A script-based workflow to calculate zooplankton community indicator for environmental status assessment in the Baltic Sea

This paper presents a script-based workflow applying widely-used R-packages to compute the core indicator Zooplankton Mean Size and Total Stock (MSTS) for assessing the ecological status of the pelagic habitat in the Baltic Sea. The script allows users to retrieve data from a database and use it for MSTS computation following data filtering and aggregation. Moreover, reference values for each indicator component, i.e., mean size of zooplankter in the community and total zooplankton biomass, can be calculated once the user provides the reference periods. Using this script, researchers and practitioners can follow temporal changes in the zooplankton community and compare them across the sub-basins. The tool is publicly available and used to implement the Marine Strategy Framework Directive in the Baltic region. •Zooplankton MSTS is a core indicator for pelagic food web status in the Baltic Sea.•A script-based workflow provides transparency of the calculations.•runMSTS facilitates environmental assessment and data processing for other needs.