StrathE2E2 {StrathE2E2}R Documentation

StrathE2E2 Package

Description

StrathE2E2 is a dynamic model of the 'big-picture', whole ecosystem effects of hydrodynamics, temperature, nutrient additions, and fishing on continental shelf marine food webs

Details

The StrathE2E2 model has two linked parts - a fishing fleet model and an ecology model. The fishing model integrates 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 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 optimisation, 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 in the package.

User community
We plan to develop a repository of open access implementations of StrathE2E for shelf sea regions. Users developing implementations which they are willing to share are encouraged to contact us to discuss inclusion in the repository.

Funding
Development of the StrathE2E2 package was supported by the UK NERC Marine Ecosystems Research Programme (grant NE/L003120/1) https://www.marine-ecosystems.org.uk/Home
Other projects which have supported aspects of the model development are:
EU-Horizon 2020 (DISCARDLESS project) http://www.discardless.eu/
Fisheries Innovation Scotland (project FIS003) https://https://fiscot.org/fis-projects/

Information on how to cite the package ... from an R session ... citation("StrathE2E2")

List of all vignettes and documentation supplied with the package:
../doc/index.html

Access the User Manual ... ../doc/StrathE2E2_User_Manual.html
or ... from an R session ... vignette("StrathE2E2_User_Manual")

Technical Manual - documentation on the structure of input and output R-objects and files:
../doc/StrathE2E2_Technical_Manual.pdf

Additional documentation:
../doc/StrathE2E2_Model_origin.html: Origin of the model (previous versions)
../doc/StrathE2E2_Model_overview.html: Overview of the model concepts and design
../doc/StrathE2E2_Ecology_model.pdf: Ecology model description
../doc/StrathE2E2_Fishing_fleet_model.pdf: Fishing fleet model description
../doc/StrathE2E2_Optimisation_sensitivity_Monte_Carlo_methodology.pdf: Optimisation, sensitivity and Monte Carlo methods
../doc/StrathE2E2_North_Sea_model.pdf: Documentation on the North Sea implementation

See Also

Model management family of functions

Basic model run family of functions

Model comparison family of functions

Parameter estimation family of functions

Sensitivity analysis family of functions

Monte Carlo analysis family of functions


[Package StrathE2E2 version 2.0.0 Index]