Man pages for pbs-assess/gfdlm
Tools for Working with openMSE (Including DLMtool, MSEtool, and SAMtool)
| change_chunk_suffix | Change the chunk and tag suffixes for a .Rmd file |
| check_tags | Check that begin and end slot-chunk tags match properly |
| chk_yrs | Check the years to summarize performance |
| create_default_rmd | Create template Rmd file describing MSEtool Objects and Slots |
| create_rmd | Create .Rmd file describing MSEtool Objects and Slots and... |
| download_om | Download an operating model from the DLMtool website |
| eval_pm | Evaluate performance petrics |
| FSP_summary | Summary of status estimates |
| get_obj_name | Get the actual name of the object for the base name object.... |
| get_probs | Summary of probabilities of performance metrics from the MSE... |
| IDX | Index-based MP from Cox et al. (2019) |
| Itarget | Itarget MP |
| ITM_hist | Historical Index Target based on natural mortality rate |
| load_data_factory | Factory to create loading functions for various species |
| MPs | Alternative versions of 'DLMtool' and 'MSEtool' MP functions |
| mse_example | Example simple MSE |
| om | Example simple operating model |
| pipe | Pipe operator |
| plot_convergence | Plot convergence |
| plot_dots | Dot plot |
| plot_factory | Make all typical plots |
| plot_historical_ts | Plot historical time series |
| plot_index | Plot sampled survey index or catch projections |
| plot_index_fits | Plot index fits from a stock reduction analysis |
| plot_kobe | Make Kobe contour plots by management procedure for B/BMSY by... |
| plot_lollipop | Make lollipop plot |
| plot_main_projections | Make a standard projection plot with SSB, F, and catch |
| plot_parallel_coords | Make parallel coordinates plot of performance metrics |
| plot_projection_ts | Plot projection time series |
| plot_radar | Create a radar plot |
| plot_rcm | Plotting functions from OM conditioning |
| plot_rcm_data | Plotting functions of data used for OM conditioning |
| plot_scenario | Plot a single time series for various scenarios and MPs |
| plot_scenario_projections | Plot projections for various scenarios on the same panels |
| plot_sensitivity | Sensitivity plot |
| plot_sensitivity_trajectory | Sensitivity trajectory plot |
| plot_tigure | Summary of performance metrics from MSE objects in a coloured... |
| plot_tradeoff | Make a trade-off scatterplot |
| plot_worms_grid | Make a Kobe "worm" timeseries plot with uncertainty |
| pm | Function factory for creating MSEtool performace metric... |
| reduce_survey | Eliminate survey data for selected years |
| sample_AddIerr | Sample additional index error |
| SP_gf | PBS groundfish surplus production wrapper function |
| theme_pbs | A ggplot2 theme |
| tidy_caa | Generate length-at-age or catch-at-age data |
| tidy_mean_length | Generate mean-length time series |
| use_AddInd | Use AddInd slot |
