# End-to-End Marine Food Web Model

## Documentation for package ‘StrathE2E2’ version 3.3.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.
StrathE2E2 | StrathE2E2 Package