sharkdata-r-download

Access physical-chemical, phytoplankton, picoplankton and chlorophyll data from the SHARKdata API using R. The data are also available in the web-interface at SHARKweb.

There are three scripts available in this repo:

download_shark_data_general.Rmd

Simple version

download_shark_data.Rmd

Added WoRMS taxonomy for phytoplankton

download_shark_data_updated_taxonomy.Rmd

Added WoRMS taxonomy for phytoplankton and updated taxonomy to follow the current AlgaeBase taxonomic database and better match the PR2 database, v5.01 (both accessed on 2023-06-02).

Instructions

List the dataset names that should be downloaded in data/shark_download/list_of_datasets.txt.

Citation

Torstensson, A. (2023). Access Swedish oceanographic monitoring data using the SHARKdata API (https://sharkdata.smhi.se/) in R (Version 1.1) [Computer software]. https://doi.org/10.5281/zenodo.8096047