Query traits at the taxonomic level — query_taxa

Retrieves trait measurements associated with taxa, with automatic resolution of taxonomic synonyms. Traits linked to synonyms are consolidated under the accepted taxon name.

Usage

query_taxa_traits(
  idtax = NULL,
  include_synonyms = TRUE,
  add_taxa_info = FALSE,
  trait_ids = NULL,
  categorical_mode = c("mode", "concat"),
  format = c("wide", "long"),
  include_remarks = FALSE,
  include_measurement_features = FALSE,
  include_citation = FALSE,
  con = NULL,
  con_taxa = NULL,
  backbone = c("internal", "wcvp")
)

Arguments

idtax: Vector of taxon IDs to query
include_synonyms: If TRUE, includes traits from all synonyms
add_taxa_info: Add taxonomic information (family, genus, species)
trait_ids: Vector of trait IDs to filter (NULL = all traits)
categorical_mode: How to aggregate categorical traits: "mode" (most frequent) or "concat" (all unique values)
format: Output format: "wide" (pivoted) or "long" (raw measurements)
include_remarks: Include measurement remarks
include_measurement_features: Add measurement-level features/metadata
con: Connection to main database (optional, defaults to call.mydb()). Used for trait measurements (taxa_traits_measures, traitlist).
con_taxa: Connection to taxa database (optional, defaults to call.mydb.taxa()). Used for synonym resolution (table_taxa) and taxonomic info enrichment.
backbone: Character. Which taxonomic backbone to use for synonym resolution. "internal" (default) uses the internal table_taxa. "wcvp" uses WCVP via wcvp_idtax_link and wcvp_names, falling back to internal for unlinked taxa.

Value

List with components: - traits_raw: Raw trait measurements with resolved taxonomy - traits_numeric: Numeric traits (aggregated if format="wide") - traits_categorical: Categorical traits (aggregated if format="wide")