BayLum 0.2.0 (2020-12-06)

Note: This package version needs at least R >= 3.5.0.

Bugfixes & changes

• AgeS_Computation()
  • Now stops if a mismatch was encountered between the number of samples and the matrix provided via THETA to prevent a ‘JAGS’ runtime error
  • The function experimentally gained a new argument jags_method to support full automated processing in parallel using the R package 'runjags'; including a ... argument for a more detailed control. By default the calculation is done simply via 'rjags' as usual
• Age_OSLC14()
  • Add additional output to enhance output table by additional information (#11)
  • The CSV-file option now returns the age and the HPD intervals
  • The bugs model for the gaussian distribution did not work due to a wrongly set index (#13); fixed.
  • If a small number of samples was used and the first was a C-14 sample JAGS crashed; now it throws are more comprehensible error message (#14).
• Generate_DataFile_MG()
  • now works only on preselected records; the limitation of OSL only was removed.
• plot_Ages()
  • The sorting of the samples in the graph did not work as expected; along with this a new argument sample_order was added.
  • The function accepts a data.frame as alternative input, if the data.frame is similar the data frames created by the computation functions (e.g., AgeS_Computation()). This option enables the manual creation of age plots from self-compiled data.
• plot_MCMC()
  • Accidentally the function could not display the chains from more than 9 samples; fixed (thanks to Maryam Heydari)
  • Now the function understand the output of AgeS_Computation() for an automated treatment
  • Wrong variable names now lead to a warning instead of a stop. This is less aggressive and it makes the function easier to use by users who only use the plot functionality of 'BayLum'
• plot_Scatterplots()
  • Line breaks and leading and trailing white space is now removed from the character (vector) provided via sample_names
  • If the number of selected samples via sample_selection was shorter than the number of names provided by sample_names the function returned an subscript out of bounds error; fixed (reported by Maryam Heydari)

Internals

• All models now come with an example showing how they can be inspected (before the examples not working)
• Fix a couple of documentation glitches (e.g., part of the documentation was missing)
• Smooth the creation of BayLum.list objects using a central internal function
• Add new C-14 calibration data and unify the names of those datasets. Allowed inputs are "IntCal13","IntCal20","Marine13","Marine20", "SHCal13", "SHCal20" or an own dataset which must be stored in a CSV-file.

New functions

• create_ThetaMatrix() this function is a helper to create the theta matrix that can be provided as input for the functions AgeS_Computation() and Age_OSLC14()
• create_FolderTemplates() creates the folder and file structures required by Generate_DataFile() and Generate_DataFile_MG() on the user’s hard drive

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 occurred 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