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) and Combes et al (2015) . This includes, amongst others, data import, export, application of age models and palaeodose model.


News

BayLum 0.1.3 (Release date: 2018-09-14)

New functions

  • plot_Ages() this function replaces code used internally by the functions AgeC14_Compution() and AgeS_Computation() to create an age overview plot. Before the user had no control over the appearance of age plot output. This is still the case if the functions AgeC14_Compution(), AgeS_Computation() and Age_OSLC14() are used (although internally only the function plot_Ages() is called), however, both functions now return a new list of class BayLum.list which is recognised by the function plot_Ages() and can be used to plot the typical age plot while providing several arguments for adjusting the plot output.

Bugfixes & changes

  • The newly introduced function combine_DataFiles() did not work on R < 3.5.0, which caused an error on CRAN; fixed.
  • The function ScatterSamples() is replaced by the function plot_Scatterplots()
  • All computation functions left text connections open after they have been exited; fixed.
  • The output of AgeC14_Compution() and AgeS_Computation() gain a new class BayLum.list
  • Redundant code in AgeC14_Compution() and AgeS_Computation() has been removed
  • The argument Nb_chaines was replaced by n.chains wherever it occured in the package (functions and documentation)
  • The function plot_Scatterplots() gained a new argument plot_type, allowing to switch between the default hexbin plot and a function developed for 'BayLum(plot_type = "smoothScatter"`)
  • The function plot_Scatterplots() gained a new argument plot_mode to allow single xy plots
  • The function plot_Scatterplots() now accepts a two column data.frame as inputbuild

Internals

  • Add new package dependency KernSmooth used in plot_Scatterplots()

BayLum 0.1.2 (Release date: 2018-06-22)

New functions

  • The function MCMC_plot() was replaced by the newly written function plot_MCMC()
  • The function Concat_DataFile() is deprecated and is basically replaced by the function combine_DataFiles()

Bugfixes

  • The functions AgeC14_Compution() and Age_OSL14() now returns age results with two digits
  • The function AgeS_Computation() now returns the MCMC information from all samples of the PDF output is set to TRUE
  • The function Age_OSLC14() never returned numerical data; fixed
  • Fix Age_OSLC14() age format, now in ka for C-14 instead of years
  • The last example in AgeS_Computation() could not be run; fixed
  • C-14 calibration datasets now show data in 'ka' and not 'a'
  • Various typo corrections.

Enhancements

  • Allow different BIN/BINX-file names as input. The functions Generate_DataFile() and Generate_DataFile_MG() do no longer expecting the name sheme bin.BIN
  • The functions Generate_DataFile() and Generate_DataFile_MG() now supports the ... argument to pass further arguments to the function Luminescene::read_BIN2R()
  • The functions Generate_DataFile() and Generate_DataFile_MG() gained a new argument verbose to control the terminal output
  • The function Age_Computation(),AgeS_Computation(),AgeC14_Computation(), Age_OSLC14() now support the argument quiet and pipe it to rjags to suppress the terminal output
  • The function AgeC14_Computation() now returns a warning if outliers are detected.
  • The function LT_RegenDose() gained two new arguments nrow and ncol became a little bit more user friendly

Internals

  • Set patch level to 0 (for 3.3.0) to account for CRAN note
  • Vignette was updated and corrected

BayLum 0.1.1 (Release date: 2017-09-01)

  • Reduce required R version to 3.3.2

BayLum 0.1.0 (Release date: 2017-08-22)

  • Initial version on CRAN

Reference manual

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install.packages("BayLum")

0.1.3 by Anne Philippe, 7 months ago


Report a bug at https://github.com/R-Lum/BayLum/issues


Browse source code at https://github.com/cran/BayLum


Authors: Claire Christophe [aut] , Anne Philippe [aut, cre] , Sebastian Kreutzer [aut] , Guillaume Guerin [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports stats, graphics, grDevices, methods, hexbin, KernSmooth, rjags, Luminescence, ArchaeoPhases

Depends on utils, coda

Suggests testthat, R.rsp


See at CRAN