get_taxonomies.species_binomials: Get NCBI Taxonomies from Species Binomials

In LocaTT: Geographically-Conscious Taxonomic Assignment for Metabarcoding

Get NCBI Taxonomies from Species Binomials

Description

Remotely fetches taxonomies from the NCBI taxonomy database for a list of species binomials. Installation of the taxize package is required to use this function.

Usage

get_taxonomies.species_binomials(
  path_to_species_binomials,
  path_to_output_file,
  path_to_taxonomy_edits = NA,
  print_queries = TRUE,
  ...
)

Arguments

path_to_species_binomials	String specifying path to input species list with common and scientific names. The file should be in CSV format and contain the following fields: 'Common_Name', 'Scientific_Name'. Values in the 'Common_Name' field are optional. Values in the 'Scientific_Name' field are required.
path_to_output_file	String specifying path to output species list with added NCBI 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. If no taxonomy edits are desired, then set this variable to NA (the default).
print_queries	Logical. Whether taxa queries should be printed. The default is TRUE.
...	Accepts former argument names for backwards compatibility.

Value

No return value. Writes an output CSV file with added taxonomies. Species which could not be found in the NCBI taxonomy database appear in the top records of the output file.

See Also

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

adjust_taxonomies for adjusting a taxonomy system.

Examples

# Get path to example input species binomials CSV file.
path_to_species_binomials<-system.file("extdata",
                                       "example_species_binomials.csv",
                                       package="LocaTT",
                                       mustWork=TRUE)

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

# Fetch taxonomies from species binomials.
get_taxonomies.species_binomials(path_to_species_binomials=path_to_species_binomials,
                                 path_to_output_file=path_to_output_file,
                                 print_queries=FALSE)

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