Add fungal host breadth (USDA Fungus-Host Dataset) — add_usda_fungus

Joins per-fungus host breadth from the USDA National Fungus Collections Fungus-Host Dataset to a taxify() result by looking up accepted_name. Each fungus species is summarised by how many distinct host plants and host plant genera it has been recorded on.

Usage

add_usda_fungus_host(x, cols = NULL, verbose = TRUE)

Arguments

x: A data.frame returned by taxify().
cols: Which columns to attach: NULL (default) the curated set, "all" every column the source carries, or a character vector of names. See enrichment_cols.
verbose: Logical. Default TRUE.

Value

The same data.frame with additional columns:

fungus_host_count: Number of distinct host plant species recorded.
fungus_host_genus_count: Number of distinct host plant genera recorded.

Details

Source: Farr, Rossman & Castlebury (2021) United States National Fungus Collections Fungus-Host Dataset, Ag Data Commons (U.S. Public Domain). Fungi only; ~99k species with at least one recorded host.

References

Farr DF, Rossman AY, Castlebury LA (2021) United States National Fungus Collections Fungus-Host Dataset. Ag Data Commons. doi:10.15482/USDA.ADC/1524414

Examples

if (FALSE) { # \dontrun{
taxify("Puccinia graminis", backbone = "gbif") |>
  add_usda_fungus_host()
} # }