BayLum 0.3.2 (2024-04-14)

This version of 'BayLum' requires R>=4.1.x!

New functions

create_DataFile()

This function attempts to ease the very pain-stacking process of input
data processing (BIN/BINX files) so that it can be used in the
'BayLum' modelling. The function is an entirely new development and
will replace the functions Generate_DataFile_MG() and
Generate_DataFile() in future versions of 'BayLum'. Key features:

• Only one function for single-grain and multiple-grain data
• Support for BIN/BINX and XSYG files and RLum.Analysis-class objects,
  i.e. the data can be imported independently of the data file creation
• A new single-file configuration based on the YAML format. This makes
  the old error-prone folder structure obsolete
• Various internal consistency checks to avoid input data are
  erroneousness; which may lead to very hard to-track-down error
  messages
• Carries information about the number of samples and the sample names

plot_RegDosePoints()

• The function will replace the deprecated fucntion LT_RegenDose(),
  which was too error-prone and complicated to maintain.

write_YAMLConfigFile()

This function supplements create_DataFile() supporting auto-generated
YAML config template files

Bugfixes and changes

Age_OSLC14()

• Determines the sample name automatically by default.

Age_Computation()

• Determines the sample name automatically by default.

AgeS_Computation()

• Determines the sample name automatically by default.

combine_DataFiles()

• Now preserves the originator attribute

SCMatrix()

• Interactive mode is now more beautiful and consistently
• Can now extract information from an object created by
  create_DataFile()

SC_Ordered()

• Can handle objects created by create_DataFile() for easier usage.

Miscellaneous

• Drop dependency to deprecated package 'ArchaeoPhases' and make
  corresponding code an internal function (PR #33, @nfrerebeau)

• Add dependencies to the packages 'yaml' and 'cli'

• Bump version requirement for 'Luminescence' to >= v0.9.22

• Add new external files example.yml and yaml_config_reference.yml

• Internal datasets DATA1, DATA2, DATA3 were updated to be
  consistent with the new function create_DataFile()

Deprecated functions

The following functions are deprecated and will be removed in future
versions of BayLum

• Generate_DataFile()
• Generate_DataFile_MG()
• LT_RegenDose()

BayLum 0.3.1 (2023-03-28)

This version of 'BayLum' requires R>=4.1.x!

Bugfixes and changes

• AgeS_Computation() & Age_OSLC14() had two instances of the
  MCMC-list. One has been removed. This essentially halves the amount of
  memory needed to store the output of these functions. (Thanks to G.
  Guérin for reporting) (#27)

• AgeS_Computation() crashed reproducibly, if the THETA matrix (as one
  possibility) was provided indeed as a file name instead of a matrix
  object; fixed (thanks to M. Heydari for reporting)

• AgeS_Computation() the function handles wrong user input for the
  Theta matrix more friendly by converting it automatically to a matrix
  if needed.

• create_ThetaMatrix() the function did not throw an error in all
  cases where sigma_s was obviously wrong; fixed (thanks to M. Heydari
  for reporting)

• Generate_DataFile_MG() the function now checks that the number of
  specified BIN/BINX-files matches the actual number of BIN/BINX-files
  present in the folders. If not, a warning is prompted. This prevents
  hard-to-track-down error messages and odd modelling results that
  erroneously encourage searching for problems with JAGS or the
  'BayLum' models.

• plot_Ages() gained a couple of new arguments. First, plot_mode
  allows to switch between the standard plot output "ages" (the
  default) and the new option "density". The latter draws probability
  density curves instead of lines. Further arguments specific to the
  plot_mode = "density" are d_scale to scale the density plots in
  height and show_ages to show the Bayes estimator. More generally,
  legend.cex was added to enable a convenient scaling of the legend
  fonts; this works for both plot modes.

• plot_MCMC() gained additional support for BayLum.list returned by
  Age_OSLC14()

• plot_Scatterplots() The functions can now handle BayLum.list
  objects if returned by certain functions. Currently:
  AgesS_Computation(), Age_OSLC14()

BayLum 0.3.0 (2022-10-28)

This version of 'BayLum' requires R>=4.1.x!

New functions

• write_BayLumFiles(): @IMHarly contributed an excellent new function
  that creates all folders and files needed for 'BayLum', making it a
  lot easier and less error-prone to work with 'BayLum'.

Bugfixes and changes

AgeS_Computation()

• The function now supports parallel processing using the package
  'rungjags' (thanks to @IMHarly)

Age_OSLC14()

• Regression error, the function tried to observe more variables than
  were actually in the model; fixed. (thanks to @IMHarly, #21)
• The function now supports parallel processing using the package
  'rungjags' (thanks to @IMHarly)

Internals

• A few fixes regarding string comparisons in if() conditions.
• Fix CRAN warning regarding Escaped LaTeX specials: \&

BayLum 0.2.1 (2022-02-20)

Note: This package version needs at least R >= 4.0.

Bugfixes & changes

AgeS_Computation()

• The function crashed if jags_method = "rjparallel" with a runtime
  error due to missing information about the RNG type; fixed (thanks
  to @IMHarly for spotting).
• If jags_method = "rjparallel" the inits were preset to a specific
  value for the random number generator. While this setting led to a
  crash of the function and probably caused no harm, the setting did
  not make any sense. Now, the random number generator settings (seed,
  type etc.) can be provided via the argument inits, which is passed
  to runjags::autorun.jags. The default is NA to maintain the
  expected behaviour if jags_method = "rjparallel" is used.
• The function gained a new argument model to inject custom models
  to run with the parameters as already defined for the model. This
  option allows to adjust priors and likelihoods to test different
  scenarios. Please not that this option works without a safety net,
  mean the function does not check whether the parameters in the model
  are actually available.
• The function now returns the used model as a character string, in
  combination with the new parameter model it can be used to modify
  the model on the fly.

Age_OSLC14()

• Add support for "rjparallel" via new argument
  jags_method = "rjparallel", like in AgeS_Computation() (thanks
  @IMHarly, #20).

Generate_DataFile_MG()

• The function gained a new argument force_run1_at_a_time. If set to
  TRUE it automatically orders the curves in the BIN/BINX-file
  following the “Run 1 at a time” option. Regardless of whether this
  option was used for the measurement or not. Please note: this cannot
  work if you have assigned a position number more than one time to
  different aliquots.
• verbose = FALSE was not respected under all circumstances; fixed.

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

CRAN submisison

CRAN submission

CRAN submission

Initial CRAN submission