{
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  "Package": "polySegratioMM",
  "Type": "Package",
  "Title": "Bayesian Mixture Models for Marker Dosage in Autopolyploids",
  "Version": "0.6-5",
  "Date": "2026-02-22",
  "Authors@R": "c(\nperson(given = \"Peter\",\nfamily = \"Baker\",\nrole = c(\"aut\", \"cre\"),\nemail = \"drpetebaker@gmail.com\",\ncomment = c(ORCID = \"0000-0002-1241-7263\")))",
  "Description": "Fits Bayesian mixture models to estimate marker dosage for\ndominant markers in autopolyploids using JAGS (1.0 or greater)\nas outlined in Baker et al \"Bayesian estimation of marker\ndosage in sugarcane and other autopolyploids\" (2010,\n<doi:10.1007/s00122-010-1283-z>). May be used in conjunction\nwith polySegratio for simulation studies and comparison with\nstandard methods.",
  "LazyData": "true",
  "URL": "https://github.com/petebaker/polysegratiomm",
  "BugReports": "https://github.com/petebaker/polysegratiomm/issues",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "Repository": "https://petebaker.r-universe.dev",
  "Date/Publication": "2026-02-27 00:09:52 UTC",
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  "NeedsCompilation": "no",
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    "User": "root"
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  "Author": "Peter Baker [aut, cre] (ORCID: <https://orcid.org/0000-0002-1241-7263>)",
  "Maintainer": "Peter Baker <drpetebaker@gmail.com>",
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    "message": "Removed TODO since all issues fixed and not required\n",
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    "diagnosticsJagsMix",
    "DistributionPlotBinomial",
    "DistributionPlotGamma",
    "DistributionPlotNorm",
    "dosagesJagsMix",
    "dumpData",
    "dumpInits",
    "plot.runJagsWrapper",
    "plot.segratioMCMC",
    "plotFitted",
    "plotTheoretical",
    "print.dosagesMCMC",
    "print.runJags",
    "print.runJagsWrapper",
    "print.segratioMCMC",
    "readJags",
    "runJags",
    "runSegratioMM",
    "setControl",
    "setInits",
    "setModel",
    "setPriors",
    "summary.segratioMCMC",
    "writeControlFile",
    "writeJagsFile"
  ],
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      "name": "hexmarkers",
      "title": "Simulated autopolyploid dominant markers from 200 hexaploid individuals",
      "object": "hexmarkers",
      "class": [
        "simAutoMarkers"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hexmarkers.overdisp",
      "title": "Simulated overdispersed autopolyploid dominant markers from 200 hexaploid individuals",
      "object": "hexmarkers.overdisp",
      "class": [
        "simAutoMarkers"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mcmcHexRun",
      "title": "Results of MCMC estimation for simulated overdispersed markers",
      "object": "mcmcHexRun",
      "class": [
        "runJagsWrapper"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "polySegratioMM-package",
      "title": "Bayesian Mixture Models for Marker Dosage in Autopolyploids",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid",
        "polyploid"
      ],
      "topics": [
        "polySegratioMM-package",
        "polySegratioMM"
      ]
    },
    {
      "page": "calculateDIC",
      "title": "Compute DIC for fitted mixture model",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "calculateDIC"
      ]
    },
    {
      "page": "diagnosticsJagsMix",
      "title": "MCMC diagnostics for polyploid segregation ratio mixture models",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "diagnosticsJagsMix"
      ]
    },
    {
      "page": "DistributionPlotBinomial",
      "title": "Distribution Plot",
      "topics": [
        "DistributionPlotBinomial",
        "DistributionPlotGamma",
        "DistributionPlotNorm"
      ]
    },
    {
      "page": "dosagesJagsMix",
      "title": "Compute dosages under specified Bayesian mixture model",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "dosagesJagsMix",
        "dosagesMCMC"
      ]
    },
    {
      "page": "dumpData",
      "title": "Dumps segregation ratio data to file for subsequent JAGS run",
      "topics": [
        "dumpData"
      ]
    },
    {
      "page": "hexmarkers",
      "title": "Simulated autopolyploid dominant markers from 200 hexaploid individuals",
      "topics": [
        "hexmarkers"
      ]
    },
    {
      "page": "hexmarkers.overdisp",
      "title": "Simulated overdispersed autopolyploid dominant markers from 200 hexaploid individuals",
      "topics": [
        "hexmarkers.overdisp"
      ]
    },
    {
      "page": "mcmcHexRun",
      "title": "Results of MCMC estimation for simulated overdispersed markers",
      "topics": [
        "mcmcHexRun"
      ]
    },
    {
      "page": "plot.segratioMCMC",
      "title": "MCMC plots for segregation ratio mixture models",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "plot.segratioMCMC"
      ]
    },
    {
      "page": "plotFitted",
      "title": "Plot observed segregation ratios and fitted and theoretical models",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "plot.runJagsWrapper",
        "plotFitted",
        "plotTheoretical"
      ]
    },
    {
      "page": "print.dosagesMCMC",
      "title": "Doses from Bayesian mixture model",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "print.dosagesMCMC",
        "print.segratioMCMC"
      ]
    },
    {
      "page": "print.runJags",
      "title": "Running JAGS",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "print.runJags",
        "print.runJagsWrapper"
      ]
    },
    {
      "page": "readJags",
      "title": "Read MCMC sample(s) from a JAGS run",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "readJags",
        "segratioMCMC"
      ]
    },
    {
      "page": "runJags",
      "title": "Run JAGS to create MCMC sample for segregation ratio mixture model",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "runJags"
      ]
    },
    {
      "page": "runSegratioMM",
      "title": "Run a Bayesian mixture model for marker dosage with minimal effort",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
      "topics": [
        "runJagsWrapper",
        "runSegratioMM"
      ]
    },
    {
      "page": "setControl",
      "title": "Set up controls for a JAGS segregation ratio model run",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
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        "setControl"
      ]
    },
    {
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      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
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        "dumpInits",
        "setInits"
      ]
    },
    {
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      "title": "Set characteristics of the Bayesian mixture model for dosages",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
      ],
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        "modelSegratioMM",
        "setModel"
      ]
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      "concept": [
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        "dominant marker",
        "autopolyploid"
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      "concept": [
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        "dominant marker",
        "autopolyploid"
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        "summary.segratioMCMC",
        "summarySegratioMCMC"
      ]
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      "page": "writeControlFile",
      "title": "Write JAGS .cmd file for running JAGS",
      "concept": [
        "segregation ratio",
        "dominant marker",
        "autopolyploid"
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      "author": "Peter Baker",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Simulated data",
        "Fitting a mixture model",
        "Assigning marker dosage",
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        "References"
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