Create Taxonomic Coverage — create_taxonomic

Create the taxonomic coverage information of a dataset based off of EML standards. The addition of taxonomic coverage is (Optional), however defaults of chinook, sturgeon, smelt, and steelhead are provided. While single or multiple taxonomies can be applied, the full set of information must be provided if chosen to be included.

create_taxonomic_coverage(
  CVPIA_common_species = NULL,
  kingdom = "kingdom",
  kingdom_value = NULL,
  phylum = "phylum",
  phylum_value = NULL,
  class = "class",
  class_value = NULL,
  order = "order",
  order_value = NULL,
  family = "family",
  family_value = NULL,
  genus = "genus",
  genus_value = NULL,
  species = "species",
  species_value = NULL,
  common_name = NULL,
  taxon_id = NULL
)

Arguments

CVPIA_common_species: Use one of the following from the helper data CVPIA_common_species: "chinook", "delta_smelt", "white_sturgeon", "green_sturgeon", or "steelhead" to get pre-selected information from ITIS.
kingdom: Kingdom level present.
kingdom_value: The kingdom name.
phylum: Phylum level present.
phylum_value: The phylum name.
class: Class level present.
class_value: The class level name.
order: Order level present.
order_value: The order level name.
family: Family level present.
family_value: The family level name.
genus: Genus level present.
genus_value: The genus level name.
species: Species level present.
species_value: The species level name.
common_name: The common name of the organism.
taxon_id: (Optional). The taxonomic serial number provided by ITIS.

Value

Taxonomic coverage information. The function should be assigned to the name taxonomic_coverage to append it to the dataset or project. Example of how to incorporate it into the add_coverage function is seen below.

CVPIA Common Species

The following frequently cited species are available for convenience:

EMLaide::CVPIA_common_species$chinook - Oncorhynchus tshawytscha (ITIS: 161980)
EMLaide::CVPIA_common_species$steelhead - Oncorhynchus mykiss (ITIS: 161989)
EMLaide::CVPIA_common_species$delta_smelt - Hypomesus transpacificus (ITIS: 162032)
EMLaide::CVPIA_common_species$white_sturgeon - Acipenser transmontanus (ITIS:161068)
EMLaide::CVPIA_common_species$green_sturgeon - Acipenser medirostris (ITIS: 161067)

For further taxonomic coverage (i.e subkingdom, infrakingdom, etc.) on any of these species, you can visit: ITIS's webpage for full coverage information.

Examples

if (FALSE) taxonomic_coverage <- create_taxonomic_coverage(CVPIA_common_species = "chinook")

if (FALSE) taxonomic_coverage <- create_taxonomic_coverage(CVPIA_common_species = "delta_smelt")

if (FALSE) taxonomic_coverage <- create_taxonomic_coverage(CVPIA_common_species = "white_sturgeon")

if (FALSE) taxonomic_coverage <- create_taxonomic_coverage(CVPIA_common_species = "green_sturgeon")

if (FALSE) taxonomic_coverage <- create_taxonomic_coverage(CVPIA_common_species = "steelhead")

if (FALSE) taxonomic_coverage <- create_taxonomic_coverage(kingdom_value = "Animalia",
                                                         phylum_value = "Chordata",
                                                         class_value = "Mammalia",
                                                         order_value = "Carnivora",
                                                         family_value = "Felidae",
                                                         genus_value = "Panthera", 
                                                         species_value = "Panthera Leo",
                                                         common_name = "Lion", 
                                                         taxon_id = "183803")
                                            
# To append this information to the dataset or project:                        
if (FALSE) create_coverage(geographic_description = "Description",
                         west_bounding_coordinate = "-160.594000", 
                         east_bounding_coordinate = "-134.104800",
                         north_bounding_coordinate = "71.238300", 
                         south_bounding_coordinate = "67.865000",
                         begin_date = "1980-01-01", 
                         end_date = "2010-12-31", 
                         taxonomic_coverage = taxonomic_coverage)