the coordinates. Both functions are very similar with slightly different implementations (Ribeiro et al. 2022; Dorey et al. In review)
bdc_coordinates_from_locality bdc Extracts occurrences with locality information that might allow geolocation (to fill gaps) (Ribeiro et al. 2022)
flagAbsent BeeBDC Flags occurrences that are marked as ”absent” under occurrenceStatus (Dorey et al. In review)
flagLicense BeeBDC Flags occurrences that are restricted by usage licences (Dorey et al. In review)
GBIFissues BeeBDC Flags occurrences based on user-defined GBIF flags (Dorey et al. In review)
clean_fossils CoordinateCleaner Flags species that occur in common fossil databases (Zizka et al. 2019)
Taxonomy bdc_clean_names bdc Cleans scientific names (e.g., removes prepended family names, removes qualifiers, etc.) and flags occurrences with name qualifiers (Ribeiro et al. 2022)
bdc_query_names_taxadb bdc Harmonizes taxonomy based on the taxadb package (Ribeiro et al. 2022)
harmoniseR BeeBDC Harmonizes taxonomy based on custom synonym lists (updated bee taxonomy provided) (Dorey et al. In review)
Space bdc_coordinates_precision & jbd_coordinates_precision bdc and BeeBDC Flags occurrences based on coordinate precision (number of decimal places). The bdc function flags occurrences if either latitude or longitude are imprecise. The BeeBDC function only flags occurrences where both latitude and longitude are imprecise (Ribeiro et al. 2022; Dorey et al. In review)
coordUncerFlagR BeeBDC Flags occurrences that do not pass a threshold of ”coordinateUncertaintyInMeters” (Dorey et al. In review)
clean_coordinates CoordinateCleaner Flags occurrences based on proximity to the centroids of capitals, countries, provinces, GBIF, and institutions; zeros for coordinates; points in seas; statistical outliers; urban areas; and coordinate validity (Zizka et al. 2019)
cd_ddmm CoordinateCleaner Flags occurrences where a significant fraction of records have been subjected to a common ‘degree minute’ to ‘decimal degree’ conversion error, where the degree sign is recognized as decimal delimiter (Zizka et al. 2019)
diagonAlley BeeBDC Flags records for fill-down errors in coordinates within datasets using a sliding window (Dorey et al. In review)
cd_round CoordinateCleaner Flags occurrences that might be from gridded datasets (Zizka et al. 2019)
countryOutlieRs BeeBDC Flags occurrences that do not match exact or adjacent country based on a custom checklist (bee country checklist is provided) BeeBDC
manualOutlierFindeR BeeBDC Flags occurrences (and their duplicates) based on expert identification BeeBDC
Time dateFindR BeeBDC Attempts to find and rescue dates hidden in other columns (Dorey et al. In review)
bdc_eventDate_empty bdc Flags occurrences without a date (Ribeiro et al. 2022)
bdc_year_outOfRange bdc Flags occurrences created prior to a user-specified year cut-off (Ribeiro et al. 2022)
Duplicates dupeSummary BeeBDC Iteratively searches out duplicates based on user-specified inputs. Duplicate clusters are merged and one occurrence is kept (based on user input) while the rest are flagged (Dorey et al. In review)
cc_dupl CoordinateCleaner Flags duplicates based on matching coordinates and species names (Zizka et al. 2019)
Filtering bdc_filter_out_flags bdc Filters occurrences using all present flag columns (starting with ”.”) (Ribeiro et al. 2022)
bdc_filter_out_names bdc Filters occurrences based only on the accepted status of taxonomy (Ribeiro et al. 2022)
summaryFun BeeBDC Filters occurrences based on flag columns and has additional inputs including: choosing filters to examine, only updating the ”.summary” flag column, and removing the flag columns (Dorey et al. In review)