Search FishLife Taxonomy for the Closest Species Match

Matches taxonomic inputs against the ParentChild_gz taxonomy tree in the FishLife database, returning the row number(s) of the closest ancestor match. Ported and adapted from the FishLife package by James Thorson.

Usage

search_species(
  Class = "predictive",
  Order = "predictive",
  Family = "predictive",
  Genus = "predictive",
  Species = "predictive",
  add_ancestors = TRUE,
  Database = marlin::FishBase_and_RAM,
  ParentChild_gz = Database$ParentChild_gz
)

Arguments

Class: Character. Taxonomic class. Default "predictive".
Order: Character. Taxonomic order. Default "predictive".
Family: Character. Taxonomic family. Default "predictive".
Genus: Character. Genus name. Default "predictive".
Species: Character. Species epithet. Default "predictive".
add_ancestors: Logical. If TRUE (default), returns row indices for all ancestor taxa as well as the matched taxon. Used by FishLife's hierarchical prediction.
Database: List. The FishLife database to search; defaults to marlin::FishBase_and_RAM.
ParentChild_gz: Data frame. The parent-child taxonomy table from Database; extracted automatically.

Value

A named list with three elements:

GroupNum: Integer vector of row indices in ParentChild_gz for the matched taxon and its ancestors.
match_taxonomy: Character vector of matched taxon strings (in "Genus_Species_predictive_..." format).
closest_match: Character. The best-matching taxon string.

Details

The function queries WORMS (World Register of Marine Species) via taxize to resolve the full taxonomy for the supplied genus/species, then sweeps from Order down to Species looking for the closest match in FishLife's ParentChild_gz. Unspecified levels are padded with "predictive" and the function falls back to the nearest ancestor if an exact species match is not found.

This function requires an internet connection. It is called internally by get_traits and create_critter.

References

Thorson, J.T. (FishLife R package). https://github.com/James-Thorson-NOAA/FishLife