Accessing and Validating Marine Environmental Data from 'SHARK' and Related Databases

Provides functions to retrieve, process, analyze, and quality-control marine physical, chemical, and biological data. The main focus is on Swedish monitoring data available through the 'SHARK' database < https://shark.smhi.se/en/>, with additional API support for 'Nordic Microalgae' < https://nordicmicroalgae.org/>, 'Dyntaxa' < https://artfakta.se/>, World Register of Marine Species ('WoRMS') < https://www.marinespecies.org>, 'AlgaeBase' < https://www.algaebase.org>, OBIS 'xylookup' web service < https://iobis.github.io/xylookup/> and Intergovernmental Oceanographic Commission (IOC) - UNESCO databases on harmful algae < https://www.marinespecies.org/hab/> and toxins < https://toxins.hais.ioc-unesco.org/>.

SHARK4R: Accessing and Validating Marine Environmental Data from 'SHARK' and Related Databases

Overview

This R package is equipped with a client application designed for integration with API functions. It facilitates access to various databases, including SHARK, SLU Artdatabanken (Dyntaxa), WoRMS, AlgaeBase, IOC-UNESCO Taxonomic Reference List of Harmful Microalgae, IOC-UNESCO Toxins database, OBIS xylookup web service and Nordic Microalgae. The package serves a dual purpose, supporting both data analysis and automatic quality control of physical, chemical, and marine biological data. Several quality control components, originally developed by Provoost and Bosch (2024), have been adapted for compatibility with the SHARK format.

Installation

You can install the latest version of SHARK4R from CRAN using:

install.packages("SHARK4R")

Or install the development version (requiring the remotes package):

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

Documentation and Tutorials

Website

For detailed information, please visit the project's webpage.

Tutorials

Explore the features and capabilities of SHARK4R through these tutorials:

• Retrieve Data From SHARK
• Retrieve Data From Dyntaxa
• Retrieve Data From WoRMS
• Retrieve Data From AlgaeBase
• Retrieve Data From IOC HAB and Toxin databases
• Retrieve Data From Nordic Microalgae
• Quality Control of SHARK Data

Reference

For a detailed overview of all available SHARK4R functions, please visit the reference section:

• Function Reference

Repository

For more details and the latest updates, visit the GitHub repository.

License

This package is licensed under the MIT License.

References

Provoost P, Bosch S (2024). obistools: Tools for data enhancement and quality control. Ocean Biodiversity Information System. Intergovernmental Oceanographic Commission of UNESCO. R package version 0.1.0, https://iobis.github.io/obistools/.