Files in r4ss/r4ss

R Code for Stock Synthesis

.Rbuildignore

.covrignore

.devcontainer/Dockerfile

.devcontainer/devcontainer.json

.devcontainer/library-scripts/common-debian.sh

.gitattributes

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.yml

.github/ISSUE_TEMPLATE/feature_request.yml

.github/workflows/call-calc-coverage.yml

.github/workflows/call-doc-and-style-r.yml

.github/workflows/call-r-cmd-check.yml

.github/workflows/call-spell-check.yml

.github/workflows/call-update-pkgdown.yml

.github/workflows/r4ss-extra-tests.yml

.gitignore

CRAN-SUBMISSION

DESCRIPTION

NAMESPACE

NEWS.md R/NegLogInt_Fn.R R/PinerPlot.R R/RebuildPlot.R R/SSMethod.Cond.TA1.8.R R/SSMethod.TA1.8.R R/SS_ForeCatch.R R/SS_Sensi_plot.R R/SS_changepars.R R/SS_decision_table_stuff.R R/SS_fitbiasramp.R R/SS_html.R R/SS_makeHTMLdiagnostictable.R R/SS_output.R R/SS_parlines.R R/SS_plots.R R/SS_read.R R/SS_read_summary.R R/SS_readctl.R R/SS_readctl_3.24.R R/SS_readctl_3.30.R R/SS_readdat.R R/SS_readdat_2.00.R R/SS_readdat_3.00.R R/SS_readdat_3.24.R R/SS_readdat_3.30.R R/SS_readforecast.R R/SS_readpar_3.24.R R/SS_readpar_3.30.R R/SS_readstarter.R R/SS_readwtatage.R R/SS_recdevs.R R/SS_splitdat.R R/SS_varadjust.R R/SS_write.R R/SS_writectl.R R/SS_writectl_3.24.R R/SS_writectl_3.30.R R/SS_writedat.R R/SS_writedat_3.24.R R/SS_writedat_3.30.R R/SS_writeforecast.R R/SS_writepar_3.24.R R/SS_writepar_3.30.R R/SS_writestarter.R R/SS_writewtatage.R R/SSbiologytables.R R/SSexecutivesummary.r R/SSgetMCMC.R R/SSgetoutput.R R/SSmakeMmatrix.R R/SSmohnsrho.R R/SSplotAgeMatrix.R R/SSplotBiology.R R/SSplotCatch.R R/SSplotCohortCatch.R R/SSplotComparisons.R R/SSplotComps.R R/SSplotData.R R/SSplotDiscard.R R/SSplotDynamicB0.R R/SSplotIndices.R R/SSplotMCMC_ExtraSelex.R R/SSplotMnwt.R R/SSplotMovementMap.R R/SSplotMovementRates.R R/SSplotNumbers.R R/SSplotPars.R R/SSplotProfile.R R/SSplotRecdevs.R R/SSplotRecdist.R R/SSplotRetroDevs.R R/SSplotRetroRecruits.R R/SSplotSPR.R R/SSplotSelex.R R/SSplotSexRatio.R R/SSplotSpawnrecruit.R R/SSplotSummaryF.R R/SSplotTags.R R/SSplotTimeseries.R R/SSplotYield.R R/SSsummarize.R R/SStableComparisons.R R/SSunavailableSpawningOutput.R R/TSCplot.R R/bubble3.R R/check_exe.R R/check_inputlist.R R/copy_SS_inputs.R R/download_models.R R/file_increment.R R/getADMBHessian.R R/get_SIS_info.R R/get_comments.r R/get_ncol.R R/get_ss3_exe.r R/helper_fxns.R R/jitter.R R/make_multifig.R R/make_multifig_sexratio.R R/mcmc.nuisance.R R/mcmc.out.R R/mountains.R R/plotCI.R R/populate_multiple_folders.R R/profile.R R/r4ss-package.R R/read.admbFit.R R/retro.R R/run.R R/selShapes.R R/stackpoly.R R/tune_comps.R R/write_fwf4.r README.md

_pkgdown.yml

codecov.yml

cran-comments.md

inst/CITATION

inst/WORDLIST

inst/extdata/simple_3.24/CompReport.sso

inst/extdata/simple_3.24/Forecast-report.sso

inst/extdata/simple_3.24/Report.sso

inst/extdata/simple_3.24/covar.sso

inst/extdata/simple_3.24/forecast.ss

inst/extdata/simple_3.24/runnumber.ss

inst/extdata/simple_3.24/simple.ctl

inst/extdata/simple_3.24/simple.dat

inst/extdata/simple_3.24/ss3.par

inst/extdata/simple_3.24/starter.ss

inst/extdata/simple_3.24/warning.sso

inst/extdata/simple_small/CompReport.sso

inst/extdata/simple_small/Forecast-report.sso

inst/extdata/simple_small/Report.sso

inst/extdata/simple_small/control.ss

inst/extdata/simple_small/covar.sso

inst/extdata/simple_small/data.ss

inst/extdata/simple_small/data_boot_001.ss

inst/extdata/simple_small/data_expval.ss

inst/extdata/simple_small/forecast.ss

inst/extdata/simple_small/ss3.par

inst/extdata/simple_small/ss_summary.sso

inst/extdata/simple_small/starter.ss

inst/extdata/simple_small/warning.sso

man-roxygen/areacols.R man-roxygen/bioscale.R man-roxygen/cex.main.R man-roxygen/deprecated_dots.R man-roxygen/dir.R man-roxygen/exe.R man-roxygen/extras.R man-roxygen/file.R man-roxygen/fleetnames.R man-roxygen/fleets.R man-roxygen/labels.R man-roxygen/legend.R man-roxygen/legendloc.R man-roxygen/lwd.R man-roxygen/mainTitle.R man-roxygen/mar.R man-roxygen/methot2011cjfas.R man-roxygen/model.R man-roxygen/overwrite.R man-roxygen/pheight.R man-roxygen/pheight_tall.R man-roxygen/plot.R man-roxygen/plotdir.R man-roxygen/print.R man-roxygen/ptsize.R man-roxygen/punits.R man-roxygen/pwidth.R man-roxygen/readctl_vars.R man-roxygen/replist.R man-roxygen/res.R man-roxygen/verbose.R man-roxygen/version.R man/DoProjectPlots.Rd man/NegLogInt_Fn.Rd man/PinerPlot.Rd man/SSMethod.Cond.TA1.8.Rd man/SSMethod.TA1.8.Rd man/SS_ForeCatch.Rd man/SS_RunJitter.Rd man/SS_Sensi_plot.Rd man/SS_changepars.Rd man/SS_decision_table_stuff.Rd man/SS_doRetro.Rd man/SS_fitbiasramp.Rd man/SS_html.Rd man/SS_makeHTMLdiagnostictable.Rd man/SS_output.Rd man/SS_parlines.Rd man/SS_plots.Rd man/SS_profile.Rd man/SS_read.Rd man/SS_read_summary.Rd man/SS_readctl.Rd man/SS_readctl_3.24.Rd man/SS_readctl_3.30.Rd man/SS_readdat.Rd man/SS_readdat_2.00.Rd man/SS_readdat_3.00.Rd man/SS_readdat_3.24.Rd man/SS_readdat_3.30.Rd man/SS_readforecast.Rd man/SS_readpar_3.24.Rd man/SS_readpar_3.30.Rd man/SS_readstarter.Rd man/SS_readwtatage.Rd man/SS_recdevs.Rd man/SS_splitdat.Rd man/SS_tune_comps.Rd man/SS_varadjust.Rd man/SS_write.Rd man/SS_writectl.Rd man/SS_writectl_3.24.Rd man/SS_writectl_3.30.Rd man/SS_writedat.Rd man/SS_writedat_3.24.Rd man/SS_writedat_3.30.Rd man/SS_writeforecast.Rd man/SS_writepar_3.24.Rd man/SS_writepar_3.30.Rd man/SS_writestarter.Rd man/SS_writewtatage.Rd man/SSbiologytables.Rd man/SSdiagsTime2Year.Rd man/SSexecutivesummary.Rd man/SSgetMCMC.Rd man/SSgetoutput.Rd man/SSmakeMmatrix.Rd man/SSmohnsrho.Rd man/SSplotAgeMatrix.Rd man/SSplotBiology.Rd man/SSplotCatch.Rd man/SSplotCohortCatch.Rd man/SSplotComparisons.Rd man/SSplotComps.Rd man/SSplotData.Rd man/SSplotDiscard.Rd man/SSplotDynamicB0.Rd man/SSplotIndices.Rd man/SSplotMCMC_ExtraSelex.Rd man/SSplotMnwt.Rd man/SSplotMovementMap.Rd man/SSplotMovementRates.Rd man/SSplotNumbers.Rd man/SSplotPars.Rd man/SSplotProfile.Rd man/SSplotRecdevs.Rd man/SSplotRecdist.Rd man/SSplotRetroRecruits.Rd man/SSplotSPR.Rd man/SSplotSelex.Rd man/SSplotSexRatio.Rd man/SSplotSpawnrecruit.Rd man/SSplotSummaryF.Rd man/SSplotTags.Rd man/SSplotTimeseries.Rd man/SSplotYield.Rd man/SSsummarize.Rd man/SStableComparisons.Rd man/SSunavailableSpawningOutput.Rd man/TSCplot.Rd man/add_legend.Rd man/bubble3.Rd man/calc_var_adjust.Rd man/check_exe.Rd man/check_inputlist.Rd man/copy_SS_inputs.Rd man/download_models.Rd

man/figures/logo.png

man/figures/logo.svg

man/file_increment.Rd man/getADMBHessian.Rd man/get_SIS_info.Rd man/get_areacols.Rd man/get_comments.Rd man/get_dat_new_name.Rd man/get_last_phase.Rd man/get_par_name.Rd man/get_ss3_exe.Rd man/get_tuning_table.Rd man/get_tv_parlabs.Rd man/is.wholenumber.Rd man/iterate_jitter.Rd man/jitter.Rd man/make_multifig.Rd man/make_multifig_sexratio.Rd man/mcmc.nuisance.Rd man/mcmc.out.Rd man/mountains.Rd man/plotCI.Rd man/populate_multiple_folders.Rd man/profile.Rd man/r4ss-package.Rd man/read.admbFit.Rd man/retro.Rd man/rich.colors.short.Rd man/run.Rd man/save_png.Rd man/selShapes.Rd man/sspar.Rd man/stackpoly.Rd man/translate_3.30_to_3.24_Q_setup.Rd man/translate_3.30_to_3.24_var_adjust.Rd man/tune_comps.Rd man/write_fwf4.Rd

pkgdown/assets/BigSkate/SPR1_series.png

pkgdown/assets/BigSkate/SPR2_minusSPRseries.png

pkgdown/assets/BigSkate/SPR3_ratiointerval.png

pkgdown/assets/BigSkate/SPR4_phase.png

pkgdown/assets/BigSkate/SR_curve.png

pkgdown/assets/BigSkate/SR_curve2.png

pkgdown/assets/BigSkate/_SS_output.html

pkgdown/assets/BigSkate/[e-mail]

pkgdown/assets/BigSkate/_SS_output_AgeComp.html

pkgdown/assets/BigSkate/_SS_output_Bio.html

pkgdown/assets/BigSkate/_SS_output_Catch.html

pkgdown/assets/BigSkate/_SS_output_CompDat.html

pkgdown/assets/BigSkate/_SS_output_Data.html

pkgdown/assets/BigSkate/_SS_output_DiagnosticTables.html

pkgdown/assets/BigSkate/_SS_output_Discard.html

pkgdown/assets/BigSkate/_SS_output_Index.html

pkgdown/assets/BigSkate/_SS_output_LenComp.html

pkgdown/assets/BigSkate/[e-mail]

pkgdown/assets/BigSkate/_SS_output_Mnwt.html

pkgdown/assets/BigSkate/_SS_output_Numbers.html

pkgdown/assets/BigSkate/_SS_output_Pars.html

pkgdown/assets/BigSkate/_SS_output_S-R.html

pkgdown/assets/BigSkate/_SS_output_SPR.html

pkgdown/assets/BigSkate/_SS_output_Sel.html

pkgdown/assets/BigSkate/_SS_output_Timeseries.html

pkgdown/assets/BigSkate/_SS_output_Yield.html

pkgdown/assets/BigSkate/bio10_spawningoutput_len.png

pkgdown/assets/BigSkate/bio11_spawningoutput_age.png

pkgdown/assets/BigSkate/bio1B_len_at_age_matrix_1.png

pkgdown/assets/BigSkate/bio1B_len_at_age_matrix_2.png

pkgdown/assets/BigSkate/bio1B_len_at_age_matrix_3.png

pkgdown/assets/BigSkate/bio1B_len_at_age_matrix_4.png

pkgdown/assets/BigSkate/bio1_sizeatage.png

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pkgdown/assets/BigSkate/bio3_sizeatage_plus_WT_and_MAT.png

pkgdown/assets/BigSkate/bio5_weightatsize.png

pkgdown/assets/BigSkate/bio6_maturity.png

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pkgdown/assets/BigSkate/bodywt_data_fltFishery_current.png

pkgdown/assets/BigSkate/bodywt_fit_fltFishery_current.png

pkgdown/assets/BigSkate/catch1 landings.png

pkgdown/assets/BigSkate/catch10 landings aggregated across seasons.png

pkgdown/assets/BigSkate/catch11 landings aggregated across seasons stacked.png

pkgdown/assets/BigSkate/catch12 total catch (if discards present) aggregated across seasons.png

pkgdown/assets/BigSkate/catch13 total catch (if discards present) aggregated across seasons stacked.png

pkgdown/assets/BigSkate/catch14 discards aggregated across seasons.png

pkgdown/assets/BigSkate/catch15 discards aggregated across seasons stacked.png

pkgdown/assets/BigSkate/catch16 landings + dead discards.png

pkgdown/assets/BigSkate/catch2 landings stacked.png

pkgdown/assets/BigSkate/catch3 observed and expected landings (if different).png

pkgdown/assets/BigSkate/catch4 total catch (including discards).png

pkgdown/assets/BigSkate/catch5 total catch (including discards) stacked.png

pkgdown/assets/BigSkate/catch6 discards.png

pkgdown/assets/BigSkate/catch7 discards stacked plot (depends on multiple fleets).png

pkgdown/assets/BigSkate/catch8 discard fraction.png

pkgdown/assets/BigSkate/catch9 harvest rate.png

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pkgdown/assets/BigSkate/comp_condAALdat_data_weighting_TA1.8_condAgeWCGBTS.png

pkgdown/assets/BigSkate/comp_condAALfit_Andre_plotsflt1mkt2_page1.png

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pkgdown/assets/BigSkate/comp_condAALfit_data_weighting_TA1.8_condAgeFishery_current.png

pkgdown/assets/BigSkate/comp_condAALfit_data_weighting_TA1.8_condAgeWCGBTS.png

pkgdown/assets/BigSkate/comp_condAALfit_residsflt1mkt2.png

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pkgdown/assets/BigSkate/comp_gstagedat_bubflt1mkt2.png

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pkgdown/assets/BigSkate/comp_gstagefit_flt1mkt2.png

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pkgdown/assets/BigSkate/comp_gstagefit_residsflt1mkt2.png

pkgdown/assets/BigSkate/comp_gstagefit_residsflt5mkt0.png

pkgdown/assets/BigSkate/comp_lendat__aggregated_across_time.png

pkgdown/assets/BigSkate/comp_lendat__multi-fleet_comparison.png

pkgdown/assets/BigSkate/comp_lendat_bubflt1mkt1.png

pkgdown/assets/BigSkate/comp_lendat_bubflt1mkt2.png

pkgdown/assets/BigSkate/comp_lendat_bubflt5mkt0.png

pkgdown/assets/BigSkate/comp_lendat_bubflt6mkt0.png

pkgdown/assets/BigSkate/comp_lendat_data_weighting_TA1.8_Fishery_current.png

pkgdown/assets/BigSkate/comp_lendat_data_weighting_TA1.8_Triennial.png

pkgdown/assets/BigSkate/comp_lendat_data_weighting_TA1.8_WCGBTS.png

pkgdown/assets/BigSkate/comp_lendat_flt1mkt1.png

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pkgdown/assets/BigSkate/comp_lenfit__aggregated_across_time.png

pkgdown/assets/BigSkate/comp_lenfit__multi-fleet_comparison.png

pkgdown/assets/BigSkate/comp_lenfit_data_weighting_TA1.8_Fishery_current.png

pkgdown/assets/BigSkate/comp_lenfit_data_weighting_TA1.8_Triennial.png

pkgdown/assets/BigSkate/comp_lenfit_data_weighting_TA1.8_WCGBTS.png

pkgdown/assets/BigSkate/comp_lenfit_flt1mkt1.png

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pkgdown/assets/BigSkate/comp_lenfit_residsflt1mkt1.png

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pkgdown/assets/BigSkate/comp_lenfit_sampsize_flt1mkt1.png

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pkgdown/assets/BigSkate/correlationcheck.html

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pkgdown/assets/BigSkate/discard_fitFishery_current.png

pkgdown/assets/BigSkate/index.html

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pkgdown/assets/BigSkate/index8_q_vs_vuln_bio_Triennial.png

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pkgdown/assets/BigSkate/parameterchecks.html

pkgdown/assets/BigSkate/plotInfoTable_28-03-2023_14.30.29.3310.csv

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pkgdown/assets/BigSkate/ts11_Age-0_recruits_(1000s).png

pkgdown/assets/BigSkate/ts11_Age-0_recruits_(1000s)_with_95_asymptotic_intervals.png

pkgdown/assets/BigSkate/ts1_Total_biomass_(mt).png

pkgdown/assets/BigSkate/ts4_Summary_biomass_(mt).png

pkgdown/assets/BigSkate/ts7_Spawning_biomass_(mt).png

pkgdown/assets/BigSkate/ts7_Spawning_biomass_(mt)_with_95_asymptotic_intervals_intervals.png

pkgdown/assets/BigSkate/ts9_Relative_spawning_biomass.png

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pkgdown/assets/BigSkate/ts_DynamicB0.png

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pkgdown/assets/BigSkate/yield4_YPR_timeseries.png

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pkgdown/favicon/favicon.ico

tests/testthat.R tests/testthat/test-SSexecutivesummary.R tests/testthat/test-TSCplot.R tests/testthat/test-basics.R tests/testthat/test-control.R tests/testthat/test-download_models.R tests/testthat/test-get_SIS_info.R tests/testthat/test-get_ss3_exe.R tests/testthat/test-older_ss3.R tests/testthat/test-par.R tests/testthat/test-plotCI.R tests/testthat/test-populate_multiple_folders.R tests/testthat/test-profile.R tests/testthat/test-readwrite.R tests/testthat/test-runs.R tests/testthat/test-test-models.R tests/testthat/test-tune_comps.R tests/testthat/test-wtatage.R tests/testthat/test_Sensi_plot.R

vignettes/.gitignore

vignettes/compare2_spawnbio_uncertainty.png

vignettes/example-plots.Rmd vignettes/r4ss-intro-vignette.Rmd

vignettes/r4ss_html_capture.png

r4ss/r4ss documentation built on April 30, 2024, 4:42 a.m.