Download the Harmful Algal Blooms (HABs) Taxonomic List

This function retrieves the taxonomic list of Harmful Algal Blooms (HABs) from the World Register of Marine Species (WoRMS). The data is returned as a dataframe, with options to customize the fields included in the download.

Usage

get_hab_list(
  aphia_id = TRUE,
  scientific_name = TRUE,
  authority = TRUE,
  fossil = TRUE,
  rank_name = TRUE,
  status_name = TRUE,
  qualitystatus_name = TRUE,
  modified = TRUE,
  lsid = TRUE,
  parent_id = TRUE,
  stored_path = TRUE,
  citation = TRUE,
  classification = TRUE,
  environment = TRUE,
  accepted_taxon = TRUE
)

Arguments

aphia_id: Logical. Include the AphiaID field. Defaults to TRUE.
scientific_name: Logical. Include the scientific name field. Defaults to TRUE.
authority: Logical. Include the authority field. Defaults to TRUE.
fossil: Logical. Include information about fossil status. Defaults to TRUE.
rank_name: Logical. Include the taxonomic rank (e.g., species, variety, forma). Defaults to TRUE.
status_name: Logical. Include the taxonomic status field. Defaults to TRUE.
qualitystatus_name: Logical. Include the quality status field. Defaults to TRUE.
modified: Logical. Include the date of last modification field. Defaults to TRUE.
lsid: Logical. Include the Life Science Identifier (LSID) field. Defaults to TRUE.
parent_id: Logical. Include the parent AphiaID field. Defaults to TRUE.
stored_path: Logical. Include the stored path field. Defaults to TRUE.
citation: Logical. Include citation information. Defaults to TRUE.
classification: Logical. Include the full taxonomic classification (e.g., kingdom, phylum, class). Defaults to TRUE.
environment: Logical. Include environmental data (e.g., marine, brackish, freshwater, terrestrial). Defaults to TRUE.
accepted_taxon: Logical. Include information about the accepted taxon (e.g., scientific name and authority). Defaults to TRUE.

Value

A dataframe containing the HABs taxonomic list, with columns based on the selected parameters.

Details

This function submits a POST request to the WoRMS database to retrieve a taxonomic list for Harmful Algal Blooms. The downloaded data can include various fields, which are controlled by the input parameters. If a field is not required, set the corresponding parameter to FALSE to exclude it from the output.

Examples

if (FALSE) { # \dontrun{
# Download the default HABs taxonomic list
habs_taxlist_df <- get_hab_list()
head(habs_taxlist_df)

# Include only specific fields in the output
habs_taxlist_df <- get_hab_list(aphia_id = TRUE, scientific_name = TRUE, authority = FALSE)
} # }