StrathE2EPolar          StrathE2EPolar Package
e2ep_calculate_hrscale
                        Calculate initial values of the scaling
                        parameters for the fishing fleet model which
                        link effort to harvest ratios.
e2ep_compare_obs        Box and whisker plots comparing annual or
                        monthly observational data with corresponding
                        model outputs.
e2ep_compare_runs_bar   Create tornado bar-plots of the differences
                        between two model runs.
e2ep_compare_runs_box   Box and whisker plots comparing annual or
                        monthly outputs from single or Monte Carlo
                        baseline and scenario model runs.
e2ep_copy               Make a copy of a named model/variant and
                        documentation in a user defined workspace
e2ep_extract_hr         Extract the values of harvest ratios generated
                        by the fleet model.
e2ep_extract_start      Extract the values of all the state variables
                        at the end of a model run and format for use as
                        new initial conditions.
e2ep_get_parmdoc        Get documentation on the parameters in the
                        model.
e2ep_get_senscrit       Get documentation on the model outputs
                        available as the basis for sensitivity
                        analysis.
e2ep_ls                 List the available models in a designated
                        workspace.
e2ep_merge_sens_mc      Combine two or more sets of raw output data
                        from parallel sensitivity or Monte Carlo
                        analysis runs performed on separate
                        machines/processors.
e2ep_optimize_act       Optimize StrathE2E fishing gear activity
                        multipliers to maximumize the likelihood of
                        either observed ecosystem target data or know
                        harvest ratios.
e2ep_optimize_eco       Optimize StrathE2EPolar ecology model
                        parameters to maximise the likelihood of
                        observed ecosystem target data.
e2ep_optimize_hr        Optimize StrathE2E harvest ratio multipliers to
                        maximum the likelihood of observed ecosystem
                        target data.
e2ep_plot_biomass       Plot showing the annual annual average biomass
                        densities of each guild in the inshore and
                        offshore zones, optionally with credible
                        intervals.
e2ep_plot_catch         Plot the distribution and composition of annual
                        catches across guild, zones and gears in the
                        final year of a model run.
e2ep_plot_eco           Plot daily data on ecological outputs from the
                        model over the final year of a run, optionally
                        with credible intervals.
e2ep_plot_edrivers      Plot climatological year of environmental
                        driving data.
e2ep_plot_fdrivers      Plot shaded-grid-cell diagrams of the
                        distributions of fishing-related drivers across
                        gears, guilds and seabed habitats.
e2ep_plot_migration     Plot daily data on migration fluxes by actively
                        mobile guilds during the final year of a run,
                        optionally with credible intervals.
e2ep_plot_opt_diagnostics
                        Plot diagnostic data on the performance of
                        parameter optimization functions.
e2ep_plot_sens_mc       Plot diagnostic data from sensitivity and Monte
                        Carlo analyses.
e2ep_plot_trophic       Plot showing the annual mean trophic level
                        index, and the omnivory index of each guild
                        during the final year of a model run,
                        optionally with credible intervals.
e2ep_plot_ts            Plot ecology model state variables or fishery
                        catches for the full duration of a model run.
e2ep_plot_ycurve        Plot fishery yield curve data for planktivorous
                        or demersal fish.
e2ep_process_sens_mc    Post-process already-created data from
                        sensitivity or Monte Carlo analysis runs.
e2ep_read               Read all the configuration, driving and
                        parameter files for a designated model and
                        compile the data into a list object.
e2ep_run                Run the StrathE2E model with a given
                        configuration.
e2ep_run_mc             Run a Monte Carlo simulation with StrathE2E and
                        derive centiles of credible values of model
                        outputs.
e2ep_run_sens           Perform a parameter sensitivity analysis on the
                        StrathE2EPolar model.
e2ep_run_ycurve         Run a set of models to generate fishery yield
                        curve data for either planktivorous or demersal
                        fish.
