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Empower-1.0: an Efficient Model of Planktonic Ecosystems Written in R : Volume 8, Issue 7 (24/07/2015)

By Anderson, T. R.

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Book Id: WPLBN0003976708
Format Type: PDF Article :
File Size: Pages 32
Reproduction Date: 2015

Title: Empower-1.0: an Efficient Model of Planktonic Ecosystems Written in R : Volume 8, Issue 7 (24/07/2015)  
Author: Anderson, T. R.
Volume: Vol. 8, Issue 7
Language: English
Subject: Science, Geoscientific, Model
Collections: Periodicals: Journal and Magazine Collection, Copernicus GmbH
Publication Date:
Publisher: Copernicus Gmbh, Göttingen, Germany
Member Page: Copernicus Publications


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Yool, A., Gentleman, W. C., & Anderson, T. R. (2015). Empower-1.0: an Efficient Model of Planktonic Ecosystems Written in R : Volume 8, Issue 7 (24/07/2015). Retrieved from http://cn.ebooklibrary.org/

Description: National Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK. 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.

EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R

Anderson, T. R.: Plankton functional type modelling: running before we can walk?, J. Plankton Res., 27, 1073–1081, 2005.; Alderkamp, A.-C., Kulk, G., Buma, G. J., Visser, R. J. W., Van Dijken, G. L., Mills, M. M., and Arrigo, K. R.: The effect of iron limitation on photophysiology of Phaeocycstis Antarctica (Prymnesiophyceae) and Flagiariopsis cylindrus (Bacillariophyceae) under dynamic irradiance, J. Phycol., 8, 45–59, 2012.; Anderson, T. R.: A spectrally averaged model of light penetration and photosynthesis, Limnol. Oceanogr., 38, 1403–1419, 1993.; Anderson, T. R.: Relating C:N ratios in zooplankton food and faecal pellets using a biochemical model, J. Exp. Mar. Biol. Ecol., 184, 183–199, 1994.; Anderson, T. R.: Progress in marine ecosystem modelling and the unreasonable effectiveness of mathematics, J. Mar. Syst., 81, 4–11, 2010.; Anderson, T. R. and Gentleman, W. C.: The legacy of Gordon Arthur Riley (1911–1985) and the development of mathematical models in biological oceanography, J. Mar. Res., 70, 1–30, 2012.; Anderson, T. R. and Hessen, D. O.: Carbon or nitrogen limitation in marine copepods?, J. Plankton Res., 17, 317–331, 1995.; Anderson, T. R. and Mitra, A.: Dysfunctionality in ecosystem models: an underrated pitfall?, Prog. Oceanogr., 84, 66–68, 2010.; Anderson, T. R. and Pondaven, P.: Non-Redfield carbon and nitrogen cycling in the Sargasso Sea: pelagic imbalances and export flux, Deep-Sea Res. Pt. I, 50, 573–591, 2003.; Anderson, T. R., Gentleman, W. C., and Sinha, B.: Influence of grazing formulations on the emergent properties of a complex ecosystem model in a global general circulation model, Prog. Oceanogr., 87, 201–213, 2010.; Anderson, T. R., Hessen, D. O., Mitra, A., Mayor, D. J., and Yool, A.: Sensitivity of secondary production and export flux to choice of trophic transfer formulation in marine ecosystem models, J. Mar. Syst., 125, 41–53, 2013.; Anderson, T. R., Christian, J. R., and Flynn, K. J.: Modeling DOM biogeochemistry, in: Biogeochemistry of marine dissolved organic matter, 2nd Edn., edited by: Hansell, D. A. and Carlson, C. A., Academic Press, 635–667, 2014.; Antonov, J. I., Seidov, D., Boyer, T. P., Locarnini, R. A., Mishonov, A. V., Garcia, H. E., Baranova, O.K., Zweng, M. M., and Johnson, D. R.: World Ocean Atlas 2009, Volume 2: Salinity, edited by: Levitus, S., NOAA Atlas NESDIS 69, U.S. Government Printing Office, Washington, DC, 184 pp., 2010.; Bar-Yam, U.: Dynamics of Complex Systems, Addison-Wesley, Reading, Massachusetts, 848 pp., 1997.; Arhonditsis, G. B., Adams-Vanharn, B. A., Nielsen, L., Stow, C. A., and Reckhow, K. H.: Evaluation of the current state of mechanistic aquatic biogeochemical modeling: Citation analysis and future perspectives, Environ. Sci. Technol., 40, 6547–6554, 2006.; Backhaus, J. O., Hegseth, E. N., Wehde, H., Irigoien, X., Hatten, K., and Logemann, K.: Convection and primary production in winter, Mar. Ecol. Prog. Ser., 251, 1–14, 2003.; Boushaba, K. and Pascual, M.: Dynamics of the echo effect in a phytoplankton system with nitrogen fixers, Bull. Math. Biol., 67, 487–507, 2005.; Blackford, J. C., Allen, J. I., and Gilbert, F. J.: Ecosystem dynamics at six contrasting sites: a generic modelling study, J. Mar. Syst., 52, 191–215, 2004.; Bouman, H. A., Platt, T., Kraay, G. W., Sathyendranath, S., and Irwin, B. D.: Bio-optical properties of the subtropical North Atlantic. I. Vertical variability, Mar. Ecol. Prog. Ser., 200, 3–18, 2000.; Bratbak, G., Egge, J. K., and Heldal, M.: Viral mortality of the marine alga Emiliania huxleyi (Haptophyceae) and termination of algal blooms, Mar. Ecol. Prog. Ser., 93, 39–48, 1993.; Bratbak, G., Willson, W., and Heldal, M.: Viral control of Emiliania huxleyi blooms?, J. Mar. Syst., 9, 75–81, 1996.; Brock, T. D.: Calculating solar radiation for ecological studies, Ecol. Modell., 14, 1–19, 1981.; Chai, F., Lindley, S. T., Toggweiler, J. R., and Barber, R. T.:


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