Luminescence

• analyse_Al2O3C_CrossTalk()
• analyse_Al2O3C_ITC()
• analyse_FadingMeasurement()
• analyse_IRSAR.RF()
• plot_AbanicoPlot()
• plot_DoseResponseCurve()
• plot_DRCSummary()
• plot_DRTResults()
• plot_Histogram()
• plot_KDE()
• plot_RadialPlot()
• We are in the process of streamlining the set of S3 methods that we export. This will not bring any loss of functionality, but will reduce some redundancy in the internal code. We don’t think that there are active users of these specific functions and, in most cases, these are of interest only to package developers. Therefore, the following S3 methods are deprecated and will be removed in v1.4.0 (#1694). | Deprecated | Replacement | |--------------------------------|-------------------| | as.data.frame.RLum.Data.* | as.data.frame() | | as.list.RLum.* | as.list() | | as.matrix.RLum.Data.* | as.matrix() | | dim.RLum.Data.* | dim() | | hist.RLum.* | hist() | | length_RLum, length.RLum.* | length() | | merge_RLum.*, merge.RLum.* | merge_RLum() | | names_RLum, names.RLum.* | names() | | plot.RLum.* | plot() | | summary.RLum.Data.* | summary() |
• The Monte Carlo error in fit_DoseResponseCurve() was slightly overestimated when any MC model failed to fit. As a way to establish whether an analysis run with Luminescence <= 1.3.0 is affected by this issue, you can count the number of failed MC runs in the results object by running sum(is.na(results$De.MC)). A value greater than 0 means that the error estimation is affected; quantifying by how much is not possible without rerunning the analysis with v1.3.1, but the size of the effect grows with the proportion of failed runs (sum(is.na(results$De.MC)) / length(results$De.MC)), and in non-pathological cases it should be very small (#1730).

analyse_Al2O3C_Measurement()

• The function now better validates the dose_points argument so that it no longer generates an incorrect data frame if the argument is provided as a list when the main input is a non-list object (#1640).

analyse_IRSAR.RF()

• The colour of the regeneration points was changed to black to guarantee greater contrast against the natural points. This should improve readability for people with red-green colour blindness and for black-and-white printing. Moreover, point colours can now be freely customised via the new col_nat and col_reg parameters (#1654; thanks to @DirkMittelstrass for reporting).
• The plot is no longer constrained to keep a fixed aspect ratio, so that it can occupy more of the available space (#1654; thanks to @DirkMittelstrass for reporting).
• The default x-axis label was changed from "Time" to "Irradiation time", (#1654; thanks to @DirkMittelstrass for reporting).
• The y-axis no longer enforces the labels to be in scientific format. The previous behaviour can be restored by setting yaxis_scientific = TRUE (#1665).
• The cores argument no longer accepts "auto" as valid input: the same functionality (using all but two of the available cores) can now be achieved by setting cores = NULL (#1668).
• A warning message shown in case of failure of the test parameters has been improved to avoid reporting a spurious NA (#1715).
• The function used to crash during plotting if any the extremes of the confidence interval built around the De value was computed as NaN. This was a very old (and presumably extremely rare) crash that affected only method = "FIT" (#1744).

analyse_pIRIRSequence()

• The function no longer crashes when presented with an empty RLum.Analysis object (#1725; thanks to Annette Kadereit for reporting).
• The check on the window size now occurs also if plot_singlePanels = TRUE. This avoids hard failures on Linux when both plot_singlePanels and plot_onePage are set to TRUE and the window size is too small; on Windows, it seems that instead of a hard error, the function would silently stop working with those settings (#1734; thanks to Annette Kadereit for reporting).

analyse_SAR.CWOSL()

• The ordering of columns in the $data field of the result object was different from expected when fit_DoseResponseCurve() returned NULL, which meant that merging the results from multiple aliquots would fail if any such result was present. This was a regression introduced in v1.1.1 (#1623).
• The POS and GRAIN columns in the $data field of the result object are now correctly populated also for XSYG files, instead of being set to NA. This was a regression introduced in v1.1.2 (#1625).
• It is now possible to set recuperation_reference = "Rmax" to select the point with highest dose as reference in the calculation of the recuperation rate (#1740; thanks to Annette Kadereit for reporting).

analyse_SAR.NCF()

• The object argument is now better validated (#1657, 1732).

analyse_SAR.TL()

• The function no longer crashes if the input object contains no TL curves (#1732).

calc_CentralDose()

• The function no longer crashes when the De values are identical and log = FALSE (#1628).
• The removal of missing values now happens only after restricting the input to the first two columns, so NA values in unrelated columns no longer affect the operation of the function (#1653; thanks to @DirkMittelstrass for reporting).

calc_FastRatio()

• Some code that adjusted the Ch_L3 setting has been removed because it had become largely superfluous since v0.9.25. Users should see no impact, except in the unlikely case when both elements of Ch_L3 are set to the last channel. In that case, the computation will now respect the user input instead of automatically moving the start of Ch_L3 back by 5 channels. That behaviour was an undocumented leftover from when user inputs were not validated (#1682).
• The number of background channels was counted as one fewer than the number used, causing the computed errors to be marginally larger than expected. This error has been present since 2016, and its impact on the results produced depends on the number of background channels used, with the inflation of errors decreasing as the size of the background region grows (#1684).

calc_FuchsLang2001()

• The function now returns an error if startDeValue exceeds the number of rows in the input data set, instead of returning only NAs in the result table (#1645).

calc_Huntley2006()

• The cores argument now can be set to NULL to use all but two of the available cores (#1668).
• The function no longer crashes when plotting in extrapolation mode if both De.measured and De.measured.error are 0 (#1672).

calc_MaxDose()

• The function is now documented alongside calc_MinDose() (#1674).

calc_MinDose()

• The removal of missing values now happens only after restricting the input to the first two columns, so NA values in unrelated columns no longer affect the operation of the function (#1659).
• The multicore argument has been deprecated and is no longer functional. Its functionality has been replaced by the cores argument, which can be set to either a numeric value or to NULL to use all but two of the available cores (#1668).
• The function now validates that the initial parameter values supplied via init.values are strictly positive, as non-positive values may cause unrecoverable crashes during fitting (#1670).
• It is now possible to disable the second-level bootstrap entirely by setting bs.N = 0. This setting corresponds to a classic bootstrap, as opposed to the recycled bootstrap that would otherwise be run by default (#1525; thanks to @MarijnvanderMeij for reporting).

calc_SourceDoseRate()

• Source type "Am-241" was misspelled in the documentation and in the function as "Am-214" and has now been corrected. The latter form is no longer accepted (#1630).

calc_Statistics()

• The function incorrectly ignored the error column whenever only some error values were exactly 0, which led to miscalculated weighted statistics. This was due to a regression introduced in v1.1.2; weighted mean, weighted median and the corresponding standard error and standard deviation are now set to NA in such cases, restoring the original behaviour (#1686).

fit_DoseResponseCurve()

• If the (optional) TnTx column contains only NAs, the column is ignored instead of causing the entire dataset to be dropped (#1632).
• The number of parameters for fit.method = "DSE" and "QDR" has been corrected to 5 and 3, respectively. For "DSE" this was a regression introduced in v1.3.0, when a new Di parameter was added to the "DSE" method without updating its parameter count; for "QDR", the behaviour regressed in v1.0.0, when predict() was introduced to replace the manual evaluation of the model fit. In both cases, this has no user-visible effect other than changing the number of dose points under which the function switches to using the “LIN” method (#1634, \#1636).
• When the root finding step failed during the Monte Carlo simulation for fit.method = "OTORX" and mode = "extrapolation", the function incorrectly reverted to the OTOR model before attempting that iteration again. This turned out to be a simple typo, with minimal impact (#1727).
• The Monte Carlo error estimation considered spurious contributions from iterations that failed to fit. This was caused by the result vector being initialised to 0 instead of NA, which resulted in a slight overestimation of errors when any MC model failed to fit (#1730).

fit_OSLLifeTimes()

• The function no longer crashes when using a list containing an empty RLum.Analysis object (#1732).

merge_Risoe.BINfileData()

• Argument objects has been renamed to object. The older name will still work, but it generates a deprecation warning (#1697).

merge_RLum()

• Argument objects has been renamed to object. The older name will still work, but it generates a deprecation warning (#1697).

merge_RLum.Analysis()

• Argument objects has been renamed to object (#1697).
• The function no longer crashes when using a list containing an empty RLum.Analysis object (#1732).

merge_RLum.Results()

• Argument objects has been renamed to object (#1697).

plot_AbanicoPlot()

• The default background colour was incorrectly set to NA, which in some very specific cases would cause some overplotting, at least on MacOS (#1649).
• The interactive plotting mode (interactive = TRUE) is more complete and renders a usable plot (#1664, \#1696).
• The function no longer crashes when using a list of data frames with different column names (#1705).
• A misspecified bw argument now reverts to the default value of "SJ" recommended by base R, instead of the historical (and somewhat deprecated) setting of "nrd0" (#1708).
• Datasets containing only one non-missing observation are no longer removed and are now plotted, but no density curve is drawn for them unless a numeric value is provided for the bw (bandwidth) argument (#1707; thanks to Annette Kadereit for reporting).
• Plot colours are now respected when one of the input data frames is automatically removed because it contains no non-missing observations (#1707; thanks to Annette Kadereit for reporting).
• The logic for the positioning of the boxplot has been slightly revised to avoid cases in which the boxplot was plotted over one of the axes or even completely outside of the visible area (#1713; thanks to Annette Kadereit for reporting).

plot_DetPlot()

• The multicore argument has been deprecated and is no longer functional. Its functionality has been replaced by the cores argument, which can be set to either a numeric value or to NULL to use all but two of the available cores (#1668).

plot_DoseResponseCurve()

• The size of the repeated point has been slightly increased to make it more distinguishable (#1722).

plot_KDE()

• The plot title is no longer drawn in a bold font, and the spacing between words in title and x-axis label has been refined so that the words no longer look attached (#1717).

plot_RadialPlot()

• The function no longer crashes when the error column contains NA values. This was a regression introduced in v1.2.0 (#1689).

plot_RLum()

• The handling of mtext has been improved so that, when specified as a list, each element is dispatched (with recycling) to each object being plotted, making mtext behave like the main argument. This was a regression introduced in v1.2.0 (#1676).

plot_RLum.Data.Curve()

• If the IRR_UNIT field is present in a BIN file (version 03 or 04), this is used as unit measure in the axis labels instead of seconds (#1721).

plot_RLum.Data.Spectrum()

• The setting legend = FALSE did not work as advertised and did not remove the legend, e.g., in plot.type = "multiple.lines" (#1702).
• The argument legend.text was removed from the function definition but it’s still available through the ... argument (#1702).

read_RF2R()

• Headers generated by the upcoming 'RLumImage' package are now supported (#1655; thanks to @DirkMittelstrass for reporting).
• Header parsing is now more robust and supports quoted strings containing spaces. Malformed header values no longer cause all headers to be lost: valid values are now stored in the info slot, while malformed entries are silently dropped and no longer produce a message (#1742; thanks to @DirkMittelstrass for reporting).

read_XSYG2R()

• The function no longer crashes when an empty <sequence /> node is found. Such a node may be present if the reader encounters an empty position and would then automatically move on to the next.

verify_SingleGrainData()

• The message reported when cleanup = TRUE is used is now shorter and more readable as it compresses consecutive record indices into a range (#1647).

write_R2BIN()

• Arguments file and version are now better validated (#1680).

Other changes

• We have expanded the family of snapshot tests by testing the function output in more cases, going from 12 to 85 output snapshots (#1638).
• Functions plot_AbanicoPlot() and plot_RLum.Data.Curve() gained a hidden .shiny flag which can be set in combination with interactive = TRUE to return the plotly object instead of printing it. This was added to improve the interactive functionality within the RLumShiny package.

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