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
Monte_Carlo_StrathE2E   Runs a Monte Carlo simulation with StrathE2E
                        and derives centiles of credible values of
                        model outputs
Sensitivity_analysis_StrathE2E
                        Performs a one-at-a-time parameter sensitivity
                        analysis on the StrathE2E model
StrathE2E               Run the StrathE2E model
StrathE2E2              StrathE2E2 Package
StrathE2E_fit           run the StrathE2E model and return objective
                        error
annealing_find_ecology_parameters
                        Optimise StrathE2E ecology model parameters to
                        maximise 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_gear_activity_mult_ecosystem_target
                        Optimise StrathE2E fishing gear activity
                        multipliers to maximum the likelihood of
                        observed ecosystem target data
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
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
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_Monte_Carlo_parameter_distributions
                        Plots the credible distributions of ecology
                        model parameters from a Monte Carlo simulation
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_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_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
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
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
write_fitted_parameters
                        Save current set of fitted parameters to file
