API for SAMtool
Stock Assessment Methods Toolkit
| Global functions | |
|---|---|
| .RCM_update_OM | Source code |
| .onUnload | Source code |
| AAV | Source code |
| Assess_I_hist | Source code |
| Assess_diagnostic | Source code |
| Assess_sim | Source code |
| Assessment | Man page |
| Assessment-class | Man page |
| Baranov | Source code |
| DDSS_4010 | Man page |
| DDSS_75MSY | Man page |
| DDSS_MSY | Man page |
| DD_ | Source code |
| DD_SS | Man page Source code |
| DD_TMB | Man page Source code |
| DD_dynamic_SSB0 | Source code |
| Data-rich-MP | Man page |
| Euler_Lotka_fn | Source code |
| HCR40_10 | Man page Source code |
| HCR60_20 | Man page Source code |
| HCR80_40MSY | Man page Source code |
| HCR_FB | Man page Source code |
| HCR_MSY | Man page Source code |
| HCR_escapement | Man page Source code |
| HCR_fixedF | Man page Source code |
| HCR_ramp | Man page Source code |
| HCR_segment | Man page Source code |
| HCRlin | Man page Source code |
| HCRlinesegment | Source code |
| LinInterp | Source code |
| MP | Man page |
| MesnilRochet_SPRcrash | Source code |
| MesnilRochet_SR | Source code |
| Model-based-MP | Man page |
| Mohn_rho | Source code |
| PRBcalc | Man page Source code |
| PRBplot | Source code |
| Perfect | Man page Source code |
| Probs | Man page Source code |
| RCM | Man page |
| RCM,OM,Data-method | Man page |
| RCM,OM,RCMdata-method | Man page |
| RCM,OM,list-method | Man page |
| RCM,list,RCMdata-method | Man page |
| RCM2MOM | Man page Source code |
| RCM_SPR | Source code |
| RCM_assess | Man page Source code |
| RCM_assess_StockPars | Source code |
| RCM_assess_ref | Source code |
| RCM_dynamic_SSB0 | Source code |
| RCM_est | Source code |
| RCM_est_data | Source code |
| RCM_est_params | Source code |
| RCM_get_likelihoods | Source code |
| RCM_int | Source code |
| RCM_nll_profile_summary | Source code |
| RCM_posthoc_adjust | Source code |
| RCM_report_samps | Source code |
| RCM_retro | Source code |
| RCM_retro_subset | Source code |
| RCM_sample_future_dev | Source code |
| RCM_sim | Source code |
| RCM_single_fit | Source code |
| RCM_update_OM | Source code |
| RCMdata | Man page |
| RCMdata-class | Man page |
| RCModel | Man page |
| RCModel-class | Man page |
| RCMstan | Man page Source code |
| R_pred | Source code |
| SAMtool | Man page |
| SAMtool-package | Man page |
| SCA | Man page Source code |
| SCA2 | Man page Source code |
| SCA_ | Source code |
| SCA_4010 | Man page |
| SCA_75MSY | Man page |
| SCA_CAL | Man page Source code |
| SCA_DDM | Man page Source code |
| SCA_MSY | Man page |
| SCA_Pope | Man page Source code |
| SCA_RWM | Man page Source code |
| SCA_catch_solver | Source code |
| SCA_dynamic_SSB0 | Source code |
| SP | Man page Source code |
| SP_ | Source code |
| SP_4010 | Man page |
| SP_75MSY | Man page |
| SP_Fox | Man page Source code |
| SP_MSY | Man page |
| SP_SS | Man page Source code |
| SP_catch_solver | Source code |
| SP_dynamic_SSB0 | Source code |
| SP_production | Man page Source code |
| SSS | Man page Source code |
| SSS_4010 | Man page |
| SSS_75MSY | Man page |
| SSS_MSY | Man page |
| Shortcut | Man page Source code |
| Shortcut2 | Man page Source code |
| TAC_MSY | Man page Source code |
| VPA | Man page Source code |
| VPA_posthoc | Source code |
| arrows | Source code |
| assign_Assessment_slots | Source code |
| cDD | Man page Source code |
| cDD_ | Source code |
| cDD_SS | Man page Source code |
| cDD_catch_solver | Source code |
| cDD_dynamic_SSB0 | Source code |
| calc_NPR | Source code |
| calc_mvlogistic_loglike | Source code |
| calculate_Mohn_rho | Source code |
| calculate_TAC | Man page Source code |
| catch_equation | Source code |
| check_OM_for_sampling | Source code |
| check_RCMdata | Man page Source code |
| check_StockPars | Source code |
| check_det | Source code |
| clean_tmb_parameters | Source code |
| compare_RCM | Man page Source code |
| compare_models | Man page Source code |
| create_sim_object | Source code |
| dev_AC | Source code |
| diagnostic | Man page Source code |
| diagnostic_AM | Man page Source code |
| dmvlogistic | Source code |
| do.call2 | Source code |
| dots_check | Source code |
| expand_V_matrix | Source code |
| expand_comp_matrix | Source code |
| extreme.outlier | Source code |
| find_na | Source code |
| generate_PLA | Source code |
| get_F01 | Source code |
| get_FSPR | Source code |
| get_Fmax | Source code |
| get_SR | Source code |
| get_ivul_len | Source code |
| get_sdreport | Source code |
| get_vul_len | Source code |
| getinds | Man page Source code |
| getsegment | Source code |
| hist.numeric | Source code |
| iVB | Source code |
| ilogit | Source code |
| ilogit2 | Source code |
| ilogitm | Source code |
| individual_array_fn | Source code |
| individual_matrix_fn | Source code |
| int_s_sel | Source code |
| int_sel | Source code |
| logit | Source code |
| logit2 | Source code |
| mahalanobis_contribution | Source code |
| mahdensplot | Source code |
| mahplot | Man page Source code |
| make_LWT | Source code |
| make_MP | Man page Source code |
| make_SL | Source code |
| make_interim_MP | Man page Source code |
| make_prior | Source code |
| make_prior_SP | Source code |
| make_projection_MP | Man page |
| make_unique_names | Source code |
| match_R_years | Source code |
| matplot | Source code |
| matrix_slot_fn | Source code |
| max | Source code |
| message | Source code |
| message_info | Source code |
| message_oops | Source code |
| mu | Source code |
| optimize_TMB_model | Source code |
| par_identical_sims_fn | Source code |
| pcod | Man page |
| plot,Assessment,missing-method | Man page |
| plot,Assessment,retro-method | Man page |
| plot,RCModel,missing-method | Man page |
| plot,prof,missing-method | Man page |
| plot,retro,missing-method | Man page |
| plot.Assessment | Man page |
| plot.RCModel | Man page |
| plot.default | Source code |
| plot.prof | Man page |
| plot.retro | Man page |
| plot_Kobe | Source code |
| plot_SR | Man page Source code |
| plot_betavar | Man page Source code |
| plot_composition | Man page Source code |
| plot_composition_RCM | Source code |
| plot_crosscorr | Man page Source code |
| plot_generic_at_age | Source code |
| plot_hessian_convergence | Source code |
| plot_iter | Source code |
| plot_lognormalvar | Man page Source code |
| plot_max_gr | Source code |
| plot_msg | Source code |
| plot_normalvar | Source code |
| plot_ogive | Source code |
| plot_residuals | Man page Source code |
| plot_steepness | Man page Source code |
| plot_surplus_production | Source code |
| plot_timeseries | Man page Source code |
| plot_yield_DD | Source code |
| plot_yield_SCA | Source code |
| plot_yield_SCA_Pope | Source code |
| plot_yield_SP | Source code |
| plot_yield_VPA | Source code |
| plot_yield_cDD | Source code |
| posterior | Man page |
| posterior,Assessment-method | Man page |
| posterior,RCModel-method | Man page |
| posterior.Assessment | Man page |
| posterior.RCModel | Man page |
| powdif | Source code |
| prelim_AM | Man page Source code |
| process_AddIndType | Source code |
| process_AddIndV | Source code |
| prof | Man page |
| prof-class | Man page |
| profile | Man page |
| profile,Assessment-method | Man page |
| profile,RCModel-method | Man page |
| profile_likelihood_DD_TMB | Source code |
| profile_likelihood_RCM | Source code |
| profile_likelihood_SCA | Source code |
| profile_likelihood_SP | Source code |
| profile_likelihood_SSS | Source code |
| profile_likelihood_VPA | Source code |
| profile_likelihood_cDD | Source code |
| profile_likelihood_spict | Source code |
| project | Man page |
| project-class | Man page |
| project_ASM | Source code |
| projection | Man page Source code |
| projection_DD_SS | Source code |
| projection_SCA | Source code |
| projection_SCA_internal | Source code |
| projection_SP | Source code |
| projection_VPA | Source code |
| projection_cDD_SS | Source code |
| pull_AddInd | Source code |
| pull_Ind | Source code |
| pull_Index | Source code |
| r_prior_fn | Source code |
| ref_pt_DD | Source code |
| ref_pt_SCA | Source code |
| ref_pt_VPA | Source code |
| ref_pt_cDD | Source code |
| report | Source code |
| retro | Man page |
| retro-class | Man page |
| retrospective | Man page |
| retrospective,Assessment-method | Man page |
| retrospective,RCModel-method | Man page |
| retrospective_AM | Man page Source code |
| retrospective_DD_SS | Source code |
| retrospective_DD_TMB | Source code |
| retrospective_SCA | Source code |
| retrospective_SP | Source code |
| retrospective_SP_SS | Source code |
| retrospective_SSS | Source code |
| retrospective_VPA | Source code |
| retrospective_cDD | Source code |
| retrospective_cDD_SS | Source code |
| retrospective_spict | Source code |
| rmd_B | Source code |
| rmd_B_B0 | Source code |
| rmd_B_B0_terminal | Source code |
| rmd_B_BMSY | Source code |
| rmd_B_BMSY_terminal | Source code |
| rmd_C_at_age | Source code |
| rmd_C_at_length | Source code |
| rmd_C_mean_age | Source code |
| rmd_C_mean_length | Source code |
| rmd_DD_SS | Source code |
| rmd_DD_TMB | Source code |
| rmd_F | Source code |
| rmd_FMSY | Source code |
| rmd_F_FMSY | Source code |
| rmd_F_FMSY_terminal | Source code |
| rmd_Kobe | Source code |
| rmd_LAA | Source code |
| rmd_LW | Source code |
| rmd_MSY | Source code |
| rmd_M_DD | Source code |
| rmd_M_prior | Source code |
| rmd_M_rw | Source code |
| rmd_N | Source code |
| rmd_N_at_age | Source code |
| rmd_R | Source code |
| rmd_R0 | Source code |
| rmd_RCM_D | Source code |
| rmd_RCM_Find | Source code |
| rmd_RCM_Hist_compare | Source code |
| rmd_RCM_Perr | Source code |
| rmd_RCM_R0 | Source code |
| rmd_RCM_R_output | Source code |
| rmd_RCM_SPR | Source code |
| rmd_RCM_SPR2 | Source code |
| rmd_RCM_SR | Source code |
| rmd_RCM_SSB_output | Source code |
| rmd_RCM_fleet_output | Source code |
| rmd_RCM_index_output | Source code |
| rmd_RCM_initD | Source code |
| rmd_RCM_likelihood_gradients | Source code |
| rmd_RCM_retrospective | Source code |
| rmd_RCM_sel | Source code |
| rmd_RCM_sel_singlefit | Source code |
| rmd_SCA | Source code |
| rmd_SP | Source code |
| rmd_SPR | Source code |
| rmd_SP_SS | Source code |
| rmd_SR | Source code |
| rmd_SSB | Source code |
| rmd_SSB_SSB0 | Source code |
| rmd_SSB_SSBMSY | Source code |
| rmd_SSS | Source code |
| rmd_U | Source code |
| rmd_U_UMSY | Source code |
| rmd_VPA | Source code |
| rmd_WAA | Source code |
| rmd_YPR | Source code |
| rmd_assess_fit | Source code |
| rmd_assess_fit_MW | Source code |
| rmd_assess_fit_series | Source code |
| rmd_assess_qq | Source code |
| rmd_assess_resid | Source code |
| rmd_assess_timeseries | Source code |
| rmd_at_age | Source code |
| rmd_bubble | Source code |
| rmd_cDD | Source code |
| rmd_cDD_SS | Source code |
| rmd_corr | Source code |
| rmd_data_MW | Source code |
| rmd_data_age_comps | Source code |
| rmd_data_length_comps | Source code |
| rmd_data_timeseries | Source code |
| rmd_dynamic_SSB0 | Source code |
| rmd_fec | Source code |
| rmd_fit_age_comps | Source code |
| rmd_fit_comps | Source code |
| rmd_fit_length_comps | Source code |
| rmd_footer | Source code |
| rmd_h | Source code |
| rmd_head | Source code |
| rmd_log_rec_dev | Source code |
| rmd_mat | Source code |
| rmd_matplot | Source code |
| rmd_persp_plot | Source code |
| rmd_residual | Source code |
| rmd_retrospective | Source code |
| rmd_sel | Source code |
| rmd_sel_annual | Source code |
| rmd_sel_persp | Source code |
| rmd_sp | Source code |
| rmd_spict | Source code |
| rmd_spict_FMSY | Source code |
| rmd_spict_yield_header | Source code |
| rmd_summary | Source code |
| rmd_yield_F | Source code |
| rmd_yield_U | Source code |
| rmd_yield_depletion | Source code |
| sample_steepness3 | Source code |
| sdreport_int | Source code |
| sim | Man page |
| sim-class | Man page |
| simulate | Man page |
| simulate,Assessment-method | Man page |
| simulate,RCModel-method | Man page |
| simulate.Assessment | Man page |
| simulate.RCModel | Man page |
| simulate_comp | Source code |
| slp | Source code |
| slp2 | Source code |
| solve_F | Source code |
| squeeze | Source code |
| stop | Source code |
| summary,Assessment-method | Man page |
| summary,retro-method | Man page |
| summary.Assessment | Man page |
| summary.retro | Man page |
| summary_DD_SS | Source code |
| summary_DD_TMB | Source code |
| summary_SCA | Source code |
| summary_SP | Source code |
| summary_SP_SS | Source code |
| summary_SSS | Source code |
| summary_VPA | Source code |
| summary_cDD | Source code |
| summary_cDD_SS | Source code |
| summary_spict | Source code |
| swordfish | Man page |
| tiny_comp | Source code |
| ts_matplot | Source code |
| userguide | Man page Source code |
| vec_slot_fn | Source code |
| warning | Source code |
| yield_fn_DD | Source code |
| yield_fn_SCA | Source code |
| yield_fn_SCA_int | Source code |
| yield_fn_cDD | Source code |
