API for tcarruth/MSEtool
Management Strategy Evaluation Toolkit
| Global functions | |
|---|---|
| AAV | Source code |
| Albacore_TwoFleet | Man page |
| Assess_I_hist | Source code |
| Assess_diagnostic | Source code |
| Assessment | Man page |
| Assessment-class | Man page |
| Awatea2OM | Man page Source code |
| AwateaRead | Source code |
| CASAL2OM | Man page Source code |
| CASALpars | Man page Source code |
| CombineMMP | 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 |
| Data-rich-MP | Man page |
| Euler_Lotka_fn | Source code |
| HCR40_10 | Man page Source code |
| HCR60_20 | Man page Source code |
| HCR_FB | Man page Source code |
| HCR_MSY | Man page Source code |
| HCR_ramp | Man page Source code |
| HCRlin | Man page Source code |
| HistMICE | Man page Source code |
| LinInt | Source code |
| MMSE-class | Man page |
| MOM-class | Man page |
| MP | Man page |
| MPCalcsNAs | Man page Source code |
| MSEtool | Man page |
| MSEtool-package | Man page |
| Model-based-MP | Man page |
| Mohn_rho | Source code |
| NIL | Man page Source code |
| PRBcalc | Man page Source code |
| PRBplot | Source code |
| Probs | Man page Source code |
| R_pred | Source code |
| ResFromRel | Man page Source code |
| SCA | Man page Source code |
| SCA2 | Man page Source code |
| SCA_4010 | Man page |
| SCA_75MSY | Man page |
| SCA_MSY | Man page |
| SCA_MSY_calc | Source code |
| SCA_Pope | Man page Source code |
| SCA_Pope_MSY_calc | Source code |
| SCA_catch_solver | Source code |
| SCA_refpt_calc | Source code |
| SIL | Man page Source code |
| SOL | Man page 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_production | Man page Source code |
| SRA | Man page |
| SRA-class | Man page |
| SRA_dynamic_SSB0 | Source code |
| SRA_get_likelihoods | Source code |
| SRA_posthoc_adjust | Source code |
| SRA_retro | Source code |
| SRA_retro_subset | Source code |
| SRA_scope | Man page |
| SRA_scope,OM,Data-method | Man page |
| SRA_scope,OM,list-method | Man page |
| SRA_scope_est | Source code |
| SRA_scope_int | Source code |
| SRA_tiny_comp | Source code |
| SRopt | Source code |
| SS2Data | Man page Source code |
| SS2Data_get_comps | Source code |
| SS2Data_get_index | Source code |
| SS2MOM | Man page Source code |
| SS2MOM_fleet | Source code |
| SS2MOM_stock | Source code |
| SS2OM | Man page Source code |
| SSS | Man page Source code |
| SSS_4010 | Man page |
| SSS_75MSY | Man page |
| SSS_MSY | Man page |
| SS_import | Source code |
| SS_steepness | Source code |
| Sub_cpars | Man page Source code |
| TAC_MSY | Man page Source code |
| TEG | Man page Source code |
| VPA | Man page Source code |
| VPA2OM | Man page Source code |
| applyMMP | Source code |
| assign_Assessment_slots | Source code |
| avail | Man page Source code |
| cDD | Man page Source code |
| cDD_ | Source code |
| cDD_SS | Man page Source code |
| cDD_catch_solver | Source code |
| calc.mcmc | Source code |
| calculate_Mohn_rho | Source code |
| calculate_TAC | Man page Source code |
| check_OM_for_sampling | Source code |
| compare_SRA | Man page Source code |
| compare_models | Man page Source code |
| diagnostic_AM | Man page Source code |
| expandHerm | Man page Source code |
| expand_comp_matrix | Source code |
| extract.area.sex.matrices | Source code |
| extract.group.matrices | Source code |
| extreme.outlier | Source code |
| fetch.file.names | Man page Source code |
| getDataList | Source code |
| getGpars | Source code |
| getGpars_r4ss_124 | Source code |
| getGpars_r4ss_134 | Source code |
| getSR | Source code |
| get_MSY_DD | Source code |
| get_MSY_cDD | Source code |
| get_s_vul_len | Source code |
| get_sdreport | Source code |
| get_vul_len | Source code |
| getclass | Source code |
| getfirstlev | Source code |
| getinds | Man page Source code |
| getnIVs | Man page Source code |
| getq_multi | Man page Source code |
| getq_multi_MICE | Man page Source code |
| getsegment | Source code |
| hrate | Man page Source code |
| iSCAM2Data | Man page Source code |
| iSCAM2OM | Man page Source code |
| iSCAMcomps | Man page Source code |
| iSCAMinds | Man page Source code |
| iVB | Source code |
| ilogit | Source code |
| ilogitm | Source code |
| int_s_sel | Source code |
| int_sel | Source code |
| ldim | Man page Source code |
| load.iscam.files | Man page Source code |
| logit | Source code |
| mahalanobis_contribution | Source code |
| mahdensplot | Source code |
| mahplot | Man page Source code |
| make_LWT | Source code |
| make_MP | Man page Source code |
| makemov | Man page Source code |
| match_R_years | Source code |
| matrix_slot_fn | Source code |
| mu | Source code |
| multiData | Man page Source code |
| multiDataS | Man page Source code |
| multiMSE | Man page Source code |
| multiMSE_int | Source code |
| multidebug | Man page Source code |
| negcorlogspace | Source code |
| nlz | Source code |
| optQ_multi | Man page Source code |
| optSR | Source code |
| optimize_TMB_model | Source code |
| par_identical_sims_fn | Source code |
| plot,Assessment,missing-method | Man page |
| plot,Assessment,retro-method | Man page |
| plot,MMSE,missing-method | Man page |
| plot,MOM,missing-method | Man page |
| plot,SRA,missing-method | Man page |
| plot,prof,missing-method | Man page |
| plot,retro,missing-method | Man page |
| plot.Assessment | Man page |
| plot.MMSE | Man page |
| plot.MOM | Man page |
| plot.SRA | Man page |
| plot.prof | Man page |
| plot.retro | Man page |
| plotRel | Man page Source code |
| plot_Kobe | Source code |
| plot_SR | Man page Source code |
| plot_betavar | Man page Source code |
| plot_composition | Man page Source code |
| plot_composition_SRA | 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_mov | Man page 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 |
| plotmulti | Man page Source code |
| plotquant | Man page Source code |
| popdynMICE | Man page Source code |
| popdynOneMICE | Man page Source code |
| 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_likelihood_DD_TMB | Source code |
| profile_likelihood_SCA | Source code |
| profile_likelihood_SCA2 | 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 |
| projection | Man page Source code |
| projection_DD_SS | Source code |
| projection_SCA2 | Source code Source code |
| projection_SCA_Pope | Source code |
| projection_SCA_internal | Source code |
| projection_SP | Source code |
| projection_VPA | Source code |
| projection_VPA_internal | Source code |
| projection_cDD_SS | Source code |
| pull_AddInd | Source code |
| pull_Ind | Source code |
| pull_Index | Source code |
| qestMICE | Man page Source code |
| r_prior_fn | Source code |
| read.control.file | Man page Source code |
| read.data.file | Man page Source code |
| read.mcmc | Man page Source code |
| read.par.file | Man page Source code |
| read.projection.file | Man page Source code |
| read.report.file | Man page Source code |
| report | Source code |
| rescale_report | Source code |
| retro | Man page |
| retro-class | Man page |
| retrospective | Man page |
| retrospective,Assessment-method | Man page |
| retrospective,SRA-method | Man page |
| retrospective_AM | Man page Source code |
| retrospective_DD_SS | Source code |
| retrospective_DD_TMB | Source code |
| retrospective_SCA | Source code |
| retrospective_SCA2 | Source code |
| retrospective_SCA_Pope | 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_mean_age | 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_N | Source code |
| rmd_N_at_age | Source code |
| rmd_R | Source code |
| rmd_R0 | Source code |
| rmd_SCA | Source code |
| rmd_SCA2 | Source code |
| rmd_SCA_Pope | Source code |
| rmd_SP | Source code |
| rmd_SP_SS | Source code |
| rmd_SR | Source code |
| rmd_SRA_D | Source code |
| rmd_SRA_Find | Source code |
| rmd_SRA_Perr | Source code |
| rmd_SRA_R0 | Source code |
| rmd_SRA_R_output | Source code |
| rmd_SRA_SR | Source code |
| rmd_SRA_SSB_output | Source code |
| rmd_SRA_fleet_output | Source code |
| rmd_SRA_initD | Source code |
| rmd_SRA_retrospective | Source code |
| rmd_SRA_sel | Source code |
| rmd_SRA_survey_output | 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_assess_fit | Source code |
| rmd_assess_fit2 | 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_data_age_comps | Source code |
| rmd_data_timeseries | Source code |
| rmd_dynamic_SSB0 | Source code |
| rmd_fit_age_comps | Source code |
| rmd_fit_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_meanR | 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_recruitment | Source code |
| sample_steepness3 | Source code |
| sdreport_int | Source code |
| simmov | Man page Source code |
| slp | Source code |
| slp2 | Source code |
| squeeze | Source code |
| strip.areas.groups | Source code |
| strip.static.params | 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_SCA2 | Source code |
| summary_SCA_Pope | 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 |
| tinyErr | Man page |
| tinyErr,MOM-method | Man page |
| tinyErr_MOM | Source code |
| ts_matplot | Source code |
| update_SRA_data | Source code |
| userguide | Man page Source code |
| validateTMB | Source code |
| vec_slot_fn | Source code |
| vector2char | Source code |
| vul_fn | Source code |
