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

Nordic Microalgae

Nordic Microalgae is an online platform providing high-quality images, illustrations, and detailed information about aquatic microalgae and related organisms in the Nordic region, including phytoplankton, microzooplankton, and benthic microalgae. It features a comprehensive species checklist, up-to-date taxonomic data linked to WoRMS and AlgaeBase, and supplementary resources such as biovolume lists and occurrence maps. Established in 1996 and supported by long-term funding from the Swedish Research Council through the Swedish Biodiversity Data Infrastructure (SBDI).

All data on Nordic Microalgae is accessible through our API. Below are examples demonstrating how to extract data using the SHARK4R package.

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 tibble libraries:

library(SHARK4R)
library(tibble)

suppressPackageStartupMessages({
  library(SHARK4R)
  library(tibble)
})

Retrieve Complete Nordic Microalgae Taxon Table

A complete Nordic Microalgae taxa list can be retrieved through the API.

# Get taxa information
taxa <- get_nua_taxa(unparsed = FALSE)

# Print data
tibble(taxa)

The full taxonomic information can be accessed as an unparsed list by enabling the unparsed parameter.

Get Nordic Microalgae External Links or Facts

Each taxon sheet on Nordic Microalgae contains facts, such as links to external webpages (e.g. AlgaeBase, WoRMS and Dyntaxa). These links can be retrieved through the API.

# Randomly select 10 taxa from shark_taxon$scientific_name
slugs <- sample(taxa$slug, size = 10)

# Get external links
external_links <- get_nua_external_links(slugs, 
                                         verbose = FALSE, 
                                         unparsed = FALSE)

# Print list
tibble(external_links)

The full list of facts can be accessed as an unparsed list by setting the unparsed parameter to TRUE.

Get Nordic Microalgae Harmfulness Information

Taxa listed in the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae contain information about harmfulness. This information can be retrieved through the API.

# Get external links
harmfulness <- get_nua_harmfulness(c("dinophysis-acuta", 
                                     "alexandrium-ostenfeldii"), 
                                   verbose = FALSE)

# Print list
tibble(harmfulness)

Get Nordic Microalgae Media Links

Links to all images present on Nordic Microalgae can be retrieved through the API. The images are available in four sizes: original (o), small (s), medium (m), and large (l).

# Get all media links
media <- get_nua_media_links(unparsed = FALSE)

# Print list
tibble(media)

Complete media information can be retrieved as an unparsed list by setting the unparsed parameter to TRUE.

Citation

# Print citation
citation("SHARK4R")

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