v0.9.26 (CRAN)

Changes in version 0.9.26 (2024-11-18)

Removed functions

• Function calc_Kars2008() (deprecated since version 0.8.1) is now
  officially defunct, calc_Huntley2006() should be used instead
  (#252, fixed in #257).

Bugfixes

analyse_pIRIRSequence()

• The function crashed with a object merge error if run in a loop
  because of a merge_RLum() error. This was caused by a regression
  while implementing the n_N calculation in plot_GrowthCurve().
  Potentially affected was also analyse_SAR.CWOSL().
• The function now shows a warning and sets plot = FALSE when option
  plot.single = FALSE is set but the device size is too small. This
  should prevent “Figure margins too large” errors.
• The function will not crash anymore during the plotting in another
  edge case related to single grain data.

analyse_SAR.CWOSL()

• The function crashed for mixed set of RLum.Analysis-class objects
  typically observed for single grain data, e.g., one object contains
  only TL curves while all others contain the OSL/IRSL data from the
  grain. As the function filters those records automatically, it
  crashed because the aliquot number assignment internally relied on
  the length of the object (regression, #373, fixed)

analyse_SAR.TL()

• The function now produces a more correct rejection.criteria data
  frame (#245, fixed in #246).
• Several edge cases that led to crashes have been fixed (#147, fixed
  in #247).

get_RLum()

• When the function was used on a list of RLum.Analysis-class
  objects with the argument null.rm = TRUE it would remove all
  NULL objects, but not elements that became list() (empty list)
  during the selection; fixed.
• Fix an edge case that caused a rather non-expected, more visible
  output problem. When curves were selected via recordType on
  RLum.Analysis-class objects (or a list of them) containing only a
  single RLum.Data-class object, the function returned the
  RLum.Data.Curve-class object regardless of the selection in
  recordType. In other words: if a user tried recordType = "TL" on
  an RLum.Analysis-class object that contained only a single IRSL
  curve, the function would still return that single IRSL curve
  instead of an empty element. The reason for this behaviour was a
  poor attempt to deal with NA in the recordType name that led to
  missing values and unexpected behaviour for a logical comparison.
  Now, before the subset happens, NA values in recordType are
  converted to "NA" (a character), allowing us to fix the incorrect
  subsetting.

plot_RLum.Data.Spectrum()

• Add support for lphi and ltheta light direction arguments for
  plot.type = "persp".
• Fix the reason for the unclear warning In col.unique == col :
longer object length is not a multiple of shorter object length

write_R2BIN()

• Recently, non-ASCII characters in comments or file names have become
  more common and that led to crashes during the file export. To avoid
  this, now all non-ASCII characters are replaced by _ before
  writing them to the BIN/BINX files.
• The function now returns the file path of the export.
• Fix a bug that left connections open if the function crashed.

Internals

• Two new internal functions .throw_warning() and .throw_error()
  sometimes flushed the terminal with messages if called (internally)
  in particular circumstances. Now we maintain a stack of function
  names, so that at any time we can report correctly the name of the
  function where an error or a warning is thrown (#254, fixed in
  #256).

What's Changed

• Post release version bump by @mcol in #240
• Don't use the bbmle::profile() try_harder option in calc_MinDose() by @mcol in #241
• Remove the windows-2019 (oldrel) instance from the CI actions by @mcol in #242
• Add the expect_snapshot_RLum() test helper and start using it by @mcol in #244
• Correct the rejection.criteria data frame created by analyse_SAR.TL() by @mcol in #246
• Fix crashes in analyse_SAR.TL() by @mcol in #247
• Silence notes raised by R CMD check by @mcol in #249
• Use add = TRUE with on.exit() by @mcol in #255
• Replace the implementation of .throw_error() and .throw_warning() by @mcol in #256
• Set calc_Kars2008() as defunct by @mcol in #257

Full Changelog: v0.9.25...v0.9.26

v0.9.25 (CRAN)

Changes in version 0.9.25 (2024-09-12)

This package version requires R >= 4.3

New functions

• read_HeliosOSL2R(): New import function to support the new zero rad
  Helios luminescence reader and its .osl file format. The output is
  an RLum.Analysis-class object.

Bugfixes

analyse_baSAR()

• Fix #183 addressing an edge-case crash when the function was called
  on an object containing no records of the appropriate type (#184,
  @mcol).

analyse_FadingMeasurements()

• Add ... support to disable the blue trend line via
  plot.trend = FALSE
• Fix #175 to deal gracefully with the case when the size of Lx and Tx
  doesn’t match (#192, @mcol).

analyse_portableOSL()

• Function did not respect argument main; fixed.

convert_Wavelength2Energy()

• Fix #133 addressing cases where R throws an uncontained error when R
  drops the object structure in very rare cases (#134; thanks @mcol)

calc_Huntley2006()

• Improve success rate of GOK fitting of the unfaded data using a two
  step approach: first an exponential fit is applied then this values
  are used as start parameters.

calc_Statistics()

• The skewness and kurtosis depended on number of MC samples (#122);
  fixed with #123 (thanks to @mcol)

calc_TLLxTxRatio()

• Function crashed for Tx.data.background = NULL (#129); fixed with
  #130 thanks to @mcol

calc_WodaFuchs2008()

• The function now officially supports numeric vectors and single-column
  data frames as input (#200).
• The function computed the number of breaks for the histogram
  incorrectly (#197, fixed with #198).
• The function now supports more types of RLum.Results objects without
  crashing, although if the object contains only one data point it will
  stop immediately to avoid problems with nls() (#199, fixed in
  #219).

extract_IrradiationTimes()

• If a BIN/BINX-file is provided, the function will now check that it
  contains the same amount of data as the corresponding XSYG file a bit
  earlier than before, thus avoiding a possible crash (#228, fixed in
  #229).

fit_CWCurve()

• Argument output.path has been removed, and a warning is raised when
  attempting to use it (#207, fixed in #209).

fit_EmissionSpectra()

• Parameter input_scale was not correctly propagated when the function
  would self-call (#160, @mcol).

fit_OSLLifeTimes()

• The validation of the minimum dataset size didn’t account for the use
  of the signal.range argument (#182, fixed by #195, @mcol).

fit_SurfaceExposure()

• Fix #162 to remove a dimension mismatch if the input data contained
  NAs, which would generate unexpected warnings (#163, @mcol).
• The function doesn’t stop anymore with an error if called on an
  RLum.Results object (#165, @mcol).

plot_AbanicoPlot()

• Argument plot.ratio will now throw an error on non-positive
  numerical values (#221, fixed in #222).
• The function doesn’t crash anymore when setting interactive = TRUE
  (#220, fixed in #233).

plot_DetPlot()

• Argument signal.integral.max is now enforced to be greater than
  signal.integral.min, as otherwise the computation of the number of
  channels would produce Inf (#203, fixed in #206).
• Fix a crash when using option
  analyse_function = "analyse_pIRIRSequence" (#210, fixed in #211).

plot_GrowthCurve()

• The function now calculates the relative saturation (n/N) using the
  ratio of the two integrates. The value is part of the output table.
• Argument na.rm has been removed: as of version 0.9.23, it was
  defunct and only accepted TRUE as valid value and produced an error
  otherwise, so there is no effective change in behaviour (#137, fixed
  in #214).

plot_Histogram()

• The function doesn’t crash anymore when setting interactive = TRUE
  (#186, fixed in #231).

plot_KDE()

• It now officially supports numeric vectors and single-column data
  frames, for which it assumes that the De error at each measurement is
  10^-9 (#189, fixed in #194, @mcol).

plot_NRt()

• The function reports an helpful message rather than crashing when
  applied to an object of unexpected type or when there is a mismatch in
  time values (#177, fixed with #179 by @mcol).

plot_RadialPlot()

• The function doesn’t crash anymore when a single-column data frame is
  provided (#191, fixed in #212).

plot_RLum.Data.Analysis()

• The function now supports all arguments from
  plot_RLum.Data.Spectrum(); before it had only basic functionality
  for RLum.Data.Spectrum-class data.

plot_RLum.Data.Spectrum()

• The plot function can now handle non-increasing column values for
  plotting (with a warning).

read_BIN2R()

• ignore.RECTYPE now supports numeric values, e.g., 128. Records for
  this type will be ignored during import.
• BINX-files with RECTYPE = 128 will not crash anymore, thanks for
  asking Anna-Maartje Boer and replying Karsten Bracht.
• The function now stops graciously when attempting to read an empty
  file (#225, fixed in #226).

read_PSL2R()

• The function is out of the beta status, hence the flag was removed.
• The RLum.Analysis-class object returned by the function gained a new
  element Sequence, which is a data frame. with the measured sequence.
  This way, if the original sequence was lost, it can still be extracted
  from the .psl data.
• If no .psl file was found the function got trapped in an infinite
  loop (#127); fixed with #128 (thanks to @mcol)

read_XSYG2R()

• Fix spectrometer data import for basically broken files.

read_Daybreak2R()

• Fix #135 to improve detection of non-ASCII files (#140, @mcol).

Risoe.BINfileData2RLum.Analysis()

• Fix a crash when reading an empty Risoe.BINfileData input (#215, fixed
  in #224).

Internals

• New internal function + tests added .get_named_list_element(). It
  just does what the names says.

What's Changed

• Don't let a 1-column matrix become a vector in convert_Wavelength2Energy() by @mcol in #134
• Check length of g_value argument in calc_Lamothe2003(). by @mcol in #132
• Fix crash in calc_TLLxTxRatio() if Tx.data.background=NULL. by @mcol in #130
• Improve input validation and complete coverage in read_PSL2R.R by @mcol in #128
• Complete coverage for read_RF2R.R. by @mcol in #126
• Increase coverage in calc_gSGC_feldspar.R. by @mcol in #125
• complete coverage in calc_Statistics.R by @mcol in #124
• Fix computation of skewness and kurtosis with MCM. by @mcol in #123
• Fix error message and awkward code in plot_GrowthCurve() by @mcol in #139
• More coverage by @mcol in #136
• More coverage by @mcol in #143
• Better detection of non-ASCII files in read_Daybreak2R.R by @mcol in #140
• Clean up input validation in calc_FiniteMixture() by @mcol in #142
• More coverage and some typos by @mcol in #145
• Don't pollute the working directory with generated output from test_write_RLum2CSV.R by @mcol in #149
• More coverage and typos by @mcol in #150
• Use nocov start/end to exclude untestable regions from coverage by @mcol in #151
• Validation of scalar variable expected to be positive by @mcol in #152
• More coverage by @mcol in #153
• Remove duplicated list of authors from the DESCRIPTION file by @mcol in #154
• Fix .throw_error() and .throw_warning() by @mcol in #155
• More coverage by @mcol in #156
• Add option null.ok to .validate_positive_scalar() by @mcol in #158
• Improve input validation in calc_FastRatio.R by @mcol in #159
• Propagate the input_scale argument in fit_EmissionSpectra() by @mcol in #160
• Remove warnings from fit_SurfaceExposure() if data contains NAs by @mcol in #163
• More coverage and fixes by @mcol in #164
• two small errors in fit_SurfaceExposure() by @mcol in #165
• Remove test results for R version < 3.6 by @mcol in #166
• Switch globally to testthat 3rd edition by @mcol in #167
• Copy the tests/testdata files to tests/testthat/_data and package them by @mcol in #170
• Some more coverage by @mcol in #171
• Include testthat/data into the package and update tests to refer to it by @mcol in #169
• More coverage by @mcol in #172
• Start silencing output from tests by @mcol in https://github.com/R-Lum/Luminescence/p...

v0.9.24 (CRAN)

Changes in version 0.9.24 (2024-06-07)

This package version requires R >= 4.3

New functions

• trim_RLum.Data(): This new function enables trimming off the number
  of channels of all supported RLum.Data-class on the time domain. For
  instance, an OSL curve (RLum.Data.Curve-class) has 1000 channels;
  one may want to extract only channels 10 to 100. Moreover, sometimes,
  RLum.Data-class objects have a different number of channels but are
  otherwise measured with the exact time resolution. Until now, it was
  possible to merge those curves, but the subsequent analysis usually
  failed because most of the analysis functions check whether the number
  of channels matches.

• import_Data(): A convenience wrapper around all functions commencing
  with read_. The functions steps through all functions and the one
  that can import a file is chosen. This function simplifies writing of
  scripts for different data formats.

The Thermochronometry functions (internal)

• Add internal function to import thermochronometry XLSX sheets into R;
  an R implementation of STAGE1, ExcelToStructure; the function has no
  user visible use for the moment.

Bugfixes and changes

analyse_IRSARRF()

• The function crashed for RF_nat.lim settings with two parameters;
  fixed (thanks to Mariana Sontag-Gonzalez for reporting)
• The function gained a new argument option for method: "VSLIDE". If
  set, the vertical sliding with the range set to "auto" is used for
  the estimation of the equivalent dose.

analyse_SAR.CWOSL()

• The function gained a new argument trim_channels. The default is
  FALSE to do not break existing code. If TRUE OSL and IRSL are
  curves are checked for the lowest number of channels on the curves and
  then all curves are trimmed accordingly using trim_RLum.Data(). This
  should fix an issue where data could not be analysed due to different
  channel numbers erroneously produced by the luminescence readers.
• The dose points names are returned as factors (which they are)
  instead of characters, with their class in the correct order. If you
  expect character values this may break existing code.
• The $data element gained two new columns ALQ and POS where the
  functions tries to store data about the running aliquot number and the
  position of the aliquot in the reader. The latter can only be accessed
  if this information was provided in measurement data (e.g., XSYG or
  BIN/BINX)
• The argument rejection.criteria gained a new option
  recuperation_reference preset to "Natural" to specify the
  regeneration reference dose point taken into account for calculating
  the recuperation rate (suggested by Anna-Maartje Boer and Jakob
  Wallinga)

calc_Huntely2006()

• If the age is NA due to Ln/Tn values lower than the smallest
  simulated Lx/Tx value, a warning with an explanation is returned.
  Thanks to Christina Neudorf for providing the test dataset.
• Better catch a few uncontrolled errors and improve the success of the
  fitting (thanks to Salome Oehler for providing scripts and datasets)
• Regression: The changes in the last version led to unexpected function
  behaviour in cases where users tried the fading correction with only a
  few dose points in the lower part of the dose-response curve because
  the fits were no longer forced through the origin. This issue is now
  corrected, and the user can use the argument
  fit.force_through_origin (which is passed down to
  plot_GrowthCurve()) to force the fit again through the origin
  (thanks to Junjie Zhang for reporting the issue).

convert_Activity2Concentration()

• The function did not work as expected if input was provided as
  abundance and the output data frame was missing values; fixed.
• The parameter input_unit now expects either "activity" (the
  default) or "abundance" instead of "Bq/kg" or "ppm/%'. The old
  input parameters are still silently accepted.
• Potentially breaking change: The naming of the output data frame
  now reports SI unit conform values, i.e. we ppm is no longer
  acceptable because it might have different interpretations. To reflect
  this change, in the function title we replaced “concentration” with
  “abundance”.

read_BIN2R()

• Argument n.records can now be provided as a vector to specifically
  select records for the import. All other records are skipped and not
  imported. This can be useful in particular for very large
  BIN/BINX-files because allows importing single records very quickly
  without parsing the entire file
• The function is now less talkative for zero byte records and stopped
  spamming the console.
• The function learned about RECTYPE 128 records and can now import
  them (before those records were skipped). As it is in the original
  format, these information are only appended to the BIN/BINX file,
  means they do not really represent measurement data. Please note that
  this support is highly experimental!
• The download of files now uses the new internal function
  .download_file()

read_Daybreak2R()

• The function gained the ... argument for compatibility reasons

read_RF2R()

• The function gained the ... argument for compatibility reasons

read_SPE2R()

• The function gained the ... argument for compatibility reasons
• The argument verbose was not fully respected; fixed

read_TIFF2R()

• The function gained the ... argument for compatibility reasons

read_XSYG2R()

• Tries a little bit harder to determine the correct file path.
• Returns the file path as @info object in the RLum.Analysis-class
  output.
• If the file is not readable it only shows the R error and not anymore
  the internal error.

plot_DetPlot()

• New argument plot: The function gained the new parameter plot to
  provide the possibility to disable the plot output for more complex
  operations
• Additional input: The function now understands lists of
  RLum.Analysis-class objects and iterates over those objects
  automatically.
• New argument multicore: As an addition to the list operation, the
  function can let it run in a multi core session
• The legend displayed the wrong labels for the equivalent dose and the
  Ln/Tn values; fixed.
• The legend is now disabled by default if no shine-down curve is shown;
  it can be activated again manually using legend.
• The par settings were not correctly reset; fixed.
• The function now supports the trim_channel argument from
  analyse_SAR.CWOSL()

plot_GrowthCurve()

• Edge case: If the Ln/Tn values was way below the fit and
  fit.method = EXP was chosen for the fitting, the function still
  returned a positive equivalent dose for mode = interpolation. Now
  the returned value is NA since no interpolation was possible.
• Minor graphical polish: the dashed lines are drawn to the end of the
  plot area.

plot_RLum()

• The function knows how to process results produces by
  analyse_SAR.CWOSL(), analyse_pIRIRSequence() and
  analyse_IRSARRF(); the functionality is very basic and for fast
  reporting situations only.

report_RLum()

• The file *.Rds file path download did not function anymore; fixed.
• The function threw an non-conclusive warning; fixed.

Risoe.BINfileData-class()

• The show method now knows about RECTYPE 128 and will account for
  it.

Risoe.BINFfileData2RLum.Analysis()

• The function learned about RECTYPE 128 records. Those records
  contain ROI data from camera measurements and are skipped for the
  moment because they do not really belong to measurement data. This may
  change future.

Internals

• Add internal download helper .download_file() for a more consistent
  approach to detect URL schemes and download files across the package
• Cover tricky edge case for the internal function
  .expand_parameters(). The function is used to recycle and expand
  function parameters if the input is a list object. It apparently
  showed odd behaviour if a function was used in a loop with objects of
  its own, e.g., f(x = i + 1), then the function would recycle i + 1
  and then evaluate i + 1 in the function environment. Usually, this
  should throw an error, but in particular, i is an object name
  commonly used in loops, so the function went upwards in the
  environments until it found the first i. However, this is not the
  i inserted by the user. The result was that the loop did not seem to
  work for no apparent reason. Now, .expand_parameters() evaluates
  input in the parent environment before passing it down.

v0.9.23 (CRAN)

Changes in version 0.9.23 (2023-11-03)

This package version requires R >= 4.2

Bugfixes and changes

analyse_portableOSL() (potentially breaking changes)

The function received a major update, including an updated output
object. Please make sure that you read the changes before updating,
because it may break your existing code!

• New argument mode added with two options 'profile' (the default)
  and 'surface'. The latter is intended for 2D surface interpolation
  of luminescence signals and was newly added.
• New argument coord added, to allow the user to provide a list or
  matrix of xy-coordinates of the sampling position. If nothing is
  provided, the coordinates are extracted from the file name or an index
  is calculated.
• The function now always translates input order in x and y coordinates,
  to have the treatment consistent.
• In profile mode, the function now returns also the dark count values
  with their standard deviation. The dark counts can also be plotted in
  the surface mode, although it probably does not make much sense.
• invert = TRUE the y-axis is now also inverted and the inversion
  works more consistently
• ... argument grid (enabled by default) for better parameter
  reading
• ... argument sample was changed to run better complying with the
  terminology of the PSL format, where
• ... argument bg_img was added to provide a background image (e.g.,
  a profile photo) for overlay the sample name is called run.
• ... supports a lot more arguments to enable better plot
  modifications in particular for the newly added surface interpolation
  mode.

calc_Huntley2006()

• The function can now handle "extrapolation" for fit.method = "GOK"
  or fit.method = "EXP" and is therefore suited to additive
  measurement protocols. This implementation has beta character and
  needs further testing.

read_PSL()

• Remove unwanted characters less aggressively from sample name; with
  this new setting, coordinates can be passed.

plot_GrowthCurve()

• The function crashed for the setting
  plot_GrowthCurve(..., mode = "alternate", fit.method = "LambertW");
  fixed (#114, @Eiskeil, thanks for reporting).
• Now throws a warning in
  mode = "extrapolation", fit.method = "LambertW" of the standard root
  estimation failed and hence the results can become inconclusive.
• fit.method = "GOK" now supports fits that are not necessarily forced
  through the origin.
• If the calculated fit weights were invalid, the parameter was not set
  always correctly set; fixed.
• Non-user visible change: the fit formula is now extracted more
  consistently and less error-prone.
• If the first Lx/Tx value was very high, the x-axis origin in the
  plot was not always shown by default. This was intended behaviour,
  however, sometimes this causes confusion. Now the axis origin is
  always shown. Still the axis limits can still be modified using ylim
  and xlim. (Thanks to Salome Oehler for flagging this issue).
• The fitted curve now always extends to the plot margins.

Internals

• Adding new dependency to 'interp'
• Remove dependency to orphaned package 'plotrix'; the code in one
  affected function was replaced using base R code

v0.9.22 (CRAN)

Changes in version 0.9.22 (2023-08-07)

This package version requires R >= 4.1

New functions

• subset_SingleGrainData(): the function provides a convenient sub
  setting of Risoe.BINFileData-class objects using a table of position
  and grain pairs

Bugfixes and changes

convert_PSL2CSV()

• The function still contained a bug if the parameters were combined in
  a certain way; fixed.

extract_IrradiationTimes()

• Now silently handles RLum.Analysis-class objects imported via
  read_BIN2R(..., fastFoward = TRUE), this allows to use the function
  in a more general manner.

merge_RisoeBINfileData()

• Does not anymore throw an error if the number of input objects was
  smaller than two. It just passes the input through unchanged.

plot_DetPlot()

• The function now returns a clear error message if the input object is
  not of type RLum.Analysis
• Edge case: the function does not crash anymore if used in a loop and
  if all equivalent doses were NA; it sill throws warnings though.
  (thanks to Annette Kadereit for reporting)

write_RLum2CSV()

• The behaviour of the parameter prefix caused confusion, because in
  combination with multiple files the function overwrote created files,
  although this was wanted behaviour now the prefix is always added to
  the automatically created files names.

v0.9.21 (CRAN)

Changes in version 0.9.21 (2023-02-03)

This package version requires R >= 4.1

Bugfixes and changes

analyse_portableOSL()

• The function can now handle a list of RLum.Analysis-class objects
  and automatically process them in a conventional way. Potential
  breaking change warning: the $summary data frame gained an
  additional column, SAMPLE. If you access columns index-based, you
  have to double-check your code. The manual was updated accordingly.
• A new ... argument sample was added to allow adding information on
  the sample for the plot
• The function did not like sequences with only one pair of OSL/IRSL and
  returned an error; fixed.

convert_PSL2CSV()

• Add new argument single_table to enable the export of PSL data into
  a single spreadsheet table (CSV file), each curve is represented by
  two columns
• Add new argument extract_raw_data, which allows extracting the raw
  data convienently. Those data are already imported by read_PSL2R()
  but they remain somewhat hidden in the @info slots of each
  RLum.Data.Curve object.

fit_LMCurve()

• If the argument fit.calcError was set to TRUE and the parameter
  confidence interval calculation failed, the function stopped with an
  uncontrolled error. Now it shows a meaningful warning instead.

plot_RadialPlot()

• Fix a few visual problems if the dataset has negative values (thanks
  to Alice Versendaal for reporting)

read_BIN2R()

• Function crashed under edge conditions while testing concise records
  returning a subscript out-of-bounds error; fixed.
• The function struggled to read files from downloads (URL instead of a
  local file path) correctly on Windows machines; fixed.

write_RLum2CSV()

• The function now accepts data.frame objects as input. This has no
  particular advantage over the base R functions, such as write.csv()
  but is used internally in combination with other functions.

Internals

• Fix outdated URL in github.R

v0.9.20 (CRAN)

Changes in version 0.9.20 (2022-07-14)

This package version requires R >= 4.1

Bugfixes and changes

analyse_Al2O3C_Measurement()

• Add support for sequences without TL curves in the sequence;
  however, the function still expects three OSL curves for natural,
  regenerated, and background signal.

merge_RLum.Data.Curve()

• The function works better if curves of different lengths are
  merged, but it still throws an error if the resolution is not
  similar.

plot_RLum.Data.Curve()

• Add support for ... arguments las and axes

plot_RLum.Data.Spectrum()

• The plot.types = "single" and plot.type = "multiple.lines" had
  two long-standing issues with the colour rug (both are fixed):

  • The colour rug showed ugly overplotting,
  • the colour rug had a resolution that depended on the x-axis
    (wavelength) scaling.

• plot.types = "single" and plot.type = "multiple.lines" now
  support a ... parameter box for removing the outer plot frame.
  The argument was named box to avoid a confusion with the term
  frames used for image stacks.

• plot.types = "single" and plot.type = "multiple.lines" now
  support a ... parameter frames for picking the frames to be
  visualised beyond the axis limitation.

plot_DRCSummary()

• The function did not know how to hand the output, if the fit was
  LambertW; added.
• The function now roughly checks whether all curves have used the
  same equation for the fitting, if not it throws an error.
• The ... arguments allowed to modify the plot are now mentioned in
  the documentation.
• The ... are better recycled to avoid a function crash in case the
  user did not provide the arguments in the required length.

plot_GrowthCurve()

• The formula returned in the output if fit.method = "LambertW" was
  not correct; fixed. The fit and the fitting were not affected;
  though.

read_BIN2R()

• The example in the documentation was a little bit too generic and is
  now replaced by an example that works.

write_R2BIN()

• The running example was not working because it used outdated example
  data. The example was replaced by a working example using an actual
  BINX-file. (thanks @JohannesFriedrich for reporting, #110)
• The terminal output of the function could not be silenced. Now the
  output (except for the progress bar, which can be switched off) is a
  message(), allowing to disable the terminal output.

Internals

• Add new internal function .add_fancy_log_axis() to provide a more
  sophisticated log-axis to plots if needed with minor ticks and
  proper labelling.
• Fix wrong usage of class() where needed

v0.9.19 (CRAN)

Changes in version 0.9.19 (2022-03-10)

This package version requires R >= 4.0.5

New functions

• extract_ROI(): Light-weighted function to extract pixel values
  from pre-defined regions-of-interest (ROI) from
  RLum.Data.Image-class, array or matrix objects and provide
  simple image processing capacity. While the function comes with a
  simple control plot output, the results can be passed also to
  plot_ROI()

• write_R2TIFF(): Export RLum.Data.Image and RLum.Data.Spectrum
  objects or a list of such to TIFF Images. A convenient wrapper
  around the function tiff::writeTIFF()

Bugfixes and changes

merge_RLum.Results()

• If elements of type matrix, data.frame or vector were merged,
  usually attributes, additional to the standard attributes (e.g.,
  class for data.frame) were lost during the merging. Now, such
  attributes are preserved so far they are not of a similar name as
  the standard object of the object element (e.g., dim for matrix
  or class for data.frame). This small addition allows to merge
  more complex objects and retain all attributes for further
  processing.

plot_DRTResults()

• The plot messed with the par() settings, which was problematic if,
  for instance, a second x-axis was wanted; fixed.
• The function examples were not anymore up-to-date; fixed.

plot_RLum.Data.Image()

• Minor correction of the colour legend, which did always show the
  highest value
• New ... argument zlim_image to maintain a consistent z-scale
  over a series of images.
• The colour stretching could fail for lin and a lot of zero values;
  fixed.

plot_RLum.Data.Spectrum()

• Fixed a bug that let plot_RLum.Data.Spectrum() crash under very
  particular circumstances due to a wrong conditional statement.
• If the count limits are oddly chosen, i.e. limit_counts is smaller
  than the actual number of counts on the z-scale, the function does
  not crash anymore but replaces the value with the lowest possible
  value.
• The argument box for the plot persp now accepts alternate for
  the customized plot without the box usually drawn around the plot.
• The function now returns the adjusted matrix used for the plotting
  regardless of whether the argument plot is set to TRUE or
  FALSE.
• If the plot type is persp, the default, the “viewing
  transformation matrix” is returned as an attribute pmat. This can
  be further used in conjunction with the function graphics::trans3d
  to add additional information to the graphic.

plot_FilterCombinations()

• The function returned a wrongly calculated optical density, using
  log() instead of log10; fixed.= Note: The shiny filter app was
  not immediately affected because the values here were taken from a
  spreadsheet.
• The output object is now invisible since the function’s main purpose
  is to plot a graphic and not return an object.

plot_ROI()

• Add support for the new function extract_ROI()
• Add new argument bg_image to support background image plotting
• The numerical output is now consistently invisble as it is for all
  plot functions in the package

v0.9.18 (CRAN)

Changes in version 0.9.18 (2022-01-17)

This package version requires R >= 4.0.5

Breaking changes

Changes in RLum.Data.Image and removal of import 'raster'

The S4 class RLum.Data.Image was heavily revised to strip
'Luminescence' of the dependency to the package 'raster' and replace
the functionality with base R functions and objects. The 'raster'
package came in at an early stage of 'Luminescence' to handle image
data. However, most of its massive feature set was never used, but
'raster' caused a lot of trouble to many users and in our automated
tests because of its own dependencies. Soon, 'raster' will be retired
and replaced by an even more powerful package called 'terra'. This was
our cue to make some serious changes instead of carrying forward this
unfortunate implementation in 'Luminescence'.

• Within the RLum.Data.Image-class image data are now stored in an
  array instead of a RasterBrick object.
• The function plot_RLum.Data.Image() does not know any more about a
  plot type plotRGB. However, the standard raster plot was even
  improved. Please watch out, however, for changed arguments.
• The image format import functions read_SPE2R() and read_TIFF2R()
  were modified to support the new class design.
• The corresponding example dataset was updated.

Removal of app_RLum()

This function was essentially a wrapper around RLumShiny::app_RLum()
written to promote 'RLumShiny'; a package providing a graphical user
interface to 'Luminescence'. 'Luminescence' is essential for
'RLumShiny'. However, this two-way dependency caused unwanted trouble
once the package 'raster' was removed. By removing app_RLum()
'Luminescence' comes lighter because it has fewer dependencies this
unfortunate reverse dependency can be avoided. RLumShiny::app_RLum()
will still work as before, but it cannot be called anymore out of
'Luminescence'. In summary, except for one function less, not much has
changed since both packages need to be installed to run the shiny
applications.

Bugfixes and changes

convert_Activity2Concentration()

• The function had had-coded conversion factors, now the factors are
  calculated, making it easier to include new data, such as updated
  half-life values.
• The documentation is extended and should now be read more clear.

use_DRAC()

• The function now supports up to 5000 datasets, instead of before 33.
  The function template_DRAC() was revised accordingly.

v0.9.17 (CRAN)

Changes in version 0.9.17 (2022-01-01)

This package version requires R >= 4.0.5

Bugfixes and changes

calc_MinDose()/calc_MaxDose()

• The error message if no likelihood profiling can be done now reads
  more clear.

fit_EmissionSpectra()

• method_control = list() gained a new sub-argument norm to
  enable/disable the normalisation of the data. The default is TRUE.

plot_AbanicoPlot()

• The keyword internally set for the font decoration 'plain' was not
  used in get_Layout(), where 'normal' was expected causing the
  function to crash in R-devel if the argument legend was used;
  fixed (#108).

plot_RadioPlot()

• An additional line, e.g., plot_RadialPlot(...,line = 1) was not
  always drawn where the user expected it to be seen; fixed (#106,
  reported by Li Bo)
• The radial z-scale did not always extend to the limits of the data,
  even if limits for the z-scale were set, leading to an odd graphical
  offset and unsuitable plots; fixed (reported by Christina Neudorf)
• The plot now always draws the lower limit of the z-scale.

plot_RLum.Analysis()

• The parameter records_max removed more curves than required;
  fixed.

plot_RLum.Data.Spectrum()

• The function gained a new argument plot that can disable the plot
  and return the matrix used for the plotting instead. This may sound
  a little bit awkward, but it adds enormous flexibility. The function
  does a lot of internal transformations, such as binning or colour
  calculations, which could not be used in other functions before. Now
  the function can be ‘misused’ to create an output object ready to be
  passed to other packages and functions, such as the package
  'plot3D'.