Add mycorrhizal type from FungalRoot — add

Joins genus-level mycorrhizal type from the FungalRoot database (Soudzilovskaia et al. 2020) to a taxify() result by looking up genus. Mycorrhizal type is phylogenetically conserved at the genus level, which is the resolution FungalRoot recommends for inference, so this enrichment joins on genus rather than accepted_name.

Usage

add_fungalroot(x, verbose = TRUE)

Arguments

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

Value

The same data.frame with three additional columns:

mycorrhizal_type: Genus-level majority-consensus type, one of AM (arbuscular), EcM (ecto), ErM (ericoid), OM (orchid), NM (non-mycorrhizal), the dual types EcM-AM / ErM-EcM / ErM-AM, Other, or uncertain. NA if the genus is not in FungalRoot.
mycorrhizal_status: Coarse status derived from the type: "mycorrhizal", "non-mycorrhizal", or "uncertain".
mycorrhizal_records: Number of FungalRoot observations supporting the genus-level consensus.

Details

Source: FungalRoot, published on GBIF as a Darwin Core Archive (doi:10.15468/a7ujmj ), CC BY-NC 4.0. The per-genus value is a majority consensus computed from the per-observation mycorrhiza type labels, not FungalRoot's own published per-genus assignment. Plant genera only. The .vtr is downloaded from the taxify release on first use and cached.

References

Soudzilovskaia NA et al. (2020) FungalRoot: global online database of plant mycorrhizal associations. New Phytologist 227:955-966.

Examples

# \donttest{
# Joins on genus, so any species in a covered genus is annotated.
taxify(c("Quercus robur", "Trifolium pratense")) |>
  add_fungalroot()
# }