Explore the taxonomic hierarchy

Here we present a practical guide to the funga_get_children_taxa() function of the fungaR package. It retrieves all child taxa — species, subspecies, varieties, and so on — below a given taxonomic name and rank, which is useful for getting every species in a genus, every genus in an order, and similar hierarchy traversals.

Function Overview

funga_get_children_taxa() first locates the parent taxon in the Flora e Funga do Brasil (FFB) checklist, then returns every taxon whose lineage includes that parent’s taxon ID. Fungi are classified in FFB by Division (phylum-equivalent, e.g. Ascomycota, Basidiomycota) rather than Class, and FFB does not register a standalone family-rank taxon record for Fungi — rank = "family" is still supported, but matched directly against the family classification column on genus/species records instead of walking a family-rank row.

Arguments

Argument Description
taxon_name Character. Scientific name to search for (e.g. "Trichoderma", "Xylariaceae", "Agaricales").
rank Character. Taxonomic rank of taxon_name: "division", "order", "family", "genus", or "species". Default "genus".
child_rank Character or NULL. Rank(s) to return as children. NULL (default) returns all descendant ranks; a single rank (e.g. "species") restricts the result to that rank only. Requesting child_rank = "family" from a division/order returns a derived summary (family name, order, and genus count) rather than real FFB rows, since none exist for Fungi.
include_synonyms Logical. If TRUE, includes synonym names in addition to accepted ones. Default FALSE.
version FFB dataset version to use. Defaults to "latest".
rm_funga_database If TRUE, deletes the cached database after the search. Default FALSE is recommended for repeated use.
verbose Logical. If TRUE (default), prints progress messages.

Get all species in a genus

library(fungaR)

species <- funga_get_children_taxa(taxon_name = "Trichoderma",
                                   rank = "genus",
                                   child_rank = "species")

Get every descendant of a genus

Species, subspecies, and varieties together:

all_descendants <- funga_get_children_taxa(taxon_name = "Trichoderma",
                                           rank = "genus",
                                           child_rank = NULL)

Get all genera in a family, including synonyms

Matched via the family classification column, since FFB has no family-rank row for Fungi:

genera <- funga_get_children_taxa(taxon_name = "Xylariaceae",
                                  rank = "family",
                                  child_rank = "genus",
                                  include_synonyms = TRUE)

Get all genera in an order

genera_in_order <- funga_get_children_taxa(taxon_name = "Agaricales",
                                            rank = "order",
                                            child_rank = "genus")

Additional Tips

  • Set child_rank = NULL when you want a complete picture of a group’s diversity, including infraspecific taxa; set it to a single rank (e.g. "species") when you specifically need a species-level checklist for downstream work.
  • rank must correctly describe taxon_name (e.g. don’t pass a genus name with rank = "order") — the function looks up the parent by matching both together.
  • Combine with funga_records() when you need geographic or trait filters in addition to hierarchy traversal (e.g. all species in a genus that are also endemic to a given state).

See Also