Files in StrathE2E2
End-to-End Marine Food Web Model

MD5

NAMESPACE

DESCRIPTION

R/plot_for_each_gear_catch_by_guild.R R/read_SD_credint.R R/e2e_process_sens_mc.R R/store_fleet_model_output.R R/write_fitted_parameters.R R/plot_final_year_time_series_data_with_ci.R R/process_sensitivity_analysis_results.R R/CredInt_make_network_results.R R/e2e_plot_opt_diagnostics.R R/e2e_copy.R R/compare_two_runs_aam.R R/read_SD_fishing.R R/CredInt_make_daily_migration_results.R R/perturb_parameters_all.R R/plot_final_year_migration_data.R R/optimize_activity_mult_hr.R R/e2e_plot_sens_mc.R R/boxplot_monthly_compare_observations.R R/e2e_merge_sens_mc.R R/plot_time_series_annual_land_disc.R R/StrathE2E_fit.R R/calculate_uptakes.R R/internal.R R/postprocess_mc_data.R R/plot_pf_yield_curve.R R/e2e_plot_ts.R R/CredInt_make_monthly_results.R R/plot_final_year_time_series_data.R R/StrathE2E2.R R/e2e_plot_ycurve.R R/plot_final_year_trophic_data_with_ci.R R/plot_seabed_abrasion_area_ratios.R R/CredInt_make_annual_flux_results.R R/e2e_ls.R R/e2e_run.R R/perturb_parameters.R R/derive_model_target_results.R R/CredInt_make_daily_flux_results.R R/plot_eco_hr_act_eco_optimization_diagnostics.R R/e2e_run_mc.R R/extract_simulated_catch_land_disc_by_gear_for_given_year.R R/read_physical_parameters.R R/build_model_run.R R/extract_final_year_of_run_plus_volumetric_data.R R/plot_final_year_trophic_data.R R/plot_final_year_migration_data_with_ci.R R/plot_gear_guild_discard_rates.R R/concatenate_raw_sensitivity_data_files.R R/postprocess_sens_data.R R/e2e_plot_biomass.R R/plot_inshore_vs_offshore_anavmass_with_ci.R R/e2e_plot_eco.R R/e2e_calculate_hrscale.R R/plot_gear_guild_harvest_ratios.R R/CredInt_make_target_results.R R/boxplot_monthly_compare_observations_with_ci.R R/read_monthly_target_data.R R/CredInt_make_daily_results.R R/boxplot_annual_compare_observations_with_ci.R R/boxplot_annual_compare_runs.R R/read_fitted_parameters.R R/read_fixed_parameters.R R/e2e_plot_catch.R R/plot_sensitivity_results.R R/generate_df_yield_curve_data.R R/calculate_error_function.R R/plot_gear_activity_distribution.R R/e2e_optimize_act.R R/read_SD_ecology.R R/plot_df_yield_curve.R R/e2e_plot_edrivers.R R/concatenate_raw_mc_data_files.R R/CredInt_make_parameter_results.R R/build_model.R R/boxplot_monthly_compare_runs.R R/monthly_averages_of_final_year.R R/e2e_plot_fdrivers.R R/plot_full_length_timeseries.R R/build_annual_drivers.R R/compare_two_runs_catch.R R/derive_annual_results_wholedomain.R R/e2e_get_parmdoc.R R/read_SD_sensitivity.R R/read_physics_drivers.R R/e2e_extract_start.R R/assemble_flow_matrix_from_model_annual_output.R R/e2e_optimize_hr.R R/e2e_read.R R/e2e_optimize_eco.R R/plot_gear_guild_offal_rates.R R/e2e_compare_runs_bar.R R/aggregate_model_output.R R/e2e_run_sens.R R/e2e_get_senscrit.R R/read_fishing_fleet_model.R R/derive_annual_results_offshore.R R/e2e_compare_runs_box.R R/generate_pf_yield_curve_data.R R/e2e_plot_trophic.R R/e2e_extract_hr.R R/disaggregate_landings_discards_by_gear.R R/plot_act_hr_optimization_diagnostics.R R/build_model_parameters.R R/interpolate_drivers.R R/extract_timeseries_annual_landings.R R/optimize_activity_mult_eco.R R/CredInt_make_aamass_results.R R/read_initial_state.R R/boxplot_annual_compare_observations.R R/read_chemistry_drivers.R R/e2e_run_ycurve.R R/fishing_fleet_model.R R/read_annual_target_data.R R/e2e_plot_migration.R R/derive_annual_results_inshore.R R/plot_inshore_vs_offshore_anavmass.R R/plot_for_each_guild_catch_by_gear.R R/plot_mc_parameter_likelihoods.R R/e2e_compare_obs.R R/build_initial_state.R R/read_biological_event_timings.R

src/init.c

src/StrathE2E2_ecology_model_function.c

inst/CITATION

inst/doc/StrathE2E2_CheatSheet.Rnw

inst/doc/StrathE2E2_CheatSheet.pdf

inst/extdata/Models/North_Sea/1970-1999/MODEL_SETUP.csv

inst/extdata/Models/North_Sea/1970-1999/Driving/chemistry_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Driving/physics_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Target/monthly_observed_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Target/region_harvest_r_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Target/annual_observed_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Target/zonal_harvest_r_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fishing_discards_NORTH_SEA.csv

inst/extdata/Models/North_Sea/1970-1999/Param/event_timing_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fishing_power_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fishing_fleet_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fishing_activity_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fishing_processing_NORTH_SEA.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fixed_miscellaneous.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fishing_gear_linkages.csv

inst/extdata/Models/North_Sea/1970-1999/Param/harvest_ratio_multiplier.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fixed_consumers_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Param/physical_parameters_NORTH_SEA.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fitted_microbiology_others_NORTH_SEA.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fishing_distribution_NORTH_SEA.csv

inst/extdata/Models/North_Sea/1970-1999/Param/food_web_flow_matrix_template.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fishing_gear_multiplier.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fitted_preference_matrix_NORTH_SEA.csv

inst/extdata/Models/North_Sea/1970-1999/Param/fitted_uptake_mort_rates_NORTH_SEA.csv

inst/extdata/Models/North_Sea/1970-1999/Param/initial_values_NORTH_SEA_1970-1999.csv

inst/extdata/Models/North_Sea/1970-1999/Param/control/sensitivity.csv

inst/extdata/Models/North_Sea/1970-1999/Param/control/optimize_fishing.csv

inst/extdata/Models/North_Sea/1970-1999/Param/control/optimize_ecology.csv

inst/extdata/Models/North_Sea/1970-1999/Param/control/monte_carlo.csv

inst/extdata/Models/North_Sea/2003-2013/MODEL_SETUP.csv

inst/extdata/Models/North_Sea/2003-2013/Driving/physics_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Driving/chemistry_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Target/monthly_observed_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Target/zonal_harvest_r_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Target/region_harvest_r_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Target/annual_observed_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fishing_discards_NORTH_SEA.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fishing_fleet_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Param/initial_values_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Param/event_timing_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fishing_processing_NORTH_SEA.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fixed_miscellaneous.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fishing_activity_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fixed_consumers_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fishing_gear_linkages.csv

inst/extdata/Models/North_Sea/2003-2013/Param/harvest_ratio_multiplier.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fishing_power_NORTH_SEA_2003-2013.csv

inst/extdata/Models/North_Sea/2003-2013/Param/physical_parameters_NORTH_SEA.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fitted_microbiology_others_NORTH_SEA.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fishing_distribution_NORTH_SEA.csv

inst/extdata/Models/North_Sea/2003-2013/Param/food_web_flow_matrix_template.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fishing_gear_multiplier.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fitted_preference_matrix_NORTH_SEA.csv

inst/extdata/Models/North_Sea/2003-2013/Param/fitted_uptake_mort_rates_NORTH_SEA.csv

inst/extdata/Models/North_Sea/2003-2013/Param/control/sensitivity.csv

inst/extdata/Models/North_Sea/2003-2013/Param/control/optimize_fishing.csv

inst/extdata/Models/North_Sea/2003-2013/Param/control/optimize_ecology.csv

inst/extdata/Models/North_Sea/2003-2013/Param/control/monte_carlo.csv

inst/extdata/Internal.data/StrathE2E_parameter_list.csv

build/vignette.rds

tests/testthat.R

tests/testdata/models/Testbed/Const/MODEL_SETUP.csv

tests/testdata/models/Testbed/Const/Driving/physics_Testbed.csv

tests/testdata/models/Testbed/Const/Driving/chemistry_Testbed.csv

tests/testdata/models/Testbed/Const/Target/region_harvest_r_Testbed.csv

tests/testdata/models/Testbed/Const/Target/zonal_harvest_r_Testbed.csv

tests/testdata/models/Testbed/Const/Target/annual_observed_Testbed.csv

tests/testdata/models/Testbed/Const/Target/monthly_observed_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fishing_power_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fixed_consumers_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fitted_microbiology_others_Testbed.csv

tests/testdata/models/Testbed/Const/Param/initial_values_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fishing_activity_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fixed_miscellaneous.csv

tests/testdata/models/Testbed/Const/Param/fitted_uptake_mort_rates_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fishing_gear_linkages.csv

tests/testdata/models/Testbed/Const/Param/harvest_ratio_multiplier.csv

tests/testdata/models/Testbed/Const/Param/event_timing_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fishing_discards_Testbed.csv

tests/testdata/models/Testbed/Const/Param/physical_parameters_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fishing_processing_Testbed.csv

tests/testdata/models/Testbed/Const/Param/food_web_flow_matrix_template.csv

tests/testdata/models/Testbed/Const/Param/fishing_gear_multiplier.csv

tests/testdata/models/Testbed/Const/Param/fishing_fleet_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fitted_preference_matrix_Testbed.csv

tests/testdata/models/Testbed/Const/Param/fishing_distribution_Testbed.csv

tests/testdata/models/Testbed/Const/Param/control/optimize_fishing.csv

tests/testdata/models/Testbed/Const/Param/control/optimize_ecology.csv

tests/testdata/models/Testbed/Const/Param/control/sensitivity_SD.csv

tests/testdata/models/Testbed/Const/Param/control/monte_carlo.csv

tests/testdata/plots/opt_act_eco.png

tests/testdata/plots/eco_benthos.png

tests/testdata/plots/eco_nut_phyt.png

tests/testdata/plots/eco_zooplankton_ci.png

tests/testdata/plots/plot_compare_runs_annual.png

tests/testdata/plots/fdrivers_harvestr.png

tests/testdata/plots/plot_sens.png

tests/testdata/plots/eco_zooplankton.png

tests/testdata/plots/eco_macrophyte.png

tests/testdata/plots/eco_fish.png

tests/testdata/plots/plot_trophic_ci.png

tests/testdata/plots/annual_compare_obs_ci.png

tests/testdata/plots/eco_predators_ci.png

tests/testdata/plots/plot_catch_by_guild.png

tests/testdata/plots/plot_biomass.png

tests/testdata/plots/eco_nut_phyt_ci.png

tests/testdata/plots/edrivers.png

tests/testdata/plots/ts_fishery_statistics.png

tests/testdata/plots/annual_compare_obs.png

tests/testdata/plots/eco_fish_ci.png

tests/testdata/plots/fdrivers_offal.png

tests/testdata/plots/plot_biomass_ci.png

tests/testdata/plots/plot_migration_ci1.png

tests/testdata/plots/plot_compare_runs_monthly.png

tests/testdata/plots/fdrivers_activity.png

tests/testdata/plots/plot_migration.png

tests/testdata/plots/plotall.R

tests/testdata/plots/eco_corp_disc.png

tests/testdata/plots/plot_ycurve_demersal.png

tests/testdata/plots/opt_hr.png

tests/testdata/plots/monthly_compare_runs.png

tests/testdata/plots/eco_predators.png

tests/testdata/plots/opt_eco.png

tests/testdata/plots/ts_ecology_variables.png

tests/testdata/plots/monthly_compare_obs.png

tests/testdata/plots/plot_trophic.png

tests/testdata/plots/plot_ycurve_planktiv.png

tests/testdata/plots/monthly_compare_obs_ci.png

tests/testdata/plots/eco_sediment_ci.png

tests/testdata/plots/opt_act_hr.png

tests/testdata/plots/fdrivers_discards.png

tests/testdata/plots/plot_compare_runs_catch.png

tests/testdata/plots/plot_compare_runs_amm.png

tests/testdata/plots/plot_pf_yield.png

tests/testdata/plots/annual_compare_runs.png

tests/testdata/plots/eco_benthos_ci.png

tests/testdata/plots/eco_sediment.png

tests/testdata/plots/eco_macrophyte_ci.png

tests/testdata/plots/eco_corp_disc_ci.png

tests/testdata/plots/plot_biomass_saved.png

tests/testdata/plots/plot_catch_by_gear.png

tests/testdata/plots/plot_mc.png

tests/testdata/plots/plot_df_yield.png

tests/testdata/plots/fdrivers_abrasion.png

vignettes/StrathE2E2_CheatSheet.Rnw

man/e2e_plot_ts.Rd man/e2e_plot_trophic.Rd man/e2e_merge_sens_mc.Rd man/e2e_plot_biomass.Rd man/e2e_plot_migration.Rd man/e2e_extract_start.Rd man/e2e_plot_fdrivers.Rd man/e2e_run.Rd man/e2e_compare_obs.Rd man/e2e_calculate_hrscale.Rd man/e2e_optimize_hr.Rd man/e2e_plot_sens_mc.Rd man/StrathE2E2-package.Rd man/e2e_process_sens_mc.Rd man/e2e_extract_hr.Rd man/e2e_compare_runs_box.Rd man/e2e_get_parmdoc.Rd man/e2e_run_mc.Rd man/e2e_plot_catch.Rd man/e2e_ls.Rd man/e2e_plot_eco.Rd man/e2e_run_ycurve.Rd man/e2e_read.Rd man/e2e_copy.Rd man/e2e_optimize_act.Rd man/e2e_run_sens.Rd man/e2e_plot_edrivers.Rd man/e2e_plot_ycurve.Rd man/e2e_optimize_eco.Rd man/e2e_compare_runs_bar.Rd man/e2e_get_senscrit.Rd man/e2e_plot_opt_diagnostics.Rd

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

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StrathE2E2
End-to-End Marine Food Web Model

Files in StrathE2E2
End-to-End Marine Food Web Model

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StrathE2E2 End-to-End Marine Food Web Model

Files in StrathE2E2 End-to-End Marine Food Web Model

R Package Documentation

Browse R Packages

We want your feedback!

StrathE2E2
End-to-End Marine Food Web Model

Files in StrathE2E2
End-to-End Marine Food Web Model