{
  "_id": "6a1f0cb5b401979e7341cdbf",
  "Package": "stockassessment",
  "Title": "State-Space Assessment Model",
  "Version": "0.12.0",
  "Date": "2025-01-20",
  "Authors@R": "c(person(\"Anders\",\"Nielsen\",role=c(\"aut\",\"cre\"), email=\"an@aqua.dtu.dk\"),\nperson(\"Casper\",\"Berg\",role=\"aut\"),\nperson(c(\"Christoffer\",\"Moesgaard\"), \"Albertsen\", role=\"aut\"),\nperson(\"Kasper\",\"Kristensen\",role=\"aut\"),\nperson(\"Mollie\", \"Brooks\", role=\"aut\"),\nperson(\"Vanessa\", \"Trijoulet\", role=\"aut\"),\nperson(c(\"Olav\",\"Nikolai\"), \"Breivik\", role=\"aut\"))",
  "Author": "Anders Nielsen [aut, cre], Casper Berg [aut], Christoffer\nMoesgaard Albertsen [aut], Kasper Kristensen [aut], Mollie\nBrooks [aut], Vanessa Trijoulet [aut], Olav Nikolai Breivik\n[aut]",
  "Maintainer": "Anders Nielsen <an@aqua.dtu.dk>",
  "Description": "Fitting SAM...",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "URL": "https://github.com/fishfollower/SAM",
  "LazyData": "TRUE",
  "BugReports": "https://github.com/fishfollower/SAM/issues",
  "Repository": "https://ices-tools-prod.r-universe.dev",
  "Date/Publication": "2026-04-17 14:52:16 UTC",
  "RemoteUrl": "https://github.com/fishfollower/SAM",
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    "message": "Merge pull request #85 from TaMie12/patch-1\n\nEnhance caytable function with NM model option",
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  "_exports": [
    "addRecruitmentCurve",
    "b0plot",
    "b0table",
    "bc",
    "catchbyfleetplot",
    "catchbyfleettable",
    "catchplot",
    "catchtable",
    "caytable",
    "componentplot",
    "corplot",
    "corplotcommon",
    "dataplot",
    "defcon",
    "defpar",
    "deterministicReferencepoints",
    "empirobscorrplot",
    "equilibriumbiomassplot",
    "equilibriumbiomasstable",
    "faytable",
    "fbarplot",
    "fbartable",
    "fitfromweb",
    "fitplot",
    "forecast",
    "forecastMSY",
    "fselectivityplot",
    "generationlengthplot",
    "generationlengthtable",
    "getAllDerivedValues",
    "getFleet",
    "getResidualFleets",
    "hcr",
    "ibc",
    "iibc",
    "jit",
    "leaveout",
    "lifeexpectancyplot",
    "lifeexpectancytable",
    "loadConf",
    "modelDescription",
    "modelforecast",
    "modeltable",
    "modelVersionInfo",
    "mohn",
    "ntable",
    "obscorrplot",
    "obscov",
    "parplot",
    "partable",
    "plotby",
    "predstdplot",
    "procres",
    "qtable",
    "qtableplot",
    "read.data.files",
    "read.ices",
    "recplot",
    "rectable",
    "reduce",
    "referencepoints",
    "residplot",
    "retro",
    "rmaxplot",
    "rmaxtable",
    "rmvnorm",
    "runwithout",
    "sam.fit",
    "saveConf",
    "sdplot",
    "setup.sam.data",
    "simstudy",
    "sprplot",
    "sprtable",
    "srplot",
    "ssbplot",
    "ssbtable",
    "tsbplot",
    "tsbtable",
    "write.data.files",
    "write.ices",
    "write.surveys",
    "yearslostplot",
    "yearslosttable",
    "ypr",
    "yprplot",
    "yprtable"
  ],
  "_datasets": [
    {
      "name": "nscodConf",
      "title": "nscodConf",
      "object": "nscodConf",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "nscodData",
      "title": "nscodData",
      "object": "nscodData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "nscodParameters",
      "title": "nscodParameters",
      "object": "nscodParameters",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "addforecast",
      "title": "SAM add forecasts",
      "topics": [
        "addforecast",
        "addforecast.samforecast"
      ]
    },
    {
      "page": "addRecruitmentCurve",
      "title": "Add stock-recruitment curve to srplot",
      "topics": [
        "addRecruitmentCurve",
        "addRecruitmentCurve.sam"
      ]
    },
    {
      "page": "b0plot",
      "title": "SAM equilibrium biomass in the absence of fishing plot",
      "topics": [
        "b0plot",
        "b0plot.default",
        "b0plot.hcr",
        "b0plot.samforecast"
      ]
    },
    {
      "page": "b0table",
      "title": "B0 biomass table",
      "topics": [
        "b0table",
        "b0table.default"
      ]
    },
    {
      "page": "bc",
      "title": "Spline basis for use with formula interface",
      "topics": [
        "bc"
      ]
    },
    {
      "page": "c.sam",
      "title": "Collect sam objects",
      "topics": [
        "c.sam"
      ]
    },
    {
      "page": "catchbyfleetplot",
      "title": "SAM catchbyfleet plot",
      "topics": [
        "catchbyfleetplot"
      ]
    },
    {
      "page": "catchbyfleettable",
      "title": "CatchByFleet table",
      "topics": [
        "catchbyfleettable"
      ]
    },
    {
      "page": "catchplot",
      "title": "SAM catch plot",
      "topics": [
        "catchplot",
        "catchplot.hcr",
        "catchplot.sam",
        "catchplot.samforecast",
        "catchplot.samset"
      ]
    },
    {
      "page": "catchtable",
      "title": "Catch table",
      "topics": [
        "catchtable",
        "catchtable.sam"
      ]
    },
    {
      "page": "caytable",
      "title": "Catch-at-age in numbers table",
      "topics": [
        "caytable"
      ]
    },
    {
      "page": "clean.void.catches",
      "title": "remove void catches",
      "topics": [
        "clean.void.catches"
      ]
    },
    {
      "page": "coef.sam",
      "title": "Extract fixed coefficients of sam object",
      "topics": [
        "coef.sam"
      ]
    },
    {
      "page": "componentplot",
      "title": "Area plot of spawning components",
      "topics": [
        "componentplot",
        "componentplot.sam"
      ]
    },
    {
      "page": "corplot",
      "title": "Plots between-age correlations by fleet, either estimated or empirical using residuals.",
      "topics": [
        "corplot",
        "corplot.sam",
        "corplot.samres"
      ]
    },
    {
      "page": "corplotcommon",
      "title": "Common function for plotting correlation matrices.",
      "topics": [
        "corplotcommon"
      ]
    },
    {
      "page": "dataplot",
      "title": "SAM Data plot",
      "topics": [
        "dataplot",
        "dataplot.sam"
      ]
    },
    {
      "page": "defcon",
      "title": "Setup basic minimal configuration for sam assessment",
      "topics": [
        "defcon"
      ]
    },
    {
      "page": "defpar",
      "title": "Setup initial values for all model parameters and random effects.",
      "topics": [
        "defpar"
      ]
    },
    {
      "page": "deterministicReferencepoints",
      "title": "Function to calculate reference points for the embedded deterministic model of a SAM fit",
      "topics": [
        "deterministicReferencepoints"
      ]
    },
    {
      "page": "deterministicReferencepoints.sam",
      "title": "Function to calculate reference points for the embedded deterministic model of a SAM fit",
      "topics": [
        "deterministicReferencepoints.sam"
      ]
    },
    {
      "page": "empirobscorrplot",
      "title": "Plots the residual between-age correlation matrices by fleet.",
      "topics": [
        "empirobscorrplot",
        "empirobscorrplot.samres"
      ]
    },
    {
      "page": "equilibriumbiomassplot",
      "title": "SAM equilibrium biomass plot",
      "topics": [
        "equilibriumbiomassplot",
        "equilibriumbiomassplot.default",
        "equilibriumbiomassplot.hcr",
        "equilibriumbiomassplot.samforecast"
      ]
    },
    {
      "page": "equilibriumbiomasstable",
      "title": "equilibrium biomass table",
      "topics": [
        "equilibriumbiomasstable",
        "equilibriumbiomasstable.default"
      ]
    },
    {
      "page": "faytable",
      "title": "F-at-age table",
      "topics": [
        "faytable",
        "faytable.sam"
      ]
    },
    {
      "page": "fbarplot",
      "title": "SAM Fbar plot",
      "topics": [
        "fbarplot",
        "fbarplot.hcr",
        "fbarplot.sam",
        "fbarplot.samforecast",
        "fbarplot.samset"
      ]
    },
    {
      "page": "fbartable",
      "title": "Fbar table",
      "topics": [
        "fbartable",
        "fbartable.default"
      ]
    },
    {
      "page": "fitfromweb",
      "title": "Read a fitted model from stockassessment.org",
      "topics": [
        "fitfromweb"
      ]
    },
    {
      "page": "fitplot",
      "title": "Plots fit to data",
      "topics": [
        "fitplot",
        "fitplot.sam"
      ]
    },
    {
      "page": "forecast",
      "title": "forecast function to do shortterm",
      "topics": [
        "forecast"
      ]
    },
    {
      "page": "forecastMSY",
      "title": "Estimating Fmsy",
      "topics": [
        "forecastMSY",
        "forecastMSY.sam"
      ]
    },
    {
      "page": "fselectivityplot",
      "title": "SAM F-selectivity plot",
      "topics": [
        "fselectivityplot",
        "fselectivityplot.sam"
      ]
    },
    {
      "page": "generationlengthplot",
      "title": "SAM generation length plot",
      "topics": [
        "generationlengthplot",
        "generationlengthplot.default",
        "generationlengthplot.hcr",
        "generationlengthplot.samforecast"
      ]
    },
    {
      "page": "generationlengthtable",
      "title": "Generation length table",
      "topics": [
        "generationlengthtable",
        "generationlengthtable.default"
      ]
    },
    {
      "page": "getAllDerivedValues",
      "title": "Update sam fit with additional derived values",
      "topics": [
        "getAllDerivedValues"
      ]
    },
    {
      "page": "getFleet",
      "title": "Extract a fleet observed or predicted value from a fitted object",
      "topics": [
        "getFleet"
      ]
    },
    {
      "page": "getLowerBounds",
      "title": "Bounds",
      "topics": [
        "getLowerBounds"
      ]
    },
    {
      "page": "getResidualFleets",
      "title": "Extract a list of catch fleets",
      "topics": [
        "getResidualFleets"
      ]
    },
    {
      "page": "getUpperBounds",
      "title": "Bounds",
      "topics": [
        "getUpperBounds"
      ]
    },
    {
      "page": "grad",
      "title": "Calculate gradient of a function",
      "topics": [
        "grad"
      ]
    },
    {
      "page": "hcr",
      "title": "Harvest control rule forecast",
      "topics": [
        "hcr",
        "hcr.sam"
      ]
    },
    {
      "page": "ibc",
      "title": "Integrated spline basis for use with formula interface",
      "topics": [
        "ibc"
      ]
    },
    {
      "page": "icesAdviceRule",
      "title": "Forecast with an ICES advice rule",
      "topics": [
        "icesAdviceRule"
      ]
    },
    {
      "page": "iibc",
      "title": "Double integrated spline basis for use with formula interface",
      "topics": [
        "iibc"
      ]
    },
    {
      "page": "is.whole.positive.number",
      "title": "Function to test if x is ...",
      "topics": [
        "is.whole.positive.number"
      ]
    },
    {
      "page": "jacobian",
      "title": "Calculate jacobian of a function",
      "topics": [
        "jacobian"
      ]
    },
    {
      "page": "jit",
      "title": "Jitter runs",
      "topics": [
        "jit"
      ]
    },
    {
      "page": "leaveout",
      "title": "leaveout run",
      "topics": [
        "leaveout"
      ]
    },
    {
      "page": "lifeexpectancyplot",
      "title": "SAM life expectancy plot",
      "topics": [
        "lifeexpectancyplot",
        "lifeexpectancyplot.default",
        "lifeexpectancyplot.hcr",
        "lifeexpectancyplot.samforecast"
      ]
    },
    {
      "page": "lifeexpectancytable",
      "title": "Life expectancy table",
      "topics": [
        "lifeexpectancytable",
        "lifeexpectancytable.default"
      ]
    },
    {
      "page": "loadConf",
      "title": "Loads a model configuration from a file",
      "topics": [
        "loadConf"
      ]
    },
    {
      "page": "logLik.sam",
      "title": "Log likelihood of sam object",
      "topics": [
        "logLik.sam"
      ]
    },
    {
      "page": "modelDescription",
      "title": "Description of model",
      "topics": [
        "modelDescription"
      ]
    },
    {
      "page": "modelforecast",
      "title": "Model based forecast function",
      "topics": [
        "modelforecast",
        "modelforecast.sam"
      ]
    },
    {
      "page": "modeltable",
      "title": "model table",
      "topics": [
        "modeltable",
        "modeltable.sam",
        "modeltable.samset"
      ]
    },
    {
      "page": "modelVersionInfo",
      "title": "Description of model",
      "topics": [
        "modelVersionInfo"
      ]
    },
    {
      "page": "mohn",
      "title": "Mohn's rho calculation",
      "topics": [
        "mohn",
        "mohn.samset"
      ]
    },
    {
      "page": "nobs.sam",
      "title": "Extract number of observations from sam object",
      "topics": [
        "nobs.sam"
      ]
    },
    {
      "page": "nscodConf",
      "title": "nscodConf",
      "topics": [
        "nscodConf"
      ]
    },
    {
      "page": "nscodData",
      "title": "nscodData",
      "topics": [
        "nscodData"
      ]
    },
    {
      "page": "nscodParameters",
      "title": "nscodParameters",
      "topics": [
        "nscodParameters"
      ]
    },
    {
      "page": "ntable",
      "title": "N table",
      "topics": [
        "ntable",
        "ntable.sam"
      ]
    },
    {
      "page": "obscorrplot",
      "title": "Plots the estimated correlation matrices by fleet.",
      "topics": [
        "obscorrplot",
        "obscorrplot.sam"
      ]
    },
    {
      "page": "obscov",
      "title": "Extract observation covariance matrices from a SAM fit",
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      "page": "parplot",
      "title": "SAM parameter plot",
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      "page": "partable",
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      "page": "plot.hcr",
      "title": "Plot hcr object",
      "topics": [
        "plot.hcr"
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    },
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      "page": "plot.sam",
      "title": "Plot sam object",
      "topics": [
        "plot.sam"
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    },
    {
      "page": "plot.samforecast",
      "title": "Plot samforecast object",
      "topics": [
        "plot.samforecast"
      ]
    },
    {
      "page": "plot.samres",
      "title": "Plot sam residuals",
      "topics": [
        "plot.samres"
      ]
    },
    {
      "page": "plot.samset",
      "title": "Plot sam object",
      "topics": [
        "plot.samset"
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    },
    {
      "page": "plot.samypr",
      "title": "Plot sam object",
      "topics": [
        "plot.samypr"
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    },
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      "page": "plotby",
      "title": "Plot by one or two",
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    },
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    },
    {
      "page": "predstdplot",
      "title": "Prediction-standard deviation plot",
      "topics": [
        "predstdplot"
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    },
    {
      "page": "print.hcr",
      "title": "Print hcr object",
      "topics": [
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    },
    {
      "page": "print.sam",
      "title": "Print sam object",
      "topics": [
        "print.sam"
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    },
    {
      "page": "print.sam_referencepoints",
      "title": "Print referencepoint object",
      "topics": [
        "print.sam_referencepoints"
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    },
    {
      "page": "print.samcoef",
      "title": "Print samcoef object",
      "topics": [
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    },
    {
      "page": "print.samforecast",
      "title": "Print samforecast object",
      "topics": [
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    {
      "page": "print.samres",
      "title": "Print samres object",
      "topics": [
        "print.samres"
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    },
    {
      "page": "print.samset",
      "title": "Print samset object",
      "topics": [
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    },
    {
      "page": "print.samypr",
      "title": "Print samypr object",
      "topics": [
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    },
    {
      "page": "procres",
      "title": "Compute process residuals (single joint sample)",
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    {
      "page": "qtable",
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      "topics": [
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    {
      "page": "qtableplot",
      "title": "plot survey catchabilities",
      "topics": [
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    {
      "page": "read.data.files",
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      "topics": [
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    },
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      "topics": [
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    },
    {
      "page": "read.surveys",
      "title": "Function to read ices survey format",
      "topics": [
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    },
    {
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      "title": "Function to supress incomplete final line warning",
      "topics": [
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    {
      "page": "recplot",
      "title": "SAM Recruits plot",
      "topics": [
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    },
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    },
    {
      "page": "reduce",
      "title": "reduce helper function to reduce data",
      "topics": [
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    },
    {
      "page": "referencepoints",
      "title": "Estimate reference points",
      "topics": [
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    },
    {
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    },
    {
      "page": "residplot",
      "title": "Compute and plot residual diagnostic tests for a SAM model fit",
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    {
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      "title": "Extract residuals from sam object",
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    },
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    {
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    {
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    },
    {
      "page": "srplot",
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      "page": "ssbplot",
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    },
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    {
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      "topics": [
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