StrathE2EPolar {StrathE2EPolar}R Documentation

StrathE2EPolar Package

Description

StrathE2EPolar is a dynamic model of the 'big-picture', whole ecosystem effects of hydrodynamics, temperature, sea ice, nutrient additions, and fishing on polar shelf marine food webs.

Details

The StrathE2EPolar 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, sea ice, 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 Barents Sea is included in the package.

Documentation

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

CheatSheet - quick-reference guide to StrathE2EPolar functions ... ../doc/StrathE2EPolar_CheatSheet.pdf
or ... from an R session ... vignette("StrathE2EPolar_CheatSheet")

StrathE2E2 Reference Manual (pdf) - compilation of function help pages generated by CRAN-check - TO BE REPLACED WITH POLAR VERSION SOON

StrathE2E2 Package User Manual (html) - guide to developing and running models - TO BE REPLACED WITH POLAR VERSION SOON

Package website: https://marineresourcemodelling.gitlab.io/index.html

Download documentation from the package website:
StrathE2E2 Technical Manual - documentation on the structure of input and output R-objects and files - TO BE REPLACED WITH POLAR VERSION SOON
Origin of the model (previous versions)
Overview of the model concepts and design - DRAFT - WORK IN PROGRESS
Ecology model description - DRAFT - WORK IN PROGRESS
Fishing fleet model description
Optimization, sensitivity and Monte Carlo methods
StrathE2E2 Documentation on the North Sea implementation of StrathE2E2 which is provided with the package - TO BE REPLACED WITH BARENTS SEA IMPLEMENTATION SOON

Repository for contributed models: (https://marineresourcemodelling.gitlab.io/resources/index.html)

Publications inventory for StrathE2E models and applications

Example data package

COMING SOON - NOT READY YET 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("StrathE2EPolarexamples", repos="https://marineresourcemodelling.gitlab.io/sran")

Once installed, load the package using ... library(StrathE2EPolarexamples)
Open documentation on the datasets using ... help(StrathE2EPolarexamples)

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:


[Package StrathE2EPolar version 1.0.0 Index]