{ "_id": "6acc7f30a14063b82c3a64dc", "Package": "taxifydb", "Title": "Build Backbones and Enrichments for the 'taxify' Package", "Version": "0.1.23.9000", "Authors@R": "person(\"Gilles\", \"Colling\", , \"gilles.colling051@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-3070-6066\"))", "Description": "Build pipeline for the 'taxify' package. Downloads raw\nsource data from official providers (WFO, COL, GBIF, ITIS, NCBI\nTaxonomy, Open Tree of Life, WoRMS, Euro+Med PlantBase, Index\nFungorum, AlgaeBase, FishBase, SeaLifeBase, the Reptile\nDatabase, the World Checklist of Vascular Plants, and the\nLeipzig Catalogue of Vascular Plants) and a wide set of trait\nand conservation datasets, normalizes to a unified Darwin\nCore-like schema, and writes pre-compiled '.vtr' files that the\n'taxify' runtime consumes. Separates build-time concerns\n(network access, parsing, schema normalization) from runtime\nconcerns so that 'taxify' itself stays lean.", "License": "MIT + file LICENSE", "URL": "https://github.com/gcol33/taxifydb", "BugReports": "https://github.com/gcol33/taxifydb/issues", "Remotes": [ "gcol33/taxify" ], "Config/testthat/edition": "3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://gcol33.r-universe.dev", "Date/Publication": "2026-10-11 23:55:23 UTC", "RemoteUrl": "https://github.com/gcol33/taxifydb", "RemoteRef": "HEAD", "RemoteSha": "540e1e9b525b242b705cc9c27a600f26835e6cde", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-12 06:26:12 UTC", "User": "root" }, "Author": "Gilles Colling [aut, cre, cph] (ORCID:\n)", "Maintainer": "Gilles Colling ", "_user": "gcol33", "_type": "src", "_file": "taxifydb_0.1.23.9000.tar.gz", "_fileid": "https://r2.ropensci.org/2863ab85ca33d5fb2790f29cea91618f20b3d57b794321647d3f05e86b0b3ef1", "_filesize": 20697592, "_sha256": "2863ab85ca33d5fb2790f29cea91618f20b3d57b794321647d3f05e86b0b3ef1", "_expires": "2027-01-20T06:33:17.000Z", "_created": "2026-10-12T06:26:12.000Z", "_published": "2026-10-12T06:33:19.914Z", "_buildurl": "https://github.com/r-universe/gcol33/actions/runs/38212232055", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114689779707, "time": 178, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11729458618" }, { "job": 114689779755, "time": 177, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11729866639" }, { "job": 114689779683, "time": 125, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11729723171" }, { "job": 114689779685, "time": 150, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11729588671" }, { "job": 114688835581, "time": 219, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11730395588" }, { "job": 114689779748, "time": 130, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11730017087" }, { "job": 114689779752, "time": 181, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11730416531" }, { "job": 114689779810, "time": 175, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11729553308" }, { "job": 114689779813, "time": 173, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11730385902" } ], "_upstream": "https://github.com/gcol33/taxifydb", "_commit": { "id": "540e1e9b525b242b705cc9c27a600f26835e6cde", "author": "Gilles Colling ", "committer": "Gilles Colling ", "message": "Update manifest: evc v4, vegcz v2026.10\n\nCo-Authored-By: Claude Opus 5.5 \nClaude-Session: https://claude.ai/code/session_01WageaoAXx9MLrMHDdzpTKa\n", "time": 1791762923 }, "_maintainer": { "name": "Gilles Colling", "email": "gilles.colling051@gmail.com", "login": "gcol33", "linkedin": "in/gilles-colling-0b3747306", "orcid": "0000-0003-3070-6066", "twitter": "@Gilles__Colling", "description": "Building tools for ecology in R, C++, and Rust.\nWhy did Microsoft have to buy it. 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"sha256", "split_scientific_name", "tsita_crosswalk", "tsita_vocab", "update_enrichment_manifest", "update_manifest", "vtr_changed", "wfo_latest_edition" ], "_help": [ { "page": "apply_delta", "title": "Apply a binary delta to produce a new .vtr", "topics": [ "apply_delta" ] }, { "page": "assert_built_matches_registry", "title": "Check that an already-built enrichment matches its registry entry", "topics": [ "assert_built_matches_registry" ] }, { "page": "attach_references", "title": "Attach a reference table to a parsed enrichment", "topics": [ "attach_references" ] }, { "page": "build_algaebase", "title": "Build the AlgaeBase backbone .vtr", "topics": [ "build_algaebase" ] }, { "page": "build_all_name_lookups", "title": "Build name-lookup tables for all installed taxify backbones", "topics": [ "build_all_name_lookups" ] }, { "page": "build_avilist", "title": "Build the AviList backbone .vtr from source", "topics": [ "build_avilist" ] }, { "page": "build_backend", "title": "Build a taxify backbone '.vtr' file from source", "topics": [ "build_backend" ] }, { "page": "build_backend_coverage", "title": "Build the backend coverage table", "topics": [ "build_backend_coverage" ] }, { "page": "build_betsi_recovery", "title": "Build a BETSI-recovery enrichment '.vtr' from its frozen matrices", "topics": [ "build_betsi_recovery" ] }, { "page": "build_col", "title": "Build the COL backbone .vtr", "topics": [ "build_col" ] }, { "page": "build_colxr", "title": "Build the COL XR backbone .vtr", "topics": [ "build_colxr" ] }, { "page": "build_enrichment", "title": "Build an enrichment '.vtr' from source", "topics": [ "build_enrichment" ] }, { "page": "build_enrichment_vtr", "title": "Write an enrichment .vtr file", "topics": [ "build_enrichment_vtr" ] }, { "page": "build_euromed", "title": "Build the Euro+Med backbone .vtr", "topics": [ "build_euromed" ] }, { "page": "build_evc", "title": "Build the EuroVegChecklist syntaxon backbone .vtr", "topics": [ "build_evc" ] }, { "page": "build_fishbase", "title": "Build the FishBase backbone .vtr", "topics": [ "build_fishbase" ] }, { "page": "build_fungorum", "title": "Build the Species Fungorum Plus backbone .vtr", "topics": [ "build_fungorum" ] }, { "page": "build_gbif", "title": "Build the GBIF backbone .vtr", "topics": [ "build_gbif" ] }, { "page": "build_gbif_occurrence_counts", "title": "Build the GBIF occurrence-count snapshot", "topics": [ "build_gbif_occurrence_counts" ] }, { "page": "build_genus_register", "title": "Build the genus register from a fixed backbone set", "topics": [ "build_genus_register" ] }, { "page": "build_itis", "title": "Build the ITIS backbone .vtr from scratch", "topics": [ "build_itis" ] }, { "page": "build_lcvp", "title": "Build the LCVP backbone .vtr from source", "topics": [ "build_lcvp" ] }, { "page": "build_lpsn", "title": "Build the LPSN backbone .vtr from source", "topics": [ "build_lpsn" ] }, { "page": "build_mdd", "title": "Build the Mammal Diversity Database backbone .vtr from source", "topics": [ "build_mdd" ] }, { "page": "build_meow", "title": "Build the MEOW ecoregion boundary '.vtr'", "topics": [ "build_meow" ] }, { "page": "build_name_lookup", "title": "Build a name-lookup .vtr from a backbone .vtr", "topics": [ "build_name_lookup" ] }, { "page": "build_ncbi", "title": "Build the NCBI backbone .vtr", "topics": [ "build_ncbi" ] }, { "page": "build_ott", "title": "Build the OTT backbone .vtr", "topics": [ "build_ott" ] }, { "page": "build_register", "title": "Build both genus_register.vtr and backend_coverage.vtr", "topics": [ "build_register" ] }, { "page": "build_reptiledb", "title": "Build the Reptile Database backbone .vtr", "topics": [ "build_reptiledb" ] }, { "page": "build_sealifebase", "title": "Build the SeaLifeBase backbone .vtr", "topics": [ "build_sealifebase" ] }, { "page": "build_vegcz", "title": "Build the Czech vegetation classification syntaxon backbone .vtr", "topics": [ "build_vegcz" ] }, { "page": "build_vtr", "title": "Write a backbone .vtr file from a precomputed data.frame", "topics": [ "build_vtr" ] }, { "page": "build_vtr_streamed", "title": "Build a backbone .vtr from a stream of normalized chunks", "topics": [ "build_vtr_streamed" ] }, { "page": "build_wcvp", "title": "Build the WCVP backbone .vtr from source", "topics": [ "build_wcvp" ] }, { "page": "build_wfo", "title": "Build the WFO backbone .vtr from source", "topics": [ "build_wfo" ] }, { "page": "build_wgsrpd", "title": "Build the WGSRPD Level 3 boundary '.vtr'", "topics": [ "build_wgsrpd" ] }, { "page": "build_worms", "title": "Build the WoRMS backbone .vtr", "topics": [ "build_worms" ] }, { "page": "check_all_enrichment_versions", "title": "Check all non-static enrichments in a manifest for version freshness", "topics": [ "check_all_enrichment_versions" ] }, { "page": "check_ckan_version", "title": "Check a CKAN resource for its last modification", "topics": [ "check_ckan_version" ] }, { "page": "check_content_md5", "title": "Check a file by the md5 of its bytes", "topics": [ "check_content_md5" ] }, { "page": "check_crossref_version", "title": "Check a journal article for corrections", "topics": [ "check_crossref_version" ] }, { "page": "check_datacite_version", "title": "Check a dataset DOI for the version DataCite records", "topics": [ "check_datacite_version" ] }, { "page": "check_dataone_version", "title": "Check a DataONE object for a newer version", "topics": [ "check_dataone_version" ] }, { "page": "check_dataverse_version", "title": "Check a Dataverse dataset for its newest released version", "topics": [ "check_dataverse_version" ] }, { "page": "check_dryad_version", "title": "Check a Dryad dataset for the latest version", "topics": [ "check_dryad_version" ] }, { "page": "check_edi_version", "title": "Check an EDI data package for a newer revision", "topics": [ "check_edi_version" ] }, { "page": "check_enrichment_source_version", "title": "Check one manifest enrichment entry against its upstream source", "topics": [ "check_enrichment_source_version" ] }, { "page": "check_figshare_version", "title": "Check a Figshare article for the latest version", "topics": [ "check_figshare_version" ] }, { "page": "check_gbif_api_version", "title": "Check the GBIF backbone API for the latest update date", "topics": [ "check_gbif_api_version" ] }, { "page": "check_gift_version", "title": "Check the GIFT database for its newest version", "topics": [ "check_gift_version" ] }, { "page": "check_github_version", "title": "Check a file on GitHub for its latest change", "topics": [ "check_github_version" ] }, { "page": "check_ipt_version", "title": "Check an IPT resource for its newest published version", "topics": [ "check_ipt_version" ] }, { "page": "check_kew_cvalues_version", "title": "Check the Kew Plant DNA C-values database for its newest release", "topics": [ "check_kew_cvalues_version" ] }, { "page": "check_last_modified", "title": "Check a file for its Last-Modified date", "topics": [ "check_last_modified" ] }, { "page": "check_lcvp_version", "title": "Check the LCVP data package for the latest version", "topics": [ "check_lcvp_version" ] }, { "page": "check_ncbi_archive_version", "title": "Check the NCBI Taxonomy monthly archive for a newer dump", "topics": [ "check_ncbi_archive_version" ] }, { "page": "check_ott_version", "title": "Check the Open Tree Taxonomy for its newest release", "topics": [ "check_ott_version" ] }, { "page": "check_pangaea_version", "title": "Check a PANGAEA dataset for changes and successors", "topics": [ "check_pangaea_version" ] }, { "page": "check_phaidra_version", "title": "Check a Phaidra object for a newer version", "topics": [ "check_phaidra_version" ] }, { "page": "check_rfishbase_version", "title": "Check an rfishbase server for its newest release", "topics": [ "check_rfishbase_version" ] }, { "page": "check_seanoe_version", "title": "Check a SEANOE dataset for its file set", "topics": [ "check_seanoe_version" ] }, { "page": "check_wayback_version", "title": "Check a Wayback Machine snapshot for a newer capture", "topics": [ "check_wayback_version" ] }, { "page": "check_wst_version", "title": "Check the World Spider Trait database for new datasets", "topics": [ "check_wst_version" ] }, { "page": "check_zenodo_version", "title": "Check a Zenodo record for the latest version", "topics": [ "check_zenodo_version" ] }, { "page": "colxr_col_publications", "title": "Publication references of the COL Base Release, keyed for COL XR", "topics": [ "colxr_col_publications" ] }, { "page": "colxr_gbif_crosswalk", "title": "Legacy GBIF keys for each COL XR usage, from the GBIF backbone", "topics": [ "colxr_gbif_crosswalk" ] }, { "page": "colxr_gbif_lookup", "title": "Look COL XR usages up in a GBIF crosswalk", "topics": [ "colxr_gbif_lookup" ] }, { "page": "colxr_latest_release", "title": "Resolve the latest Catalogue of Life Extended Release", "topics": [ "colxr_latest_release" ] }, { "page": "colxr_request_export", "title": "Request a ChecklistBank export and wait for it", "topics": [ "colxr_request_export" ] }, { "page": "count_gbif_occurrences", "title": "Count GBIF occurrence records per taxon key", "topics": [ "count_gbif_occurrences" ] }, { "page": "count_vtr_rows", "title": "Count rows in a .vtr file", "topics": [ "count_vtr_rows" ] }, { "page": "create_delta", "title": "Create a binary diff between two .vtr files", "topics": [ "create_delta" ] }, { "page": "delim_chunk_feed", "title": "Feed a delimited file to 'build_vtr_streamed()' a chunk at a time", "topics": [ "delim_chunk_feed" ] }, { "page": "delim_fk_lookup", "title": "Build an id -> value lookup for the ids a file's foreign keys reference", "topics": [ "delim_fk_lookup" ] }, { "page": "download_algaebase", "title": "Fetch all AlgaeBase records via /nameusage/search", "topics": [ "download_algaebase" ] }, { "page": "download_and_unzip", "title": "Download a ZIP and extract, returning the path to a matching file", "topics": [ "download_and_unzip" ] }, { "page": "download_avilist", "title": "Download the AviList extended checklist workbook", "topics": [ "download_avilist" ] }, { "page": "download_cf_file", "title": "Download a Cloudflare-fronted file via the curl_cffi helper", "topics": [ "download_cf_file" ] }, { "page": "download_col", "title": "Download and extract the COL DwC-A", "topics": [ "download_col" ] }, { "page": "download_colxr", "title": "Download and extract the COL XR Darwin Core Archive", "topics": [ "download_colxr" ] }, { "page": "download_curl_file", "title": "Download a file via curl", "topics": [ "download_curl_file" ] }, { "page": "download_dryad_file", "title": "Download a Dryad data file (handles the Anubis bot challenge)", "topics": [ "download_dryad_file" ] }, { "page": "download_edi_file", "title": "Download a file from EDI's PASTA repository, authenticated", "topics": [ "download_edi_file" ] }, { "page": "download_euromed", "title": "Download the frozen Euro+Med CDM snapshot", "topics": [ "download_euromed" ] }, { "page": "download_evc", "title": "Download the frozen EuroVegChecklist snapshot", "topics": [ "download_evc" ] }, { "page": "download_fungorum", "title": "Download and extract the Species Fungorum Plus ColDP archive", "topics": [ "download_fungorum" ] }, { "page": "download_gbif", "title": "Download the GBIF backbone simple.txt.gz", "topics": [ "download_gbif" ] }, { "page": "download_gbif_api_pages", "title": "Fetch paginated GBIF API results", "topics": [ "download_gbif_api_pages" ] }, { "page": "download_gbif_occurrence_counts", "title": "Download the published GBIF occurrence-count snapshot", "topics": [ "download_gbif_occurrence_counts" ] }, { "page": "download_groot", "title": "Download both GRooT files (species aggregate + full per-record version)", "topics": [ "download_groot" ] }, { "page": "download_itis", "title": "Download and extract the ITIS SQLite database", "topics": [ "download_itis" ] }, { "page": "download_lcvp", "title": "Download the LCVP 'tab_lcvp' data file", "topics": [ "download_lcvp" ] }, { "page": "download_lpsn", "title": "Download the LPSN ColDP archive from ChecklistBank", "topics": [ "download_lpsn" ] }, { "page": "download_mdd", "title": "Download and unpack the Mammal Diversity Database archive", "topics": [ "download_mdd" ] }, { "page": "download_meow", "title": "Download the MEOW ecoregion GeoJSON snapshot", "topics": [ "download_meow" ] }, { "page": "download_ncbi", "title": "Download and extract NCBI taxdump", "topics": [ "download_ncbi" ] }, { "page": "download_ott", "title": "Download and extract OTT taxonomy", "topics": [ "download_ott" ] }, { "page": "download_reptiledb", "title": "Download the Reptile Database bulk files", "topics": [ "download_reptiledb" ] }, { "page": "download_vegcz", "title": "Download the frozen Pladias vegetation snapshot", "topics": [ "download_vegcz" ] }, { "page": "download_wcvp", "title": "Download and extract the WCVP names file", "topics": [ "download_wcvp" ] }, { "page": "download_wfo", "title": "Download and extract the WFO classification file", "topics": [ "download_wfo" ] }, { "page": "download_wgsrpd", "title": "Download the WGSRPD Level 3 GeoJSON", "topics": [ "download_wgsrpd" ] }, { "page": "download_wiley_supplement", "title": "Download a Wiley/Atypon supporting-information file", "topics": [ "download_wiley_supplement" ] }, { "page": "download_worms", "title": "Download and extract WoRMS DwC-A", "topics": [ "download_worms" ] }, { "page": "enrichment_emergency_fallback", "title": "Build enrichment from source and return the raw data.frame", "topics": [ "enrichment_emergency_fallback" ] }, { "page": "enrichment_trait_cols", "title": "Trait columns of an enrichment", "topics": [ "enrichment_trait_cols" ] }, { "page": "gbif_count_keys", "title": "Taxon keys whose occurrence count can decide a GBIF pick", "topics": [ "gbif_count_keys" ] }, { "page": "gen_spe", "title": "Six-letter GEN_SPE species code", "topics": [ "gen_spe" ] }, { "page": "gunzip_file", "title": "Decompress a gzipped file to a plain file", "topics": [ "gunzip_file" ] }, { "page": "harvest_ckan_datastore", "title": "Harvest an entire CKAN datastore resource past the offset window", "topics": [ "harvest_ckan_datastore" ] }, { "page": "harvest_plazi_dwca", "title": "Harvest the Plazi Darwin Core archives covering a taxon", "topics": [ "harvest_plazi_dwca" ] }, { "page": "has_xdelta3", "title": "Check if xdelta3 is available on PATH", "topics": [ "has_xdelta3" ] }, { "page": "inrae_genus_dict", "title": "INRAE genus-abbreviation dictionary", "topics": [ "inrae_genus_dict" ] }, { "page": "list_backends", "title": "List available backend builders", "topics": [ "list_backends" ] }, { "page": "list_betsi_recovery", "title": "List the BETSI-recovery enrichments", "topics": [ "list_betsi_recovery" ] }, { "page": "list_build_only_enrichments", "title": "List build-only (non-redistributable) candidate trait sources", "topics": [ "list_build_only_enrichments" ] }, { "page": "list_enrichments", "title": "List available enrichment builders", "topics": [ "list_enrichments" ] }, { "page": "list_geometry", "title": "List available reference-geometry builders", "topics": [ "list_geometry" ] }, { "page": "list_scrape_only_enrichments", "title": "List scrape-only (non-redistributed) trait sources", "topics": [ "list_scrape_only_enrichments" ] }, { "page": "normalize_backbone", "title": "Normalize a raw backbone data.frame to the unified schema", "topics": [ "normalize_backbone" ] }, { "page": "normalize_colxr", "title": "Normalize one block of COL XR rows to the unified schema", "topics": [ "normalize_colxr" ] }, { "page": "normalize_gbif", "title": "Normalize one block of GBIF rows to the unified schema", "topics": [ "normalize_gbif" ] }, { "page": "normalize_wcvp", "title": "Normalize one block of WCVP rows to the unified schema", "topics": [ "normalize_wcvp" ] }, { "page": "normalize_wfo", "title": "Normalize one block of WFO rows to the unified schema", "topics": [ "normalize_wfo" ] }, { "page": "normalize_worms", "title": "Normalize one block of WoRMS rows to the unified schema", "topics": [ "normalize_worms" ] }, { "page": "parse_algae_traits", "title": "Parse AlgaeTraits macroalgal traits (WoRMS ZIP export)", "topics": [ "parse_algae_traits" ] }, { "page": "parse_alien_first_records", "title": "Parse the Seebens et al. global first-record database", "topics": [ "parse_alien_first_records" ] }, { "page": "parse_alpine_carabids", "title": "Parse the Alpine elevational-gradient carabid trait table", "topics": [ "parse_alpine_carabids" ] }, { "page": "parse_amniote", "title": "Parse the Amniote Life History Database", "topics": [ "parse_amniote" ] }, { "page": "parse_amphibio", "title": "Parse AmphiBIO amphibian traits (CSV from ZIP)", "topics": [ "parse_amphibio" ] }, { "page": "parse_anage", "title": "Parse AnAge longevity and life-history traits (TSV from ZIP)", "topics": [ "parse_anage" ] }, { "page": "parse_animaltraits", "title": "Parse AnimalTraits observations CSV (aggregate to species medians)", "topics": [ "parse_animaltraits" ] }, { "page": "parse_arctic", "title": "Parse Arctic Traits Database (marine benthos)", "topics": [ "parse_arctic" ] }, { "page": "parse_arthropod_traits", "title": "Parse NW European Arthropod DwC-A (taxon + measurement + description)", "topics": [ "parse_arthropod_traits" ] }, { "page": "parse_austraits", "title": "Parse the AusTraits plant trait database", "topics": [ "parse_austraits" ] }, { "page": "parse_avonet", "title": "Parse AVONET bird morphology XLSX", "topics": [ "parse_avonet" ] }, { "page": "parse_bacdive", "title": "Parse the BacDive strain snapshot into per-species microbial traits", "topics": [ "parse_bacdive" ] }, { "page": "parse_baseflor", "title": "Parse Baseflor (Catminat / Julve) French flora trait spreadsheet", "topics": [ "parse_baseflor" ] }, { "page": "parse_bee_ostwald", "title": "Parse Ostwald global bee morphometrics", "topics": [ "parse_bee_ostwald" ] }, { "page": "parse_bet", "title": "Parse the Bryophytes of Europe Traits (BET) table", "topics": [ "parse_bet" ] }, { "page": "parse_betsi_collembola_body_length", "title": "Parse the BETSI Collembola body-length export into per-species values", "topics": [ "parse_betsi_collembola_body_length" ] }, { "page": "parse_betsi_recovery", "title": "Parse a per-taxon BETSI-recovery matrix into per-species trait columns", "topics": [ "parse_betsi_recovery" ] }, { "page": "parse_beukhof", "title": "Parse Beukhof marine fish traits", "topics": [ "parse_beukhof" ] }, { "page": "parse_bien", "title": "Parse BIEN trait data (queried via the BIEN R package)", "topics": [ "parse_bien" ] }, { "page": "parse_birdbase", "title": "Parse the BIRDBASE bird trait database", "topics": [ "parse_birdbase" ] }, { "page": "parse_blanchard", "title": "Parse Blanchard & Moreau ant genus defensive traits", "topics": [ "parse_blanchard" ] }, { "page": "parse_brot", "title": "Parse BROT 2.0 Mediterranean plant traits", "topics": [ "parse_brot" ] }, { "page": "parse_bryoatt", "title": "Parse BRYOATT (attributes of British and Irish bryophytes)", "topics": [ "parse_bryoatt" ] }, { "page": "parse_ccdb", "title": "Parse the Chromosome Counts Database (CCDB)", "topics": [ "parse_ccdb" ] }, { "page": "parse_cefas_btrait", "title": "Parse the Cefas biological-traits database (North-West European benthos)", "topics": [ "parse_cefas_btrait" ] }, { "page": "parse_chelonians", "title": "Parse the CheloniansTraits turtle database", "topics": [ "parse_chelonians" ] }, { "page": "parse_chowdhury", "title": "Parse the Chowdhury et al. 2025 German carabid trend + trait table", "topics": [ "parse_chowdhury" ] }, { "page": "parse_clopla", "title": "Parse CLO-PLA (clonal and bud-bank traits of the Central European flora)", "topics": [ "parse_clopla" ] }, { "page": "parse_combine", "title": "Parse the COMBINE mammal trait database (reported values)", "topics": [ "parse_combine" ] }, { "page": "parse_common_names", "title": "Parse common names from GBIF, NCBI, and OTT", "topics": [ "parse_common_names" ] }, { "page": "parse_copepod_traits", "title": "Parse the Brun et al. marine copepod trait database", "topics": [ "parse_copepod_traits" ] }, { "page": "parse_coral_traits", "title": "Parse the Coral Trait Database release", "topics": [ "parse_coral_traits" ] }, { "page": "parse_diaz_traits", "title": "Parse Diaz et al. 2022 supplementary traits (XLSX)", "topics": [ "parse_diaz_traits" ] }, { "page": "parse_disperse", "title": "Parse DISPERSE European aquatic-invertebrate dispersal traits", "topics": [ "parse_disperse" ] }, { "page": "parse_eberswalde", "title": "Parse the Eberswalde long-term carabid monitoring trait table", "topics": [ "parse_eberswalde" ] }, { "page": "parse_ecoflora", "title": "Parse the Ecoflora scrape snapshot (British Isles plant traits)", "topics": [ "parse_ecoflora" ] }, { "page": "parse_ecomorphosis", "title": "Parse the Bonfanti et al. Collembola ecomorphosis list into per-species rows", "topics": [ "parse_ecomorphosis" ] }, { "page": "parse_edwards_phyto", "title": "Parse Edwards phytoplankton nutrient-utilization traits", "topics": [ "parse_edwards_phyto" ] }, { "page": "parse_eive", "title": "Parse EIVE 1.0 ecological indicator values (XLSX)", "topics": [ "parse_eive" ] }, { "page": "parse_ellers_collembola", "title": "Parse the Ellers et al. Collembola trait table into per-species values", "topics": [ "parse_ellers_collembola" ] }, { "page": "parse_elton_traits", "title": "Parse EltonTraits 1.0 birds + mammals TSVs", "topics": [ "parse_elton_traits" ] }, { "page": "parse_epa_freshwater", "title": "Parse the EPA Freshwater Biological Traits database (macroinvertebrates)", "topics": [ "parse_epa_freshwater" ] }, { "page": "parse_eupolltrait", "title": "Parse EuPollTrait (European bees + hoverflies)", "topics": [ "parse_eupolltrait" ] }, { "page": "parse_eurobat", "title": "Parse the EuroBaTrait European bat trait dataset", "topics": [ "parse_eurobat" ] }, { "page": "parse_euromed_distribution", "title": "Parse the Euro+Med distribution snapshot", "topics": [ "parse_euromed_distribution" ] }, { "page": "parse_faprotax", "title": "Parse FAPROTAX, the functional annotation of prokaryotic taxa", "topics": [ "parse_faprotax" ] }, { "page": "parse_finand", "title": "Parse the Finand & Kotze Helsinki urban-forest carabid trait table", "topics": [ "parse_finand" ] }, { "page": "parse_fishbase", "title": "Parse FishBase species traits (via rfishbase)", "topics": [ "parse_fishbase" ] }, { "page": "parse_fishmorph", "title": "Parse FISHMORPH freshwater fish morphological traits (CSV)", "topics": [ "parse_fishmorph" ] }, { "page": "parse_fishtraits", "title": "Parse the FishTraits v14 database (Frimpong & Angermeier)", "topics": [ "parse_fishtraits" ] }, { "page": "parse_floraweb", "title": "Parse the FloraWeb scrape snapshot (German-flora plant traits)", "topics": [ "parse_floraweb" ] }, { "page": "parse_frugivoria", "title": "Parse Frugivoria (Neotropical frugivore traits)", "topics": [ "parse_frugivoria" ] }, { "page": "parse_fungal_traits", "title": "Parse FungalTraits XLSX (Table S1, genus-level traits)", "topics": [ "parse_fungal_traits" ] }, { "page": "parse_fungalroot", "title": "Parse the FungalRoot database (GBIF Darwin Core Archive) to genus-level types", "topics": [ "parse_fungalroot" ] }, { "page": "parse_funguild", "title": "Parse FUNGuild JSON database dump", "topics": [ "parse_funguild" ] }, { "page": "parse_fw_insects_conus", "title": "Parse the Freshwater Insects CONUS genus trait table (EDI edi.481)", "topics": [ "parse_fw_insects_conus" ] }, { "page": "parse_gbif_common_names", "title": "Parse GBIF vernacular names (VernacularName.tsv + Taxon.tsv)", "topics": [ "parse_gbif_common_names" ] }, { "page": "parse_gidias", "title": "Parse the GIDIAS impact database into per-species EICAT/SEICAT aggregates", "topics": [ "parse_gidias" ] }, { "page": "parse_gift", "title": "Parse GIFT species-level plant traits (via the GIFT package)", "topics": [ "parse_gift" ] }, { "page": "parse_globi", "title": "Parse the GloBI distinct-edge snapshot into per-species interaction degree", "topics": [ "parse_globi" ] }, { "page": "parse_globtherm", "title": "Parse the GlobTherm thermal-tolerance database", "topics": [ "parse_globtherm" ] }, { "page": "parse_glonaf", "title": "Parse GloNAF taxon-region data (multiple CSVs/XLSXs from ZIP)", "topics": [ "parse_glonaf" ] }, { "page": "parse_gmpd", "title": "Parse the Global Mammal Parasite Database (GMPD 2.0)", "topics": [ "parse_gmpd" ] }, { "page": "parse_griis", "title": "Parse GRIIS Country Compendium CSV", "topics": [ "parse_griis" ] }, { "page": "parse_groot", "title": "Parse the GRooT species-aggregate root-trait table", "topics": [ "parse_groot" ] }, { "page": "parse_gwdd", "title": "Parse the Global Wood Density Database v2 (species aggregate)", "topics": [ "parse_gwdd" ] }, { "page": "parse_homerange", "title": "Parse HomeRange mammal home-range database", "topics": [ "parse_homerange" ] }, { "page": "parse_hosts", "title": "Parse NHM HOSTS Lepidoptera hostplant records into per-insect host breadth", "topics": [ "parse_hosts" ] }, { "page": "parse_huang_amph", "title": "Parse Huang amphibian morphology", "topics": [ "parse_huang_amph" ] }, { "page": "parse_hydraulics", "title": "Parse the Sanchez-Martinez et al. 2020 plant hydraulics compilation", "topics": [ "parse_hydraulics" ] }, { "page": "parse_imageomics_neon", "title": "Parse the Imageomics NEON ground-beetle image measurements", "topics": [ "parse_imageomics_neon" ] }, { "page": "parse_invacost", "title": "Parse the InvaCost economic-cost database into per-species aggregates", "topics": [ "parse_invacost" ] }, { "page": "parse_italic", "title": "Parse the ITALIC lichen taxon-page snapshot", "topics": [ "parse_italic" ] }, { "page": "parse_iucn", "title": "Parse IUCN Red List conservation status from the GBIF Darwin Core Archive", "topics": [ "parse_iucn" ] }, { "page": "parse_kew_cvalues", "title": "Parse the Kew Plant DNA C-values database (genome size)", "topics": [ "parse_kew_cvalues" ] }, { "page": "parse_kew_sid", "title": "Parse SER-SID (Kew Seed Information Database) tables to per-species traits", "topics": [ "parse_kew_sid" ] }, { "page": "parse_leda", "title": "Parse LEDA trait files", "topics": [ "parse_leda" ] }, { "page": "parse_leptraits", "title": "Parse LepTraits 1.0 butterfly consensus CSV", "topics": [ "parse_leptraits" ] }, { "page": "parse_madin", "title": "Parse the Madin et al. bacteria/archaea trait database", "topics": [ "parse_madin" ] }, { "page": "parse_marine_distribution", "title": "Parse WoRMS marine distributions rolled up to MEOW ecoregions", "topics": [ "parse_marine_distribution" ] }, { "page": "parse_monograph_body_length", "title": "Mine body length (mm) from an OCR'd taxonomic monograph", "topics": [ "parse_monograph_body_length" ] }, { "page": "parse_monograph_collembola", "title": "Aggregate the frozen monograph body-length extraction to one row per species", "topics": [ "parse_monograph_collembola" ] }, { "page": "parse_ncbi_common_names", "title": "Parse NCBI common names from names.dmp", "topics": [ "parse_ncbi_common_names" ] }, { "page": "parse_nesttrait", "title": "Parse Bird Nest Traits (NestTrait v2)", "topics": [ "parse_nesttrait" ] }, { "page": "parse_noddb", "title": "Parse NodDB, the global database of root-symbiotic nitrogen fixation", "topics": [ "parse_noddb" ] }, { "page": "parse_nztd", "title": "Parse NZTD New Zealand marine benthos traits", "topics": [ "parse_nztd" ] }, { "page": "parse_octocoral", "title": "Parse Octocoral Trait Database (v2.2)", "topics": [ "parse_octocoral" ] }, { "page": "parse_odonata", "title": "Parse Odonate Phenotypic Database (categorical traits)", "topics": [ "parse_odonata" ] }, { "page": "parse_ott_common_names", "title": "Parse OTT common names from synonyms.tsv + taxonomy.tsv", "topics": [ "parse_ott_common_names" ] }, { "page": "parse_pantheria", "title": "Parse PanTHERIA mammal life-history traits (TSV)", "topics": [ "parse_pantheria" ] }, { "page": "parse_parravicini", "title": "Parse Parravicini reef-fish trophic guilds", "topics": [ "parse_parravicini" ] }, { "page": "parse_pelagic", "title": "Parse Pelagic Species Trait Database", "topics": [ "parse_pelagic" ] }, { "page": "parse_phylacine", "title": "Parse PHYLACINE v1.2 trait data", "topics": [ "parse_phylacine" ] }, { "page": "parse_plantatt", "title": "Parse PLANTATT (attributes of British and Irish plants)", "topics": [ "parse_plantatt" ] }, { "page": "parse_plazi_collembola_body_length", "title": "Parse Plazi Collembola treatments into per-species body length", "topics": [ "parse_plazi_collembola_body_length" ] }, { "page": "parse_pottier", "title": "Parse Pottier amphibian heat tolerance", "topics": [ "parse_pottier" ] }, { "page": "parse_quimbayo", "title": "Parse Quimbayo reef-fish traits", "topics": [ "parse_quimbayo" ] }, { "page": "parse_ramond", "title": "Parse the Ramond et al. plankton protist trait database", "topics": [ "parse_ramond" ] }, { "page": "parse_repttraits", "title": "Parse ReptTraits (Etard et al. 2024) reptile traits (XLSX from Figshare)", "topics": [ "parse_repttraits" ] }, { "page": "parse_rimet_phyto", "title": "Parse Rimet & Druart phytoplankton metrics", "topics": [ "parse_rimet_phyto" ] }, { "page": "parse_saproxylic", "title": "Parse Hagge saproxylic beetle morphology", "topics": [ "parse_saproxylic" ] }, { "page": "parse_sealifebase", "title": "Parse SeaLifeBase species traits (via rfishbase)", "topics": [ "parse_sealifebase" ] }, { "page": "parse_sharkipedia", "title": "Parse Sharkipedia elasmobranch life-history traits", "topics": [ "parse_sharkipedia" ] }, { "page": "parse_sheld", "title": "Parse SHELD US freshwater mussel traits", "topics": [ "parse_sheld" ] }, { "page": "parse_spider_traits", "title": "Parse the World Spider Trait Database CSV export", "topics": [ "parse_spider_traits" ] }, { "page": "parse_sworm", "title": "Parse the sWorm global earthworm dataset into per-species ecological groups", "topics": [ "parse_sworm" ] }, { "page": "parse_tetradensity", "title": "Parse TetraDENSITY population density", "topics": [ "parse_tetradensity" ] }, { "page": "parse_thermofresh", "title": "Parse the Freshwater thermal-tolerance database (ThermoFresh)", "topics": [ "parse_thermofresh" ] }, { "page": "parse_tree_of_sex", "title": "Parse the Tree of Sex database (plants + vertebrates + invertebrates)", "topics": [ "parse_tree_of_sex" ] }, { "page": "parse_usda_fungus_host", "title": "Parse USDA Fungus-Host records into per-fungus host breadth", "topics": [ "parse_usda_fungus_host" ] }, { "page": "parse_useful_plants", "title": "Parse the World Checklist of Useful Plant Species PDF", "topics": [ "parse_useful_plants" ] }, { "page": "parse_virion", "title": "Parse VIRION into per-host virus association breadth", "topics": [ "parse_virion" ] }, { "page": "parse_wcvp", "title": "Parse WCVP names + distribution (from extracted ZIP directory)", "topics": [ "parse_wcvp" ] }, { "page": "parse_zanne", "title": "Parse Zanne et al. 2014 woodiness CSV", "topics": [ "parse_zanne" ] }, { "page": "parse_zooplankton", "title": "Parse Global Zooplankton Trait Database", "topics": [ "parse_zooplankton" ] }, { "page": "precompute_backbone", "title": "Full precompute pipeline: keys + synonym embedding", "topics": [ "precompute_backbone" ] }, { "page": "probe_upstream_identity", "title": "Ask a source host what identity its newest version carries", "topics": [ "probe_upstream_identity" ] }, { "page": "publish_enrichment_release", "title": "Publish enrichment '.vtr' files to the rolling enrichment release", "topics": [ "publish_enrichment_release" ] }, { "page": "publish_release", "title": "Create a GitHub release and upload backbone artifacts", "topics": [ "publish_release" ] }, { "page": "read_algaebase", "title": "Read and normalize a fetched list of AlgaeBase records", "topics": [ "read_algaebase" ] }, { "page": "read_avilist", "title": "Read and normalize the AviList checklist", "topics": [ "read_avilist" ] }, { "page": "read_col", "title": "Read and normalize the COL Taxon.tsv", "topics": [ "read_col" ] }, { "page": "read_colxr", "title": "Read and normalize the COL XR export", "topics": [ "read_colxr" ] }, { "page": "read_dmp", "title": "Read a pipe-delimited NCBI .dmp file", "topics": [ "read_dmp" ] }, { "page": "read_euromed", "title": "Read and normalize the Euro+Med CDM snapshot", "topics": [ "read_euromed" ] }, { "page": "read_evc", "title": "Read and normalize the EuroVegChecklist into the syntaxon backbone schema", "topics": [ "read_evc" ] }, { "page": "read_fungorum", "title": "Read and normalize the Species Fungorum Plus ColDP files", "topics": [ "read_fungorum" ] }, { "page": "read_gbif", "title": "Read and normalize the GBIF backbone", "topics": [ "read_gbif" ] }, { "page": "read_gbif_occurrence_counts", "title": "Read a GBIF occurrence-count snapshot", "topics": [ "read_gbif_occurrence_counts" ] }, { "page": "read_itis", "title": "Read and normalize the ITIS SQLite database", "topics": [ "read_itis" ] }, { "page": "read_lcvp", "title": "Read and normalize the LCVP reference table", "topics": [ "read_lcvp" ] }, { "page": "read_lpsn", "title": "Read and normalize the LPSN checklist", "topics": [ "read_lpsn" ] }, { "page": "read_mdd", "title": "Read and normalize the Mammal Diversity Database", "topics": [ "read_mdd" ] }, { "page": "read_meow", "title": "Parse the MEOW ecoregion GeoJSON into a long-format vertex table", "topics": [ "read_meow" ] }, { "page": "read_ncbi", "title": "Read and normalize the NCBI taxonomy dump", "topics": [ "read_ncbi" ] }, { "page": "read_ott", "title": "Read and normalize the OTT taxonomy", "topics": [ "read_ott" ] }, { "page": "read_reptiledb", "title": "Read and normalize the Reptile Database", "topics": [ "read_reptiledb" ] }, { "page": "read_vegcz", "title": "Read the Czech vegetation classification into the syntaxon backbone schema", "topics": [ "read_vegcz" ] }, { "page": "read_wcvp", "title": "Read and normalize the WCVP names file", "topics": [ "read_wcvp" ] }, { "page": "read_wfo", "title": "Read and normalize the WFO classification file", "topics": [ "read_wfo" ] }, { "page": "read_wgsrpd", "title": "Parse the WGSRPD Level 3 GeoJSON into a long-format vertex table", "topics": [ "read_wgsrpd" ] }, { "page": "read_worms", "title": "Read and normalize the WoRMS taxonomy", "topics": [ "read_worms" ] }, { "page": "register_backbones", "title": "Names of the backbones the genus register and backend coverage union", "topics": [ "register_backbones" ] }, { "page": "resolve_betsi_codes", "title": "Resolve BETSI species codes to binomials", "topics": [ "resolve_betsi_codes" ] }, { "page": "resolve_enrichment_names", "title": "Resolve enrichment names against all taxify backends", "topics": [ "resolve_enrichment_names" ] }, { "page": "resolve_hierarchy", "title": "Resolve family/genus by walking a parent-child hierarchy", "topics": [ "resolve_hierarchy" ] }, { "page": "resolve_name_map", "title": "Map names to their cross-backbone accepted names", "topics": [ "resolve_name_map" ] }, { "page": "rfishbase_release", "title": "Latest rfishbase data release for a server", "topics": [ "rfishbase_release" ] }, { "page": "sha256", "title": "Compute 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