{
  "_id": "6ac217b7773a0037682c1d69",
  "Package": "FLSAM",
  "Title": "An Implementation of the State-Space Assessment Model for FLR",
  "Version": "3.0.0.9005",
  "Date": "2023-04-18",
  "Authors@R": "c(\nperson(\"N.T.\", \"Hintzen\", email = \"nhintzen@pelagicfish.eu\", role = \"cre\"),\nperson(\"M.R.\", \"Payne\", email = \"mpa@aqua.dtu.dk\", role = \"aut\"))",
  "Description": "This package provides an FLR wrapper to the SAM\nstate-space assessment model.",
  "Collate": "\"FLSAM.control.R\" \"FLSAM.R\" \"FLSAM.MSE.R\" \"FLSAM.out.R\"\n\"FLR2SAM.R\" \"SAM2FLR.R\" \"accessors.R\" \"af.R\" \"anf.r\"\n\"diagnostics.R\" \"kobe-FLSAM.R\" \"looi_retro.R\" \"methods_plots.R\"\n\"methods.R\" \"monteCarloStock.R\" \"pin.R\" \"zzz.R\"",
  "License": "GPL (>= 2)",
  "LazyLoad": "no",
  "Repository": "https://flr.r-universe.dev",
  "Date/Publication": "2025-05-03 07:00:09 UTC",
  "RemoteUrl": "https://github.com/flr/FLSAM",
  "RemoteRef": "HEAD",
  "RemoteSha": "89bb528f43026bedbc27b02cf897d0ffc5f5b31e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-04 08:54:42 UTC",
    "User": "root"
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  "Author": "N.T. Hintzen [cre],\nM.R. Payne [aut]",
  "Maintainer": "N.T. Hintzen <nhintzen@pelagicfish.eu>",
  "_user": "flr",
  "_type": "src",
  "_file": "FLSAM_3.0.0.9005.tar.gz",
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  "_expires": "2027-01-12T09:09:09.000Z",
  "_created": "2026-10-04T08:54:42.000Z",
  "_published": "2026-10-04T09:09:10.933Z",
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    "message": "adding option for setting seed in simulate function\nadding cohort option in methods_plots for retro\n",
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  "_tags": [],
  "_stars": 5,
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/manual.pdf",
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    "extra/readme.md"
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  "_exports": [
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    "catch.scale",
    "catchabilities",
    "clean.void.catches",
    "coef",
    "coefficients",
    "comp.plot",
    "components",
    "components<-",
    "conf2ctrl",
    "cor.F",
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    "cor.plot",
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    "FLSAM.control",
    "FLSAM.fast",
    "FLSAM.MSE",
    "FLSAM.out",
    "FLSAM2par",
    "FLSAM2SAM",
    "FLSAMs",
    "formatMatrix",
    "formatQuant",
    "fpart.plot",
    "getLowerBounds",
    "getUpperBounds",
    "info",
    "info<-",
    "kobeFLSAM",
    "kobeFLSamFn",
    "loi",
    "loo",
    "looi",
    "lr.test",
    "mohns.rho",
    "monteCarloStock",
    "monteCarloStockMscan",
    "n.states",
    "n.states<-",
    "n.var",
    "nlogl",
    "nlogl<-",
    "nopar",
    "nopar<-",
    "obs.var",
    "obscor.plot",
    "obscov",
    "obscov<-",
    "obscv.plot",
    "obsvar.plot",
    "otolith",
    "plotkobe",
    "power.law.exps",
    "procerr.plot",
    "rec.pars",
    "rescov",
    "rescov<-",
    "residual.diagnostics",
    "retro",
    "retroParams",
    "retroResiduals",
    "retroSelectivity",
    "sam.fitfast",
    "sam.out",
    "SAM2FLR",
    "SIM2FLR",
    "simulate",
    "states",
    "states<-"
  ],
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      "name": "HERAS.sams",
      "title": "North Sea Autumn Spawning Herring Stock Assessment",
      "object": "HERAS.sams",
      "file": "HERAS.sams.RData",
      "class": [
        "FLSAMs"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "NSH",
      "title": "North Sea Autumn Spawning Herring Stock Assessment",
      "object": "NSH",
      "file": "NSH.RData",
      "class": [
        "FLStock"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "NSH.ctrl",
      "title": "North Sea Autumn Spawning Herring Stock Assessment",
      "object": "NSH",
      "file": "NSH.RData",
      "class": [
        "FLSAM.control"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "NSH.sam",
      "title": "North Sea Autumn Spawning Herring Stock Assessment",
      "object": "NSH.sam",
      "file": "NSH.sam.RData",
      "class": [
        "FLSAM"
      ],
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      "table": false,
      "tojson": false
    },
    {
      "name": "NSH.tun",
      "title": "North Sea Autumn Spawning Herring Stock Assessment",
      "object": "NSH",
      "file": "NSH.RData",
      "class": [
        "FLIndices"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SOL",
      "title": "",
      "object": "SOL",
      "file": "SOL.RData",
      "class": [
        "FLStock"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SOL.ctrl",
      "title": "",
      "object": "SOL",
      "file": "SOL.RData",
      "class": [
        "FLSAM.control"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SOL.sam",
      "title": "",
      "object": "SOL.sam",
      "file": "SOL.sam.RData",
      "class": [
        "FLSAM"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SOL.tun",
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      "object": "SOL",
      "file": "SOL.RData",
      "class": [
        "FLIndices"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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  ],
  "_help": [
    {
      "page": "accessors",
      "title": "Accessor functions for FLSAM",
      "topics": [
        "accessors",
        "catch",
        "catchabilities",
        "f",
        "fbar",
        "n",
        "obs.var",
        "power.law.exps",
        "rec",
        "ssb",
        "tsb"
      ]
    },
    {
      "page": "AIC",
      "title": "Akaike's information criterion for FLSAM",
      "topics": [
        "AIC"
      ]
    },
    {
      "page": "cor.plot",
      "title": "FLSAM sam variable correlation plot",
      "topics": [
        "cor.plot"
      ]
    },
    {
      "page": "drop",
      "title": "Drop an element from an FLSAM.control object",
      "topics": [
        "drop.from.control"
      ]
    },
    {
      "page": "FLSAM",
      "title": "FLR Wrapper for the State-space assessment model (FLSAM)",
      "topics": [
        "FLR2SAM",
        "FLSAM",
        "runSAM",
        "SAM2FLR",
        "update"
      ]
    },
    {
      "page": "FLSAM.control",
      "title": "FLSAM.control",
      "topics": [
        "FLSAM.control"
      ]
    },
    {
      "page": "FLSAM.out",
      "title": "Create FLSAM formatted output file",
      "topics": [
        "FLSAM.out",
        "sam.out"
      ]
    },
    {
      "page": "FLSAMs",
      "title": "Class '\"FLSAMs\"'",
      "topics": [
        "FLSAMs",
        "FLSAMs-class"
      ]
    },
    {
      "page": "looi",
      "title": "Run a sequence of assessments leaving one fleet (non-catch) in or out",
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        "loo",
        "looi"
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    },
    {
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      "topics": [
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      ]
    },
    {
      "page": "monteCarloStock",
      "title": "Generate new starting conditions of numbers and f-at-age.",
      "topics": [
        "monteCarloStock"
      ]
    },
    {
      "page": "data",
      "title": "North Sea Autumn Spawning Herring Stock Assessment",
      "topics": [
        "HERAS.sams",
        "NSH",
        "NSH.ctrl",
        "NSH.sam",
        "NSH.tun"
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    {
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      "title": "Create diagnostic observation variance v.s. CV plot.",
      "topics": [
        "obscv.plot"
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    },
    {
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      "title": "Create diagnostic observation variance plot.",
      "topics": [
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        "otolith"
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    },
    {
      "page": "parameter.accesors",
      "title": "Parameter accessor functions for FLSAM",
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        "coef",
        "coefficients",
        "params"
      ]
    },
    {
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      "title": "Produce diagnostics on process error in the SAM Model",
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        "procerr.plot"
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    },
    {
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      "title": "FLSAM assessment diagnostics",
      "topics": [
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    },
    {
      "page": "retro",
      "title": "Retrospective stock assessment for FLSAM",
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        "retro"
      ]
    }
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