{ "_id": "6a3242653efcd9bda4377f63", "Type": "Package", "Package": "SSMSE", "Title": "Management Strategy Evaluation (MSE) using Stock Synthesis (SS)", "Version": "0.3.0", "Authors@R": "c(\nperson(\"Kathryn\", \"Doering\", , \"kathryn.doering@noaa.gov\", role = c(\"aut\", \"cre\")),\nperson(\"Nathan\", \"Vaughan\", , \"nathan.vaughan@noaa.gov\", role = \"aut\")\n)", "Description": "An R package for performing Management Strategy Evaluation\n(MSE) using Stock Synthesis (SS3). SS3 is used as the Operating\nModel (OM) and, if the user desires, the Estimation model (EM).\nSSMSE allows existing SS3 models to be used as the basis for an\nOM. These OMs are used in the MSE framework provided by SSMSE\nto evaluate the implications of management actions on a\npopulation given uncertainty.", "License": "MIT + file LICENSE.md", "URL": "https://github.com/nmfs-ost/SSMSE", "BugReports": "https://github.com/nmfs-ost/SSMSE/issues", "Remotes": [ "cran/assertive.base@master", "cran/assertive.properties@master", "cran/assertive.types@master", "r4ss/r4ss@main", "ss3sim/ss3sim@main" ], "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "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://noaa-fisheries-integrated-toolbox.r-universe.dev", "Date/Publication": "2025-06-16 23:36:03 UTC", "RemoteUrl": "https://github.com/nmfs-ost/SSMSE", "RemoteRef": "HEAD", "RemoteSha": "7e84e38d4a57becdef8a6e3d4710cddd1bfc18ee", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-17 00:33:56 UTC", "User": "root" }, "Author": "Kathryn Doering [aut, cre],\nNathan Vaughan [aut]", "Maintainer": "Kathryn Doering ", "MD5sum": "aa0b09b98a53990f19ee76b576edb8d0", "_user": "noaa-fisheries-integrated-toolbox", "_type": "src", "_file": "SSMSE_0.3.0.tar.gz", "_fileid": "682b6bdcee439d22ce83d9b1cfdc3ffe7df3f776ef5c2d1db3e45334ccd96e29", "_filesize": 10105120, "_sha256": "682b6bdcee439d22ce83d9b1cfdc3ffe7df3f776ef5c2d1db3e45334ccd96e29", "_created": "2026-06-17T00:33:56.000Z", "_published": "2026-06-17T06:44:53.693Z", "_distro": "noble", "_jobs": [ { "job": 81834193720, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "FAIL", "artifact": "" }, { "job": 81834193851, "time": 168, "config": "linux-release-x86_64", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 81834194056, "time": 82, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 81834193774, "time": 88, "config": "macos-release-arm64", "r": "4.6.0", 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"_maintainer": { "name": "Kathryn Doering", "email": "kathryn.doering@noaa.gov", "login": "k-doering-noaa", "description": "", "uuid": 48930335 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "assertive.base", "role": "Imports" }, { "package": "assertive.properties", "role": "Imports" }, { "package": "assertive.types", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "r4ss", "version": ">= 1.50.0", "role": "Imports" }, { "package": "ss3sim", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "nmfs-ost", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 7 } ], "_tags": [ { "name": "v0.2.9", "date": "2025-09-20" } ], "_topics": [ "stock-synthesis" ], "_stars": 21, "_contributors": [ { "user": "k-doering-noaa", "count": 721, "uuid": 48930335 }, { "user": "nathanvaughan-noaa", "count": 107, "uuid": 53061482 }, { "user": "corinnebassin-noaa", "count": 9, "uuid": 47904818 }, { "user": "kellijohnson-noaa", "count": 6, "uuid": 4108564 }, { "user": "cassidypeterson-noaa", "count": 2, "uuid": 90650166 } ], "_userbio": { "uuid": 49974461, "type": "organization", "name": "NOAA Fisheries Integrated Toolbox", "followers": 9, "description": "GitHub Organization to manage the NOAA FIT" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SSMSE" }, "_devurl": "https://github.com/nmfs-ost/ssmse", "_searchresults": 60, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/SSMSE.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "check_convergence", "create_future_om_list", "create_sample_struct", "create_scen_list", "develop_OMs", "get_avg_catch", "get_bin", "get_catch_cv", "get_catch_sd", "get_rel_SSB_avg", "get_SSB_avg", "get_total_catch", "parse_MS", "plot_comp_sampling", "plot_index_sampling", "run_EM", "run_ss_model", "run_SSMSE", "set_MSE_seeds", "SSMSE_summary_all" ], "_help": [ { "page": "add_dev_changes", "title": "Add the deviation changes from the list obj to an existing df", "topics": [ "add_dev_changes" ] }, { "page": "add_new_dat", "title": "Add new data to an existing EM dataset", "topics": [ "add_new_dat" ] }, { "page": "add_OM_devs", "title": "Add in future parameter values", "topics": [ "add_OM_devs" ] }, { "page": "add_sample_struct", "title": "Add in years of sampling data needed", "topics": [ "add_sample_struct" ] }, { "page": "calc_comp_var", "title": "Calculate uncertainty and biases in historic composition data", "topics": [ "calc_comp_var" ] }, { "page": "calc_par_trend", "title": "Calculate the parameter trend", "topics": [ "calc_par_trend" ] }, { "page": "change_dat", "title": "Change dataset from OM into format for EM", "topics": [ "change_dat" ] }, { "page": "change_yrs_fcast", "title": "Change the years in the forecast file", "topics": [ "change_yrs_fcast" ] }, { "page": "check_avail_dat", "title": "check all index years/fleets in EM available in OM. (but not vice versa) a general function that can be used", "topics": [ "check_avail_dat" ] }, { "page": "check_catch_df", "title": "Check the catch dataframe", "topics": [ "check_catch_df" ] }, { "page": "check_convergence", "title": "Flag potential convergence issues in SS3 model runs", "topics": [ "check_convergence" ] }, { "page": "check_dir", "title": "Check that the directory for an OM is valid", "topics": [ "check_dir" ] }, { "page": "check_EM_forecast", "title": "Check structure of forecast is suitable to use in the EM", "topics": [ "check_EM_forecast" ] }, { "page": "check_future_catch", "title": "Check future catch smaller than the last year's population size.", "topics": [ "check_future_catch" ] }, { "page": "check_future_om_list_str", "title": "Check the general structure of a future OM list and standardize values", "topics": [ "check_future_om_list_str" ] }, { "page": "check_future_om_list_vals", "title": "Check structure of a future OM list against the scen_list and standardize output", "topics": [ "check_future_om_list_vals" ] }, { "page": "check_OM_dat", "title": "check that an OM data set has at least the same data as an estimation model", "topics": [ "check_OM_dat" ] }, { "page": "check_sample_struct", "title": "Check sample_struct_list", "topics": [ "check_sample_struct" ] }, { "page": "check_scen_list", "title": "Check structure of the object scen_list", "topics": [ "check_scen_list" ] }, { "page": "clean_init_mod_files", "title": "clean the initial model files", "topics": [ "clean_init_mod_files" ] }, { "page": "combine_cols", "title": "function that creates a combined column to the list_item of interest", "topics": [ "combine_cols" ] }, { "page": "convert_future_om_list_to_devs_df", "title": "Create the devs dataframe for a scenario and iteration from user input", "topics": [ "convert_future_om_list_to_devs_df" ] }, { "page": "convert_to_r4ss_names", "title": "Convert user input to r4ss data names", "topics": [ "convert_to_r4ss_names" ] }, { "page": "copy_model_files", "title": "Copy OM and EM model files", "topics": [ "copy_model_files" ] }, { "page": "create_future_om_list", "title": "Helper function to create future om list objects", "topics": [ "create_future_om_list" ] }, { "page": "create_OM", "title": "Create the OM", "topics": [ "create_OM" ] }, { "page": "create_out_dirs", "title": "create the OM directory", "topics": [ "create_out_dirs" ] }, { "page": "create_sample_struct", "title": "Create the sample_struct list", "topics": [ "create_sample_struct" ] }, { "page": "create_scen_list", "title": "Create scen_list object to use in run_SSMSE function.", "topics": [ "create_scen_list" ] }, { "page": "develop_OMs", "title": "Develop different operating models", "topics": [ "develop_OMs" ] }, { "page": "EM", "title": "Use EM as the management strategy option.", "topics": [ "EM" ] }, { "page": "get_avg_catch", "title": "Example Performance Metric: Calculate average catch over a range of years", "topics": [ "get_avg_catch" ] }, { "page": "get_bin", "title": "Get SS3 binary/executable location in package", "topics": [ "get_bin" ] }, { "page": "get_catch_cv", "title": "Example Performance Metric: Calculate the coefficient of variation of catch", "topics": [ "get_catch_cv" ] }, { "page": "get_catch_sd", "title": "Example Performance Metric: Calculate Standard Deviation of Catch", "topics": [ "get_catch_sd" ] }, { "page": "get_dead_catch", "title": "Get dead catch from the timeseries Report.sso table", "topics": [ "get_dead_catch" ] }, { "page": "get_EM_catch_df", "title": "Get the EM catch data frame", "topics": [ "get_EM_catch_df" ] }, { "page": "get_EM_dat", "title": "Change the OM data to match the format of the original EM data", "topics": [ "get_EM_dat" ] }, { "page": "get_F", "title": "Get the Fishing mortality from the timeseries Report.sso table", "topics": [ "get_F" ] }, { "page": "get_full_sample_struct", "title": "Get the full sample structure from user input", "topics": [ "get_full_sample_struct" ] }, { "page": "get_impl_error_matrix", "title": "Put implementation error of 0 into a matrix", "topics": [ "get_impl_error_matrix" ] }, { "page": "get_init_samp_scheme", "title": "Get the sampling scheme in a data file.", "topics": [ "get_init_samp_scheme" ] }, { "page": "get_input_value", "title": "return a value from a data frame", "topics": [ "get_input_value" ] }, { "page": "get_no_EM_catch_df", "title": "Get the data frame of catch for the next iterations when not using an estimation model.", "topics": [ "get_no_EM_catch_df" ] }, { "page": "get_performance_metrics", "title": "get basic data to calculate performance metrics", "topics": [ "get_performance_metrics" ] }, { "page": "get_rel_SSB_avg", "title": "Example Performance Metric: Calculate the avg relative SSB (SSB/SSB unfished) over a range of years for each iteration", "topics": [ "get_rel_SSB_avg" ] }, { "page": "get_retained_catch", "title": "Get retained catch from the timeseries Report.sso table", "topics": [ "get_retained_catch" ] }, { "page": "get_SSB_avg", "title": "Example Performance Metric: calculate the average SSB over a range of years for each iteration", "topics": [ "get_SSB_avg" ] }, { "page": "get_total_catch", "title": "Example Performance Metric: Calculate total catch over a range of years", "topics": [ "get_total_catch" ] }, { "page": "Interim", "title": "Interim assessment management strategy", "topics": [ "Interim" ] }, { "page": "last_yr_catch", "title": "Last year catch used in the future for management strategy", "topics": [ "last_yr_catch" ] }, { "page": "locate_in_dirs", "title": "Locate the OM model files", "topics": [ "locate_in_dirs" ] }, { "page": "match_parname", "title": "Match parameter name to parameter names in the par file", "topics": [ "match_parname" ] }, { "page": "no_catch", "title": "No Catch in the future management strategy", "topics": [ "no_catch" ] }, { "page": "parse_MS", "title": "Parse management strategy options", "topics": [ "parse_MS" ] }, { "page": "plot_comp_sampling", "title": "Plot comp data, expected values, and sampled data for 1 scenario", "topics": [ "plot_comp_sampling" ] }, { "page": "plot_index_sampling", "title": "Plot index data, expected values, and sampled data for 1 scenario", "topics": [ "plot_index_sampling" ] }, { "page": "r4ss_obj_err", "title": "Error if object is not an r4ss object", "topics": [ "r4ss_obj_err" ] }, { "page": "rm_sample_struct_hist", "title": "Remove the historical sampling structure", "topics": [ "rm_sample_struct_hist" ] }, { "page": "rm_vals", "title": "remove vals in 2 list components with the same name", "topics": [ "rm_vals" ] }, { "page": "run_EM", "title": "Run the estimation model", "topics": [ "run_EM" ] }, { "page": "run_OM", "title": "Initial run of the OM", "topics": [ "run_OM" ] }, { "page": "run_ss_model", "title": "Run an operating or estimation model", "topics": [ "run_ss_model" ] }, { "page": "run_SSMSE", "title": "run an MSE using SS3 OMs", "topics": [ "run_SSMSE" ] }, { "page": "run_SSMSE_iter", "title": "Run one iteration of an MSE using SS3 OM", "topics": [ "run_SSMSE_iter" ] }, { "page": "run_SSMSE_scen", "title": "Run an MSE scenario using SS3 OM", "topics": [ "run_SSMSE_scen" ] }, { "page": "sample_vals", "title": "Sample vals from normal random, lognormal random, or modified AR-1 process.", "topics": [ "sample_vals" ] }, { "page": "set_MSE_seeds", "title": "Set the initial global, scenario, and iteration seeds", "topics": [ "set_MSE_seeds" ] }, { "page": "Sim_comp", "title": "Calculate uncertainty and biases in historic composition data", "topics": [ "Sim_comp" ] }, { "page": "SSMSE", "title": "SSMSE: A package for Management Strategy Evaluation (MSE) using Stock Synthesis (SS3)", "topics": [ "SSMSE-package", "SSMSE" ] }, { "page": "SSMSE_summary_all", "title": "Get results in a list for 1 scenario", "topics": [ "SSMSE_summary_all" ] }, { "page": "SSMSE_summary_iter", "title": "Get results in a list for 1 iteration", "topics": [ "SSMSE_summary_iter" ] }, { "page": "SSMSE_summary_scen", "title": "Get results in a list for 1 scenario", "topics": [ "SSMSE_summary_scen" ] }, { "page": "test_no_par", "title": "Change a model from running with par to running without par", "topics": [ "test_no_par" ] }, { "page": "update_basevals_blocks", "title": "Update a sequence of base parameter annual values to account for a time varying block effects", "topics": [ "update_basevals_blocks" ] }, { "page": "update_basevals_dev", "title": "Update a sequence of base parameter annual values to account for a time varying deviation effects", "topics": [ "update_basevals_dev" ] }, { "page": "update_basevals_env", "title": "Update a sequence of base parameter annual values to account for a time varying environmental effects", "topics": [ "update_basevals_env" ] }, { "page": "update_OM", "title": "Extend the OM forward using next years' catch", "topics": [ "update_OM" ] } ], "_readme": 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