StrathE2E2 {StrathE2E2} | R Documentation |
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 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
Model management family of functions
list_models
: List the available models in a designated workspace
copy_model
: Make a copy of a named model/variant in a user defined workspace
read_model
: Read a model setup from a given workspace - this is a core function in the package
Basic model run family of functions
StrathE2E
: Run the model for a prescribed number of years
extract_new_initial_cond_from_end_of_run
: Create a new initial values file from the end-state of a model run
plot_full_length_timeseries
: Plot time series of state variables for the full duration of a model run
plot_final_year
: Plot whole domian data for the final year of a run
plot_final_year_LTL_inshore_vs_offshore
: Plot inshore and offshore lower trophic level data for the final year
plot_final_year_HTL_inshore_vs_offshore
: Plot inshore and offshore upper trophic level data for the final year
plot_sediment_habitats_final_year
: Plot sediment nutrients and detritus for the final year
box_and_whisker_annual_plots
: Plot comparison of observed annual data and derived model results
box_and_whisker_monthly_plots
: Plot comparison of observed monthly data with derived model results
plot_time_series_annual_land_disc
: Plot time series of annual landings and discards for a full run
plot_for_each_gear_catch_by_guild
: Plot annual catch composition of each gear for the final year of a run
plot_for_each_guild_catch_by_gear
: Plot distribution of catches across gear for each guild in the final yea
Model comparison family of functions
compare_two_runs_aam
: Plot a tornado diagram comparing annual average mass data from two model runs
compare_two_runs_catch
: Plot a tornado diagram comparing annual landings and discards data from two model runs
Parameter estimation family of functions
annealing_find_ecology_parameters
: Find ecology model parameters maximising the likelihood of observed ecosystem data
annealing_find_harvest_ratio_mult
: Find harvest ratio multipliers maximising the likelihood of observed ecosystem data
calculate_hr_scale_values
: Calculate fishing fleet model parameters which link effort to harvest ratios
annealing_find_gear_activity_mult_ecosystem_target
: Find gear activity multipliers maximising the likelihood of observed ecosystem data
annealing_find_gear_activity_mult_HR_target
: Find gear activity multipliers maximising the likelihood of known harvest ratios
Sensitivity analysis family of functions
Sensitivity_analysis_StrathE2E
: Run a Morris Method global sensitivity analysis
concatenate_raw_sensitivity_analysis_results
: Merge raw analysis data from parallel runs into a single file
process_sensitivity_analysis_results_offline
: Process raw data offline to create final outputs
plot_sensitivity_analysis_results
: Plot sensitivity analysis results
Monte Carlo analysis family of functions
Monte_Carlo_StrathE2E
: Monte Carlo simulation to generate credible intervals of model outputs
plot_Monte_Carlo_parameter_distributions
: Plot credible intervals of model parameters
plot_final_year_time_series_data_with_credible_intervals
: Plot time series of state variables for the final year of a model run
plot_final_year_migration_data_with_credible_intervals
: Plot migration fluxes between offshore and inshore zones
plot_final_year_trophic_data_with_credible_intervals
: Plot annual mean trophic level and omnivory indices for model guilds
plot_inshore_vs_offshore_anavmass_with_credible_intervals
: Plot inshore and offshore annual average mass densities for the final year
box_and_whisker_annual_plots_with_credible_intervals
: Plot comparison of observed ecosystem data with equivalent model outputs
box_and_whisker_monthly_plots_with_credible_intervals
: Plot comparison of observed nutrient and plankton data with model outputs