Download, Clean, Classify, Enrich and Export Biodiversity
Occurrence Data
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Documentation for package ‘biofetchR’ version 0.1.0
Help Pages
| append_summary_row | Append a row to a GBIF processing summary table |
| bf_apply_manual_taxonomy_fixes | Apply manual taxonomy name and rank fixes to a data frame |
| bf_attach_gbif_taxonomy | Attach GBIF taxonomy to a data frame |
| bf_attach_griis_status | Attach GRIIS status to a species or species-country table |
| bf_attach_native_status | Attach native/non-native recipient status to a data frame |
| bf_available_marine_overlays | List package-supported marine overlays |
| bf_available_native_web_sources | List web sources supported for native-range evidence |
| bf_bind_gbif_chunks | Harmonise and bind GBIF result chunks |
| bf_cache_dir | Get a writable cache directory for biofetchR spatial layers |
| bf_check_taxonomic_resolution | Check taxonomic resolution quality |
| bf_clean_taxon_names | Clean taxon names before taxonomy resolution |
| bf_download_griis | Download the GRIIS country compendium |
| bf_download_sinas_resources | Download and locate required SInAS resources |
| bf_enrich_raster_context | Enrich GBIF points with raster context layers |
| bf_enrich_raster_context_from_sources | Enrich point occurrences from explicitly supplied raster context layers |
| bf_fetch_native_ranges_sinas | Fetch native-origin evidence from SInAS |
| bf_fetch_native_ranges_web | Compile species-level native-origin evidence from web sources |
| bf_filter_griis_invasive | Keep rows flagged as invasive in GRIIS |
| bf_filter_native | Filter a data frame to confirmed native recipient records |
| bf_filter_non_native | Filter a data frame to confirmed non-native recipient records |
| bf_find_griis_table | Find the most likely GRIIS table in an unpacked archive |
| bf_griis_lookup | Build a compact GRIIS lookup table |
| bf_load_basins | Load nested basins (HydroBASINS; Pfafstetter) |
| bf_load_biosphere_reserve | Load UNESCO biosphere reserve locations |
| bf_load_feow | Load Freshwater Ecoregions of the World polygons |
| bf_load_gdw_barriers | Load Global Dam Watch river barrier points |
| bf_load_gdw_reservoirs | Load Global Dam Watch reservoir polygons |
| bf_load_global_mining | Load global mining polygons |
| bf_load_gloric | Load GloRiC river reach lines |
| bf_load_hydrowaste | Load HydroWASTE wastewater treatment plant points |
| bf_load_lakes | Load global lake polygons (HydroLAKES) |
| bf_load_marine_regions_overlay | Load a package-managed Marine Regions overlay |
| bf_load_ne_admin1 | Load Natural Earth Admin-1 (States/Provinces) (auto-download + cache) |
| bf_load_ne_urban | Load Natural Earth Urban Areas (auto-download + cache) |
| bf_load_ne_urban_areas | Load Natural Earth Urban Areas (polygons), auto-downloaded and cached |
| bf_load_ramsar | Load Ramsar wetland polygons for selected countries |
| bf_load_resolve2017 | Load RESOLVE Ecoregions (2017) (auto-download + cache) |
| bf_load_resolve_ecoregions2017 | Load RESOLVE Ecoregions 2017 (polygons), auto-downloaded and cached |
| bf_load_rivers | Load global river reaches (HydroRIVERS) with optional caching |
| bf_load_teow | Load & cache WWF Terrestrial Ecoregions (TEOW) |
| bf_load_wdpa | Load WDPA protected-area polygons for selected countries |
| bf_marine_overlay_canonical | Resolve a marine overlay alias to its canonical name |
| bf_name_rivers_osm | Annotate HydroRIVERS reaches with OSM river names |
| bf_native_range_lookup | Build a native-range lookup table |
| bf_native_status_summary | Summarise native-origin status columns |
| bf_prepare_taxa_for_gbif | Prepare taxon names for GBIF download pipelines |
| bf_read_griis | Read and standardise the GRIIS country compendium |
| bf_reconcile_griis_native_status | Reconcile GRIIS and native-origin evidence |
| bf_resolve_gbif_taxonomy | Resolve one taxon name against GBIF |
| bf_resolve_gbif_taxonomy_batch | Resolve a vector of taxon names against GBIF |
| bf_sinas_default_urls | Return default SInAS 3.1.1 resource URLs |
| bf_standardise_griis | Standardise a raw GRIIS table |
| bf_standardise_native_ranges | Standardise native-range evidence to a species-level lookup |
| bf_taxonomic_summary | Summarise taxonomy resolution outcomes |
| bf_tax_extract_genus | Extract the genus component from a taxon name |
| bf_tax_is_genus_level | Detect genus-level or open-nomenclature names |
| bf_tax_looks_non_taxon | Detect likely non-taxonomic strings |
| bf_teow_cache_info | Return cache path/info for TEOW |
| bf_teow_clear_cache | Clear the cached TEOW dataset |
| bf_unpack_griis | Unpack a cached GRIIS archive |
| bf_web_native_gbif | Fetch native-range evidence from the GBIF Species API |
| bf_web_native_worms | Fetch native-range evidence from WoRMS REST distributions |
| bf_write_native_web_outputs | Write native-range web evidence outputs |
| check_entrez_key | Check for NCBI Entrez API Key |
| check_gbif_presence | Check whether GBIF has coordinate-based records for a species |
| download_gbif_batch | Submit global GBIF download jobs for species-level workflows |
| download_gbif_batch_gadm | Submit country-filtered GBIF downloads for terrestrial/freshwater workflows |
| eez_join | Join GBIF points to Exclusive Economic Zone polygons |
| filter_by_status | Filter or normalise records by native/alien status |
| gadm_join | Attach GADM labels to occurrence points |
| get_taxon_key | Retrieve a GBIF taxonKey for a scientific name |
| initialize_summary | Initialise a GBIF processing summary table |
| install_optional_deps | Report optional biofetchR dependencies |
| is_marine_species | Determine if a species is likely marine from taxonomy |
| list_status_presets | List available native/non-native status presets |
| load_all_gadm | Load and bind GADM geometries for multiple countries |
| load_gadm | Load GADM administrative geometries |
| overlay_join | Join GBIF points to Marine Regions overlays (robust, with s2 fallback) |
| process_gbif_eez_pipeline | Run the marine pipeline through the legacy EEZ wrapper |
| process_gbif_marine_pipeline | Process marine GBIF occurrences using package-managed marine overlays |
| process_gbif_terrestrial_freshwater_pipeline | Process terrestrial and freshwater GBIF occurrences |
| resolve_species_names | Resolve and standardise species names |
| thin_spatial_points | Clean and spatially thin GBIF-style occurrence points |
| wait_and_import_gbif | Wait for GBIF occurrence downloads and import completed records |
| wait_and_import_gbif_safe | Import GBIF downloads through the package import helper |