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 #173
• Small improvement in input validation in template_DRAC() by @mcol in #174
• Silence some more test output by @mcol in #176
• More coverage by @mcol in #178
• Silence some more test outputs by @mcol in #180
• fixes for crashes in plot_NRt() by @mcol in #179
• Don't pollute the workspace with example data when running tests by @mcol in #181
• Check that there are records in an object before subsetting from them by @mcol in #184
• Some more coverage by @mcol in #185
• More coverage by @mcol in #188
• Simplify and correct the check for Inf in plot_KDE() by @mcol in #190
• Fix crash in analyse_FadingMeasurement() with different length objects by @mcol in #192
• Some more coverage and removal of unreachable code by @mcol in #193
• Support vectors and single-column data frames in plot_KDE() by @mcol in #194
• Add a check for zero-row input data to plot_KDE() by @mcol in #196
• Improve validation of data size in fit_OSLLifeTimes() by @mcol in #195
• Fix computation of number of breaks in calc_WodaFuchs2008() by @mcol in #198
• Support vectors and single-colums dataframes in calc_WodaFuchs2008() by @mcol in #200
• More coverage by @mcol in #201
• More coverage by @mcol in #204
• Validate signal and background integral values in plot_DetPlot() by @mcol in #206
• Finish silencing the test ouput by @mcol in #205
• Remove the output.path argument from fit_CWCurve() by @mcol in #209
• Add full support for single-column data frames to plot_RadialPlot() by @mcol in #212
• Fix crash in plot_DetPlot(..., analyse_function = "analyse_pIRIRSequence") by @mcol in #211
• Remove the defunct na.rm option from plot_GrowthCurve() by @mcol in #214
• Better validation of the par argument of calc_MinDose() by @mcol in #218
• More coverage by @mcol in #213
• Validate the plot.ratio argument of plot_AbanicoPlot() by @mcol in #222
• Make calc_WodaFuchs2008() work on more RLum.Results objects by @mcol in #219
• Make Risoe.BINfileData2RLum.Analysis() deal with empty input objects by @mcol in #224
• Make .Risoe.BINfileData2RLum.Data.Curve() work without the id argument by @mcol in #227
• Make read_BIN2R() not crash when forcing a version on an empty file by @mcol in #226
• Improve consistency check in extract_IrradiationTime() by @mcol in #229
• More coverage by @mcol in #230
• Fix crash when using interactive mode for plot_Histogram() by @mcol in #231
• Make interactive mode in plot_AbanicoPlot() functional again by @mcol in #233
• Fix S3 methods that didn't work by @mcol in #232
• Exclude untestable functions from coverage by @mcol in #235
• Remove duplicate check in write_R2BIN() and reword error message by @mcol in #236

New Contributors

• @mcol made their first contribution in #134

Full Changelog: v0.9.24...v0.9.25