Journal cover Journal topic
Geoscientific Model Development An interactive open-access journal of the European Geosciences Union
Geosci. Model Dev., 8, 2231-2262, 2015
© Author(s) 2015. This work is distributed
under the Creative Commons Attribution 3.0 License.
Model description paper
24 Jul 2015
EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R
T. R. Anderson1, W. C. Gentleman2, and A. Yool1 1National Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK
2Department of Engineering Mathematics, Dalhousie University, 5269 Morris St., Halifax, Nova Scotia, B3H 4R2, Canada
Abstract. Modelling marine ecosystems requires insight and judgement when it comes to deciding upon appropriate model structure, equations and parameterisation. Many processes are relatively poorly understood and tough decisions must be made as to how to mathematically simplify the real world. Here, we present an efficient plankton modelling testbed, EMPOWER-1.0 (Efficient Model of Planktonic ecOsystems WrittEn in R), coded in the freely available language R. The testbed uses simple two-layer "slab" physics whereby a seasonally varying mixed layer which contains the planktonic marine ecosystem is positioned above a deep layer that contains only nutrient. As such, EMPOWER-1.0 provides a readily available and easy to use tool for evaluating model structure, formulations and parameterisation. The code is transparent and modular such that modifications and changes to model formulation are easily implemented allowing users to investigate and familiarise themselves with the inner workings of their models. It can be used either for preliminary model testing to set the stage for further work, e.g. coupling the ecosystem model to 1-D or 3-D physics, or for undertaking front line research in its own right. EMPOWER-1.0 also serves as an ideal teaching tool. In order to demonstrate the utility of EMPOWER-1.0, we implemented a simple nutrient–phytoplankton–zooplankton–detritus (NPZD) ecosystem model and carried out both a parameter tuning exercise and structural sensitivity analysis. Parameter tuning was demonstrated for four contrasting ocean sites, focusing on station BIOTRANS in the North Atlantic (47° N, 20° W), highlighting both the utility of undertaking a planned sensitivity analysis for this purpose, yet also the subjectivity which nevertheless surrounds the choice of which parameters to tune. Structural sensitivity tests were then performed comparing different equations for calculating daily depth-integrated photosynthesis, as well as mortality terms for both phytoplankton and zooplankton. Regarding the calculation of daily photosynthesis, for example, results indicated that the model was relatively insensitive to the choice of photosynthesis–irradiance curve, but markedly sensitive to the method of calculating light attenuation in the water column. The work highlights the utility of EMPOWER-1.0 as a means of comprehending, diagnosing and formulating equations for the dynamics of marine ecosystems.

Citation: Anderson, T. R., Gentleman, W. C., and Yool, A.: EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R, Geosci. Model Dev., 8, 2231-2262, doi:10.5194/gmd-8-2231-2015, 2015.
Publications Copernicus
Short summary
Ecosystem models provide a powerful tool for simulating ocean biology. Care must be exercised when selecting appropriate equations and parameter values to represent chosen marine ecosystems. Here, we present an efficient plankton model testbed, using simplified physics and coded in the freely available language R. Multiple runs can be undertaken for different ocean sites, permitting thorough evaluation of ecosystem model performance. The testbed also serves as an excellent resource for teaching.
Ecosystem models provide a powerful tool for simulating ocean biology. Care must be exercised...