Package: taxifydb 0.1.0

taxifydb: Build Backbones and Enrichments for the 'taxify' Package

Build pipeline for the 'taxify' package. Downloads raw source data from official providers (WFO, COL, GBIF, ITIS, NCBI Taxonomy, Open Tree of Life, WoRMS, Euro+Med PlantBase, Index Fungorum, AlgaeBase) and a wide set of trait and conservation datasets, normalizes to a unified Darwin Core-like schema, and writes pre-compiled '.vtr' files that the 'taxify' runtime consumes. Separates build-time concerns (network access, parsing, schema normalization) from runtime concerns so that 'taxify' itself stays lean.

Authors:Gilles Colling [aut, cre, cph]

taxifydb_0.1.0.tar.gz
taxifydb_0.1.0.zip(r-4.7)taxifydb_0.1.0.zip(r-4.6)taxifydb_0.1.0.zip(r-4.5)
taxifydb_0.1.0.tgz(r-4.6-any)taxifydb_0.1.0.tgz(r-4.5-any)
taxifydb_0.1.0.tar.gz(r-4.7-any)taxifydb_0.1.0.tar.gz(r-4.6-any)
taxifydb_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
taxifydb/json (API)

# Install 'taxifydb' in R:
install.packages('taxifydb', repos = c('https://gcol33.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gcol33/taxifydb/issues

On CRAN:

Conda:

biodiversitydarwin-coretaxonomy

1.70 score 1 stars 2 scripts 90 exports 12 dependencies

Last updated from:76810a268e. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING134
source / vignettesOK166
linux-release-x86_64WARNING136
macos-release-arm64WARNING108
macos-oldrel-arm64WARNING103
windows-develWARNING113
windows-releaseWARNING110
windows-oldrelWARNING92
wasm-releaseOK132

Exports:apply_deltabuild_algaebasebuild_all_name_lookupsbuild_backendbuild_colbuild_enrichmentbuild_enrichment_vtrbuild_euromedbuild_fungorumbuild_gbifbuild_itisbuild_name_lookupbuild_ncbibuild_ottbuild_vtrbuild_wfobuild_wormscheck_all_enrichment_versionscheck_dryad_versioncheck_enrichment_source_versioncheck_figshare_versioncheck_gbif_api_versioncheck_gbif_versioncheck_wcvp_versioncheck_zenodo_versioncount_vtr_rowscreate_deltadownload_algaebasedownload_and_unzipdownload_coldownload_curl_filedownload_euromeddownload_fungorumdownload_gbifdownload_gbif_api_pagesdownload_itisdownload_ncbidownload_ottdownload_wfodownload_wormsenrichment_emergency_fallbackhas_xdelta3list_backendslist_enrichmentsnormalize_backboneparse_algae_traitsparse_alien_first_recordsparse_amphibioparse_anageparse_animaltraitsparse_arthropod_traitsparse_avonetparse_common_namesparse_conservation_statusparse_diaz_traitsparse_eiveparse_elton_traitsparse_fish_traitsparse_fishbaseparse_fungal_traitsparse_funguildparse_gbif_common_namesparse_glonafparse_griisparse_ledaparse_leptraitsparse_lizard_traitsparse_ncbi_common_namesparse_ott_common_namesparse_pantheriaparse_wcvpparse_woodinessprecompute_backbonepublish_releaseread_algaebaseread_colread_dmpread_euromedread_fungorumread_gbifread_itisread_ncbiread_ottread_wforead_wormsresolve_enrichment_namesresolve_hierarchysha256update_enrichment_manifestupdate_manifest

Dependencies:clicurldigestgluejsonlitelifecyclerlangtaxifytidyselectvctrsvectrawithr

Readme and manuals

Help Manual

Help pageTopics
Apply a binary delta to produce a new .vtrapply_delta
Build the AlgaeBase backbone .vtrbuild_algaebase
Build name-lookup tables for all installed taxify backbonesbuild_all_name_lookups
Build a taxify backbone '.vtr' file from sourcebuild_backend
Build the COL backbone .vtrbuild_col
Build an enrichment '.vtr' from sourcebuild_enrichment
Write an enrichment .vtr filebuild_enrichment_vtr
Build the Euro+Med backbone .vtrbuild_euromed
Build the Species Fungorum Plus backbone .vtrbuild_fungorum
Build the GBIF backbone .vtrbuild_gbif
Build the ITIS backbone .vtr from scratchbuild_itis
Build a name-lookup .vtr from a backbone .vtrbuild_name_lookup
Build the NCBI backbone .vtrbuild_ncbi
Build the OTT backbone .vtrbuild_ott
Write a backbone .vtr file from a precomputed data.framebuild_vtr
Build the WFO backbone .vtr from sourcebuild_wfo
Build the WoRMS backbone .vtrbuild_worms
Check all non-static enrichments in a manifest for version freshnesscheck_all_enrichment_versions
Check a Dryad dataset for the latest versioncheck_dryad_version
Dispatch version check based on a manifest entry's source formatcheck_enrichment_source_version
Check a Figshare article for the latest versioncheck_figshare_version
Check the GBIF backbone API for the latest update datecheck_gbif_api_version
Check a GBIF hosted dataset for the Last-Modified datecheck_gbif_version
Check Kew WCVP for the latest versioncheck_wcvp_version
Check a Zenodo record for the latest versioncheck_zenodo_version
Count rows in a .vtr filecount_vtr_rows
Create a binary diff between two .vtr filescreate_delta
Fetch all AlgaeBase records via /nameusage/searchdownload_algaebase
Download a ZIP and extract, returning the path to a matching filedownload_and_unzip
Download and extract the COL DwC-Adownload_col
Download a file via curldownload_curl_file
Download and extract the Euro+Med CSVdownload_euromed
Download and extract the Species Fungorum Plus ColDP archivedownload_fungorum
Download the GBIF backbone simple.txt.gzdownload_gbif
Fetch paginated GBIF API resultsdownload_gbif_api_pages
Download and extract the ITIS SQLite databasedownload_itis
Download and extract NCBI taxdumpdownload_ncbi
Download and extract OTT taxonomydownload_ott
Download and extract the WFO classification filedownload_wfo
Download and extract WoRMS DwC-Adownload_worms
Build enrichment from source and return the raw data.frameenrichment_emergency_fallback
Check if xdelta3 is available on PATHhas_xdelta3
List available backend builderslist_backends
List available enrichment builderslist_enrichments
Normalize a raw backbone data.frame to the unified schemanormalize_backbone
Parse AlgaeTraits macroalgal traits (WoRMS ZIP export)parse_algae_traits
Parse Seebens et al. Global Alien Species First Record Databaseparse_alien_first_records
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 NW European Arthropod DwC-A (taxon + measurement + description)parse_arthropod_traits
Parse AVONET bird morphology XLSXparse_avonet
Parse common names from GBIF, NCBI, and OTTparse_common_names
Parse IUCN Red List conservation status from the GBIF Darwin Core Archiveparse_conservation_status
Parse Diaz et al. 2022 supplementary traits (XLSX)parse_diaz_traits
Parse EIVE 1.0 ecological indicator values (XLSX)parse_eive
Parse EltonTraits 1.0 birds + mammals TSVsparse_elton_traits
Parse FISHMORPH freshwater fish morphological traits (CSV)parse_fish_traits
Parse FishBase species and ecology tables (via rfishbase)parse_fishbase
Parse FungalTraits XLSX (Table S1, genus-level traits)parse_fungal_traits
Parse FUNGuild JSON database dumpparse_funguild
Parse GBIF vernacular names (VernacularName.tsv + Taxon.tsv)parse_gbif_common_names
Parse GloNAF taxon-region data (multiple CSVs/XLSXs from ZIP)parse_glonaf
Parse GRIIS Country Compendium CSVparse_griis
Parse LEDA trait files (multiple semicolon/tab-delimited files)parse_leda
Parse LepTraits 1.0 butterfly consensus CSVparse_leptraits
Parse Meiri (2018) lizard traits (XLSX from Figshare)parse_lizard_traits
Parse NCBI common names from names.dmpparse_ncbi_common_names
Parse OTT common names from synonyms.tsv + taxonomy.tsvparse_ott_common_names
Parse PanTHERIA mammal life-history traits (TSV)parse_pantheria
Parse WCVP names + distribution (from extracted ZIP directory)parse_wcvp
Parse Zanne et al. 2014 woodiness CSVparse_woodiness
Full precompute pipeline: keys + synonym embeddingprecompute_backbone
Create a GitHub release and upload backbone artifactspublish_release
Read and normalize a fetched list of AlgaeBase recordsread_algaebase
Read and normalize the COL Taxon.tsvread_col
Read a pipe-delimited NCBI .dmp fileread_dmp
Read and normalize the Euro+Med CSVread_euromed
Read and normalize the Species Fungorum Plus ColDP filesread_fungorum
Read and normalize the GBIF backboneread_gbif
Read and normalize the ITIS SQLite databaseread_itis
Read and normalize the NCBI taxonomy dumpread_ncbi
Read and normalize the OTT taxonomyread_ott
Read and normalize the WFO classification fileread_wfo
Read and normalize the WoRMS taxonomyread_worms
Resolve enrichment names against all taxify backendsresolve_enrichment_names
Resolve family/genus by walking a parent-child hierarchyresolve_hierarchy
Compute SHA-256 checksum of a filesha256
Update manifest.json enrichment entry from built meta.jsonupdate_enrichment_manifest
Update manifest.json after a successful backbone buildupdate_manifest