get_taxonomies.IUCN: Get Taxonomies from IUCN Red List Files

In LocaTT: Geographically-Conscious Taxonomic Assignment for Metabarcoding

Get Taxonomies from IUCN Red List Files

Description

Formats taxonomies from IUCN Red List taxonomy.csv and common_names.csv files for use with the local_taxa_tool function.

Usage

get_taxonomies.IUCN(
  path_to_taxonomies,
  path_to_common_names,
  path_to_output_file,
  domain = "Eukaryota",
  path_to_taxonomy_edits = NA,
  ...
)

Arguments

path_to_taxonomies	String specifying path to input IUCN Red List taxonomy.csv file.
path_to_common_names	String specifying path to input IUCN Red List common_names.csv file.
path_to_output_file	String specifying path to output species list (in CSV format) with formatted taxonomies.
domain	String specifying the domain name to use for all species. The IUCN Red List files do not include domain information, so a domain name must be provided. If using a reference database from UNITE, provide a kingdom name here (e.g., 'Fungi'). The default is 'Eukaryota'.
path_to_taxonomy_edits	String specifying path to taxonomy edits file in CSV format. The file must contain the following fields: 'Old_Taxonomy', 'New_Taxonomy', 'Notes'. Old taxonomies are replaced with new taxonomies in the order the records appear in the file. The taxonomic levels in the 'Old_Taxonomy' and 'New_Taxonomy' fields should be delimited by a semi-colon. If no taxonomy edits are desired, then set this variable to NA (the default).
...	Accepts former argument names for backwards compatibility.

Value

No return value. Writes an output CSV file with formatted taxonomies.

See Also

get_taxonomies.species_binomials for remotely fetching NCBI taxonomies from species binomials.

adjust_taxonomies for adjusting a taxonomy system.

Examples

# Get path to example taxonomy CSV file.
path_to_taxonomies<-system.file("extdata",
                                "example_taxonomy.csv",
                                package="LocaTT",
                                mustWork=TRUE)

# Get path to example common names CSV file.
path_to_common_names<-system.file("extdata",
                                  "example_common_names.csv",
                                  package="LocaTT",
                                  mustWork=TRUE)

# Create a temporary file path for the output CSV file.
path_to_output_file<-tempfile(fileext=".csv")

# Format common names and taxonomies.
get_taxonomies.IUCN(path_to_taxonomies=path_to_taxonomies,
                    path_to_common_names=path_to_common_names,
                    path_to_output_file=path_to_output_file)

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