Coastal generalized ecosystem model (CGEM) 1.0: Flexible model formulations for simulating complex biogeochemical processes in aquatic ecosystems.

The Coastal Generalized Ecosystem Model (CGEM) is a biogeochemical model developed to study regulating processes of water-column optical properties, water-column and benthic carbon, oxygen, and nutrient cycles, and phytoplankton and zooplankton dynamics. CGEM offers numerous formulations for important rate processes, providing users flexibility in altering model structure. This flexibility also provides a means for evaluating model structural uncertainty and impacts on simulations, which are rarely evaluated with numerical ecosystem models. As an open-source model, CGEM also offers users the option to implement new formulations or modify existing routines. We also provide a full description of the model formulations, state variables, and model parameters in CGEM. Using two published case studies, we explore how different formulations for light attenuation, phytoplankton temperature growth response, and sediment processes impact simulations. We discuss CGEM's role as a new ecosystem model within the modeling community and opportunities to address current and future water quality issues.