Man pages for strathclyde-marine-resource-modelling/StrathE2E2
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 |
