Finding a dataset | Attaching one dataset | Datasets with one value per place or language | One trait from several datasets | Where each value came from | Coverage | How the values are joined | Downloads and versions | Where next | References
Package: taxify 0.7.0
taxify: Offline Taxonomic Name Matching Against Darwin Core Backbones
Matches taxonomic names against local copies of published backbones ('Catalogue of Life', 'GBIF Backbone Taxonomy', 'ITIS', 'World Flora Online', 'WoRMS', 'NCBI Taxonomy', 'Open Tree of Life', 'Euro+Med', 'Species Fungorum', 'AlgaeBase', 'FishBase', 'SeaLifeBase', 'Reptile Database', 'LCVP', 'WCVP', 'Mammal Diversity Database', 'AviList', 'LPSN') and two vegetation classifications, and resolves each name to its accepted name. It performs the name-resolution step of 'taxize' and 'WorldFlora', run offline against these files. Names are cleaned of authors and qualifiers, matched exactly and then by edit distance within their genus, and followed from synonym to accepted name, with the backbone version recorded on every row. Published trait, status and distribution datasets are joined on the accepted name, and so is a table the user supplies. Matching runs in the 'vectra' column-store engine.
Authors:
taxify_0.7.0.tar.gz
taxify_0.7.0.zip(r-4.7-any)taxify_0.7.0.zip(r-4.6-any)taxify_0.7.0.zip(r-4.5-any)
taxify_0.7.0.tgz(r-4.6-any)taxify_0.7.0.tgz(r-4.5-any)
taxify_0.7.0.tar.gz(r-4.7-any)taxify_0.7.0.tar.gz(r-4.6-any)
taxify_0.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
taxify/json (API)
| # Install 'taxify' in R: |
| install.packages('taxify', repos = c('https://gcol33.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gcol33/taxify/issues
Pkgdown/docs site:https://gillescolling.com
biodiversitydarwin-coreecologyfuzzy-matchinggbifname-matchingnomenclatureofflinespecies-namessynonymstaxonomy
Last updated from:23db251444. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 268 | ||
| source / vignettes | OK | 275 | ||
| linux-release | OK | 235 | ||
| macos-release | OK | 184 | ||
| macos-oldrel | OK | 164 | ||
| windows-devel | OK | 356 | ||
| windows-release | OK | 296 | ||
| windows-oldrel | OK | 283 | ||
| wasm-release | OK | 136 |
Exports:add_algae_traitsadd_alien_first_recordsadd_alpine_carabidsadd_amnioteadd_amphibioadd_anageadd_animaltraitsadd_arctic_traitsadd_arthropod_traitsadd_austraitsadd_avonetadd_bacdiveadd_basefloradd_bee_ostwaldadd_betadd_betsi_collembola_body_lengthadd_betsi_collembola_traitsadd_betsi_earthworm_traitsadd_beukhofadd_bienadd_birdbaseadd_blanchardadd_brotadd_bryoattadd_ccdbadd_cefas_btraitadd_cheloniansadd_chowdhuryadd_classificationadd_cloplaadd_col_infoadd_combineadd_combine_imputedadd_combine_reportedadd_common_namesadd_copepod_traitsadd_coral_traitsadd_dataadd_diaz_traitsadd_disperseadd_eberswaldeadd_ecofloraadd_ecomorphosisadd_edwards_phytoadd_eiveadd_ellers_collembolaadd_elton_traitsadd_epa_freshwateradd_eupolltraitadd_eurobatadd_euromed_distributionadd_faprotaxadd_finandadd_fishbaseadd_fishmorphadd_fishtraitsadd_florawebadd_freshwater_insects_conusadd_frugivoriaadd_fungal_traitsadd_fungalrootadd_funguildadd_gbif_infoadd_gidiasadd_giftadd_globiadd_globthermadd_glonafadd_gmpdadd_griisadd_grootadd_gwddadd_homerangeadd_hostsadd_huang_amphadd_hybrid_infoadd_hydraulicsadd_imageomics_neonadd_inrae_collembola_traitsadd_invacostadd_italicadd_iucnadd_kew_cvaluesadd_kew_sidadd_ledaadd_leptraitsadd_madinadd_monograph_collembola_body_lengthadd_nesttraitadd_noddbadd_nztdadd_octocoraladd_odonataadd_pantheriaadd_parraviciniadd_pelagicadd_phylacineadd_pignattiadd_plantattadd_plazi_collembola_body_lengthadd_pottieradd_quimbayoadd_ramondadd_repttraitsadd_rimet_phytoadd_saproxylicadd_sealifebaseadd_sharkipediaadd_sheldadd_spider_traitsadd_swormadd_tetradensityadd_thermofreshadd_traitadd_tree_of_sexadd_usda_fungus_hostadd_useful_plantsadd_virionadd_wcvpadd_wfo_infoadd_zanneadd_zooplanktonbackbone_codebackbone_fixed_kingdombasionym_placementcandidate_orderchildrenciteclass2treecomm2scidownstreamembed_acceptedenrichment_authorship_colenrichment_colsenrichment_groupseuromed_areasexport_datagbif_backmatchgbif_fetchgbif_requestgift_traitsid2nameinspectinstall_backbonesis_aggregate_namelist_backboneslist_enrichmentslist_traitslookup_genuslowest_commonnormalize_aggregate_namenormalize_epithetsnormalize_kingdom_groupnormalize_syntaxon_nameparse_nameprecompute_keysreconcilesci2commscore_candidatessynonymstaxifytaxify_buildtaxify_build_registertaxify_clear_cachetaxify_data_dirtaxify_databasestaxify_downloadtaxify_download_enrichmenttaxify_example_datataxify_idstaxify_load_registertaxify_locktaxify_longtaxify_pintaxify_refresh_manifesttaxify_regionstaxify_register_coveragetaxify_restoretaxify_storetrait_infoupstream
Dependencies:clicurlgluejsonlitelibgeoslifecyclerlangtidyselectvctrsvectrawithr
Attaching published data
Last update: 2026-10-13
Started: 2026-04-04
Checking a name list
Checks without matching | Checks on matched names | Labels and tiers | Checks against a region | Using the report | Comparing a checklist with a backbone | Where next
Last update: 2026-10-13
Started: 2026-06-29
Choosing and combining backbones
The default fallback chain | Naming the backbones | Checking names outside a backbone | Comparing backbones | Columns from one backbone | How the backbones differ in output | Downloading and pinning versions | Choosing backbones for a list | Where next
Last update: 2026-10-13
Started: 2026-07-22
Compatibility with taxize and WorldFlora
Matching the same names in both packages | Agreement on a sample of WFO names | Functions of taxize | Functions of WorldFlora | Differences | Timings against WorldFlora | When taxize or WorldFlora fits better | Where next | References
Last update: 2026-10-13
Started: 2026-04-04
Exploring the backbone
Synonyms | Taxa below a genus or family | Ranks above a taxon | IDs | The parts of a name | Common names | Comparing a list | Where next
Last update: 2026-10-13
Started: 2026-10-13
Get started
Installation | Matching a list of names | Common errors when matching | Checking the matches | Joining your own data | Joining published data | Recording what was used | Where next
Last update: 2026-10-13
Started: 2026-10-13
How names are matched
The stages | Cleaning | Fuzzy matching | Distance methods | The threshold | Misspelt genera | Checking fuzzy matches | Names with more than one accepted taxon | Synonyms and basionyms | Infraspecific names | Names no backbone matches | Where next
Last update: 2026-10-13
Started: 2026-04-04
Hybrids and aggregates
Hybrid names | Hybrid parents | How hybrids are detected | Aggregates | Traits for hybrids and aggregates | Where next
Last update: 2026-10-13
Started: 2026-07-09
Joining your own data
Joining a data frame | Joining a file | Choosing columns | Repeated species | Matching options | Combining with published data | Exporting the result | How the join works | Where next
Last update: 2026-10-13
Started: 2026-04-04
Matching large lists
How long matching takes | Lists that need no fuzzy matching | Ordering the backbones | Long lists in parts | Memory | Downloads before a run | Where the files are | Where next
Last update: 2026-10-13
Started: 2026-04-04
Matching vegetation units
Names of vegetation units | The two backbones | Matching unit names | The units above each name | From a national association to a European alliance | Mixing taxa and vegetation units | How the backbones were built | Where next | References
Last update: 2026-10-13
Started: 2026-10-13
Matching within a region
A misspelling with two candidates | How the region filter decides | Naming the region | Coordinates | Native or introduced records | Marine regions | Where next | References
Last update: 2026-10-13
Started: 2026-06-29
Requesting GBIF data for a species list
Matching the names to keys | Several keys for one name | What a request covers | Results matched against another backbone | Setting up rgbif | Sending the request | Linking records to the requested names | Citing the download | Where next
Last update: 2026-10-13
Started: 2026-09-23
