Abstract
Abstract 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. 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. 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. The package includes functions for parameter optimization, global sensitivity analysis and Monte Carlo estimation of credible intervals for model outputs. A fully developed and documented implementation for the North Sea is included with the package.
Highlights
The effects of anthropogenic or natural pressures applied to any part of an ecosystem are eventually felt everywhere to some extent through the phenomenon known as a ‘trophic cascade’ (Pace et al, 1999)
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
There is no simple answer to the question of an appropriate spatial, taxonomic and biological granularity for an ecosystem/food web model (Fulton, 2010; Giricheva, 2015; Iwasa et al, 1987)
Summary
The effects of anthropogenic or natural pressures applied to any part of an ecosystem are eventually felt everywhere to some extent through the phenomenon known as a ‘trophic cascade’ (Pace et al, 1999). Cascading effects are attenuated or amplified as they propagate through the food web, depending on the nature of the pressure and details of the ecology (Heath et al, 2014). Diagnosing the type and magnitude of pressures that an ecosystem can sustain before being fundamentally altered requires simulation with mathematical models that aim to represent the key ecological components and processes which govern cascades. The model takes a macroscopic view of ecology, aggregating over the many microscopic details of taxonomy, demography and spatial structure (Giricheva, 2015). The aim is to represent the gross dynamics with a tolerable parameter count and fast run-time, so as
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