get_taxonomies.IUCN {LocaTT}

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_IUCN_taxonomies,
  path_to_IUCN_common_names,
  path_to_output_local_taxa_list,
  domain_name = "Eukaryota",
  path_to_taxonomy_edits = NA
)

Arguments

path_to_IUCN_taxonomies

String specifying path to input IUCN Red List taxonomy.csv file.

path_to_IUCN_common_names

String specifying path to input IUCN Red List common_names.csv file.

path_to_output_local_taxa_list

String specifying path to output species list (in CSV format) with formatted taxonomies.

domain_name

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).

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.

Examples

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

# Get path to example common names CSV file.
path_to_common_names_file<-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_IUCN_taxonomies=path_to_taxonomy_file,
                    path_to_IUCN_common_names=path_to_common_names_file,
                    path_to_output_local_taxa_list=path_to_output_file)