{
  "_id": "6a1f20f1b401979e734204f7",
  "Package": "BayLum",
  "Type": "Package",
  "Title": "Chronological Bayesian Models Integrating Optically Stimulated\nLuminescence and Radiocarbon Age Dating",
  "Version": "0.3.3",
  "Date": "2025-09-19",
  "Authors@R": "c(\nperson(\"Claire\", \"Christophe\", role = \"aut\"),\nperson(\"Anne\", \"Philippe\", , \"anne.philippe@univ-nantes.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-5331-5087\")),\nperson(\"Sebastian\", \"Kreutzer\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-0734-2199\")),\nperson(\"Guillaume\", \"Guérin\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-6298-5579\")),\nperson(\"Frederik Harly\", \"Baumgarten\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-4374-5948\")),\nperson(\"Nicolas\", \"Frerebeau\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-5759-4944\")),\nperson(\"Université Bordeaux Montaigne\", role = c(\"cph\", \"fnd\")),\nperson(\"CNRS\", role = \"fnd\"),\nperson(\"LabEx Sciences archéologiques de Bordeaux\", role = \"fnd\")\n)",
  "Maintainer": "Anne Philippe <anne.philippe@univ-nantes.fr>",
  "Description": "Bayesian analysis of luminescence data and C-14 age\nestimates. Bayesian models are based on the following\npublications: Combes, B. & Philippe, A. (2017)\n<doi:10.1016/j.quageo.2017.02.003> and Combes et al. (2015)\n<doi:10.1016/j.quageo.2015.04.001>. This includes, amongst\nothers, data import, export, application of age models and\npalaeodose model.",
  "License": "GPL-3",
  "URL": "https://CRAN.r-project.org/package=BayLum,\nhttps://crp2a.github.io/BayLum/",
  "BugReports": "https://github.com/crp2a/BayLum/issues",
  "VignetteBuilder": "knitr",
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  "Repository": "https://crp2a.r-universe.dev",
  "Date/Publication": "2025-09-19 09:54:04 UTC",
  "RemoteUrl": "https://github.com/crp2a/BayLum",
  "RemoteRef": "v0.3.3",
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  "Packaged": {
    "Date": "2026-05-16 07:44:41 UTC",
    "User": "root"
  },
  "Author": "Claire Christophe [aut],\nAnne Philippe [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5331-5087>),\nSebastian Kreutzer [aut] (ORCID:\n<https://orcid.org/0000-0002-0734-2199>),\nGuillaume Guérin [aut] (ORCID: <https://orcid.org/0000-0001-6298-5579>),\nFrederik Harly Baumgarten [aut] (ORCID:\n<https://orcid.org/0000-0002-4374-5948>),\nNicolas Frerebeau [aut] (ORCID:\n<https://orcid.org/0000-0001-5759-4944>),\nUniversité Bordeaux Montaigne [cph, fnd],\nCNRS [fnd],\nLabEx Sciences archéologiques de Bordeaux [fnd]",
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  "_user": "crp2a",
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  "_created": "2026-05-16T07:44:41.000Z",
  "_published": "2026-06-02T18:29:05.122Z",
  "_distro": "noble",
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    "message": "Recompile vignettes\n",
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    "bayesian-statistics",
    "geochronology",
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    "cpp"
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    "name": "Archéosciences Bordeaux",
    "description": "Archaeological Science Laboratory at Bordeaux Montaigne University"
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  "_downloads": {
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BayLum"
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  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
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    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/crp2a/baylum",
  "_realowner": "crp2a",
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  "_releases": [
    {
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      "date": "2017-09-01"
    },
    {
      "version": "0.1.1",
      "date": "2017-09-07"
    },
    {
      "version": "0.1.2",
      "date": "2018-06-22"
    },
    {
      "version": "0.1.3",
      "date": "2018-09-19"
    },
    {
      "version": "0.2.0",
      "date": "2020-12-06"
    },
    {
      "version": "0.2.1",
      "date": "2022-02-21"
    },
    {
      "version": "0.3.1",
      "date": "2023-04-13"
    },
    {
      "version": "0.3.2",
      "date": "2024-06-16"
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    {
      "version": "0.3.3",
      "date": "2025-09-25"
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  ],
  "_exports": [
    "Age_Computation",
    "Age_OSLC14",
    "AgeC14_Computation",
    "AgeS_Computation",
    "combine_DataFiles",
    "Concat_DataFile",
    "create_DataFile",
    "create_FolderTemplates",
    "create_ThetaMatrix",
    "Generate_DataFile",
    "Generate_DataFile_MG",
    "LT_RegenDose",
    "Palaeodose_Computation",
    "plot_Ages",
    "plot_MCMC",
    "plot_RegDosePoints",
    "plot_Scatterplots",
    "SC_Ordered",
    "ScatterSamples",
    "SCMatrix",
    "write_BayLumFiles",
    "write_YAMLConfigFile"
  ],
  "_datasets": [
    {
      "name": "AgeS",
      "title": "Output of 'AgeS_Computation' function for the samples: \"GDB5\" and \"GDB3\"",
      "object": "AgeS",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "DATA_C14",
      "title": "C14 cal age estiamte and its error",
      "object": "DATA_C14",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "DATA1",
      "title": "DATA of sample named GDB3",
      "object": "DATA1",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "DATA2",
      "title": "DATA on sample named GDB5",
      "object": "DATA2",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "DATA3",
      "title": "DATA of sample named FER1",
      "object": "DATA3",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "IntCal13",
      "title": "Atmospheric North data for calibration of 14C age",
      "object": "IntCal13",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CAL.BP",
        "X14C.age",
        "Error"
      ],
      "rows": 5141,
      "table": true,
      "tojson": true
    },
    {
      "name": "IntCal20",
      "title": "Atmospheric North data for calibration of 14C age",
      "object": "IntCal20",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CAL.BP",
        "X14C.age",
        "Error"
      ],
      "rows": 9501,
      "table": true,
      "tojson": true
    },
    {
      "name": "Marine13",
      "title": "Marine data for calibration of 14C age",
      "object": "Marine13",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CAL.BP",
        "X14C.age",
        "Error"
      ],
      "rows": 4801,
      "table": true,
      "tojson": true
    },
    {
      "name": "Marine20",
      "title": "Marine data for calibration of 14C age",
      "object": "Marine20",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CAL.BP",
        "X14C.age",
        "Error"
      ],
      "rows": 5501,
      "table": true,
      "tojson": true
    },
    {
      "name": "MCMCsample",
      "title": "MCMC sample from the posterior distribution of the dataset GDB5",
      "object": "MCMCsample",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "D",
        "sD"
      ],
      "rows": 6000,
      "table": true,
      "tojson": true
    },
    {
      "name": "Model_Age",
      "title": "JAGS models use in 'Age_Computation'",
      "object": "Model_Age",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "Model_AgeC14",
      "title": "JAGS models use in 'AgeC14_Computation'",
      "object": "Model_AgeC14",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "Model_AgeS",
      "title": "JAGS models use in 'AgeS_Computation'",
      "object": "Model_AgeS",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "Model_Palaeodose",
      "title": "JAGS models use in 'Palaeodose_Computation'",
      "object": "Model_Palaeodose",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "ModelC14",
      "title": "Likelihood of C14 samples for JAGS models use in 'Age_OSLC14'",
      "object": "ModelC14",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "ModelOSL",
      "title": "Likelihood of OSL samples for JAGS models use in 'Age_OSLC14'",
      "object": "ModelOSL",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "ModelPrior",
      "title": "Prior for JAGS models use in 'Age_OSLC14'",
      "object": "ModelPrior",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "SHCal13",
      "title": "Atmospheric South data for calibration of 14C age",
      "object": "SHCal13",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CAL.BP",
        "X14C.age",
        "Error"
      ],
      "rows": 5141,
      "table": true,
      "tojson": true
    },
    {
      "name": "SHCal20",
      "title": "Atmospheric South data for calibration of 14C age",
      "object": "SHCal20",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CAL.BP",
        "X14C.age",
        "Error"
      ],
      "rows": 9501,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Age_Computation",
      "title": "Bayesian analysis for the OSL age estimation of one sample",
      "topics": [
        "Age_Computation"
      ]
    },
    {
      "page": "Age_OSLC14",
      "title": "Bayesian analysis for age estimation of OSL measurements and C-14 ages of various samples",
      "topics": [
        "Age_OSLC14"
      ]
    },
    {
      "page": "AgeC14_Computation",
      "title": "Bayesian analysis for C-14 age estimations of various samples",
      "topics": [
        "AgeC14_Computation"
      ]
    },
    {
      "page": "AgeS",
      "title": "Output of 'AgeS_Computation' function for the samples: \"GDB5\" and \"GDB3\"",
      "topics": [
        "AgeS"
      ]
    },
    {
      "page": "AgeS_Computation",
      "title": "Bayesian analysis for OSL age estimation of various samples",
      "topics": [
        "AgeS_Computation"
      ]
    },
    {
      "page": "combine_DataFiles",
      "title": "Combine objects",
      "topics": [
        "combine_DataFiles",
        "Concat_DataFile"
      ]
    },
    {
      "page": "create_DataFile",
      "title": "Prepare input data for subsequent BayLum Analysis",
      "topics": [
        "create_DataFile"
      ]
    },
    {
      "page": "create_FolderTemplates",
      "title": "Create Folder Templates",
      "topics": [
        "create_FolderTemplates"
      ]
    },
    {
      "page": "create_ThetaMatrix",
      "title": "Create Theta Matrix",
      "topics": [
        "create_ThetaMatrix"
      ]
    },
    {
      "page": "DATA_C14",
      "title": "C14 cal age estiamte and its error",
      "topics": [
        "DATA_C14"
      ]
    },
    {
      "page": "DATA1",
      "title": "DATA of sample named GDB3",
      "topics": [
        "DATA1"
      ]
    },
    {
      "page": "DATA2",
      "title": "DATA on sample named GDB5",
      "topics": [
        "DATA2"
      ]
    },
    {
      "page": "DATA3",
      "title": "DATA of sample named FER1",
      "topics": [
        "DATA3"
      ]
    },
    {
      "page": "Generate_DataFile_MG-deprecated",
      "title": "Generates, from one (or several) BIN file(s) of Multi-grain OSL measurements a list of luminescence data and information before statistical analysis (DEPRECATED)",
      "topics": [
        "Generate_DataFile_MG",
        "Generate_DataFile_MG-deprecated"
      ]
    },
    {
      "page": "Generate_DataFile-deprecated",
      "title": "Generates, from one (or several) BIN-file(s) of Single-grain OSL measurements, a list of luminescence data and information before statistical analysis (DEPRECATED)",
      "topics": [
        "Generate_DataFile",
        "Generate_DataFile-deprecated"
      ]
    },
    {
      "page": "IntCal13",
      "title": "Atmospheric North data for calibration of 14C age",
      "topics": [
        "IntCal13"
      ]
    },
    {
      "page": "IntCal20",
      "title": "Atmospheric North data for calibration of 14C age",
      "topics": [
        "IntCal20"
      ]
    },
    {
      "page": "LT_RegenDose-deprecated",
      "title": "Plots Lx/Tx as a function of the regenerative dose (DEPRECATED)",
      "topics": [
        "LT_RegenDose",
        "LT_RegenDose-deprecated"
      ]
    },
    {
      "page": "Marine13",
      "title": "Marine data for calibration of 14C age",
      "topics": [
        "Marine13"
      ]
    },
    {
      "page": "Marine20",
      "title": "Marine data for calibration of 14C age",
      "topics": [
        "Marine20"
      ]
    },
    {
      "page": "MCMCsample",
      "title": "MCMC sample from the posterior distribution of the dataset GDB5",
      "topics": [
        "MCMCsample"
      ]
    },
    {
      "page": "Model_Age",
      "title": "JAGS models use in 'Age_Computation'",
      "topics": [
        "Model_Age"
      ]
    },
    {
      "page": "Model_AgeC14",
      "title": "JAGS models use in 'AgeC14_Computation'",
      "topics": [
        "Model_AgeC14"
      ]
    },
    {
      "page": "Model_AgeS",
      "title": "JAGS models use in 'AgeS_Computation'",
      "topics": [
        "Model_AgeS"
      ]
    },
    {
      "page": "Model_Palaeodose",
      "title": "JAGS models use in 'Palaeodose_Computation'",
      "topics": [
        "Model_Palaeodose"
      ]
    },
    {
      "page": "ModelC14",
      "title": "Likelihood of C14 samples for JAGS models use in 'Age_OSLC14'",
      "topics": [
        "ModelC14"
      ]
    },
    {
      "page": "ModelOSL",
      "title": "Likelihood of OSL samples for JAGS models use in 'Age_OSLC14'",
      "topics": [
        "ModelOSL"
      ]
    },
    {
      "page": "ModelPrior",
      "title": "Prior for JAGS models use in 'Age_OSLC14'",
      "topics": [
        "ModelPrior"
      ]
    },
    {
      "page": "Palaeodose_Computation",
      "title": "Bayesian analysis for the palaeodose estimation of various samples",
      "topics": [
        "Palaeodose_Computation"
      ]
    },
    {
      "page": "plot_Ages",
      "title": "Create Age Plot",
      "topics": [
        "plot_Ages"
      ]
    },
    {
      "page": "plot_MCMC",
      "title": "Plot MCMC trajectories and posterior distributions",
      "topics": [
        "plot_MCMC"
      ]
    },
    {
      "page": "plot_RegDosePoints",
      "title": "Plot Regeneration Dose Points",
      "topics": [
        "plot_RegDosePoints"
      ]
    },
    {
      "page": "plot_Scatterplots",
      "title": "Display Scatter Plot Matrix of the Bayesian Age Results",
      "topics": [
        "plot_Scatterplots",
        "ScatterSamples"
      ]
    },
    {
      "page": "SC_Ordered",
      "title": "Create Stratigraphically Ordered Sample Matrix",
      "topics": [
        "SC_Ordered"
      ]
    },
    {
      "page": "SCMatrix",
      "title": "Construct the Stratigraphic Constrain Matrix Interactively",
      "topics": [
        "SCMatrix"
      ]
    },
    {
      "page": "SHCal13",
      "title": "Atmospheric South data for calibration of 14C age",
      "topics": [
        "SHCal13"
      ]
    },
    {
      "page": "SHCal20",
      "title": "Atmospheric South data for calibration of 14C age",
      "topics": [
        "SHCal20"
      ]
    },
    {
      "page": "write_BayLumFiles",
      "title": "Write BayLum .csv-files",
      "topics": [
        "write_BayLumFiles"
      ]
    },
    {
      "page": "write_YAMLConfigFile",
      "title": "Write Auto Generated YAML BayLum Configuration File to the Disc",
      "topics": [
        "write_YAMLConfigFile"
      ]
    }
  ],
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    "matrixStats",
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    "R6",
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    "RcppEigen",
    "RcppParallel",
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  ],
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      "headers": "jags",
      "source": "jags",
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      "name": "jags",
      "homepage": "https://mcmc-jags.sourceforge.io",
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    {
      "source": "BayLum.Rmd",
      "filename": "BayLum.html",
      "title": "BayLum: An Introduction",
      "author": "Claire Christophe, Anne Philippe, Sebastian Kreutzer, Guillaume Guérin, Frederik Baumgarten",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installing `BayLum' package",
        "First steps: age analysis of one sample",
        "Option 1: Import information from a BIN/BINX-file.",
        "Remarks",
        "Data import/export",
        "Data structure",
        "Visualise Lx/Tx values and dose points",
        "Generate data file from BIN/BINX-files of multi-grain OSL measurements",
        "Option 2: Import data using create_DataFile()",
        "Age computation",
        "Remark 1: MCMC trajectories",
        "Remark 2: LIN_fit and Origin_fit, dose-response curves option",
        "Remark 3: distribution, equivalent dose dispersion option",
        "Remark 4: SavePdf and SaveEstimates option",
        "Remark 4: PriorAge option",
        "Multiple BIN/BINX-files for one sample",
        "Age analysis of various samples",
        "Generate data file from BIN/BINX-files",
        "Combine files using the function combine_DataFiles()",
        "Age analysis without stratigraphic constraints",
        "Age analysis with stratigraphic constraints",
        "Ordering samples",
        "Define matrix to set stratigraphic constraints",
        "When MCMC trajectories did not converge",
        "References",
        "Further reading",
        "For more details on the diagnostic of Markov chains",
        "For details on the here used dataset"
      ],
      "created": "2017-06-01 10:06:23",
      "modified": "2025-09-19 09:54:04",
      "commits": 40
    },
    {
      "source": "ConfigFile_Specification.Rmd",
      "filename": "ConfigFile_Specification.html",
      "title": "BayLum: Specification of the YAML config file",
      "author": "Sebastian Kreutzer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Background and scope",
        "Key concepts",
        "Examples and detailed specifications",
        "A single sample entry",
        "Multiple records",
        "Paramter specifcation",
        "Top level (sample, files)",
        "sample",
        "files",
        "settings level",
        "rules level",
        "Final remarks",
        "Auto-generate the config file using write_YAMLConfigFile()",
        "Show available parameters",
        "Write YAML file",
        "Internals"
      ],
      "created": "2023-08-03 09:29:34",
      "modified": "2024-09-17 23:13:03",
      "commits": 5
    }
  ],
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