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

Description

This function retrieves the IOC-UNESCO Taxonomic Reference List of Harmful Microalgae (Lundholm et al. 2009) 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(
  species_only = TRUE,
  harmful_non_toxic_only = FALSE,
  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,
  verbose = TRUE
)

Value

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

Arguments

species_only: Logical. If TRUE, only species-level records are returned (i.e., rows where the Species column is not NA). Note that this filter is only applied when harmful_non_toxic_only = FALSE; it is ignored when harmful_non_toxic_only = TRUE.
harmful_non_toxic_only: Logical. If TRUE, retrieves only non-toxigenic marine microalgal species flagged with harmful effects. Defaults to FALSE.
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.
verbose: Logical. Whether to display progress information. Default is TRUE.

Details

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

References

Lundholm, N.; Bernard, C.; Churro, C.; Escalera, L.; Hoppenrath, M.; Iwataki, M.; Larsen, J.; Mertens, K.; Murray, S.; Probert, I.; Salas, R.; Tillmann, U.; Zingone, A. (Eds) (2009 onwards). IOC-UNESCO Taxonomic Reference List of Harmful Microalgae. https://www.marinespecies.org/hab/. doi:10.14284/362

Examples

Run this code

# \donttest{
# Download the default HABs taxonomic list
try(habs_taxlist_df <- get_hab_list())
if (exists("habs_taxlist_df")) head(habs_taxlist_df)

# Include higher taxa records
try(habs_taxlist_df <- get_hab_list(species_only = FALSE))
if (exists("habs_taxlist_df")) head(habs_taxlist_df)

# Retrieve only non-toxigenic harmful species (experimental stage)
try(habs_taxlist_df <- get_hab_list(harmful_non_toxic_only = TRUE, verbose = FALSE))
if (exists("habs_taxlist_df")) head(habs_taxlist_df)

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

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