v0.9.16 (CRAN)

Changes in version 0.9.16 (2021-11-18)

This package version requires R >= 4.0.5

New functions

• combine_Dr_De() This function allows to model dose rate and equivalent dose distributions to obtain an age from Bayesian modelling using both distributions. In the back, a couple of additional functions have been added to support this novel approach. This function requires JAGS (supported through 'rjags') on your computer along with a couple of other R packages prompted to you when you first try to use this function.

• plot_OSLAgeSummary() Posterior distribution plot of ages. This function is used by combine_De_Dr(), however, it can be used as stand-alone plot.

Bugfixes and changes

analyse_FadingMeasurement()

• If run in a loop (e.g., with lapply()), merging of the results with merge_RLum() failed because the returned objects were not always strictly identical; fixed.

analyse_SAR.CWOSL()

• If all dose points were 0, the function crashed; fixed.

calc_CentralDose()

• The output in element output$summary was confusing for log = FALSE. While the terminal output was correct, no differentiation was made between absolute and relative values in the output object depending on the log mode. Now two more columns were added to report the overdispersion always in absolute units (whatever that may be) and relative (thanks to Li Bo for reporting this problem).
• No claim on the unit (e.g., Gy or s) is made in the terminal output anymore because we do not determine this information. Instead, now ‘abs.’ for absolute is used.

read_BIN2R()

• The function crashed if it was run in a loop and encountered non-supported files; fixed.
• The function does not crash anymore for zero-byte files but skips the import, returns a message and NULL.
• For BINX files created using an EM-CCD camera, the function created, under particular circumstances, invalid records that could not be further transformed; fixed (thanks to Anna-Maartje de Boer for reporting).

plot_RadialPlot()

• The function does not mess anymore with the par() settings of other subsequent plots

plot_GrowthCurve()

• The function crashed in combination with analyse_SAR.CWOSL(...,fit.weights = TRUE) for unfortunate Lx/Tx error values (means, Inf) caused by noise-like OSL data; fixed. Thanks to Frederik Baumgarten for reporting the issue.

Internals

• New dependency to the package 'mclust' is required by the two new functions.

v0.9.15 (CRAN)

New functions

• fit_EmissionSpectra(): this new functions allows you to fit
  luminescence emission spectra (e.g., TL, RF) with a semi-automated
  start parameter estimation. The function was around quite some time
  but was finalised only recently.

Bugfixes and changes

General

• We removed 'magrittr' from the dependency. It was never used
  within the package or required for examples, but loaded for
  convenience reasons to smooth the data analysis. However, with
  R >=4.1, a native pipe operator (|>) became available and
  'magrittr' is no longer needed (but can still be loaded by the
  user via library(magrittr) if needed).

analyse_FadingMeasurement()

• Minor graphical issue in the plot output: if the shine-down curve
  did not start at 0 s, the integration limits were drawn incorrectly
  (the calculation was correct, though); fixed.

analyse_SAR.CWOSL()

• The extraction of irradiation times, if irradiation curves were
  provided (e.g., usually part of XSYG files), did not work reliably;
  fixed.

calc_AverageDose()

• The function aggressively reset plot areas also in cases nothing was
  plotted; fixed.

plot_AbanicoPlot()

• If the input was of type data.frame the function struggled if the
  data.frame had more than two columns. While this was clearly
  indicated in the documentation, the behaviour was annoying, because
  it made always an extra sub-setting necessary when working with
  data.frames comprising more than two columns. Now the function
  discards all other columns except for the first two if the input is
  a data.frame.

plot_GrowthCurve()

• The function crashed if fit.method = "LambertW" and the Ln/Tn
  largely exceeded the highest Lx/Tx point; fixed.

plot_RLum.Data.Spectrum()

• For plot.type = "image" the labels for the contour did not scale
  for changed cex settings; fixed.

v0.9.14 (CRAN)

Changes in version 0.9.14 (2021-07-21)

This package version requires at least R >= 4.0.5

Bugfixes and changes

plot_AbanicoPlot()

• The function lost the parameter output (default TRUE), which was
  superfluous because the output was calculated regardless this
  option. Now the output is always returned, but invisible on the
  terminal. This has no user-visible effect and does not break old
  code.
• The function had a long-standing nasty bug that caused overplotting
  if the function was called repeatedly
  with par settings different from the default par(mfrow = c(1,1));
  fixed.
• In the case, the plot was shown on different panels (e.g.,
  par(mfrow = c(1,2))) in combination with the option dots = TRUE,
  the function crashed with the cryptic message:
  Error in rep(20, length(dots.x.i) - 1) : invalid 'times' argument;
  fixed.

analyse_FadingMeasurement()

• Apparently, the function never worked as intended for XSYG files;
  fixed. To prevent further problems, a test was added that monitors
  this functionality.
• The parameter t_star now supports half_complex, which uses the
  long equation from Auclair et al. (2003). The difference is of
  theoretical nature, however, now the two values can be compared.
• The plotting speed was improved by limiting the number of shine-down
  curves to a maximum of ten. Likewise, the lines showing the error
  range is now a polygon instead of single lines.

plot_RLum.Analysis()

• The function gained a new argument records_max enabling only a
  limited number of curves to be shown in the mode combine = TRUE.
  This avoids that a large number of curves become indistinguishable.
  The first and the last curve are always shown, all other curves are
  shown following an evenly distributed index interval.
• The ... argument sub (sub title of the plot) for
  combine = TRUE did not work properly due the R’s partial matching
  of arguments that conflicted with the argument subset. The
  argument sub was now renamed to sub_title to prevent this error
  from happening and support again subtitles.

verify_SingleGrainData()

• Improve terminal and plot output
• Add minimal support for ... to control plot output if wanted

v0.9.13 (CRAN)

Changes in version 0.9.13 (2021-06-03) (v0.9.12 was never released)

• read_TIFF2R() Wrapper function to import TIF/TIFF files and TIFF
  image stack data

Bugfixes and changes

calc_FadingCorr()

• If no solution could be found (usually the case for unrealistically
  large g-values), the function crashed with a non-helpful error
  message. Now a meaningful message is shown and the function returns
  NULL.
• The function did not flag a problem but just crashed for non-numeric
  input; changed.
• The function is now a little bit less forgiving if tc was not set.

RLum.Data.Image-class

• Add S4-methods to coerce from and to list and array

plot_AbanicoPlot()

• Documentation for the parameter y.axis clarified along with a new
  list of supported ... parameters.
• Add supported for graphics::par() yaxt parameter to suppress the
  y-axis using yaxt == "n". Please note that in a such a case a
  newly added axis via axis(2) needs to be adjusted otherwise the
  scale is not correct.

plot_Histogramm()

• If the input is of RLum.Results-class always the first element
  will be plotted. The function will not search anymore for an element
  'data'

plot_RLum.Data.Image()

• Various minor improvements to better support image data plotting +
  update documentation

plot_RLum.Data.Spectrum()

• Plot type "image" added based on graphics::image() added.

report_RLum()

• Due to changes in R, the full report was not always visible or
  complete; fixed.
• Now supports report distribution plotting for calc_AverageDose()
  model.

verify_SingleGrainData()

• The function stops flooding the terminal with the same warning over
  and over again if run over a list.

Internals

• mclust added as new package dependency to support the new Bayesian
  models
• tiff added as new suggested package to support the new function
  read_TIFF2R()
• report_RLum() was a little bit too aggressive when trying to close
  connections on exit (CRAN email from 2021-05-11)

v0.9.11 (CRAN)

Changes in version 0.9.11 (2021-04-29)

This package version requires R (>= 3.6.0).

New functions

• convert_SG2MG() Convert single-grain data to multiple-grain data
  by adding curve signals from one disc. Works only for files created
  by Risø TL/OSL readers.

• calc_gSGC_feldspar() Function to support the calculation of the
  equivalent dose using the global standardised growth curve (gSGC)
  for feldspar proposed by Li et al. (2015)

Bugfixes and changes

analyse_SAR.CWOSL()

• The function, applied to a list of RLum.Analysis objects, crashed
  with a merge error under very particular circumstances after
  throwing a fitting error; fixed (reported by Brice Lebrun).

fit_LMCurve()

• The function additionally returns a component_matrix (if the
  fitting was successful). The matrix contains xy-values obtained from
  the fitting with the resolution of the input data.

plot_GrowthCurve()

• The quality index for the comparison of the D_e and
  the D_e estimated from the Monte-Carlo yielded > 100%
  if mode = 'extrapolation'; spooky and fixed.
• The function caused a crash in analyse_SAR.CWOSL() for very small
  D_e error values and returned a user unfriendly error
  message (Error in temp.GC[, 2]/temp.GC[, 1]). This was caused by
  an unintentional type conversion to a character for very small
  values (#103, thanks to @IMHarly for spotting).
• Add support for the Lambert W dose-response curve fitting as
  suggested by Pagonis et al. (2020) (thanks to @vpagonis for
  developing the math)
• Minor tweaks to improve the graphical output and avoid various
  errors

read_BIN2R()

• Only for BIN/BINX-file version 3 and 4: if the numbers of runs
  exceeded 128, the number became negative; fixed.

Internals

• 'lamW' added as new package dependency. This is needed to support
  the Lambert W function as in the function plot_GrowthCurve()

v0.9.10 (CRAN)

Changes in version 0.9.10 (2020-12-10)

Bugfixes and changes

analyse_SAR.CWOSLOSL()

• The recent changes in 0.9.9 improving the self-call had unwanted
  side effects if the input parameters were itself objects. For
  example: signal.integral.min = setting led to a
  missing parameter error; fixed (thanks to Thomas Kolb for
  reporting).

• Note: While investigating the previous bug, it turned out that
  some users provide rejection criteria as unnamed list, albeit the
  manual says that is has to be a named list.

calc_FuchsLang2001()

• The function caused a fatal error on the CRAN R-devel resources
  after recent changes in R and did not work anymore on R-devel. This
  is fixed now and has no user visible effects.
• Minor code polish and better test coverage.

v0.9.9

Changes in version 0.9.9 (2020-11-29)

New functions

• calc_OSLLxTxDecomposed() Calculate Lx/Tx ratio for decomposed
  CW-OSL signal components by Dirk Mittelstrass

Bugfixes and changes

analyse_SAR.CWOSLOSL()

• The default value for rejection.criteria is now list() instead
  of NULL. As before, the default value means that internally set
  rejection criteria are applied and hence this change should not
  affect the behaviour of the function, but it allowed us to greatly
  simplify the underlying code.
• The function did not check correctly for all record types, under
  particular circumstances, some of the non-support curves could slip
  through; corrected.
• If the input records were not of type OSL, IRSL or POSL the
  function was supposed to return NULL but crashed instead; fixed.
• As implemented by calc_OSLLxTxRatio() the function now supports
  NA values for the integrals. If set, sum curves are taken for the
  calculation. This option enables a bunch of new possibilities to
  test more experimental protocols without modifying the function.
• Following the NA support, all integral arguments are now preset to
  NA. To avoid user errors, a warning is thrown each time the
  function runs with integral limits set to NA.
• The identification of the allowed curves was further improved to
  cover cases where users may want to provide experimental OSL curves.
  Allowed are combinations where OSL is combined with additional
  letters [a-zA-Z]. Everything else is, as before, ignored.
• The function now supports the input from the upcoming R package
  'OSLdecomposition' by Dirk Mittelstrass and hence gained a new
  argument called OSL.component.
• In particular circumstances, when no TL-curves were detected as
  preheat, the function crashed; fixed (flagged by Dirk Mittelstrass).

calc_OSLLxTxRatio()

• The function now supports NA as input for the signal.integral
  and/or background.integral. If set to NA the sum of the count
  values is used. This is useful if the users wants to process
  component data that were already extracted and do not need integral
  limits.
• The output of the function is not anymore invisible. This should
  have no further effect.

plot_GrowthCurve()

• Users sometimes complained about large uncertainties produced by the
  Monte-Carlo runs to estimate the error on the D_e,
  which returns the standard deviation of the MC runs. Large standard
  deviations are a result of large individual uncertainties (e.g.,
  noisy data) provided as input. The function now returns,
  experimentally, estimates of the highest probability density
  intervals as an alternative. Beyond we may recall that the results
  of the MC runs are always returned as a separate object by the
  function. Means, users ca run any statistic of choice to best
  estimate the uncertainties on the D_e.

read_Daybreak()

• The function threw a lot of warnings for the *.DAT after
  R >= 4.0.0 started to be more strict about embedded null bytes
  within a character. The code was updated to a newer version and no
  further warnings are shown.
• Under particular circumstances the function left open connections
  behind; fixed.

Internals

• The automated tests now use consistently testthat >= 3.0.0.
  Naturally this has no user visible effect, however, we found a
  couple of minor bugs while updating the tests.

v0.9.8

Changes in version 0.9.8 (2020-11-16)

Important user affecting changes

• The version requires R (>= 3.5.0)
• We removed a few of our vignettes from the package. They are now
  available on https://r-luminescence.org/tutorials/

New functions

• read_RF2R() Add support for importing spatially resolved RF
  measurement results.

• plot_ROI() Visualisation of ROI data imported by read_RF2R().

• convert_Concentration2DoseRate() by Svenja Riedesel and Martin
  Autzen. This function converts radionuclide concentrations (K in %,
  Th and U in ppm) into dose rates (Gy/ka). Beta dose rates are also
  attenuated for the grain size. Beta and gamma dose rates are
  corrected for the water content.

• calc_CobbleDoseRate() by Svenja Riedesel and Martin Autzen. The
  function calculates the dose rate profile through the cobble based
  on Riedesel and Autzen (2020).

Datasets

• ExampleData.CobbleDate new example dataset to be used in
  conjunction with the function calc_CobbleDoseRate(). Contributed
  by Svenja Riedesel and Martin Autzen.

• BaseDateSet.Conversion, Cresswelletal2019 was changed to
  Cresswelletal2018. The corresponding function scale_GammaDose()
  was updated.

• BaseDateSet.GrainSizeAttenuation.rda: Grain size correction data
  for beta-dose rates published by Guérin et al. (2012). Dataset
  contributed by Svenja Riedesel and Martin Autzen.

Bugfixes and changes

analyse_SAR.CWOSLOSL()

• The function gained a new argument plot_onePage. If set to TRUE,
  the plot output is gathered in one single plot window instead of
  three.
• If the user decided for odd reasons to mix preheat steps recorded as
  TL (signal recorded) and simple preheat (no signal recorded) the
  function stopped with an uncontrolled error. Now the function is
  more flexible. However, this comes at a cost, e.g., if the user
  accidentally swaps the sequence order (such as OSL-TL, instead of
  TL-OSL) this may remain unnoticed.
• For zero count data (e.g., observed in single grain curves), the
  function crashed with a non-indicative error message because NaN
  are usually produced if the recycling ratio is calculated; fixed
  (thanks to Brice Lebrun for reporting the issue).

analyse_FadingMeasurements()

• Typo correction in the manual and a better documentation of
  supported ... arguments
• The ylim argument can now be used to control the 'signal fading'
  plot output.
• While the x-axis of the fading curve output was correct, it probably
  caused too much confusion, and now the values are shown with
  superscripts, e.g., 10^0, 10^1 etc. If the number of data points
  is too small, the function will fall back to the old representation.
• The function did not work properly for less than five data points
  and stopped with
  Error in rep(rgb(0, 0, 0, 0.3), length(TIMESINCEIRR) - 5) (thanks
  to Annette Kadereit for flagging this issue)
• The function now shows also the normalised log-values under the
  time-scale (#97)
• As it turned out, t_star did not work if the input was produced by
  read_BIN2R(); fixed along with (#97)
• t_star now can be a function, e.g., function(x) x+100, which
  would add a constant value to all TIMESINCEIRR values (#97).

analyse_IRSAR.RF()

• The function learned to recognise input from read_RF2R and changes
  the header labelling accordingly.
• An edge case crash that might occur in combination with the vertical
  sliding has be sanitized.
• The text progress bar was not closed correctly, this could lead to
  artefacts in the terminal output; fixed.
• The internal C++ function used for the curve sliding now uses
  Armadillo vectors via RcppArmadillo. Depending on the platform
  this gives a performance plus free house by at least 50%. However,
  it comes at the cost of a reduced maximum vertical sliding range of
  1e+07 (before 1e+08).

plot_RLum.Data.Curve()

• The argument norm now supports the options "max" for a
  normalisation to the highest point (the default), "min" for a
  normalisation to the lowest point and huot for a normalisation
  suggested by Sébastien Huot (#87) via GitHub

plot_RLum.Analysis()

• The argument norm now supports the options "max" for a
  normalisation to the highest point (the default), "min" for a
  normalisation to the lowest point and huot for a normalisation
  suggested by Sébastien Huot (#87) via GitHub. Please note that
  norm only works if combine = TRUE.

report_RLum()

• Function complained about missing header; fixed.
• Function threw warnings Duplicate identifier 'root'; fixed.

read_SPE2R()

• The function threw a warning about truncated strings; the warning
  was not relevant and is no suppressed.

verify_SingleGrainData()

• The function did not always return a plot: Fixed.

Internals

• Risoe.BINfileData-class objects got a as.data.frame() S3-method
  to allow a direct conversion into a single data.frames. Count values
  are added in columns for each record (thanks to Annette Kadereit for
  the idea).

• structure_RLum() for RLum.Analysis-class recycled rows in the
  output data.frame if objects had more than one parent id (.pid).
  This led to odd behaviour if functions expected (correctly) that the
  number of entries in the data.frame returned by
  structure_RLum(), cannot not have more rows than number of records
  in the object. This could happen, e.g., after merging
  RLum.Data.Curve-class objects. ow multiple .pid entries still
  create only one string and the number of rows matches the number of
  records in the object.

v0.9.7

Changes in version 0.9.7 (2020-01-04)

Bugfixes and changes

analyse_Al2O3C_Measurements()

• Supplementary argument main never worked; fixed.
• New supplementary argument title which allows to pass further
  names of a sample to the plot output.

plot_AbanicoPlot()

• The plot now can handle negative values, fixed in combination with
  #88 (reported by Sébastien Huot)

plot_RadialPlot()

• Fix display problem when log.z = FALSE combined with negative
  values (#88, reported by Sébastien Huot)

read_BIN2R()

• Due to a typo, some bytes were read in the wrong order (big-endian
  instead of little-endian). While the fix does not affect the
  behaviour of the function, the non-fixed function would have soon
  crashed on CRAN servers. A big thanks to Tomas Kalibera from the
  CRAN team for his support and for pointing out this issue.

internal_as.latex.table()

• The function gained a new argument rm.zero which is preset to
  TRUE. If set, all columns containing zero values only are removed.
  The new argument enables a better fine tuning of the latex output.

v0.9.6

Changes in version 0.9.6 (2019-12-05)

Bugfixes and changes

analyse_SAR_CWOSL()

• Setting the argument plot.single = TRUE does not any longer
  interferes with the global par settings for the rejection criteria
  plot.

fit_OSLLifeTimes()

• The function gained a new argument plot_simple to produce plots
  without residuals that can be combined using standard R layout plot
  functionality, e.g., par(mfrow = c(2,1)).
• Function now handles the log = "x", log = "y" and log = "xy"
  options better.
• In the self-call mode (input is RLum.Analysis-class object), all
  ... objects are supported as list and get recycled if the list
  does not equal the number of objects

plot_GrowthCurve()

• The y-axis labelling of the test-dose response plot finally shows
  what was done since the beginning: the Tx values are normalised by
  the Tn values, i.e. Tn/Tx and not Tn/Tx. Thanks to Andrea Junge for
  spotting this flaw.

read_XSYG2R()

• The function now supports the temperature recalculation of TL curves
  even they consist of only a single point value.

Internals

• Changes in the development version of R caused error messages on
  CRAN and would have stopped the package from function properly in
  the future. This was corrected; the changes do not have any
  user-visible effect.
• The internal function for the DRAC output .as.latex.table() gained
  a new argument tabular_only which gives a little bit more
  flexibility at hand of the output the DRAC is combined with LaTeX.