Files in r4ss

R Code for Stock Synthesis

NEWS.md README.md R/SStableComparisons.R R/SSplotRetroDevs.R R/SS_RunJitter.R R/SS_readstarter.R R/SS_readforecast.R R/make_multifig_sexratio.R R/SSplotYield.R R/get_ncol.R R/SS_readctl_3.24.R R/SSplotMCMC_ExtraSelex.R R/SS_makeHTMLdiagnostictable.R R/SSplotMovementRates.R R/SS_writedat_3.30.R R/plotCI.R R/SSMethod.Cond.TA1.8.R R/SS_writestarter.R R/PinerPlot.R R/SS_writewtatage.R R/SS_readpar_3.24.R R/r4ss-package.R R/SS_writectl.R R/SS_decision_table_stuff.R R/SS_readctl_3.30.R R/RebuildPlot.R R/SS_readwtatage.R R/SS_readdat.R R/SSplotCatch.R R/SS_fitbiasramp.R R/SS_profile.R R/SS_writedat.R R/stackpoly.R R/SSplotSelex.R R/SS_output.R R/SS_doRetro.R R/r4ss_logo.R R/SS_varadjust.R R/SSMethod.TA1.8.R R/SS_writectl_3.30.R R/SS_writedat_3.24.R R/SSgetoutput.R R/SS_splitdat.R R/SS_write.R R/mcmc.out.R R/SS_readpar_3.30.R R/SSunavailableSpawningOutput.R R/check_model.R R/SS_readdat_2.00.R R/selShapes.R R/SSbootstrap.R R/SS_parlines.R R/SSplotProfile.R R/getADMBHessian.R R/populate_multiple_folders.R R/SSplotIndices.R R/bubble3.R R/file_increment.R R/SSexecutivesummary.r R/SSplotTimeseries.R R/SS_readdat_3.24.R R/SSmohnsrho.R R/TSCplot.R R/SSplotNumbers.R R/mountains.R R/SSplotDynamicB0.R R/SSplotCohortCatch.R R/SSplotDiscard.R R/SS_readctl.R R/SSplotRetroRecruits.R R/SSplotComps.R R/SSplotSexRatio.R R/SS_html.R R/SSplotMnwt.R R/SSplotSPR.R R/SS_writepar_3.30.R R/SS_writectl_3.24.R R/SSplotMovementMap.R R/check_inputlist.R R/copy_SS_inputs.R R/run_SS_models.R R/SSplotData.R R/SS_writeforecast.R R/SSplotSummaryF.R R/SS_read_summary.R R/write_fwf4.r R/SS_readdat_3.00.R R/SSplotAgeMatrix.R R/SSmakeMmatrix.R R/mcmc.nuisance.R R/SSplotRecdevs.R R/SSplotComparisons.R R/SSplotPars.R R/SSbiologytables.R R/SS_changepars.R R/make_multifig.R R/read.admbFit.R R/NegLogInt_Fn.R R/SS_tune_comps.R R/SS_writepar_3.24.R R/helper_fxns.R R/SS_Sensi_plot.R R/SS_recdevs.R R/SSplotRecdist.R R/SS_readdat_3.30.R R/SSplotSpawnrecruit.R R/SS_ForeCatch.R R/SSplotBiology.R R/SSplotTags.R R/SSgetMCMC.R R/SSsummarize.R R/SS_read.R R/get_comments.r R/SS_plots.R R/get_SIS_info.R man/read.admbFit.Rd man/SS_writepar_3.30.Rd man/SSgetMCMC.Rd man/mcmc.nuisance.Rd man/SSsummarize.Rd man/PinerPlot.Rd man/SSplotComps.Rd man/SSMethod.Cond.TA1.8.Rd man/SSplotSPR.Rd man/write_fwf4.Rd man/SS_readwtatage.Rd man/SSplotCatch.Rd man/SS_html.Rd man/SSplotData.Rd man/SSplotComparisons.Rd man/SSplotRetroRecruits.Rd man/add_legend.Rd man/SS_plots.Rd man/SS_makeHTMLdiagnostictable.Rd man/SS_output.Rd man/SSplotDynamicB0.Rd man/SSplotMnwt.Rd man/SSexecutivesummary.Rd man/SSbootstrap.Rd man/SS_writectl_3.30.Rd man/get_tv_parlabs.Rd man/stackpoly.Rd man/SS_recdevs.Rd man/SSbiologytables.Rd man/SS_RunJitter.Rd man/SSplotDiscard.Rd man/SS_writedat.Rd man/SSplotBiology.Rd man/run_SS_models.Rd man/SS_writeforecast.Rd man/SS_writectl_3.24.Rd man/SS_readdat_3.24.Rd man/SS_writectl.Rd man/SSplotPars.Rd man/TSCplot.Rd man/SSmohnsrho.Rd man/SSplotMovementMap.Rd man/SS_readstarter.Rd man/SSplotMCMC_ExtraSelex.Rd man/SS_varadjust.Rd man/SS_splitdat.Rd man/is.wholenumber.Rd man/get_tuning_table.Rd man/make_multifig_sexratio.Rd man/r4ss_logo.Rd man/SSdiagsTime2Year.Rd man/SS_readdat_3.30.Rd man/SSplotRecdevs.Rd man/selShapes.Rd man/SS_writedat_3.24.Rd man/SSgetoutput.Rd man/copy_SS_inputs.Rd man/translate_3.30_to_3.24_Q_setup.Rd man/SS_readforecast.Rd man/SStableComparisons.Rd man/SS_read_summary.Rd man/get_comments.Rd man/SS_readpar_3.24.Rd man/SS_ForeCatch.Rd man/SS_writepar_3.24.Rd man/SS_Sensi_plot.Rd man/get_dat_new_name.Rd man/SSplotSummaryF.Rd man/SS_profile.Rd man/SS_readdat.Rd man/SSplotCohortCatch.Rd man/SS_read.Rd man/SSplotNumbers.Rd man/SS_decision_table_stuff.Rd man/SSplotMovementRates.Rd man/SS_readctl_3.24.Rd man/SS_writewtatage.Rd man/SS_parlines.Rd man/sspar.Rd man/SS_readpar_3.30.Rd man/SS_writestarter.Rd man/SS_write.Rd man/NegLogInt_Fn.Rd man/save_png.Rd man/file_increment.Rd man/SS_readdat_3.00.Rd man/get_SIS_info.Rd man/r4ss-package.Rd man/mcmc.out.Rd man/SSplotTags.Rd man/SS_readctl.Rd man/SSplotRecdist.Rd man/mountains.Rd man/SSplotSelex.Rd man/plotCI.Rd man/SSplotTimeseries.Rd man/SSplotIndices.Rd man/check_model.Rd man/SS_readctl_3.30.Rd man/SSplotYield.Rd man/make_multifig.Rd man/SSplotAgeMatrix.Rd man/SSmakeMmatrix.Rd man/DoProjectPlots.Rd man/rich.colors.short.Rd man/SSplotSexRatio.Rd man/SS_readdat_2.00.Rd man/check_inputlist.Rd man/populate_multiple_folders.Rd man/SSunavailableSpawningOutput.Rd man/translate_3.30_to_3.24_var_adjust.Rd man/getADMBHessian.Rd man/SS_fitbiasramp.Rd man/SS_doRetro.Rd man/SS_writedat_3.30.Rd man/bubble3.Rd man/SS_tune_comps.Rd man/SS_changepars.Rd man/SSMethod.TA1.8.Rd man/SSplotSpawnrecruit.Rd man/get_last_phase.Rd man/SSplotProfile.Rd