Taxa

pbdb_taxon(; kwargs...)

Get information about a single taxonomic name (by name or id).

Arguments

• kwargs...: One of the following must be provided (but not both):
  • name: Taxonomic name string; % and _ may be used as wildcards.
  • id: PBDB identifier (integer or extended identifier).
  Additional options:
  • show: Extra blocks (e.g. "attr" attribution, "app" first/last appearance, "size" number of subtaxa).
  • vocab: Vocabulary for field names ("pbdb" for full names, "com" for compact).

Returns

A DataFrame with information about the selected taxon.

Examples

pbdb_taxon(name = "Canis"; show = ["attr", "app", "size"])

pbdb_taxa(; kwargs...)

Get information about multiple taxonomic names.

Arguments

• kwargs...: Filtering and output parameters. Common options include:
  • name: Name string (wildcards allowed).
  • id: Identifier (vector allowed).
  • rel: Relationship selector (e.g. "synonyms", "children", "all_children", "all_parents", "common").
  • extant: Logical, select only extant or non-extant taxa.
  • show: Extra blocks ("attr", "app", "size", "class").
  • vocab: Vocabulary for field names.

Returns

A DataFrame of taxa matching the query.

Examples

pbdb_taxa(name = "Canidae"; rel = "all_parents", show = ["attr", "app", "size", "class"])

pbdb_taxa_auto(; kwargs...)

Autocomplete: list of taxonomic names matching a prefix or partial name.

Arguments

• kwargs...: Common options include:
  • name: A partial name or prefix (at least 3 significant characters).
  • limit: Maximum number of matches to return.

Returns

A DataFrame of candidate taxonomic names, including rank and occurrence counts. This endpoint returns JSON in PBDB; the wrapper converts to a DataFrame.

Examples

pbdb_taxa_auto(name = "Cani"; limit = 10)

pbdb_ref_taxa(; kwargs...)

Get bibliographic references associated with taxonomic names.

This mirrors pbdb_taxa filters but returns reference records instead of taxa.

Arguments

• kwargs...: Accepts the same taxon selectors as pbdb_taxa, e.g.:
  • name or id: Base taxon.
  • rel: Relationship (e.g. "synonyms", "children", "allchildren", "allparents").
  • extant: Logical; restrict to extant/non-extant taxa.
  • show: Extra blocks (e.g. "both", "comments").
  • vocab: Field naming vocabulary.

Returns

A DataFrame with references linked to the selected taxa.

Examples

pbdb_ref_taxa(name = "Canidae"; show = ["both", "comments"])

pbdb_opinions_taxa(; kwargs...)

Get taxonomic opinions about taxa, used to build the PBDB taxonomic hierarchy.

Arguments

• kwargs...: Filtering options, e.g.:
  • base_name: Taxon (and descendants).
  • name or id: Base taxon selector.
  • rel: Relationship filter (e.g. "synonyms", "children").
  • vocab: Vocabulary for field names.

Returns

A DataFrame with taxonomic opinions for the selected taxa.

Examples

pbdb_opinions_taxa(base_name = "Canis")