{
  "_id": "6ad1f131d3c80a766859c925",
  "Package": "coda",
  "Version": "0.19-4.1",
  "Date": "2020-09-30",
  "Title": "Output Analysis and Diagnostics for MCMC",
  "Authors@R": "c(person(\"Martyn\", \"Plummer\", role=c(\"aut\",\"cre\",\"trl\"),\nemail=\"martyn.plummer@gmail.com\"),\nperson(\"Nicky\", \"Best\", role=\"aut\"),\nperson(\"Kate\", \"Cowles\", role=\"aut\"),\nperson(\"Karen\", \"Vines\", role=\"aut\"),\nperson(\"Deepayan\", \"Sarkar\", role=\"aut\"),\nperson(\"Douglas\", \"Bates\", role=\"aut\"),\nperson(\"Russell\", \"Almond\", role=\"aut\"),\nperson(\"Arni\", \"Magnusson\", role=\"aut\"))",
  "Description": "Provides functions for summarizing and plotting the output\nfrom Markov Chain Monte Carlo (MCMC) simulations, as well as\ndiagnostic tests of convergence to the equilibrium distribution\nof the Markov chain.",
  "License": "GPL (>= 2)",
  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "Maintainer": "Martyn Plummer <martyn.plummer@gmail.com>",
  "Repository": "https://martynplummer.r-universe.dev",
  "Date/Publication": "2024-01-31 17:20:45 UTC",
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  "_exports": [
    "acfplot",
    "as.array.mcmc.list",
    "as.mcmc",
    "as.mcmc.list",
    "autocorr",
    "autocorr.diag",
    "autocorr.plot",
    "batchSE",
    "bugs2jags",
    "chanames",
    "coda.options",
    "codamenu",
    "crosscorr",
    "crosscorr.plot",
    "cumuplot",
    "densplot",
    "display.coda.options",
    "effectiveSize",
    "gelman.diag",
    "gelman.plot",
    "geweke.diag",
    "geweke.plot",
    "heidel.diag",
    "HPDinterval",
    "is.mcmc",
    "is.mcmc.list",
    "mcmc",
    "mcmc.list",
    "mcmcUpgrade",
    "mcpar",
    "multi.menu",
    "nchain",
    "niter",
    "nvar",
    "pcramer",
    "raftery.diag",
    "read.and.check",
    "read.coda",
    "read.coda.interactive",
    "read.jags",
    "read.openbugs",
    "rejectionRate",
    "spectrum0",
    "spectrum0.ar",
    "thin",
    "traceplot",
    "varnames",
    "varnames<-"
  ],
  "_datasets": [
    {
      "name": "line",
      "title": "Simple linear regression example",
      "object": "line",
      "file": "line.rda",
      "class": [
        "mcmc.list"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "as.ts.mcmc",
      "title": "Coerce mcmc object to time series",
      "topics": [
        "as.ts.mcmc"
      ]
    },
    {
      "page": "autocorr",
      "title": "Autocorrelation function for Markov chains",
      "topics": [
        "autocorr"
      ]
    },
    {
      "page": "autocorr.diag",
      "title": "Autocorrelation function for Markov chains",
      "topics": [
        "autocorr.diag",
        "autocorr.diag.mcmc",
        "autocorr.diag.mcmc.list"
      ]
    },
    {
      "page": "autocorr.plot",
      "title": "Plot autocorrelations for Markov Chains",
      "topics": [
        "autocorr.plot"
      ]
    },
    {
      "page": "batchSE",
      "title": "Batch Standard Error",
      "topics": [
        "batchSE"
      ]
    },
    {
      "page": "bugs2jags",
      "title": "Convert WinBUGS data file to JAGS data file",
      "topics": [
        "bugs2jags"
      ]
    },
    {
      "page": "coda.options",
      "title": "Options settings for the codamenu driver",
      "topics": [
        ".Coda.Options",
        ".Coda.Options.Default",
        "coda.options",
        "display.coda.options"
      ]
    },
    {
      "page": "codamenu",
      "title": "Main menu driver for the coda package",
      "topics": [
        "codamenu"
      ]
    },
    {
      "page": "Cramer",
      "title": "The Cramer-von Mises Distribution",
      "topics": [
        "pcramer"
      ]
    },
    {
      "page": "crosscorr",
      "title": "Cross correlations for MCMC output",
      "topics": [
        "crosscorr"
      ]
    },
    {
      "page": "crosscorr.plot",
      "title": "Plot image of correlation matrix",
      "topics": [
        "crosscorr.plot"
      ]
    },
    {
      "page": "cumuplot",
      "title": "Cumulative quantile plot",
      "topics": [
        "cumuplot"
      ]
    },
    {
      "page": "densplot",
      "title": "Probability density function estimate from MCMC output",
      "topics": [
        "densplot"
      ]
    },
    {
      "page": "effectiveSize",
      "title": "Effective sample size for estimating the mean",
      "topics": [
        "effectiveSize"
      ]
    },
    {
      "page": "gelman.diag",
      "title": "Gelman and Rubin's convergence diagnostic",
      "topics": [
        "gelman.diag"
      ]
    },
    {
      "page": "gelman.plot",
      "title": "Gelman-Rubin-Brooks plot",
      "topics": [
        "gelman.plot"
      ]
    },
    {
      "page": "geweke.diag",
      "title": "Geweke's convergence diagnostic",
      "topics": [
        "geweke.diag"
      ]
    },
    {
      "page": "geweke.plot",
      "title": "Geweke-Brooks plot",
      "topics": [
        "geweke.plot"
      ]
    },
    {
      "page": "heidel.diag",
      "title": "Heidelberger and Welch's convergence diagnostic",
      "topics": [
        "heidel.diag"
      ]
    },
    {
      "page": "HPDinterval",
      "title": "Highest Posterior Density intervals",
      "topics": [
        "HPDinterval",
        "HPDinterval.mcmc",
        "HPDinterval.mcmc.list"
      ]
    },
    {
      "page": "linepost",
      "title": "Simple linear regression example",
      "topics": [
        "line"
      ]
    },
    {
      "page": "mcmc",
      "title": "Markov Chain Monte Carlo Objects",
      "topics": [
        "as.mcmc",
        "as.mcmc.default",
        "is.mcmc",
        "mcmc",
        "print.mcmc"
      ]
    },
    {
      "page": "mcmc.convert",
      "title": "Conversions of MCMC objects",
      "topics": [
        "as.array.mcmc.list",
        "as.matrix.mcmc",
        "as.matrix.mcmc.list",
        "as.mcmc.mcmc.list"
      ]
    },
    {
      "page": "mcmc.list",
      "title": "Replicated Markov Chain Monte Carlo Objects",
      "topics": [
        "as.mcmc.list",
        "as.mcmc.list.default",
        "is.mcmc.list",
        "mcmc.list",
        "plot.mcmc.list"
      ]
    },
    {
      "page": "mcmc.subset",
      "title": "Extract or replace parts of MCMC objects",
      "topics": [
        "[.mcmc",
        "[.mcmc.list"
      ]
    },
    {
      "page": "mcmcUpgrade",
      "title": "Upgrade mcmc objects in obsolete format",
      "topics": [
        "mcmcUpgrade"
      ]
    },
    {
      "page": "mcpar",
      "title": "Mcpar attribute of MCMC objects",
      "topics": [
        "mcpar"
      ]
    },
    {
      "page": "multi.menu",
      "title": "Choose multiple options from a menu",
      "topics": [
        "multi.menu"
      ]
    },
    {
      "page": "nchain",
      "title": "Dimensions of MCMC objects",
      "topics": [
        "nchain",
        "niter",
        "nvar"
      ]
    },
    {
      "page": "plot.mcmc",
      "title": "Summary plots of mcmc objects",
      "topics": [
        "plot.mcmc"
      ]
    },
    {
      "page": "raftery.diag",
      "title": "Raftery and Lewis's diagnostic",
      "topics": [
        "raftery.diag"
      ]
    },
    {
      "page": "read.and.check",
      "title": "Read data interactively and check that it satisfies conditions",
      "topics": [
        "read.and.check"
      ]
    },
    {
      "page": "read.coda",
      "title": "Read output files in CODA format",
      "topics": [
        "read.coda",
        "read.jags"
      ]
    },
    {
      "page": "read.coda.interactive",
      "title": "Read CODA output files interactively",
      "topics": [
        "read.coda.interactive"
      ]
    },
    {
      "page": "read.openbugs",
      "title": "Read CODA output files produced by OpenBUGS",
      "topics": [
        "read.openbugs"
      ]
    },
    {
      "page": "rejectionRate",
      "title": "Rejection Rate for Metropolis-Hastings chains",
      "topics": [
        "rejectionRate",
        "rejectionRate.mcmc",
        "rejectionRate.mcmc.list"
      ]
    },
    {
      "page": "spectrum0",
      "title": "Estimate spectral density at zero",
      "topics": [
        "spectrum0"
      ]
    },
    {
      "page": "spectrum0.ar",
      "title": "Estimate spectral density at zero",
      "topics": [
        "spectrum0.ar"
      ]
    },
    {
      "page": "summary.mcmc",
      "title": "Summary statistics for Markov Chain Monte Carlo chains",
      "topics": [
        "summary.mcmc",
        "summary.mcmc.list"
      ]
    },
    {
      "page": "thin",
      "title": "Thinning interval",
      "topics": [
        "thin"
      ]
    },
    {
      "page": "time.mcmc",
      "title": "Time attributes for mcmc objects",
      "topics": [
        "end.mcmc",
        "end.mcmc.list",
        "frequency.mcmc",
        "start.mcmc",
        "start.mcmc.list",
        "thin.mcmc",
        "thin.mcmc.list",
        "time.mcmc",
        "time.mcmc.list"
      ]
    },
    {
      "page": "traceplot",
      "title": "Trace plot of MCMC output",
      "topics": [
        "traceplot"
      ]
    },
    {
      "page": "trellisplots",
      "title": "Trellis plots for mcmc objects",
      "topics": [
        "acfplot",
        "acfplot.mcmc",
        "acfplot.mcmc.list",
        "densityplot.mcmc",
        "densityplot.mcmc.list",
        "levelplot.mcmc",
        "levelplot.mcmc.list",
        "qqmath.mcmc",
        "qqmath.mcmc.list",
        "xyplot.mcmc",
        "xyplot.mcmc.list"
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    {
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      "title": "Named dimensions of MCMC objects",
      "topics": [
        "chanames",
        "chanames<-",
        "varnames",
        "varnames<-"
      ]
    },
    {
      "page": "window.mcmc",
      "title": "Time windows for mcmc objects",
      "topics": [
        "window.mcmc",
        "window.mcmc.list"
      ]
    }
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  "_nocasepkg": "coda",
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