{
  "_id": "6a1c06f41d7bb097a0a2b6fe",
  "Package": "FLjjm",
  "Title": "Running the JJM Stock Assessment Model Inside the MSE FLR System",
  "Version": "0.3.3",
  "AuthorR": "c( person(given = 'Iago', family = 'Mosqueira', role =\nc('aut', 'cre'), email = 'iago.mosqueira@wur.nl'), person(given\n= 'Karolina', family = 'Molla Gazi', role = c('aut'), email =\n'karolina.mollagazi@wur.nl'))",
  "Description": "Runs the JJM stock assessment model for Chilean Jack\nMackerel inside the MSE system of FLR's mse package.",
  "Additional_repositories": "https://sprfmo.r-universe.dev,\nhttps://flr.r-universe.dev",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "License": "EUPL",
  "LazyLoad": "Yes",
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  "Packaged": {
    "Date": "2026-05-31 09:53:59 UTC",
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  "Author": "Iago Mosqueira [aut, cre], Karolina Molla Gazi [aut]",
  "Maintainer": "Iago Mosqueira <iago.mosqueira@wur.nl>",
  "Config/pak/sysreqs": "bwidget cmake make libicu-dev libjpeg-dev\nlibpng-dev libuv1-dev libxml2-dev",
  "Repository": "https://sprfmo.r-universe.dev",
  "Date/Publication": "2026-05-31 08:45:04 UTC",
  "RemoteUrl": "https://github.com/SPRFMO/FLjjm",
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  "_created": "2026-05-31T09:53:59.000Z",
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      "tojson": false
    },
    {
      "name": "indicators",
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      "object": "indicators",
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      "tojson": false
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      "table": false,
      "tojson": false
    },
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      "title": "",
      "object": "cjmstk",
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "mods",
      "title": "",
      "object": "cjmstks",
      "file": "cjmstks.RData",
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
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      "name": "oem",
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      "class": [
        "FLombf"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "statistics",
      "title": "",
      "object": "statistics",
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "table": false,
      "tojson": false
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "page": "dot-combinejjmsout",
      "title": "Combine Fisheries Model Results",
      "topics": [
        ".combinejjmsout"
      ]
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    {
      "page": "AgeToLengthComp",
      "title": "Convert Age Composition to Length Composition",
      "topics": [
        "AgeToLengthComp"
      ]
    },
    {
      "page": "build",
      "title": "Build Functions for FLjjm Package",
      "topics": [
        "build"
      ]
    },
    {
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      "title": "Build an FLBiol from a jjm.output object",
      "topics": [
        "buildFLBjjm"
      ]
    },
    {
      "page": "buildFLFsjjm",
      "title": "Build FLFisheries from JJMS Model Output",
      "topics": [
        "buildFLFsjjm"
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    },
    {
      "page": "buildFLIsjjm",
      "title": "Construct FLIndices from a jjm.output object",
      "topics": [
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    {
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    {
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      "title": "Build FLStock from jjm.output",
      "topics": [
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    },
    {
      "page": "buildFLSojjm",
      "title": "Build FLStock with areas from jjm.output",
      "topics": [
        "buildFLSojjm"
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    {
      "page": "buildFLSsjjm",
      "title": "Build multiple FLStock objects from jjm.output",
      "topics": [
        "buildFLSsjjm"
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    {
      "page": "buildjjmctl",
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      "topics": [
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    },
    {
      "page": "catch-FLStocks-method",
      "title": "Calculate Total Catch across FLStocks",
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        "catch,FLStocks-method"
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      "title": "Observation Error Model wrapper for CJM within MSE workflows",
      "topics": [
        "cjm.oem"
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    {
      "page": "cjmage2len",
      "title": "Convert Age Composition to Length Composition for Landings",
      "topics": [
        "cjmage2len"
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    },
    {
      "page": "cjmfwc",
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      "topics": [
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      "title": "Execute JJMS Model",
      "topics": [
        "exejjms"
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    },
    {
      "page": "fbar-FLStocks-method",
      "title": "Calculate Average Fishing Mortality across FLStocks",
      "topics": [
        "fbar,FLStocks-method"
      ]
    },
    {
      "page": "FLjjm",
      "title": "FLjjm: An R Package for Interacting with JJMS Stock Assessment Model in FLR",
      "topics": [
        "FLjjm"
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      "page": "fwdmov",
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      "topics": [
        "fwdmov"
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      "topics": [
        "fwdmov.om"
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      "topics": [
        "jjms"
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    {
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      "title": "JJMS Stock Assessment",
      "topics": [
        "jjms.sa"
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    },
    {
      "page": "loadFLSjjms",
      "title": "Load FLStocks from JJMS Model",
      "topics": [
        "loadFLSjjms"
      ]
    },
    {
      "page": "loadJJMS",
      "title": "Load JJMS Model Components",
      "topics": [
        "loadJJMS"
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    },
    {
      "page": "namejjms",
      "title": "Get Name of JJMS Model",
      "topics": [
        "namejjms"
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    },
    {
      "page": "nStocksjjms",
      "title": "Get Number of Stocks in JJMS Model",
      "topics": [
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      ]
    },
    {
      "page": "packjjmsrun",
      "title": "Clean Up JJMS Model Run Directory",
      "topics": [
        "packjjmsrun"
      ]
    },
    {
      "page": "readFLBjjm",
      "title": "Create an FLBiol from a JJMS model run directory",
      "topics": [
        "readFLBjjm"
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    },
    {
      "page": "readFLFsjjm",
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      "topics": [
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    {
      "page": "readFLIsjjm",
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      "topics": [
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    },
    {
      "page": "readFLoemjjm",
      "title": "Read FLIndices with OEM iterations and MC outputs",
      "topics": [
        "readFLoemjjm"
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    {
      "page": "readFLomjjm",
      "title": "Create an FLombf object from a JJMS model run directory",
      "topics": [
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    {
      "page": "readFLRPsjjm",
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      "topics": [
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    {
      "page": "ssb-FLStocks-method",
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  "_vignettes": [
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      "filename": "FLjjm.html",
      "title": "Description of the FLjjm package",
      "author": "Name SURNAME",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Using the FLjjm package",
        "Loading jjms outputs",
        "Running jjms",
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        "Observation Error Model (oem)",
        "Indices of abundance to generate in MP:",
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        "More information",
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      "created": "2024-01-19 17:41:21",
      "modified": "2026-05-31 08:45:04",
      "commits": 3
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