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

Heath, Michael R. and Speirs, Douglas C. and Thurlbeck, Ian and Wilson, Robert J. (2020) StrathE2E2 : an R package for modelling the dynamics of marine food webs and fisheries. Methods in Ecology and Evolution. ISSN 2041-210X

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    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.