Add fungal lifestyle and trait data (FungalTraits)

Joins FungalTraits (Polme et al. 2020) genus-level trait data to a taxify() result by looking up genus. Unlike other enrichments that join on species-level accepted_name, FungalTraits is a genus-level database and joins on the genus column already present in taxify output.

Usage

add_fungal_traits(x, verbose = TRUE)

Arguments

x: A data.frame returned by taxify().
verbose: Logical. Default TRUE.

Value

The same data.frame with additional columns:

primary_lifestyle: Primary ecological role (e.g., saprotroph, mycorrhizal, pathogen, endophyte, lichenized, parasite).
secondary_lifestyle: Secondary ecological role, if any.
growth_form: Morphological growth form (e.g., agaricoid, corticioid, polyporoid, yeast).
fruitbody_type: Fruiting body morphology (e.g., gasteroid, pileate, resupinate).
decay_substrate: Substrate type for saprotrophic genera (e.g., wood, litter, dung, soil).
plant_pathogenic_capacity: Capacity to cause plant disease (e.g., high, medium, low, none).
animal_biotrophic_capacity: Capacity for animal biotrophy.
endophytic_interaction_capability: Capacity for endophytic interactions with plants.
ectomycorrhiza_exploration_type: Exploration type for ectomycorrhizal genera (e.g., contact, short, medium, long).

Details

Source: FungalTraits (Polme et al. 2020, Fungal Diversity, CC BY 4.0). Coverage: ~10k fungal genera. Genus-level only (not species-level).

References

Polme S et al. (2020) FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity 105:1-16. doi:10.1007/s13225-020-00466-2

Examples

# Runs offline against the bundled example database.
old <- options(taxify.data_dir = taxify_example_data())

taxify("Amanita muscaria", backend = "gbif") |>
  add_fungal_traits()

options(old)