v0.9.5

Changes in version 0.9.4/0.9.5 (2019-09-20/2019-09-21)

Important user visible changes

1. plot_KDE() wrong error bars As it turned out, unfortunately,
   the error bars produced by plot_KDE() had been wrong since 2014.
   The input error values (2nd column in the data.frame) had been, for
   reasons we cannot recall anymore, divided by two leading to an
   improved visualisation of uncertainties. A big thank goes to Andrea
   Junge (#93) who made us aware of this bug.

2. The way the x-axis channels from BIN/BINX-files are generated
   changed So far, during the file import, minimum and maximum values
   were taken, and channels were distributed equally according to the
   number of available data points. Thanks to Sébastien Huot for a
   constructive discussion.

• Example old behaviour: For an OSL curve recorded over 40 s with 100
  channels, the first channel was set at 0 s, the last channel to at
  40 s. Thus, the width of each channel was 0.404 s.

• Example new behaviour: For an OSL curve recorded over 40 s with 100
  channels, the first channel is set to 0.4 s, the last channel to at
  40 s. Thus, the width of each channel is 0.4 s.

• In other words, the first channel does not start anymore at 0 s, as
  it is the case, e.g., in the Analyst.

Please note that these changes will impact your analysis results!

Difference between version 0.9.4 and 0.9.5

Non-used dependency to 'interp' removed.

Bugfixes and changes

analyse_SAR.CWOSL()

• The automated curve type recognition introduced with the last
  release broke the vignette of the R package 'RLum.Model'; now
  refactored code prevent other people’s code from breaking.

calc_CentralDose()

• The function does not crash anymore with an odd error if NA values
  are provided (#82 reported by Sébastien Huot).
• The function gained a new argument na.rm which is set to FALSE
  by default.

plot_DetPlot()

• The argument analyse_function.control now understands the
  arguments fit.method and fit.force_through_origin.

calc_MinDose()

• The final parameter estimates and their confidence intervals in the
  console output are now always reported in their absolute values,
  independent of whether the logged or non-logged model was used (#84
  suggested by Sébastien Huot). This is a purely cosmetic change, and
  no changes to the calculations were made.
• The values in the profile log-likelihood plots are now always given
  in their absolute values, independent of whether the logged or
  non-logged model was used (#84 suggested by Sébastien Huot). This is
  a purely cosmetic change, and no changes to the calculations were
  made. The output object still returns the original profile objects
  with the logged values.
• Improved handling of values close to zero if bootstrap = TRUE
  (#91, reported by Andrea Junge).

plot_GrowthCurve()

• Remove rounding from numerical output values (#81 suggested by
  Sébastien Huot); this affects all subsequent functions. However,
  terminal and graphical output do not change.

Internals

• The package data/datalist file listing the example data shipped
  with the package was not correct (#85, CRAN comment); now corrected.

v0.9.4

CRAN release

v0.9.3 (CRAN)

Changes in version 0.9.3 (2019-07-31)

• This version takes care of a CRAN note complaining about a non-used
  package declared in the Import fields.

v0.9.2 (CRAN)

Changes in version 0.9.2 (2019-07-30)

• This version fixes an URL problem discovered by the CRAN pre-check

v0.9.1 (never released on CRAN)

Changes in version 0.9.1 (2019-07-30)

Removed functions

• model_LuminescenceSignals(): This wrapper function for the R
  package 'RLumModel' was removed due to changes on CRAN inflicting
  a warning because the object is masked from 'package:Luminescence'
  each time 'RLumModel' was loaded. In 'Luminescence' the function
  had no real scope, but provided a place holder to point the users on
  the existence of the package 'RLumModel'.

Bugfixes and changes

apply_EfficiencyCorrection()

• The function now supports RLum.Analysis objects as input
• All allowed input objects can now be provided as list (self-call
  support)
• Minor code polish

analyse_baSAR()

• The manual stated that RLum.Analysis-class are supported, but
  actually this is not true, it supports a list of RLum.Analysis
  objects only.
• Some minor manual corrections.

analyse_SAR.CWOLS()

• Add support for POSL data,before the function crashed (reported by
  Alice Versendaal). POSL curves had been not listed as supported
  curve types though.
• Improve dataset recognition (OSL, IRSL, POSL).

calc_Lamothe2003()

• The documentation wrongly stated that an input data.frame should
  have the columns dose, De and De error, indeed dose, LxTx
  and LxTx error are expected (spotted by Jeong-Heon Choi)

calc_TLLxTxRatio()

• The LxTx.Error is no longer negative, even if the subtraction lead
  to negative count values (#78, reported by Sébastien Huot)

calc_SourceDoseRate()

• The function learned about the half-life of Cs-137

fit_OSLLifeTimes()

• 0 count values crashed the function for obvious reasons
  (a / 0 = Inf), this can happen in particular for artificial
  datasets. Now, if 0 is detected, count values are increased by
  0.1 (reported by Dirk Mittelstrass)

plot_AbanicoPlot()

• If summary = "se.abs" was chosen, the abanico plot showed se.rel
  instead; corrected (reported by Maryam Heydari)

plot_DRTResults()

• Correct documentation, where it was erroneously implicated that the
  ... argument pipes all arguments,
• add support for argument las.

plot_GrowthCurve()

• If the dose points included NA values the function crashed
  unexpectedly.

S4-classes and methods

• RLum.Analysis-class
  • Code polish (no visible changes)
• RLum.Data.Curve-class
  • Code polish and clarifying the documentation
• RLum.Data.Image-class
  • Conversion methods to a matrix and from and to data.frame
    never worked as intended.
  • Code housekeeping

Internals

• The DESCRIPTION file contained the string “[upcoming]”. This was
  a left-over from the development version and is now removed.

• Version numbering is now again more R canonical consisting only of
  three numbers (stable.major.minor). Development versions are only
  indicated by .9000 in the version number. Numbers after 9000
  (e.g., 9000-1) indicate build numbers. Both is used for GitHub
  build versions only.

• The file name RisoeBINfileData-class.R was changed to
  Risoe.BINfileData-class.R for consistency reasons, however, this
  has no further visible effect (#76, spotted by Sébastien Huot)

v0.9.0 (CRAN)

Changes in version 0.9.0 (2019-04-21)

'Luminescence' 0.9.X releases will be the last versions supporting
R < 3.5.0.

Important R related changes (R >= 3.6.0)

The behaviour of the base R function sample() was changed / corrected
(see news on https://www.r-project.org for details). This function is
used heavily within functions by 'Luminescence' (e.g.,
plot_GrowthCurve()). That being said, it means that old data
re-analysed by 'Luminescence' using R versions >= 3.6.0 will not give
the same results. Differences are small, however, they may significant.
If you want to reproduce your data, we recommend to use one of our
Docker images which include the R
version from the package release date.

New functions

• convert_Wavelength2Energy() Smooth and quick emission spectra
  conversion from wavelength to energy scales
• fit_OSLLifeTimes() Fit and deconvolution of OSL lifetimes using
  off-time measurements, i.e. after the stimulation was switched off.
• plot_DRCSummary() Summarise all dose-response curves from your SAR
  OSL analysis in one single plot.
• scale_GammaDose() Scale the gamma dose rate considering
  layer-to-layer variations in soil radioactivity. Contributed by S.
  Riedesel and M. Autzen.
• fit_ThermalQuenching() Provide an easy option to fit thermal
  quenching data and determine the activation energy.

Bugfixes and changes

apply_CosmicRayRemoval()

• Thanks to black magic, this function now runs also over a list of
  RLum.Data.Spectrum objects and and RLum.Analysis objects (also
  nested in a list)

apply_EfficiencyCorrection()

• The function produced a warning (“collapsing to unique x values”)
  on R-devel; fixed.

analyse_SAR.CWOSL()

• If the function was used in a self-call mode (object of type
  list), the arguments contrary to what is written in the manual,
  the arguments such as signal.integral.min had not been expanded
  properly; no one complained, however, corrected.
• The argument main no also supports the input list in the
  self-call mode.

analyse_SAR.TL()

• The plot legend was not correct, if no dose points had been
  provided; fixed
• The function returned a confusion warning; fixed.
• If background signals are provided, now the background subtracted
  signal is shown automatically instead of the uncorrected curves
  (suggestion by Tilmann Wolpert)
• The function now supports a list of RLum.Analysis objects as input
• The plot settings were sufficiently reset; fixed.
• Code polish

analyse_FadingMeasurements()

• Enable support for data imported from a BIN/BINX-file
• If the g-value is negative, now it also returns a negative g-value;
  before always the absolute values was taken, which was not
  meaningful
• If rho was negative, the log10 value could not be calculated, this
  caused an unwanted warning; now suppressed
• It showed a warning on R-devel due to changes in stats::approx();
  fixed
• Records with negative time since irradiation are now automatically
  removed (thanks to input by Sébastien Huot)
• Function is now more relaxed when odd data a provided and it is less
  talkative

calc_Huntley2006()

• The function now checks if rho (rhop) is a sensible non-zero
  positive value and, if otherwise, stops with a more meaningful error
  message. (Issue #74)
• Now the function is a little bit less talkative if extreme dataset
  are provided as input

read_BIN2R()

• Add support for missing BINX-file version 5 (pointed out by Harrison
  Gray)
• In the auto-file recognition (only a path instead of a file is
  provided), sometimes the found BIN/BINX-files were imported twice.
  The corresponding code was simplified to avoid such errors in future
• Sometimes the time stamp is invalid since it is missing a leading
  0. For BINX-files >= version 6 such timestamps now get corrected
  during the import

read_XSYG2R()

• The function failed for R-devel importing spectrometer data
  (approx(..., ties = -2)); fixed.

plot_GrowthCurve()

• The function crashed with
  Error in data.MC[, i] : incorrect number of dimensions under very
  particular circumstances (reported by Alice Versendaal). This was
  due to unwanted internal object conversion; fixed.

plot_RLum.Data.Spectrum()

• The wavelength to energy scale conversion was not correct. This was
  corrected and internally, the function now calls consistently the
  new function convert_Wavelength2Enegy() (the corresponding code
  and documentation have been updated or removed).
• The function gained a new argument norm for normalising the data
  to the highest or the lowest count value.
• The function gained a new argument bg.spectrum allow to pass a
  background spectrum that can be used for the subtraction
• The function returned a warning if a single matrix was used but
  plot.type was already set to single; fixed.
• Wrong settings in bg.channels crashed the function. Now it
  auto-corrects the wrong values.
• Channel binning now consistently calls the internal function
  Luminescence:::.matrix_binning(), which is more efficient cleaner
  than the code used before
• The function now longer crashes for plot.type = 'persp' if
  'xaxis.energy = TRUE.
• The colour picking option was not always working; fixed.
• Warnings are formatted more nicely.

verify_SingeGrainData()

• The function crashed for crazy datasets; fixed
• Cleaning-up RLum.Analysis-class objects did not worked; fixed

write_RLum2CSV()

• The function gained a new argument compact which is set TRUE be
  default, and keeps the element output as simple as possible, which
  is in particular helpful for RLum.Results objects
• The function now behaves more friendly to RLum.Results objects,
  before the output was hard to understand.

write_RLum2BIN()

• The export failed if the time stamp was invalid (NA); now NA
  values are consistently replaced by 000000 (other values are not
  possible, otherwise the re-import of such file would fail) (reported
  by Alice Versendaal via email, 2019-03-06)

Changes in S4-objects and methods

get_RLum

• The method working on list elements got a new argument class to
  remove unwanted RLum objects in from list of RLum objects

RLum.Analysis-class

• The show-method crashed under very rare circumstances if
  inconsistent objects had been combined; fixed.

RLum.Data.Spectrum-class

• Support added for bin_RLum.Data()

New example datasets

• ExampleData.TR_OSL provides a single fast-pulsing OSL curve that
  can be used to test the function fit_OSLLifeTimes().

Internals

• Package news are now provided as markdown document (NEWS.md) which
  is supported by CRAN
• The package version numbering scheme has been modified to simplify
  the distinction between different developer versions. While relevant
  numbers for CRAN remain X.X.X, which reads stable.major.minor
  version, a 4th number indicates the running package build number,
  e.g., 0.9.0.7.
• New internal function Luminescence:::.matrix_binning() to get the
  matrix (and curve) binning consistent; so far used only by the the
  bin_RLum.Data() method for RLum.Data.Spectrum-class
• Vignette S4-class object structure updated
• Internal changes to address changes in R-devel checking logical
  arguments with length more than one (e.g., if(is.na(x)) returned
  an error if x was not a vector of length 1)
• src/Makevars file removed to prevent unconditional stripping in
  response to a recent CRAN request; in return the installation size
  of the package increased in size on some platforms.

v0.8.6

CRAN submission

v0.8.5

CRAN submission

v0.8.4

CRAN submission

v0.8.3

CRAN submission
This release fails on the Solaris platform on CRAN and will be replaced
by 0.8.4.