Files in strathclyde-marine-resource-modelling/StrathE2E2
End-to-end marine food web model
.gitignore
DESCRIPTION
NAMESPACE
R/StrathE2E.R
R/aggregate_model_output.R
R/annealing_fit_ecology_parameters.R
R/assemble_flow_matrix_from_model_annual_output.R
R/box_and_whisker_annual_plots.R
R/box_and_whisker_monthly_plots.R
R/build_annual_drivers.R
R/build_initial_state.R
R/build_model.R
R/build_model_parameters.R
R/build_model_run.R
R/calculate_error_function.R
R/calculate_uptakes.R
R/copy_model.R
R/derive_annual_results_inshore.R
R/derive_annual_results_offshore.R
R/derive_annual_results_wholedomain.R
R/derive_model_target_results.R
R/disaggregate_landings_discards_by_gear.R
R/extract_simulated_catch_land_disc_by_gear_for_given_year.R
R/extract_timeseries_annual_landings.R
R/fishing_fleet_model.R
R/internal.R
R/interpolate_drivers.R
R/list_models.R
R/monthly_averages_of_final_year.R
R/perturb_parameters.R
R/plot_final_year.R
R/plot_final_year_MERP_HTL_inshore_vs_offshore.R
R/plot_final_year_MERP_LTL_inshore_vs_offshore.R
R/plot_for_each_gear_catch_by_group.R
R/plot_for_each_group_catch_by_gear.R
R/plot_full_length_timeseries.R
R/plot_sediment_habitats_final_year.R
R/plot_time_series_annual_land_disc.R
R/read_SD_control_file.R
R/read_annual_target_data.R
R/read_biological_event_timings.R
R/read_chemistry_drivers.R
R/read_fishing_fleet_model.R
R/read_fitted_parameters.R
R/read_fixed_parameters.R
R/read_initial_state.R
R/read_model.R
R/read_monthly_target_data.R
R/read_physical_parameters.R
R/read_physics_drivers.R
R/sensitivity_analysis.R
R/store_fleet_model_output.R
R/write_fitted_parameters.R
R/zzz.R
README.md
inst/doc/strathe2e2_user_guide.pdf
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Driving_data/2003-2013_boundary_data_2surf_SInitadjusted-CLYDE_WOAtlas.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Driving_data/2003-2013_physics_drivers_2surf_pdistreordered-CLYDE.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/MODEL_SETUP.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/2003-2013_biological_event_timing_parameters_clyde.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/Parameter_SD_control/CredIntSim_SD.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/Parameter_SD_control/OATsensitivity_SD.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/Parameter_SD_control/annealing_SD.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/Parameter_SD_control/annealing_SD_ecology.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/Parameter_SD_control/annealing_SD_fishing.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/Price_per_tonne_and_nitrogen_WW_conversions.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_activity_parameters_2003-2013_CLYDE.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_activity_scaling_values.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_costs_per_activity_2003_2013.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_discard_parameters_BMbycatch_tp_kelp-CLYDE.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_distribution_parameters_tp_kelp_CLYDE.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_fleet_parameters_CLYDE-V11-12(4)EXTdisc.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_fleet_parameters_REVISED_MF_DPupscaled_selSW_tp_kelp_incNOK-NEW-6EXTdisc.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_gear_net_profit_margins.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_power_parameters_BMbycatch_tp_kelp_incNOK-CLYDE.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_power_parameters_BMbycatch_tp_kelp_incNOK-NEW-4.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fishing_processing_at_sea_parameters_BMbycatch_tp_kelp-WESTSCOT.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fitted_parameters_microbiology_and_others-MERP_North_Sea_tp_kelp_40.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fitted_parameters_microbiology_and_others-MERP_North_Sea_tp_kelp_VERSION11-12.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fitted_parameters_preference_matrix-MERP_North_Sea_tp_kelp_40.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fitted_parameters_preference_matrix-MERP_North_Sea_tp_kelp_VERSION11-12.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fitted_parameters_uptake_and_mortality_rates-MERP_North_Sea_tp_kelp_40.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fitted_parameters_uptake_and_mortality_rates-MERP_North_Sea_tp_kelp_VERSION11-12.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fixed_parameters_for_consumer_groups-NEWYEAR18_tp_kelp_e30_2003-2013.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/fixed_parameters_miscellaneous_tp_kelp_lowQ10.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/food_web_flow_matrix_template_tp_kelp.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/harvest_ratio_scaling_values_tp_kelp.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/model_endstate_export-MERP_CLYDE1.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/model_endstate_export-MERP_CLYDE2.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/model_endstate_export-MERP_CLYDE3.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/model_endstate_export-MERP_North_Sea_2003-2013_baseline.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Parameters/physical_parameters_CLYDE-v13.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Target_data/annual_target_data_2SURF_V15tp_kelp-2_2003-2013_Clyde.csv
inst/extdata/Models/MERP_Clyde_Bias_corrected_KELP/2003-13_First_draft/Target_data/monthly_target_data.csv
inst/extdata/Models/North_Sea/1970-1999/Driving_data/boundary_data_NORTH_SEA_1970-1999.csv
inst/extdata/Models/North_Sea/1970-1999/Driving_data/physics_drivers_NORTH_SEA_1970-1999.csv
inst/extdata/Models/North_Sea/1970-1999/MODEL_SETUP.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/Parameter_SD_control/CredIntSim_SD.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/Parameter_SD_control/OATsensitivity_SD.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/Parameter_SD_control/annealing_SD_ecology.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/Parameter_SD_control/annealing_SD_fishing.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/biological_event_timing_parameters_NORTH_SEA_1970-1999.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fishing_activity_parameters_NORTH_SEA_1970-1999.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fishing_activity_scaling_values.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fishing_discard_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fishing_distribution_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fishing_fleet_parameters_NORTH_SEA_1970-1999.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fishing_power_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fishing_processing_at_sea_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fitted_parameters_microbiology_and_others_NORTH_SEA.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fitted_parameters_preference_matrix_NORTH_SEA.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fitted_parameters_uptake_and_mortality_rates_NORTH_SEA.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fixed_parameters_for_consumer_groups_NORTH_SEA_1970-1999.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/fixed_parameters_miscellaneous.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/food_web_flow_matrix_template.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/harvest_ratio_scaling_values.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/model_endstate_export_NORTH_SEA_1970-1999.csv
inst/extdata/Models/North_Sea/1970-1999/Parameters/physical_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/1970-1999/Target_data/annual_target_data_NORTH_SEA_1970-1999.csv
inst/extdata/Models/North_Sea/1970-1999/Target_data/monthly_target_data_NORTH_SEA_1970-1999.csv
inst/extdata/Models/North_Sea/2003-2013/Driving_data/boundary_data_NORTH_SEA_2003-2013.csv
inst/extdata/Models/North_Sea/2003-2013/Driving_data/physics_drivers_NORTH_SEA_2003-2013.csv
inst/extdata/Models/North_Sea/2003-2013/MODEL_SETUP.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/Parameter_SD_control/CredIntSim_SD.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/Parameter_SD_control/OATsensitivity_SD.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/Parameter_SD_control/annealing_SD_ecology.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/Parameter_SD_control/annealing_SD_fishing.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/biological_event_timing_parameters_NORTH_SEA_2003-2013.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fishing_activity_parameters_NORTH_SEA_2003-2013.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fishing_activity_scaling_values.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fishing_discard_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fishing_distribution_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fishing_fleet_parameters_NORTH_SEA_2003-2013.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fishing_power_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fishing_processing_at_sea_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fitted_parameters_microbiology_and_others_NORTH_SEA.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fitted_parameters_preference_matrix_NORTH_SEA.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fitted_parameters_uptake_and_mortality_rates_NORTH_SEA.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fixed_parameters_for_consumer_groups_NORTH_SEA_2003-2013.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/fixed_parameters_miscellaneous.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/food_web_flow_matrix_template.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/harvest_ratio_scaling_values.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/model_endstate_export_NORTH_SEA_2003-2013.csv
inst/extdata/Models/North_Sea/2003-2013/Parameters/physical_parameters_NORTH_SEA.csv
inst/extdata/Models/North_Sea/2003-2013/Target_data/annual_target_data_NORTH_SEA_2003-2013.csv
inst/extdata/Models/North_Sea/2003-2013/Target_data/monthly_target_data_NORTH_SEA_2003-2013.csv
man/StrathE2E.Rd
man/aggregate_model_output.Rd
man/annealing_fit_ecology_parameters.Rd
man/assemble_flow_matrix_from_model_annual_output.Rd
man/box_and_whisker_annual_plots.Rd
man/box_and_whisker_monthly_plots.Rd
man/build_annual_drivers.Rd
man/build_initial_state.Rd
man/build_model.Rd
man/build_model_parameters.Rd
man/build_model_run.Rd
man/calculate_error_function.Rd
man/calculate_uptakes.Rd
man/copy_model.Rd
man/derive_annual_results_inshore.Rd
man/derive_annual_results_offshore.Rd
man/derive_annual_results_wholedomain.Rd
man/derive_model_target_results.Rd
man/disaggregate_landings_discards_by_gear.Rd
man/extract_simulated_catch_land_disc_by_gear_for_given_year.Rd
man/extract_timeseries_annual_landings.Rd
man/fishing_fleet_model.Rd
man/interpolate_drivers.Rd
man/list_models.Rd
man/monthly_averages_of_final_year.Rd
man/perturb_parameters.Rd
man/plot_final_year.Rd
man/plot_final_year_MERP_HTL_inshore_vs_offshore.Rd
man/plot_final_year_MERP_LTL_inshore_vs_offshore.Rd
man/plot_for_each_gear_catch_by_group.Rd
man/plot_for_each_group_catch_by_gear.Rd
man/plot_full_length_timeseries.Rd
man/plot_sediment_habitats_final_year.Rd
man/plot_time_series_annual_land_disc.Rd
man/read_SD_control_ecology.Rd
man/read_annual_target_data.Rd
man/read_biological_event_timings.Rd
man/read_chemistry_drivers.Rd
man/read_fishing_fleet_model.Rd
man/read_fitted_parameters.Rd
man/read_fixed_parameters.Rd
man/read_initial_state.Rd
man/read_model.Rd
man/read_monthly_target_data.Rd
man/read_physical_parameters.Rd
man/read_physics_drivers.Rd
man/sensitivity_analysis.Rd
man/store_fleet_model_output.Rd
man/write_fitted_parameters.Rd
releases/StrathE2E2_2.0.0.zip
releases/latest.zip
src/E2E_Foodweb_MERP_OFFAL_KELP_clean_MODEL_FUNCTION_2SURF_REV_2ZOO_V9_ROWBACK_V12L_extra2-V11_LO.c
vignettes/StrathE2E2.Rmd
