## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", eval = FALSE ) ## ----list-enrichments--------------------------------------------------------- # library(taxify) # # list_enrichments() # #> name version nrow static trait_cols ... # #> 1 conservation_status ... 166000 TRUE conservation_status ... # #> 2 griis ... 23000 FALSE invasive_status ... # #> 3 wcvp ... 340000 FALSE native_status ... # #> ... ## ----pre-download------------------------------------------------------------- # # Download a single enrichment # taxify_download_enrichment("conservation_status") # # # Download several at once # taxify_download_enrichment(c("woodiness", "eive", "leda")) # # # Download all of them # taxify_download_enrichment(c( # "conservation_status", "griis", "wcvp", "eive", # "elton_traits", "avonet", "pantheria", "amphibio", # "common_names", "woodiness", "diaz_traits", "leda", # "fungal_traits", "funguild", "algae_traits", # "fish_traits", "fishbase", "lizard_traits", "anage", "glonaf", # "leptraits", "animaltraits", "arthropod_traits", "alien_first_records", # "baseflor", "ecoflora", "floraweb" # )) ## ----woodiness---------------------------------------------------------------- # plants <- taxify(c( # "Quercus robur", "Betula pendula", "Arrhenatherum elatius", # "Festuca rubra", "Salix caprea", "Cornus sanguinea" # )) # # plants |> add_woodiness() # #> input_name accepted_name woodiness # #> 1 Quercus robur Quercus robur woody # #> 2 Betula pendula Betula pendula woody # #> 3 Arrhenatherum elatius Arrhenatherum elatius herbaceous # #> 4 Festuca rubra Festuca rubra herbaceous # #> 5 Salix caprea Salix caprea woody # #> 6 Cornus sanguinea Cornus sanguinea woody ## ----eive--------------------------------------------------------------------- # grasses <- taxify(c( # "Arrhenatherum elatius", "Bromus erectus", "Festuca rubra", # "Dactylis glomerata", "Lolium perenne", "Poa pratensis" # )) # # grasses |> add_eive() # #> input_name eive_light eive_temperature eive_moisture eive_reaction eive_nutrients # #> 1 Arrhenatherum ... 7.2 5.8 4.3 7.1 6.5 # #> 2 Bromus erectus 7.6 5.5 3.1 7.8 3.2 # #> ... ## ----diaz-traits-------------------------------------------------------------- # trees <- taxify(c( # "Quercus robur", "Fagus sylvatica", "Picea abies", # "Pinus sylvestris", "Acer pseudoplatanus" # )) # # trees |> add_diaz_traits() # #> input_name seed_mass_mg plant_height_m # #> 1 Quercus robur 3200.0 25.0 # #> 2 Fagus sylvatica 2200.0 30.0 # #> 3 Picea abies 7.9 40.0 # #> 4 Pinus sylvestris 6.5 25.0 # #> 5 Acer pseudoplatanus 120.0 25.0 ## ----leda--------------------------------------------------------------------- # meadow_spp <- taxify(c( # "Arrhenatherum elatius", "Trifolium pratense", # "Leucanthemum vulgare", "Plantago lanceolata", # "Achillea millefolium", "Centaurea jacea" # )) # # meadow_spp |> add_leda() # #> input_name raunkiaer_life_form dispersal_type sla_mm2_mg canopy_height_m ... # #> 1 Arrhenatherum ... hemicryptophyte anemochory 25.1 0.90 ... # #> 2 Trifolium pratense hemicryptophyte zoochory 22.3 0.30 ... # #> ... ## ----regional-plants, eval=FALSE---------------------------------------------- # taxify(c("Bellis perennis", "Achillea millefolium", "Calluna vulgaris")) |> # add_ecoflora() |> # add_floraweb() ## ----conservation-status------------------------------------------------------ # species <- taxify(c( # "Panthera tigris", "Ailuropoda melanoleuca", # "Gorilla gorilla", "Vulpes vulpes", # "Passer domesticus", "Quercus robur" # )) # # species |> add_conservation_status() # #> input_name conservation_status # #> 1 Panthera tigris EN # #> 2 Ailuropoda melanoleuca VU # #> 3 Gorilla gorilla CR # #> 4 Vulpes vulpes LC # #> 5 Passer domesticus LC # #> 6 Quercus robur LC ## ----avonet------------------------------------------------------------------- # birds <- taxify(c( # "Parus major", "Cyanistes caeruleus", "Erithacus rubecula", # "Turdus merula", "Falco peregrinus", "Aquila chrysaetos" # )) # # birds |> add_avonet() # #> input_name beak_length wing_length avonet_body_mass_g migration trophic_niche ... # #> 1 Parus major 11.2 75.1 18.5 sedentary Invertivore ... # #> 2 Cyanistes caeruleus 9.8 67.2 11.0 sedentary Invertivore ... # #> 3 Erithacus rubecula 11.5 72.3 17.1 partial Invertivore ... # #> 4 Turdus merula 20.8 130.5 95.0 partial Omnivore ... # #> 5 Falco peregrinus 15.2 312.0 750.0 full Vertivore ... # #> 6 Aquila chrysaetos 37.5 607.0 4000.0 partial Vertivore ... ## ----elton-traits------------------------------------------------------------- # birds <- taxify(c( # "Parus major", "Dendrocopos major", "Alcedo atthis", # "Tyto alba", "Apus apus" # )) # # birds |> add_elton_traits() # #> input_name diet_inv diet_fruit diet_seed foraging_canopy foraging_aerial nocturnal ... # #> 1 Parus major 60 10 20 50 0 0 ... # #> 2 Dendrocopos major 75 5 10 80 0 0 ... # #> 3 Alcedo atthis 0 0 0 0 0 0 ... # #> 4 Tyto alba 10 0 0 0 0 1 ... # #> 5 Apus apus 100 0 0 0 100 0 ... ## ----pantheria---------------------------------------------------------------- # mammals <- taxify(c( # "Vulpes vulpes", "Canis lupus", "Ursus arctos", # "Mustela nivalis", "Lutra lutra", "Lynx lynx" # )) # # mammals |> add_pantheria() # #> input_name pantheria_body_mass_g longevity_mo litter_size home_range_km2 ... # #> 1 Vulpes vulpes 5480.0 144 5.0 8.55 ... # #> 2 Canis lupus 31757.0 192 5.4 242.00 ... # #> 3 Ursus arctos 139000.0 396 2.0 488.00 ... # #> 4 Mustela nivalis 67.0 72 5.5 0.03 ... # #> 5 Lutra lutra 8000.0 180 2.3 15.00 ... # #> 6 Lynx lynx 20500.0 252 2.6 168.00 ... ## ----amphibio----------------------------------------------------------------- # amphibians <- taxify(c( # "Bufo bufo", "Rana temporaria", "Salamandra salamandra", # "Triturus cristatus", "Hyla arborea", "Bombina variegata" # )) # # amphibians |> add_amphibio() # #> input_name body_size_mm arboreal aquatic direct_development nocturnal_amphibio ... # #> 1 Bufo bufo 150.0 0 0 0 1 ... # #> 2 Rana temporaria 110.0 0 1 0 0 ... # #> 3 Salamandra salamandra 200.0 0 0 0 1 ... # #> 4 Triturus cristatus 160.0 0 1 0 1 ... # #> 5 Hyla arborea 50.0 1 0 0 1 ... # #> 6 Bombina variegata 50.0 0 1 0 0 ... ## ----fungal-traits------------------------------------------------------------ # fungi <- taxify(c( # "Amanita muscaria", "Boletus edulis", "Trametes versicolor", # "Agaricus bisporus", "Cantharellus cibarius" # )) # # fungi |> add_fungal_traits() # #> input_name primary_lifestyle growth_form fruitbody_type decay_substrate ... # #> 1 Amanita muscaria ectomycorrhizal agaricoid agaricoid ... # #> 2 Boletus edulis ectomycorrhizal boletoid boletoid ... # #> 3 Trametes versicolor saprotroph polyporoid polyporoid wood ... # #> 4 Agaricus bisporus saprotroph agaricoid agaricoid litter ... # #> 5 Cantharellus cibarius ectomycorrhizal cantharelloid cantharelloid ... ## ----funguild----------------------------------------------------------------- # fungi <- taxify(c( # "Amanita muscaria", "Boletus edulis", "Trametes versicolor", # "Agaricus bisporus", "Cantharellus cibarius" # )) # # fungi |> add_funguild() # #> input_name trophic_mode guild funguild_growth_form confidence_ranking # #> 1 Amanita muscaria Symbiotroph Ectomycorrhizal Agaricoid Highly Probable # #> 2 Boletus edulis Symbiotroph Ectomycorrhizal Boletoid Highly Probable # #> 3 Trametes versicolor Saprotroph Wood Saprotroph Polyporoid Highly Probable # #> 4 Agaricus bisporus Saprotroph Litter Saprotroph Agaricoid Highly Probable # #> 5 Cantharellus cibarius Symbiotroph Ectomycorrhizal Cantharelloid Highly Probable ## ----algae-traits------------------------------------------------------------- # seaweeds <- taxify(c( # "Fucus vesiculosus", "Ulva lactuca", "Laminaria digitata", # "Chondrus crispus", "Sargassum muticum" # )) # # seaweeds |> add_algae_traits() # #> input_name algae_body_size_cm algae_growth_form algae_calcification algae_tidal_zone ... # #> 1 Fucus vesiculosus 60.0 foliose none intertidal ... # #> 2 Ulva lactuca 30.0 foliose none intertidal ... # #> 3 Laminaria digitata 200.0 foliose none subtidal ... # #> 4 Chondrus crispus 15.0 foliose none intertidal ... # #> 5 Sargassum muticum 300.0 foliose none subtidal ... ## ----fish-traits-------------------------------------------------------------- # freshwater_fish <- taxify(c( # "Salmo trutta", "Esox lucius", "Cyprinus carpio", # "Perca fluviatilis", "Silurus glanis" # )) # # freshwater_fish |> add_fish_traits() # #> input_name fish_body_elongation fish_eye_size fish_oral_gape_position fish_body_lateral_shape ... # #> 1 Salmo trutta 0.22 0.08 0.42 0.18 ... # #> 2 Esox lucius 0.18 0.06 0.50 0.15 ... # #> 3 Cyprinus carpio 0.35 0.05 0.38 0.25 ... # #> 4 Perca fluviatilis 0.30 0.07 0.40 0.22 ... # #> 5 Silurus glanis 0.15 0.03 0.48 0.12 ... ## ----fishbase----------------------------------------------------------------- # fish <- taxify(c( # "Gadus morhua", "Thunnus thynnus", "Hippocampus hippocampus", # "Squalus acanthias", "Salmo trutta" # )) # # fish |> add_fishbase() # #> input_name fb_body_length_cm fb_body_mass_g fb_trophic_level fb_depth_min_m fb_depth_max_m ... # #> 1 Gadus morhua 132.0 55500.0 4.4 0.0 600.0 ... # #> 2 Thunnus thynnus 458.0 684000.0 4.2 0.0 1000.0 ... # #> 3 Hippocampus hippocampus 15.0 NA 3.1 1.0 60.0 ... # #> 4 Squalus acanthias 160.0 11000.0 4.3 16.0 900.0 ... # #> 5 Salmo trutta 140.0 50000.0 3.4 0.0 332.0 ... ## ----lizard-traits------------------------------------------------------------ # lizards <- taxify(c( # "Pogona vitticeps", "Lacerta agilis", "Iguana iguana", # "Varanus komodoensis", "Gekko gecko" # )) # # lizards |> add_lizard_traits() # #> input_name lizard_body_mass_g lizard_svl_mm lizard_tail_length_mm lizard_clutch_size ... # #> 1 Pogona vitticeps 350.0 230.0 250.0 18.0 ... # #> 2 Lacerta agilis 10.0 70.0 100.0 8.0 ... # #> 3 Iguana iguana 4000.0 450.0 700.0 35.0 ... # #> 4 Varanus komodoensis 70000.0 1500.0 1400.0 18.0 ... # #> 5 Gekko gecko 60.0 140.0 130.0 2.0 ... ## ----anage-------------------------------------------------------------------- # vertebrates <- taxify(c( # "Vulpes vulpes", "Aquila chrysaetos", "Crocodylus niloticus", # "Bufo bufo", "Salmo salar" # ), backend = c("col", "gbif")) # # vertebrates |> add_anage() # #> input_name max_longevity_yr anage_body_mass_g metabolic_rate_w ... # #> 1 Vulpes vulpes 15.2 5480.0 10.41 ... # #> 2 Aquila chrysaetos 46.0 4210.0 8.94 ... # #> 3 Crocodylus niloticus 44.0 242500.0 NA ... # #> 4 Bufo bufo 36.0 48.0 NA ... # #> 5 Salmo salar 13.0 3400.0 NA ... ## ----animaltraits------------------------------------------------------------- # arthropods <- taxify(c( # "Drosophila melanogaster", "Apis mellifera", # "Tenebrio molitor", "Gryllus campestris" # ), backend = c("col", "gbif")) # # arthropods |> add_animaltraits() # #> input_name animaltraits_body_mass_kg animaltraits_metabolic_rate_w # #> 1 Drosophila melanogaster 0.000001030 0.000000218 # #> 2 Apis mellifera 0.000100000 0.000012600 # #> 3 Tenebrio molitor 0.000140000 0.000004850 # #> 4 Gryllus campestris 0.000800000 NA ## ----leptraits---------------------------------------------------------------- # butterflies <- taxify(c( # "Vanessa cardui", "Pieris rapae", "Papilio machaon", # "Lycaena phlaeas", "Colias crocea" # ), backend = c("col", "gbif")) # # butterflies |> add_leptraits() # #> input_name wingspan_mm voltinism diapause_stage canopy_affinity ... # #> 1 Vanessa cardui 62.5 3.0 NA Open canopy ... # #> 2 Pieris rapae 47.5 4.0 pupa Open canopy ... # #> 3 Papilio machaon 75.0 2.0 pupa Open canopy ... # #> 4 Lycaena phlaeas 30.0 3.0 larva Open canopy ... # #> 5 Colias crocea 48.5 3.0 adult Open canopy ... ## ----arthropod-traits--------------------------------------------------------- # insects <- taxify(c( # "Abax parallelepipedus", "Pterostichus melanarius", # "Chorthippus parallelus", "Araneus diadematus" # ), backend = c("col", "gbif")) # # insects |> add_arthropod_traits() # #> input_name arthropod_body_size_mm arthropod_dispersal arthropod_voltinism arthropod_feeding_guild ... # #> 1 Abax parallelepipedus 18.5 0.01 1.0 carnivore ... # #> 2 Pterostichus melanarius 15.0 0.32 1.0 carnivore ... # #> 3 Chorthippus parallelus 17.0 0.10 1.0 herbivore ... # #> 4 Araneus diadematus 13.0 0.45 1.0 carnivore ... ## ----invasive-single---------------------------------------------------------- # plants <- taxify(c( # "Robinia pseudoacacia", "Ailanthus altissima", # "Impatiens glandulifera", "Quercus robur", # "Reynoutria japonica", "Solidago canadensis" # )) # # plants |> add_invasive_status(country = "AT") # #> input_name invasive_status # #> 1 Robinia pseudoacacia invasive # #> 2 Ailanthus altissima invasive # #> 3 Impatiens glandulifera invasive # #> 4 Quercus robur native # #> 5 Reynoutria japonica invasive # #> 6 Solidago canadensis invasive ## ----invasive-multi----------------------------------------------------------- # plants |> add_invasive_status(country = c("AT", "DE", "GB")) # #> input_name invasive_status_AT invasive_status_DE invasive_status_GB # #> 1 Robinia pseudoacacia invasive invasive invasive # #> 2 Ailanthus altissima invasive invasive introduced # #> 3 Impatiens glandulifera invasive invasive invasive # #> 4 Quercus robur native native native # #> 5 Reynoutria japonica invasive invasive invasive # #> 6 Solidago canadensis invasive invasive introduced ## ----invasive-filter---------------------------------------------------------- # result <- plants |> add_invasive_status(country = c("AT", "DE")) # # Species invasive in Austria but not in Germany # result[result$invasive_status_AT == "invasive" & # result$invasive_status_DE != "invasive", ] ## ----invasive-all------------------------------------------------------------- # plants |> add_invasive_status(country = "all") # # Adds invasive_status_AD, invasive_status_AE, ..., invasive_status_ZW ## ----alien-fr-single---------------------------------------------------------- # aliens <- taxify(c( # "Robinia pseudoacacia", "Ailanthus altissima", # "Impatiens glandulifera", "Quercus robur", # "Ambrosia artemisiifolia", "Solidago canadensis" # )) # # aliens |> add_alien_first_records(country = "AT") # #> input_name alien_first_record alien_first_record_source alien_first_record_reference # #> 1 Robinia pseudoacacia 1850 NOBANIS NOBANIS # #> 2 Ailanthus altissima 1870 NOBANIS NOBANIS # #> 3 Impatiens glandulifera 1900 NOBANIS NOBANIS # #> 4 Quercus robur NA # #> 5 Ambrosia artemisiifolia 1863 NOBANIS NOBANIS # #> 6 Solidago canadensis 1850 NOBANIS NOBANIS ## ----alien-fr-multi----------------------------------------------------------- # aliens |> add_alien_first_records(country = c("AT", "DE", "GB")) # #> input_name alien_first_record_AT alien_first_record_DE alien_first_record_GB ... # #> 1 Robinia pseudoacacia 1850 1630 1640 ... # #> 2 Ailanthus altissima 1870 1780 1751 ... # #> 3 Impatiens glandulifera 1900 1839 1855 ... ## ----alien-fr-long------------------------------------------------------------ # aliens |> # add_alien_first_records(country = c("AT", "DE", "GB")) |> # taxify_long() # #> input_name country_code alien_first_record alien_first_record_source ... # #> 1 Robinia pseudoacacia AT 1850 NOBANIS ... # #> 2 Ailanthus altissima AT 1870 NOBANIS ... # #> ... # #> 7 Robinia pseudoacacia DE 1630 Long (2003) ... # #> ... ## ----taxify-long-griis-------------------------------------------------------- # aliens |> # add_invasive_status(country = c("AT", "DE")) |> # taxify_long() ## ----taxify-long-combined----------------------------------------------------- # aliens |> # add_invasive_status(country = c("AT", "DE")) |> # add_alien_first_records(country = c("AT", "DE", "CH")) |> # taxify_long() ## ----wcvp-single-------------------------------------------------------------- # trees <- taxify(c( # "Quercus robur", "Quercus suber", "Eucalyptus globulus", # "Nothofagus pumilio", "Sequoiadendron giganteum" # )) # # trees |> add_wcvp(region = "EUR") # #> input_name native_status # #> 1 Quercus robur native # #> 2 Quercus suber native # #> 3 Eucalyptus globulus NA # #> 4 Nothofagus pumilio NA # #> 5 Sequoiadendron giganteum NA ## ----wcvp-multi--------------------------------------------------------------- # trees |> add_wcvp(region = c("EUR", "AUS", "SAM")) # #> input_name native_status_EUR native_status_AUS native_status_SAM # #> 1 Quercus robur native NA NA # #> 2 Quercus suber native NA NA # #> 3 Eucalyptus globulus NA native NA # #> 4 Nothofagus pumilio NA NA native # #> 5 Sequoiadendron giganteum NA NA NA ## ----glonaf------------------------------------------------------------------- # plants <- taxify(c( # "Robinia pseudoacacia", "Ailanthus altissima", # "Impatiens glandulifera", "Quercus robur" # )) # # plants |> add_glonaf(region = "EUR") # #> input_name naturalized # #> 1 Robinia pseudoacacia 1 # #> 2 Ailanthus altissima 1 # #> 3 Impatiens glandulifera 1 # #> 4 Quercus robur NA ## ----common-names-en---------------------------------------------------------- # species <- taxify(c( # "Quercus robur", "Parus major", "Vulpes vulpes", # "Bufo bufo", "Picea abies" # )) # # species |> add_common_names() # #> input_name common_name # #> 1 Quercus robur Pedunculate Oak # #> 2 Parus major Great Tit # #> 3 Vulpes vulpes Red Fox # #> 4 Bufo bufo Common Toad # #> 5 Picea abies Norway Spruce ## ----common-names-de---------------------------------------------------------- # species |> add_common_names(lang = "de") # #> input_name common_name # #> 1 Quercus robur Stieleiche # #> 2 Parus major Kohlmeise # #> 3 Vulpes vulpes Rotfuchs # #> 4 Bufo bufo Erdkroete # #> 5 Picea abies Gemeine Fichte ## ----stacking-plants---------------------------------------------------------- # library(taxify) # # plant_result <- taxify(c( # "Quercus robur", "Fagus sylvatica", "Picea abies", # "Arrhenatherum elatius", "Festuca rubra", "Plantago lanceolata" # )) |> # add_conservation_status() |> # add_woodiness() |> # add_eive() |> # add_diaz_traits() ## ----stacking-birds----------------------------------------------------------- # bird_result <- taxify(c( # "Parus major", "Cyanistes caeruleus", "Erithacus rubecula", # "Turdus merula", "Falco peregrinus" # )) |> # add_conservation_status() |> # add_avonet() |> # add_elton_traits() |> # add_common_names() ## ----stacking-mammals--------------------------------------------------------- # mammal_result <- taxify(c( # "Vulpes vulpes", "Canis lupus", "Ursus arctos", # "Lutra lutra", "Lynx lynx" # )) |> # add_conservation_status() |> # add_pantheria() |> # add_elton_traits() |> # add_common_names(lang = "de") ## ----stacking-fungi----------------------------------------------------------- # fungal_result <- taxify(c( # "Amanita muscaria", "Boletus edulis", "Trametes versicolor" # )) |> # add_conservation_status() |> # add_fungal_traits() |> # add_funguild() ## ----stacking-fish------------------------------------------------------------ # fish_result <- taxify(c( # "Salmo trutta", "Esox lucius", "Gadus morhua" # )) |> # add_conservation_status() |> # add_fish_traits() |> # add_fishbase() ## ----coverage-example--------------------------------------------------------- # mixed <- taxify(c( # "Quercus robur", # plant # "Parus major", # bird # "Vulpes vulpes", # mammal # "Bufo bufo", # amphibian # "Amanita muscaria", # fungus # "Salmo trutta" # fish # )) # # mixed |> # add_woodiness() |> # add_avonet() |> # add_pantheria() |> # add_amphibio() |> # add_fungal_traits() |> # add_fishbase() # #> input_name woodiness beak_length pantheria_body_mass_g body_size_mm primary_lifestyle fb_trophic_level ... # #> 1 Quercus robur woody NA NA NA NA ... # #> 2 Parus major NA 11.2 NA NA NA ... # #> 3 Vulpes vulpes NA NA 5480.0 NA NA ... # #> 4 Bufo bufo NA NA NA 150.0 NA ... # #> 5 Amanita muscaria NA NA NA NA ectomycorrhizal NA ... # #> 6 Salmo trutta NA NA NA NA 3.4 ... ## ----coverage-check----------------------------------------------------------- # result <- taxify(species_list) |> add_woodiness() # # Fraction of matched species with woodiness data # mean(!is.na(result$woodiness[!is.na(result$accepted_name)])) ## ----summary-enrichments------------------------------------------------------ # result <- taxify(c("Quercus robur", "Fagus sylvatica", "Pinus sylvestris")) |> # add_conservation_status() |> # add_woodiness() |> # add_eive() # # summary(result) # #> -- taxify results -------------------------------------------------------- # #> backend: WFO v2024.12 | 3 names submitted # #> # #> matched 3 (exact: 3, case-insensitive: 0, fuzzy: 0) # #> -------------------------------------------------------- # #> taxon groups: plant: 3 # #> # #> enrichments: # #> conservation_status (IUCN Red List 2025.1) -- 3 of 3 matched # #> woodiness (Zanne et al. 2014 1.0) -- 3 of 3 matched # #> eive (EIVE 1.0 2023.1) -- 3 of 3 matched ## ----guide-euro-plants-------------------------------------------------------- # result <- taxify(species_list, backend = "wfo") |> # add_conservation_status() |> # add_woodiness() |> # add_eive() |> # add_diaz_traits() |> # add_leda() |> # add_wcvp(region = "EUR") |> # add_common_names() ## ----guide-global-plants------------------------------------------------------ # result <- taxify(species_list, backend = "wfo") |> # add_conservation_status() |> # add_woodiness() |> # add_diaz_traits() |> # add_wcvp(region = c("NAM", "SAM", "AFR")) |> # add_common_names() ## ----guide-birds-------------------------------------------------------------- # result <- taxify(species_list, backend = "col") |> # add_conservation_status() |> # add_avonet() |> # add_elton_traits() |> # add_common_names() ## ----guide-mammals------------------------------------------------------------ # result <- taxify(species_list, backend = "col") |> # add_conservation_status() |> # add_pantheria() |> # add_elton_traits() |> # add_common_names() ## ----guide-amphibians--------------------------------------------------------- # result <- taxify(species_list, backend = "col") |> # add_conservation_status() |> # add_amphibio() |> # add_common_names() ## ----guide-fish--------------------------------------------------------------- # result <- taxify(species_list, backend = "worms") |> # add_conservation_status() |> # add_fish_traits() |> # add_fishbase() |> # add_common_names() ## ----guide-lizards------------------------------------------------------------ # result <- taxify(species_list, backend = "col") |> # add_conservation_status() |> # add_lizard_traits() |> # add_common_names() ## ----guide-butterflies-------------------------------------------------------- # result <- taxify(species_list, backend = "col") |> # add_conservation_status() |> # add_leptraits() |> # add_common_names() ## ----guide-arthropods--------------------------------------------------------- # result <- taxify(species_list, backend = c("col", "gbif")) |> # add_conservation_status() |> # add_arthropod_traits() |> # add_animaltraits() |> # add_common_names() ## ----guide-fungi-------------------------------------------------------------- # result <- taxify(species_list, backend = "col") |> # add_conservation_status() |> # add_fungal_traits() |> # add_funguild() |> # add_common_names() ## ----guide-algae-------------------------------------------------------------- # result <- taxify(species_list, backend = "worms") |> # add_conservation_status() |> # add_algae_traits() |> # add_common_names() ## ----guide-mixed-all---------------------------------------------------------- # result <- taxify(species_list) |> # add_conservation_status() |> # add_woodiness() |> # add_avonet() |> # add_pantheria() |> # add_amphibio() |> # add_elton_traits() ## ----guide-mixed-split-------------------------------------------------------- # result <- taxify(species_list) # # plants <- result[result$kingdom == "Plantae", ] # birds <- result[result$family %in% bird_families, ] # mammals <- result[result$family %in% mammal_families, ] # # plants <- plants |> add_woodiness() |> add_eive() # birds <- birds |> add_avonet() |> add_elton_traits() # mammals <- mammals |> add_pantheria() |> add_elton_traits() ## ----add-data-csv------------------------------------------------------------- # result <- taxify(c("Quercus robur", "Pinus sylvestris", "Fagus sylvatica")) # # # From a CSV file (auto-detect species column) # result |> add_data("my_traits.csv") ## ----add-data-df-------------------------------------------------------------- # # From a data.frame with explicit species column # my_traits <- data.frame( # species = c("Quercus robur", "Pinus sylvestris", "Fagus sylvatica"), # bark_thickness_mm = c(25, 15, 8), # shade_tolerance = c(0.6, 0.3, 0.8) # ) # result |> add_data(my_traits, species_col = "species")