{
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  "Package": "fishSim",
  "Title": "Simulate Populations With Multiple Stocks, Movement, Mating,\nMortality, and Parentage",
  "Version": "0.0.0.9000",
  "Authors@R": "person(\"Shane\", \"Baylis\", email = \"shane.m.baylis@gmail.com\", role = c(\"aut\", \"cre\"))",
  "Description": "Simulates population demography of an arbitrary number of\nstocks potentially connected by movement, with full parentage\nrecord-keeping. Includes functions for movement, mating,\nmortality, and aging, plus convenience functions to handle data\narchiving.",
  "License": "MIT + file LICENSE",
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  "Repository": "https://smbaylis.r-universe.dev",
  "Date/Publication": "2026-03-24 02:17:32 UTC",
  "RemoteUrl": "https://github.com/SMBaylis/fishSim",
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    "capture",
    "check_growthrate",
    "findRelatives",
    "findRelativesPar",
    "grandparents",
    "great.grandparents",
    "great2.grandparents",
    "great3.grandparents",
    "great4.grandparents",
    "lookAtPair",
    "make_archive",
    "makeFounders",
    "mate",
    "mort",
    "move",
    "namedRelatives",
    "oldmove",
    "parents",
    "PoNG",
    "quickin",
    "remove_dead",
    "rTruncPoisson",
    "sexSwitch"
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    {
      "page": "addmtDNA",
      "title": "add mtDNA haplotypes to a completed simulation",
      "topics": [
        "addmtDNA"
      ]
    },
    {
      "page": "altMate",
      "title": "Breeding based on mature females",
      "topics": [
        "altMate"
      ]
    },
    {
      "page": "archive_dead",
      "title": "Take dead individuals and copy them to an archive",
      "topics": [
        "archive_dead"
      ]
    },
    {
      "page": "birthdays",
      "title": "Add one to each individual's age",
      "topics": [
        "birthdays"
      ]
    },
    {
      "page": "bondedMate",
      "title": "mating between bonded pairs",
      "topics": [
        "bondedMate"
      ]
    },
    {
      "page": "both",
      "title": "Unique reals from ordered pairs of integers",
      "topics": [
        "both"
      ]
    },
    {
      "page": "capture",
      "title": "Identify genetic captures/samples in population",
      "topics": [
        "capture"
      ]
    },
    {
      "page": "check_growthrate",
      "title": "Estimate population growth under some 'mate()' and 'mort()' conditions",
      "topics": [
        "check_growthrate"
      ]
    },
    {
      "page": "dfify",
      "title": "convert an early 'makeFounders'-type matrix to 'data.frame'",
      "topics": [
        "dfify"
      ]
    },
    {
      "page": "findRelatives",
      "title": "Find shared ancestors between pairs of individuals",
      "topics": [
        "findRelatives"
      ]
    },
    {
      "page": "findRelativesPar",
      "title": "Partially-parallelized 'findRelatives()'",
      "topics": [
        "findRelativesPar"
      ]
    },
    {
      "page": "fishSim",
      "title": "fishSim",
      "topics": [
        "fishSim-package",
        "fishSim"
      ]
    },
    {
      "page": "grandparents",
      "title": "Look up the grandparents of one or more individuals",
      "topics": [
        "grandparents"
      ]
    },
    {
      "page": "great.grandparents",
      "title": "look up the great-grandparents of one or more individuals",
      "topics": [
        "great.grandparents"
      ]
    },
    {
      "page": "great2.grandparents",
      "title": "Look up the great-great-grandparents of one or more individuals",
      "topics": [
        "great2.grandparents"
      ]
    },
    {
      "page": "great3.grandparents",
      "title": "Look up the great-great-great-grandparents of one or more individuals.",
      "topics": [
        "great3.grandparents"
      ]
    },
    {
      "page": "great4.grandparents",
      "title": "Look up the great-great-great-great-grandparents of one or more individuals",
      "topics": [
        "great4.grandparents"
      ]
    },
    {
      "page": "lookAtPair",
      "title": "Show a readable relationship summary for a pair of relatives",
      "topics": [
        "lookAtPair"
      ]
    },
    {
      "page": "make_archive",
      "title": "Set up an archive matrix for storing simulation outputs",
      "topics": [
        "make_archive"
      ]
    },
    {
      "page": "make_sim_names",
      "title": "Make sim names, as a list",
      "topics": [
        "make_sim_names"
      ]
    },
    {
      "page": "makeFounders",
      "title": "Make a founding population",
      "topics": [
        "makeFounders"
      ]
    },
    {
      "page": "mate",
      "title": "Find male-female pairs and breed until a quota is filled",
      "topics": [
        "mate"
      ]
    },
    {
      "page": "mort",
      "title": "Kill some members of the population",
      "topics": [
        "mort"
      ]
    },
    {
      "page": "move",
      "title": "Age- and/or sex-specific Markovian movement between breeding stocks",
      "topics": [
        "move"
      ]
    },
    {
      "page": "namedRelatives",
      "title": "Show numbers of pairs in named relationship classes",
      "topics": [
        "namedRelatives"
      ]
    },
    {
      "page": "oldmove",
      "title": "Markovian movement between breeding stocks",
      "topics": [
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      ]
    },
    {
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      "title": "Look up the parents of one or more individuals",
      "topics": [
        "parents"
      ]
    },
    {
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      "title": "Find a Point of No Growth (by tweaking first-year mortality)",
      "topics": [
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      ]
    },
    {
      "page": "quickin",
      "title": "Quick lookup of CKMR-relevant relationships",
      "topics": [
        "quickin"
      ]
    },
    {
      "page": "remove_dead",
      "title": "Remove the dead from a population",
      "topics": [
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      ]
    },
    {
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      "title": "Draw from a zero-truncated Poisson dist",
      "topics": [
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      ]
    },
    {
      "page": "sexSwitch",
      "title": "Induce sex-switching in a subset of the population",
      "topics": [
        "sexSwitch"
      ]
    },
    {
      "page": "xpairs",
      "title": "Look up shared ancestors for 'quickin'-style kinship reporting",
      "topics": [
        "xpairs"
      ]
    }
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  "_readme": "https://github.com/SMBaylis/fishSim/raw/HEAD/README.md",
  "_rundeps": [
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        "Setup",
        "Mating",
        "Mortality",
        "Birthdays",
        "Sampling from the population",
        "What's my population doing? Can I make it stay the same size?",
        "Turning processes into a simple simulation",
        "Looking up relationships between pairs of animals",
        "The 'bells and whistles' scenario",
        "Setting up the data objects",
        "Parameterising movement, survival, and maturity structures",
        "Checking population growth rates with the new parameters",
        "Running the simulation",
        "Addenda",
        "A note on mark-dependent survival or movement",
        "Arbitrary variables to affect the simulation",
        "Custom functions in fishSim",
        "Pair-bonded mating"
      ],
      "created": "2021-02-15 01:28:03",
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