End-to-End Marine Food Web Model

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Documentation for package ‘StrathE2E2’ version 3.3.0

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