Offline Taxonomic Name Matching Against Darwin Core Backbones
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Documentation for package ‘taxify’ version 0.4.0
Help Pages
-- A --
| add_algae_traits | Add macroalgal functional traits (AlgaeTraits) |
| add_alien_first_records | Add alien species first record years |
| add_amniote | Add amniote life-history traits (Amniote Life History Database) |
| add_amphibio | Add amphibian life-history traits (AmphiBIO) |
| add_anage | Add longevity and life-history traits (AnAge) |
| add_animaltraits | Add cross-taxon body mass and metabolic rate (AnimalTraits) |
| add_arctic_traits | Add Arctic marine benthos traits |
| add_arthropod_traits | Add arthropod life-history traits (NW European Arthropods) |
| add_austraits | Add Australian plant traits (AusTraits) |
| add_avonet | Add bird morphology and migration (AVONET) |
| add_bacdive | Add bacterial and archaeal strain phenotypes (BacDive) |
| add_baseflor | Add plant traits from Baseflor (Catminat / Julve) |
| add_bee_ostwald | Add bee morphometrics (Ostwald) |
| add_bet | Add bryophyte traits (Bryophytes of Europe Traits) |
| add_beukhof | Add marine fish traits (Beukhof) |
| add_bien | Add plant traits (BIEN) |
| add_birdbase | Add bird traits (BIRDBASE) |
| add_blanchard | Add ant genus defensive traits (Blanchard & Moreau) |
| add_brot | Add Mediterranean plant traits (BROT 2.0) |
| add_bryoatt | Add British and Irish bryophyte attributes (BRYOATT) |
| add_ccdb | Add plant chromosome numbers (Chromosome Counts Database) |
| add_cefas_btrait | Add benthic invertebrate traits (Cefas) |
| add_chelonians | Add turtle traits (CheloniansTraits) |
| add_classification | Add the full higher classification to a taxify result |
| add_clopla | Add clonal and bud-bank traits (CLO-PLA) |
| add_col_info | Add COL-specific columns |
| add_combine | Add mammal traits (COMBINE) |
| add_combine_imputed | Add mammal traits from COMBINE (phylogenetically imputed values) |
| add_combine_reported | Add mammal traits from COMBINE (reported values) |
| add_common_names | Add common (vernacular) names |
| add_copepod_traits | Add copepod traits (Brun et al. 2017) |
| add_coral_traits | Add scleractinian coral traits (Coral Trait Database) |
| add_data | Add custom data by taxonomic matching |
| add_diaz_traits | Add seed mass and plant height (Diaz et al. 2022) |
| add_disperse | Add aquatic-invertebrate dispersal traits (DISPERSE) |
| add_ecoflora | Add British plant traits from Ecoflora |
| add_edwards_phyto | Add phytoplankton nutrient-uptake traits (Edwards et al.) |
| add_eive | Add EIVE ecological indicator values |
| add_elton_traits | Add diet, foraging, and body mass (EltonTraits 1.0) |
| add_epa_freshwater | Add freshwater invertebrate traits (US EPA) |
| add_eupolltrait | Add European pollinator traits (EuPollTrait) |
| add_eurobat | Add European bat traits (EuroBaTrait) |
| add_fishbase | Add fish traits (FishBase) |
| add_fishmorph | Add freshwater fish morphological traits (FISHMORPH) |
| add_fishtraits | Add United States freshwater fish traits (FishTraits) |
| add_floraweb | Add German plant traits from FloraWeb |
| add_freshwater_insects_conus | Add freshwater-insect genus traits (Freshwater Insects CONUS) |
| add_frugivoria | Add Neotropical frugivore traits (Frugivoria) |
| add_fungalroot | Add mycorrhizal type from FungalRoot |
| add_fungal_traits | Add fungal lifestyle and trait data (FungalTraits) |
| add_funguild | Add fungal functional guild data (FUNGuild) |
| add_gbif_info | Add GBIF-specific columns |
| add_gidias | Add invasive-species impact (EICAT / SEICAT, GIDIAS) |
| add_gift | Add plant traits from GIFT |
| add_globi | Add biotic interaction degree (GloBI) |
| add_globtherm | Add thermal tolerance limits (GlobTherm) |
| add_glonaf | Add naturalized alien flora status (GloNAF) |
| add_gmpd | Add mammal parasite burden (GMPD 2.0) |
| add_griis | Add invasive species status (GRIIS) |
| add_groot | Add root traits (GRooT) |
| add_gwdd | Add wood density (Global Wood Density Database v2) |
| add_homerange | Add mammal home-range size (HomeRange) |
| add_hosts | Add Lepidoptera hostplant breadth (NHM HOSTS) |
| add_huang_amph | Add amphibian morphometrics (Huang) |
| add_hybrid_info | Add hybrid parent and type information |
| add_invacost | Add economic cost of biological invasions (InvaCost) |
| add_italic | Add Italian-lichen taxon-page traits (ITALIC) |
| add_iucn | Add IUCN Red List conservation status |
| add_kew_cvalues | Add plant genome size (Kew Plant DNA C-values) |
| add_kew_sid | Add seed traits from the Kew Seed Information Database (SER-SID) |
| add_leda | Add plant traits from LEDA Traitbase |
| add_leptraits | Add butterfly traits (LepTraits) |
| add_madin | Add bacterial and archaeal traits (Madin et al.) |
| add_nesttrait | Add bird nest traits (NestTrait) |
| add_nztd | Add NZ marine benthos traits (NZTD) |
| add_octocoral | Add octocoral traits (Octocoral Trait Database) |
| add_odonata | Add odonate behavioural/ecological traits (OPD) |
| add_pantheria | Add mammal life-history traits (PanTHERIA) |
| add_parravicini | Add reef-fish trophic guild (Parravicini) |
| add_pelagic | Add pelagic species traits |
| add_phylacine | Add mammal traits including extinct species (PHYLACINE) |
| add_pignatti | Add Italian plant traits from Pignatti (on demand, via TR8) |
| add_plantatt | Add British and Irish plant attributes (PLANTATT) |
| add_pottier | Add amphibian heat tolerance (Pottier) |
| add_quimbayo | Add reef-fish traits (Quimbayo) |
| add_ramond | Add marine protist functional traits (Ramond et al.) |
| add_repttraits | Add reptile ecological traits and distribution (ReptTraits) |
| add_rimet_phyto | Add phytoplankton cell metrics (Rimet & Druart) |
| add_saproxylic | Add saproxylic beetle morphology (Hagge) |
| add_sealifebase | Add aquatic-life traits (SeaLifeBase) |
| add_sharkipedia | Add elasmobranch life-history traits (Sharkipedia) |
| add_sheld | Add freshwater mussel traits (SHELD) |
| add_spider_traits | Add spider traits (World Spider Trait Database) |
| add_tetradensity | Add population density (TetraDENSITY) |
| add_thermofresh | Add freshwater thermal-tolerance traits (ThermoFresh) |
| add_trait | Add a trait from every source that carries it |
| add_tree_of_sex | Add sex-determination traits (Tree of Sex) |
| add_usda_fungus_host | Add fungal host breadth (USDA Fungus-Host Dataset) |
| add_useful_plants | Add human-use categories (World Checklist of Useful Plant Species) |
| add_wcvp | Add WCVP native range status |
| add_wfo_info | Add WFO-specific columns |
| add_zanne | Add woodiness (Zanne et al. 2014) |
| add_zooplankton | Add marine zooplankton traits |
-- C --
| children | List the accepted taxa within a genus or family |
| cite | Cite data sources used in a taxify result |
| class2tree | Build a taxonomy tree from resolved names |
| comm2sci | Resolve common (vernacular) names to scientific names |
-- D --
| downstream | List all descendants of a taxon down to a target rank |
-- E --
| enrichment_cols | Browse the trait columns an enrichment door can attach |
| enrichment_groups | Browse the group values a grouped enrichment can filter on |
| export_data | Export a taxify result to file |
-- G --
| gift_traits | Browse the bundled GIFT trait columns |
-- I --
| id2name | Resolve backbone IDs to names |
| inspect | Inspect a name list for probable typos and other anomalies |
| install_backbones | Install taxonomic backbones for offline matching |
-- L --
| list_backbones | List supported taxonomic backbones |
| list_enrichments | List available enrichments |
| list_traits | List the traits available to add_trait() |
| lookup_genus | Look up a genus in the register |
| lowest_common | Lowest common taxon of a set of names |
-- P --
| parse_name | Parse taxonomic names into their structural parts |
| print.taxify_tree | Build a taxonomy tree from resolved names |
-- R --
| reconcile | Reconcile a checklist against a backbone's current treatment |
-- S --
| sci2comm | Resolve scientific names to common (vernacular) names |
| synonyms | List the synonyms of a name |
-- T --
| taxify | Match taxonomic names against local backbone databases |
| taxify_build | Build a backbone database from source |
| taxify_build_register | Build the genus register from source |
| taxify_candidates | Expand ambiguous matches into their candidate taxa |
| taxify_clear_cache | Clear all cached backbones |
| taxify_databases | One overview of every database taxify knows about |
| taxify_data_dir | Get the taxify data directory |
| taxify_download | Download a pre-built taxify backbone |
| taxify_download_enrichment | Download one or more enrichment .vtr files |
| taxify_download_vtr | Download a pre-built taxify backbone |
| taxify_example_data | Path to the bundled example database |
| taxify_load_register | Load the unified genus register into memory |
| taxify_lock | Record the exact backbone and enrichment versions behind a result |
| taxify_long | Reshape grouped enrichment columns to long format |
| taxify_refresh_manifest | Invalidate the session manifest cache |
| taxify_regions | List the regions accepted by region= |
| taxify_register_coverage | Show backbone coverage for a genus |
| taxify_restore | Check an install against a lockfile |
| trait_info | Describe a trait's sources and units |
-- U --
| upstream | List the higher classification (ancestors) of a taxon |