R: Offline Taxonomic Name Matching Against Darwin Core Backbones

# Offline Taxonomic Name Matching Against Darwin Core Backbones

## Documentation for package ‘taxify’ version 0.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E G I L P R S T U

## -- 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