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  "Package": "runjags",
  "Title": "Interface Utilities, Model Templates, Parallel Computing Methods\nand Additional Distributions for MCMC Models in JAGS",
  "Version": "2.2.2-5",
  "Date": "2025-04-09",
  "Authors@R": "c(person(\"Matthew\", \"Denwood\", role=c(\"aut\",\"cre\"), email=\"md@sund.ku.dk\"),\nperson(\"Martyn\", \"Plummer\", role=\"cph\",\ncomment=\"Copyright holder of the code in src/distributions/DPar1.*, configure.ac, R/rjags_functions.R, and original copyright holder of some modified code where indicated\"))",
  "Description": "User-friendly interface utilities for MCMC models via Just\nAnother Gibbs Sampler (JAGS), facilitating the use of parallel\n(or distributed) processors for multiple chains, automated\ncontrol of convergence and sample length diagnostics, and\nevaluation of the performance of a model using drop-k\nvalidation or against simulated data. Template model\nspecifications can be generated using a standard lme4-style\nformula interface to assist users less familiar with the BUGS\nsyntax.  A JAGS extension module provides additional\ndistributions including the Pareto family of distributions, the\nDuMouchel prior and the half-Cauchy prior.",
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      "date": "2015-04-14"
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      "date": "2015-09-14"
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      "date": "2016-03-31"
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    "add.summary",
    "as.jags",
    "as.runjags",
    "ask",
    "autoextend.jags",
    "autoextend.JAGS",
    "autorun.jags",
    "autorun.JAGS",
    "cleanup.jags",
    "cleanup.JAGS",
    "combine.jags",
    "combine.JAGS",
    "combine.mcmc",
    "combine.MCMC",
    "contrasts.mcmc",
    "contrasts.MCMC",
    "divide.jags",
    "divide.JAGS",
    "drop.k",
    "drop.k.jags",
    "drop.k.JAGS",
    "dump.format",
    "extend.jags",
    "extend.JAGS",
    "extract",
    "extract.runjags",
    "failed.jags",
    "failed.JAGS",
    "failedjags",
    "findjags",
    "findJAGS",
    "is.runjags",
    "list.format",
    "load.runjagsmodule",
    "load.runJAGSmodule",
    "new_unique",
    "prec2sd",
    "read.jagsfile",
    "read.JAGSfile",
    "read.winbugs",
    "read.WinBUGS",
    "results.jags",
    "results.JAGS",
    "run.jags",
    "run.JAGS",
    "run.jags.study",
    "run.JAGS.study",
    "runjags.getOption",
    "runjags.options",
    "template_huiwalter",
    "template.jags",
    "template.JAGS",
    "testjags",
    "testJAGS",
    "timestring",
    "unload.runjagsmodule",
    "unload.runJAGSmodule",
    "write.jagsfile",
    "write.JAGSfile"
  ],
  "_help": [
    {
      "page": "add.summary",
      "title": "Summary statistics and plot methods for runjags class objects",
      "topics": [
        "add.summary",
        "plot.runjags",
        "plot.runjagsplots",
        "print.runjags",
        "print.runjagsplots",
        "summary.runjags"
      ]
    },
    {
      "page": "ask",
      "title": "Obtain Input from User With Error Handling",
      "topics": [
        "ask"
      ]
    },
    {
      "page": "autorun.jags",
      "title": "Run or extend a user-specified Bayesian MCMC model in JAGS with automatically calculated run-length and convergence diagnostics",
      "topics": [
        "autoextend.JAGS",
        "autoextend.jags",
        "autorun.JAGS",
        "autorun.jags"
      ]
    },
    {
      "page": "combine.mcmc",
      "title": "Combining and dividing runjags and MCMC objects",
      "topics": [
        "combine.JAGS",
        "combine.jags",
        "combine.MCMC",
        "combine.mcmc",
        "divide.JAGS",
        "divide.jags"
      ]
    },
    {
      "page": "dump.list.format",
      "title": "Conversion Between a Named List and a Character String in the R Dump Format",
      "topics": [
        "dump.format",
        "dump.list.format",
        "list.format"
      ]
    },
    {
      "page": "extract.runjags",
      "title": "Extract peripheral information from runjags objects",
      "topics": [
        "dic.runjags",
        "extract",
        "extract.jags",
        "extract.runjags"
      ]
    },
    {
      "page": "findjags",
      "title": "Attempt to Locate a JAGS Install",
      "topics": [
        "findJAGS",
        "findjags"
      ]
    },
    {
      "page": "load.runjagsmodule",
      "title": "Load the internal JAGS module provided by runjags",
      "topics": [
        "load.runJAGSmodule",
        "load.runjagsmodule",
        "unload.runJAGSmodule",
        "unload.runjagsmodule"
      ]
    },
    {
      "page": "mutate.functions",
      "title": "Mutate functions to be used with runjags summary methods",
      "topics": [
        "contrasts.MCMC",
        "contrasts.mcmc",
        "mutate.functions",
        "prec2sd"
      ]
    },
    {
      "page": "new_unique",
      "title": "Create a Unique Filename",
      "topics": [
        "new_unique"
      ]
    },
    {
      "page": "read.jagsfile",
      "title": "Extract Any Models, Data, Monitored Variables or Initial Values As Character Vectors from a JAGS or WinBUGS Format Textfile",
      "topics": [
        "read.JAGSfile",
        "read.jagsfile",
        "read.WinBUGS",
        "read.winbugs"
      ]
    },
    {
      "page": "results.jags",
      "title": "Importing of saved JAGS simulations with partial error recovery",
      "topics": [
        "results.JAGS",
        "results.jags"
      ]
    },
    {
      "page": "run.jags",
      "title": "Run or extend a user-specified Bayesian MCMC model in JAGS from within R",
      "topics": [
        "extend.JAGS",
        "extend.jags",
        "run.JAGS",
        "run.jags"
      ]
    },
    {
      "page": "run.jags.study",
      "title": "Drop-k and simulated dataset studies using JAGS",
      "topics": [
        "drop.k",
        "drop.k.JAGS",
        "drop.k.jags",
        "run.JAGS.study",
        "run.jags.study"
      ]
    },
    {
      "page": "runjags-class",
      "title": "The runjags class and available S3 methods",
      "topics": [
        "as.jags",
        "as.jags.default",
        "as.jags.runjags",
        "as.mcmc.list.runjags",
        "as.mcmc.runjags",
        "as.runjags",
        "as.runjags.default",
        "as.runjags.jags",
        "cleanup.JAGS",
        "cleanup.jags",
        "failed.JAGS",
        "failed.jags",
        "failedjags",
        "fitted.runjags",
        "is.runjags",
        "predict.runjags",
        "residuals.runjags",
        "runjags-class",
        "runjagsclass",
        "runjagsstudy-class",
        "runjagsstudyclass"
      ]
    },
    {
      "page": "runjags.options",
      "title": "Options for the runjags package",
      "topics": [
        "runJAGS.getOption",
        "runjags.getOption",
        "runJAGS.options",
        "runjags.options"
      ]
    },
    {
      "page": "runjags.printmethods",
      "title": "Print methods for runjags helper classes",
      "topics": [
        "plot.runjagsstudy",
        "print.crosscorrstats",
        "print.dicstats",
        "print.failedjags",
        "print.gelman.with.target",
        "print.gelmanwithtarget",
        "print.mcsestats",
        "print.rjagsoutput",
        "print.runjagsbginfo",
        "print.runjagsdata",
        "print.runjagsinits",
        "print.runjagsmodel",
        "print.runjagsoutput",
        "print.runjagsstudy",
        "runjags.printmethods",
        "summary.runjagsstudy"
      ]
    },
    {
      "page": "template_huiwalter",
      "title": "Create a Hui-Walter model based on paired test data for an arbitrary number of tests and populations",
      "topics": [
        "template_huiwalter"
      ]
    },
    {
      "page": "template.jags",
      "title": "Generate a generalised linear mixed model (GLMM) specification in JAGS",
      "topics": [
        "template.JAGS",
        "template.jags"
      ]
    },
    {
      "page": "testjags",
      "title": "Analyse the System to Check That JAGS Is Installed",
      "topics": [
        "testJAGS",
        "testjags"
      ]
    },
    {
      "page": "timestring",
      "title": "Calculate the Elapsed Time in Sensible Units",
      "topics": [
        "timestring"
      ]
    },
    {
      "page": "write.jagsfile",
      "title": "Write a complete JAGS model to a text file",
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        "write.JAGSfile",
        "write.jagsfile"
      ]
    }
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      "filename": "quickjags.html",
      "title": "A quick-start guide to running models in JAGS",
      "engine": "knitr::knitr",
      "headings": [
        "A quick-start guide to using the runjags package",
        "Preparation",
        "Running models using run.jags",
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        "Generating a GLMM template",
        "Model evaluation",
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      "title": "Using the runjags package",
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        "Package functions",
        "Illustration of usage with a simulation study",
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