StrathE2E2: an R package for modelling the dynamics of marine food webs and fisheries

Michael R. Heath; Douglas C. Speirs; Ian Thurlbeck; Robert J. Wilson

doi:10.1111/2041-210X.13510

StrathE2E2: an R package for modelling the dynamics of marine food webs and fisheries

Michael R. Heath, Douglas C. Speirs, Ian Thurlbeck, Robert J. Wilson

Research output: Contribution to journal › Article › peer-review

11 Citations (Scopus)

119 Downloads (Pure)

Abstract

1. We present StrathE2E2, an R package for modelling the whole ecosystem, or ‘big-picture’ effects of hydrodynamics, temperature, nutrient additions, and fishing on continental shelf marine food webs.
2. StrathE2E2 has two linked parts – a fishing fleet model and an ecology model. The fishing model combines harvesting, discarding and seabed disturbance rates across a range of gears and passes the results into the ecology model.
3. The ecology model is a network of coupled ordinary differential equations representing the rates of change in nitrogen mass of organic detritus, dissolved inorganic nutrient, and coarse guilds of living biomass spanning microbes to megafauna. The equations include representations of feeding, metabolism, reproduction, active migrations, advection and mixing. Environmental driving data include temperature, irradiance, hydrodynamics, and nutrient inputs from rivers, atmosphere and ocean boundaries.
4. The package includes functions for parameter optimization, global sensitivity analysis, and Monte Carlo estimation of credible intervals for model outputs
5. A fully developed and documented implementation for the North Sea is included with the package.

Original language	English
Pages (from-to)	280-287
Number of pages	8
Journal	Methods in Ecology and Evolution
Volume	12
Early online date	11 Oct 2020
DOIs	https://doi.org/10.1111/2041-210X.13510
Publication status	Published - 4 Feb 2021

Keywords

ecosystem modelling
fisheries
food webs

Access to Document

10.1111/2041-210X.13510Licence: CC BY 4.0

Heath-etal-MEE-2020-StrathE2E2-an-R-package-for-modelling-the-dynamics-of-marine-foodFinal published version, 710 KBLicence: CC BY 4.0

Mike Heath
- m.heathstrath.acuk
- Mathematics And Statistics - Professor
- MASTS
- People, Place and Policy
Person: Academic

1 Active
3 Finished

Mission Atlantic. Towards the Sustainable Development of the Atlantic Ocean
Speirs, D. (Principal Investigator), Heath, M. (Co-investigator) & Laverick, J. (Researcher)
European Commission - Horizon Europe + H2020
1/09/20 → 31/08/25
Project: Research
DiscardLess – Strategies for the gradual elimination of discards in European fisheries (H2020 SC2 SFS)
Heath, M. (Principal Investigator) & Cook, R. (Co-investigator)
European Commission - Horizon Europe + H2020
1/03/15 → 28/02/19
Project: Research
Modelling the impacts of trawling on the marine ecosystem
Heath, M. (Principal Investigator) & Speirs, D. (Co-investigator)
Fisheries Innovation Scotland
1/01/15 → 31/08/15
Project: Research

StrathE2E2 - End-to-End Marine Food Web Model
Heath, M. (Creator) & Thurlbeck, I. (Contributor), University of Strathclyde, 13 Jul 2020
https://CRAN.R-project.org/package=StrathE2E2 and one more link, https://marineresourcemodelling.gitlab.io/resources/index.html (show fewer)
Dataset

11 Citations
11 Article
1 Commissioned report
1 Other report
1 Comment/debate

Can we use recovery timescales to define good environmental status?
Thorpe, R. B., Heath, M. & Lynam, C. P., 30 Nov 2023, In: Ecological Indicators. 155, 17 p., 110984.
Research output: Contribution to journal › Article › peer-review

Open Access
File
2 Citations (Scopus)

44 Downloads (Pure)
Synthetic shelf sediment maps for the Greenland Sea and Barents Sea
Laverick, J. H., Speirs, D. C. & Heath, M. R., 5 Apr 2022, In: Geoscience Data Journal. 10, 2, p. 220-230 11 p.
Research output: Contribution to journal › Article › peer-review

Open Access
File
1 Citation (Scopus)

45 Downloads (Pure)
The response of North Sea ecosystem functional groups to warming and changes in fishing
Thorpe, R. B., Arroyo, N. L., Safi, G., Niquil, N., Heath, M., Pace, M. C. & Lynam, C. P., 4 Apr 2022, In: Frontiers in Marine Science. 9, 13 p., 841909.
Research output: Contribution to journal › Article › peer-review

Open Access
File
8 Citations (Scopus)

48 Downloads (Pure)

Royal Society of Edinburgh, Sir James Black Medal
Heath, M. (Recipient), 6 Aug 2017
Prize: Prize (including medals and awards)

2 Oral presentation

Modelling fisheries displacement in the North Sea and its ecosystem and economic consequences
Heath, M. (Speaker), Doherty, T. (Contributor), Laverick, J. (Contributor) & Speirs, D. (Contributor)
6 Dec 2023
Activity: Talk or presentation types › Oral presentation
Big-picture modelling to help inform marine management trade-offs in the North Sea
Heath, M. (Speaker), Doherty, T. (Contributor), Laverick, J. (Contributor) & Speirs, D. (Contributor)
13 Sept 2023
Activity: Talk or presentation types › Oral presentation

Cite this

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title = "StrathE2E2: an R package for modelling the dynamics of marine food webs and fisheries",

abstract = "1. We present StrathE2E2, an R package for modelling the whole ecosystem, or {\textquoteleft}big-picture{\textquoteright} effects of hydrodynamics, temperature, nutrient additions, and fishing on continental shelf marine food webs.2. StrathE2E2 has two linked parts – a fishing fleet model and an ecology model. The fishing model combines harvesting, discarding and seabed disturbance rates across a range of gears and passes the results into the ecology model.3. The ecology model is a network of coupled ordinary differential equations representing the rates of change in nitrogen mass of organic detritus, dissolved inorganic nutrient, and coarse guilds of living biomass spanning microbes to megafauna. The equations include representations of feeding, metabolism, reproduction, active migrations, advection and mixing. Environmental driving data include temperature, irradiance, hydrodynamics, and nutrient inputs from rivers, atmosphere and ocean boundaries.4. The package includes functions for parameter optimization, global sensitivity analysis, and Monte Carlo estimation of credible intervals for model outputs5. A fully developed and documented implementation for the North Sea is included with the package. ",

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AU - Heath, Michael R.

AU - Speirs, Douglas C.

AU - Thurlbeck, Ian

AU - Wilson, Robert J.

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N2 - 1. We present StrathE2E2, an R package for modelling the whole ecosystem, or ‘big-picture’ effects of hydrodynamics, temperature, nutrient additions, and fishing on continental shelf marine food webs.2. StrathE2E2 has two linked parts – a fishing fleet model and an ecology model. The fishing model combines harvesting, discarding and seabed disturbance rates across a range of gears and passes the results into the ecology model.3. The ecology model is a network of coupled ordinary differential equations representing the rates of change in nitrogen mass of organic detritus, dissolved inorganic nutrient, and coarse guilds of living biomass spanning microbes to megafauna. The equations include representations of feeding, metabolism, reproduction, active migrations, advection and mixing. Environmental driving data include temperature, irradiance, hydrodynamics, and nutrient inputs from rivers, atmosphere and ocean boundaries.4. The package includes functions for parameter optimization, global sensitivity analysis, and Monte Carlo estimation of credible intervals for model outputs5. A fully developed and documented implementation for the North Sea is included with the package.

AB - 1. We present StrathE2E2, an R package for modelling the whole ecosystem, or ‘big-picture’ effects of hydrodynamics, temperature, nutrient additions, and fishing on continental shelf marine food webs.2. StrathE2E2 has two linked parts – a fishing fleet model and an ecology model. The fishing model combines harvesting, discarding and seabed disturbance rates across a range of gears and passes the results into the ecology model.3. The ecology model is a network of coupled ordinary differential equations representing the rates of change in nitrogen mass of organic detritus, dissolved inorganic nutrient, and coarse guilds of living biomass spanning microbes to megafauna. The equations include representations of feeding, metabolism, reproduction, active migrations, advection and mixing. Environmental driving data include temperature, irradiance, hydrodynamics, and nutrient inputs from rivers, atmosphere and ocean boundaries.4. The package includes functions for parameter optimization, global sensitivity analysis, and Monte Carlo estimation of credible intervals for model outputs5. A fully developed and documented implementation for the North Sea is included with the package.

KW - ecosystem modelling

KW - fisheries

KW - food webs

U2 - 10.1111/2041-210X.13510

DO - 10.1111/2041-210X.13510

M3 - Article

SN - 2041-210X

VL - 12

SP - 280

EP - 287

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

ER -

StrathE2E2: an R package for modelling the dynamics of marine food webs and fisheries

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