List, extract taxa

Query taxa from the taxonomic backbone database using hierarchical matching. For species queries, if exact matching fails, the function automatically falls back to intelligent fuzzy matching. For higher taxonomic ranks (family, genus, order), exact matching is used by default.

Usage

query_taxa(
  class = NULL,
  family = NULL,
  genus = NULL,
  order = NULL,
  species = NULL,
  only_genus = FALSE,
  only_family = FALSE,
  only_class = FALSE,
  ids = NULL,
  verbose = TRUE,
  exact_match = TRUE,
  check_synonymy = TRUE,
  extract_traits = TRUE,
  min_similarity = 0.3
)

Arguments

class

character string of class

family

string or character vector of family names

genus

string or character vector of genus names

order

string or character vector of order names

species

string or character vector of full species names (genus + species)

only_genus

logical whether to return only genus-level taxa

only_family

logical whether to return only family-level taxa

only_class

logical whether to return only class-level taxa

ids

integer vector of idtax_n to retrieve directly

verbose

logical whether to show progress messages

exact_match

logical if TRUE (default), only exact matches returned. If FALSE, uses intelligent fuzzy matching. Note: fuzzy matching is generally only useful for species names; for family/genus/order queries, exact matching is recommended.

check_synonymy

logical whether to resolve synonyms and include them

extract_traits

logical whether to add trait information

min_similarity

numeric (0-1) minimum similarity score for fuzzy matching (default: 0.3)

tax_nam01

string (currently not used in matching)

tax_nam02

string (currently not used in matching)

Value

A tibble of all taxa

A tibble of taxa with taxonomic hierarchy and optionally traits

Author

Gilles Dauby, gilles.dauby@ird.fr