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r4ss  

R Code for Stock Synthesis
View on CRAN: Click here


Download and install r4ss package within the R console
Install from CRAN:
install.packages("r4ss")

Install from Github:
library("remotes")
install_github("cran/r4ss")

Install by package version:
library("remotes")
install_version("r4ss", "1.44.0")



Attach the package and use:
library("r4ss")
Maintained by
Ian G. Taylor
[Scholar Profile | Author Map]
First Published: 2009-11-10
Latest Update: 2022-05-26
Description:
A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.19.01, from April 2022).
How to cite:
Ian G. Taylor (2009). r4ss: R Code for Stock Synthesis. R package version 1.44.0, https://cran.r-project.org/web/packages/r4ss. Accessed 26 Mar. 2025.
Previous versions and publish date:
1.0 (2009-11-10 11:15), 1.01 (2009-11-16 08:45), 1.02 (2009-12-06 11:08), 1.03 (2010-01-13 08:46), 1.04 (2010-01-22 08:48), 1.05 (2010-03-26 19:06), 1.06 (2010-05-16 18:20), 1.07 (2010-07-24 22:42), 1.08 (2010-08-11 06:48), 1.10 (2010-08-17 21:03), 1.11 (2010-09-21 10:15), 1.12 (2010-11-03 08:42), 1.13 (2011-01-05 07:45), 1.14 (2011-02-18 18:30), 1.15 (2011-04-15 07:22), 1.16 (2011-06-29 11:42), 1.17 (2012-06-15 21:42), 1.18 (2012-08-24 08:10), 1.20 (2013-03-15 07:25), 1.22.1 (2014-07-12 07:14), 1.22 (2014-07-09 08:20), 1.24.0 (2015-12-23 23:28), 1.36.1 (2019-10-18 06:50)
Other packages that cited r4ss R package
View r4ss citation profile
Other R packages that r4ss depends, imports, suggests or enhances
Complete documentation for r4ss
Functions, R codes and Examples using the r4ss R package
Some associated functions: DoProjectPlots . NegLogInt_Fn . PinerPlot . SSMethod.Cond.TA1.8 . SSMethod.TA1.8 . SS_ForeCatch . SS_RunJitter . SS_Sensi_plot . SS_changepars . SS_decision_table_stuff . SS_doRetro . SS_fitbiasramp . SS_html . SS_makeHTMLdiagnostictable . SS_output . SS_parlines . SS_plots . SS_profile . SS_read . SS_read_summary . SS_readctl . SS_readctl_3.24 . SS_readctl_3.30 . SS_readdat . SS_readdat_2.00 . SS_readdat_3.00 . SS_readdat_3.24 . SS_readdat_3.30 . SS_readforecast . SS_readpar_3.24 . SS_readpar_3.30 . SS_readstarter . SS_readwtatage . SS_recdevs . SS_splitdat . SS_tune_comps . SS_varadjust . SS_write . SS_writectl . SS_writectl_3.24 . SS_writectl_3.30 . SS_writedat . SS_writedat_3.24 . SS_writedat_3.30 . SS_writeforecast . SS_writepar_3.24 . SS_writepar_3.30 . SS_writestarter . SS_writewtatage . SSbiologytables . SSbootstrap . SSdiagsTime2Year . SSexecutivesummary . SSgetMCMC . SSgetoutput . SSmakeMmatrix . SSmohnsrho . SSplotAgeMatrix . SSplotBiology . SSplotCatch . SSplotCohortCatch . SSplotComparisons . SSplotComps . SSplotData . SSplotDiscard . SSplotDynamicB0 . SSplotIndices . SSplotMCMC_ExtraSelex . SSplotMnwt . SSplotMovementMap . SSplotMovementRates . SSplotNumbers . SSplotPars . SSplotProfile . SSplotRecdevs . SSplotRecdist . SSplotRetroRecruits . SSplotSPR . SSplotSelex . SSplotSexRatio . SSplotSpawnrecruit . SSplotSummaryF . SSplotTags . SSplotTimeseries . SSplotYield . SSsummarize . SStableComparisons . SSunavailableSpawningOutput . TSCplot . add_legend . bubble3 . check_inputlist . check_model . copy_SS_inputs . file_increment . getADMBHessian . get_SIS_info . get_comments . get_dat_new_name . get_last_phase . get_tuning_table . get_tv_parlabs . is.wholenumber . make_multifig . make_multifig_sexratio . mcmc.nuisance . mcmc.out . mountains . plotCI . populate_multiple_folders . r4ss-package . r4ss_logo . read.admbFit . rich.colors.short . run_SS_models . save_png . selShapes . sspar . stackpoly . translate_3.30_to_3.24_Q_setup . translate_3.30_to_3.24_var_adjust . write_fwf4 . 
Some associated R codes: NegLogInt_Fn.R . PinerPlot.R . RebuildPlot.R . SSMethod.Cond.TA1.8.R . SSMethod.TA1.8.R . SS_ForeCatch.R . SS_RunJitter.R . SS_Sensi_plot.R . SS_changepars.R . SS_decision_table_stuff.R . SS_doRetro.R . SS_fitbiasramp.R . SS_html.R . SS_makeHTMLdiagnostictable.R . SS_output.R . SS_parlines.R . SS_plots.R . SS_profile.R . SS_read.R . SS_read_summary.R . SS_readctl.R . SS_readctl_3.24.R . SS_readctl_3.30.R . SS_readdat.R . SS_readdat_2.00.R . SS_readdat_3.00.R . SS_readdat_3.24.R . SS_readdat_3.30.R . SS_readforecast.R . SS_readpar_3.24.R . SS_readpar_3.30.R . SS_readstarter.R . SS_readwtatage.R . SS_recdevs.R . SS_splitdat.R . SS_tune_comps.R . SS_varadjust.R . SS_write.R . SS_writectl.R . SS_writectl_3.24.R . SS_writectl_3.30.R . SS_writedat.R . SS_writedat_3.24.R . SS_writedat_3.30.R . SS_writeforecast.R . SS_writepar_3.24.R . SS_writepar_3.30.R . SS_writestarter.R . SS_writewtatage.R . SSbiologytables.R . SSbootstrap.R . SSgetMCMC.R . SSgetoutput.R . SSmakeMmatrix.R . SSmohnsrho.R . SSplotAgeMatrix.R . SSplotBiology.R . SSplotCatch.R . SSplotCohortCatch.R . SSplotComparisons.R . SSplotComps.R . SSplotData.R . SSplotDiscard.R . SSplotDynamicB0.R . SSplotIndices.R . SSplotMCMC_ExtraSelex.R . SSplotMnwt.R . SSplotMovementMap.R . SSplotMovementRates.R . SSplotNumbers.R . SSplotPars.R . SSplotProfile.R . SSplotRecdevs.R . SSplotRecdist.R . SSplotRetroDevs.R . SSplotRetroRecruits.R . SSplotSPR.R . SSplotSelex.R . SSplotSexRatio.R . SSplotSpawnrecruit.R . SSplotSummaryF.R . SSplotTags.R . SSplotTimeseries.R . SSplotYield.R . SSsummarize.R . SStableComparisons.R . SSunavailableSpawningOutput.R . TSCplot.R . bubble3.R . check_inputlist.R . check_model.R . copy_SS_inputs.R . file_increment.R . getADMBHessian.R . get_SIS_info.R . get_ncol.R . helper_fxns.R . make_multifig.R . make_multifig_sexratio.R . mcmc.nuisance.R . mcmc.out.R . mountains.R . plotCI.R . populate_multiple_folders.R . r4ss-package.R . r4ss_logo.R . read.admbFit.R . run_SS_models.R . selShapes.R . stackpoly.R .  Full r4ss package functions and examples
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