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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ftnerc:oai:nora.nerc.ac.uk:511910 2023-05-15T17:36:06+02:00 EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R Anderson, T.R. Gentleman, W.C. Yool, A. 2015-07-24 text http://nora.nerc.ac.uk/id/eprint/511910/ https://nora.nerc.ac.uk/id/eprint/511910/1/gmd-8-2231-2015.pdf https://doi.org/10.5194/gmd-8-2231-2015 en eng https://nora.nerc.ac.uk/id/eprint/511910/1/gmd-8-2231-2015.pdf Anderson, T.R. orcid:0000-0002-7408-1566 Gentleman, W.C.; Yool, A. orcid:0000-0002-9879-2776 . 2015 EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R. Geoscientific Model Development, 8 (7). 2231-2262. https://doi.org/10.5194/gmd-8-2231-2015 <https://doi.org/10.5194/gmd-8-2231-2015> cc_by CC-BY Marine Sciences Publication - Article PeerReviewed 2015 ftnerc https://doi.org/10.5194/gmd-8-2231-2015 2023-02-04T19:42:12Z 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 Natural Environment Research Council: NERC Open Research Archive Geoscientific Model Development 8 7 2231 2262 |
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Open Polar |
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Natural Environment Research Council: NERC Open Research Archive |
op_collection_id |
ftnerc |
language |
English |
topic |
Marine Sciences |
spellingShingle |
Marine Sciences Anderson, T.R. Gentleman, W.C. Yool, A. EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R |
topic_facet |
Marine Sciences |
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 |
Anderson, T.R. Gentleman, W.C. Yool, A. |
author_facet |
Anderson, T.R. Gentleman, W.C. Yool, A. |
author_sort |
Anderson, T.R. |
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 |
publishDate |
2015 |
url |
http://nora.nerc.ac.uk/id/eprint/511910/ https://nora.nerc.ac.uk/id/eprint/511910/1/gmd-8-2231-2015.pdf https://doi.org/10.5194/gmd-8-2231-2015 |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_relation |
https://nora.nerc.ac.uk/id/eprint/511910/1/gmd-8-2231-2015.pdf Anderson, T.R. orcid:0000-0002-7408-1566 Gentleman, W.C.; Yool, A. orcid:0000-0002-9879-2776 . 2015 EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R. Geoscientific Model Development, 8 (7). 2231-2262. https://doi.org/10.5194/gmd-8-2231-2015 <https://doi.org/10.5194/gmd-8-2231-2015> |
op_rights |
cc_by |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.5194/gmd-8-2231-2015 |
container_title |
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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