Files in nissandjac/PacifichakeMSE
Management strategy evaluation of Pacific hake
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/AAV.R
R/Check_Identifiable_vs2.R
R/PacifichakeMSE-package.R
R/calcF.R
R/calcMeanAge.R
R/calcSE.R
R/calcSSB0.R
R/create_TMB_data.R
R/df_MSE.R
R/df_lists.R
R/df_lists_OM.R
R/fnMSE.R
R/fn_plot_MSE.R
R/fn_rerun_OM.R
R/getF.R
R/getParameters.R
R/getParameters_OM.R
R/getParameters_csv.R
R/getParameters_ss.R
R/getParms_noAge.R
R/getRefpoint.R
R/getSelec.R
R/getUncertainty.R
R/hake_objectives.R
R/hake_objectives_vs2.R
R/hake_violin.R
R/load_data.R
R/load_data_seasons.R
R/load_data_ss.R
R/load_files.R
R/load_files_OM.R
R/plotMSE.R
R/plotMSE_biasadjustment.R
R/plotSelectivity.R
R/plotUncertainty.R
R/plotValues.R
R/plotViolin.R
R/roxygen.R
R/roxygentags.R
R/run_agebased_model_true_Catch.R
R/run_multiple_MSEs.R
R/run_multiple_OMs.R
R/run_multiple_unfished.R
R/runfuture_OM.R
R/summarizeMSE.R
README.md
R_scripts/TAC_function.R
R_scripts/hake_map.R
R_scripts/plotCatchSeasons.R
R_scripts/plotMovementSensitivity.R
R_scripts/plot_climate_MSE.R
R_scripts/plot_climate_movement.R
R_scripts/plot_conditioned_model.R
R_scripts/plot_relative_MSE.R
R_scripts/plot_sensitivity.R
R_scripts/runHakeassessment.R
R_scripts/run_MSE_climate.R
R_scripts/run_MSE_perfect.R
R_scripts/update_assessment_data.R
inst/extdata/2018hake_control.ss
inst/extdata/2018hake_data.ss
inst/extdata/CompReport.sso
inst/extdata/F0.csv
inst/extdata/Fin.csv
inst/extdata/FleetAgeComp_byNation.csv
inst/extdata/Forecast-report.sso
inst/extdata/Mage.csv
inst/extdata/Ninit_MLE.csv
inst/extdata/PSEL.csv
inst/extdata/Rdev.csv
inst/extdata/Rdev_MLE.csv
inst/extdata/Report.sso
inst/extdata/SS32018/CompReport.sso
inst/extdata/SS32018/CumReport.sso
inst/extdata/SS32018/Forecast-report.sso
inst/extdata/SS32018/ParmTrace.sso
inst/extdata/SS32018/Report.sso
inst/extdata/SS32018/SIS_table.sso
inst/extdata/SS32018/checkup.sso
inst/extdata/SS32018/control.ss_new
inst/extdata/SS32018/covar.sso
inst/extdata/SS32018/data.ss_new
inst/extdata/SS32018/derived_posteriors.sso
inst/extdata/SS32018/echoinput.sso
inst/extdata/SS32018/forecast.ss
inst/extdata/SS32018/forecast.ss_new
inst/extdata/SS32018/hake_control.ss
inst/extdata/SS32018/hake_data.ss
inst/extdata/SS32018/posterior_obj_func.sso
inst/extdata/SS32018/posterior_vectors.sso
inst/extdata/SS32018/posteriors.sso
inst/extdata/SS32018/rebuild.sso
inst/extdata/SS32018/runnumber.ss
inst/extdata/SS32018/ss_summary.sso
inst/extdata/SS32018/starter.ss
inst/extdata/SS32018/starter.ss_new
inst/extdata/SS32018/warning.sso
inst/extdata/SS32018/wtatage.ss
inst/extdata/SS32018/wtatage.ss_new
inst/extdata/SS32018_norec/CompReport.sso
inst/extdata/SS32018_norec/Forecast-report.sso
inst/extdata/SS32018_norec/Report.sso
inst/extdata/SS32018_norec/control.ss
inst/extdata/SS32018_norec/control.ss_new
inst/extdata/SS32018_norec/covar.sso
inst/extdata/SS32018_norec/data.ss
inst/extdata/SS32018_norec/data.ss_new
inst/extdata/SS32018_norec/echoinput.sso
inst/extdata/SS32018_norec/forecast.ss
inst/extdata/SS32018_norec/forecast.ss_new
inst/extdata/SS32018_norec/runnumber.ss
inst/extdata/SS32018_norec/ss_summary.sso
inst/extdata/SS32018_norec/starter.ss
inst/extdata/SS32018_norec/starter.ss_new
inst/extdata/SS32018_norec/warning.sso
inst/extdata/SS32018_norec/wtatage.ss
inst/extdata/SS32018_norec/wtatage.ss_new
inst/extdata/SS32019/CompReport.sso
inst/extdata/SS32019/CumReport.sso
inst/extdata/SS32019/Forecast-report.sso
inst/extdata/SS32019/ParmTrace.sso
inst/extdata/SS32019/Report.sso
inst/extdata/SS32019/SIS_table.sso
inst/extdata/SS32019/admodel.cov
inst/extdata/SS32019/admodel.dep
inst/extdata/SS32019/admodel.hes
inst/extdata/SS32019/control.ss_new
inst/extdata/SS32019/covar.sso
inst/extdata/SS32019/data.ss_new
inst/extdata/SS32019/derived_posteriors.sso
inst/extdata/SS32019/echoinput.sso
inst/extdata/SS32019/fmin.log
inst/extdata/SS32019/forecast.ss
inst/extdata/SS32019/forecast.ss_new
inst/extdata/SS32019/gradient.dat
inst/extdata/SS32019/hake_control.ss
inst/extdata/SS32019/hake_data.ss
inst/extdata/SS32019/posterior_obj_func.sso
inst/extdata/SS32019/posterior_vectors.sso
inst/extdata/SS32019/posteriors.sso
inst/extdata/SS32019/rebuild.sso
inst/extdata/SS32019/runnumber.ss
inst/extdata/SS32019/ss.bar
inst/extdata/SS32019/ss.cor
inst/extdata/SS32019/ss.eva
inst/extdata/SS32019/ss.par
inst/extdata/SS32019/ss.rep
inst/extdata/SS32019/ss.std
inst/extdata/SS32019/ss_summary.sso
inst/extdata/SS32019/starter.ss
inst/extdata/SS32019/starter.ss_new
inst/extdata/SS32019/suggested_tuning.ss
inst/extdata/SS32019/warning.sso
inst/extdata/SS32019/wtatage.ss
inst/extdata/SS32019/wtatage.ss_new
inst/extdata/TAC.csv
inst/extdata/ac_catch_new.csv
inst/extdata/ac_data.csv
inst/extdata/ac_survey_country.csv
inst/extdata/acoustic survey.csv
inst/extdata/adjusted_tac_fn.csv
inst/extdata/age_catch_ss.csv
inst/extdata/age_error_head.csv
inst/extdata/age_in_catch_obs.csv
inst/extdata/age_survey_ss.csv
inst/extdata/agecomps_fishery.csv
inst/extdata/agecomps_fishery_old.csv
inst/extdata/agecomps_survey.csv
inst/extdata/assessment_MLE.csv
inst/extdata/assesssment.csv
inst/extdata/asssessment_MLE.csv
inst/extdata/asssessment_MLE_old.csv
inst/extdata/b_input.csv
inst/extdata/catch_per_country.csv
inst/extdata/catch_per_sector.csv
inst/extdata/catch_table.csv
inst/extdata/catches.csv
inst/extdata/covar.sso
inst/extdata/data.ss_new
inst/extdata/df_survey.csv
inst/extdata/fishing_mortalities.csv
inst/extdata/forecast.ss
inst/extdata/hake_totcatch.csv
inst/extdata/initN.csv
inst/extdata/maturity.csv
inst/extdata/minmaxSSB.csv
inst/extdata/p_MLE.csv
inst/extdata/p_estimated.csv
inst/extdata/parms_scalar.csv
inst/extdata/performancemetrics.csv
inst/extdata/selectivity.csv
inst/extdata/spawnbio.csv
inst/extdata/starter.ss
inst/extdata/survey.csv
inst/extdata/survey_country.csv
inst/extdata/temp100_annual.csv
inst/extdata/unfished_waa.csv
inst/extdata/waa.csv
inst/extdata/wage_ss.csv
inst/extdata/wtatage.ss
inst/extdata/wtatage.ss_new
man/AAV.Rd
man/PacifichakeMSE-package.Rd
man/calcF.Rd
man/calcMeanAge.Rd
man/calcSE.Rd
man/calcSSB0.Rd
man/create_TMB_data.Rd
man/df_lists.Rd
man/df_lists_OM.Rd
man/dummy.Rd
man/extract_fixed.Rd
man/fnMSE.Rd
man/fn_plot_MSE.Rd
man/fn_rerun_OM.Rd
man/fnsum.Rd
man/getF.Rd
man/getParameters.Rd
man/getParameters_OM.Rd
man/getParameters_csv.Rd
man/getParameters_ss.Rd
man/getRefpoint.Rd
man/getSelec.Rd
man/getUncertainty.Rd
man/hake_objectives.Rd
man/hake_violin.Rd
man/load_data.Rd
man/load_data_seasons.Rd
man/load_data_ss.Rd
man/plotSelectivity.Rd
man/plotValues.Rd
man/plotViolin.Rd
man/processMSE.Rd
man/run.agebased.true.catch.Rd
man/run_multiple_MSEs.Rd
man/run_multiple_OMs.Rd
man/runfuture_OM.Rd
man/summarizeMSE.Rd
manual.Rmd
results/Climate/Catch_quota_tot.png
results/Climate/F0.png
results/Climate/Movement.png
results/Climate/Publication/Figure1.pdf
results/Climate/Publication/Figure2.pdf
results/Climate/Publication/Figure3.pdf
results/Climate/Publication/Figure4.pdf
results/Climate/Publication/Figure5.pdf
results/Climate/Publication/Figure6.pdf
results/Climate/Publication/Figure7.pdf
results/Climate/Publication/Figure8.pdf
results/Climate/Publication/Figure9.pdf
results/Climate/Publication/Resubmission/Figure1.pdf
results/Climate/Publication/Resubmission/Figure1.png
results/Climate/Publication/Resubmission/Figure2.pdf
results/Climate/Publication/Resubmission/Figure2.png
results/Climate/Publication/Resubmission/Figure3.pdf
results/Climate/Publication/Resubmission/Figure3.png
results/Climate/Publication/Resubmission/Figure4.pdf
results/Climate/Publication/Resubmission/Figure4.png
results/Climate/Publication/Resubmission/Figure5.pdf
results/Climate/Publication/Resubmission/Figure5.png
results/Climate/Publication/Resubmission/Figure6.pdf
results/Climate/Publication/Resubmission/Figure6.png
results/Climate/Publication/Resubmission/Figure7.pdf
results/Climate/Publication/Resubmission/Figure7.png
results/Climate/Publication/Resubmission/Figures.zip
results/Climate/Publication/Resubmission/Supplementary/EE_tvTAC.png
results/Climate/Publication/Resubmission/Supplementary/Figure9.pdf
results/Climate/Publication/Resubmission/Supplementary/movement_history.png
results/Climate/Publication/Resubmission/Supplementary/objectives_decade.png
results/Climate/Publication/Resubmission/Supplementary/relative_catch.png
results/Climate/Publication/Resubmission/Supplementary/risk.png
results/Climate/Publication/climate_EE.png
results/Climate/Publication/climate_alternative_all.png
results/Climate/Publication/objectives_decade.png
results/Climate/Publication/risklines.png
results/Climate/Publication/tacs.png
results/Climate/Publication/violin_publication.png
results/Climate/Realized_catch.png
results/Climate/SE_SSB.png
results/Climate/SSB_country.png
results/Climate/SSB_mid_year.png
results/Climate/SSB_presentation.png
results/Climate/SSB_total.png
results/Climate/average_age_catch_country.png
results/Climate/average_age_survey_country.png
results/Climate/biasadjustment_ssb.png
results/Climate/catch_table.csv
results/Climate/catch_table.xlsx
results/Climate/climate_EE.png
results/Climate/climate_alternative.png
results/Climate/climate_alternative_all.png
results/Climate/hakedistribution.pdf
results/Climate/hakedistribution.png
results/Climate/hakedistribution.svg
results/Climate/movement_history.png
results/Climate/objective_bars.png
results/Climate/objective_violin.png
results/Climate/objectives_decade.png
results/Climate/objectives_decade_median.png
results/Climate/objectives_presentation.png
results/Climate/objectives_publication.png
results/Climate/objectives_publication_perfect.png
results/Climate/objectives_risklines.png
results/Climate/risklines.png
results/Climate/risklines_perfect.png
results/Climate/sp_objective_bars.png
results/Climate/sp_violin.png
results/Climate/summed_results_test.png
results/Climate/tacs.png
results/Climate/total_average_age_catch.png
results/Climate/total_average_age_surv.png
results/Climate/total_average_ags.png
results/Climate/total_catch.png
results/Climate/violin_publication.png
results/Climate/violin_publication_TAC4.png
results/Figs/AC_catch.png
results/Figs/AC_survey.png
results/Figs/Biomass_survey.png
results/Figs/Climate/ Catch_quota_tot.png
results/Figs/Climate/ F0.png
results/Figs/Climate/ Realized_catch.png
results/Figs/Climate/ SE_SSB.png
results/Figs/Climate/ SSB_country.png
results/Figs/Climate/ SSB_mid_year.png
results/Figs/Climate/ SSB_total.png
results/Figs/Climate/ average_age_catch_country.png
results/Figs/Climate/ average_age_survey_country.png
results/Figs/Climate/ objective_bars.png
results/Figs/Climate/ objective_bars_presentation.png
results/Figs/Climate/ total_average_age_catch.png
results/Figs/Climate/ total_average_age_surv.png
results/Figs/Climate/ total_catch.png
results/Figs/Climate/objective_bars.png
results/Figs/F_country.png
results/Figs/Movement.png
results/Figs/Movement/ SE_SSB.png
results/Figs/Movement/ SSB_country.png
results/Figs/Movement/ SSB_mid_year.png
results/Figs/Movement/ average_age_catch_country.png
results/Figs/Movement/ average_age_survey_country.png
results/Figs/Movement/ objective_bars.png
results/Figs/Movement/ total_average_age_catch.png
results/Figs/Movement/ total_average_age_surv.png
results/Figs/Movement/ total_catch.png
results/Figs/Presentation/Violin plot.emf
results/Figs/SSB.png
results/Figs/age_s.png
results/Figs/b = 0.5/ SE_SSB.png
results/Figs/b = 0.5/ SSB_country.png
results/Figs/b = 0.5/ SSB_mid_year.png
results/Figs/b = 0.5/ average_age_catch_country.png
results/Figs/b = 0.5/ average_age_survey_country.png
results/Figs/b = 0.5/ objective_bars.png
results/Figs/b = 0.5/ total_average_age_catch.png
results/Figs/b = 0.5/ total_average_age_surv.png
results/Figs/b = 0.5/ total_catch.png
results/Figs/climate_movement.png
results/Figs/condition_all.png
results/Figs/selectivity/ F0.png
results/Figs/selectivity/ SE_SSB.png
results/Figs/selectivity/ SSB_country.png
results/Figs/selectivity/ SSB_mid_year.png
results/Figs/selectivity/ average_age_catch_country.png
results/Figs/selectivity/ average_age_survey_country.png
results/Figs/selectivity/ objective_bars.png
results/Figs/selectivity/ total_average_age_catch.png
results/Figs/selectivity/ total_average_age_surv.png
results/Figs/selectivity/ total_catch.png
results/Figs/selectivity/selecplot.png
results/Figs/survey_combined.png
results/Figs/survey_total.png
results/Figs/tacplot.png
results/HCR/Catch_quota_tot.png
results/HCR/F0.png
results/HCR/Realized_catch.png
results/HCR/SE_SSB.png
results/HCR/SSB_country.png
results/HCR/SSB_mid_year.png
results/HCR/SSB_total.png
results/HCR/average_age_catch_country.png
results/HCR/average_age_survey_country.png
results/HCR/objective_bars.png
results/HCR/objective_violin.png
results/HCR/sp_objective_bars.png
results/HCR/sp_violin.png
results/HCR/total_average_age_catch.png
results/HCR/total_average_age_surv.png
results/HCR/total_average_ags.png
results/HCR/total_catch.png
results/Selectivity/Catch_quota_tot.png
results/Selectivity/F0.png
results/Selectivity/Realized_catch.png
results/Selectivity/SE_SSB.png
results/Selectivity/SSB_country.png
results/Selectivity/SSB_mid_year.png
results/Selectivity/SSB_total.png
results/Selectivity/Selectivity_difference.png
results/Selectivity/average_age_catch_country.png
results/Selectivity/average_age_survey_country.png
results/Selectivity/objective_bars.png
results/Selectivity/objective_violin.png
results/Selectivity/seeds.csv
results/Selectivity/sp_objective_bars.png
results/Selectivity/sp_violin.png
results/Selectivity/total_average_age_catch.png
results/Selectivity/total_average_age_surv.png
results/Selectivity/total_average_ags.png
results/Selectivity/total_catch.png
results/bias adjustment/SSB_0.png
results/bias adjustment/SSB_country.png
results/climate_alternative.png
results/sensitivity/R0_dist.png
results/survey/JMC/Catch_quota_tot.png
results/survey/JMC/F0.png
results/survey/JMC/Realized_catch.png
results/survey/JMC/SE_SSB.png
results/survey/JMC/SSB_country.png
results/survey/JMC/SSB_mid_year.png
results/survey/JMC/SSB_total.png
results/survey/JMC/average_age_catch_country.png
results/survey/JMC/average_age_survey_country.png
results/survey/JMC/objective_bars.png
results/survey/JMC/total_average_age_catch.png
results/survey/JMC/total_average_age_surv.png
results/survey/JMC/total_catch.png
results/survey/JTC/Catch_quota_tot.png
results/survey/JTC/F0.png
results/survey/JTC/Realized_catch.png
results/survey/JTC/SE_SSB.png
results/survey/JTC/SSB_country.png
results/survey/JTC/SSB_mid_year.png
results/survey/JTC/SSB_total.png
results/survey/JTC/average_age_catch_country.png
results/survey/JTC/average_age_survey_country.png
results/survey/JTC/objective_bars.png
results/survey/JTC/objective_violin.png
results/survey/JTC/sp_objective_bars.png
results/survey/JTC/sp_violin.png
results/survey/JTC/total_average_age_catch.png
results/survey/JTC/total_average_age_surv.png
results/survey/JTC/total_average_ags.png
results/survey/JTC/total_catch.png
results/survey/Realized/Catch_quota_tot.png
results/survey/Realized/F0.png
results/survey/Realized/Realized_catch.png
results/survey/Realized/SE_SSB.png
results/survey/Realized/SSB_country.png
results/survey/Realized/SSB_mid_year.png
results/survey/Realized/SSB_total.png
results/survey/Realized/average_age_catch_country.png
results/survey/Realized/average_age_survey_country.png
results/survey/Realized/objective_bars.png
results/survey/Realized/total_average_age_catch.png
results/survey/Realized/total_average_age_surv.png
results/survey/Realized/total_catch.png
src/runHakeassessment.cpp
