expand_taxonomies: Expand Taxonomies

In LocaTT: Geographically-Conscious Taxonomic Assignment for Metabarcoding

Expand Taxonomies

Description

Extracts each taxonomic level from a vector of taxonomic strings.

Usage

expand_taxonomies(
  taxonomies,
  levels = c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  full_names = TRUE,
  delimiter = ";",
  ignore
)

Arguments

taxonomies	A character vector of taxonomic strings.
levels	A character vector of taxonomic level names. The length of levels determines the number of taxonomic levels to extract from the taxonomies, and the order of elements in levels is assumed to match the order of taxonomic levels in the taxonomies. levels is also used as the field names of the returned data frame (see return value section). The default vector includes: "Domain", "Phylum", "Class", "Order", "Family", "Genus", and "Species".
full_names	Logical. If TRUE (the default), then full taxonomies are returned down to the extracted taxonomic level. If FALSE, then only the extracted taxonomic level is returned.
delimiter	A character string of the delimiter between taxonomic levels in the input taxonomies. The default is ";".
ignore	An optional character vector of taxonomic strings for which taxonomic expansion will be skipped. In the returned data frame (see return value section), the record for each skipped taxonomic string will be filled with NAs.

Value

Returns a data frame of extracted taxonomic levels. One record for each element of taxonomies, and one field for each element of levels. Field names are inherited from levels. If a taxonomic level is not present in a taxonomic string, then the respective cell in the returned data frame will contain NA.

See Also

get_taxonomic_level for extracting a taxonomic level from taxonomic strings.

get_consensus_taxonomy for generating a consensus taxonomy from taxonomic strings.

Examples

expand_taxonomies(taxonomies=
   c("Eukaryota;Chordata;Amphibia;Caudata;Ambystomatidae;Ambystoma;Ambystoma mavortium",
     "Eukaryota;Chordata;Amphibia;Anura;Bufonidae;Anaxyrus;Anaxyrus boreas",
     "Eukaryota;Chordata;Amphibia;Anura;Ranidae;Rana;Rana luteiventris"),
                       full_names=FALSE,
                       delimiter=";")

LocaTT documentation built on June 14, 2026, 1:06 a.m.