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

IOC-UNESCO Databases

The Intergovernmental Oceanographic Commission of UNESCO (IOC) is the United Nations body dedicated to supporting global ocean science, services, and governance. The IOC-UNESCO Taxonomic Reference List of Harmful Microalgae focuses on species known to produce toxins or exhibit toxic effects, along with a few species suspected of toxin production. All toxic species in the list are verified with WoRMS to ensure accurate taxonomy.

The IOC-UNESCO Toxins database complements this list by providing detailed reference information about toxins, some of which are associated with harmful algal events.

The information from these databases can be access through APIs, as demonstrated in this tutorial using SHARK4R.

Getting Started

Installation

You can install the package from GitHub using the devtools package:

# install.packages("devtools")
devtools::install_github("sharksmhi/SHARK4R",
                         dependencies = TRUE)

Load the SHARK4R and dplyr libraries:

library(SHARK4R)
library(dplyr)

suppressPackageStartupMessages({
  library(SHARK4R)
  library(dplyr)
})

Retrieve HAB List From IOC Taxonomic List

The complete HAB list, including scientific names and AphiaIDs, can be downloaded from the IOC-UNESCO Taxonomic Reference List of Harmful Microalgae. The output fields are customizable through function parameters—for example, setting classification = FALSE excludes higher taxonomic information from the results.

# Retrieve complete HAB list
hab_list <- get_hab_list()

# Print result as tibble
tibble(hab_list)

Retrieve HAB Toxins From IOC Toxins Database

The complete Toxin list can be downloaded from the IOC-UNESCO Toxins database using the get_toxin_list function.

# Retrieve complete toxin list
toxin_list <- get_toxin_list()

# Print result as tibble
tibble(toxin_list)

Citation

# Print citation
citation("SHARK4R")

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