{ "_id": "6a1025aeacfb0bcc41c8ed89", "Type": "Package", "Package": "ss3sim", "Title": "Fisheries Stock Assessment Simulation Testing with Stock\nSynthesis", "Version": "1.24.0", "Authors@R": "c(\nperson(c(\"Kelli\", \"F.\"), \"Johnson\", , \"kelli.johnson@noaa.gov\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-5149-451X\")),\nperson(c(\"Sean\", \"C.\"), \"Anderson\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-9563-1937\")),\nperson(c(\"Kathryn\", \"L.\"), \"Doering\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-0396-7044\")),\nperson(c(\"Cole\", \"C.\"), \"Monnahan\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-0871-6700\")),\nperson(c(\"Christine\", \"C.\"), \"Stawitz\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-3122-4501\")),\nperson(\"Curry\", \"Cunningham\", role = \"ctb\"),\nperson(\"Allan\", \"Hicks\", role = \"ctb\"),\nperson(\"Felipe\", \"Hurtado-Ferro\", role = \"ctb\"),\nperson(\"Peter\", \"Kuriyama\", role = \"ctb\"),\nperson(\"Roberto\", \"Licandeo\", role = \"ctb\"),\nperson(\"Carey\", \"McGilliard\", role = \"ctb\"),\nperson(c(\"Giancarlo\", \"H.\"), \"Moron Correa\", role = \"ctb\"),\nperson(\"Melissa\", \"Murdian\", role = \"ctb\"),\nperson(\"Kotaro\", \"Ono\", role = \"ctb\"),\nperson(\"Merrill\", \"Rudd\", role = \"ctb\"),\nperson(\"Cody\", \"Szuwalski\", role = \"ctb\"),\nperson(c(\"Ian\", \"G.\"), \"Taylor\", role = \"ctb\"),\nperson(\"Juan\", \"Valero\", role = \"ctb\"),\nperson(\"Athol\", \"Whitten\", role = \"ctb\"),\nperson(c(\"Kiva\", \"L.\"), \"Oken\", role = \"ctb\")\n)", "Description": "A framework for fisheries stock assessment simulation\ntesting with Stock Synthesis (SS3) as described in Anderson et\nal. (2014) .", "License": "MIT + file LICENSE", "URL": "https://github.com/ss3sim/ss3sim", "BugReports": "https://github.com/ss3sim/ss3sim/issues", "VignetteBuilder": "knitr", "Remotes": [ "github::r4ss/r4ss@main" ], "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "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://ss3sim.r-universe.dev", "Date/Publication": "2026-04-13 16:42:44 UTC", "RemoteUrl": "https://github.com/ss3sim/ss3sim", "RemoteRef": "HEAD", "RemoteSha": "11e7466603202ab8724839fe394fd1e10c1434fe", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-13 09:33:05 UTC", "User": "root" }, "Author": "Kelli F. Johnson [aut, cre] (ORCID:\n),\nSean C. Anderson [aut] (ORCID: ),\nKathryn L. Doering [aut] (ORCID:\n),\nCole C. Monnahan [aut] (ORCID: ),\nChristine C. 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"name": "scalar_dat", "title": "Example scalar data from the Introduction vignette", "object": "scalar_dat", "class": [ "data.frame" ], "fields": [ "SSB_Unfished", "Totbio_Unfished", "SmryBio_Unfished", "Recr_Unfished", "SSB_Btgt", "SPR_Btgt", "F_Btgt", "TotYield_Btgt", "SSB_SPR", "F_SPR", "TotYield_SPR", "SSB_MSY", "SPR_MSY", "F_MSY", "TotYield_MSY", "Ret_Catch_MSY", "max_grad", "depletion", "alt_sigma_r", "last_yr_early", "first_yr_full", "last_yr_full", "first_yr_recent", "max_bias_adj", "params_on_bound", "params_stuck_low", "params_stuck_high", "NatM_p_1_Fem_GP_1", "L_at_Amin_Fem_GP_1", "L_at_Amax_Fem_GP_1", "VonBert_K_Fem_GP_1", "CV_young_Fem_GP_1", "CV_old_Fem_GP_1", "Wtlen_1_Fem_GP_1", "Wtlen_2_Fem_GP_1", "Mat50._Fem_GP_1", "Mat_slope_Fem_GP_1", "Eggs.kg_inter_Fem_GP_1", "Eggs.kg_slope_wt_Fem_GP_1", "RecrDist_GP_1", "RecrDist_Area_1", "RecrDist_month_1", "CohortGrowDev", "FracFemale_GP_1", "SR_LN_R0", "SR_BH_steep", "SR_sigmaR", "SR_regime", "SR_autocorr", "Early_InitAge_25", 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At time of writing, this method will work for MG, selectivity, and catchability time varying, but not for SR", "topics": [ "add_tv_parlines" ] }, { "page": "calculate_bias", "title": "Calculate bias adjustment for recruitment deviations", "topics": [ "calculate_bias" ] }, { "page": "calculate_data_units", "title": "Calculate fleets, years, and data types needed given sampling parameters", "topics": [ "calculate_data_units" ] }, { "page": "calculate_re", "title": "Calculate relative error", "topics": [ "calculate_re" ] }, { "page": "change_catch", "title": "Change catch in the Stock Synthesis data list", "topics": [ "change_catch" ] }, { "page": "change_comp", "title": "Change composition data to dummy data for running the operating model", "topics": [ "change_comp" ] }, { "page": "change_dat_bin", "title": "Change the bins for a composition object", "topics": [ "change_dat_bin" ] }, { "page": "change_data", "title": "Change the data that is available from a list object", "concept": [ "change functions" ], "topics": [ "change_data" ] }, { "page": "change_e", "title": "Methods to alter the parameters estimated in a Stock Synthesis model", "concept": [ "change functions" ], "topics": [ "change_e" ] }, { "page": "change_em_ageerr", "title": "Change ageing-error matrix in estimation model", "concept": [ "change functions" ], "topics": [ "change_em_ageerr" ] }, { "page": "change_em_binning", "title": "Change population and observed length-composition bins", "concept": [ "change functions", "sample functions" ], "topics": [ "change_em_binning" ] }, { "page": "change_f", "title": "Specify fishing mortality, F, using the Stock Synthesis control file", "concept": [ "change functions" ], "topics": [ "change_f" ] }, { "page": "change_lcomp_constant", "title": "Set the robustification constant for length-composition data", "topics": [ "change_lcomp_constant" ] }, { "page": "change_o", "title": "Methods to include parameters in a Stock Synthesis operating model", "concept": [ "change functions" ], "topics": [ "change_o" ] }, { "page": "change_pop_bin", "title": "Set up population length bin structure", "topics": [ "change_pop_bin" ] }, { "page": "change_q", "title": "Adds or removes catchability parameters from a control file", "topics": [ "change_q" ] }, { "page": "change_rec_devs", "title": "Replace recruitment deviations", "topics": [ "change_rec_devs" ] }, { "page": "change_recyear", "title": "Change start year main recruitment deviations in control file", "topics": [ "change_recyear" ] }, { "page": "change_retro", "title": "Alter a starter file for a retrospective analysis", "concept": [ "change functions" ], "topics": [ "change_retro" ] }, { "page": "change_startyear", "title": "Change start year of the data file", "topics": [ "change_startyear" ] }, { "page": "change_tail_compression", "title": "Replace tail compression value for length composition data", "topics": [ "change_tail_compression" ] }, { "page": "change_tv", "title": "Methods to include time-varying parameters in a Stock Synthesis operating model", "concept": [ "change functions" ], "topics": [ "change_tv" ] }, { "page": "change_year", "title": "Change the years estimated", "topics": [ "change_year" ] }, { "page": "check_data", "title": "Check that the Stock Synthesis data file looks correct", "topics": [ "check_data" ] }, { "page": "check_data_str_range", "title": "Check input arguments for data", "topics": [ "check_data_str_range" ] }, { "page": "check_eqlength", "title": "Check if input arguments have the same length", "topics": [ "check_eqlength" ] }, { "page": "check_forecast", "title": "Check input forecast file values", "topics": [ "check_forecast" ] }, { "page": "check_q", "title": "Check if desired q parameters exist in control file list", "topics": [ "check_q" ] }, { "page": "clean_data", "title": "Given sampling arguments, remove unneeded data from a .dat file", "concept": [ "sampling functions" ], "topics": [ "clean_data" ] }, { "page": "codemctl", "title": "Control file for the cod estimation method", "topics": [ "codemctl" ] }, { "page": "codomctl", "title": "Control file for the cod operating model", "topics": [ "codomctl" ] }, { "page": "codomdat", "title": "Data for the cod operating model", "topics": [ "codomdat" ] }, { "page": "convert_to_wide", "title": "Convert long-style ss3sim output to wide format", "topics": [ "convert_to_wide" ] }, { "page": "copy_ss3models", "title": "Copy the OM or EM into a scenario directory", "topics": [ "copy_ss3models" ] }, { "page": "create_em", "title": "Create an EM from an OM", "topics": [ "create_em" ] }, { "page": "create_logo", "title": "Create the ss3sim logo", "topics": [ "create_logo" ] }, { "page": "facet_form", "title": "Helper function for building a ggplot facet", "topics": [ "facet_form" ] }, { "page": "fill_across", "title": "Fill in matrix across rows of weight-at-age data by interpolation", "topics": [ "fill_across" ] }, { "page": "find_position", "title": "Find integer reference to fleet names", "topics": [ "find_position" ] }, { "page": "get_bin", "title": "Get Stock Synthesis binary/executable location", "topics": [ "get_bin" ] }, { "page": "get_compfit", "title": "Get summaries of fits to composition data from report file list", "topics": [ "get_compfit" ] }, { "page": "get_model_folder", "title": "Get the folder location of an included Stock Synthesis model configuration", "topics": [ "get_model_folder" ] }, { "page": "get_nll_components", "title": "Get negative log likelihood (NLL) values from a report file list", "topics": [ "get_nll_components" ] }, { "page": "get_recdevs", "title": "Return a set of recruitment deviations", "topics": [ "get_recdevs" ] }, { "page": "get_results_all", "title": "Extract Stock Synthesis simulation output", "concept": [ "get-results" ], "topics": [ "get_results_all" ] }, { "page": "get_results_derived", "title": "Extract time series from a model run with the associated standard deviation.", "concept": [ "get-results" ], "topics": [ "get_results_derived" ] }, { "page": "get_results_iter", "title": "Get results for 1 iteration", "topics": [ "get_results_iter" ] }, { "page": "get_results_mod", "title": "Get results for 1 model run", "topics": [ "get_results_mod" ] }, { "page": "get_results_scalar", "title": "Extract scalar quantities from a model run.", "concept": [ "get-results" ], "topics": [ "get_results_scalar" ] }, { "page": "get_results_scenario", "title": "Extract Stock Synthesis simulation results for one scenario", "concept": [ "get-results" ], "topics": [ "get_results_scenario" ] }, { "page": "get_results_timeseries", "title": "Return the time series information from an iteration", "concept": [ "get-results" ], "topics": [ "get_results_timeseries" ] }, { "page": "get_scenarios", "title": "Identify scenarios in 'directory'", "concept": [ "get results" ], "topics": [ "get_scenarios" ] }, { "page": "get_sigmar", "title": "Get Variability About Recruitment Deviations (sigma_R)", "topics": [ "get_sigmar" ] }, { "page": "get_success", "title": "Determine if a Stock Synthesis run was successful", "topics": [ "get_success" ] }, { "page": "make_df", "title": "Make a list of lists with dataframe components into a dataframes", "topics": [ "make_df" ] }, { "page": "plot_boxplot", "title": "Plot results of a simulation as boxplots", "topics": [ "plot_boxplot" ] }, { "page": "plot_cummean", "title": "Plot the cumulative mean for a parameter", "topics": [ "plot_cummean" ] }, { "page": "plot_lines", "title": "Plot time-series values as lines", "topics": [ "plot_lines" ] }, { "page": "plot_points", "title": "Plot results of a simulation as a scatterplot", "topics": [ "plot_points" ] }, { "page": "plot_ss3sim", "title": "Base plot for 'ss3sim' data", "topics": [ "plot_ss3sim" ] }, { "page": "profile_fmsy", "title": "Determine Fmsy for a given operating model", "topics": [ "profile_fmsy" ] }, { "page": "replace_x", "title": "Replace a 'NULL' value with 'NA' in a list", 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"topics": [ "scalar_dat" ] }, { "page": "setup_bins", "title": "Set up bin structure for composition data", "topics": [ "setup_bins" ] }, { "page": "setup_parallel", "title": "Setup parallel processing", "topics": [ "setup_parallel" ] }, { "page": "setup_scenarios", "title": "Get scenario information from a data frame of specifications", "topics": [ "setup_scenarios" ] }, { "page": "setup_scenarios_defaults", "title": "Set up a generic scenario", "topics": [ "setup_scenarios_defaults" ] }, { "page": "setup_scenarios_fleet", "title": "Set up fleet-specific information", "topics": [ "setup_scenarios_fleet" ] }, { "page": "setup_scenarios_lookup", "title": "Create a named vector to look up full names for types of arguments", "topics": [ "setup_scenarios_lookup" ] }, { "page": "setup_scenarios_name", "title": "Create a name for an unnamed scenario", "topics": [ "setup_scenarios_name" ] }, { "page": "ss3sim_base", "title": "High-level wrapper to run a simulation", "topics": [ "ss3sim_base" 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