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  "_rbuild": "4.6.2",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/FLa4a.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
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  "_cranurl": false,
  "_exports": [
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    "a4aFitMCMC",
    "a4aFitMCMCs",
    "a4aFits",
    "a4aFitSA",
    "a4aFitSAs",
    "a4aGr",
    "a4aM",
    "a4aSCA",
    "as.mcmc",
    "breakpts",
    "bubbles",
    "burnin",
    "clock",
    "coef",
    "coefficients",
    "coefficients<-",
    "collapseSeasons",
    "computeCatchDiagnostics",
    "covar",
    "defaultFmod",
    "defaultN1mod",
    "defaultQmod",
    "defaultSRmod",
    "defaultVmod",
    "dims",
    "distr",
    "distr<-",
    "fCovar",
    "fFrml",
    "fitSumm",
    "fmodel",
    "formula",
    "formula<-",
    "fPars",
    "genFLIndex",
    "genFLQuant",
    "genFLStock",
    "getAcor",
    "getADMBCallArgs",
    "getADMBCovariance",
    "getADMBHessian",
    "getCov",
    "getK",
    "getN",
    "getTPL",
    "getX",
    "getYidx",
    "grInvMod",
    "grInvMod<-",
    "grMod",
    "grMod<-",
    "is.empty",
    "iter",
    "l2a",
    "level",
    "level<-",
    "m",
    "ma",
    "model",
    "mvrcop",
    "mvrnorm",
    "mvrtriangle",
    "n1model",
    "niters",
    "params",
    "params<-",
    "pars",
    "pars2dim",
    "plot",
    "predict",
    "qCovar",
    "qFrml",
    "qmodel",
    "qPars",
    "qqmath",
    "replaceZeros",
    "residuals",
    "sca",
    "sca.sa",
    "SCAMCMC",
    "SCAPars",
    "scas",
    "sep.sa",
    "shape",
    "shape<-",
    "simulate",
    "srCovar",
    "srFrml",
    "srmodel",
    "srPars",
    "stdlogres",
    "stkmodel",
    "submodel",
    "submodels",
    "trend",
    "trend<-",
    "vCovar",
    "vFrml",
    "vmodel",
    "vPars",
    "wireframe",
    "wt"
  ],
  "_datasets": [
    {
      "name": "dps567",
      "title": "dps567",
      "object": "dps567",
      "class": [
        "FLStock"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dps567.idx",
      "title": "dps567.idx",
      "object": "dps567.idx",
      "class": [
        "FLIndex"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hakeGSA7",
      "title": "hakeGSA7",
      "object": "hakeGSA7",
      "class": [
        "FLStock"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hakeGSA7.idx",
      "title": "hakeGSA7.idx",
      "object": "hakeGSA7.idx",
      "class": [
        "FLIndices"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hke1567",
      "title": "hke1567",
      "object": "hke1567",
      "class": [
        "FLStock"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hke1567.idx",
      "title": "hke1567.idx",
      "object": "hke1567.idx",
      "class": [
        "FLIndex"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "index_cd_len",
      "title": "index_cd_len",
      "object": "southernHakeLen",
      "class": [
        "FLIndex"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "index_pt_len",
      "title": "index_pt_len",
      "object": "southernHakeLen",
      "class": [
        "FLIndex"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "index_sp_len",
      "title": "index_sp_len",
      "object": "southernHakeLen",
      "class": [
        "FLIndex"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mut09",
      "title": "mut09",
      "object": "mut09",
      "class": [
        "FLStock"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mut09.idx",
      "title": "mut09.idx",
      "object": "mut09.idx",
      "class": [
        "FLIndices"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "rfLen.stk",
      "title": "rfLen.stk",
      "object": "rfLen",
      "class": [
        "FLStockLen"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "rfTrawl.idx",
      "title": "rfTrawl.idx",
      "object": "rfLen",
      "class": [
        "FLIndex"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "rfTrawlJmp.idx",
      "title": "rfTrawlJmp.idx",
      "object": "rfLen",
      "class": [
        "FLIndex"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "rfTrawlTrd.idx",
      "title": "rfTrawlTrd.idx",
      "object": "rfLen",
      "class": [
        "FLIndex"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "shake_len",
      "title": "shake_len",
      "object": "southernHakeLen",
      "class": [
        "FLStockLen"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "multiplication-methods",
      "title": "* methods",
      "topics": [
        "*",
        "*,FLIndices,a4aFitSA-method",
        "*,FLIndices,SCAPars-method",
        "*,FLStock,a4aFitSA-method",
        "*,FLStock,SCAPars-method"
      ]
    },
    {
      "page": "a4aFit-class",
      "title": "S4 class 'a4aFit'",
      "topics": [
        "a4aFit",
        "a4aFit-class",
        "a4aFit-methods",
        "a4aFits",
        "a4aFits,a4aFit-method",
        "a4aFits,list-method",
        "a4aFits,missing-method",
        "a4aFits-class",
        "a4aFits-methods",
        "catch.n,a4aFit-method",
        "clock",
        "clock,a4aFit-method",
        "clock-methods",
        "computeCatchDiagnostics,a4aFit-method",
        "fitSumm",
        "fitSumm,a4aFit-method",
        "fitSumm-methods",
        "harvest,a4aFit,ANY-method",
        "index,a4aFit-method",
        "iter,a4aFit-method",
        "logLik,a4aFit-method",
        "show,a4aFit-method",
        "stock.n,a4aFit-method"
      ]
    },
    {
      "page": "a4aFitCatchDiagn-class",
      "title": "S4 class 'a4aFitCatchDiagn'",
      "topics": [
        "a4aFitCatchDiagn",
        "a4aFitCatchDiagn-class",
        "a4aFitCatchDiagn-methods",
        "computeCatchDiagnostics"
      ]
    },
    {
      "page": "a4aFitMCMC-class",
      "title": "S4 class 'a4aFitMCMC'",
      "topics": [
        "a4aFit,a4aFitMCMC-method",
        "a4aFitMCMC",
        "a4aFitMCMC-class",
        "a4aFitMCMC-methods",
        "a4aFitMCMCs",
        "a4aFitMCMCs,a4aFitMCMC-method",
        "a4aFitMCMCs,list-method",
        "a4aFitMCMCs,missing-method",
        "a4aFitMCMCs-class",
        "a4aFitMCMCs-methods",
        "a4aFitSA,a4aFitMCMC-method",
        "as.mcmc",
        "as.mcmc,a4aFitMCMC-method",
        "as.mcmc-methods",
        "burnin",
        "burnin,a4aFitMCMC-method",
        "burnin-methods"
      ]
    },
    {
      "page": "a4aFitResiduals-class",
      "title": "S4 class 'a4aFitResiduals'",
      "topics": [
        "a4aFitResiduals",
        "a4aFitResiduals-class",
        "a4aFitResiduals-methods",
        "residuals,a4aFit-method"
      ]
    },
    {
      "page": "a4aFitSA-class",
      "title": "S4 class 'a4aFitSA'",
      "topics": [
        "a4aFit,a4aFitSA-method",
        "a4aFitSA",
        "a4aFitSA-class",
        "a4aFitSA-methods",
        "a4aFitSAs",
        "a4aFitSAs,a4aFitSA-method",
        "a4aFitSAs,list-method",
        "a4aFitSAs,missing-method",
        "a4aFitSAs-class",
        "a4aFitSAs-methods",
        "fmodel,a4aFitSA-method",
        "iter,a4aFitSA-method",
        "m,a4aFitSA-method",
        "n1model,a4aFitSA-method",
        "pars",
        "pars,a4aFitSA-method",
        "pars-methods",
        "qmodel,a4aFitSA-method",
        "show,a4aFitSA-method",
        "srmodel,a4aFitSA-method",
        "stkmodel,a4aFitSA-method",
        "submodels,a4aFitSA-method",
        "vmodel,a4aFitSA-method",
        "wt,a4aFitSA-method"
      ]
    },
    {
      "page": "a4aGr-class",
      "title": "Individual growth class",
      "topics": [
        "a4aGr",
        "a4aGr,missing-method",
        "a4aGr-class",
        "a4aGr-methods",
        "distr,a4aGr-method",
        "distr<-,a4aGr,character-method",
        "grInvMod",
        "grInvMod,a4aGr-method",
        "grInvMod-methods",
        "grInvMod<-",
        "grInvMod<-,a4aGr,formula-method",
        "grInvMod<--methods",
        "grMod",
        "grMod,a4aGr-method",
        "grMod-methods",
        "grMod<-",
        "grMod<-,a4aGr,formula-method",
        "grMod<--methods",
        "params,a4aGr-method",
        "params<-,a4aGr,FLPar-method",
        "vcov,a4aGr-method",
        "vcov<-,a4aGr,numeric-method"
      ]
    },
    {
      "page": "a4aInternal",
      "title": "Stock assessment model advanced method",
      "topics": [
        "a4aInternal"
      ]
    },
    {
      "page": "a4aM-class",
      "title": "Natural mortality class",
      "topics": [
        "a4aM",
        "a4aM,missing-method",
        "a4aM-class",
        "a4aM-methods",
        "level",
        "level,a4aM-method",
        "level-methods",
        "level<-",
        "level<-,a4aM-method",
        "level<--methods",
        "shape",
        "shape,a4aM-method",
        "shape-methods",
        "shape<-",
        "shape<-,a4aM-method",
        "shape<--methods",
        "show,a4aM-method",
        "trend",
        "trend,a4aM-method",
        "trend-methods",
        "trend<-",
        "trend<-,a4aM-method",
        "trend<--methods"
      ]
    },
    {
      "page": "a4aStkParams-class",
      "title": "Stock parameters class",
      "topics": [
        "a4aStkParams",
        "a4aStkParams,missing-method",
        "a4aStkParams-class",
        "a4aStkParams-methods",
        "coefficients",
        "coefficients,a4aStkParams-method",
        "coefficients-methods",
        "coefficients<-",
        "coefficients<-,a4aStkParams,FLPar-method",
        "coefficients<--methods",
        "distr,a4aStkParams-method",
        "distr<-,a4aStkParams,character-method",
        "fMod",
        "fMod,a4aStkParams-method",
        "fMod-methods",
        "fMod<-",
        "fMod<-,a4aStkParams,formula-method",
        "fMod<--methods",
        "iter,a4aStkParams-method",
        "m,a4aStkParams-method",
        "mat,a4aStkParams-method",
        "n1Mod",
        "n1Mod,a4aStkParams-method",
        "n1Mod-methods",
        "n1Mod<-",
        "n1Mod<-,a4aStkParams,formula-method",
        "n1Mod<--methods",
        "params,a4aStkParams-method",
        "params<-,a4aStkParams,FLPar-method",
        "propagate,a4aStkParams-method",
        "rMod-methods",
        "srMod",
        "srMod,a4aStkParams-method",
        "srMod<-",
        "srMod<-,a4aStkParams,formula-method",
        "srMod<--methods",
        "vcov,a4aStkParams-method",
        "vcov<-,a4aStkParams,array-method",
        "wt,a4aStkParams-method"
      ]
    },
    {
      "page": "addition-methods",
      "title": "+ methods",
      "topics": [
        "+,FLIndices,a4aFit-method",
        "+,FLStock,a4aFit-method",
        "+,FLStocks,a4aFits-method",
        "addition"
      ]
    },
    {
      "page": "assorted-methods",
      "title": "Assorted methods needed by FLa4a",
      "topics": [
        "assorted methods",
        "dims,a4aStkParams-method",
        "getYidx",
        "getYidx,FLQuant-method",
        "getYidx-methods",
        "is.empty",
        "niters",
        "niters,a4aGr-method",
        "niters,FLModelSim-method",
        "niters-methods",
        "replaceZeros",
        "replaceZeros,FLI-method",
        "replaceZeros,FLIndices-method",
        "replaceZeros,FLQuant-method",
        "replaceZeros,FLStock-method",
        "replaceZeros-methods"
      ]
    },
    {
      "page": "breakpts",
      "title": "Breakpoints",
      "topics": [
        "breakpts",
        "breakpts,numeric-method",
        "breakpts-methods"
      ]
    },
    {
      "page": "bubbles-methods",
      "title": "Bubbles plot of standardized log residuals",
      "topics": [
        "bubble plot of residuals",
        "bubbles,a4aFitResiduals,missing-method"
      ]
    },
    {
      "page": "collapseSeasons",
      "title": "Collapse seasons",
      "topics": [
        "collapseSeasons"
      ]
    },
    {
      "page": "defaultsubmodels",
      "title": "Default sub-models",
      "topics": [
        "defaultFmod",
        "defaultN1mod",
        "defaultQmod",
        "defaultSRmod",
        "defaultSubModels",
        "defaultVmod"
      ]
    },
    {
      "page": "deprecated",
      "title": "deprecated",
      "topics": [
        "a4aSCA",
        "deprecated"
      ]
    },
    {
      "page": "dps567",
      "title": "dps567",
      "topics": [
        "dps567"
      ]
    },
    {
      "page": "dps567.idx",
      "title": "dps567.idx",
      "topics": [
        "dps567.idx"
      ]
    },
    {
      "page": "coef-methods",
      "title": "coefficients extract and replacement",
      "topics": [
        "coef",
        "coef,a4aFitSA-method",
        "coef,a4aFitSA-methods",
        "coef,a4aStkParams-method",
        "coef,SCAPars-method",
        "coef,submodel-method",
        "coef,submodels-method",
        "coef<-",
        "coef<-,a4aFitSA,numeric-method",
        "coef<-,a4aFitSA-methods",
        "coef<-,a4aStkParams,FLPar-method",
        "coef<-,a4aStkParams,matrix-method",
        "coef<-,a4aStkParams,numeric-method",
        "coef<-,SCAPars,numeric-method",
        "coef<-,submodel,FLPar-method",
        "coef<-,submodel,numeric-method",
        "coef<-,submodels,numeric-method",
        "formula<-",
        "formula<-,submodel,formula-method"
      ]
    },
    {
      "page": "genFLIndex-methods",
      "title": "Methods to generate FLIndex objects",
      "topics": [
        "genFLIndex",
        "genFLIndex,FLQuant-method",
        "genFLIndex-methods"
      ]
    },
    {
      "page": "genFLQuant-methods",
      "title": "Methods to generate FLQuant objects",
      "topics": [
        "genFLQuant",
        "genFLQuant,a4aStkParams-method",
        "genFLQuant,FLQuant-method",
        "genFLQuant,submodel-method",
        "genFLQuant,submodels-method",
        "genFLQuant-methods"
      ]
    },
    {
      "page": "genFLStock-methods",
      "title": "Methods to generate FLStock objects",
      "topics": [
        "genFLStock",
        "genFLStock,FLStock,FLQuant,FLQuant,missing-method",
        "genFLStock,FLStock,FLQuant,missing,FLQuant-method",
        "genFLStock,FLStock,missing,FLQuant,FLQuant-method",
        "genFLStock-methods"
      ]
    },
    {
      "page": "getAcor-methods",
      "title": "compute log-correlation matrix",
      "topics": [
        "getAcor",
        "getAcor,FLQuant-method",
        "getAcor-methods"
      ]
    },
    {
      "page": "getADMBHessian",
      "title": "Get ADMB Hessian",
      "topics": [
        "getADMBCovariance",
        "getADMBHessian"
      ]
    },
    {
      "page": "getCov-methods",
      "title": "Get covariance matrix",
      "topics": [
        "getCov"
      ]
    },
    {
      "page": "getK",
      "title": "Get K",
      "topics": [
        "getK",
        "getK,a4aGr-method",
        "getK-methods"
      ]
    },
    {
      "page": "getTPL",
      "title": "Get TPL with ADMB code",
      "topics": [
        "getTPL"
      ]
    },
    {
      "page": "getX-methods",
      "title": "Get model matrix",
      "topics": [
        "getX",
        "getX,formula-method",
        "getX-methods"
      ]
    },
    {
      "page": "hakeGSA7",
      "title": "hakeGSA7",
      "topics": [
        "hakeGSA7"
      ]
    },
    {
      "page": "hakeGSA7.idx",
      "title": "hakeGSA7.idx",
      "topics": [
        "hakeGSA7.idx"
      ]
    },
    {
      "page": "hke1567",
      "title": "hke1567",
      "topics": [
        "hke1567"
      ]
    },
    {
      "page": "hke1567.idx",
      "title": "hke1567.idx",
      "topics": [
        "hke1567.idx"
      ]
    },
    {
      "page": "index_cd_len",
      "title": "index_cd_len",
      "topics": [
        "index_cd_len"
      ]
    },
    {
      "page": "index_pt_len",
      "title": "index_pt_len",
      "topics": [
        "index_pt_len"
      ]
    },
    {
      "page": "index_sp_len",
      "title": "index_sp_len",
      "topics": [
        "index_sp_len"
      ]
    },
    {
      "page": "l2a",
      "title": "Method to convert length-based data to age-based",
      "topics": [
        "l2a",
        "l2a,FLIndex,a4aGr-method",
        "l2a,FLQuant,a4aGr-method",
        "l2a,FLStockLen,a4aGr-method",
        "l2a-methods"
      ]
    },
    {
      "page": "m",
      "title": "natural mortality",
      "topics": [
        "m",
        "m,a4aM-method"
      ]
    },
    {
      "page": "ma-methods",
      "title": "Model averaging (experimental)",
      "topics": [
        "ma",
        "ma,a4aFitSAs-method",
        "ma-methods"
      ]
    },
    {
      "page": "mut09",
      "title": "mut09",
      "topics": [
        "mut09"
      ]
    },
    {
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