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Changelog

Source: NEWS.md

Changes in version 0.9.26 (2024-11-18)

CRAN release: 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).

Changes in version 0.9.25 (2024-09-12)

CRAN release: 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, 1).

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, 1).

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

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 1)

calc_TLLxTxRatio()

  • Function crashed for Tx.data.background = NULL (#129); fixed with #130 thanks to 1

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, 1).

fit_OSLLifeTimes()

  • The validation of the minimum dataset size didn’t account for the use of the signal.range argument (#182, fixed by #195, 1).

fit_SurfaceExposure()

  • Fix #162 to remove a dimension mismatch if the input data contained NAs, which would generate unexpected warnings (#163, 1).
  • The function doesn’t stop anymore with an error if called on an RLum.Results object (#165, 1).

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, 1).

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 1).

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 1)

read_XSYG2R()

  • Fix spectrometer data import for basically broken files.

read_Daybreak2R()

  • Fix #135 to improve detection of non-ASCII files (#140, 1).

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.