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 presen...
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ftdoajarticles:oai:doaj.org/article:8ac7fba82df64023acf568d7bd48740f 2023-05-15T17:35:59+02:00 EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R T. R. Anderson W. C. Gentleman A. Yool 2015-07-01T00:00:00Z https://doi.org/10.5194/gmd-8-2231-2015 https://doaj.org/article/8ac7fba82df64023acf568d7bd48740f EN eng Copernicus Publications http://www.geosci-model-dev.net/8/2231/2015/gmd-8-2231-2015.pdf https://doaj.org/toc/1991-959X https://doaj.org/toc/1991-9603 1991-959X 1991-9603 doi:10.5194/gmd-8-2231-2015 https://doaj.org/article/8ac7fba82df64023acf568d7bd48740f Geoscientific Model Development, Vol 8, Iss 7, Pp 2231-2262 (2015) Geology QE1-996.5 article 2015 ftdoajarticles https://doi.org/10.5194/gmd-8-2231-2015 2022-12-31T04:04:16Z 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 ... Article in Journal/Newspaper North Atlantic Directory of Open Access Journals: DOAJ Articles Geoscientific Model Development 8 7 2231 2262 |
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language |
English |
topic |
Geology QE1-996.5 |
spellingShingle |
Geology QE1-996.5 T. R. Anderson W. C. Gentleman A. Yool EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R |
topic_facet |
Geology QE1-996.5 |
description |
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 ... |
format |
Article in Journal/Newspaper |
author |
T. R. Anderson W. C. Gentleman A. Yool |
author_facet |
T. R. Anderson W. C. Gentleman A. Yool |
author_sort |
T. R. Anderson |
title |
EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R |
title_short |
EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R |
title_full |
EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R |
title_fullStr |
EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R |
title_full_unstemmed |
EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R |
title_sort |
empower-1.0: an efficient model of planktonic ecosystems written in r |
publisher |
Copernicus Publications |
publishDate |
2015 |
url |
https://doi.org/10.5194/gmd-8-2231-2015 https://doaj.org/article/8ac7fba82df64023acf568d7bd48740f |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_source |
Geoscientific Model Development, Vol 8, Iss 7, Pp 2231-2262 (2015) |
op_relation |
http://www.geosci-model-dev.net/8/2231/2015/gmd-8-2231-2015.pdf https://doaj.org/toc/1991-959X https://doaj.org/toc/1991-9603 1991-959X 1991-9603 doi:10.5194/gmd-8-2231-2015 https://doaj.org/article/8ac7fba82df64023acf568d7bd48740f |
op_doi |
https://doi.org/10.5194/gmd-8-2231-2015 |
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Geoscientific Model Development |
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8 |
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7 |
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2231 |
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2262 |
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