get_hab_list: Download the Harmful Algal Blooms (HABs) Taxonomic List

In sharksmhi/SHARK4R: Retrieving, Analyzing, and Validating Marine Data from SHARK and Nordic Microalgae

Download the Harmful Algal Blooms (HABs) Taxonomic List

Description

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.

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.

Value

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

Examples

## Not run: 
# 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)

## End(Not run)

sharksmhi/SHARK4R documentation built on Jan. 9, 2025, 5:15 p.m.