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BayLum

An R package for chronological Bayesian models integrated for Optically Stimulated (OSL) Luminescence Dating

Installation

To install the latest development builds directly from GitHub, run

if(!require("devtools"))
  install.packages("devtools")
devtools::install_github("crp2a/BayLum@master")

To install a developer build other than ‘master’, replace the term ‘master’ in the codeline by the name of the wanted developer build.

Please note that you need to have JAGS installed on your computer

Note

The package comes without any guarantee!

Please further note that this version is a development version and may change day by day. For stable branches please visit the package on CRAN ‘BayLum’.

Funding

The development of 'BayLum' was supported by LabEx LaScArBx (ANR -n.ANR-10-LABX-52) between 2015 and 2018 (in particular through the MAM and COVADIM projects).

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

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Version

Install

install.packages('BayLum')

Monthly Downloads

325

Version

0.3.2

License

GPL-3

Maintainer

Anne Philippe

Last Published

June 16th, 2024

Functions in BayLum (0.3.2)

DATA2

DATA on sample named GDB5
AgeS_Computation

Bayesian analysis for OSL age estimation of various samples
DATA3

DATA of sample named FER1
AgeC14_Computation

Bayesian analysis for C-14 age estimations of various samples
Age_OSLC14

Bayesian analysis for age estimation of OSL measurements and C-14 ages of various samples
Age_Computation

Bayesian analysis for the OSL age estimation of one sample
DATA1

DATA of sample named GDB3
BayLum-deprecated

Deprecated functions in package BayLum.
AgeS

Output of AgeS_Computation function for the samples: "GDB5" and "GDB3"
BayLum-package

Chronological Bayesian Models Integrating Optically Stimulated Luminescence and C-14 Dating

LT_RegenDose-deprecated

Plots Lx/Tx as a function of the regenerative dose (DEPRECATED)
Generate_DataFile-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)
DATA_C14

C14 cal age estiamte and its error
IntCal20

Atmospheric North data for calibration of 14C age
Marine20

Marine data for calibration of 14C age
Generate_DataFile_MG-deprecated

Generates, from one (or several) BIN file(s) of Multi-grain OSL measurements a list of luminescence data and information before statistical analysis (DEPRECATED)
IntCal13

Atmospheric North data for calibration of 14C age
Marine13

Marine data for calibration of 14C age
MCMCsample

MCMC sample from the posterior distribution of the dataset GDB5
ModelPrior

Prior for JAGS models use in Age_OSLC14
ModelOSL

Likelihood of OSL samples for JAGS models use in Age_OSLC14
Model_AgeS

JAGS models use in AgeS_Computation
ModelC14

Likelihood of C14 samples for JAGS models use in Age_OSLC14
SC_Ordered

Create Stratigraphically Ordered Sample Matrix
SHCal13

Atmospheric South data for calibration of 14C age
Model_Age

JAGS models use in Age_Computation
plot_MCMC

Plot MCMC trajectories and posterior distributions
SCMatrix

Construct the Stratigraphic Constrain Matrix Interactively
plot_RegDosePoints

Plot Regeneration Dose Points
Palaeodose_Computation

Bayesian analysis for the palaeodose estimation of various samples
plot_Scatterplots

Display Scatter Plot Matrix of the Bayesian Age Results
write_BayLumFiles

Write BayLum .csv-files
Model_Palaeodose

JAGS models use in Palaeodose_Computation
write_YAMLConfigFile

Write Auto Generated YAML BayLum Configuration File to the Disc
create_ThetaMatrix

Create Theta Matrix
plot_Ages

Create Age Plot
combine_DataFiles

Combine objects
SHCal20

Atmospheric South data for calibration of 14C age
create_DataFile

Prepare input data for subsequent BayLum Analysis
Model_AgeC14

JAGS models use in AgeC14_Computation
create_FolderTemplates

Create Folder Templates