The University of Southampton
University of Southampton Institutional Repository

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

EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R
EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R
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.
1991-9603
2231-2262
Anderson, T.R.
dfed062f-e747-48d3-b59e-2f5e57a8571d
Gentleman, W.C.
60ef3257-66ea-4792-882f-91c35d6d6195
Yool, A.
882aeb0d-dda0-405e-844c-65b68cce5017
Anderson, T.R.
dfed062f-e747-48d3-b59e-2f5e57a8571d
Gentleman, W.C.
60ef3257-66ea-4792-882f-91c35d6d6195
Yool, A.
882aeb0d-dda0-405e-844c-65b68cce5017

Anderson, T.R., Gentleman, W.C. and Yool, A. (2015) EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R. Geoscientific Model Development, 8 (7), 2231-2262. (doi:10.5194/gmd-8-2231-2015).

Record type: Article

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.

Text
gmd-8-2231-2015.pdf - Version of Record
Available under License Other.
Download (824kB)

More information

Published date: 2015
Organisations: Marine Systems Modelling

Identifiers

Local EPrints ID: 382241
URI: https://eprints.soton.ac.uk/id/eprint/382241
ISSN: 1991-9603
PURE UUID: afce5591-2373-430c-bd38-90705105755e

Catalogue record

Date deposited: 30 Sep 2015 14:51
Last modified: 19 Jul 2019 20:31

Export record

Altmetrics

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of https://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×