End-to-end marine food web model

aggregate_model_output | create some aggregates of various columns in the output... |

annealing_fit_ecology_parameters | Finds the best-fit values of the ecology model parameters... |

assemble_flow_matrix_from_model_annual_output | process the whole domain annual flux results held in the... |

box_and_whisker_annual_plots | plot observed and modelled distributions of the annual... |

box_and_whisker_monthly_plots | plot some monthly result sumamries |

build_annual_drivers | uses monthly values of time-series drivers over a... |

build_initial_state | adjust initial state taking notice of physical parameters |

build_model | build model for invocation of StrathE2E |

build_model_parameters | Build entire set of model parameters combining fixed,... |

build_model_run | build model run |

calculate_error_function | measure current model fit |

calculate_uptakes | Apply perturbed preference values to fitted parameters to... |

copy_model | make a copy of the named model/variant |

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... |

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_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 available models |

monthly_averages_of_final_year | Summarise the final year for nitrate ammonia and chl |

perturb_parameters | perturb parameters a bit |

plot_final_year | Plot final year time series |

plot_final_year_MERP_HTL_inshore_vs_offshore | Plot full time series of out |

plot_final_year_MERP_LTL_inshore_vs_offshore | Plot full time series of out |

plot_for_each_gear_catch_by_group | plot results as lineplots by group |

plot_for_each_group_catch_by_gear | plot results as lineplots by group |

plot_full_length_timeseries | Plot full time series of output |

plot_sediment_habitats_final_year | Plot full time series of out |

plot_time_series_annual_land_disc | plot results as lineplots by group |

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... |

read_model | read designated model |

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_control_ecology | return list of annealing paramters |

sensitivity_analysis | performs a one-at-a-time sensitivity analysis using the... |

store_fleet_model_output | grab the 'gear_group_prop_effort' and... |

StrathE2E | run the StrathE2E model |

write_fitted_parameters | Save current set of fitted parameters to file |

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