Files in ichimomo/frasyr

Fisheries Research Agency (FRA) provides the method for calculating sustainable yield (SY) with R

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yml

.github/workflows/pkgdown.yaml

.github/workflows/workflow.yml

.gitignore

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

R/diagnostics_vpa.R R/future.r R/graphics.r R/inner_tools.R R/rvpa.r R/sr_selection.R R/stock_recruit.r R/tables.R R/two-patchSR.R R/ui.R R/use_rvpa_tmb.r R/utilities.r README.md

_config.yml

codecov.yml

data-raw/all_dummy_data_base.csv

data-raw/ex1_M.csv

data-raw/ex1_caa.csv

data-raw/ex1_index.csv

data-raw/ex1_maa.csv

data-raw/ex1_waa.csv

data-raw/ex2_caa.csv

data-raw/ex2_maa.csv

data-raw/ex2_vpa.csv

data-raw/ex2_waa.csv

data-raw/process.R

data/data_future_HSL1.rda

data/data_future_HSL2.rda

data/res_MSY_HSL1.rda

data/res_MSY_HSL2.rda

data/res_future_HSL1.rda

data/res_future_HSL2.rda

data/res_sr_HSL1.rda

data/res_sr_HSL2.rda

data/res_vpa_estb.rda

data/res_vpa_example.rda

data/res_vpa_org.rda

data/vpadat_base0.rda

data/vpadat_estb.rda

frasyr.Rproj

inst/executable/HMM_SR.cpp

inst/executable/TwoPatchSR.cpp

inst/executable/est_MSY_tmb.cpp

inst/executable/rvpa_tmb.cpp

inst/extdata/Fc_at_age_pma_check.csv

inst/extdata/SRdata_pma.rda

inst/extdata/SRpma_BH_L1_AR0_outAR0.rda

inst/extdata/SRpma_BH_L1_AR0_outAR1.rda

inst/extdata/SRpma_BH_L1_AR1_outAR0.rda

inst/extdata/SRpma_BH_L1_AR1_outAR1.rda

inst/extdata/SRpma_BH_L2_AR0_outAR0.rda

inst/extdata/SRpma_BH_L2_AR0_outAR1.rda

inst/extdata/SRpma_BH_L2_AR1_outAR0.rda

inst/extdata/SRpma_BH_L2_AR1_outAR1.rda

inst/extdata/SRpma_HS_L1_AR0_outAR0.rda

inst/extdata/SRpma_HS_L1_AR0_outAR1.rda

inst/extdata/SRpma_HS_L1_AR1_outAR0.rda

inst/extdata/SRpma_HS_L1_AR1_outAR0_repoptT.rda

inst/extdata/SRpma_HS_L1_AR1_outAR1.rda

inst/extdata/SRpma_HS_L2_AR0_outAR0.rda

inst/extdata/SRpma_HS_L2_AR0_outAR1.rda

inst/extdata/SRpma_HS_L2_AR1_outAR0.rda

inst/extdata/SRpma_HS_L2_AR1_outAR1.rda

inst/extdata/SRpma_RI_L1_AR0_outAR0.rda

inst/extdata/SRpma_RI_L1_AR0_outAR1.rda

inst/extdata/SRpma_RI_L1_AR1_outAR0.rda

inst/extdata/SRpma_RI_L1_AR1_outAR1.rda

inst/extdata/SRpma_RI_L2_AR0_outAR0.rda

inst/extdata/SRpma_RI_L2_AR0_outAR1.rda

inst/extdata/SRpma_RI_L2_AR1_outAR0.rda

inst/extdata/SRpma_RI_L2_AR1_outAR1.rda

inst/extdata/ac_res_pma.rda

inst/extdata/all_dummy_data_base.csv

inst/extdata/all_dummy_data_estb.csv

inst/extdata/all_dummy_data_lst0.csv

inst/extdata/all_dummy_data_pgc_estb.csv

inst/extdata/all_dummy_data_plus_group_change.csv

inst/extdata/all_dummy_data_rec.csv

inst/extdata/all_dummy_data_rec2.csv

inst/extdata/baa_pma_check.csv

inst/extdata/boot_res_pma_median_pars.rda

inst/extdata/caa_pma.csv

inst/extdata/check_calc_rel_abund.csv

inst/extdata/code_pma_check.csv

inst/extdata/data_released.csv

inst/extdata/faa_pma_check.csv

inst/extdata/fres_pma_BH_L1_AR0_outAR0.rda

inst/extdata/fres_pma_BH_L1_AR0_outAR1.rda

inst/extdata/fres_pma_BH_L1_AR1_outAR0.rda

inst/extdata/fres_pma_BH_L1_AR1_outAR1.rda

inst/extdata/fres_pma_BH_L2_AR0_outAR0.rda

inst/extdata/fres_pma_BH_L2_AR0_outAR1.rda

inst/extdata/fres_pma_BH_L2_AR1_outAR0.rda

inst/extdata/fres_pma_BH_L2_AR1_outAR1.rda

inst/extdata/fres_pma_HS_L1_AR0_outAR0.rda

inst/extdata/fres_pma_HS_L1_AR0_outAR1.rda

inst/extdata/fres_pma_HS_L1_AR1_outAR0.rda

inst/extdata/fres_pma_HS_L1_AR1_outAR1.rda

inst/extdata/fres_pma_HS_L2_AR0_outAR0.rda

inst/extdata/fres_pma_HS_L2_AR0_outAR1.rda

inst/extdata/fres_pma_HS_L2_AR1_outAR0.rda

inst/extdata/fres_pma_HS_L2_AR1_outAR1.rda

inst/extdata/fres_pma_RI_L1_AR0_outAR0.rda

inst/extdata/fres_pma_RI_L1_AR0_outAR1.rda

inst/extdata/fres_pma_RI_L1_AR1_outAR0.rda

inst/extdata/fres_pma_RI_L1_AR1_outAR1.rda

inst/extdata/fres_pma_RI_L2_AR0_outAR0.rda

inst/extdata/fres_pma_RI_L2_AR0_outAR1.rda

inst/extdata/fres_pma_RI_L2_AR1_outAR0.rda

inst/extdata/fres_pma_RI_L2_AR1_outAR1.rda

inst/extdata/future_BHpar0_AIC_pma_check.csv

inst/extdata/future_BHpar0_AICc_pma_check.csv

inst/extdata/future_BHpar0_BIC_pma_check.csv

inst/extdata/future_BHpar0_k_pma_check.csv

inst/extdata/future_BHpar0_loglik_pma_check.csv

inst/extdata/future_BHpar0_opt_convergence_pma_check.csv

inst/extdata/future_BHpar0_opt_counts_pma_check.csv

inst/extdata/future_BHpar0_opt_par_pma_check.csv

inst/extdata/future_BHpar0_opt_value_pma_check.csv

inst/extdata/future_BHpar0_pars_pma_check.csv

inst/extdata/future_BHpar0_pred_pma_check.csv

inst/extdata/future_BHpar0_resid2_pma_check.csv

inst/extdata/future_BHpar0_resid_pma_check.csv

inst/extdata/future_BHpar1_AIC_pma_check.csv

inst/extdata/future_BHpar1_AICc_pma_check.csv

inst/extdata/future_BHpar1_BIC_pma_check.csv

inst/extdata/future_BHpar1_k_pma_check.csv

inst/extdata/future_BHpar1_loglik_pma_check.csv

inst/extdata/future_BHpar1_opt_convergence_pma_check.csv

inst/extdata/future_BHpar1_opt_counts_pma_check.csv

inst/extdata/future_BHpar1_opt_par_pma_check.csv

inst/extdata/future_BHpar1_opt_value_pma_check.csv

inst/extdata/future_BHpar1_pars_pma_check.csv

inst/extdata/future_BHpar1_pred_pma_check.csv

inst/extdata/future_BHpar1_resid2_pma_check.csv

inst/extdata/future_BHpar1_resid_pma_check.csv

inst/extdata/future_HSpar0_AIC_pma_check.csv

inst/extdata/future_HSpar0_AICc_pma_check.csv

inst/extdata/future_HSpar0_BIC_pma_check.csv

inst/extdata/future_HSpar0_k_pma_check.csv

inst/extdata/future_HSpar0_loglik_pma_check.csv

inst/extdata/future_HSpar0_opt_convergence_pma_check.csv

inst/extdata/future_HSpar0_opt_counts_pma_check.csv

inst/extdata/future_HSpar0_opt_par_pma_check.csv

inst/extdata/future_HSpar0_opt_value_pma_check.csv

inst/extdata/future_HSpar0_pars_pma_check.csv

inst/extdata/future_HSpar0_pred_pma_check.csv

inst/extdata/future_HSpar0_resid2_pma_check.csv

inst/extdata/future_HSpar0_resid_pma_check.csv

inst/extdata/future_HSpar1_AIC_pma_check.csv

inst/extdata/future_HSpar1_AICc_pma_check.csv

inst/extdata/future_HSpar1_BIC_pma_check.csv

inst/extdata/future_HSpar1_k_pma_check.csv

inst/extdata/future_HSpar1_loglik_pma_check.csv

inst/extdata/future_HSpar1_opt_convergence_pma_check.csv

inst/extdata/future_HSpar1_opt_counts_pma_check.csv

inst/extdata/future_HSpar1_opt_par_pma_check.csv

inst/extdata/future_HSpar1_opt_value_pma_check.csv

inst/extdata/future_HSpar1_pars_pma_check.csv

inst/extdata/future_HSpar1_pred_pma_check.csv

inst/extdata/future_HSpar1_resid2_pma_check.csv

inst/extdata/future_HSpar1_resid_pma_check.csv

inst/extdata/future_RIpar0_AIC_pma_check.csv

inst/extdata/future_RIpar0_AICc_pma_check.csv

inst/extdata/future_RIpar0_BIC_pma_check.csv

inst/extdata/future_RIpar0_k_pma_check.csv

inst/extdata/future_RIpar0_loglik_pma_check.csv

inst/extdata/future_RIpar0_opt_convergence_pma_check.csv

inst/extdata/future_RIpar0_opt_counts_pma_check.csv

inst/extdata/future_RIpar0_opt_par_pma_check.csv

inst/extdata/future_RIpar0_opt_value_pma_check.csv

inst/extdata/future_RIpar0_pars_pma_check.csv

inst/extdata/future_RIpar0_pred_pma_check.csv

inst/extdata/future_RIpar0_resid2_pma_check.csv

inst/extdata/future_RIpar0_resid_pma_check.csv

inst/extdata/future_RIpar1_AIC_pma_check.csv

inst/extdata/future_RIpar1_AICc_pma_check.csv

inst/extdata/future_RIpar1_BIC_pma_check.csv

inst/extdata/future_RIpar1_k_pma_check.csv

inst/extdata/future_RIpar1_loglik_pma_check.csv

inst/extdata/future_RIpar1_opt_convergence_pma_check.csv

inst/extdata/future_RIpar1_opt_counts_pma_check.csv

inst/extdata/future_RIpar1_opt_par_pma_check.csv

inst/extdata/future_RIpar1_opt_value_pma_check.csv

inst/extdata/future_RIpar1_pars_pma_check.csv

inst/extdata/future_RIpar1_pred_pma_check.csv

inst/extdata/future_RIpar1_resid2_pma_check.csv

inst/extdata/future_RIpar1_resid_pma_check.csv

inst/extdata/future_SRdata0_pma_check.csv

inst/extdata/future_SRdata0usingPeriodFrom1990To2000_pma_check.csv

inst/extdata/future_SRdata_pma_check.csv

inst/extdata/future_ref_F_F01_check.csv

inst/extdata/future_ref_F_Fcurrent_check.csv

inst/extdata/future_ref_F_Fhigh_check.csv

inst/extdata/future_ref_F_Flow_check.csv

inst/extdata/future_ref_F_Fmax_check.csv

inst/extdata/future_ref_F_Fmean_check.csv

inst/extdata/future_ref_F_Fmed_check.csv

inst/extdata/future_ref_F_FpSPR_check.csv

inst/extdata/future_ref_F_maa_check.csv

inst/extdata/future_ref_F_max_age_check.csv

inst/extdata/future_ref_F_min_age_check.csv

inst/extdata/future_ref_F_rps-data_check.csv

inst/extdata/future_ref_F_rps-q_check.csv

inst/extdata/future_ref_F_sel_check.csv

inst/extdata/future_ref_F_spr-q_check.csv

inst/extdata/future_ref_F_spr0_check.csv

inst/extdata/future_ref_F_summary_check.csv

inst/extdata/future_ref_F_waa-catch_check.csv

inst/extdata/future_ref_F_waa_check.csv

inst/extdata/future_ref_F_ypr-spr_check.csv

inst/extdata/future_vpa_fres_BH_ABC_pma_check.csv

inst/extdata/future_vpa_fres_BH_M1_pma_check.csv

inst/extdata/future_vpa_fres_BH_M2_pma_check.csv

inst/extdata/future_vpa_fres_BH_M3_pma_check.csv

inst/extdata/future_vpa_fres_BH_alpha_pma_check.csv

inst/extdata/future_vpa_fres_BH_baa1_pma_check.csv

inst/extdata/future_vpa_fres_BH_baa2_pma_check.csv

inst/extdata/future_vpa_fres_BH_baa3_pma_check.csv

inst/extdata/future_vpa_fres_BH_biom1_pma_check.csv

inst/extdata/future_vpa_fres_BH_biom2_pma_check.csv

inst/extdata/future_vpa_fres_BH_biom3_pma_check.csv

inst/extdata/future_vpa_fres_BH_caa1_pma_check.csv

inst/extdata/future_vpa_fres_BH_caa2_pma_check.csv

inst/extdata/future_vpa_fres_BH_caa3_pma_check.csv

inst/extdata/future_vpa_fres_BH_currentF_pma_check.csv

inst/extdata/future_vpa_fres_BH_eaa_pma_check.csv

inst/extdata/future_vpa_fres_BH_faa1_pma_check.csv

inst/extdata/future_vpa_fres_BH_faa2_pma_check.csv

inst/extdata/future_vpa_fres_BH_faa3_pma_check.csv

inst/extdata/future_vpa_fres_BH_fyear_year_pma_check.csv

inst/extdata/future_vpa_fres_BH_maa1_pma_check.csv

inst/extdata/future_vpa_fres_BH_maa2_pma_check.csv

inst/extdata/future_vpa_fres_BH_maa3_pma_check.csv

inst/extdata/future_vpa_fres_BH_maa_year_pma_check.csv

inst/extdata/future_vpa_fres_BH_multi_pma_check.csv

inst/extdata/future_vpa_fres_BH_multi_year_pma_check.csv

inst/extdata/future_vpa_fres_BH_naa1_pma_check.csv

inst/extdata/future_vpa_fres_BH_naa2_pma_check.csv

inst/extdata/future_vpa_fres_BH_naa3_pma_check.csv

inst/extdata/future_vpa_fres_BH_naa_all1_pma_check.csv

inst/extdata/future_vpa_fres_BH_naa_all2_pma_check.csv

inst/extdata/future_vpa_fres_BH_naa_all3_pma_check.csv

inst/extdata/future_vpa_fres_BH_rec-arg_a_pma_check.csv

inst/extdata/future_vpa_fres_BH_rec-arg_b_pma_check.csv

inst/extdata/future_vpa_fres_BH_rec-arg_resid_pma_check.csv

inst/extdata/future_vpa_fres_BH_rec-arg_rho_pma_check.csv

inst/extdata/future_vpa_fres_BH_rec-arg_sd2_pma_check.csv

inst/extdata/future_vpa_fres_BH_rec-arg_sd_pma_check.csv

inst/extdata/future_vpa_fres_BH_recruit_pma_check.csv

inst/extdata/future_vpa_fres_BH_rps_pma_check.csv

inst/extdata/future_vpa_fres_BH_ssb1_pma_check.csv

inst/extdata/future_vpa_fres_BH_ssb2_pma_check.csv

inst/extdata/future_vpa_fres_BH_ssb3_pma_check.csv

inst/extdata/future_vpa_fres_BH_thisyear-ssb_pma_check.csv

inst/extdata/future_vpa_fres_BH_vbiom_pma_check.csv

inst/extdata/future_vpa_fres_BH_vssb_pma_check.csv

inst/extdata/future_vpa_fres_BH_vwcaa_pma_check.csv

inst/extdata/future_vpa_fres_BH_waa-catch1_pma_check.csv

inst/extdata/future_vpa_fres_BH_waa-catch2_pma_check.csv

inst/extdata/future_vpa_fres_BH_waa-catch3_pma_check.csv

inst/extdata/future_vpa_fres_BH_waa1_pma_check.csv

inst/extdata/future_vpa_fres_BH_waa2_pma_check.csv

inst/extdata/future_vpa_fres_BH_waa3_pma_check.csv

inst/extdata/future_vpa_fres_BH_waa_year_pma_check.csv

inst/extdata/future_vpa_fres_BH_wcaa1_pma_check.csv

inst/extdata/future_vpa_fres_BH_wcaa2_pma_check.csv

inst/extdata/future_vpa_fres_BH_wcaa3_pma_check.csv

inst/extdata/future_vpa_fres_BH_years_pma_check.csv

inst/extdata/future_vpa_fres_HS_ABC_pma_check.csv

inst/extdata/future_vpa_fres_HS_M1_pma_check.csv

inst/extdata/future_vpa_fres_HS_M2_pma_check.csv

inst/extdata/future_vpa_fres_HS_M3_pma_check.csv

inst/extdata/future_vpa_fres_HS_alpha_pma_check.csv

inst/extdata/future_vpa_fres_HS_baa1_pma_check.csv

inst/extdata/future_vpa_fres_HS_baa2_pma_check.csv

inst/extdata/future_vpa_fres_HS_baa3_pma_check.csv

inst/extdata/future_vpa_fres_HS_biom1_pma_check.csv

inst/extdata/future_vpa_fres_HS_biom2_pma_check.csv

inst/extdata/future_vpa_fres_HS_biom3_pma_check.csv

inst/extdata/future_vpa_fres_HS_caa1_pma_check.csv

inst/extdata/future_vpa_fres_HS_caa2_pma_check.csv

inst/extdata/future_vpa_fres_HS_caa3_pma_check.csv

inst/extdata/future_vpa_fres_HS_currentF_pma_check.csv

inst/extdata/future_vpa_fres_HS_eaa_pma_check.csv

inst/extdata/future_vpa_fres_HS_faa1_pma_check.csv

inst/extdata/future_vpa_fres_HS_faa2_pma_check.csv

inst/extdata/future_vpa_fres_HS_faa3_pma_check.csv

inst/extdata/future_vpa_fres_HS_fyear_year_pma_check.csv

inst/extdata/future_vpa_fres_HS_maa1_pma_check.csv

inst/extdata/future_vpa_fres_HS_maa2_pma_check.csv

inst/extdata/future_vpa_fres_HS_maa3_pma_check.csv

inst/extdata/future_vpa_fres_HS_maa_year_pma_check.csv

inst/extdata/future_vpa_fres_HS_multi_pma_check.csv

inst/extdata/future_vpa_fres_HS_multi_year_pma_check.csv

inst/extdata/future_vpa_fres_HS_naa1_pma_check.csv

inst/extdata/future_vpa_fres_HS_naa2_pma_check.csv

inst/extdata/future_vpa_fres_HS_naa3_pma_check.csv

inst/extdata/future_vpa_fres_HS_naa_all1_pma_check.csv

inst/extdata/future_vpa_fres_HS_naa_all2_pma_check.csv

inst/extdata/future_vpa_fres_HS_naa_all3_pma_check.csv

inst/extdata/future_vpa_fres_HS_rec-arg_a_pma_check.csv

inst/extdata/future_vpa_fres_HS_rec-arg_b_pma_check.csv

inst/extdata/future_vpa_fres_HS_rec-arg_resid_pma_check.csv

inst/extdata/future_vpa_fres_HS_rec-arg_rho_pma_check.csv

inst/extdata/future_vpa_fres_HS_rec-arg_sd2_pma_check.csv

inst/extdata/future_vpa_fres_HS_rec-arg_sd_pma_check.csv

inst/extdata/future_vpa_fres_HS_recruit_pma_check.csv

inst/extdata/future_vpa_fres_HS_rps_pma_check.csv

inst/extdata/future_vpa_fres_HS_ssb1_pma_check.csv

inst/extdata/future_vpa_fres_HS_ssb2_pma_check.csv

inst/extdata/future_vpa_fres_HS_ssb3_pma_check.csv

inst/extdata/future_vpa_fres_HS_thisyear-ssb_pma_check.csv

inst/extdata/future_vpa_fres_HS_vbiom_pma_check.csv

inst/extdata/future_vpa_fres_HS_vssb_pma_check.csv

inst/extdata/future_vpa_fres_HS_vwcaa_pma_check.csv

inst/extdata/future_vpa_fres_HS_waa-catch1_pma_check.csv

inst/extdata/future_vpa_fres_HS_waa-catch2_pma_check.csv

inst/extdata/future_vpa_fres_HS_waa-catch3_pma_check.csv

inst/extdata/future_vpa_fres_HS_waa1_pma_check.csv

inst/extdata/future_vpa_fres_HS_waa2_pma_check.csv

inst/extdata/future_vpa_fres_HS_waa3_pma_check.csv

inst/extdata/future_vpa_fres_HS_waa_year_pma_check.csv

inst/extdata/future_vpa_fres_HS_wcaa1_pma_check.csv

inst/extdata/future_vpa_fres_HS_wcaa2_pma_check.csv

inst/extdata/future_vpa_fres_HS_wcaa3_pma_check.csv

inst/extdata/future_vpa_fres_HS_years_pma_check.csv

inst/extdata/gradient_pma_check.csv

inst/extdata/hessian_pma_check.csv

inst/extdata/jack_res_pma_pars.rda

inst/extdata/maa_pma.csv

inst/extdata/minimum_pma_check.csv

inst/extdata/naa_pma_check.csv

inst/extdata/np_pma_check.csv

inst/extdata/prof_lik_res_pma.rda

inst/extdata/refs_base_pma.rda

inst/extdata/refs_base_pma_pre.rda

inst/extdata/res_MSY_pma.rda

inst/extdata/res_MSY_pma_mean_samplesize100.rda

inst/extdata/res_MSY_pma_mean_samplesize1000.rda

inst/extdata/res_MSY_pma_mean_samplesize10000.rda

inst/extdata/res_MSY_pma_old.rda

inst/extdata/res_MSY_pma_pre.rda

inst/extdata/res_MSY_pma_sd_samplesize100.rda

inst/extdata/res_MSY_pma_sd_samplesize1000.rda

inst/extdata/res_MSY_pma_sd_samplesize10000.rda

inst/extdata/res_corSR_pma_BH_L1_AR0_outAR0.rda

inst/extdata/res_corSR_pma_BH_L1_AR0_outAR1.rda

inst/extdata/res_corSR_pma_BH_L1_AR1_outAR0.rda

inst/extdata/res_corSR_pma_BH_L1_AR1_outAR1.rda

inst/extdata/res_corSR_pma_BH_L2_AR0_outAR0.rda

inst/extdata/res_corSR_pma_BH_L2_AR0_outAR1.rda

inst/extdata/res_corSR_pma_BH_L2_AR1_outAR0.rda

inst/extdata/res_corSR_pma_BH_L2_AR1_outAR1.rda

inst/extdata/res_corSR_pma_HS_L1_AR0_outAR0.rda

inst/extdata/res_corSR_pma_HS_L1_AR0_outAR1.rda

inst/extdata/res_corSR_pma_HS_L1_AR1_outAR0.rda

inst/extdata/res_corSR_pma_HS_L1_AR1_outAR1.rda

inst/extdata/res_corSR_pma_HS_L2_AR0_outAR0.rda

inst/extdata/res_corSR_pma_HS_L2_AR0_outAR1.rda

inst/extdata/res_corSR_pma_HS_L2_AR1_outAR0.rda

inst/extdata/res_corSR_pma_HS_L2_AR1_outAR1.rda

inst/extdata/res_corSR_pma_RI_L1_AR0_outAR0.rda

inst/extdata/res_corSR_pma_RI_L1_AR0_outAR1.rda

inst/extdata/res_corSR_pma_RI_L1_AR1_outAR0.rda

inst/extdata/res_corSR_pma_RI_L1_AR1_outAR1.rda

inst/extdata/res_corSR_pma_RI_L2_AR0_outAR0.rda

inst/extdata/res_corSR_pma_RI_L2_AR0_outAR1.rda

inst/extdata/res_corSR_pma_RI_L2_AR1_outAR0.rda

inst/extdata/res_corSR_pma_RI_L2_AR1_outAR1.rda

inst/extdata/res_future_Fcurrent_pma.rda

inst/extdata/res_future_Fcurrent_pma_pre.rda

inst/extdata/res_ref_f_pma.rda

inst/extdata/res_ref_f_pma_old.rda

inst/extdata/res_steepness_pma_BH_L1_AR0_outAR0.rda

inst/extdata/res_steepness_pma_BH_L1_AR0_outAR1.rda

inst/extdata/res_steepness_pma_BH_L1_AR1_outAR0.rda

inst/extdata/res_steepness_pma_BH_L1_AR1_outAR1.rda

inst/extdata/res_steepness_pma_BH_L2_AR0_outAR0.rda

inst/extdata/res_steepness_pma_BH_L2_AR0_outAR1.rda

inst/extdata/res_steepness_pma_BH_L2_AR1_outAR0.rda

inst/extdata/res_steepness_pma_BH_L2_AR1_outAR1.rda

inst/extdata/res_steepness_pma_HS_L1_AR0_outAR0.rda

inst/extdata/res_steepness_pma_HS_L1_AR0_outAR1.rda

inst/extdata/res_steepness_pma_HS_L1_AR1_outAR0.rda

inst/extdata/res_steepness_pma_HS_L1_AR1_outAR1.rda

inst/extdata/res_steepness_pma_HS_L2_AR0_outAR0.rda

inst/extdata/res_steepness_pma_HS_L2_AR0_outAR1.rda

inst/extdata/res_steepness_pma_HS_L2_AR1_outAR0.rda

inst/extdata/res_steepness_pma_HS_L2_AR1_outAR1.rda

inst/extdata/res_steepness_pma_RI_L1_AR0_outAR0.rda

inst/extdata/res_steepness_pma_RI_L1_AR0_outAR1.rda

inst/extdata/res_steepness_pma_RI_L1_AR1_outAR0.rda

inst/extdata/res_steepness_pma_RI_L1_AR1_outAR1.rda

inst/extdata/res_steepness_pma_RI_L2_AR0_outAR0.rda

inst/extdata/res_steepness_pma_RI_L2_AR0_outAR1.rda

inst/extdata/res_steepness_pma_RI_L2_AR1_outAR0.rda

inst/extdata/res_steepness_pma_RI_L2_AR1_outAR1.rda

inst/extdata/res_vpa_dummy.csv

inst/extdata/res_vpa_dummy_age2.csv

inst/extdata/res_vpa_dummy_release_fish.csv

inst/extdata/res_vpa_dummy_release_fish_new.csv

inst/extdata/res_vpa_pma.rda

inst/extdata/saa_pma_check.csv

inst/extdata/srr_check1_pma.rda

inst/extdata/srr_check2_pma.rda

inst/extdata/ssb_pma_check.csv

inst/extdata/ssbcoef_pma_check.csv

inst/extdata/termf_pma_check.csv

inst/extdata/vpa.csv

inst/extdata/waa_pma.csv

inst/extdata/wcaa_pma_check.csv

man/Generation.Time.Rd man/SRregime_plot.Rd man/adhoc_table.Rd man/apply_year_colum.Rd man/arrange_weight.Rd man/autocalc_ridgevpa.Rd man/autocor.plot.Rd man/average_SR_mat.Rd man/beta.simulation.Rd man/boo.vpa.Rd man/boot.SR.Rd man/bootSR.ggplot.Rd man/bootSR.plot.Rd man/boot_steepness.Rd man/bubble_plot2.Rd man/caa.est.mat.Rd man/caa.est.mat_wrong.Rd man/calc.StdResid.Rd man/calc.rel.abund.Rd man/calc.residAR.Rd man/calc_Fratio.Rd man/calc_future_perSPR.Rd man/calc_perspr.Rd man/calc_steepness.Rd man/calculate_all_pm.Rd man/check.SRdist.Rd man/check.SRfit.Rd man/check_MSE_sd0.Rd man/check_consistent_w.Rd man/check_fix_CVoption.Rd man/colorize_table.Rd man/compare_MSY.Rd man/compare_SRfit.Rd man/compare_eq_stat.Rd man/compare_future_performance.Rd man/compare_kobeII.Rd man/convert_Fvector.Rd man/convert_SR_tibble.Rd man/convert_faa_perSPR.Rd man/convert_future_list_table.Rd man/convert_future_table.Rd man/convert_vpa_tibble.Rd man/corSR.Rd man/create_dummy_vpa.Rd man/data.handler.Rd man/derive_RP_value.Rd man/derive_biopar.Rd man/derive_future_summary.Rd man/detect_plus_group.Rd man/do_caaboot_vpa.Rd man/do_estcheck_vpa.Rd man/do_jackknife_vpa.Rd man/do_retrospective_vpa.Rd man/do_sensitivity_vpa.Rd man/draw_SRline.Rd man/est_MSYRP.Rd man/export_formattable.Rd man/export_kobeII_table.Rd man/export_kobeII_tables.Rd man/export_tables.Rd man/extract_x.Rd man/fit.SR.Rd man/fit.SR_pen.Rd man/fit.SR_tol.Rd man/fit.SRmig.Rd man/fit.SRregime.Rd man/fit_draw_SRline.Rd man/format_beta_table.Rd man/future_vpa.Rd man/get.SPR.Rd man/get.SRdata.Rd man/get.ab.bh.Rd man/get_performance.Rd man/ggsave_SH.Rd man/ggsave_SH_large.Rd man/give_agename.Rd man/hmm_SR.Rd man/jackknife.SR.Rd man/load_folder.Rd man/make_RP_table.Rd man/make_SR_dframe.Rd man/make_abctable.Rd man/make_array.Rd man/make_future_data.Rd man/make_kobeII_table.Rd man/make_kobe_ratio.Rd man/make_msytable.Rd man/make_stock_table2.Rd man/make_table.Rd man/out.SR.Rd man/out.vpa.Rd man/plot_Fcurrent.Rd man/plot_Fref.Rd man/plot_HCR.Rd man/plot_HCR_by_catch.Rd man/plot_SR.Rd man/plot_SR_AReffect.Rd man/plot_SRdata.Rd man/plot_future_simple.Rd man/plot_futures.Rd man/plot_futures_simple.Rd man/plot_kobe_gg.Rd man/plot_resboot_vpa.Rd man/plot_residual_vpa.Rd man/plot_sprypr.Rd man/plot_vpa.Rd man/plot_yield.Rd man/prof.lik.Rd man/prof.likSR.Rd man/profile_likelihood.vpa.Rd man/pull_df_from_list.Rd man/pull_var_from_kobeII_table.Rd man/rank_HCR.Rd man/read.vpa.Rd man/redo_future.Rd man/ref.F.Rd man/retrieve_input.Rd man/retro.est.Rd man/safe_call.Rd man/sample_backward.Rd man/set_SR_mat.Rd man/source_lines.Rd man/specify.Mesnil.gamma.Rd man/summary_kobe_table.Rd man/table1.Rd man/table2.Rd man/table4.Rd man/take_interval.Rd man/test_sd0_future.Rd man/theme_SH.Rd man/to_vpa_data.Rd man/tryall_SR.Rd man/use_rvpa_tmb.Rd man/validate_sr.Rd man/vpa.Rd tests/testthat.R

tests/testthat/.gitignore

tests/testthat/data_future_test.rda

tests/testthat/helper-future.R

tests/testthat/resSRcomp.png

tests/testthat/res_vpa_files.rda

tests/testthat/res_vpa_no_global_minimum_example.rda

tests/testthat/test-data.handler.R tests/testthat/test-future-dummy-data.R tests/testthat/test-future-option.R tests/testthat/test-future-part.R tests/testthat/test-graphics.R tests/testthat/test-inner_tools.R tests/testthat/test-refF-part.R tests/testthat/test-release.R tests/testthat/test-rvpa-part.R tests/testthat/test-sr-para-cor-steepness.R tests/testthat/test-srmodels.R tests/testthat/test-srr-part.R tests/testthat/test-stock-recruit-part.R tests/testthat/test-tables.R tests/testthat/test-test.R tests/testthat/test-ui.R tests/testthat/test-utilities.R tests/testthat/tmp.pdf

tests/testthat/vpa.csv

tests/testthat/vpa.pdf tools/estMSY.Rmd tools/est_MSY_tmb_test.R tools/future-old.Rmd tools/future_new.Rmd

tools/generate-testdata/check.calc.rel.abund.xlsx

tools/generate-testdata/future2.1.r tools/generate-testdata/generate_res_MSY_for_ensemble.R tools/generate-testdata/generate_res_MSY_for_test.R tools/generate-testdata/generate_res_SRR_for_test.R tools/generate-testdata/generate_res_SRdata_for_test.R tools/generate-testdata/generate_res_corSR_steepness_for_test.R tools/generate-testdata/generate_res_fit_SR_for_test.R tools/generate-testdata/generate_res_future_vpa_for_test.R tools/generate-testdata/generate_res_ref_f_for_test.R tools/generate-testdata/generate_res_vpa_for_test.R tools/generate-testdata/rvpa1.9.4.r tools/generate-testdata/stock_recruit.r tools/generate-testdata/stock_recruit_pulreq446.R tools/generate-testdata/utilities-future-vpa.r tools/make_report_SC.Rmd tools/make_report_SC_digest.Rmd tools/mse_test.R vignettes/Diagnostics-for-VPA.Rmd vignettes/fittingSR.Rmd vignettes/vpa.Rmd

vignettes/vpa.csv

ichimomo/frasyr documentation built on Dec. 11, 2023, 12:50 a.m.