{ "_id": "6a17359aacfb0bcc41d94be1", "Type": "Package", "Package": "r4ss", "Title": "R Code for Stock Synthesis", "Version": "1.54.0", "Authors@R": "c(\nperson(\"Ian G.\", \"Taylor\", , \"Ian.Taylor@noaa.gov\", role = c(\"aut\", \"cre\")),\nperson(\"Ian J.\", \"Stewart\", role = \"aut\"),\nperson(\"Allan C.\", \"Hicks\", role = \"aut\"),\nperson(\"Tommy M.\", \"Garrison\", role = \"aut\"),\nperson(\"Andre E.\", \"Punt\", role = \"aut\"),\nperson(\"R.I.C. Chris\", \"Francis\", role = \"aut\"),\nperson(\"John R.\", \"Wallace\", role = \"aut\"),\nperson(\"Chantel R.\", \"Wetzel\", role = \"aut\"),\nperson(\"James T.\", \"Thorson\", role = \"aut\"),\nperson(\"Yukio\", \"Takeuchi\", role = \"aut\"),\nperson(\"Kotaro\", \"Ono\", role = \"aut\"),\nperson(\"Cole C.\", \"Monnahan\", role = \"aut\"),\nperson(\"Christine C.\", \"Stawitz\", role = \"aut\"),\nperson(\"Z. Teresa\", \"A'mar\", role = \"aut\"),\nperson(\"Athol R.\", \"Whitten\", role = \"aut\"),\nperson(\"Kelli F.\", \"Johnson\", role = \"aut\"),\nperson(\"Robbie L.\", \"Emmet\", role = \"aut\"),\nperson(\"Sean C.\", \"Anderson\", role = \"aut\"),\nperson(\"Gwladys I.\", \"Lambert\", role = \"aut\"),\nperson(\"Megan M.\", \"Stachura\", role = \"aut\"),\nperson(\"Andrew B.\", \"Cooper\", role = \"aut\"),\nperson(\"Andi\", \"Stephens\", role = \"aut\"),\nperson(\"Neil L.\", \"Klaer\", role = \"aut\"),\nperson(\"Carey R.\", \"McGilliard\", role = \"aut\"),\nperson(\"Iago\", \"Mosqueira\", role = \"aut\"),\nperson(\"Watal M.\", \"Iwasaki\", role = \"aut\"),\nperson(\"Kathryn L.\", \"Doering\", role = \"aut\"),\nperson(\"Andrea M.\", \"Havron\", role = \"aut\"),\nperson(\"Nathan R.\", \"Vaughan\", role = \"aut\"),\nperson(\"LaTreese S.\", \"Denson\", role = \"aut\"),\nperson(\"Ashleigh J.\", \"Novak\", role = \"aut\"),\nperson(\"Henning\", \"Winker\", role = \"aut\"),\nperson(\"Lee\", \"Qi\", role = \"aut\"),\nperson(\"Megumi\", \"Oshima\", role = \"aut\"),\nperson(\"Eric\", \"Fletcher\", role = \"aut\"),\nperson(\"Elizabeth\", \"Perl\", role = \"aut\"),\nperson(\"Kiva L.\", \"Oken\", role = \"aut\"),\nperson(\"Arni\", \"Magnusson\", role = \"aut\"),\nperson(\"Peter\", \"Kuriyama\", role = \"aut\")\n)", "Description": "A collection of R functions for use with Stock Synthesis,\na fisheries stock assessment modeling platform written in ADMB\nby Dr. Richard D. Methot at the NOAA Northwest Fisheries\nScience Center. The functions include tools for summarizing and\nplotting results, manipulating files, visualizing model\nparameterizations, and various other common stock assessment\ntasks. This version of '{r4ss}' is compatible with Stock\nSynthesis versions 3.24 through 3.30 (specifically version\n3.30.24.00-prerel, from July 2025). Support for 3.24 models is\nonly through the core functions for reading output and\nplotting.", "License": "GPL-3", "URL": "https://github.com/r4ss/r4ss, https://r4ss.github.io/r4ss/", "BugReports": "https://github.com/r4ss/r4ss/issues", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Encoding": "UTF-8", "Language": "en-US", "LazyLoad": "yes", "Roxygen": "list(markdown = TRUE)", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev git make libharfbuzz-dev libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev", "Repository": "https://ices-tools-prod.r-universe.dev", "Date/Publication": "2026-05-27 16:18:37 UTC", "RemoteUrl": "https://github.com/r4ss/r4ss", "RemoteRef": "HEAD", "RemoteSha": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 18:12:22 UTC", "User": "root" }, "Author": "Ian G. Taylor [aut, cre],\nIan J. Stewart [aut],\nAllan C. Hicks [aut],\nTommy M. Garrison [aut],\nAndre E. Punt [aut],\nR.I.C. Chris Francis [aut],\nJohn R. Wallace [aut],\nChantel R. Wetzel [aut],\nJames T. Thorson [aut],\nYukio Takeuchi [aut],\nKotaro Ono [aut],\nCole C. Monnahan [aut],\nChristine C. Stawitz [aut],\nZ. Teresa A'mar [aut],\nAthol R. Whitten [aut],\nKelli F. Johnson [aut],\nRobbie L. Emmet [aut],\nSean C. Anderson [aut],\nGwladys I. Lambert [aut],\nMegan M. Stachura [aut],\nAndrew B. Cooper [aut],\nAndi Stephens [aut],\nNeil L. Klaer [aut],\nCarey R. McGilliard [aut],\nIago Mosqueira [aut],\nWatal M. Iwasaki [aut],\nKathryn L. Doering [aut],\nAndrea M. Havron [aut],\nNathan R. Vaughan [aut],\nLaTreese S. Denson [aut],\nAshleigh J. Novak [aut],\nHenning Winker [aut],\nLee Qi [aut],\nMegumi Oshima [aut],\nEric Fletcher [aut],\nElizabeth Perl [aut],\nKiva L. Oken [aut],\nArni Magnusson [aut],\nPeter Kuriyama [aut]", "Maintainer": "Ian G. Taylor ", "MD5sum": "4c744b7e80ada88e75a84c5e5f90cb41", "_user": "ices-tools-prod", "_type": "src", "_file": "r4ss_1.54.0.tar.gz", "_fileid": "8af343c6ff065b555afa5ed48da7dbe7445b36ef1d1ecef3af17168dea1ed2fc", "_filesize": 3112492, "_sha256": "8af343c6ff065b555afa5ed48da7dbe7445b36ef1d1ecef3af17168dea1ed2fc", "_created": "2026-05-27T18:12:22.000Z", "_published": "2026-05-27T18:19:06.378Z", "_distro": "noble", "_jobs": [ { "job": 78143314252, "time": 318, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7248328436" }, { "job": 78143314393, "time": 317, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7248328248" }, { "job": 78143314238, "time": 187, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7248281383" }, { "job": 78143314269, "time": 197, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7248284922" }, { "job": 78142233550, "time": 357, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7248210705" }, { "job": 78143314176, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7248269073" }, { "job": 78143314300, "time": 328, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7248332052" }, { "job": 78143314424, "time": 308, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7248325179" }, { "job": 78143314272, "time": 333, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7248335853" } ], "_buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26529539651", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/r4ss/r4ss", "_commit": { "id": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "author": "Ian Taylor <4992918+iantaylor-NOAA@users.noreply.github.com>", "committer": "GitHub ", "message": "fix issue with max.print with long forecast (#1079)\n\n* fix issue with max.print with long forecast\n\n- fixes #1078\n- thanks to @g7liniers for\n\n* style and docs: run devtools::document() and style with styler or air", "time": 1779898717 }, "_maintainer": { "name": "Ian G. Taylor", "email": "ian.taylor@noaa.gov", "login": "iantaylor-noaa", "description": "Fisheries stock assessment scientist at NOAA's Northwest Fisheries Science Center", "uuid": 4992918 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "corpcor", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.2.0", "role": "Imports" }, { "package": "forcats", "role": "Imports" }, { "package": "furrr", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "gh", "role": "Imports" }, { "package": "kableExtra", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "flextable", 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"2010-08-17" }, { "version": "1.11", "date": "2010-09-21" }, { "version": "1.12", "date": "2010-11-03" }, { "version": "1.13", "date": "2011-01-05" }, { "version": "1.14", "date": "2011-02-18" }, { "version": "1.15", "date": "2011-04-15" }, { "version": "1.16", "date": "2011-06-29" }, { "version": "1.17", "date": "2012-06-15" }, { "version": "1.18", "date": "2012-08-24" }, { "version": "1.20", "date": "2013-03-15" }, { "version": "1.22", "date": "2014-07-09" }, { "version": "1.22.1", "date": "2014-07-12" }, { "version": "1.24.0", "date": "2015-12-23" }, { "version": "1.36.1", "date": "2019-10-18" }, { "version": "1.44.0", "date": "2022-05-26" } ], "_exports": [ "add_legend", "age2long", "calc_var_adjust", "check_dir", "check_exe", "comp2long", "copy_SS_inputs", "DoProjectPlots", "download_models", "get_SIS_info", "get_ss3_exe", "get_values", "getADMBHessian", "is.wholenumber", "jitter", "make_multifig", "make_multifig_sexratio", "mcmc.nuisance", "mcmc.out", "mountains", "NegLogInt_Fn", "PinerPlot", "plot_twopanel_comparison", "populate_multiple_folders", "profile", "read.admbFit", "retro", "rich.colors.short", "run", "save_png", "selShapes", "signif_string", "size2long", "SS_changepars", "SS_decision_table_stuff", "SS_doRetro", "SS_fitbiasramp", "SS_ForeCatch", "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_RunJitter", "SS_Sensi_plot", "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", "ss3_data_to_fims", "SSbiologytables", "SSdiagsTime2Year", "SSexecutivesummary", "SSgetMCMC", "SSgetoutput", "SSmakeMmatrix", "SSMethod.Cond.TA1.8", "SSMethod.TA1.8", "SSmohnsrho", "sspar", "SSplotAgeMatrix", "SSplotBiology", "SSplotCatch", "SSplotCohortCatch", "SSplotComparisons", "SSplotComps", "SSplotData", "SSplotDiscard", "SSplotDynamicB0", "SSplotIndices", "SSplotMCMC_ExtraSelex", "SSplotMnwt", "SSplotMovementMap", "SSplotMovementRates", "SSplotNumbers", "SSplotPars", "SSplotProfile", "SSplotRecdevs", "SSplotRecdist", "SSplotRetroRecruits", "SSplotSelex", "SSplotSexRatio", "SSplotSpawnrecruit", "SSplotSPR", "SSplotSummaryF", "SSplotTags", "SSplotTimeseries", "SSplotYield", "SSsummarize", "SStableComparisons", "SSunavailableSpawningOutput", "stackpoly", "table_all", "table_biology", "table_compweight", "table_config", "table_exec_summary", "table_parcounts", "table_pars", "table_ts", "TSCplot", "tune_comps", "write_fwf4" ], "_help": [ { "page": "add_file_header", "title": "Add header comments to the input files", "topics": [ "add_file_header" ] }, { "page": "add_legend", "title": "Add legend to plots", "topics": [ "add_legend" ] }, { "page": "bubble3", "title": "Create a bubble plot.", "topics": [ "bubble3" ] }, { "page": "calc_var_adjust", "title": "Calculate variance adjustments for discard or mean body weight data", "topics": [ "calc_var_adjust" ] }, { "page": "check_dir", "title": "Directory check", "topics": [ "check_dir" ] }, { "page": "check_exe", "title": "Find location of executable within path or specified directory", "topics": [ "check_exe" ] }, { "page": "check_inputlist", "title": "Check input argument 'inputlist'", "topics": [ "check_inputlist" ] }, { "page": "check_replist", "title": "Check if the replist input is something that was created by SS_output()", "topics": [ "check_replist" ] }, { "page": "comp2long", "title": "Convert composition data to long format", "topics": [ "age2long", "comp2long", "size2long" ] }, { "page": "copy_SS_inputs", "title": "Copy a the Stock Synthesis input files from one directory to another", "concept": [ "run functions" ], "topics": [ "copy_SS_inputs" ] }, { "page": "DoProjectPlots", "title": "Deprecated function to make plots from Andre Punt's Rebuilder program.", "topics": [ "DoProjectPlots" ] }, { "page": "download_models", "title": "Download SS3 test models", "topics": [ "download_models" ] }, { "page": "file_increment", "title": "Rename key Stock Synthesis output files by adding integer value", "topics": [ "file_increment" ] }, { "page": "get_areacols", "title": "Get default vector of colors for each area", "topics": [ "get_areacols" ] }, { "page": "get_comments", "title": "Collect comments lines starting from \"#C\" in datfile, ctlfile, starter.ss, forecast.ss etc", "topics": [ "get_comments" ] }, { "page": "get_dat_new_name", "title": "Get the name of the data .ss_new file in a directory", "topics": [ "get_dat_new_name" ] }, { "page": "get_last_phase", "title": "Get the highest phase used in the control file", "topics": [ "get_last_phase" ] }, { "page": "get_par_name", "title": "Get the name of the .par file in a directory", "topics": [ "get_par_name" ] }, { "page": "get_SIS_info", "title": "Gather information for the NOAA Species Information System (SIS)", "topics": [ "get_SIS_info" ] }, { "page": "get_ss3_exe", "title": "Download the Stock Synthesis (SS3) executable", "topics": [ "get_ss3_exe" ] }, { "page": "get_tuning_table", "title": "Get the tuning table", "topics": [ "get_tuning_table" ] }, { "page": "get_tv_parlabs", "title": "Get time varying parameter labels", "topics": [ "get_tv_parlabs" ] }, { "page": "get_values", "title": "Function to pull values and calculate confidence intervals from model output called from 'r4ss::table_exec_summary()'.", "topics": [ "get_values" ] }, { "page": "getADMBHessian", "title": "Read admodel.hes file", "topics": [ "getADMBHessian" ] }, { "page": "is.wholenumber", "title": "Utility function to test if x is \"numerically\" integer wrt machine epsilon taken from example section of help of is.integer", "topics": [ "is.wholenumber" ] }, { "page": "iterate_jitter", "title": "Execute a single jittered model run", "topics": [ "iterate_jitter" ] }, { "page": "jitter", "title": "Iteratively run Stock Synthesis with jittered starting values", "concept": [ "run functions" ], "topics": [ "jitter" ] }, { "page": "make_multifig", "title": "Create multi-figure plots.", "topics": [ "make_multifig" ] }, { "page": "make_multifig_sexratio", "title": "Create multi-figure sex ratio plots.", "topics": [ "make_multifig_sexratio" ] }, { "page": "mcmc.nuisance", "title": "Summarize nuisance MCMC output", "topics": [ "mcmc.nuisance" ] }, { "page": "mcmc.out", "title": "Summarize, analyze and plot key MCMC output.", "topics": [ "mcmc.out" ] }, { "page": "mountains", "title": "Make shaded polygons with a mountain-like appearance", "topics": [ "mountains" ] }, { "page": "NegLogInt_Fn", "title": "Perform SS implementation of Laplace Approximation", "topics": [ "NegLogInt_Fn" ] }, { "page": "PinerPlot", "title": "Make plot of likelihood contributions by fleet", "concept": [ "profile functions" ], "topics": [ "PinerPlot" ] }, { "page": "plot_twopanel_comparison", "title": "Plot a two-panel comparison using SSplotComparisons", "topics": [ "plot_twopanel_comparison" ] }, { "page": "plotCI", "title": "Plot points with confidence intervals.", "topics": [ "plotCI" ] }, { "page": "populate_multiple_folders", "title": "Populate multiple Stock Synthesis folders with input files", "concept": [ "run functions" ], "topics": [ "populate_multiple_folders" ] }, { "page": "profile", "title": "Run a likelihood profile in Stock Synthesis.", "concept": [ "profile functions", "run functions" ], "topics": [ "profile" ] }, { "page": "read.admbFit", "title": "Read ADMB .par and .cor files.", "topics": [ "read.admbFit" ] }, { "page": "retro", "title": "Run a retrospective analyses", "concept": [ "run functions" ], "topics": [ "retro" ] }, { "page": "rich.colors.short", "title": "Make a vector of colors.", "topics": [ "rich.colors.short" ] }, { "page": "run", "title": "Run a Stock Synthesis model", "concept": [ "run functions" ], "topics": [ "run" ] }, { "page": "save_png", "title": "Open png device and return info on the file being created", "topics": [ "save_png" ] }, { "page": "selShapes", "title": "Launch a shiny app that displays various selectivity curves", "topics": [ "selShapes" ] }, { "page": "signif_string", "title": "Convert a numeric vector to character with chosen significant digits", "topics": [ "signif_string" ] }, { "page": "SS_changepars", "title": "Change parameters, bounds, or phases in the control file.", "topics": [ "SS_changepars" ] }, { "page": "SS_decision_table_stuff", "title": "Extract total catch, spawning output, and fraction unfished from forecast years", "topics": [ "SS_decision_table_stuff" ] }, { "page": "SS_doRetro", "title": "Deprecated function to run a retrospective analyses, renamed to retro()", "topics": [ "SS_doRetro" ] }, { "page": "SS_fitbiasramp", "title": "Estimate bias adjustment for recruitment deviates", "topics": [ "SS_fitbiasramp" ] }, { "page": "SS_ForeCatch", "title": "Create table of fixed forecast catches", "topics": [ "SS_ForeCatch" ] }, { "page": "SS_html", "title": "Create HTML files to view figures in browser.", "topics": [ "SS_html" ] }, { "page": "SS_makeHTMLdiagnostictable", "title": "Make html diagnostic tables", "topics": [ "SS_makeHTMLdiagnostictable" ] }, { "page": "SS_output", "title": "A function to create a list object for the output from Stock Synthesis", "topics": [ "SS_output" ] }, { "page": "SS_parlines", "title": "Get parameter lines from Stock Synthesis control file", "topics": [ "SS_parlines" ] }, { "page": "SS_plots", "title": "plot many quantities related to output from Stock Synthesis", "topics": [ "SS_plots" ] }, { "page": "SS_profile", "title": "Deprecated function to run a likelihood profile, renamed to profile().", "topics": [ "SS_profile" ] }, { "page": "SS_read", "title": "Read all Stock Synthesis input files for a model", "concept": [ "read/write functions" ], "topics": [ "SS_read" ] }, { "page": "SS_read_summary", "title": "read ss_summary file", "topics": [ "SS_read_summary" ] }, { "page": "SS_readctl", "title": "Read control file from SS", "concept": [ "read/write functions" ], "topics": [ "SS_readctl" ] }, { "page": "SS_readctl_3.24", "title": "Deprecated: read control file from SS version 3.24", "topics": [ "SS_readctl_3.24" ] }, { "page": "SS_readctl_3.30", "title": "read control file from SS version 3.30", "topics": [ "SS_readctl_3.30" ] }, { "page": "SS_readdat", "title": "read Stock Synthesis data file", "concept": [ "read/write functions" ], "topics": [ "SS_readdat" ] }, { "page": "SS_readdat_2.00", "title": "Deprecated: read data file from SS version 2.00", "topics": [ "SS_readdat_2.00" ] }, { "page": "SS_readdat_3.00", "title": "Deprecate: read data file from SS version 3.00", "topics": [ "SS_readdat_3.00" ] }, { "page": "SS_readdat_3.24", "title": "Deprecated: read data file from SS version 3.24", "topics": [ "SS_readdat_3.24" ] }, { "page": "SS_readdat_3.30", "title": "read data file from SS version 3.30", "topics": [ "SS_readdat_3.30" ] }, { "page": "SS_readforecast", "title": "read forecast file", "concept": [ "read/write functions" ], "topics": [ "SS_readforecast" ] }, { "page": "SS_readpar_3.24", "title": "Deprecated: read ss.par file from SS version 3.24", "topics": [ "SS_readpar_3.24" ] }, { "page": "SS_readpar_3.30", "title": "read .par file from SS version 3.30", "topics": [ "SS_readpar_3.30" ] }, { "page": "SS_readstarter", "title": "Read Stock Synthesis starter file as a list", "concept": [ "read/write functions" ], "topics": [ "SS_readstarter" ] }, { "page": "SS_readwtatage", "title": "Read in a weight-at-age data file as a data frame", "topics": [ "SS_readwtatage" ] }, { "page": "SS_recdevs", "title": "Insert a vector of recruitment deviations into the control file.", "topics": [ "SS_recdevs" ] }, { "page": "SS_RunJitter", "title": "Deprecated function to run jitters, renamed to jitter()", "topics": [ "SS_RunJitter" ] }, { "page": "SS_Sensi_plot", "title": "Create relative sensitivity plots as described in Cope and Gertseva (2020)", "topics": [ "SS_Sensi_plot" ] }, { "page": "SS_tune_comps", "title": "Deprecated function to tune composition data, renamed to tune_comps()", "topics": [ "SS_tune_comps" ] }, { "page": "SS_varadjust", "title": "Modify variance and sample size adjustments in the control file", "topics": [ "SS_varadjust" ] }, { "page": "SS_write", "title": "Write all Stock Synthesis input files for a model", "concept": [ "read/write functions" ], "topics": [ "SS_write" ] }, { "page": "SS_writectl", "title": "Write Stock Synthesis control file", "concept": [ "read/write functions" ], "topics": [ "SS_writectl" ] }, { "page": "SS_writectl_3.24", "title": "Deprecated: write 3.24 control file", "topics": [ "SS_writectl_3.24" ] }, { "page": "SS_writectl_3.30", "title": "write control file for SS3 version 3.30", "topics": [ "SS_writectl_3.30" ] }, { "page": "SS_writedat", "title": "write Stock Synthesis data file", "concept": [ "read/write functions" ], "topics": [ "SS_writedat" ] }, { "page": "SS_writedat_3.24", "title": "Deprecated: write data file for SS version 3.24", "topics": [ "SS_writedat_3.24" ] }, { "page": "SS_writedat_3.30", "title": "write data file for SS version 3.30", "topics": [ "SS_writedat_3.30" ] }, { "page": "SS_writeforecast", "title": "write forecast file", "concept": [ "read/write functions" ], "topics": [ "SS_writeforecast" ] }, { "page": "SS_writepar_3.24", "title": "Deprecated: write ss.par file from SS version 3.24", "topics": [ "SS_writepar_3.24" ] }, { "page": "SS_writepar_3.30", "title": "write .par file from SS version 3.30", "topics": [ "SS_writepar_3.30" ] }, { "page": "SS_writestarter", "title": "write starter file", "concept": [ "read/write functions" ], "topics": [ "SS_writestarter" ] }, { "page": "SS_writewtatage", "title": "Write weight-at-age file", "topics": [ "SS_writewtatage" ] }, { "page": "ss3_data_to_fims", "title": "Convert SS3 data into format required by FIMS", "topics": [ "ss3_data_to_fims" ] }, { "page": "SSbiologytables", "title": "Deprecated function to create a table of biology for assessment reporting: length, weight, % mature, fecundity, and selectivity", "topics": [ "SSbiologytables" ] }, { "page": "SSdiagsTime2Year", "title": "Convert Time-Steps", "topics": [ "SSdiagsTime2Year" ] }, { "page": "SSexecutivesummary", "title": "Deprecated function to create executive summary tables from an SS3 Report.sso file", "topics": [ "SSexecutivesummary" ] }, { "page": "SSgetMCMC", "title": "Read MCMC output.", "topics": [ "SSgetMCMC" ] }, { "page": "SSgetoutput", "title": "Get output from multiple Stock Synthesis models.", "concept": [ "model comparison functions" ], "topics": [ "SSgetoutput" ] }, { "page": "SSmakeMmatrix", "title": "Convert a matrix of natural mortality values into inputs for Stock Synthesis", "topics": [ "SSmakeMmatrix" ] }, { "page": "SSMethod.Cond.TA1.8", "title": "Apply Francis composition weighting method TA1.8 for conditional age-at-length fits", "concept": [ "tuning functions" ], "topics": [ "SSMethod.Cond.TA1.8" ] }, { "page": "SSMethod.TA1.8", "title": "Apply Francis composition weighting method TA1.8", "concept": [ "tuning functions" ], "topics": [ "SSMethod.TA1.8" ] }, { "page": "SSmohnsrho", "title": "Calculate Mohn's rho values for select quantities", "topics": [ "SSmohnsrho" ] }, { "page": "sspar", "title": "Allow Multi-Plots Set the par() to options suitable for ss3diags multi plots.", "topics": [ "sspar" ] }, { "page": "SSplotAgeMatrix", "title": "Plot matrix of either length or observed age at true age", "topics": [ "SSplotAgeMatrix" ] }, { "page": "SSplotBiology", "title": "Plot biology related quantities.", "topics": [ "SSplotBiology" ] }, { "page": "SSplotCatch", "title": "Plot catch related quantities.", "topics": [ "SSplotCatch" ] }, { "page": "SSplotCohortCatch", "title": "Plot cumulative catch by cohort.", "topics": [ "SSplotCohortCatch" ] }, { "page": "SSplotComparisons", "title": "plot model comparisons", "concept": [ "model comparison functions" ], "topics": [ "SSplotComparisons" ] }, { "page": "SSplotComps", "title": "Plot composition data and fits.", "topics": [ "SSplotComps" ] }, { "page": "SSplotData", "title": "Timeline of presence/absence of data by type, year, and fleet.", "topics": [ "SSplotData" ] }, { "page": "SSplotDiscard", "title": "Plot fit to discard fraction.", "topics": [ "SSplotDiscard" ] }, { "page": "SSplotDynamicB0", "title": "Plot Dynamic B0", "topics": [ "SSplotDynamicB0" ] }, { "page": "SSplotIndices", "title": "Plot indices of abundance and associated quantities.", "topics": [ "SSplotIndices" ] }, { "page": "SSplotMCMC_ExtraSelex", "title": "Plot uncertainty around chosen selectivity ogive from MCMC.", "topics": [ "SSplotMCMC_ExtraSelex" ] }, { "page": "SSplotMnwt", "title": "Plot mean weight data and fits.", "topics": [ "SSplotMnwt" ] }, { "page": "SSplotMovementMap", "title": "Show movement rates on a map.", "topics": [ "SSplotMovementMap" ] }, { "page": "SSplotMovementRates", "title": "Plot movement rates from model output", "topics": [ "SSplotMovementRates" ] }, { "page": "SSplotNumbers", "title": "Plot numbers-at-age related data and fits.", "topics": [ "SSplotNumbers" ] }, { "page": "SSplotPars", "title": "Plot distributions of priors, posteriors, and estimates.", "topics": [ "SSplotPars" ] }, { "page": "SSplotProfile", "title": "Plot likelihood profile results", "concept": [ "profile functions" ], "topics": [ "SSplotProfile" ] }, { "page": "SSplotRecdevs", "title": "Plot recruitment deviations", "topics": [ "SSplotRecdevs" ] }, { "page": "SSplotRecdist", "title": "Plot of recruitment distribution among areas and seasons", "topics": [ "SSplotRecdist" ] }, { "page": "SSplotRetroRecruits", "title": "Make squid plot of retrospectives of recruitment deviations.", "topics": [ "SSplotRetroRecruits" ] }, { "page": "SSplotSelex", "title": "Plot selectivity", "topics": [ "SSplotSelex" ] }, { "page": "SSplotSexRatio", "title": "Plot sex-ratio data and fits for two sex models", "topics": [ "SSplotSexRatio" ] }, { "page": "SSplotSpawnrecruit", "title": "Plot spawner-recruit curve.", "topics": [ "SSplotSpawnrecruit" ] }, { "page": "SSplotSPR", "title": "Plot Spawning Potential Ratio (SPR) quantities.", "topics": [ "SSplotSPR" ] }, { "page": "SSplotSummaryF", "title": "Plot the summary F (or harvest rate).", "topics": [ "SSplotSummaryF" ] }, { "page": "SSplotTags", "title": "Plot tagging data and fits", "topics": [ "SSplotTags" ] }, { "page": "SSplotTimeseries", "title": "Plot timeseries data", "topics": [ "SSplotTimeseries" ] }, { "page": "SSplotYield", "title": "Plot yield and surplus production.", "topics": [ "SSplotYield" ] }, { "page": "SSsummarize", "title": "Summarize the output from multiple Stock Synthesis models.", "concept": [ "model comparison functions" ], "topics": [ "SSsummarize" ] }, { "page": "SStableComparisons", "title": "make table comparing quantities across models", "concept": [ "model comparison functions" ], "topics": [ "SStableComparisons" ] }, { "page": "SSunavailableSpawningOutput", "title": "Plot unavailable spawning output", "topics": [ "SSunavailableSpawningOutput" ] }, { "page": "stackpoly", "title": "modified from \"stackpoly\" by Jim Lemon from \"plotrix\" package", "topics": [ "stackpoly" ] }, { "page": "table_all", "title": "Run all the tables functions", "concept": [ "table functions" ], "topics": [ "table_all" ] }, { "page": "table_biology", "title": "Create a table of biology for assessment reporting: length, weight, % mature, fecundity, and selectivity", "concept": [ "table functions" ], "topics": [ "table_biology" ] }, { "page": "table_compweight", "title": "Table of length and age comp Francis weights (doesn't yet include other data types)", "concept": [ "table functions" ], "topics": [ "table_compweight" ] }, { "page": "table_config", "title": "Create a table to summarize the configuration of the SS3 model", "concept": [ "table functions" ], "topics": [ "table_config" ] }, { "page": "table_exec_summary", "title": "Create executive summary tables from an SS3 Report.sso file", "concept": [ "table functions" ], "topics": [ "table_exec_summary" ] }, { "page": "table_parcounts", "title": "Summarize the estimated parameters based on an SS3 control file", "concept": [ "table functions" ], "topics": [ "table_parcounts" ] }, { "page": "table_pars", "title": "Table of parameters", "concept": [ "table functions" ], "topics": [ "table_pars" ] }, { "page": "table_ts", "title": "Table of estimated time series", "concept": [ "table functions" ], "topics": [ "table_ts" ] }, { "page": "translate_3.30_to_3.24_Q_setup", "title": "Use 3.30 q options to create the 3.24 q setup", "topics": [ "translate_3.30_to_3.24_Q_setup" ] }, { "page": "translate_3.30_to_3.24_var_adjust", "title": "Use 3.30 variance adjustments to create the 3.24 formatting", "topics": [ "translate_3.30_to_3.24_var_adjust" ] }, { "page": "tryCatch.W.E", "title": "tryCatch both warnings (with value) and errors", "topics": [ "tryCatch.W.E" ] }, { "page": "TSCplot", "title": "Create a plot for the TSC report", "topics": [ "TSCplot" ] }, { "page": "tune_comps", "title": "Calculate new tunings for length and age compositions and (re)run models", "concept": [ "run functions", "tuning functions" ], "topics": [ "tune_comps" ] }, { "page": "write_fwf4", "title": "Function to write formatted table similar to table written by gdata::write.fwf from data.frame or matrix This function does not accept columns or logical with factor", "topics": [ "write_fwf4" ] }, { "page": "writeComment", "title": "Add a comment line to the input files", "topics": [ "writeComment" ] } ], "_pkglogo": "https://github.com/r4ss/r4ss/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/r4ss/r4ss/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bslib", "cachem", "cli", "coda", "codetools", "corpcor", "cpp11", "curl", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "forcats", "fs", "furrr", "future", "generics", "ggplot2", "gh", "gitcreds", "globals", "glue", "gridExtra", "gtable", "highr", "htmltools", "httr2", "ini", "isoband", "jquerylib", "jsonlite", "kableExtra", "knitr", "labeling", "lattice", "lifecycle", "listenv", "magrittr", "memoise", "mime", "openssl", "parallelly", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "RColorBrewer", "rlang", "rmarkdown", "rstudioapi", "S7", "sass", "scales", "stringi", "stringr", "svglite", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "xml2", "yaml" ], "_vignettes": [ { "source": "r4ss-plots-ghpages.Rmd", "filename": "r4ss-plots-ghpages.html", "title": "Customizing {r4ss} output and posting to github pages", "author": "Ian Taylor and Kathryn Doering", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Creating plots", "Example: Creating plots from simple and adding a custom tab", "read model output", "make the default plots and associated HTML files", "Make custom plots and write CSV file with info about them", "Add custom plots to the .csv", "Getting the plots onto github" ], "created": "2026-04-30 23:14:18", "modified": "2026-04-30 23:14:18", "commits": 1 }, { "source": "example-plots.Rmd", "filename": "example-plots.html", "title": "Example r4ss plots", "author": "Ian G. Taylor", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-03-28 00:01:45", "modified": "2023-03-28 21:44:34", "commits": 3 }, { "source": "r4ss-intro-vignette.Rmd", "filename": "r4ss-intro-vignette.html", "title": "Introduction to r4ss", "author": "Ian G. Taylor and Kathryn L. Doering", "engine": "knitr::rmarkdown", "headings": [ "Installing the r4ss R package", "Basic installation", "Loading the package and reading help pages", "Alternative versions", "Reading model output and making default plots", "Creating select plots", "Scripting Stock Synthesis workflows with r4ss", "Read in Stock Synthesis files", "Investigate the model", "Modify the model", "Write out the modified models", "Download the Stock Synthesis executable from GitHub", "Run the modified model", "Investigate the model run", "Should I script my whole Stock Synthesis workflow?", "Functions for common stock assessment tasks", "Running retrospectives", "Jittering", "Tuning composition data" ], "created": "2018-01-11 20:38:07", "modified": "2024-09-19 21:22:15", "commits": 19 } ], "_score": 11.964731512673476, "_indexed": false, "_nocasepkg": "r4ss", "_universes": [ "ices-tools-prod" ], "_indexurl": "https://r4ss.r-universe.dev/r4ss", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.54.0", "date": "2026-05-27T18:15:46.000Z", "distro": "noble", "commit": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "fileid": "666643085e017890b33f9bee5f60d779b6ed942d4737ad635005e8c960e87202", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26529539651" }, { "r": "4.6.0", "os": "linux", "version": "1.54.0", "date": "2026-05-27T18:15:47.000Z", "distro": "noble", "commit": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "fileid": "9a4b7a82e8163b8aa62cd98ebd915a4169558054454f8eafc070aeedb9c2603d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26529539651" }, { "r": "4.5.3", "os": "mac", "version": "1.54.0", "date": "2026-05-27T18:14:38.000Z", "commit": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "fileid": "088e69483c0b3904d7e94704ed2002645a49cd8e5ae5e0400f21df05e71a6552", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26529539651" }, { "r": "4.6.0", "os": "mac", "version": "1.54.0", "date": "2026-05-27T18:14:49.000Z", "commit": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "fileid": "8c1606bac542d3dce4d78be112bcbf2cd274693572639c3dacfaa9703b4d0b18", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26529539651" }, { "r": "4.6.0", "os": "wasm", "version": "1.54.0", "date": "2026-05-27T18:15:45.000Z", "commit": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "fileid": "96ae1359b3bfc414cf02fb11d40e778170bd7ea4be059b31b84bcc6921743740", "status": "success", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26529539651" }, { "r": "4.7.0", "os": "win", "version": "1.54.0", "date": "2026-05-27T18:14:47.000Z", "commit": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "fileid": "ee510fa39c651713eab71c20edb2d2518254f362278ca9b51a75133c98a1636d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26529539651" }, { "r": "4.5.3", "os": "win", "version": "1.54.0", "date": "2026-05-27T18:14:54.000Z", "commit": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "fileid": "f95b2a155ac26e44873dc6b8b36aeeea2de6b33f88cd71e19a4d6b2a238d4550", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26529539651" }, { "r": "4.6.0", "os": "win", "version": "1.54.0", "date": "2026-05-27T18:14:28.000Z", "commit": "1ef0a05030e4a70477afdbdfb91a45bfd35b75c9", "fileid": "4cdfd6edd3df34b4217d4e2cd0e99eae4c99ca69f5a06c68f14697c33909d7da", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26529539651" } ] }