{
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  "Package": "FLjjm",
  "Title": "Running the JJM Stock Assessment Model Inside the MSE FLR System",
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  "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",
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  "Packaged": {
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  "Author": "Iago Mosqueira [aut, cre], Karolina Molla Gazi [aut]",
  "Maintainer": "Iago Mosqueira <iago.mosqueira@wur.nl>",
  "Repository": "https://jimianelli.r-universe.dev",
  "Date/Publication": "2026-06-09 07:13:50 UTC",
  "RemoteUrl": "https://github.com/SPRFMO/FLjjm",
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      "table": false,
      "tojson": true
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      "page": "AgeToLengthComp",
      "title": "Convert Age Composition to Length Composition",
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    },
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      "title": "Build Functions for FLjjm Package",
      "topics": [
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      "topics": [
        "buildFLBjjm"
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    },
    {
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      "topics": [
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    {
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    {
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      "topics": [
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      "page": "FLjjm",
      "title": "FLjjm: An R Package for Interacting with JJMS Stock Assessment Model in FLR",
      "topics": [
        "FLjjm"
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    {
      "page": "loadFLSjjms",
      "title": "Load FLStocks from JJMS Model",
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    {
      "page": "loadJJMS",
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    {
      "page": "namejjms",
      "title": "Get Name of JJMS Model",
      "topics": [
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    {
      "page": "nStocksjjms",
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      "page": "packjjmsrun",
      "title": "Clean Up JJMS Model Run Directory",
      "topics": [
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      "page": "readFLBjjm",
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      "topics": [
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    {
      "page": "readFLFsjjm",
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      "topics": [
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    {
      "page": "readFLoemjjm",
      "title": "Read FLIndices with OEM iterations and MC outputs",
      "topics": [
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      "page": "readFLomjjm",
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      "page": "readFLRPsjjm",
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      "engine": "knitr::rmarkdown",
      "headings": [
        "Using the FLjjm package",
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      "created": "2024-01-19 17:41:21",
      "modified": "2026-05-31 08:45:04",
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