{
  "_id": "6a49e0922c82cd361482563d",
  "Package": "baytaAAR",
  "Type": "Package",
  "Title": "Bayesian Transition Analysis with Markov Chain Monte Carlo",
  "Version": "1.0.3",
  "Authors@R": "c(person(given = \"Nils\", family = \"Müller-Scheeßel\",\nemail = \"nils.mueller-scheessel@ufg.uni-kiel.de\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-7992-8722\")),\nperson(given = \"Christoph\", family = \"Rinne\",\nemail = \"crinne@ufg.uni-kiel.de\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9829-6182\")))",
  "Maintainer": "Nils Müller-Scheeßel\n<nils.mueller-scheessel@ufg.uni-kiel.de>",
  "Description": "Provides Bayesian age estimation for bioarchaeological\nskeletal data using ordinal probit regression models\nimplemented in 'JAGS' and 'NIMBLE'. The package is designed to\nhandle multiple ordinal traits of adult individuals and\nincorporates a Gompertz prior on age to reflect\npopulation-level mortality. It accounts for estimation\nuncertainties and supports full customization of model\nparameters and Markov Chain Monte Carlo settings. For more\ndetails see Müller-Scheeßel et al. (2026)\n<doi:10.1002/ajpa.70289>.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "RdMacros": "Rdpack",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "URL": "https://github.com/ISAAKiel/baytaAAR,\nhttps://isaakiel.github.io/baytaAAR/",
  "BugReports": "https://github.com/ISAAKiel/baytaAAR/issues",
  "Config/Needs/website": "rmarkdown",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-15 15:55:15 UTC",
    "User": "root"
  },
  "Author": "Nils Müller-Scheeßel [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-7992-8722>), Christoph Rinne [aut]\n(ORCID: <https://orcid.org/0000-0002-9829-6182>)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-06-15 14:40:21 UTC",
  "RemoteUrl": "https://github.com/cran/baytaAAR",
  "RemoteRef": "HEAD",
  "RemoteSha": "e006a1ec1e304750c8290dabfbf72be23753fa5e",
  "_user": "cran",
  "_type": "src",
  "_file": "baytaAAR_1.0.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/b041ac49d02498fea8ffe4fa6c16a52e925765b3649d1828edca20ef6bb9a81a",
  "_filesize": 3483219,
  "_sha256": "b041ac49d02498fea8ffe4fa6c16a52e925765b3649d1828edca20ef6bb9a81a",
  "_expires": "2026-10-13T04:41:52.000Z",
  "_created": "2026-06-15T15:55:15.000Z",
  "_published": "2026-07-05T04:41:54.128Z",
  "_jobs": [
    {
      "job": 85193249706,
      "time": 192,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7643635328"
    },
    {
      "job": 85193249879,
      "time": 181,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7643632805"
    },
    {
      "job": 85193249647,
      "time": 335,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7643548490"
    },
    {
      "job": 85193249690,
      "time": 149,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7643617990"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/27558441915",
  "_status": "success",
  "_upstream": "https://github.com/cran/baytaAAR",
  "_commit": {
    "id": "e006a1ec1e304750c8290dabfbf72be23753fa5e",
    "author": "Nils Müller-Scheeßel <nils.mueller-scheessel@ufg.uni-kiel.de>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.3\n",
    "time": 1781534421
  },
  "_maintainer": {
    "name": "Nils Müller-Scheeßel",
    "email": "nils.mueller-scheessel@ufg.uni-kiel.de",
    "orcid": "0000-0001-7992-8722"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "nimble",
      "role": "Depends"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "Rdpack",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "scoringRules",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "flexsurv",
      "role": "Imports"
    },
    {
      "package": "coda",
      "role": "Imports"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "withr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "gridExtra",
      "role": "Suggests"
    },
    {
      "package": "bayesplot",
      "role": "Suggests"
    },
    {
      "package": "tidybayes",
      "role": "Suggests"
    },
    {
      "package": "rjags",
      "role": "Suggests"
    },
    {
      "package": "runjags",
      "role": "Suggests"
    },
    {
      "package": "ggridges",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-25",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.0.3",
      "date": "2026-06-15"
    }
  ],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 609,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/baytaAAR"
  },
  "_devurl": "https://github.com/isaakiel/baytaaar",
  "_pkgdown": "https://isaakiel.github.io/baytaAAR/",
  "_searchresults": 6,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/baytaAAR.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.3",
      "date": "2026-06-15"
    }
  ],
  "_exports": [
    "age.comp.plot",
    "age.comp.summary",
    "age.estim.summary",
    "bay.ta",
    "bay.ta.jags",
    "bay.ta.nimble",
    "corr.mat.mean",
    "diagnostic.summary",
    "diagnostics.max.min",
    "prob.cat",
    "sequential.binom.test",
    "threshold.chains",
    "threshold.matrix"
  ],
  "_datasets": [
    {
      "name": "sorsum_as",
      "title": "Sorsum: Example dataset",
      "object": "sorsum_as",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "auricular_surface"
      ],
      "rows": 38,
      "table": true,
      "tojson": true
    },
    {
      "name": "spitalfields",
      "title": "Spitalfields: Example dataset",
      "object": "spitalfields",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "TO",
        "ST",
        "MI",
        "MA",
        "AP",
        "Sex"
      ],
      "rows": 180,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "age.comp.plot",
      "title": "Plots of quality measures of age estimation",
      "topics": [
        "age.comp.plot"
      ]
    },
    {
      "page": "age.comp.summary",
      "title": "Quality measures of age estimation",
      "topics": [
        "age.comp.summary"
      ]
    },
    {
      "page": "age.estim.summary",
      "title": "Summary of age estimates",
      "topics": [
        "age.estim.summary"
      ]
    },
    {
      "page": "bay.ta",
      "title": "Bayesian Transition Analysis with JAGS or NIMBLE",
      "topics": [
        "bay.ta"
      ]
    },
    {
      "page": "corr.mat.mean",
      "title": "Extract correlation matrix from Cholesky factor",
      "topics": [
        "corr.mat.mean"
      ]
    },
    {
      "page": "diagnostic.summary",
      "title": "Diagnostic summary of MCMC samples",
      "topics": [
        "diagnostic.summary"
      ]
    },
    {
      "page": "diagnostics.max.min",
      "title": "Maximum and minimum diagnostic values",
      "topics": [
        "diagnostics.max.min"
      ]
    },
    {
      "page": "prob.cat",
      "title": "Summed or mean probability densities per category",
      "topics": [
        "prob.cat"
      ]
    },
    {
      "page": "sequential.binom.test",
      "title": "Sequential cumulative binomial test",
      "topics": [
        "sequential.binom.test"
      ]
    },
    {
      "page": "sorsum_as",
      "title": "Sorsum: Example dataset",
      "concept": [
        "examples"
      ],
      "topics": [
        "sorsum_as"
      ]
    },
    {
      "page": "spitalfields",
      "title": "Spitalfields: Example dataset",
      "concept": [
        "examples"
      ],
      "topics": [
        "spitalfields"
      ]
    },
    {
      "page": "threshold.chains",
      "title": "Compute thresholds for chains",
      "topics": [
        "threshold.chains"
      ]
    },
    {
      "page": "threshold.matrix",
      "title": "Extract thresholds",
      "topics": [
        "threshold.matrix"
      ]
    }
  ],
  "_pkglogo": "https://github.com/cran/baytaAAR/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/cran/baytaAAR/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "assertthat",
    "backports",
    "bbmle",
    "bdsmatrix",
    "boot",
    "broom",
    "car",
    "carData",
    "checkmate",
    "cli",
    "coda",
    "colorspace",
    "corrplot",
    "cowplot",
    "cpp11",
    "data.table",
    "Deriv",
    "deSolve",
    "doBy",
    "dplyr",
    "evaluate",
    "farver",
    "fastGHQuad",
    "flexsurv",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "igraph",
    "isoband",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "lsoda",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "mstate",
    "muhaz",
    "mvtnorm",
    "nimble",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "polynom",
    "pracma",
    "purrr",
    "quadprog",
    "quantreg",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "rstatix",
    "rstpm2",
    "S7",
    "scales",
    "scoringRules",
    "SparseM",
    "statmod",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "computation_framework.Rmd",
      "filename": "computation_framework.html",
      "title": "Computation framework",
      "engine": "knitr::rmarkdown",
      "headings": [
        "JAGS vs. NIMBLE vs. Stan",
        "Parallel processing and number of chains",
        "References"
      ],
      "created": "2026-06-15 14:40:21",
      "modified": "2026-06-15 14:40:21",
      "commits": 1
    },
    {
      "source": "data_preparation.Rmd",
      "filename": "data_preparation.html",
      "title": "Data input",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2026-06-15 14:40:21",
      "modified": "2026-06-15 14:40:21",
      "commits": 1
    },
    {
      "source": "baytaAAR.Rmd",
      "filename": "baytaAAR.html",
      "title": "Introduction to baytaAAR",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Load libraries",
        "Introduction",
        "Data layout",
        "Running a first analysis",
        "Running the analysis with JAGS",
        "Going further",
        "References"
      ],
      "created": "2026-06-15 14:40:21",
      "modified": "2026-06-15 14:40:21",
      "commits": 1
    },
    {
      "source": "mathematical_background.Rmd",
      "filename": "mathematical_background.html",
      "title": "Mathematical background",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Benjamin Gompertz and the Gompertz distribution",
        "The Gompertz distribution with NIMBLE and JAGS",
        "Mathematical notation",
        "References"
      ],
      "created": "2026-06-15 14:40:21",
      "modified": "2026-06-15 14:40:21",
      "commits": 1
    },
    {
      "source": "known_age.Rmd",
      "filename": "known_age.html",
      "title": "Spitalfields: Comparison with known age-at-death",
      "engine": "knitr::rmarkdown",
      "headings": [
        "References"
      ],
      "created": "2026-06-15 14:40:21",
      "modified": "2026-06-15 14:40:21",
      "commits": 1
    }
  ],
  "_score": 3.3979400086720375,
  "_indexed": true,
  "_nocasepkg": "baytaaar",
  "_universes": [
    "cran",
    "isaakiel"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-06-15T15:57:55.000Z",
      "distro": "noble",
      "commit": "e006a1ec1e304750c8290dabfbf72be23753fa5e",
      "fileid": "https://r2.ropensci.org/f1b9d7408354239d21d5412c03c299e2aea1f40737b8b0584d2df4b0440e8e84",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/27558441915"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-06-15T15:57:53.000Z",
      "distro": "noble",
      "commit": "e006a1ec1e304750c8290dabfbf72be23753fa5e",
      "fileid": "https://r2.ropensci.org/32aae36d8bee2330329cfec7008b5447c82b37a2354000f34824b5cb4c05eefc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/27558441915"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.3",
      "date": "2026-06-15T15:58:07.000Z",
      "commit": "e006a1ec1e304750c8290dabfbf72be23753fa5e",
      "fileid": "https://r2.ropensci.org/94953e0f5b06d76e10a046b09d0d96ef428b8c46a36390a7cbe83a33eb1f3e04",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/27558441915"
    }
  ]
}