Package index • taxify

Match and inspect names

Resolve a vector of names against local backbones and check a list before you trust it.

taxify(): Match taxonomic names against local backbone databases
parse_name(): Parse taxonomic names into their structural parts
comm2sci(): Resolve common (vernacular) names to scientific names
sci2comm(): Resolve scientific names to common (vernacular) names
id2name(): Resolve backbone IDs to names
inspect(): Inspect a name list for probable typos and other anomalies
reconcile(): Reconcile a checklist against a backbone's current treatment
taxify_regions(): List the regions accepted by region=
taxify_long(): Reshape grouped enrichment columns to long format
export_data(): Export a taxify result to file
cite(): Cite data sources used in a taxify result

Explore the backbone

Read the backbone the other ways — list synonyms, list the taxa within or beneath a group, attach the full classification, build a taxonomy tree.

synonyms(): List the synonyms of a name
children(): List the accepted taxa within a genus or family
downstream(): List all descendants of a taxon down to a target rank
upstream(): List the higher classification (ancestors) of a taxon
add_classification(): Add the full higher classification to a taxify result
class2tree() print(<taxify_tree>): Build a taxonomy tree from resolved names
lowest_common(): Lowest common taxon of a set of names
taxify_candidates(): Expand ambiguous matches into their candidate taxa

Backbone data and cache

Download, cache, and inspect backbone snapshots and the unified genus register.

install_backbones(): Install taxonomic backbones for offline matching
taxify_download(): Download a pre-built taxify backbone
taxify_download_enrichment(): Download one or more enrichment .vtr files
taxify_data_dir(): Get the taxify data directory
taxify_example_data(): Path to the bundled example database
taxify_clear_cache(): Clear all cached backbones
taxify_refresh_manifest(): Invalidate the session manifest cache
taxify_build_register(): Build the genus register from source
taxify_load_register(): Load the unified genus register into memory
taxify_register_coverage(): Show backbone coverage for a genus
lookup_genus(): Look up a genus in the register
taxify_lock(): Record the exact backbone and enrichment versions behind a result
taxify_restore(): Check an install against a lockfile

Backend-specific columns

Attach extra columns from the backbone that matched.

add_col_info(): Add COL-specific columns
add_gbif_info(): Add GBIF-specific columns
add_wfo_info(): Add WFO-specific columns
add_hybrid_info(): Add hybrid parent and type information

Traits across sources

Name one trait; gather and harmonize it from every source that carries it.

add_trait(): Add a trait from every source that carries it
list_traits(): List the traits available to add_trait()
trait_info(): Describe a trait's sources and units

Browse and discover

See every backbone, enrichment, and trait taxify offers, and join your own table.

taxify_databases(): One overview of every database taxify knows about
list_backbones(): List supported taxonomic backbones
list_enrichments(): List available enrichments
enrichment_cols(): Browse the trait columns an enrichment door can attach
enrichment_groups(): Browse the group values a grouped enrichment can filter on
add_data(): Add custom data by taxonomic matching

Enrichments — distribution and status

add_iucn(): Add IUCN Red List conservation status
add_griis(): Add invasive species status (GRIIS)
add_glonaf(): Add naturalized alien flora status (GloNAF)
add_invacost(): Add economic cost of biological invasions (InvaCost)
add_gidias(): Add invasive-species impact (EICAT / SEICAT, GIDIAS)
add_alien_first_records(): Add alien species first record years
add_wcvp(): Add WCVP native range status
add_common_names(): Add common (vernacular) names
add_globi(): Add biotic interaction degree (GloBI)

Enrichments — plants

add_zanne(): Add woodiness (Zanne et al. 2014)
add_eive(): Add EIVE ecological indicator values
add_diaz_traits(): Add seed mass and plant height (Diaz et al. 2022)
add_leda(): Add plant traits from LEDA Traitbase
add_groot(): Add root traits (GRooT)
add_hydraulics(): Add plant hydraulic traits (Sanchez-Martinez et al.)
add_noddb(): Add root-nodule nitrogen fixation (NodDB)
add_baseflor(): Add plant traits from Baseflor (Catminat / Julve)
add_ecoflora(): Add British plant traits from Ecoflora
add_floraweb(): Add German plant traits from FloraWeb
add_plantatt(): Add British and Irish plant attributes (PLANTATT)
add_bryoatt(): Add British and Irish bryophyte attributes (BRYOATT)
add_clopla(): Add clonal and bud-bank traits (CLO-PLA)
add_austraits(): Add Australian plant traits (AusTraits)
add_bien(): Add plant traits (BIEN)
add_brot(): Add Mediterranean plant traits (BROT 2.0)
add_bet(): Add bryophyte traits (Bryophytes of Europe Traits)
add_kew_sid(): Add seed traits from the Kew Seed Information Database (SER-SID)
add_kew_cvalues(): Add plant genome size (Kew Plant DNA C-values)
add_ccdb(): Add plant chromosome numbers (Chromosome Counts Database)
add_useful_plants(): Add human-use categories (World Checklist of Useful Plant Species)
add_gwdd(): Add wood density (Global Wood Density Database v2)
add_pignatti(): Add Italian plant traits from Pignatti (on demand, via TR8)
add_gift(): Add plant traits from GIFT
gift_traits(): Browse the bundled GIFT trait columns

Enrichments — fungi, algae, lichens, and microbes

add_fungal_traits(): Add fungal lifestyle and trait data (FungalTraits)
add_fungalroot(): Add mycorrhizal type from FungalRoot
add_funguild(): Add fungal functional guild data (FUNGuild)
add_usda_fungus_host(): Add fungal host breadth (USDA Fungus-Host Dataset)
add_italic(): Add Italian-lichen taxon-page traits (ITALIC)
add_algae_traits(): Add macroalgal functional traits (AlgaeTraits)
add_bacdive(): Add bacterial and archaeal strain phenotypes (BacDive)
add_madin(): Add bacterial and archaeal traits (Madin et al.)
add_faprotax(): Add prokaryote metabolic and ecological functions (FAPROTAX)
add_rimet_phyto(): Add phytoplankton cell metrics (Rimet & Druart)
add_edwards_phyto(): Add phytoplankton nutrient-uptake traits (Edwards et al.)
add_ramond(): Add marine protist functional traits (Ramond et al.)

Enrichments — birds and mammals

add_avonet(): Add bird morphology and migration (AVONET)
add_birdbase(): Add bird traits (BIRDBASE)
add_nesttrait(): Add bird nest traits (NestTrait)
add_elton_traits(): Add diet, foraging, and body mass (EltonTraits 1.0)
add_frugivoria(): Add Neotropical frugivore traits (Frugivoria)
add_pantheria(): Add mammal life-history traits (PanTHERIA)
add_phylacine(): Add mammal traits including extinct species (PHYLACINE)
add_combine(): Add mammal traits (COMBINE)
add_combine_reported(): Add mammal traits from COMBINE (reported values)
add_combine_imputed(): Add mammal traits from COMBINE (phylogenetically imputed values)
add_homerange(): Add mammal home-range size (HomeRange)
add_tetradensity(): Add population density (TetraDENSITY)
add_eurobat(): Add European bat traits (EuroBaTrait)
add_gmpd(): Add mammal parasite burden (GMPD 2.0)

Enrichments — reptiles, amphibians, and fish

add_repttraits(): Add reptile ecological traits and distribution (ReptTraits)
add_chelonians(): Add turtle traits (CheloniansTraits)
add_amphibio(): Add amphibian life-history traits (AmphiBIO)
add_huang_amph(): Add amphibian morphometrics (Huang)
add_pottier(): Add amphibian heat tolerance (Pottier)
add_fishbase(): Add fish traits (FishBase)
add_fishmorph(): Add freshwater fish morphological traits (FISHMORPH)
add_fishtraits(): Add United States freshwater fish traits (FishTraits)
add_beukhof(): Add marine fish traits (Beukhof)
add_quimbayo(): Add reef-fish traits (Quimbayo)
add_parravicini(): Add reef-fish trophic guild (Parravicini)
add_pelagic(): Add pelagic species traits
add_sharkipedia(): Add elasmobranch life-history traits (Sharkipedia)

Enrichments — invertebrates and aquatic life

add_arthropod_traits(): Add arthropod life-history traits (NW European Arthropods)
add_spider_traits(): Add spider traits (World Spider Trait Database)
add_bee_ostwald(): Add bee morphometrics (Ostwald)
add_eupolltrait(): Add European pollinator traits (EuPollTrait)
add_leptraits(): Add butterfly traits (LepTraits)
add_odonata(): Add odonate behavioural/ecological traits (OPD)
add_saproxylic(): Add saproxylic beetle morphology (Hagge)
add_chowdhury(): Add German ground-beetle traits and occupancy trends (Chowdhury et al. 2025)
add_finand(): Add Helsinki urban-forest carabid traits (Finand & Kotze)
add_eberswalde(): Add Eberswalde long-term carabid monitoring traits and trends
add_alpine_carabids(): Add Alpine ground-beetle traits (Chamberlain et al.)
add_imageomics_neon(): Add North American ground-beetle elytra measurements (Imageomics / NEON)
add_sworm(): Add earthworm ecological groups (sWorm)
add_betsi_earthworm_traits(): Add earthworm traits (Pelosi et al. 2014)
add_betsi_collembola_traits(): Add Collembola traits (Lu et al. 2025)
add_ellers_collembola(): Add Collembola traits (Ellers et al. 2018)
add_inrae_collembola_traits(): Add Collembola traits (Data INRAE deposits)
add_ecomorphosis(): Add Collembola ecomorphosis (Bonfanti et al. 2022)
add_betsi_collembola_body_length(): Add Collembola body length (BETSI export)
add_monograph_collembola_body_length(): Add Collembola body length (monographs)
add_plazi_collembola_body_length(): Add Collembola body length (Plazi treatments)
add_hosts(): Add Lepidoptera hostplant breadth (NHM HOSTS)
add_blanchard(): Add ant genus defensive traits (Blanchard & Moreau)
add_coral_traits(): Add scleractinian coral traits (Coral Trait Database)
add_octocoral(): Add octocoral traits (Octocoral Trait Database)
add_zooplankton(): Add marine zooplankton traits
add_arctic_traits(): Add Arctic marine benthos traits
add_nztd(): Add NZ marine benthos traits (NZTD)
add_disperse(): Add aquatic-invertebrate dispersal traits (DISPERSE)
add_freshwater_insects_conus(): Add freshwater-insect genus traits (Freshwater Insects CONUS)
add_thermofresh(): Add freshwater thermal-tolerance traits (ThermoFresh)
add_sheld(): Add freshwater mussel traits (SHELD)
add_copepod_traits(): Add copepod traits (Brun et al. 2017)
add_epa_freshwater(): Add freshwater invertebrate traits (US EPA)
add_cefas_btrait(): Add benthic invertebrate traits (Cefas)
add_sealifebase(): Add aquatic-life traits (SeaLifeBase)

Enrichments — cross-taxon

add_amniote(): Add amniote life-history traits (Amniote Life History Database)
add_anage(): Add longevity and life-history traits (AnAge)
add_animaltraits(): Add cross-taxon body mass and metabolic rate (AnimalTraits)
add_globtherm(): Add thermal tolerance limits (GlobTherm)
add_tree_of_sex(): Add sex-determination traits (Tree of Sex)
add_virion(): Add host-virus association breadth (VIRION)

Low-level building blocks

Exported internals for power users and custom pipelines.

taxify_build(): Build a backbone database from source
score_candidates(): Score match candidates by resolution priority
embed_accepted(): Embed accepted taxon info at build time (synonym self-join)
precompute_keys(): Precompute matching keys at build time
normalize_epithets(): Vectorized Latin orthographic normalization
is_aggregate_name(): Test whether a canonical name carries an aggregate marker
normalize_aggregate_name(): Normalize aggregate markers on canonical names (build-time)