Package: BayLum 0.3.3

Anne Philippe

BayLum: Chronological Bayesian Models Integrating Optically Stimulated Luminescence and Radiocarbon Age Dating

Bayesian analysis of luminescence data and C-14 age estimates. Bayesian models are based on the following publications: Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003> and Combes et al. (2015) <doi:10.1016/j.quageo.2015.04.001>. This includes, amongst others, data import, export, application of age models and palaeodose model.

Authors:Claire Christophe [aut], Anne Philippe [aut, cre], Sebastian Kreutzer [aut], Guillaume Guérin [aut], Frederik Harly Baumgarten [aut], Nicolas Frerebeau [aut], Université Bordeaux Montaigne [cph, fnd], CNRS [fnd], LabEx Sciences archéologiques de Bordeaux [fnd]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BayLum/json (API)

# Install 'BayLum' in R:
install.packages('BayLum', repos = c('https://crp2a.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/crp2a/baylum/issues

Pkgdown/docs site:https://crp2a.github.io

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • AgeS - Output of 'AgeS_Computation' function for the samples: "GDB5" and "GDB3"
  • DATA_C14 - C14 cal age estiamte and its error
  • DATA1 - DATA of sample named GDB3
  • DATA2 - DATA on sample named GDB5
  • DATA3 - DATA of sample named FER1
  • IntCal13 - Atmospheric North data for calibration of 14C age
  • IntCal20 - Atmospheric North data for calibration of 14C age
  • Marine13 - Marine data for calibration of 14C age
  • Marine20 - Marine data for calibration of 14C age
  • MCMCsample - MCMC sample from the posterior distribution of the dataset GDB5
  • Model_Age - JAGS models use in 'Age_Computation'
  • Model_AgeC14 - JAGS models use in 'AgeC14_Computation'
  • Model_AgeS - JAGS models use in 'AgeS_Computation'
  • Model_Palaeodose - JAGS models use in 'Palaeodose_Computation'
  • ModelC14 - Likelihood of C14 samples for JAGS models use in 'Age_OSLC14'
  • ModelOSL - Likelihood of OSL samples for JAGS models use in 'Age_OSLC14'
  • ModelPrior - Prior for JAGS models use in 'Age_OSLC14'
  • SHCal13 - Atmospheric South data for calibration of 14C age
  • SHCal20 - Atmospheric South data for calibration of 14C age

On CRAN:

Conda:

archaeometrybayesian-statisticsgeochronologyluminescence-datingradiocarbon-datesjagscpp

6.26 score 9 stars 40 scripts 320 downloads 1 mentions 22 exports 36 dependencies

Last updated from:9844fafdf1 (on v0.3.3). Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK143
source / vignettesOK225
linux-release-x86_64OK127
macos-release-arm64OK133
macos-oldrel-arm64OK125
windows-develOK103
windows-releaseOK96
windows-oldrelOK111
wasm-releaseOK117

Exports:Age_ComputationAge_OSLC14AgeC14_ComputationAgeS_Computationcombine_DataFilesConcat_DataFilecreate_DataFilecreate_FolderTemplatescreate_ThetaMatrixGenerate_DataFileGenerate_DataFile_MGLT_RegenDosePalaeodose_Computationplot_Agesplot_MCMCplot_RegDosePointsplot_ScatterplotsSC_OrderedScatterSamplesSCMatrixwrite_BayLumFileswrite_YAMLConfigFile

Dependencies:askpassbbmlebdsmatrixclicodacurldata.tabledeldirDEoptimhexbinhttrinterpjsonliteKernSmoothlamWlatticeLuminescenceMASSMatrixmatrixStatsmclustmimeminpack.lmmvtnormnumDerivopensslR6RcppRcppEigenRcppParallelrjagsrunjagsshapesysXMLyaml

BayLum: An Introduction
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
Rendered fromBayLum.Rmdusingknitr::rmarkdown

Last update: 2025-09-19
Started: 2017-06-01

BayLum: Specification of the YAML config file
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
Rendered fromConfigFile_Specification.Rmdusingknitr::rmarkdown

Last update: 2024-09-17
Started: 2023-08-03

Readme and manuals

Help Manual

Help pageTopics
Bayesian analysis for the OSL age estimation of one sampleAge_Computation
Bayesian analysis for age estimation of OSL measurements and C-14 ages of various samplesAge_OSLC14
Bayesian analysis for C-14 age estimations of various samplesAgeC14_Computation
Output of 'AgeS_Computation' function for the samples: "GDB5" and "GDB3"AgeS
Bayesian analysis for OSL age estimation of various samplesAgeS_Computation
Combine objectscombine_DataFiles Concat_DataFile
Prepare input data for subsequent BayLum Analysiscreate_DataFile
Create Folder Templatescreate_FolderTemplates
Create Theta Matrixcreate_ThetaMatrix
C14 cal age estiamte and its errorDATA_C14
DATA of sample named GDB3DATA1
DATA on sample named GDB5DATA2
DATA of sample named FER1DATA3
Generates, from one (or several) BIN file(s) of Multi-grain OSL measurements a list of luminescence data and information before statistical analysis (DEPRECATED)Generate_DataFile_MG Generate_DataFile_MG-deprecated
Generates, from one (or several) BIN-file(s) of Single-grain OSL measurements, a list of luminescence data and information before statistical analysis (DEPRECATED)Generate_DataFile Generate_DataFile-deprecated
Atmospheric North data for calibration of 14C ageIntCal13
Atmospheric North data for calibration of 14C ageIntCal20
Plots Lx/Tx as a function of the regenerative dose (DEPRECATED)LT_RegenDose LT_RegenDose-deprecated
Marine data for calibration of 14C ageMarine13
Marine data for calibration of 14C ageMarine20
MCMC sample from the posterior distribution of the dataset GDB5MCMCsample
JAGS models use in 'Age_Computation'Model_Age
JAGS models use in 'AgeC14_Computation'Model_AgeC14
JAGS models use in 'AgeS_Computation'Model_AgeS
JAGS models use in 'Palaeodose_Computation'Model_Palaeodose
Likelihood of C14 samples for JAGS models use in 'Age_OSLC14'ModelC14
Likelihood of OSL samples for JAGS models use in 'Age_OSLC14'ModelOSL
Prior for JAGS models use in 'Age_OSLC14'ModelPrior
Bayesian analysis for the palaeodose estimation of various samplesPalaeodose_Computation
Create Age Plotplot_Ages
Plot MCMC trajectories and posterior distributionsplot_MCMC
Plot Regeneration Dose Pointsplot_RegDosePoints
Display Scatter Plot Matrix of the Bayesian Age Resultsplot_Scatterplots ScatterSamples
Create Stratigraphically Ordered Sample MatrixSC_Ordered
Construct the Stratigraphic Constrain Matrix InteractivelySCMatrix
Atmospheric South data for calibration of 14C ageSHCal13
Atmospheric South data for calibration of 14C ageSHCal20
Write BayLum .csv-fileswrite_BayLumFiles
Write Auto Generated YAML BayLum Configuration File to the Discwrite_YAMLConfigFile