get_taxonomies.species_binomials {LocaTT}

Get NCBI Taxonomies from Species Binomials

Description

Remotely fetches taxonomies from the NCBI taxonomy database for a list of species binomials.

Usage

get_taxonomies.species_binomials(
  path_to_input_species_binomials,
  path_to_output_local_taxa_list,
  path_to_taxonomy_edits = NA,
  print_taxize_queries = TRUE
)

Arguments

path_to_input_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_local_taxa_list

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_taxize_queries

Logical. Whether taxa queries should be printed. The default is TRUE.

Value

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

See Also

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

Examples

# Get path to example input species binomials CSV file.
path_to_input_file<-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_input_species_binomials=path_to_input_file,
                                 path_to_output_local_taxa_list=path_to_output_file,
                                 print_taxize_queries=FALSE)