| Apply a binary delta to produce a new .vtr | apply_delta |
| Check that an already-built enrichment matches its registry entry | assert_built_matches_registry |
| Attach a reference table to a parsed enrichment | attach_references |
| Build the AlgaeBase backbone .vtr | build_algaebase |
| Build name-lookup tables for all installed taxify backbones | build_all_name_lookups |
| Build the AviList backbone .vtr from source | build_avilist |
| Build a taxify backbone '.vtr' file from source | build_backend |
| Build the backend coverage table | build_backend_coverage |
| Build a BETSI-recovery enrichment '.vtr' from its frozen matrices | build_betsi_recovery |
| Build the COL backbone .vtr | build_col |
| Build the COL XR backbone .vtr | build_colxr |
| Build an enrichment '.vtr' from source | build_enrichment |
| Write an enrichment .vtr file | build_enrichment_vtr |
| Build the Euro+Med backbone .vtr | build_euromed |
| Build the EuroVegChecklist syntaxon backbone .vtr | build_evc |
| Build the FishBase backbone .vtr | build_fishbase |
| Build the Species Fungorum Plus backbone .vtr | build_fungorum |
| Build the GBIF backbone .vtr | build_gbif |
| Build the GBIF occurrence-count snapshot | build_gbif_occurrence_counts |
| Build the genus register from a fixed backbone set | build_genus_register |
| Build the ITIS backbone .vtr from scratch | build_itis |
| Build the LCVP backbone .vtr from source | build_lcvp |
| Build the LPSN backbone .vtr from source | build_lpsn |
| Build the Mammal Diversity Database backbone .vtr from source | build_mdd |
| Build the MEOW ecoregion boundary '.vtr' | build_meow |
| Build a name-lookup .vtr from a backbone .vtr | build_name_lookup |
| Build the NCBI backbone .vtr | build_ncbi |
| Build the OTT backbone .vtr | build_ott |
| Build both genus_register.vtr and backend_coverage.vtr | build_register |
| Build the Reptile Database backbone .vtr | build_reptiledb |
| Build the SeaLifeBase backbone .vtr | build_sealifebase |
| Build the Czech vegetation classification syntaxon backbone .vtr | build_vegcz |
| Write a backbone .vtr file from a precomputed data.frame | build_vtr |
| Build a backbone .vtr from a stream of normalized chunks | build_vtr_streamed |
| Build the WCVP backbone .vtr from source | build_wcvp |
| Build the WFO backbone .vtr from source | build_wfo |
| Build the WGSRPD Level 3 boundary '.vtr' | build_wgsrpd |
| Build the WoRMS backbone .vtr | build_worms |
| Check all non-static enrichments in a manifest for version freshness | check_all_enrichment_versions |
| Check a CKAN resource for its last modification | check_ckan_version |
| Check a file by the md5 of its bytes | check_content_md5 |
| Check a journal article for corrections | check_crossref_version |
| Check a dataset DOI for the version DataCite records | check_datacite_version |
| Check a DataONE object for a newer version | check_dataone_version |
| Check a Dataverse dataset for its newest released version | check_dataverse_version |
| Check a Dryad dataset for the latest version | check_dryad_version |
| Check an EDI data package for a newer revision | check_edi_version |
| Check one manifest enrichment entry against its upstream source | check_enrichment_source_version |
| Check a Figshare article for the latest version | check_figshare_version |
| Check the GBIF backbone API for the latest update date | check_gbif_api_version |
| Check the GIFT database for its newest version | check_gift_version |
| Check a file on GitHub for its latest change | check_github_version |
| Check an IPT resource for its newest published version | check_ipt_version |
| Check the Kew Plant DNA C-values database for its newest release | check_kew_cvalues_version |
| Check a file for its Last-Modified date | check_last_modified |
| Check the LCVP data package for the latest version | check_lcvp_version |
| Check the NCBI Taxonomy monthly archive for a newer dump | check_ncbi_archive_version |
| Check the Open Tree Taxonomy for its newest release | check_ott_version |
| Check a PANGAEA dataset for changes and successors | check_pangaea_version |
| Check a Phaidra object for a newer version | check_phaidra_version |
| Check an rfishbase server for its newest release | check_rfishbase_version |
| Check a SEANOE dataset for its file set | check_seanoe_version |
| Check a Wayback Machine snapshot for a newer capture | check_wayback_version |
| Check the World Spider Trait database for new datasets | check_wst_version |
| Check a Zenodo record for the latest version | check_zenodo_version |
| Publication references of the COL Base Release, keyed for COL XR | colxr_col_publications |
| Legacy GBIF keys for each COL XR usage, from the GBIF backbone | colxr_gbif_crosswalk |
| Look COL XR usages up in a GBIF crosswalk | colxr_gbif_lookup |
| Resolve the latest Catalogue of Life Extended Release | colxr_latest_release |
| Request a ChecklistBank export and wait for it | colxr_request_export |
| Count GBIF occurrence records per taxon key | count_gbif_occurrences |
| Count rows in a .vtr file | count_vtr_rows |
| Create a binary diff between two .vtr files | create_delta |
| Feed a delimited file to 'build_vtr_streamed()' a chunk at a time | delim_chunk_feed |
| Build an id -> value lookup for the ids a file's foreign keys reference | delim_fk_lookup |
| Fetch all AlgaeBase records via /nameusage/search | download_algaebase |
| Download a ZIP and extract, returning the path to a matching file | download_and_unzip |
| Download the AviList extended checklist workbook | download_avilist |
| Download a Cloudflare-fronted file via the curl_cffi helper | download_cf_file |
| Download and extract the COL DwC-A | download_col |
| Download and extract the COL XR Darwin Core Archive | download_colxr |
| Download a file via curl | download_curl_file |
| Download a Dryad data file (handles the Anubis bot challenge) | download_dryad_file |
| Download a file from EDI's PASTA repository, authenticated | download_edi_file |
| Download the frozen Euro+Med CDM snapshot | download_euromed |
| Download the frozen EuroVegChecklist snapshot | download_evc |
| Download and extract the Species Fungorum Plus ColDP archive | download_fungorum |
| Download the GBIF backbone simple.txt.gz | download_gbif |
| Fetch paginated GBIF API results | download_gbif_api_pages |
| Download the published GBIF occurrence-count snapshot | download_gbif_occurrence_counts |
| Download both GRooT files (species aggregate + full per-record version) | download_groot |
| Download and extract the ITIS SQLite database | download_itis |
| Download the LCVP 'tab_lcvp' data file | download_lcvp |
| Download the LPSN ColDP archive from ChecklistBank | download_lpsn |
| Download and unpack the Mammal Diversity Database archive | download_mdd |
| Download the MEOW ecoregion GeoJSON snapshot | download_meow |
| Download and extract NCBI taxdump | download_ncbi |
| Download and extract OTT taxonomy | download_ott |
| Download the Reptile Database bulk files | download_reptiledb |
| Download the frozen Pladias vegetation snapshot | download_vegcz |
| Download and extract the WCVP names file | download_wcvp |
| Download and extract the WFO classification file | download_wfo |
| Download the WGSRPD Level 3 GeoJSON | download_wgsrpd |
| Download a Wiley/Atypon supporting-information file | download_wiley_supplement |
| Download and extract WoRMS DwC-A | download_worms |
| Build enrichment from source and return the raw data.frame | enrichment_emergency_fallback |
| Trait columns of an enrichment | enrichment_trait_cols |
| Taxon keys whose occurrence count can decide a GBIF pick | gbif_count_keys |
| Six-letter GEN_SPE species code | gen_spe |
| Decompress a gzipped file to a plain file | gunzip_file |
| Harvest an entire CKAN datastore resource past the offset window | harvest_ckan_datastore |
| Harvest the Plazi Darwin Core archives covering a taxon | harvest_plazi_dwca |
| Check if xdelta3 is available on PATH | has_xdelta3 |
| INRAE genus-abbreviation dictionary | inrae_genus_dict |
| List available backend builders | list_backends |
| List the BETSI-recovery enrichments | list_betsi_recovery |
| List build-only (non-redistributable) candidate trait sources | list_build_only_enrichments |
| List available enrichment builders | list_enrichments |
| List available reference-geometry builders | list_geometry |
| List scrape-only (non-redistributed) trait sources | list_scrape_only_enrichments |
| Normalize a raw backbone data.frame to the unified schema | normalize_backbone |
| Normalize one block of COL XR rows to the unified schema | normalize_colxr |
| Normalize one block of GBIF rows to the unified schema | normalize_gbif |
| Normalize one block of WCVP rows to the unified schema | normalize_wcvp |
| Normalize one block of WFO rows to the unified schema | normalize_wfo |
| Normalize one block of WoRMS rows to the unified schema | normalize_worms |
| Parse AlgaeTraits macroalgal traits (WoRMS ZIP export) | parse_algae_traits |
| Parse the Seebens et al. global first-record database | parse_alien_first_records |
| Parse the Alpine elevational-gradient carabid trait table | parse_alpine_carabids |
| Parse the Amniote Life History Database | parse_amniote |
| Parse AmphiBIO amphibian traits (CSV from ZIP) | parse_amphibio |
| Parse AnAge longevity and life-history traits (TSV from ZIP) | parse_anage |
| Parse AnimalTraits observations CSV (aggregate to species medians) | parse_animaltraits |
| Parse Arctic Traits Database (marine benthos) | parse_arctic |
| Parse NW European Arthropod DwC-A (taxon + measurement + description) | parse_arthropod_traits |
| Parse the AusTraits plant trait database | parse_austraits |
| Parse AVONET bird morphology XLSX | parse_avonet |
| Parse the BacDive strain snapshot into per-species microbial traits | parse_bacdive |
| Parse Baseflor (Catminat / Julve) French flora trait spreadsheet | parse_baseflor |
| Parse Ostwald global bee morphometrics | parse_bee_ostwald |
| Parse the Bryophytes of Europe Traits (BET) table | parse_bet |
| Parse the BETSI Collembola body-length export into per-species values | parse_betsi_collembola_body_length |
| Parse a per-taxon BETSI-recovery matrix into per-species trait columns | parse_betsi_recovery |
| Parse Beukhof marine fish traits | parse_beukhof |
| Parse BIEN trait data (queried via the BIEN R package) | parse_bien |
| Parse the BIRDBASE bird trait database | parse_birdbase |
| Parse Blanchard & Moreau ant genus defensive traits | parse_blanchard |
| Parse BROT 2.0 Mediterranean plant traits | parse_brot |
| Parse BRYOATT (attributes of British and Irish bryophytes) | parse_bryoatt |
| Parse the Chromosome Counts Database (CCDB) | parse_ccdb |
| Parse the Cefas biological-traits database (North-West European benthos) | parse_cefas_btrait |
| Parse the CheloniansTraits turtle database | parse_chelonians |
| Parse the Chowdhury et al. 2025 German carabid trend + trait table | parse_chowdhury |
| Parse CLO-PLA (clonal and bud-bank traits of the Central European flora) | parse_clopla |
| Parse the COMBINE mammal trait database (reported values) | parse_combine |
| Parse common names from GBIF, NCBI, and OTT | parse_common_names |
| Parse the Brun et al. marine copepod trait database | parse_copepod_traits |
| Parse the Coral Trait Database release | parse_coral_traits |
| Parse Diaz et al. 2022 supplementary traits (XLSX) | parse_diaz_traits |
| Parse DISPERSE European aquatic-invertebrate dispersal traits | parse_disperse |
| Parse the Eberswalde long-term carabid monitoring trait table | parse_eberswalde |
| Parse the Ecoflora scrape snapshot (British Isles plant traits) | parse_ecoflora |
| Parse the Bonfanti et al. Collembola ecomorphosis list into per-species rows | parse_ecomorphosis |
| Parse Edwards phytoplankton nutrient-utilization traits | parse_edwards_phyto |
| Parse EIVE 1.0 ecological indicator values (XLSX) | parse_eive |
| Parse the Ellers et al. Collembola trait table into per-species values | parse_ellers_collembola |
| Parse EltonTraits 1.0 birds + mammals TSVs | parse_elton_traits |
| Parse the EPA Freshwater Biological Traits database (macroinvertebrates) | parse_epa_freshwater |
| Parse EuPollTrait (European bees + hoverflies) | parse_eupolltrait |
| Parse the EuroBaTrait European bat trait dataset | parse_eurobat |
| Parse the Euro+Med distribution snapshot | parse_euromed_distribution |
| Parse FAPROTAX, the functional annotation of prokaryotic taxa | parse_faprotax |
| Parse the Finand & Kotze Helsinki urban-forest carabid trait table | parse_finand |
| Parse FishBase species traits (via rfishbase) | parse_fishbase |
| Parse FISHMORPH freshwater fish morphological traits (CSV) | parse_fishmorph |
| Parse the FishTraits v14 database (Frimpong & Angermeier) | parse_fishtraits |
| Parse the FloraWeb scrape snapshot (German-flora plant traits) | parse_floraweb |
| Parse Frugivoria (Neotropical frugivore traits) | parse_frugivoria |
| Parse FungalTraits XLSX (Table S1, genus-level traits) | parse_fungal_traits |
| Parse the FungalRoot database (GBIF Darwin Core Archive) to genus-level types | parse_fungalroot |
| Parse FUNGuild JSON database dump | parse_funguild |
| Parse the Freshwater Insects CONUS genus trait table (EDI edi.481) | parse_fw_insects_conus |
| Parse GBIF vernacular names (VernacularName.tsv + Taxon.tsv) | parse_gbif_common_names |
| Parse the GIDIAS impact database into per-species EICAT/SEICAT aggregates | parse_gidias |
| Parse GIFT species-level plant traits (via the GIFT package) | parse_gift |
| Parse the GloBI distinct-edge snapshot into per-species interaction degree | parse_globi |
| Parse the GlobTherm thermal-tolerance database | parse_globtherm |
| Parse GloNAF taxon-region data (multiple CSVs/XLSXs from ZIP) | parse_glonaf |
| Parse the Global Mammal Parasite Database (GMPD 2.0) | parse_gmpd |
| Parse GRIIS Country Compendium CSV | parse_griis |
| Parse the GRooT species-aggregate root-trait table | parse_groot |
| Parse the Global Wood Density Database v2 (species aggregate) | parse_gwdd |
| Parse HomeRange mammal home-range database | parse_homerange |
| Parse NHM HOSTS Lepidoptera hostplant records into per-insect host breadth | parse_hosts |
| Parse Huang amphibian morphology | parse_huang_amph |
| Parse the Sanchez-Martinez et al. 2020 plant hydraulics compilation | parse_hydraulics |
| Parse the Imageomics NEON ground-beetle image measurements | parse_imageomics_neon |
| Parse the InvaCost economic-cost database into per-species aggregates | parse_invacost |
| Parse the ITALIC lichen taxon-page snapshot | parse_italic |
| Parse IUCN Red List conservation status from the GBIF Darwin Core Archive | parse_iucn |
| Parse the Kew Plant DNA C-values database (genome size) | parse_kew_cvalues |
| Parse SER-SID (Kew Seed Information Database) tables to per-species traits | parse_kew_sid |
| Parse LEDA trait files | parse_leda |
| Parse LepTraits 1.0 butterfly consensus CSV | parse_leptraits |
| Parse the Madin et al. bacteria/archaea trait database | parse_madin |
| Parse WoRMS marine distributions rolled up to MEOW ecoregions | parse_marine_distribution |
| Mine body length (mm) from an OCR'd taxonomic monograph | parse_monograph_body_length |
| Aggregate the frozen monograph body-length extraction to one row per species | parse_monograph_collembola |
| Parse NCBI common names from names.dmp | parse_ncbi_common_names |
| Parse Bird Nest Traits (NestTrait v2) | parse_nesttrait |
| Parse NodDB, the global database of root-symbiotic nitrogen fixation | parse_noddb |
| Parse NZTD New Zealand marine benthos traits | parse_nztd |
| Parse Octocoral Trait Database (v2.2) | parse_octocoral |
| Parse Odonate Phenotypic Database (categorical traits) | parse_odonata |
| Parse OTT common names from synonyms.tsv + taxonomy.tsv | parse_ott_common_names |
| Parse PanTHERIA mammal life-history traits (TSV) | parse_pantheria |
| Parse Parravicini reef-fish trophic guilds | parse_parravicini |
| Parse Pelagic Species Trait Database | parse_pelagic |
| Parse PHYLACINE v1.2 trait data | parse_phylacine |
| Parse PLANTATT (attributes of British and Irish plants) | parse_plantatt |
| Parse Plazi Collembola treatments into per-species body length | parse_plazi_collembola_body_length |
| Parse Pottier amphibian heat tolerance | parse_pottier |
| Parse Quimbayo reef-fish traits | parse_quimbayo |
| Parse the Ramond et al. plankton protist trait database | parse_ramond |
| Parse ReptTraits (Etard et al. 2024) reptile traits (XLSX from Figshare) | parse_repttraits |
| Parse Rimet & Druart phytoplankton metrics | parse_rimet_phyto |
| Parse Hagge saproxylic beetle morphology | parse_saproxylic |
| Parse SeaLifeBase species traits (via rfishbase) | parse_sealifebase |
| Parse Sharkipedia elasmobranch life-history traits | parse_sharkipedia |
| Parse SHELD US freshwater mussel traits | parse_sheld |
| Parse the World Spider Trait Database CSV export | parse_spider_traits |
| Parse the sWorm global earthworm dataset into per-species ecological groups | parse_sworm |
| Parse TetraDENSITY population density | parse_tetradensity |
| Parse the Freshwater thermal-tolerance database (ThermoFresh) | parse_thermofresh |
| Parse the Tree of Sex database (plants + vertebrates + invertebrates) | parse_tree_of_sex |
| Parse USDA Fungus-Host records into per-fungus host breadth | parse_usda_fungus_host |
| Parse the World Checklist of Useful Plant Species PDF | parse_useful_plants |
| Parse VIRION into per-host virus association breadth | parse_virion |
| Parse WCVP names + distribution (from extracted ZIP directory) | parse_wcvp |
| Parse Zanne et al. 2014 woodiness CSV | parse_zanne |
| Parse Global Zooplankton Trait Database | parse_zooplankton |
| Full precompute pipeline: keys + synonym embedding | precompute_backbone |
| Ask a source host what identity its newest version carries | probe_upstream_identity |
| Publish enrichment '.vtr' files to the rolling enrichment release | publish_enrichment_release |
| Create a GitHub release and upload backbone artifacts | publish_release |
| Read and normalize a fetched list of AlgaeBase records | read_algaebase |
| Read and normalize the AviList checklist | read_avilist |
| Read and normalize the COL Taxon.tsv | read_col |
| Read and normalize the COL XR export | read_colxr |
| Read a pipe-delimited NCBI .dmp file | read_dmp |
| Read and normalize the Euro+Med CDM snapshot | read_euromed |
| Read and normalize the EuroVegChecklist into the syntaxon backbone schema | read_evc |
| Read and normalize the Species Fungorum Plus ColDP files | read_fungorum |
| Read and normalize the GBIF backbone | read_gbif |
| Read a GBIF occurrence-count snapshot | read_gbif_occurrence_counts |
| Read and normalize the ITIS SQLite database | read_itis |
| Read and normalize the LCVP reference table | read_lcvp |
| Read and normalize the LPSN checklist | read_lpsn |
| Read and normalize the Mammal Diversity Database | read_mdd |
| Parse the MEOW ecoregion GeoJSON into a long-format vertex table | read_meow |
| Read and normalize the NCBI taxonomy dump | read_ncbi |
| Read and normalize the OTT taxonomy | read_ott |
| Read and normalize the Reptile Database | read_reptiledb |
| Read the Czech vegetation classification into the syntaxon backbone schema | read_vegcz |
| Read and normalize the WCVP names file | read_wcvp |
| Read and normalize the WFO classification file | read_wfo |
| Parse the WGSRPD Level 3 GeoJSON into a long-format vertex table | read_wgsrpd |
| Read and normalize the WoRMS taxonomy | read_worms |
| Names of the backbones the genus register and backend coverage union | register_backbones |
| Resolve BETSI species codes to binomials | resolve_betsi_codes |
| Resolve enrichment names against all taxify backends | resolve_enrichment_names |
| Resolve family/genus by walking a parent-child hierarchy | resolve_hierarchy |
| Map names to their cross-backbone accepted names | resolve_name_map |
| Latest rfishbase data release for a server | rfishbase_release |
| Compute SHA-256 checksum of a file | sha256 |
| Split a scientific name into genus and epithets | split_scientific_name |
| The enrichment-to-T-SITA crosswalk | tsita_crosswalk |
| The T-SITA thesaurus as a flat concept table | tsita_vocab |
| Update manifest.json enrichment entry from built meta.json | update_enrichment_manifest |
| Update manifest.json after a successful backbone build | update_manifest |
| Does a build warrant a release? | vtr_changed |
| Resolve the newest WFO Plant List edition on Zenodo | wfo_latest_edition |
