Man pages for timjmiller/wham
Woods Hole Assessment Model (WHAM)
| check_convergence | Check convergence of WHAM model |
| check_estimability | Check for identifiability of fixed effects Originally... |
| compare_wham_models | Compare multiple WHAM (or ASAP) models |
| do_reference_points | Add reporting of biological reference points to WHAM model |
| do_retro_peels | Fit retrospective peels and add them to the fitted model... |
| do_sdreport | Add TMB sdreport object to WHAM model |
| extract_fixed | Extract fixed effects Originally provided by... |
| fit_peel | Fit model peeling off _i_ years of data |
| fit_tmb | Fit TMB model using nlminb |
| fit_wham | Fit WHAM model |
| jitter_wham | Jitter starting values of a fitted WHAM model |
| make_osa_residuals | Calculate one-step-ahead residuals |
| mohns_rho | Calculate Mohn's rho for a WHAM model with peels |
| pipe | Pipe function |
| plot_wham_output | Plot WHAM output |
| prepare_projection | Prepare input data and parameters to project an already fit... |
| prepare_wham_input | Prepare input data and parameters for WHAM model |
| project_wham | Project a fit WHAM model |
| read_asap3_dat | Read an ASAP3 .dat file into R |
| read_asap3_fit | Read ASAP3 fit |
| read_wham_fit | Read WHAM fit |
| reduce_input | Reduce the years of the model |
| retro | Run retrospective analysis |
| self_test | Perform self-test simulation and estimation of a fitted WHAM... |
| set_age_comp | Specify the age composition models for fleet(s) and indices. |
| set_catch | Specify catch selectivity blocks and aggregate and age... |
| set_ecov | Specify configuration for environmental covariates, effects... |
| set_F | Specify configuration for fully-selected fishing mortality |
| set_indices | Specify index selectivity blocks and aggregate and age... |
| set_L | Specify model and parameter configuration for "extra"... |
| set_M | Specify model and parameter configuration for natural... |
| set_move | Specify model and parameter configuration for movement when... |
| set_NAA | Specify model and parameter configuration for numbers at age |
| set_osa_obs | Set up observation vector that is used by the model for... |
| set_q | Specify model and parameter configuration for catchability |
| set_selectivity | Specify model and parameter configuration for selectivity |
| wham_html | Create HTML file to view output plots in browser |
