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| annealing_find_ecology_parameters | Optimise StrathE2E ecology model parameters to maximise the likelihood of observed ecosystem target data |
| annealing_find_gear_activity_mult_ecosystem_target | Optimise StrathE2E fishing gear activity multipliers to maximum the likelihood of observed ecosystem target data |
| annealing_find_gear_activity_mult_HR_target | Optimise fishing gear activity multipliers to maximum the likelihood of known harvest ratios |
| annealing_find_harvest_ratio_mult | Optimise StrathE2E harvest ratio multipliers to maximum the likelihood of observed ecosystem target data |
| assemble_flow_matrix_from_model_annual_output | process the whole domain annual flux results held in the dataframe annual_flux_results to produce a flow-matrix defining all of the annual integrated mass fluxes been every pair of prey and predator guilds in the food web, alf the geochemical flows, and all of the boundary flows |
| box_and_whisker_annual_plots | Box-and-whisker plots of observed annual target data on the state of the ecosystem with equivalent properties derived from a StrathE2E run |
| box_and_whisker_annual_plots_with_credible_intervals | Box-and-whisker plots of observed annual target data on the state of the ecosystem with equivalent properties derived from a Monte Carlo StrathE2E run |
| box_and_whisker_monthly_plots | Box-and-whisker plots of observed monthly data on the state of the ecosystem with equivalent properties derived from a StrathE2E run |
| box_and_whisker_monthly_plots_with_credible_intervals | Box-and-whisker plots of observed monthly data on the state of the ecosystem with equivalent properties derived from a Monte Carlo StrathE2E run |
| build_annual_drivers | uses monthly values of time-series drivers over a climatological annual cycle and makes them into functions for #interpolating values at any given time. |
| build_initial_state | adjust initial state taking notice of physical parameters |
| build_model_parameters | Build entire set of model parameters combining fixed, physical, fleet model output, plus some biomass thresholds |
| build_model_run | build model run |
| calculate_error_function | measure current model fit |
| calculate_hr_scale_values | Calculate rough values of the scaling parameters for the fishing fleet model which link effort to harvest ratios |
| calculate_uptakes | Apply perturbed preference values to fitted parameters to calculate uptakes |
| compare_two_runs_aam | Create a tornado plot of the differences in annual averaged masses of variable in two model runs |
| compare_two_runs_catch | Create a tornado plot of the differences in landings and discards in two model runs |
| concatenate_raw_sensitivity_analysis_results | Combine two or more sets of raw output data from sensitivity analysis runs performed on separate machine/processors |
| copy_model | Make a copy of a named model/variant and documentation in a user defined workspace |
| CredInt_make_aamass_results | Save current set of fitted parameters to file |
| CredInt_make_annual_flux_results | Save current set of fitted parameters to file |
| CredInt_make_daily_flux_results | Save current set of fitted parameters to file |
| CredInt_make_daily_migration_results | Save current set of fitted parameters to file |
| CredInt_make_daily_results | Save current set of fitted parameters to file |
| CredInt_make_monthly_results | Save current set of fitted parameters to file |
| CredInt_make_network_results | Save current set of fitted parameters to file |
| CredInt_make_parameter_results | Save current set of fitted parameters to file |
| CredInt_make_target_results | Save current set of fitted parameters to file |
| derive_annual_results_inshore | derive set of results for inshore only and write to files |
| derive_annual_results_offshore | derive set of results for offshore only and write to files |
| derive_annual_results_wholedomain | extract annual average biomass in the final year for the whole model domain |
| derive_model_target_results | derive annual target results and write to file |
| disaggregate_landings_discards_by_gear | disaggregate group annual landings and discards by gear |
| extract_final_year_of_run_plus_volumetric_data | extract the final year of model output and add columns of the volumetric data needed to process the results |
| extract_new_initial_cond_from_end_of_run | Extract the values of all the state variables at the end of a run and format for use as new initial conditions |
| extract_simulated_catch_land_disc_by_gear_for_given_year | extract simulated catch |
| extract_timeseries_annual_landings | read designated model |
| fishing_fleet_model | defines the fishing fleet model |
| interpolate_drivers | Interpolate drivers over time that model is to be run |
| list_models | List the available models in a designated workspace |
| Monte_Carlo_StrathE2E | Runs a Monte Carlo simulation with StrathE2E and derives centiles of credible values of model outputs |
| monthly_averages_of_final_year | Summarise the final year for nitrate ammonia and chl |
| perturb_parameters | perturb parameters a bit |
| perturb_parameters_all | perturb parameters a bit |
| plot_final_year | Multi-panel time series plots of state variable data for the final year of a model run generated by the StrathE2E() function |
| plot_final_year_HTL_inshore_vs_offshore | Plots of inshore and offshore high trophic level state variables for the final year of a model run |
| plot_final_year_LTL_inshore_vs_offshore | Plots of inshore and offshore low trophic level state variables for the final year of a model run |
| plot_final_year_migration_data_with_credible_intervals | Plots of active migration fluxes over the final year of a simulation generated by the Monte_Carlo_StrathE2E() function |
| plot_final_year_time_series_data_with_credible_intervals | Create multi-panel plots showing the credible intervals of state variable densities over the final year of a simulation generated by the Monte_Carlo_StrathE2E() function |
| plot_final_year_trophic_data_with_credible_intervals | Plots of credible value distributions mean trophic level and omnivory index generated by the Monte_Carlo_StrathE2E() function |
| plot_for_each_gear_catch_by_guild | Plots of annual integrated catch compositions by each gears for the final year of a model run |
| plot_for_each_guild_catch_by_gear | Plots of the distributions of annual integrated catches of each guild across gears for the final year of a model run |
| plot_full_length_timeseries | Plot state variable data for the full duration of a model run |
| plot_inshore_vs_offshore_anavmass_with_credible_intervals | Plots of annual average inshore and offshore mass densities generated a Monte_Carlo StrathE2E simulation |
| plot_Monte_Carlo_parameter_distributions | Plots the credible distributions of ecology model parameters from a Monte Carlo simulation |
| plot_sediment_habitats_final_year | Plots of inshore and offshore sediment habitat state variables |
| plot_sensitivity_analysis_results | Create a plot of results from the Morris method sensitivity analysis |
| plot_time_series_annual_land_disc | Time series plots of annual integrated catches from the inshore and offshore zones |
| process_sensitivity_analysis_results | post-process data from a one-at-a-time sensitivity analysis using the Morris Method for factorial sampling of the ecology model parameters, the fishing fleet model parameters, and the environmental forcings |
| process_sensitivity_analysis_results_offline | Read and post-process raw data saved as a csv file from the Sensitivity_analysis_StrathE2E() function |
| read_annual_target_data | read annual target data |
| read_biological_event_timings | Read the biological event timing parameters |
| read_chemistry_drivers | Read the default set of chemistry drivers |
| read_fishing_fleet_model | read fishing fleet model configuration |
| read_fitted_parameters | Load fitted parameter values for model |
| read_fixed_parameters | load the fixed parameters used in the model |
| read_initial_state | read and set the initial values of the state variables used in the model |
| read_model | Read all the configuration, driving and parameter files for a designated model and compiles the data into a list object |
| read_monthly_target_data | read monthly target data |
| read_physical_parameters | set up the physical configuration of the model |
| read_physics_drivers | Read the default set of physics drivers |
| read_SD_credint | return list of annealing parameters |
| read_SD_ecology | return list of annealing parameters |
| read_SD_fishing | return list of annealing parameters |
| read_SD_sensitivity | return list of annealing parameters |
| Sensitivity_analysis_StrathE2E | Performs a one-at-a-time parameter sensitivity analysis on the StrathE2E model |
| store_fleet_model_output | grab the 'gear_group_prop_effort' and 'gear_group_prob_discard' matrices, reorganise and store them for use after the main model run to derive the landings and discards from each gear, from inshore and offshore zones |
| StrathE2E | Run the StrathE2E model |
| StrathE2E2 | StrathE2E2 Package |
| StrathE2E_fit | run the StrathE2E model and return objective error |
| write_fitted_parameters | Save current set of fitted parameters to file |