StrathE2E2              StrathE2E2 Package
e2e_calculate_hrscale   Calculate initial values of the scaling
                        parameters for the fishing fleet model which
                        link effort to harvest ratios.
e2e_compare_obs         Box and whisker plots comparing annual or
                        monthly observational data with corresponding
                        model outputs.
e2e_compare_runs_bar    Create tornado bar-plots of the differences
                        between two model runs.
e2e_compare_runs_box    Box and whisker plots comparing annual or
                        monthly outputs from single or Monte Carlo
                        baseline and scenario model runs.
e2e_copy                Make a copy of a named model/variant and
                        documentation in a user defined workspace
e2e_extract_hr          Extract the values of harvest ratios generated
                        by the fleet model.
e2e_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.
e2e_get_parmdoc         Get documentation on the parameters in the
                        model.
e2e_get_senscrit        Get documentation on the model outputs
                        available as the basis for sensitivity
                        analysis.
e2e_ls                  List the available models in a designated
                        workspace.
e2e_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.
e2e_optimize_act        Optimize StrathE2E fishing gear activity
                        multipliers to maximumize the likelihood of
                        either observed ecosystem target data or know
                        harvest ratios.
e2e_optimize_eco        Optimize StrathE2E ecology model parameters to
                        maximise the likelihood of observed ecosystem
                        target data.
e2e_optimize_hr         Optimize StrathE2E harvest ratio multipliers to
                        maximum the likelihood of observed ecosystem
                        target data.
e2e_plot_biomass        Plot showing the annual annual average biomass
                        densities of each guild in the inshore and
                        offshore zones, optionally with credible
                        intervals.
e2e_plot_catch          Plot the distribution and composition of annual
                        catches across guild, zones and gears in the
                        final year of a model run.
e2e_plot_eco            Plot daily data on ecological outputs from the
                        model over the final year of a run, optionally
                        with credible intervals.
e2e_plot_edrivers       Plot climatological year of environmental
                        driving data.
e2e_plot_fdrivers       Plot shaded-grid-cell diagrams of the
                        distributions of fishing-related drivers across
                        gears, guilds and seabed habitats.
e2e_plot_migration      Plot daily data on migration fluxes by actively
                        mobile guilds during the final year of a run,
                        optionally with credible intervals.
e2e_plot_opt_diagnostics
                        Plot diagnostic data on the performance of
                        parameter optimization functions.
e2e_plot_sens_mc        Plot diagnostic data from sensitivity and Monte
                        Carlo analyses.
e2e_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.
e2e_plot_ts             Plot ecology model state variables or fishery
                        catches for the full duration of a model run.
e2e_plot_ycurve         Plot fishery yield curve data for planktivorous
                        or demersal fish.
e2e_process_sens_mc     Post-process already-created data from
                        sensitivity or Monte Carlo analysis runs.
e2e_read                Read all the configuration, driving and
                        parameter files for a designated model and
                        compile the data into a list object.
e2e_run                 Run the StrathE2E model with a given
                        configuration.
e2e_run_mc              Run a Monte Carlo simulation with StrathE2E and
                        derive centiles of credible values of model
                        outputs.
e2e_run_sens            Perform a parameter sensitivity analysis on the
                        StrathE2E model.
e2e_run_ycurve          Run a set of models to generate fishery yield
                        curve data for either planktivorous or demersal
                        fish.
