{ "_id": "6a35cc0d3efcd9bda43f0b83", "Package": "taxifydb", "Title": "Build Backbones and Enrichments for the 'taxify' Package", "Version": "0.1.0", "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) and a wide set of trait and conservation\ndatasets, normalizes to a unified Darwin Core-like schema, and\nwrites pre-compiled '.vtr' files that the 'taxify' runtime\nconsumes. Separates build-time concerns (network access,\nparsing, schema normalization) from runtime concerns so that\n'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": "8.0.0", "Config/pak/sysreqs": "make libssl-dev", "Repository": "https://gcol33.r-universe.dev", "Date/Publication": "2026-06-19 21:26:26 UTC", "RemoteUrl": "https://github.com/gcol33/taxifydb", "RemoteRef": "HEAD", "RemoteSha": "76810a268e76024e760fc2d9de53e60993800e48", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-19 23:06:13 UTC", "User": "root" }, "Author": "Gilles Colling [aut, cre, cph] (ORCID:\n)", "Maintainer": "Gilles Colling ", "MD5sum": "0f924081ed619669c48a77d51ff7ddfe", "_user": "gcol33", "_type": "src", "_file": "taxifydb_0.1.0.tar.gz", "_fileid": "1a06af6abbc26d4731e657e46c7f433909eb55f1150fca389e2e8dcd37962042", "_filesize": 254726, "_sha256": "1a06af6abbc26d4731e657e46c7f433909eb55f1150fca389e2e8dcd37962042", "_created": "2026-06-19T23:06:13.000Z", "_published": "2026-06-19T23:09:01.330Z", "_distro": "noble", "_jobs": [ { "job": 82433711112, "time": 134, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7759668522" }, { "job": 82433711143, "time": 136, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7759668802" }, { "job": 82433711140, "time": 103, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7759664317" }, { "job": 82433711111, "time": 108, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7759664933" }, { "job": 82433487985, "time": 166, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7759650242" }, { "job": 82433711096, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7759668355" }, { "job": 82433711119, "time": 113, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7759665611" }, { "job": 82433711118, "time": 92, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7759662872" }, { "job": 82433711134, "time": 110, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7759665233" } ], "_buildurl": "https://github.com/r-universe/gcol33/actions/runs/27852311365", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/gcol33/taxifydb", "_commit": { "id": "76810a268e76024e760fc2d9de53e60993800e48", "author": "Gilles Colling ", "committer": "Gilles Colling ", "message": "data: bump 8 backbones to 2026.06 (accepted_authorship)\n\nPoints wfo, col, gbif, itis, worms, euromed, fungorum, algaebase at the\n2026.06 release builds, which carry the new accepted_authorship column.\nNCBI and OTT are unchanged (their sources have no authorship). col/worms\nspecies_profile extras are preserved at their existing tags.\n\nCo-Authored-By: Claude Opus 4.8 \nClaude-Session: https://claude.ai/code/session_01BpMyNDYhCVaurz8Qk1cmD4\n", "time": 1781904386 }, "_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. Sadge :(", "uuid": 25009600 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "curl", "role": "Imports" }, { "package": "digest", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "taxify", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "vectra", "role": "Imports" }, { "package": "DBI", "role": "Suggests" }, { "package": "openxlsx2", "role": "Suggests" }, { "package": "rfishbase", "role": "Suggests" }, { "package": "RSQLite", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "gcol33", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 1 }, { "week": "2026-20", "n": 10 }, { "week": "2026-21", "n": 5 }, { "week": "2026-22", "n": 2 }, { "week": "2026-25", "n": 4 } ], "_tags": [ { "name": "col-2025-r1", "date": "2026-05-16" }, { "name": "gbif-2026.05", "date": "2026-05-16" }, { "name": "wfo-2024-12-r1", "date": "2026-05-16" }, { "name": "algaebase-2026.05", "date": "2026-05-19" }, { "name": "enrichment-2026.05", "date": "2026-05-19" }, { "name": "euromed-2020", "date": "2026-05-19" }, { "name": "fungorum-2026.05", "date": "2026-05-19" }, { "name": "itis-2026.05", "date": "2026-05-19" }, { "name": "ncbi-2026.05", "date": "2026-05-19" }, { "name": "ott-3.7.3", "date": "2026-05-19" }, { "name": "worms-2026.05", "date": "2026-05-19" }, { "name": "algaebase-2026.06", "date": "2026-06-19" }, { "name": "col-2026.06", "date": "2026-06-19" }, { "name": "enrichment-2026.06", "date": "2026-06-19" }, { "name": "euromed-2026.06", "date": "2026-06-19" }, { "name": "fungorum-2026.06", "date": "2026-06-19" }, { "name": "gbif-2026.06", "date": "2026-06-19" }, { "name": "itis-2026.06", "date": "2026-06-19" }, { "name": "wfo-2026.06", "date": "2026-06-19" }, { "name": "worms-2026.06", "date": "2026-06-19" } ], "_topics": [ "biodiversity", "darwin-core", "taxonomy" ], "_stars": 1, "_contributors": [ { "user": "gcol33", "count": 17, "uuid": 25009600 } ], "_userbio": { "uuid": 25009600, "type": "user", "name": "Gilles Colling", "followers": 7, "description": "Building tools for ecology in R, C++, and Rust.\nWhy did Microsoft have to buy it. Sadge :(" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/taxifydb" }, "_devurl": "https://github.com/gcol33/taxifydb", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/taxifydb.html", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "apply_delta", "build_algaebase", "build_all_name_lookups", "build_backend", "build_col", "build_enrichment", "build_enrichment_vtr", "build_euromed", "build_fungorum", "build_gbif", "build_itis", "build_name_lookup", "build_ncbi", "build_ott", "build_vtr", "build_wfo", "build_worms", "check_all_enrichment_versions", "check_dryad_version", "check_enrichment_source_version", "check_figshare_version", "check_gbif_api_version", "check_gbif_version", "check_wcvp_version", "check_zenodo_version", "count_vtr_rows", "create_delta", "download_algaebase", "download_and_unzip", "download_col", "download_curl_file", "download_euromed", "download_fungorum", "download_gbif", "download_gbif_api_pages", "download_itis", "download_ncbi", "download_ott", "download_wfo", "download_worms", "enrichment_emergency_fallback", "has_xdelta3", "list_backends", "list_enrichments", "normalize_backbone", "parse_algae_traits", "parse_alien_first_records", "parse_amphibio", "parse_anage", "parse_animaltraits", "parse_arthropod_traits", "parse_avonet", "parse_common_names", "parse_conservation_status", "parse_diaz_traits", "parse_eive", "parse_elton_traits", "parse_fish_traits", "parse_fishbase", "parse_fungal_traits", "parse_funguild", "parse_gbif_common_names", "parse_glonaf", "parse_griis", "parse_leda", "parse_leptraits", "parse_lizard_traits", "parse_ncbi_common_names", "parse_ott_common_names", "parse_pantheria", "parse_wcvp", "parse_woodiness", "precompute_backbone", "publish_release", "read_algaebase", "read_col", "read_dmp", "read_euromed", "read_fungorum", "read_gbif", "read_itis", "read_ncbi", "read_ott", "read_wfo", "read_worms", "resolve_enrichment_names", "resolve_hierarchy", "sha256", "update_enrichment_manifest", "update_manifest" ], "_help": [ { "page": "apply_delta", "title": "Apply a binary delta to produce a new .vtr", "topics": [ "apply_delta" ] }, { "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_backend", "title": "Build a taxify backbone '.vtr' file from source", "topics": [ "build_backend" ] }, { "page": "build_col", "title": "Build the COL backbone .vtr", "topics": [ "build_col" ] }, { "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_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_itis", "title": "Build the ITIS backbone .vtr from scratch", "topics": [ "build_itis" ] }, { "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_vtr", "title": "Write a backbone .vtr file from a precomputed data.frame", "topics": [ "build_vtr" ] }, { "page": "build_wfo", "title": "Build the WFO backbone .vtr from source", "topics": [ "build_wfo" ] }, { "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_dryad_version", "title": "Check a Dryad dataset for the latest version", "topics": [ "check_dryad_version" ] }, { "page": "check_enrichment_source_version", "title": "Dispatch version check based on a manifest entry's source format", "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_gbif_version", "title": "Check a GBIF hosted dataset for the Last-Modified date", "topics": [ "check_gbif_version" ] }, { "page": "check_wcvp_version", "title": "Check Kew WCVP for the latest version", "topics": [ "check_wcvp_version" ] }, { "page": "check_zenodo_version", "title": "Check a Zenodo record for the latest version", "topics": [ "check_zenodo_version" ] }, { "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": "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_col", "title": "Download and extract the COL DwC-A", "topics": [ "download_col" ] }, { "page": "download_curl_file", "title": "Download a file via curl", "topics": [ "download_curl_file" ] }, { "page": "download_euromed", "title": "Download and extract the Euro+Med CSV", "topics": [ "download_euromed" ] }, { "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_itis", "title": "Download and extract the ITIS SQLite database", "topics": [ "download_itis" ] }, { "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_wfo", "title": "Download and extract the WFO classification file", "topics": [ "download_wfo" ] }, { "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": "has_xdelta3", "title": "Check if xdelta3 is available on PATH", "topics": [ "has_xdelta3" ] }, { "page": "list_backends", "title": "List available backend builders", "topics": [ "list_backends" ] }, { "page": "list_enrichments", "title": "List available enrichment builders", "topics": [ "list_enrichments" ] }, { "page": "normalize_backbone", "title": "Normalize a raw backbone data.frame to the unified schema", "topics": [ "normalize_backbone" ] }, { "page": "parse_algae_traits", "title": "Parse AlgaeTraits macroalgal traits (WoRMS ZIP export)", "topics": [ "parse_algae_traits" ] }, { "page": "parse_alien_first_records", "title": "Parse Seebens et al. Global Alien Species First Record Database", "topics": [ "parse_alien_first_records" ] }, { "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_arthropod_traits", "title": "Parse NW European Arthropod DwC-A (taxon + measurement + description)", "topics": [ "parse_arthropod_traits" ] }, { "page": "parse_avonet", "title": "Parse AVONET bird morphology XLSX", "topics": [ "parse_avonet" ] }, { "page": "parse_common_names", "title": "Parse common names from GBIF, NCBI, and OTT", "topics": [ "parse_common_names" ] }, { "page": "parse_conservation_status", "title": "Parse IUCN Red List conservation status from the GBIF Darwin Core Archive", "topics": [ "parse_conservation_status" ] }, { "page": "parse_diaz_traits", "title": "Parse Diaz et al. 2022 supplementary traits (XLSX)", "topics": [ "parse_diaz_traits" ] }, { "page": "parse_eive", "title": "Parse EIVE 1.0 ecological indicator values (XLSX)", "topics": [ "parse_eive" ] }, { "page": "parse_elton_traits", "title": "Parse EltonTraits 1.0 birds + mammals TSVs", "topics": [ "parse_elton_traits" ] }, { "page": "parse_fish_traits", "title": "Parse FISHMORPH freshwater fish morphological traits (CSV)", "topics": [ "parse_fish_traits" ] }, { "page": "parse_fishbase", "title": "Parse FishBase species and ecology tables (via rfishbase)", "topics": [ "parse_fishbase" ] }, { "page": "parse_fungal_traits", "title": "Parse FungalTraits XLSX (Table S1, genus-level traits)", "topics": [ "parse_fungal_traits" ] }, { "page": "parse_funguild", "title": "Parse FUNGuild JSON database dump", "topics": [ "parse_funguild" ] }, { "page": "parse_gbif_common_names", "title": "Parse GBIF vernacular names (VernacularName.tsv + Taxon.tsv)", "topics": [ "parse_gbif_common_names" ] }, { "page": "parse_glonaf", "title": "Parse GloNAF taxon-region data (multiple CSVs/XLSXs from ZIP)", "topics": [ "parse_glonaf" ] }, { "page": "parse_griis", "title": "Parse GRIIS Country Compendium CSV", "topics": [ "parse_griis" ] }, { "page": "parse_leda", "title": "Parse LEDA trait files (multiple semicolon/tab-delimited files)", "topics": [ "parse_leda" ] }, { "page": "parse_leptraits", "title": "Parse LepTraits 1.0 butterfly consensus CSV", "topics": [ "parse_leptraits" ] }, { "page": "parse_lizard_traits", "title": "Parse Meiri (2018) lizard traits (XLSX from Figshare)", "topics": [ "parse_lizard_traits" ] }, { "page": "parse_ncbi_common_names", "title": "Parse NCBI common names from names.dmp", "topics": [ "parse_ncbi_common_names" ] }, { "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_wcvp", "title": "Parse WCVP names + distribution (from extracted ZIP directory)", "topics": [ "parse_wcvp" ] }, { "page": "parse_woodiness", "title": "Parse Zanne et al. 2014 woodiness CSV", "topics": [ "parse_woodiness" ] }, { "page": "precompute_backbone", "title": "Full precompute pipeline: keys + synonym embedding", "topics": [ "precompute_backbone" ] }, { "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_col", "title": "Read and normalize the COL Taxon.tsv", "topics": [ "read_col" ] }, { "page": "read_dmp", "title": "Read a pipe-delimited NCBI .dmp file", "topics": [ "read_dmp" ] }, { "page": "read_euromed", "title": "Read and normalize the Euro+Med CSV", "topics": [ "read_euromed" ] }, { "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_itis", "title": "Read and normalize the ITIS SQLite database", "topics": [ "read_itis" ] }, { "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_wfo", "title": "Read and normalize the WFO classification file", "topics": [ "read_wfo" ] }, { "page": "read_worms", "title": "Read and normalize the WoRMS taxonomy", "topics": [ "read_worms" ] }, { "page": "resolve_enrichment_names", "title": "Resolve enrichment names against all taxify backends", "topics": [ "resolve_enrichment_names" ] }, { "page": "resolve_hierarchy", 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