Search_species: Search species

In James-Thorson/FishLife: Predict Life History Parameters For Any Fish

Search species

Description

Match taxonomic inputs to a given row of ParentChild_gz or its closest ancestor

Usage

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

Arguments

Class	Character input for taxonomic class
Order	Character input for taxonomic class
Family	Character input for taxonomic class
Genus	Character input for taxonomic class
Species	Character input for taxonomic class
add_ancestors	Boolean whether to add ancestors for matching species or not
ParentChild_gz	vector providing index of parent-taxon for every child-taxa

Details

This function attempts to do a smart match to elements of ParentChild_gz. It sweeps from Order to Species and ignores any taxonomic input listed as "predictive" until it finds something else. It then appends "predictive" to any lower taxonomic level that is missing, and checks whether this specification yields a single, unique taxon. If it does, it then returns the row number and potentially any ancestors (higher taxonomic levels)

Value

integer of row numbers of ParentChild_gz matching genus_species

James-Thorson/FishLife documentation built on Feb. 29, 2024, 3:47 a.m.