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_DoseResponseCurve() by @mcol in #848
Add more graphical snapshot tests by @mcol in #850
Fix the cex setting in legend() of calc_AliquotSize() by @mcol in #851
Add some snapshot and graphical snapshot tests by @mcol in #853
Fix the cex setting in legend() of plot_RLum.Analysis(). by @mcol in #855
Add more flexibility to the message reported by .throw_message() by @mcol in #856
Improve positioning of y-axis label in plot_AbanicoPlot() by @mcol in #858
Fix incorrect drawing of the minor grid lines on a rotated plot by @mcol in #860
Respect the cex in plot_AbanicoPlot() by @mcol in #862
Support the frame argument also for a rotated Abanico plot. by @mcol in #864
Improve z-axis label positioning and tickmarks in plot_AbanicoPlot() by @mcol in #866
Fix performance regression in calc_Huntley2006() if n.MC is set by @mcol in #868
Don't crash in analyse_SAR.CWOSL() if recordType is NA by @mcol in #870
Don't crash if both trim_range values exceed the number of channels by @mcol in #872
Don't crash if record.id removes all records by @mcol in #874
Vectorize translation to regular expression in get_RLum() by @mcol in #876
Fix z-axis ticks and labels if log.z = FALSE by @mcol in #878
Use relative values in the cex argument of points() by @mcol in #880
Remove defunct functions PSL2Risoe.BINfileData() and Second2Gray() by @mcol in #881
Improve validation against a single-column data frame by @mcol in #883
Summarize the parameters of interest in fit_IsothermalHolding() by @mcol in #884
Improve validation against a list of 1-column data frames by @mcol in #886
Improve validation against a data frame with non-numeric fields by @mcol in #888
Improve validation against a data.frame with only a character column by @mcol in #890
Improve validation against data frames with only NA values by @mcol in #892
Improve validation against lists of length 2 by @mcol in #894
Cosmetic improvements to .warningCatcher() by @mcol in #895
Don't crash in fit_OSLLifeTimes() if signal_range has negatives values by @mcol in #897
Remove any non-finite values from the profile in calc_MinDose() by @mcol in #899
Fix crash by ensuring that bs.M is at least 2 in calc_MinDose() by @mcol in #901
Return the validated value from .validate_[positive|logical]_scalar() by @mcol in #902
Improve validation against data frames with an NA column by @mcol in #904
Make calc_Statistics() compute the weighted median correctly by @mcol in #906
Don't assume that class always returns a single value in .rm_nonRLum() by @mcol in #908
Improve validation against a numeric vector with NaN by @mcol in #910
Improve validation against an empty numeric vector by @mcol in #913
Improve validation against a numeric vector with Inf by @mcol in #914
Check that after removal of NAs there is still data in calc_MinDose() by @mcol in #916
Improve validation against data frame with first column of NAs by @mcol in #918
add correct_PMTLinearity() by @RLumSK in #920
Don't crash in .validate_positive_scalar(Inf, int = TRUE) by @mcol in #923
Improve validation against data frame with a NA column by @mcol in #925
Improve validation against a 0-row data frame by @mcol in #927
Don't leave FNAME empty in read_BIN2R() by @mcol in #929
Fix validation of cross_talk_correction in analyse_Al2O3C_Measurement() by @mcol in #931
Improve validation against a 1-row matrix by @mcol in #933
Improve validation against 0-row or 0-col matrices by @mcol in #935
Compute the correct dimension in report_RLum() by @mcol in #939
Improve validation against a list containing an empty lists by @mcol in #941
Implement the Poisson smoother of Carter et al. (2018) by @mcol in #937
Improve validation against an empty RLum.Analysis object by @mcol in #943
Restore the docs for the RLum.* classes in the pdf file by @mcol in #944
Don't allow assigning NULL in add_metadata() and rename_metadata() by @mcol in #947
Remove get_Risoe.BINfileData() and the corresponding generic by @mcol in #949
Add snapshot tests for the merge_*() functions by @mcol in #951
Add the verbose argument to merge_Risoe.BINfileData() by @mcol in #952
Cap the maximum number of components to be fitted in fit_CWCurve() by @mcol in #954
Introduce the default value for NULL %||% operator and start using it by @mcol in #956
Return a De.raw field from fit_DoseResponseCurve() by @mcol in #958
Add option to control the legend position in plot_DoseResponseCurve() by @mcol in #960
Report correctly the fit outcome for QDR in fit_DoseResponseCurve() by @mcol in #962
Add a workaround for R-devel failure by @mcol in #968
Improve validation in plot_RisoeBINfileData() by @mcol in #965
Add more graphical snapshots by @mcol in #966
Fix regression in drawing the dose-response curve in plot_DRCSummary() by @mcol in #970
Fix x-axis label for TL plots in plot_Risoe.BINfileData() by @mcol in #972
Try to get debug info from coverage runs by @mcol in #973
Correct computation of De.MC, De.error and HPDI for interpolation mode in fit_DoseResponseCurve() by @mcol in #975
Compute the HPDIs in more cases in fit_DoseResponseCurve() by @mcol in #977
More snapshot and graphical snapshot tests by @mcol in #978
Return early from analyse_Al2O3C_ITC() if fitting the GC curves fails by @mcol in #980
Reorder and rename fields in object returned by fit_DoseResponseCurve() by @mcol in #981
Extract the error field more reliably in use_DRAC() by @mcol in #983
Operate on logged values in .smoothing() for method = Carter_etal_2018 by @mcol in #986
Fix crash in apply_CosmicRayRemoval() by @mcol in #988

Full Changelog: v1.1.0...v1.1.1

v1.1.1 (CRAN)

Changes in version 1.1.1 (2025-09-11)

New functions

Removed functions and deprecations

Bugfixes and changes

add_metadata<-()

analyse_Al2O3C_ITC()

analyse_Al2O3C_Measurement()

analyse_SAR.CWOSL()

apply_CosmicRayRemoval()

calc_AliquotSize()

calc_Huntley2006()

calc_MaxDose()

calc_MinDose()

calc_Statistics()

fit_CWCurve()

fit_DoseResponseCurve()

fit_LMCurve()

fit_OSLLifeTimes()

get_RLum()

merge_Risoe.BINfileData()

plot_AbanicoPlot()

plot_DoseResponseCurve()

plot_DRCSummary()

plot_DRTResults()

plot_Histogram()

plot_KDE()

plot_RadialPlot()

plot_Risoe.BINfileData()

plot_RLum.Analysis()

plot_RLum.Data.Curve()

plot_RLum.Data.Spectrum()

read_BIN2R()

read_XSYG2R()

smooth_RLum()

trim_RLum.Data()

use_DRAC()

What's Changed

Contributors

Uh oh!

`add_metadata<-()`

`analyse_Al2O3C_ITC()`

`analyse_Al2O3C_Measurement()`

`analyse_SAR.CWOSL()`

`apply_CosmicRayRemoval()`

`calc_AliquotSize()`

`calc_Huntley2006()`

`calc_MaxDose()`

`calc_MinDose()`

`calc_Statistics()`

`fit_CWCurve()`

`fit_DoseResponseCurve()`

`fit_LMCurve()`

`fit_OSLLifeTimes()`

`get_RLum()`

`merge_Risoe.BINfileData()`

`plot_AbanicoPlot()`

`plot_DoseResponseCurve()`

`plot_DRCSummary()`

`plot_DRTResults()`

`plot_Histogram()`

`plot_KDE()`

`plot_RadialPlot()`

`plot_Risoe.BINfileData()`

`plot_RLum.Analysis()`

`plot_RLum.Data.Curve()`

`plot_RLum.Data.Spectrum()`

`read_BIN2R()`

`read_XSYG2R()`

`smooth_RLum()`

`trim_RLum.Data()`

`use_DRAC()`