adjust_taxonomies: Adjust Taxonomies

In LocaTT: Geographically-Conscious Taxonomic Assignment for Metabarcoding

Adjust Taxonomies

Description

Performs adjustments to a taxonomy system according to a taxonomy edits file.

Usage

adjust_taxonomies(
  path_to_input_file,
  path_to_output_file,
  path_to_taxonomy_edits
)

Arguments

path_to_input_file	String specifying path to list of species (in CSV format) whose taxonomies are to be adjusted. The file should contain the following fields: 'Common_Name', 'Domain', 'Phylum', 'Class', 'Order', 'Family', 'Genus', 'Species'. There should be no NAs or blanks in the taxonomy fields, and the species field should contain the binomial name. Additional fields may be present in the input file, and fields can be in any order.
path_to_output_file	String specifying path to output species list with adjusted taxonomies. The output file will be in CSV format.
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.

Value

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

See Also

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

get_taxonomies.IUCN for formatting taxonomies from the IUCN Red List.

Examples

# Get path to input file.
path_to_input_file<-system.file("extdata",
                                "example_local_taxa_list.csv",
                                package="LocaTT",
                                mustWork=TRUE)

# Get path to taxonomy edits.
path_to_taxonomy_edits<-system.file("extdata",
                                    "example_taxonomy_edits.csv",
                                    package="LocaTT",
                                    mustWork=TRUE)

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

# Adjust taxonomies.
adjust_taxonomies(path_to_input_file=path_to_input_file,
                  path_to_output_file=path_to_output_file,
                  path_to_taxonomy_edits=path_to_taxonomy_edits)

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