Man pages for ShotaNishijima/messir
Management and Evaluation for Sustainability of Surume-Ika (Japanese flying squid) with R)
| convert_samuika_estMSY | Function for converting samuika result to the data for... |
| det_BRF | Calculating deterministic biological reference points |
| est_MSY | Estimating MSY-based management reference points for... |
| future_sim | future simulation for Surume-Ika |
| get_mohn | Calculation of Mohn's rho from retrospective analysis of... |
| get_prob_ref | Function for calculating probability of achiveing biological... |
| get_rec_pars | Function for deriving stock-recruitment parameters |
| get_SRdata | Function to get stock-recruit data from samuika object |
| integrate_detBRF | Output summary table with deterministic biological reference... |
| make_named_list | Making a combined list with original list name(s) |
| make_tmb_data | Function for making input data for est_MSY with TMB |
| out_beta_table | output summary table when changing beta |
| out_Fmulti_table | output summary table when changing Fmulti |
| out_summary_estimate | output a table of samuika results |
| out_summary_estimate_n | output a table of samuika results (Stock number and... |
| plot_catch | Function for plotting time series of catch biomass |
| plot_F | Function for plotting time-series of fishing mortality... |
| plot_retro_samuika | plotting retrospective analyses of samuika |
| plot_samuika_estimates | plotting (multiple) samuika results |
| plot_spawning_biomass | Function for plotting time-series of spawning biomass |
| plot_spawning_number | Function for plotting time-series of spawning number |
| plot_SR_regime | plotting stock-recruitment curve with regimes from a samuika... |
| plot_SR_samuika | plotting stock-recruitment curve from samuika objects |
| plot_stock_biomass | Function for plotting time-series of stock biomass |
| plot_stock_number | Function for plotting time-series of stock number |
| retro_samuika | Retrospective analysis for samuika |
| samuika | State-Space Assessment model Used for surume-IKA (samuika) – |
| simulate_rec_resid | Function for simulating recruitment residuals with... |
| SRF | Stock-recruitment function |
| trace_future | Tracing for future_sim results with different F values |
| use_est_MSY_tmb | Function for activating cpp file for samuuika with TMB |
| use_saumika_tmb | Function for activating cpp file for samuuika with TMB |
| visualize_future | Function for plotting future_res |
| visualize_kobe_chart | plotting Kobe chart |
| visualize_yield_curve | Function for visualizing yield curve from trace_future |
