{
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  "Type": "Package",
  "Title": "Stock Assessment Methods Toolkit",
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  "Authors@R": "c(person(\"Quang\", \"Huynh\", email = \"quang@bluematterscience.com\", role = c(\"aut\", \"cre\")), \nperson(\"Tom\", \"Carruthers\", email = \"tom@bluematterscience.com\", role = \"aut\"),\nperson(\"Adrian\", \"Hordyk\", email = \"adrian@bluematterscience.com\", role = \"aut\"))",
  "Date": "2026-06-04",
  "Maintainer": "Quang Huynh <quang@bluematterscience.com>",
  "Description": "Simulation tools for closed-loop simulation are provided\nfor the 'MSEtool' operating model to inform data-rich\nfisheries. 'SAMtool' provides a conditioning model, assessment\nmodels of varying complexity with standardized reporting,\nmodel-based management procedures, and diagnostic tools for\nevaluating assessments inside closed-loop simulation.",
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  "BugReports": "https://github.com/Blue-Matter/SAMtool/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://blue-matter.r-universe.dev",
  "Date/Publication": "2026-06-04 18:26:42 UTC",
  "RemoteUrl": "https://github.com/Blue-Matter/SAMtool",
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    "Date": "2026-06-08 20:38:29 UTC",
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  "Author": "Quang Huynh [aut, cre],\nTom Carruthers [aut],\nAdrian Hordyk [aut]",
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  "_exports": [
    "Assessment",
    "cDD",
    "cDD_SS",
    "check_RCMdata",
    "compare_models",
    "compare_RCM",
    "DD_SS",
    "DD_TMB",
    "DDSS_4010",
    "DDSS_75MSY",
    "DDSS_MSY",
    "diagnostic",
    "diagnostic_AM",
    "getinds",
    "HCR_escapement",
    "HCR_FB",
    "HCR_fixedF",
    "HCR_MSY",
    "HCR_ramp",
    "HCR_segment",
    "HCR40_10",
    "HCR60_20",
    "HCR80_40MSY",
    "HCRlin",
    "mahplot",
    "make_interim_MP",
    "make_MP",
    "make_projection_MP",
    "Perfect",
    "plot",
    "plot_betavar",
    "plot_composition",
    "plot_crosscorr",
    "plot_lognormalvar",
    "plot_residuals",
    "plot_SR",
    "plot_steepness",
    "plot_timeseries",
    "posterior",
    "PRBcalc",
    "prelim_AM",
    "Probs",
    "prof",
    "profile",
    "project",
    "projection",
    "RCM",
    "RCM_assess",
    "RCM2MOM",
    "RCMdata",
    "RCModel",
    "RCMstan",
    "retro",
    "retrospective",
    "retrospective_AM",
    "SCA",
    "SCA_4010",
    "SCA_75MSY",
    "SCA_CAL",
    "SCA_DDM",
    "SCA_MSY",
    "SCA_Pope",
    "SCA_RWM",
    "SCA2",
    "Shortcut",
    "Shortcut2",
    "sim",
    "simulate",
    "SP",
    "SP_4010",
    "SP_75MSY",
    "SP_Fox",
    "SP_MSY",
    "SP_production",
    "SP_SS",
    "SSS",
    "SSS_4010",
    "SSS_75MSY",
    "SSS_MSY",
    "summary",
    "TAC_MSY",
    "userguide",
    "VPA"
  ],
  "_datasets": [
    {
      "name": "pcod",
      "title": "Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada",
      "object": "pcod",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "swordfish",
      "title": "North Atlantic Swordfish dataset",
      "object": "swordfish",
      "class": [
        "Data"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "SAMtool-package",
      "title": "Stock Assessment Methods Toolkit",
      "topics": [
        "SAMtool-package",
        "SAMtool"
      ]
    },
    {
      "page": "Assessment-class",
      "title": "Class-'Assessment'",
      "topics": [
        "Assessment",
        "Assessment-class"
      ]
    },
    {
      "page": "cDD",
      "title": "Continuous Delay-differential assessment model",
      "topics": [
        "cDD",
        "cDD_SS"
      ]
    },
    {
      "page": "RCM",
      "title": "Rapid Conditioning Model (RCM)",
      "topics": [
        "check_RCMdata",
        "RCM",
        "RCM,list,RCMdata-method",
        "RCM,OM,Data-method",
        "RCM,OM,list-method",
        "RCM,OM,RCMdata-method"
      ]
    },
    {
      "page": "compare_models",
      "title": "Compare output from several assessment models",
      "topics": [
        "compare_models"
      ]
    },
    {
      "page": "DD_TMB",
      "title": "Delay - Difference Stock Assessment in TMB",
      "topics": [
        "DD_SS",
        "DD_TMB"
      ]
    },
    {
      "page": "diagnostic",
      "title": "Diagnostic of assessments in MSE: did Assess models converge during MSE?",
      "topics": [
        "diagnostic",
        "diagnostic_AM"
      ]
    },
    {
      "page": "getinds",
      "title": "Characterize posterior predictive data",
      "topics": [
        "getinds"
      ]
    },
    {
      "page": "HCR_escapement",
      "title": "Fixed escapement harvest control rule",
      "topics": [
        "HCR_escapement"
      ]
    },
    {
      "page": "HCR_FB",
      "title": "A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE.",
      "topics": [
        "HCR_FB"
      ]
    },
    {
      "page": "HCR_fixedF",
      "title": "Simple fixed F harvest control rule",
      "topics": [
        "HCR_fixedF"
      ]
    },
    {
      "page": "HCR_MSY",
      "title": "Harvest control rule to fish at some fraction of maximum sustainable yield",
      "topics": [
        "HCR_MSY"
      ]
    },
    {
      "page": "HCR_ramp",
      "title": "Linearly ramped harvest control rules",
      "topics": [
        "HCR40_10",
        "HCR60_20",
        "HCR80_40MSY",
        "HCR_ramp"
      ]
    },
    {
      "page": "HCR_segment",
      "title": "Segmented harvest control rules",
      "topics": [
        "HCR_segment"
      ]
    },
    {
      "page": "HCRlin",
      "title": "Generic linear harvest control rule based on biomass",
      "topics": [
        "HCRlin"
      ]
    },
    {
      "page": "mahplot",
      "title": "Plot statistical power of the indicator with increasing time blocks",
      "topics": [
        "mahplot"
      ]
    },
    {
      "page": "make_MP",
      "title": "Make a custom management procedure (MP)",
      "topics": [
        "make_interim_MP",
        "make_MP",
        "make_projection_MP"
      ]
    },
    {
      "page": "Model-based-MP",
      "title": "Model-based management procedures",
      "topics": [
        "Data-rich-MP",
        "DDSS_4010",
        "DDSS_75MSY",
        "DDSS_MSY",
        "Model-based-MP",
        "MP",
        "SCA_4010",
        "SCA_75MSY",
        "SCA_MSY",
        "SP_4010",
        "SP_75MSY",
        "SP_MSY",
        "SSS_4010",
        "SSS_75MSY",
        "SSS_MSY"
      ]
    },
    {
      "page": "pcod",
      "title": "Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada",
      "topics": [
        "pcod"
      ]
    },
    {
      "page": "plot_betavar",
      "title": "Plots a beta variable",
      "topics": [
        "plot_betavar"
      ]
    },
    {
      "page": "plot_composition",
      "title": "Plot composition data",
      "topics": [
        "plot_composition"
      ]
    },
    {
      "page": "plot_crosscorr",
      "title": "Produce a cross-correlation plot of the derived data arising from getinds(MSE_object)",
      "topics": [
        "plot_crosscorr"
      ]
    },
    {
      "page": "plot_lognormalvar",
      "title": "Plots a lognormal variable",
      "topics": [
        "plot_lognormalvar"
      ]
    },
    {
      "page": "plot_residuals",
      "title": "Plot residuals",
      "topics": [
        "plot_residuals"
      ]
    },
    {
      "page": "plot_SR",
      "title": "Plot stock-recruitment function",
      "topics": [
        "plot_SR"
      ]
    },
    {
      "page": "plot_steepness",
      "title": "Plots probability distribution function of stock-recruit steepness",
      "topics": [
        "plot_steepness"
      ]
    },
    {
      "page": "plot_timeseries",
      "title": "Plot time series of data",
      "topics": [
        "plot_timeseries"
      ]
    },
    {
      "page": "plot.Assessment",
      "title": "Plot Assessment object",
      "topics": [
        "plot,Assessment,missing-method",
        "plot,Assessment,retro-method",
        "plot.Assessment"
      ]
    },
    {
      "page": "plot.prof",
      "title": "Plot profile object",
      "topics": [
        "plot,prof,missing-method",
        "plot.prof"
      ]
    },
    {
      "page": "plot.RCModel",
      "title": "Plot RCM scope output",
      "topics": [
        "compare_RCM",
        "plot,RCModel,missing-method",
        "plot.RCModel"
      ]
    },
    {
      "page": "plot.retro",
      "title": "Methods for retro object",
      "topics": [
        "plot,retro,missing-method",
        "plot.retro",
        "summary,retro-method",
        "summary.retro"
      ]
    },
    {
      "page": "posterior",
      "title": "Sample posterior of TMB models in SAMtool",
      "topics": [
        "posterior",
        "posterior,Assessment-method",
        "posterior,RCModel-method",
        "posterior.Assessment",
        "posterior.RCModel",
        "RCMstan"
      ]
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