{
  "_id": "6a10575facfb0bcc41ca2f6c",
  "Package": "dclone",
  "Type": "Package",
  "Title": "Data Cloning and MCMC Tools for Maximum Likelihood Methods",
  "Version": "2.3-3",
  "Date": "2025-07-12",
  "Authors@R": "c(person(given = \"Peter\",\nfamily = \"Solymos\",\ncomment = c(ORCID = \"0000-0001-7337-1740\"),\nrole = c(\"aut\", \"cre\"),\nemail = \"psolymos@gmail.com\"))",
  "Maintainer": "Peter Solymos <psolymos@gmail.com>",
  "Description": "Low level functions for implementing maximum likelihood\nestimating procedures for complex models using data cloning and\nBayesian Markov chain Monte Carlo methods as described in\nSolymos 2010 <doi:10.32614/RJ-2010-011>. Sequential and\nparallel MCMC support for 'JAGS', 'WinBUGS', 'OpenBUGS', and\n'Stan'.",
  "License": "GPL-2",
  "SystemRequirements": "none, one or more of JAGS (>= 3.0.0), WinBUGS (>=\n1.4), OpenBUGS (>= 3.2.2), Stan",
  "URL": "https://groups.google.com/forum/#!forum/dclone-users,\nhttps://datacloning.org, https://github.com/datacloning/dclone",
  "BugReports": "https://github.com/datacloning/dclone/issues",
  "LazyLoad": "yes",
  "LazyData": "true",
  "Config/pak/sysreqs": "make jags",
  "Repository": "https://psolymos.r-universe.dev",
  "Date/Publication": "2025-07-13 17:38:22 UTC",
  "RemoteUrl": "https://github.com/datacloning/dclone",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-09 07:22:49 UTC",
    "User": "root"
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  "Author": "Peter Solymos [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7337-1740>)",
  "MD5sum": "fc118781db605d996f26369033418763",
  "_user": "psolymos",
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  "_created": "2026-05-09T07:22:49.000Z",
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  "_topics": [
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    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_realowner": "datacloning",
  "_cranurl": true,
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    {
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      "date": "2016-03-12"
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      "date": "2018-02-04"
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    {
      "version": "2.3-0",
      "date": "2019-03-22"
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      "date": "2023-07-03"
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      "date": "2025-07-13"
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  "_exports": [
    ".dcFit",
    "as.mcmc.list.bugs",
    "bugs.fit",
    "bugs.parfit",
    "chisq.diag",
    "chisq.diag.mcmc.list",
    "clean.jags.model",
    "clearDcloneEnv",
    "clusterSize",
    "clusterSplitSB",
    "codaSamples",
    "coef.mcmc.list",
    "confint.mcmc.list.dc",
    "custommodel",
    "dc.fit",
    "dc.parfit",
    "dcdiag",
    "dcdiag.default",
    "dcdim",
    "dciid",
    "dclone",
    "dclone.dcdim",
    "dclone.dciid",
    "dclone.dctr",
    "dclone.default",
    "dclone.environment",
    "dclone.list",
    "dcoptions",
    "dcsd",
    "dcsd.mcmc.list",
    "dctable",
    "dctable.default",
    "dctr",
    "errlines",
    "errlines.default",
    "evalParallelArgument",
    "existsDcloneEnv",
    "extractdcdiag",
    "extractdcdiag.default",
    "extractdctable",
    "extractdctable.default",
    "jags.fit",
    "jags.parfit",
    "jagsModel",
    "lambdamax.diag",
    "lambdamax.diag.mcmc.list",
    "listDcloneEnv",
    "make.symmetric",
    "mclapplySB",
    "mcmcapply",
    "nclones",
    "nclones.default",
    "nclones.list",
    "pairs.mcmc.list",
    "parallel.inits",
    "parCodaSamples",
    "parDosa",
    "parJagsModel",
    "parLapplySB",
    "parLapplySLB",
    "parListFactories",
    "parListModules",
    "parLoadModule",
    "parSetFactory",
    "parUnloadModule",
    "parUpdate",
    "plot.dcdiag",
    "plot.dctable",
    "plotClusterSize",
    "pullDcloneEnv",
    "pushDcloneEnv",
    "quantile.mcmc.list",
    "stack.mcmc.list",
    "stan.fit",
    "stan.model",
    "stan.parfit",
    "update.mcmc.list",
    "updated.model",
    "vcov.mcmc.list",
    "vcov.mcmc.list.dc",
    "write.jags.model"
  ],
  "_datasets": [
    {
      "name": "ovenbird",
      "title": "Abundances of ovenbird in Alberta",
      "object": "ovenbird",
      "class": [
        "data.frame"
      ],
      "fields": [
        "count",
        "site",
        "year",
        "ecosite",
        "dsucc",
        "dalien",
        "long",
        "lat",
        "uplow",
        "thd"
      ],
      "rows": 182,
      "table": true,
      "tojson": true
    },
    {
      "name": "regmod",
      "title": "Exemplary MCMC list object",
      "object": "regmod",
      "class": [
        "mcmc.list"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "dclone-package",
      "title": "Data Cloning",
      "topics": [
        "dclone-package"
      ]
    },
    {
      "page": "dcFit",
      "title": "Internal function for iterative model fitting with data cloning",
      "topics": [
        ".dcFit"
      ]
    },
    {
      "page": "bugs.fit",
      "title": "Fit BUGS models with cloned data",
      "topics": [
        "as.mcmc.list.bugs",
        "bugs.fit"
      ]
    },
    {
      "page": "bugs.parfit",
      "title": "Parallel computing with WinBUGS/OpenBUGS",
      "topics": [
        "bugs.parfit"
      ]
    },
    {
      "page": "clusterSize",
      "title": "Optimizing the number of workers",
      "topics": [
        "clusterSize",
        "plotClusterSize"
      ]
    },
    {
      "page": "clusterSplitSB",
      "title": "Size balancing",
      "topics": [
        "clusterSplitSB",
        "parLapplySB",
        "parLapplySLB"
      ]
    },
    {
      "page": "codaSamples",
      "title": "Generate posterior samples in mcmc.list format",
      "topics": [
        "codaSamples"
      ]
    },
    {
      "page": "dc.fit",
      "title": "Iterative model fitting with data cloning",
      "topics": [
        "dc.fit"
      ]
    },
    {
      "page": "dc.parfit",
      "title": "Parallel model fitting with data cloning",
      "topics": [
        "dc.parfit"
      ]
    },
    {
      "page": "dclone",
      "title": "Cloning R objects",
      "topics": [
        "dcdim",
        "dciid",
        "dclone",
        "dclone.dcdim",
        "dclone.dciid",
        "dclone.dctr",
        "dclone.default",
        "dclone.environment",
        "dclone.list",
        "dctr"
      ]
    },
    {
      "page": "DcloneEnv",
      "title": "Manipulating dclone environments",
      "topics": [
        ".DcloneEnvModel",
        ".DcloneEnvResults",
        "clearDcloneEnv",
        "DcloneEnv",
        "existsDcloneEnv",
        "listDcloneEnv",
        "pullDcloneEnv",
        "pushDcloneEnv"
      ]
    },
    {
      "page": "dcoptions",
      "title": "Setting Options",
      "topics": [
        "dcoptions"
      ]
    },
    {
      "page": "dctable",
      "title": "Retrieve descriptive statistics from fitted objects to evaluate convergence",
      "topics": [
        "dcdiag",
        "dcdiag.default",
        "dctable",
        "dctable.default",
        "extractdcdiag",
        "extractdcdiag.default",
        "extractdctable",
        "extractdctable.default",
        "plot.dcdiag",
        "plot.dctable"
      ]
    },
    {
      "page": "errlines",
      "title": "Plot error bars",
      "topics": [
        "errlines",
        "errlines.default"
      ]
    },
    {
      "page": "evalParallelArgument",
      "title": "Evaluates parallel argument",
      "topics": [
        "evalParallelArgument"
      ]
    },
    {
      "page": "jags.fit",
      "title": "Fit JAGS models with cloned data",
      "topics": [
        "jags.fit"
      ]
    },
    {
      "page": "jags.parfit",
      "title": "Parallel computing with JAGS",
      "topics": [
        "jags.parfit"
      ]
    },
    {
      "page": "jagsModel",
      "title": "Create a JAGS model object",
      "topics": [
        "jagsModel"
      ]
    },
    {
      "page": "lambdamax.diag",
      "title": "Data Cloning Diagnostics",
      "topics": [
        "chisq.diag",
        "chisq.diag.mcmc.list",
        "lambdamax.diag",
        "lambdamax.diag.mcmc.list"
      ]
    },
    {
      "page": "make.symmetric",
      "title": "Make a square matrix symmetric by averaging.",
      "topics": [
        "make.symmetric"
      ]
    },
    {
      "page": "mclapplySB",
      "title": "Size balancing version of mclapply",
      "topics": [
        "mclapplySB"
      ]
    },
    {
      "page": "coef.mcmc.list",
      "title": "Methods for the 'mcmc.list' class",
      "topics": [
        "coef.mcmc.list",
        "confint.mcmc.list.dc",
        "dcsd",
        "dcsd.mcmc.list",
        "quantile.mcmc.list",
        "vcov.mcmc.list",
        "vcov.mcmc.list.dc"
      ]
    },
    {
      "page": "mcmcapply",
      "title": "Calculations on 'mcmc.list' objects",
      "topics": [
        "mcmcapply",
        "stack.mcmc.list"
      ]
    },
    {
      "page": "nclones",
      "title": "Number of Clones",
      "topics": [
        "nclones",
        "nclones.default",
        "nclones.list"
      ]
    },
    {
      "page": "ovenbird",
      "title": "Abundances of ovenbird in Alberta",
      "topics": [
        "ovenbird"
      ]
    },
    {
      "page": "pairs.mcmc.list",
      "title": "Scatterplot Matrices for 'mcmc.list' Objects",
      "topics": [
        "pairs.mcmc.list"
      ]
    },
    {
      "page": "parallel.inits",
      "title": "Parallel RNGs for initial values",
      "topics": [
        "parallel.inits"
      ]
    },
    {
      "page": "parCodaSamples",
      "title": "Generate posterior samples in 'mcmc.list' format on parallel workers",
      "topics": [
        "parCodaSamples"
      ]
    },
    {
      "page": "parDosa",
      "title": "Parallel wrapper function to call from within a function",
      "topics": [
        "parDosa"
      ]
    },
    {
      "page": "parJagsModel",
      "title": "Create a JAGS model object on parallel workers",
      "topics": [
        "parJagsModel"
      ]
    },
    {
      "page": "parLoadModule",
      "title": "Dynamically load JAGS modules on parallel workers",
      "topics": [
        "parListModules",
        "parLoadModule",
        "parUnloadModule"
      ]
    },
    {
      "page": "parSetFactory",
      "title": "Advanced control over JAGS on parallel workers",
      "topics": [
        "parListFactories",
        "parSetFactory"
      ]
    },
    {
      "page": "parUpdate",
      "title": "Update jags models on parallel workers",
      "topics": [
        "parUpdate"
      ]
    },
    {
      "page": "regmod",
      "title": "Exemplary MCMC list object",
      "topics": [
        "regmod"
      ]
    },
    {
      "page": "stan.fit",
      "title": "Fit Stan models with cloned data",
      "topics": [
        "stan.fit",
        "stan.model",
        "stan.parfit"
      ]
    },
    {
      "page": "update.mcmc.list",
      "title": "Automatic updating of an MCMC object from JAGS",
      "topics": [
        "update.mcmc.list",
        "updated.model"
      ]
    },
    {
      "page": "write.jags.model",
      "title": "Write and remove model file",
      "topics": [
        "clean.jags.model",
        "custommodel",
        "write.jags.model"
      ]
    }
  ],
  "_readme": "https://github.com/datacloning/dclone/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "BH",
    "boot",
    "callr",
    "checkmate",
    "cli",
    "coda",
    "cpp11",
    "desc",
    "distributional",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "inline",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "loo",
    "magrittr",
    "Matrix",
    "matrixStats",
    "numDeriv",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "posterior",
    "processx",
    "ps",
    "QuickJSR",
    "R2OpenBUGS",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppParallel",
    "rjags",
    "rlang",
    "rstan",
    "S7",
    "scales",
    "StanHeaders",
    "tensorA",
    "tibble",
    "utf8",
    "vctrs",
    "viridisLite",
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  "_sysdeps": [
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      "shlib": "libjags",
      "package": "jags",
      "headers": "jags",
      "source": "jags",
      "version": "4.3.2-2.2404.0",
      "name": "jags",
      "homepage": "https://mcmc-jags.sourceforge.io",
      "description": "Just Another Gibbs Sampler for Bayesian MCMC - binary\nJAGS is Just Another Gibbs Sampler.  It is a program for analysis of\nBayesian hierarchical models using Markov Chain Monte Carlo (MCMC)\nsimulation not wholly unlike BUGS.\n\nJAGS was written with three aims in mind:\n* To have an engine for the BUGS language that runs on Unix\n* To be extensible, allowing users to write their own functions,\ndistributions and samplers.\n* To be a plaftorm for experimentation with ideas in Bayesian modelling\n\nThis package contains the 'jags' binary as well as the associated\nshared library modules loaded by the binary."
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 7.0136544468779825,
  "_indexed": false,
  "_nocasepkg": "dclone",
  "_universes": [
    "psolymos"
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