get_hab_list: Download the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae

Description

This function retrieves the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae 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
)

Value

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

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.

Details

This function submits a POST request to the WoRMS database to retrieve the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae. 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

Run this code

# \donttest{
# 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)
head(habs_taxlist_df)
# }