StrathE2E2-package: StrathE2E2 Package

Description Details Documentation Example data package See Also


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.


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 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 in the package.


List of all vignettes and documentation supplied with the package:

CheatSheet - quick-reference guide to StrathE2E2 functions ... ../doc/StrathE2E2_CheatSheet.pdf
or ... from an R session ... vignette("StrathE2E2_CheatSheet")

Reference Manual (pdf) - compilation of function help pages generated by CRAN-check

Package User Manual (html) - guide to developing and running models

Package website:

Download documentation from the package website:
Technical Manual - documentation on the structure of input and output R-objects and files
Origin of the model (previous versions)
Overview of the model concepts and design
Ecology model description
Fishing fleet model description
Optimization, sensitivity and Monte Carlo methods
Documentation on the North Sea implementation of StrathE2E2 which is provided with the package

Repository for contributed models: (

Publications inventory for StrathE2E models and applications

Example data package

Example outputs from the more computationally intensive model functions are provided as a supplementary data package.

The data package auto-installs when example data are first invoked. Alternatively, to install manually:
... from an R session ... install.packages("StrathE2E2examples", repos="")

Once installed, load the package using ... library(StrathE2E2examples)
Open documentation on the datasets using ... help(StrathE2E2examples)

See Also

Model management:

Basic model operations:

Parameter estimation:

Sensitivity and Monte Carlo analyses:

Compare model runs:

Fishery yield analysis:

Visualize model inputs:

Visualize model outputs:

StrathE2E2 documentation built on Jan. 23, 2021, 1:07 a.m.