{
  "_id": "69e09f4fc5259ad4cd90fda2",
  "Type": "Package",
  "Package": "SPoRC",
  "Title": "A Generalized Stochastic (S) Population (Po) Model Over Regional\n(R) Components (C)",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(\"Matthew\", \"Cheng\", , \"lhcheng@alaska.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Dan\", \"Goethel\", role = \"ctb\"),\nperson(\"Pete\", \"Hulson\", role = \"ctb\"),\nperson(\"Curry\", \"Cunningham\", role = \"ctb\")\n)",
  "Description": "A generalized spatial population model for stock\nassessment, written in RTMB.",
  "License": "GPL-3",
  "URL": "https://chengmatt.github.io/SPoRC",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "LazyDataCompression": "xz",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://jimianelli.r-universe.dev",
  "Date/Publication": "2025-11-27 04:12:55 UTC",
  "RemoteUrl": "https://github.com/jimianelli/SPoRC",
  "RemoteRef": "HEAD",
  "RemoteSha": "8060533a3831a2f3179cba9745ee92ecf79b6259",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-04-16 08:28:46 UTC",
    "User": "root"
  },
  "Author": "Matthew Cheng [aut, cre],\nDan Goethel [ctb],\nPete Hulson [ctb],\nCurry Cunningham [ctb]",
  "Maintainer": "Matthew Cheng <lhcheng@alaska.edu>",
  "MD5sum": "f98e4594e637254a373b7379f5359bec",
  "_user": "jimianelli",
  "_type": "src",
  "_file": "SPoRC_0.1.0.tar.gz",
  "_fileid": "daefa368fde6c7cfc394ee9f75695b84ef0515e076644a908f8aaefb2889b447",
  "_filesize": 26335212,
  "_sha256": "daefa368fde6c7cfc394ee9f75695b84ef0515e076644a908f8aaefb2889b447",
  "_created": "2026-04-16T08:28:46.000Z",
  "_published": "2026-06-02T20:54:29.401Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 71604844145,
      "time": 321,
      "config": "linux-devel-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6469147919"
    },
    {
      "job": 71604844164,
      "time": 222,
      "config": "linux-release-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6469120511"
    },
    {
      "job": 71604844269,
      "time": 177,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6469107210"
    },
    {
      "job": 71604844238,
      "time": 161,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6469102620"
    },
    {
      "job": 71603977165,
      "time": 365,
      "config": "source",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6469057668"
    },
    {
      "job": 71604844167,
      "time": 228,
      "config": "wasm-release",
      "r": "4.5.1",
      "check": "OK",
      "artifact": "6469122418"
    },
    {
      "job": 71604844256,
      "time": 203,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "6469115004"
    },
    {
      "job": 71604844233,
      "time": 196,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6469112527"
    },
    {
      "job": 71604844223,
      "time": 187,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6469110108"
    }
  ],
  "_buildurl": "https://github.com/r-universe/jimianelli/actions/runs/24499969591",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/jimianelli/SPoRC",
  "_commit": {
    "id": "8060533a3831a2f3179cba9745ee92ecf79b6259",
    "author": "Matt Cheng <84427627+chengmatt@users.noreply.github.com>",
    "committer": "Matt Cheng <84427627+chengmatt@users.noreply.github.com>",
    "message": "quick fixes on ln_InitDevs dimensions in sim\n",
    "time": 1764216775
  },
  "_maintainer": {
    "name": "Matthew Cheng",
    "email": "lhcheng@alaska.edu",
    "login": "chengmatt",
    "twitter": "@MLCheng3",
    "uuid": 84427627
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "RTMB",
      "role": "Depends"
    },
    {
      "package": "abind",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "here",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "progressr",
      "role": "Imports"
    },
    {
      "package": "randtests",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "TMB",
      "role": "Imports"
    },
    {
      "package": "compResidual",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "purrr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "jimianelli",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-16",
      "n": 15
    },
    {
      "week": "2025-17",
      "n": 1
    },
    {
      "week": "2025-18",
      "n": 21
    },
    {
      "week": "2025-19",
      "n": 1
    },
    {
      "week": "2025-20",
      "n": 4
    },
    {
      "week": "2025-21",
      "n": 5
    },
    {
      "week": "2025-22",
      "n": 6
    },
    {
      "week": "2025-23",
      "n": 6
    },
    {
      "week": "2025-24",
      "n": 3
    },
    {
      "week": "2025-25",
      "n": 5
    },
    {
      "week": "2025-26",
      "n": 4
    },
    {
      "week": "2025-27",
      "n": 15
    },
    {
      "week": "2025-28",
      "n": 8
    },
    {
      "week": "2025-29",
      "n": 9
    },
    {
      "week": "2025-30",
      "n": 4
    },
    {
      "week": "2025-31",
      "n": 3
    },
    {
      "week": "2025-32",
      "n": 5
    },
    {
      "week": "2025-34",
      "n": 4
    },
    {
      "week": "2025-35",
      "n": 1
    },
    {
      "week": "2025-40",
      "n": 13
    },
    {
      "week": "2025-41",
      "n": 3
    },
    {
      "week": "2025-42",
      "n": 4
    },
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-46",
      "n": 2
    },
    {
      "week": "2025-48",
      "n": 4
    }
  ],
  "_tags": [
    {
      "name": "v1.0.0-alpha",
      "date": "2025-08-05"
    },
    {
      "name": "v1.0.0-beta",
      "date": "2025-09-30"
    },
    {
      "name": "v1.0.0",
      "date": "2025-11-24"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "chengmatt",
      "count": 164,
      "uuid": 84427627
    },
    {
      "user": "benwilliams-noaa",
      "count": 4,
      "uuid": 64659151
    }
  ],
  "_userbio": {
    "uuid": 2715618,
    "type": "user",
    "name": "Jim Ianelli"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SPoRC"
  },
  "_devurl": "https://github.com/chengmatt/sporc",
  "_pkgdown": "https://chengmatt.github.io/SPoRC",
  "_searchresults": 51,
  "_rbuild": "4.5.3",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SPoRC.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "bisection_F",
    "condition_closed_loop_simulations",
    "do_francis_reweighting",
    "do_jitter",
    "do_likelihood_profile",
    "Do_Population_Projection",
    "do_retrospective",
    "do_runs_test",
    "fit_model",
    "get_biological_plot",
    "get_catch_fits_plot",
    "get_closed_loop_reference_points",
    "get_comp_prop",
    "get_data_fitted_plot",
    "get_idx_fits",
    "get_idx_fits_plot",
    "get_key_quants",
    "get_logistN_Sigma",
    "get_model_rep_from_mcmc",
    "get_nLL_plot",
    "get_osa",
    "get_par_est_info",
    "Get_Reference_Points",
    "get_retrospective_plot",
    "get_retrospective_relative_difference",
    "get_selex_plot",
    "get_ts_plot",
    "marg_AIC",
    "plot_all_basic",
    "plot_resids",
    "post_optim_sanity_checks",
    "rho_trans",
    "run_annual_cycle",
    "run_francis",
    "set_data_indicator_unused",
    "Setup_Mod_Biologicals",
    "Setup_Mod_Catch_and_F",
    "Setup_Mod_Dim",
    "Setup_Mod_FishIdx_and_Comps",
    "Setup_Mod_Fishsel_and_Q",
    "Setup_Mod_Movement",
    "Setup_Mod_Rec",
    "Setup_Mod_SrvIdx_and_Comps",
    "Setup_Mod_Srvsel_and_Q",
    "Setup_Mod_Tagging",
    "Setup_Mod_Weighting",
    "Setup_Sim_Biologicals",
    "Setup_Sim_Containers",
    "Setup_Sim_Dim",
    "Setup_sim_env",
    "Setup_Sim_Fishing",
    "Setup_Sim_Rec",
    "Setup_Sim_Survey",
    "Setup_Sim_Tagging",
    "Simulate_Pop_Static",
    "simulation_data_to_SPoRC",
    "simulation_self_test",
    "theme_sablefish"
  ],
  "_datasets": [
    {
      "name": "dusky_rtmb_model",
      "title": "Dusky model outputs from single regino model",
      "object": "dusky_rtmb_model",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mlt_rg_sable_data",
      "title": "Sablefish data for multi region (5 area) case study",
      "object": "mlt_rg_sable_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "mlt_rg_sable_rep",
      "title": "Sablefish report for 5 region case study",
      "object": "mlt_rg_sable_rep",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "sgl_rg_dusky_data",
      "title": "Dusky data for single region assessment case study",
      "object": "sgl_rg_dusky_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "sgl_rg_ebswp_data",
      "title": "EBS Walleye Pollock data for single region case study",
      "object": "sgl_rg_ebswp_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "sgl_rg_sable_data",
      "title": "Sablefish data for single region case study",
      "object": "sgl_rg_sable_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "sgl_rg_sable_rep",
      "title": "Sablefish report for single region case study",
      "object": "sgl_rg_sable_rep",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "three_rg_sable_data",
      "title": "Sablefish data for multi region (3 area) case study",
      "object": "three_rg_sable_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bisection_F",
      "title": "Go from TAC to Fishing Mortality using bisection",
      "concept": [
        "Closed Loop Simulations"
      ],
      "topics": [
        "bisection_F"
      ]
    },
    {
      "page": "condition_closed_loop_simulations",
      "title": "Set up simulation list for closed-loop projections",
      "concept": [
        "Closed Loop Simulations"
      ],
      "topics": [
        "condition_closed_loop_simulations"
      ]
    },
    {
      "page": "do_francis_reweighting",
      "title": "Get Francis Weights",
      "concept": [
        "Francis Reweighting"
      ],
      "topics": [
        "do_francis_reweighting"
      ]
    },
    {
      "page": "do_jitter",
      "title": "Run Jitter Analysis",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "do_jitter"
      ]
    },
    {
      "page": "do_likelihood_profile",
      "title": "Run Likelihood Profile",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "do_likelihood_profile"
      ]
    },
    {
      "page": "Do_Population_Projection",
      "title": "Do Population Projections",
      "concept": [
        "Reference Points and Projections"
      ],
      "topics": [
        "Do_Population_Projection"
      ]
    },
    {
      "page": "do_retrospective",
      "title": "Run retrospective analyses for RTMB models",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "do_retrospective"
      ]
    },
    {
      "page": "do_runs_test",
      "title": "Runs test function taken from SS3 diags.",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "do_runs_test"
      ]
    },
    {
      "page": "dusky_rtmb_model",
      "title": "Dusky model outputs from single regino model",
      "topics": [
        "dusky_rtmb_model"
      ]
    },
    {
      "page": "fit_model",
      "title": "Run RTMB model",
      "concept": [
        "Utility"
      ],
      "topics": [
        "fit_model"
      ]
    },
    {
      "page": "get_biological_plot",
      "title": "Get Plots of Biological Quantities",
      "concept": [
        "Plotting"
      ],
      "topics": [
        "get_biological_plot"
      ]
    },
    {
      "page": "get_catch_fits_plot",
      "title": "Title Get Catch Fits Plot",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "get_catch_fits_plot"
      ]
    },
    {
      "page": "get_closed_loop_reference_points",
      "title": "Get Closed Loop Reference Points",
      "concept": [
        "Closed Loop Simulations"
      ],
      "topics": [
        "get_closed_loop_reference_points"
      ]
    },
    {
      "page": "get_comp_prop",
      "title": "Gets composition data proportions normalized according to the assessment specifications from RTMB",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "get_comp_prop"
      ]
    },
    {
      "page": "get_data_fitted_plot",
      "title": "Get Data Fitted to Plot",
      "concept": [
        "Plotting"
      ],
      "topics": [
        "get_data_fitted_plot"
      ]
    },
    {
      "page": "get_idx_fits",
      "title": "Gets index fits results",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "get_idx_fits"
      ]
    },
    {
      "page": "get_idx_fits_plot",
      "title": "Get Index Fits Plot",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "get_idx_fits_plot"
      ]
    },
    {
      "page": "get_key_quants",
      "title": "Generate Key Projection Quantities and Table Plot",
      "concept": [
        "Reference Points and Projections"
      ],
      "topics": [
        "get_key_quants"
      ]
    },
    {
      "page": "get_logistN_Sigma",
      "title": "Construct logistic-normal covariance matrix",
      "concept": [
        "Utility"
      ],
      "topics": [
        "get_logistN_Sigma"
      ]
    },
    {
      "page": "get_model_rep_from_mcmc",
      "title": "Extract model report from MCMC posterior samples",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "get_model_rep_from_mcmc"
      ]
    },
    {
      "page": "get_nLL_plot",
      "title": "Get plot of negative log likelihood values",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "get_nLL_plot"
      ]
    },
    {
      "page": "get_osa",
      "title": "Compute OSA residuals for composition data",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "get_osa"
      ]
    },
    {
      "page": "get_par_est_info",
      "title": "Helper function for extracting parameter information and names from TMB",
      "concept": [
        "Utility"
      ],
      "topics": [
        "get_par_est_info"
      ]
    },
    {
      "page": "Get_Reference_Points",
      "title": "Wrapper function to get reference points",
      "concept": [
        "Reference Points and Projections"
      ],
      "topics": [
        "Get_Reference_Points"
      ]
    },
    {
      "page": "get_retrospective_plot",
      "title": "Get Retrospective Plot",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "get_retrospective_plot"
      ]
    },
    {
      "page": "get_retrospective_relative_difference",
      "title": "Derive relative difference from terminal year from a retrospective analysis.",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "get_retrospective_relative_difference"
      ]
    },
    {
      "page": "get_selex_plot",
      "title": "Get Fishery and Survey Selectivity Plots",
      "concept": [
        "Plotting"
      ],
      "topics": [
        "get_selex_plot"
      ]
    },
    {
      "page": "get_ts_plot",
      "title": "Get Time Series Plots",
      "concept": [
        "Plotting"
      ],
      "topics": [
        "get_ts_plot"
      ]
    },
    {
      "page": "marg_AIC",
      "title": "Calculate the Corrected marginal AIC (AICc) from Optimization Results",
      "topics": [
        "marg_AIC"
      ]
    },
    {
      "page": "mlt_rg_sable_data",
      "title": "Sablefish data for multi region (5 area) case study",
      "topics": [
        "mlt_rg_sable_data"
      ]
    },
    {
      "page": "mlt_rg_sable_rep",
      "title": "Sablefish report for 5 region case study",
      "topics": [
        "mlt_rg_sable_rep"
      ]
    },
    {
      "page": "plot_all_basic",
      "title": "Plotting function for all basic quantities",
      "concept": [
        "Plotting"
      ],
      "topics": [
        "plot_all_basic"
      ]
    },
    {
      "page": "plot_resids",
      "title": "Plots OSA residuals from outputs from get_osa. Much of this code is taken from the afscOM package, but with modificaitons to plot features.",
      "concept": [
        "Model Diagnostics"
      ],
      "topics": [
        "plot_resids"
      ]
    },
    {
      "page": "post_optim_sanity_checks",
      "title": "Post Optimization Model Convergence Checks",
      "concept": [
        "Utility"
      ],
      "topics": [
        "post_optim_sanity_checks"
      ]
    },
    {
      "page": "rho_trans",
      "title": "Title Constrains value between -1 and 1",
      "concept": [
        "Utility"
      ],
      "topics": [
        "rho_trans"
      ]
    },
    {
      "page": "run_annual_cycle",
      "title": "Run Annual Cycle in Simulation Environment",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "run_annual_cycle"
      ]
    },
    {
      "page": "run_francis",
      "title": "Run Iterative Francis Reweighting Procedure",
      "concept": [
        "Francis Reweighting"
      ],
      "topics": [
        "run_francis"
      ]
    },
    {
      "page": "set_data_indicator_unused",
      "title": "Set Data Indicators to Unused for Specified Years",
      "concept": [
        "Utility"
      ],
      "topics": [
        "set_data_indicator_unused"
      ]
    },
    {
      "page": "Setup_Mod_Biologicals",
      "title": "Setup biological inputs for estimation model",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_Biologicals"
      ]
    },
    {
      "page": "Setup_Mod_Catch_and_F",
      "title": "Setup fishing mortality and catch observations",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_Catch_and_F"
      ]
    },
    {
      "page": "Setup_Mod_Dim",
      "title": "Set up model dimensions",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_Dim"
      ]
    },
    {
      "page": "Setup_Mod_FishIdx_and_Comps",
      "title": "Setup observed fishery indices and composition data (age and length comps)",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_FishIdx_and_Comps"
      ]
    },
    {
      "page": "Setup_Mod_Fishsel_and_Q",
      "title": "Setup fishery selectivity and catchability specifications",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_Fishsel_and_Q"
      ]
    },
    {
      "page": "Setup_Mod_Movement",
      "title": "Setup Movement Processes for SPoRC",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_Movement"
      ]
    },
    {
      "page": "Setup_Mod_Rec",
      "title": "Setup model objects for specifying recruitment module and associated processes",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_Rec"
      ]
    },
    {
      "page": "Setup_Mod_SrvIdx_and_Comps",
      "title": "Setup observed survey indices and composition data (age and length comps)",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_SrvIdx_and_Comps"
      ]
    },
    {
      "page": "Setup_Mod_Srvsel_and_Q",
      "title": "Setup survey selectivity and catchability specifications",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_Srvsel_and_Q"
      ]
    },
    {
      "page": "Setup_Mod_Tagging",
      "title": "Setup tagging processes and parameters",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_Tagging"
      ]
    },
    {
      "page": "Setup_Mod_Weighting",
      "title": "Set up SPoRC model weighting",
      "concept": [
        "Model Setup"
      ],
      "topics": [
        "Setup_Mod_Weighting"
      ]
    },
    {
      "page": "Setup_Sim_Biologicals",
      "title": "Set up simulation containers and inputs for biological parameters",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "Setup_Sim_Biologicals"
      ]
    },
    {
      "page": "Setup_Sim_Containers",
      "title": "Setup containers for simulation and output",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "Setup_Sim_Containers"
      ]
    },
    {
      "page": "Setup_Sim_Dim",
      "title": "Initialize Simulation Dimension Settings",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "Setup_Sim_Dim"
      ]
    },
    {
      "page": "Setup_sim_env",
      "title": "Constructs simulation objects in a new simulation environment for use in simulation functions",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "Setup_sim_env"
      ]
    },
    {
      "page": "Setup_Sim_Fishing",
      "title": "Setup values and dimensions of fishing processes",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "Setup_Sim_Fishing"
      ]
    },
    {
      "page": "Setup_Sim_Rec",
      "title": "Set up recruitment dynamics for simulation",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "Setup_Sim_Rec"
      ]
    },
    {
      "page": "Setup_Sim_Survey",
      "title": "Setup values for survey parameterization",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "Setup_Sim_Survey"
      ]
    },
    {
      "page": "Setup_Sim_Tagging",
      "title": "Set up simulated tagging dynamics",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "Setup_Sim_Tagging"
      ]
    },
    {
      "page": "sgl_rg_dusky_data",
      "title": "Dusky data for single region assessment case study",
      "topics": [
        "sgl_rg_dusky_data"
      ]
    },
    {
      "page": "sgl_rg_ebswp_data",
      "title": "EBS Walleye Pollock data for single region case study",
      "topics": [
        "sgl_rg_ebswp_data"
      ]
    },
    {
      "page": "sgl_rg_sable_data",
      "title": "Sablefish data for single region case study",
      "topics": [
        "sgl_rg_sable_data"
      ]
    },
    {
      "page": "sgl_rg_sable_rep",
      "title": "Sablefish report for single region case study",
      "topics": [
        "sgl_rg_sable_rep"
      ]
    },
    {
      "page": "Simulate_Pop_Static",
      "title": "Simulates a static spatial, sex, and age-structured population (no feedback loop)",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "Simulate_Pop_Static"
      ]
    },
    {
      "page": "simulation_data_to_SPoRC",
      "title": "Extract simulation data into SPoRC format",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "simulation_data_to_SPoRC"
      ]
    },
    {
      "page": "simulation_self_test",
      "title": "Conduct a Simulation Self Test",
      "concept": [
        "Simulation Setup"
      ],
      "topics": [
        "simulation_self_test"
      ]
    },
    {
      "page": "theme_sablefish",
      "title": "ggplot theme for sablefish",
      "concept": [
        "Plotting"
      ],
      "topics": [
        "theme_sablefish"
      ]
    },
    {
      "page": "three_rg_sable_data",
      "title": "Sablefish data for multi region (3 area) case study",
      "topics": [
        "three_rg_sable_data"
      ]
    }
  ],
  "_readme": "https://github.com/jimianelli/SPoRC/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "cli",
    "codetools",
    "cowplot",
    "cpp11",
    "data.table",
    "digest",
    "dplyr",
    "farver",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "globals",
    "glue",
    "gridExtra",
    "gtable",
    "here",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "MASS",
    "Matrix",
    "parallelly",
    "pillar",
    "pkgconfig",
    "plyr",
    "progressr",
    "purrr",
    "R6",
    "randtests",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "reshape2",
    "rlang",
    "rprojroot",
    "RTMB",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "TMB",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "a_model_dimensions.Rmd",
      "filename": "a_model_dimensions.html",
      "title": "Description of Model and Data Dimensions",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Data Inputs for Defining Model Dimensions",
        "Data Inputs for Defining Recruitment Processes",
        "Data Inputs for Defining Biological Processes",
        "Data Inputs for Defining Movement Processes",
        "Data Inputs for Defining Tagging Processes",
        "Data Inputs for Defining Catch and Fishing Mortality Processes",
        "Data Inputs for Defining Fishery Indices and Compositions",
        "Data Inputs for Defining Survey Indices and Compositions",
        "Data Inputs for Defining Fishery Selectivity and Catchability",
        "Data Inputs for Defining Survey Selectivity and Catchability",
        "Data Inputs for Defining Model Weighting"
      ],
      "created": "2025-04-29 03:44:29",
      "modified": "2025-10-27 14:05:43",
      "commits": 26
    },
    {
      "source": "b_model_parameters.Rmd",
      "filename": "b_model_parameters.html",
      "title": "Description of Model Parameters",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Fishery Removals",
        "Fishery Selectivity",
        "Fishery Catchability",
        "Fishery Composition Likelihoods",
        "Survey Selectivity",
        "Survey Catchability",
        "Survey Composition Likelihoods",
        "Natural Mortality",
        "Recruitment",
        "Movement",
        "Tagging"
      ],
      "created": "2025-04-29 03:44:29",
      "modified": "2025-10-06 23:29:04",
      "commits": 15
    },
    {
      "source": "c_model_equations.Rmd",
      "filename": "c_model_equations.html",
      "title": "Description of Model Equations",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Process Equations",
        "Population Initialization",
        "Recruitment Processes",
        "Population Projection",
        "Observation Equations",
        "Fishery Observation Model",
        "Survey Observation Model",
        "Tagging Observation Model",
        "Fishery and Survey Selectivity",
        "Likelihoods",
        "Observation Likelihoods",
        "Fishery Catches",
        "Fishery and Survey Indices",
        "Fishery and Survey Compositions",
        "Structuring Compositions and Ageing Error",
        "Tagging",
        "Parameter Priors and Process Error Penalties",
        "Parameter Priors",
        "Natural Mortality",
        "Fishery and Survey Catchability",
        "Steepness",
        "Recruitment Proportions",
        "Movement",
        "Tag Reporting Rates",
        "Process Error Penalties",
        "Initial Age Deviations",
        "Recruitment Deviations",
        "Fishing Mortality Deviations",
        "Joint Likelihood",
        "References"
      ],
      "created": "2025-04-29 03:44:29",
      "modified": "2025-10-27 14:05:43",
      "commits": 38
    },
    {
      "source": "d_model_report.Rmd",
      "filename": "d_model_report.html",
      "title": "Description of Model Report",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Biological Processes",
        "Fishery Processes",
        "Survey Processes",
        "Tagging Processes",
        "Likelihoods",
        "Parameter Deviations",
        "Derived Quantities"
      ],
      "created": "2025-05-19 17:02:42",
      "modified": "2025-10-06 23:29:04",
      "commits": 8
    },
    {
      "source": "e_single_region_sablefish_case_study.Rmd",
      "filename": "e_single_region_sablefish_case_study.html",
      "title": "Setting up a Single Region Model (Alaska Sablefish)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup Model Dimensions",
        "Setup Recruitment Dynamics",
        "Setup Biological Dynamics",
        "Setup Movement and Tagging Dynamics",
        "Setup Catch and Fishing Mortality",
        "Setup Index and Composition Data (Fishery and Survey)",
        "Setup Selectivity and Catchability (Fishery and Survey)",
        "Setup Model Weighting",
        "Fit Model and Plot"
      ],
      "created": "2025-04-29 03:44:29",
      "modified": "2025-09-30 01:20:06",
      "commits": 11
    },
    {
      "source": "f_single_region_ebs_pollock_case_study.Rmd",
      "filename": "f_single_region_ebs_pollock_case_study.html",
      "title": "Setting up a Single Region Model (Eastern Bering Sea Pollock)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup Model Dimensions",
        "Setup Recruitment Dynamics",
        "Setup Biological Dynamics",
        "Setup Movement and Tagging",
        "Setup Catch and Fishing Mortality",
        "Setup Fishery Indices and Compositions",
        "Setup Survey Indices and Compositions",
        "Setting up Fishery Selectivity and Catchability",
        "Setting up Survey Selectivity and Catchability",
        "Setup Model Weighting",
        "Fit Model and Plot"
      ],
      "created": "2025-07-08 02:13:32",
      "modified": "2025-11-24 16:53:18",
      "commits": 9
    },
    {
      "source": "g_spatial_sablefish_case_study.Rmd",
      "filename": "g_spatial_sablefish_case_study.html",
      "title": "Setting up a Spatial Model (Alaska Sablefish)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup Model Dimensions",
        "Setup Recruitment Dynamics",
        "Setup Biological Dynamics",
        "Setup Movement and Tagging Dynamics",
        "Setup Catch and Fishing Mortality",
        "Setup Index and Composition Data (Fishery and Survey)",
        "Setup Selectivity and Catchability (Fishery and Survey)",
        "Setup Model Weighting",
        "Fit Model and Plot"
      ],
      "created": "2025-04-29 03:44:29",
      "modified": "2025-10-16 14:01:39",
      "commits": 12
    },
    {
      "source": "h_closed_loop_simulations.Rmd",
      "filename": "h_closed_loop_simulations.html",
      "title": "Run Closed Loop Simulations",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Define Operating Model",
        "Define Management Options",
        "Define Estimation Model",
        "Define and Run Closed-Loop Simulation"
      ],
      "created": "2025-05-24 03:04:02",
      "modified": "2025-11-24 16:53:18",
      "commits": 12
    },
    {
      "source": "i_reference_points.Rmd",
      "filename": "i_reference_points.html",
      "title": "Deriving Reference Points, Catch Advice, and Projections",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Reference Points",
        "Single Region",
        "Spawning Potential Ratio",
        "Maximum Sustainable Yield (Beverton-Holt)",
        "Multi-Region",
        "Independent",
        "Global",
        "Local",
        "Deriving Catch Advice and Projections",
        "Code Demonstration",
        "Getting Reference Points",
        "Multi Region",
        "Conducting Catch Projections to Derive Catch Advice (Deterministic Recruitment)",
        "Conducting Stochastic Population Projections",
        "References"
      ],
      "created": "2025-06-18 21:00:50",
      "modified": "2025-11-24 16:53:18",
      "commits": 14
    },
    {
      "source": "j_starting_mapping.Rmd",
      "filename": "j_starting_mapping.html",
      "title": "Starting Values and Fixing (and Sharing) Parameters",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Starting Values",
        "Mapping",
        "Fixing Parameters",
        "Sharing Parameters"
      ],
      "created": "2025-07-01 20:22:31",
      "modified": "2025-09-30 01:20:06",
      "commits": 6
    },
    {
      "source": "k_defining_priors.Rmd",
      "filename": "k_defining_priors.html",
      "title": "Defining Priors",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Steepness",
        "Natural Mortality",
        "Catchability",
        "Selectivity",
        "Movement",
        "Tag Reporting Rates",
        "Recruitment Proportions"
      ],
      "created": "2025-07-16 20:56:23",
      "modified": "2025-09-30 01:20:06",
      "commits": 4
    },
    {
      "source": "l_simulation_testing.Rmd",
      "filename": "l_simulation_testing.html",
      "title": "Simulation Testing (Cross and Self Tests)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Simulation Cross-Testing in SPoRC",
        "Define Model Dimensions",
        "Fishing Processes",
        "Survey Processes",
        "Biological Dynamics",
        "Tagging and Movement",
        "Recruitment",
        "Run the Operating Model",
        "Define Estimation Model",
        "Run Cross-Test Analysis",
        "Self Testing"
      ],
      "created": "2025-09-30 01:20:06",
      "modified": "2025-10-15 21:02:10",
      "commits": 2
    },
    {
      "source": "m_simulation_dimensions.Rmd",
      "filename": "m_simulation_dimensions.html",
      "title": "Description of Simulation Dimensions",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Simulation Settings",
        "Population, Recruitment, and Biological Processes",
        "Fishery Processes",
        "Survey Processes",
        "Tagging"
      ],
      "created": "2025-10-02 16:55:09",
      "modified": "2025-10-23 14:47:31",
      "commits": 2
    },
    {
      "source": "n_single_region_ebs_pollock_randomeff_case_study.Rmd",
      "filename": "n_single_region_ebs_pollock_randomeff_case_study.html",
      "title": "Random Effects (Selectivity Example; Eastern Bering Sea Pollock)",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2025-10-03 22:22:19",
      "modified": "2025-11-27 03:59:28",
      "commits": 4
    },
    {
      "source": "o_get_started.Rmd",
      "filename": "o_get_started.html",
      "title": "Running a Simple Assessment (The Basics)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Load data and packages",
        "Setup model",
        "Setup Recruitment Dynamics",
        "Setup biological dynamics",
        "Setup Movement and Tagging",
        "Setup Catch and Fishing Mortality",
        "Setup Fishery Indices and Compositions",
        "Setup Survey Indices and Compositions",
        "Setup Fishery Selectivity and Catchability",
        "Setup Survey Selectivity and Catchability",
        "Setup Model Weighting",
        "Fit model",
        "Fit model (Without Francis)",
        "Fit model (With Francis)",
        "Check Model Results",
        "Convergence",
        "Time Series Results",
        "Catch and Index Fits",
        "Composition Fits",
        "Fishery Ages",
        "Fishery Lengths",
        "Survey Ages",
        "Retrospectives",
        "Retrospectives (Without Francis)",
        "Retrospectives (With Francis)",
        "Likelihood Profiles",
        "Jitter Analysis",
        "MCMC",
        "Reference Points and Projections",
        "Reference Points",
        "Projections",
        "Spawning Biomass Projections",
        "Catch Projections",
        "Catch Advice under $F_{40%}$",
        "Fishing Mortality Projections"
      ],
      "created": "2025-07-18 01:58:48",
      "modified": "2025-10-15 21:02:10",
      "commits": 7
    },
    {
      "source": "p_single_region_dusky_alt_mp_testing.Rmd",
      "filename": "p_single_region_dusky_alt_mp_testing.html",
      "title": "Testing Management Procedures via Closed Loop Simulations (Dusky Rockfish)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Estimation Model",
        "Projection Options",
        "Functions to Determine Catch",
        "Management Procedures",
        "Simulation Loop (Single Replicate)",
        "Simulation Loop (Parrallelized)",
        "Condition Closed Loop Simulation",
        "Run Simulations",
        "Process Results",
        "Visualize"
      ],
      "created": "2025-10-13 15:26:22",
      "modified": "2025-11-24 16:53:18",
      "commits": 3
    }
  ],
  "_score": 6.025633511060698,
  "_indexed": true,
  "_nocasepkg": "sporc",
  "_universes": [
    "jimianelli",
    "chengmatt"
  ],
  "_progress_url": "https://github.com/r-universe/jimianelli/actions/runs/26847422353",
  "_binaries": [
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-04-16T08:33:29.000Z",
      "distro": "noble",
      "commit": "8060533a3831a2f3179cba9745ee92ecf79b6259",
      "fileid": "a8b8e21a45ffa9ec242a1f5159039d5687cf0667dad8501ea59af24808ed426d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/jimianelli/actions/runs/24499969591"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-04-16T08:31:22.000Z",
      "commit": "8060533a3831a2f3179cba9745ee92ecf79b6259",
      "fileid": "722ce5fc99e64cd482378dc67de7e598cbe5322b683ec90f653b1f18b3395388",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/jimianelli/actions/runs/24499969591"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-04-16T08:31:11.000Z",
      "commit": "8060533a3831a2f3179cba9745ee92ecf79b6259",
      "fileid": "e3791966f2a3ae22d5176ee9e320af0ee2513033ce035e4949b728d18debadeb",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/jimianelli/actions/runs/24499969591"
    },
    {
      "r": "4.5.1",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-04-16T08:33:18.000Z",
      "commit": "8060533a3831a2f3179cba9745ee92ecf79b6259",
      "fileid": "846066c72e26a5c569a0cc2ac9a03131d94d6e8b2101451d4250a42c115b2374",
      "status": "success",
      "buildurl": "https://github.com/r-universe/jimianelli/actions/runs/24499969591"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-04-16T08:31:18.000Z",
      "commit": "8060533a3831a2f3179cba9745ee92ecf79b6259",
      "fileid": "da07be71b6da0e4594795e049a4bc1217be0d410fec8e133c3941a688c411ee4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/jimianelli/actions/runs/24499969591"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-04-16T08:31:05.000Z",
      "commit": "8060533a3831a2f3179cba9745ee92ecf79b6259",
      "fileid": "cb7c121a86231020d7f4614158f907e805240249efc125b82563b5e4633bc1de",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/jimianelli/actions/runs/24499969591"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-04-16T08:31:02.000Z",
      "commit": "8060533a3831a2f3179cba9745ee92ecf79b6259",
      "fileid": "6c75ec5f0f38f6f41fe4efa7af6660b7e16e009b3800f14c1334869cbc514404",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/jimianelli/actions/runs/24499969591"
    }
  ]
}