v1.1.2 (CRAN)

Changes in version 1.1.2 (2025-12-12)

This package version requires R >= 4.4

Removed functions and deprecations

• The functions CW2pHMi(), CW2pLM(), CW2pLMi() and CW2pPMi()
  (deprecated since 1.0.0) have been removed, but their functionality
  remains in the corresponding convert_CW2*() functions (#992).

• Functions github_commits(), github_branches() and
  github_issues() are now deprecated and will be removed in a future
  release (#1026).

• Functions is.RLum(), is.RLum.Data(), is.RLum.Data.Curve(),
  is.RLum.Data.Spectrum(), is.RLum.Data.Image(),
  is.RLum.Analysis() and is.RLum.Results(), and are now deprecated
  and will be removed in a future release. The best way of testing
  whether an object is of a given type is by using the inherits()
  function, as in inherits(object, "RLum.Data.Curve") (#1034).

Bugfixes and changes

analyse_Al2O3C_CrossTalk()

• The function no longer crashes if dose_point is misspecified
  (#1073).

• The function no longer crashes when called on an RLum.Analysis
  object rather than on a list of them (#1182).

analyse_Al2O3C_Measurement()

• The function no longer crashes when called on RLum.Analysis objects
  that do not contain records of type "OSL (UVVIS)" or "TL (UVVIS)"
  (#1232).

analyse_baSAR()

• The function no longer crashes if all objects in the input list are
  removed because empty (#1041).

• The dose response curves are no longer overplotted when there are
  fewer than 1000 MCMC iterations (#1058).

analyse_FadingMeasurement()

• The function no longer crashes when called on an object with missing
  originator (#1130, #1154).

• When called with a list containing object with multiple classes, the
  message produced reports the correct number of objects removed from
  the analysis (#1132).

• The function no longer crashes if the normalisation term is zero,
  which should never happen in real-life analyses, but it may occur if
  the input data is somewhat malformed (#1144).

• The function no longer crashes when attempting to remove undesired
  objects from a list-like class that overloads the [<- S3 method
  (#1236).

analyse_IRSAR.RF()

• The function no longer crashes when n.MC = NULL is used with the
  FIT method (#1055).

• The function has been optimized to be faster during the bootstrap and
  sliding phases for the SLIDE and VSLIDE methods, with speed-ups in
  the region of 45% (#1210, #1230).

analyse_pIRIRSequence()

• The names in the curves legend are no longer cut off (#1206).

• Labels and legend in the rejection criteria plot are better positioned
  and no longer cut off (#1208).

• The dashed lines in the summarised DRC plot have been extended to
  reach the outer box instead of leaving small white gaps at the
  extremes (#1215).

• The space around the plots when using plot_singlePanels = FALSE has
  been reduced, so that plots can be a bit more detailed (#1219).

analyse_portableOSL()

• The size of the contour labels for mode = "surface" can now be
  controlled with the ... argument labcex and scale with cex
  (#1075).

• The size of the interpolation grid can be controlled via the ...
  arguments nx and ny (#1077).

• The coord argument is now better validated to avoid a crash in case
  of misspecification (#1097).

analyse_SAR.CWOSL()

• Empty subplots are inserted when onlyLxTxTable = TRUE to preserve
  the usual plot ordering. This prevents a crash that would otherwise
  occur if the option was set from analyse_pIRIRSequence() (#1186).

• The function crashed when applied to an object generated by
  OSLdecomposition::RLum.OSL_decomposition() with plot = TRUE; this
  was a regression introduced in v1.1.0 (#1188; thanks to
  @DirkMittelstrass for reporting).

• The visualisation of the ‘Checks’ (former rejection criteria) was not
  very intuitive. To improve the situation, we now display correct
  inequality symbols, such as <= or >= instead of <> (which was
  meant to be understood as a comparator). Furthermore, the recycling
  ratio now shows better the threshold depending on whether the ratio is
  smaller or larger than one.

• The function crashed if the rejection.criteria list specified a
  NULL value for recuperation_reference (#1204).

• The space around the plots when using plot_onePage = TRUE has been
  reduced, so that plots can be a bit more detailed (#1219).

• The labels in the rejection criteria plot are now shortened only when
  the available horizontal space is not wide enough (#1222).

bin_RLum.Data()

• Validation of the bin_size (for RLum.Data.Curve), bin_size.row
  and bin_size.col (for RLum.Data.Spectrum) has been made stricter,
  so that invalid values produce an error (#1104).

calc_AliquotSize()

• The function no longer hangs when grain.size is set to a small value
  and its minimum and maximum values are the same (#1114).

• The number of MC iteration is now correctly reported in the plot
  subtitle (#1115).

• The function now validates the MC.iter argument to avoid an ugly
  crash if a non-positive value is provided (#1124).

• The function now better validates its grain.size argument (#1152).

calc_CentralDose()

• The profile log-likelihood plot is now cut at a log-likelihood of
  -100, so that for profiles with log-likelihoods more negative than
  that don’t get too squashed in the region of interest (#1227; thanks
  to @DirkMittelstrass for reporting).

calc_CosmicDoseRate()

• The function is now more robust against NA values in its input
  arguments (#1101).

calc_EED_Model()

• A crash that occurred with a small number of simulation was fixed
  (#1051).

• The error message in case of failed surface interpolation is now
  clearer and more complete (#1053).

calc_FadingCorr()

• The function produces an error if g_value is an RLum.Results
  object with an unsupported originator instead of returning NULL
  (#1136).

calc_FiniteMixture()

• The function no longer crashes if the De column contains zeros or
  missing values (#1146, #1148).

• The legend for the components is positioned consistently also at cex
  values other than 1 and is drawn also when pdf.colors = "gray"
  (#1175).

calc_HomogeneityTest()

• The function ignores all columns after the first two, as they could
  lead to crashes if they contained non-numeric values (#1224).

calc_Huntley()

• A warning raised in rare occasions if the number of Monte Carlo
  iterations is very small has been fixed (#1048).

calc_OSLLxTxRatio()

• The Lx.data and Tx.data arguments are now better validated
  (#1178).

calc_SourceDoseRate()

• The function returns a clearer error message if dates are specified in
  an unexpected or ambiguous format (#1162).

calc_Statistics()

• The function could crash if an error was exactly zero. This affected
  also the plotting functions that use calc_Statistics() (#1160).

combine_De_Dr()

• It is now possible to control the random seeds used by the JAGS MCMC
  chains via the method_control argument (#1038).

fit_CWCurve()

• If model fitting failed but an object named fit was present in the
  workspace, the function tried to use that one, which would lead to a
  crash or to unexpected results (#1081).

• The output.table field of the RLum.Results object returned now
  contains only columns corresponding to the components effectively
  fitted (#1083).

fit_EmissionSpectra()

• The function makes better use of the plot area, leaving smaller
  margins around the plot (#1011).

fit_OSLLifeTimes()

• The function throws a warning when the fit fails (#1005).

• The function makes better use of the plot area, leaving smaller
  margins around the plot (#1011).

install_DevelopmentVersion()

• The function has been refactored so that it no longer depends on the
  deprecated github_branches() function (#1079).

plot_AbanicoPlot()

• A warning was raised if the function returned early (for example due
  to invalid inputs) and the graphical device was off (#1001).

• The function now validates the frame argument in order to avoid
  crashing on misspecified values (#1036).

• The function no longer crashes when a small plot.ratio value is
  specified (#1062).

• The function now validates the zlim argument to avoid a crash if
  negative values are used with log.z = TRUE (#1063).

• The legend text now scales better at high cex values (#1066).

• If summary.pos contains multiple valid positions, the first one is
  used rather than generating warnings and not showing the summary
  (#1093).

plot_DoseResponseCurve()

• The plot symbols are now correctly assigned for
  mode = "extrapolation" and in the legend. If reg_points_pch is
  specified, it must now be a vector of 3 elements, corresponding to the
  symbols to use for normal points, point 0 and repeated points,
  respectively (#1072).

• The baseline line in the sensitivity plot has been extended to reach
  the outer box instead of leaving small white gaps at the extremes
  (#1213).

• The space around the plots has been reduced, so that plots can be a
  bit more detailed (#1219).

plot_DRTResponse()

• The function now suppresses the warnings generated by
  graphics::arrows() when datasets having wildly different
  distributions are plotted (#1184).

plot_Histogram()

• Since version 1.0.0, setting summary.pos to one of “left”, “center”
  or “right” and normal_curve = TRUE resulted in the summary table not
  being visible (#1118).

plot_KDE()

• Space a...

v1.1.1 (CRAN)

Changes in version 1.1.1 (2025-09-11)

New functions

• correct_PMTLinearity(): A helper function to correct luminescence
  signals measured with a PMT for count linearity (#920).

Removed functions and deprecations

• Functions calc_Kars2008() (defunct since 0.9.26),
  Analyse_SAR.OSLdata() (since 1.0.0), PSL2Risoe.BINfileData()
  (since 1.0.0) and Second2Gray() (since 1.0.0) have been removed from
  the package. Their functionality can be found in functions
  calc_Huntley2006(), analyse_SAR.CWOSL(),
  convert_PSL2Risoe.BINfileData() and convert_Second2Gray(),
  respectively.

• Function get_Risoe.BINfileData() has been removed as it was not used
  and provided no benefits to the user (#945).

Bugfixes and changes

add_metadata<-()

• The function throws an error if trying to assign a NULL value
  instead of silently ignoring it (#946).

analyse_Al2O3C_ITC()

• The function returns early if the fitting of the dose response curve
  fails (#979).

analyse_Al2O3C_Measurement()

• The function allows to specify the cross_talk_argument as a numeric
  vector of length 3, as was already documented (#930).

analyse_SAR.CWOSL()

• The function crashed if any of the curves had NA as its recordType
  (#867).

apply_CosmicRayRemoval()

• The method argument of smooth_RLum() was not reachable via ...
  as the apply_CosmicRayRemoval() already has an argument called
  method. Now the ... argument is called method_smooth_RLum and
  works as expected (9b27467).

• The function crashed if method = “Pych”andMARGIN = 1` were
  specified. The function now better validates its inputs and no longer
  returns invisibly but normally (#987).

calc_AliquotSize()

• The legend text now scales better at non-default cex settings (#849).

calc_Huntley2006()

• If the user set the n.MC argument, this was also used in the fitting
  of the dose response curve. This was not the expected behaviour, and
  resulted in poor performance (a 2x slowdown for n.MC = 10000). This
  regression was introduced in version 1.0.0 (#867).

calc_MaxDose()

• The function crashed if sigmab was set to a very small value (#898).

calc_MinDose()

• The function crashed when bootstrapping with bs.M = 1. Now the
  bs.M parameter is silently reset to 2 in that case, although such
  low values are discouraged as they may trigger a warning during loess
  fitting (#900).

• The function crashed when all rows in the input data set contained
  NA values (#915).

calc_Statistics()

• The computation of the weighted median is now correct, while before it
  corresponded to the simple (unweighted) median (#905).

fit_CWCurve()

• The function hanged on particularly small datasets as it tried to fit
  too many components for the available data (#953).

fit_DoseResponseCurve()

• The object returned now contains an additional .De.raw column to
  store the calculated De value computed by the fitting function “as
  is”, without setting meaningless results to NA. The De and
  .De.raw columns differ only for mode = "interpolation", where the
  first sets the De to NA if negative, while the latter doesn’t. It is
  then up to the user to decide what to do with those values, bearing in
  mind that they may be arbitrary when negative (#957).

• The message reported for fit.method = "QDR" now states correctly
  whether the fit succeeded or failed (#961).

• The computation of De.MC, De.Error and HPDI for
  mode = "interpolation" has been modified to account correctly for
  possible negative De values resulting from the fit (#963).

• Previously, a single NA value in the Monte Carlo results prevented
  the computation of Highest Density Intervals (HPDI). This limitation
  has been removed, and now HPDIs are reported in more cases (#976).

• The columns of the results$De data frame are now reported in a
  different order; an additional “Mode” column reports the value of the
  mode argument; columns meant for internal use have been moved to the
  end and their names are now prefixed with . (#974).

fit_LMCurve()

• The automatic correction of the x-axis limits when log = "x" is
  specified and the lowest value is set to 0 threw the correct warning
  but actually did nothing (38e4324).

fit_OSLLifeTimes()

• The function ensures that the signal_range argument doesn’t contain
  negative values instead of crashing (#896).

get_RLum()

• The function doesn’t crash anymore on RLum.Analysis objects if using
  the record.id argument removes all available records (#873).

• An internal optimization increased the performance of the function.
  The difference is not perceivable on single calls to get_RLum(), but
  the change brings a visible speed up when merge_RLum() is called
  over a sufficiently large number of RLum.Analysis objects (#875).

merge_Risoe.BINfileData()

• The function gained argument verbose to allow disabling the output
  from read_BIN2R() and write_R2BIN() (#950).

plot_AbanicoPlot()

• The positioning of the y-axis label has been improved to be centred
  around the zero line (#847). The z-axis tickmarks and labels are
  better drawn at non-default cex values (#865).

• The minor grid lines were drawn incorrectly in a rotated plot (#849).

• Some plot elements didn’t scale correctly at non-default cex values
  (#861, #879).

• The frame argument is now respected also when the plot is rotated
  (#863).

• The weighted median is computed correctly when summary = "median"
  and summary.method = "weighted" are used (#905).

plot_DoseResponseCurve()

• We added support for the log graphical parameter, which can be used
  if the fit was obtained with mode other than "extrapolation" (#820).

• The normal curve drawn as part of the histogram plot could appear very
  jagged or even as a straight line, as it could happen that too few
  points were actually used when drawing the curve (#843).

• The legend symbols did not match anymore the plotted regeneration/dose
  points. This also affected functions such as analyse_SAR.CWOSL() and
  analyse_pIRIRSequence() (9ba54e6).

• The legend positioning can now be controlled via the ... argument
  legend.pos (#959).

plot_DRCSummary()

• The dose-response curve is now plotted as expected, after a regression
  in 1.1.0 caused the function to produce an empty plot (#969).

plot_DRTResults()

• Points didn’t scale correctly at non-default cex values (#879).

• Option summary = "weighted$median" is now officially supported
  (#905).

plot_Histogram()

• Option summary = "median.weighted" is now officially supported
  (#905).

plot_KDE()

• Outlier points didn’t scale correctly at non-default cex values
  (#879).

• The weighted median is computed correctly when summary = "median"
  and summary.method = "weighted" are used (#905).

plot_RadialPlot()

• Option summary = "median.weighted" is now officially supported
  (#905).

plot_Risoe.BINfileData()

• Input arguments are validate more strictly to avoid unexpected crashes
  in case of misspecification (#964).

• The x-axis label for TL curves now reports temperature rather than
  time, consistently with the data shown (#971).

plot_RLum.Analysis()

• The legend text now scales better at non-default cex settings
  (#854).

plot_RLum.Data.Curve()

• The function gained a new logical argument interactive that enables
  interactive plotting of curves using plotly::plot_ly(). It requires
  the suggested package 'plotly' to be installed (e4746ea).

plot_RLum.Data.Spectrum()

• Types image and contour gained more control of the contour line
  labels through the argument labcex.

• For plot types "image" and "multiple.lines" the ... logical
  argument legend was added.

• Plot type "image" further gained a legend with support through ...
  for legend.pos, legend.horiz and n_breaks to control the number
  of colours in the graphic.

read_BIN2R()

• The FNAME metadata field is no longer left empty if the BIN-file
  didn’t specify one, but it’s populated with the BIN-file name without
  extension. This is the behaviour that was present up to version
  0.9.26, but version 1.0.0 had regressed it (#928).

read_XSYG2R()

• Add support for the new function correct_PMTLinearity() (#920).

smooth_RLum()

• Add support for the Poisson smoother of Carter et al. (2018), which
  can be accessed by setting method = "Carter_etal_2018". This is
  helpful to ensure that the dark-background counts signals measured by
  a photomultiplier tube follow a Poisson statistic, and smooths
  non-conforming values according to an average over four neighbours
  (#921).

trim_RLum.Data()

• The function crashed if both values specified in the trim_range
  argument exceeded the number of channels available (#871).

use_DRAC()

• Report the message produced by the DRAC server more reliably in case
  of error (#982).

What's Changed

• Remove defunct functions calc_Kars2008() and Analyse_SAR.OSLdata() by @mcol in #841
• Add support for log transformation in plot_DoseResponseCurve() by @mcol in #842
• Make normal curve not appear jagged in plot_DoseResponseCurve() by @mcol in #844
• Use uniformly-spaced points when log = "x" in plot_DoseResponseCurve() by @mcol in #846
• Ensure that the density polygon is closed correctly in plot_DoseR...

v1.1.0 (CRAN)

Changes in version 1.1.0 (2025-06-11)

New functions

• remove_SignalBackground(): A user-friendly method to subtract
  background signals from various curves in RLum.Analysis objects
  without resorting to lapply() loops. Depending on the record type,
  the function identifies pairs of curves; for instance, if in a
  sequence, a TL curve is immediately followed by another TL curve,
  the second curve is recognised as the background signal, subtracted
  using merge_RLum() and subsequently removed from the object (if
  desired). Alternatively, a set of potential background curves can be
  specified.

• remove_RLum(): This function further completes the set of methods
  that can handle and modify RLum-class objects. It operates on
  RLum.Analysis objects or a list of such objects to remove unwanted
  records from datasets. Although the function calls get_RLum() and
  relies on its functionality, the new implementation facilitates a more
  logical workflow and analysis pipeline.

• .as.latex.table(): Converts RLum.Results objects where suitable to
  LaTeX ready tables, for instance, objects produced by use_DRAC().
  The function has been present in the package as an internal function
  for many years; now it is exported and better linked to make it
  discoverable.

New datasets

• RF70Curves is a new dataset consisting of two IR-RF curves measured
  with the RF70 protocol. This new dataset provides a more realistic
  example for analyse_IRSAR.RF().

Breaking changes

• Function get_Quote() is no longer exported, but remains available as
  an internal function. This is unlikely to affect any user of the
  package, as the function was only meant to report a random quote at
  startup (#644).

• In the functions fit_DoseResponseCurve() and plot_GrowthCurve(),
  the fit.method option LambertW was replaced by the more correct
  term OTOR.

• Argument cex.global has been removed from plot_DoseResponseCurve()
  (and consequently also from plot_GrowthCurve()), and if set it will
  be silently ignored. Users can set the cex graphical parameter via
  ... in its place (#831).

• The fit.method and fit.advanced arguments of function
  fit_LMCurve() have been removed. The default fitting method has been
  changed from port to LM, and support for the port algorithm has
  been removed. From now on, argument fit.method is silently ignored,
  unless fit.method = 'port' is used, in which case a deprecation
  warning is thrown (#793).

• The fundamental physical constants used in the package (such as
  Boltzmann constant, Planck constant, etc.) have been uniformed to
  those reported in the NIST Reference on Constants, Units and
  Uncertainty. This may affect
  the numerical results of the following functions: calc_FastRatio(),
  calc_Huntley2006(), calc_SourceDoseRate(),
  calc_ThermalLifetime(), convert_Activity2Concentration(),
  convert_Wavelength2Energy(), fit_CWCurve(), fit_LMCurve(),
  fit_SurfaceExposure(), fit_ThermalQuenching() (#693).

Bugfixes and changes

analyse_baSAR()

• The function crashed if only one aliquot was kept (#834).

analyse_FadingMeasurement()

• The function crashed if the number of Lx and Tx curves was not
  equal when structure = c("Lx", "Tx"), which is the default. The
  check that the number of points within each pair of curves has also
  been improved, and the function now produces more helpful error
  messages (#616).

• The function tests are now less rigorous for different Lx and Tx
  sizes. While they should match, numerical rounding issues in the data
  returned by the measurement devices could previously result in
  rejection of records, although this had no actual meaning for the data
  analysis.

analyse_IRSAR.RF()

• The legend and subtitle texts now scale better at non-default cex
  settings (#803).

• The printing of progress bars and messages to the terminal can now be
  controlled via the ... argument verbose. Previously this could
  only be done via the txtProgressBar argument (which is still
  supported), but the new option makes the interface consistent with
  most other functions (#805).

• The mtext and cex options are respected if method = "None"
  (#807).

• The residual plot correctly respects the logarithmic transformation of
  the x-axis when log = "x" or log = "xy" are specified (#814,
  #825).

• The function now deals correctly also with input objects containing
  multiple curves (#816).

• The residual indicator rectangle, which is drawn when method is
  either SLIDE or VSLIDE, is also drawn when log = "x" (#821).

• The plotting of the density is silently disabled if n.MC = NULL,
  which avoids a spurious warning (#823).

analyse_pIRIRSequence()

• The function now respects the cex graphical argument, and its plot
  output has been subtly improved thanks to various fixes that have
  occurred especially in plot_DoseResponseCurve() (#831).

analyse_portableOSL()

• The function now returns an error if mode is something other than
  "profile" or "surface".

• The mode argument was not respected when operating over a list of
  objects (#673).

• The function crashed when using mode = "surface" if the plotting
  limits were too tight and left only one point (#675).

• The check on the validity of the signal.integral argument has been
  improved, and now it occurs only once, so at most one warning is
  raised if the argument is set to a value exceeding the valid range
  (#678, #680).

• The function returns a clearer message when no x-coordinates were
  measured and mode = "surface" was used (#682).

• The cex and type graphical parameters can now configured via the
  ... argument (#684).

• The expected sequence pattern of the input object is validated more
  thoroughly to avoid crashes in case of misspecification (#687).

• The graphical ... argument contour never produced a meaningful
  contour plot due to an internal error (#686). Along, arguments
  contour_nlevels and contour_col are now supported through ... to
  better control the number and colour of contour lines.

analyse_SAR.CWOSL()

• Add support for fit.method = 'OTORX' following the changes in
  fit_DoseResponseCurve(); this change includes the new argument
  dose.points.test that is only of use in combination with the OTORX
  fit.

• Add new graphical output if the measurements were single grain
  measurements, in such case a disc with the position and grain number
  marked in shown. This plot replaces the IRSL curve check plot, but
  only for single grain data (#797).

• The rejection criteria plot was rewritten and now provides an easier
  to grasp visual feedback (#797, #798).

• The IRSL/Single Grain panel swapped place with the rejection
  criteria panel; the plot numbers remained unchanged to avoid
  regression.

• More code optimisation for better readability (#802)

analyse_SAR.TL()

• A check on the sequence.structure argument ensures that a “SIGNAL”
  entry has been specified (#779).

calc_AliquotSize()

• The new argument sample_carrier.diameter allows to specify a value
  for the diameter of the sample carrier, which up to now was hardcoded
  to the very common 9.8 mm size (#623).

• Several graphical parameters can now configured via ... arguments,
  so that the plot appearance can be fully customized (#671).

calc_AverageDose()

• A bug in the implementation prevented the default plot settings from
  being modified via ... as advertised. Now custom settings are
  respected (#658).

calc_FiniteMixture()

• The function doesn’t crash anymore if the n.components argument
  specifies non-consecutive values (#691).

• The function sometimes failed to plot some of the densities when the
  number of components was set to a value of 8 or more (#704).

• The density plots would not always be coloured completely, but
  especially for high values of sigmab there would be an unfilled area
  at the base of the densities (#706).

• If the very first iteration over the components during plotting was
  skipped, then the function crashed as a quantity computed only in that
  iteration was not available. This happened for very specific
  combinations of sigmab and n.components (#708).

• Another crash occurred when height of the largest density curve could
  not be estimated due to the presence of too many NA values in the
  intermediate computations (#710).

• The check for significance of each component added to the model has
  been corrected to be more statistically rigorous (#703).

• Blank gaps appearing to the sides of the proportion of components plot
  for high number of components have been removed (#713), as well as
  extra slices appearing due to rounding errors (#715).

• The plot can be better configured via the new plot.criteria argument
  to control whether the statistical criteria curves should be drawn.
  Moreover, support for the ... options has been added: cex to
  control the overall scaling, main.densities, main.proportions and
  main.criteria to set the subplot titles (#717).

• Plots are now generated even when results contain NA values, as they
  in general don’t affect the plot. However, when that happens we report
  it in the plot subtitle (#718).

calc_Huntley2006()

• Support was added for multicore computations via the cores argument,
  and for the nls-fitting control options maxiter and trace.

• The fitting of the simulated curve with the GOK model has been made
  more robust: when an initial fit of the model fails, the ...

v1.0.1 (CRAN)

Changes in version 1.0.1 (2025-03-07)

Bugfixes

analyse_baSAR()

• The number of aliquots used was only partially reported if no aliquots
  were removed, resulting in an incomplete message in the output to the
  terminal.

analyse_FadingMeasurement()

• The function now checks that an input object generated from an XSYG
  file contains irradiation steps and returns an error if none are
  available, instead of producing an unhelpful output (#588).

• A regression in plot_RLum.Analysis() caused part of the plot of the
  luminescence curves to be garbled (#589).

• The function crashed on a file generated by read_XSYG2R() if the
  number of curves available after removal of the irradiation step was
  not enough for the the fading measurement to be analysed (#603).

analyse_pIRIRSequence()

• The check on the minimum device plot size used to fail if only one
  dimension was below our minimum threshold, and when it was incorrectly
  triggered by the floating point values computed by
  grDevices::dev.size(), which sometimes could be spuriously just
  below threshold. We also changed the minimum device size from 18 to 16
  inches (#593).

calc_CosmicDoseRate()

• The function crashed if the number of depths provided exceeded that of
  the densities and the latter contained more than one value (#595).

calc_FadingCorr()

• The function sporadically returned an implausibly large error estimate
  if any of the Monte Carlo simulations produced an outlier solution
  (#597).

• The function now allocates only as much memory as required if the user
  specifies a value for n.MC other than "auto", which brings a small
  speed-up if fewer than 10 million samples are requested.

• Input arguments are now more thoroughly checked to avoid warnings or
  unhelpful messages (#599).

calc_FastRatio()

• The function crashed if the input was an RLum.Analysis object (#586).

plot_AbanicoPlot()

• The xlim, ylim and zlim parameters are now better validated to
  avoid possible crashes if misspecified (#581).

plot_RLum.Analysis()

• The function reset incorrectly the graphical parameters for the case
  plot_singlePanels = TRUE. This caused a regression in the plot
  output from analyse_FadingMeasurement() (#589).

sort_RLum()

• The function doesn’t crash when multiple fields are specified,
  although the actual sort at the moment occurs only on the first field
  (#606).

• Attempting to sort an empty object returns the object itself instead
  of crashing (#608).

What's Changed

• Validate xlim, ylim and zlim in plot_AbanicoPlot() by @mcol in #582
• Complete coverage for calc_CosmicDoseRate.R by @mcol in #583
• Replace sapply(x, length) and similar with lengths() by @mcol in #585
• Fix crash in calc_FastRatio() on RLum.Analysis objects by @mcol in #587
• Check that irradiation steps are available if the originator is read_XSYG2R by @mcol in #590
• Fix regression in plot generated by analyse_FadingMeasurement() by @mcol in #591
• Fix the minimum device plot size checks in analyse_pIRIRSequence() by @mcol in #594
• Tighten checks on inputs and consolidate code in calc_CosmicDoseRate() by @mcol in #596
• Tighten the outlier threshold in calc_FadingCorr() by @mcol in #598
• Improve validation and documentation of calc_FadingCorr() arguments by @mcol in #600
• Improve validation against a character vector by @mcol in #602
• Fix crash in analyse_FadingMeasurement() if not enough curves are available by @mcol in #604
• Fix crashes in sort_RLum() if more than one field is specified by @mcol in #607
• Don't crash when sorting an empty RLum.Analysis object by @mcol in #609

Full Changelog: v1.0.0...v1.0.1

v1.0.0 (CRAN)

Changes in version 1.0.0 (2024-02-21)

New functions

• apply_Crosstalk(), calc_MoransI(), plot_SingleGrainDisc() and
  plot_MoranScatterplot() were contributed by Anna-Maartje de Boer and Luc
  Steinbuch (#560). An introductory example on how to use these functions
  is available by executing vignette("crosstalk").

• calc_EED_Model() models incomplete and heterogeneous bleaching of
  mobile grains after Guibert et al. (2017). Along with the function, the
  new ExampleData.MortarData data set was added.

• fit_DoseResponseCurve() and plot_DoseResponseCurve() are two new
  functions derived from plot_GrowthCurve(): the first only performs the
  fitting of a dose-response curve, while the second plots it. This brings
  greater flexibility and increased speed, as plotting is now independent of
  fitting (#141, fixed in #318).

• melt_RLum(): Creates a new flat data.frame that can be used for instance
  in combination with 'ggplot2'. It works only on RLum.Data.Curve-class
  and RLum.Analysis-class objects and lists of such objects.

• merge_RLum.Data.Spectrum(): This new function allows to merge two or
  more RLum.Data.Spectrum objects in different ways (#368, fixed in #419).

• add_metadata(), rename_metadata(), replace_metadata():
  These function allow to manipulate the metadata of
  Risoe.BINfileData, RLum.Analysis and RLum.Data objects (#480, fixed
  in #514, #524, #525, #527, #534, #545).

• sort_RLum(): Allows to sort the records of RLum.Analysis and
  Risoe.BINfileData objects according to a given slot or info element
  (#528, fixed in #571 and #576).

• view(): Provides a shortcut to the utils::View() spreadsheet-like data
  viewer tailored to the objects in the package (#489, fixed in #490).

Breaking changes

• We have dropped our dependency on the readxl package: functions
  analyse_baSAR() and use_DRAC() now do not accept XLS files anymore but
  CSV files instead (#237, fixed in #270). CSV files can be easily generated
  from XLS files by Excel or similar applications, or by reading them with
  readxl::read_excel() and saving them with write.csv().

• The plot.single option, which was available for several functions,
  sometimes under a slightly different name, has now been renamed to
  plot_singlePanels for overall consistency and clarity. Function
  scale_GammaDose() used that option but gave it the opposite meaning: now
  also this function conforms to the rest of the package. The use of the
  older names is now deprecated and will produce a warning (#351, fixed in #408).

• The NumberIterations.MC option of plot_GrowthCurve() has now been
  renamed to n.MC for consistency with other functions. Potentially affected
  are also analyse_Al2O3C_ITC(), analyse_baSAR(), analyse_SAR.CWOSL(),
  analyse_SAR.TL(), calc_Huntley2006(), calc_Lamothe2003(),
  as they may pass that option plot_GrowthCurve() via their ... argument.
  The use of the older name is now deprecated and will produce a warning (#546,
  fixed in #547).

Renamed functions and deprecations

• Function Analyse_SAR.OSLdata() is now officially deprecated,
  analyse_SAR.CWOSL() should be used instead (#216, fixed in #264).

• Functions CW2pHMi(), CW2pLM(), CW2pLMi() and CW2pPMi() have been
  renamed to convert_CW2pHMi(), convert_CW2pLM(), convert_CW2pLMi()
  and convert_CW2pPMi(), respectively. The use of the older names is now
  deprecated and will produce a warning (#499, fixed in #503).

• Function Second2Gray() has been renamed to convert_Second2Gray()
  (#498, fixed in #500).

• Function PSL2Risoe.BINfileData() has been renamed to convert_PSL2Risoe.BINfileData()
  (#555, fixed in #556).

New dependencies

• We have added package ’vdiffr’ as dependency in suggests. The package
  enables us to automatically verify the consistency of plot outputs generated
  by package functions against reference figures captured earlier. Although
  this new dependency does not have any user-visible impact, it is required
  when building ’Luminescence’ from source. The primary advantage lies in the
  developer's domain, as it ensures that modifications to functions do not
  inadvertently alter plot outputs.

Bugfixes

analyse_Al2O3C_CrossTalk()

• The function doesn't crash anymore if option recordType is specified and
  none of the records in the data set is of that type (#487, fixed in #488).

analyse_baSAR()

• Argument XLS_file has been replaced by CSV_file and, as mentioned
  above, the function now only accepts CSV files as input (#237, fixed in #270).
• Add support for recordType passed to get_RLum in the additional arguments.
• Option plot.single has been renamed to plot_singlePanels (#351, fixed
  in #408).
• The function crashed if the number of MCMC iterations was set equal to the
  thinning interval; on the other hand, we saw errors reported from JAGS if the
  number of MCMC iterations was not at least double the thinning interval. To
  address this, we slightly retouched our automatic setting of the thinning
  interval (which was problematic only if the number of MCMC iterations was
  extremely low); on the other hand, if a user sets a thinning interval that
  is too high, we now reset it to a lower value and raise a warning (#407,
  fixed in #409).
• The function crashed if a Risoe.BINFileData object was provided and the
  argument irradiation_times was set; fixed.
• The function was supposed to remove non-OSL curves from the dataset, but
  it almost never did; fixed.
• The function is more robust against input that may have been subset
  inconsistently (#517, fixed in #518).
• The function doesn't crash but reports more helpful messages in case the
  user overrides the default set of monitored variables using variable.names
  within the method_control argument (#521, fixed in #522).

analyse_SAR.CWOSL()

• The function crashed for a list input that led to NULL for various
  reasons (e.g., unsuitable set of curves). Here the self-call attempted to
  extract information from the results that did not exist in the first place
  instead of returning NULL; fixed.
• The produced RLum.Results object now also contains a column for the
  grain (#553, fixed in #554).

analyse_FadingMeasurement()

• The function now checks for the version of the BIN-file that originated the
  RLum.Analysis object given as input, and reports a message if a version
  older than 5 was used (#281, fixed in #282).
• The function doesn't crash anymore on some RLum.Analysis input files
  (#283, fixed in #288).
• Option plot.single has been renamed to plot_singlePanels (#351, fixed
  in #408).
• The function doesn't crash anymore if no record is left after removal of
  records with negative time since irradiation (#454, fixed in #456).
• The function has been made more robust in the calculation of rho' (#558,
  fixed in #559).

analyse_IRSAR.RF()

• The performance of this function has been improved for the "SLIDE" and
  "VSLIDE" methods, thanks both to tweaks in the C++ implementation of the
  sliding algorithm and in how that is managed on the R side. In particular,
  the default number of sliding windows tested in the algorithm has been
  reduced from 10 to 3: this value is no longer hardcoded, but can be tuned
  through the new num_slide_windows setting (part of the method.control
  option), thus allowing to find a balance between computation time and
  quality of fit (#372, fixed in #388, #398 and #399).
• The function is more robust against sequence_structure misspecifications
  (#393, fixed in #394).
• Some data preparation steps where not correctly applied for method = "VSLIDE"
  (#396, fixed in #397).
• Option method.control has been renamed to method_control for consistency
  with all other functions in the package (#411, fixed in #412).

analyse_pIRIRSequence()

• Option plot.single has been renamed to plot_singlePanels (#351, fixed
  in #408).
• The produced RLum.Results object now also contains a column for the
  grain (#553, fixed in #554).
• The function now checks that the sequence.structure argument contains
  at least one IR step (#579, fixed in #580).

analyse_SAR.CWOSL()

• Option plot.single has been renamed to plot_singlePanels (#351, fixed
  in #408).
• The function shifted the curves correctly in cases where the first channel
  is zero and a log-transformation on the x-axis is requested (#580, fixed in
  #531).

apply_CosmicRayRamoval()

• Support has been added for the internal function smooth_RLum that can
  be passed as new argument for method.

calc_AverageDose()

• The function crashed if the data contained non-positive values: now these
  are removed before proceeding (#532, fixed in #533).

calc_CentralDose()

• Argument na.rm is now deprecated: the function will now always remove
  missing values, as otherwise the presence of any NA would propagate and
  produce unusable results (all NAs) or buggy behaviour (#302, fixed in #304).
• The function stops the fixed-point iteration for the computation of the
  profile log-likelihood as soon as sigma < 1e-16, as allowing sigma to
  become zero leads to infinities and buggy behaviour (also fixed in #304).

calc_FastRatio()

• A number of crashes related to input validation have been fixed (#471,
  fixed in #472).

calc_FiniteMixture()

• Arguments dose.scale and pdf.scale were not used and have been
  removed (#566, fixed in #567).

calc_gSGC()

• The function crashed if the data contained negative errors: to avoid this,
  we now take the absolute values of errors (#479, fixed in #481).

calc_Huntley2006()

• Some crashes in case of model misspecification have been solved (#538,
  fixed in #539).
• Some details in the implementation of the function have been optimized, and
  now it is much faster than before. As ...

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.