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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.
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().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).
analyse_baSAR()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()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()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()... 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 fit is
attempted again with 10 different values for D0 and the
best fit is used. This should reduce the number of occasions in which
the error message “Could not fit simulated model curve, check
suitability of model and parameters” is reported (#660).
The function crashed if all simulated Lx/Tx values were identical
and approximately zero, which could happen if the rhop
argument was set to a large enough value (#725).
An error message has been improved so that it doesn’t suggest setting the ‘fit.bounds = FALSE’ argument if it has already been set (#729).
The computation of the x-axis limits has been improved to avoid
having too much unused horizontal space, especially for
mode = "extrapolation" (#731).
The scaling of the plot can now be controlled via the
cex argument (#735).
The plot margins are set more precisely and avoid the summary text to be cut off (#737).
calc_MinDose()calc_OSLLxTxRatio()The function returned a warning for wrong integral settings for
the Tx curve even if no Tx curve was
provided.
The function does not check any more of different object types
for Lx.data and Tx.data but validate objects
for allowed types (this should have no user-visible effects).
convert_Concentration2DoseRate()extract_IrradiationTimes()The function tries a little bit harder to extract the correct duration of TL steps, rendering the data output hopefully a little bit more intelligible (#651).
The function gained a new argument called
return_same_as_input, with default value of
FALSE. If set to TRUE, the input object
(usually an RLum.Analysis object or a list of
them) is returned with updated info elements for IRR_TIME
and TIMESINCEIRR. This makes the RLum.Analysis
object compatible with functions that explicitly search for those two
objects, such as those in the 'OSLdecomposition' package
(#752).
fit_DoseResponseCurve()The function now allocates less memory for storing intermediate values (#610).
Add initial support for OTORX fitting following
Lawless and Timar-Gabor
a set if
fit.force_through_origin = FALSE. This also enables to
support mode = "extrapolation" (thanks to John Lawless for
his input).The code of the function was optimised in several places to improve code readability and reduce redundant calls.
The models for EXP, EXP+LIN,
EXP+EXP and GOK are now available in C++. This
cut the required computation times in half in benchmark scenarios. More
importantly, this performance scales with the number of Monte Carlo
runs.
fit_EmissionSpectra()fit_LMCurve()If the user asks logarithmic scaling in the y-axis, using either
log = "y" or log = "xy", this is now ignored
when plotting residuals and component contributions (#755).
The plot has been slightly reworked to reduce the cases of
“margin too large” errors and to work better at high settings of
cex (#757).
Missing values in the input data are now silently removed (#759, #763).
The plotting of residuals, component contributions and legend can now be disabled, and the legend position can be controlled (#785).
The error computed when using option
fit.calcError = TRUE is now returned correctly, instead of
being left to NA (#789).
Argument bg.subtraction also accepts the option
"none" to disable background subtraction even if
values.bg is provided (#795).
fit_SurfaceExposure()mu when a list of input data is
provided (#667).fit_ThermalQuenching()The trace option, which can be specified via the
method_control argument, is now respected.
The model now get internally reformulated into a mathematically equivalent expression that is easier to fit. This should reduce the number of occasions when the function fails to find a valid solution and improve the uncertainty estimation (#696).
get_RLum()subset can now be provided as a character
that represents a logical expression. Before, it always required a
logical expression, but this may lead to odd effects due to the early
evaluation happening in R and might not be wanted. Providing
subset as a character is now a viable workaround in those
situations.import_Data()merge_RLum.Data.Curve()plot_DetPlot()multicore = FALSE (#742).plot_DoseResponseCurve()The response curve always tries to the get the 0 point in the
mode interpolation and alternate
(#677).
Minor graphical polish to limit overplotting and also plot a
density curve for the L_n/T_n signal.
If mode = "alternate", the message that the
equivalent dose could not be fitted is no longer shown.
Argument cex.global has been removed and will be
silently ignored (#831).
plot_DRCSummary()fit.method = 'OTORX' following the
change in fit_DoseResponseCurve() (#677).plot_DRTResults()The summary and legend texts now scale better at non-default cex settings (#765).
Argument given.dose is better validated against
misspecifications, and setting it to 0 is equivalent to leaving it at
its default NULL value, which corresponds to avoiding data
normalization (#767, #799).
The function crashed when multiple inputs were used with
boxplot = TRUE and all preheat values were identical
(#769).
Plot title, summary text and legend are now better positioned (#773, #774, #781).
A bug in the way colours and symbols are assigned to plot points has been fixed (#777).
The horizontal axis doesn’t include anymore a spurious extra tick that didn’t correspond to any aliquot (#783).
plot_GrowthCurve()Add support for fit.method = 'OTORX' following the
change in fit_DoseResponseCurve() (#677).
Argument cex.global has been removed and will be
silently ignored (#831).
plot_Histogram()The function now doesn’t produce warnings when the input consists of a single-column data frame, as it assumes that the De error is 10^-9 (#744).
The right margin is now smaller when errors are not plotted, as there is no need to leave space for the standard error axis (#748).
The summary text now scales better at non-default cex settings (#750).
plot_KDE()The function validates its input values more thoroughly (#635).
Setting summary.pos to one of “left”, “center” or
“right” resulted in the summary table not being visible (#642).
Argument output has been removed, and it will be
ignored if set (#700).
plot_RadialPlot()The function validates its input values more thoroughly (#639).
The legend text now scales better at non-default cex settings (#746).
plot_RLum.Data.Curve()We added comprehensive support for base R plotting arguments
utilised by plot.default() and par(). This
enhancement ensures that all available arguments are fully supported
(#646).
The function gained a new logical argument named
auto_scale. When set in conjunction with either
xlim or ylim, this argument automatically
adjusts the plot range to align with the corresponding settings for
xlim or ylim. For instance, if a user intends
to plot OSL curves but initially selects the xlim range
c(10:30) to examine the background, the initial count
values may be excessively large, resulting in limited visibility. With
the introduction of the auto_scale option, the
ylim values are automatically adjusted to compensate for
this scenario. The auto_scale argument is also accessible
through plot_RLum.Analysis() and plot_RLum()
(#646).
plot_RLum.Data.Spectrum()The channel-wise background subtraction was essentially broken if a background spectrum with the same setting was provided. The function always calculated the arithmetic mean. This was fixed, and the manual updated accordingly.
If a background spectrum was provided, the behaviour of the plot
output was sometimes hard to understand without knowledge of the
underlying code. This behaviour was improved and now ylim
will also affect the background spectrum if
bg.channels = NULL (the default).
The function could crash if column names were missing and the 1bg.spectrum` argument was used (#726).
read_TIFF2R()The argument file can now be provided as a
list or a character vector.
The function gained a new logical argument called
merge2stack that can be used if file is either
a list or a character vector of length > 1. If set to
TRUE, images are combined into one image stack.
read_XSYG2R()A redundant computation has been removed, and the function is now marginally faster on files when the detector is not a spectrometer (#753).
Prepare import for an updated version of LexStudio2
(>=v2.31.1) where the horizontal hardware binning finally works after
>10 years, but the changes introduce a lot of NaN values
that would cause a crash of the function.
Minor code refactoring for a small speed boost if spectrometer measurements are imported.
scale_GammaDose()plot_singlePanels now works as documented,
that is it produces all plots in a single page when set to
FALSE (default), and one plot per page when set to
TRUE (#698).sort_RLum()The sorting mechanism for RLum.Analysis objects has
been enhanced. It now enables sorting based on multiple parameters,
including sorting all available info_elements in a
prioritised manner (#606, #620).
Sorting now works on a list of RLum.Analysis
objects. If the list contains elements of a different type, they are
passed through unchanged. The output is again a list (#620).
structure_RLum().pid and info as lists within the
data frame. The function is primarily used internally to facilitate a
rapid exploration of RLum.Analysis object structures.
However, the change may potentially break existing code in extremely
rare circumstances.template_DRAC()use_DRAC() to fail.use_DRAC()The function now checks for DRAC specific URL parts if a custom URL is provided; this avoids long searches for unspecific errors.
Due to the internal masking of submitted values, the initial row order got mixed up; regression from #438. The order is maintained and the row index corrected; in other words, the masking should now be again invisible to the user.
verify_SingleGrainData()read_XSYG2R() contained positions in its info
field (#740).write_R2TIFF()create_UID() has undergone
further optimisation for speed, resulting in a significant performance
improvement. Additionally, it now generates a hash value with a
consistent length instead of a time stamp with a random number.analyse_baSAR()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()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()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()plot_AbanicoPlot()xlim, ylim and zlim
parameters are now better validated to avoid possible crashes if
misspecified (#581).plot_RLum.Analysis()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).
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).
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).
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).
view(): Provides a shortcut to the
utils::View() spreadsheet-like data viewer tailored to the
objects in the package (#489).
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). 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).
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).
Function Analyse_SAR.OSLdata() is now officially
deprecated, analyse_SAR.CWOSL() should be used instead
(#216).
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).
Function Second2Gray() has been renamed to
convert_Second2Gray() (#498).
Function PSL2Risoe.BINfileData() has been renamed to
convert_PSL2Risoe.BINfileData() (#555).
’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.analyse_Al2O3C_CrossTalk()recordType
is specified and none of the records in the data set is of that type
(#487).analyse_baSAR()XLS_file has been replaced by
CSV_file and, as mentioned above, the function now only
accepts CSV files as input (#237).recordType passed to
get_RLum in the additional arguments.plot.single has been renamed to
plot_singlePanels (#351).Risoe.BINFileData object was
provided and the argument irradiation_times was set;
fixed.variable.names within the method_control
argument (#521).analyse_SAR.CWOSL()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.RLum.Results object now also contains a
column for the grain (#553).analyse_FadingMeasurement()RLum.Analysis object given as input, and
reports a message if a version older than 5 was used (#281).RLum.Analysis input files (#283).plot.single has been renamed to
plot_singlePanels (#351).analyse_IRSAR.RF()num_slide_windows setting (part of the
method.control option), thus allowing to find a balance
between computation time and quality of fit (#372).sequence_structure
misspecifications (#393).method = "VSLIDE" (#396).method.control has been renamed to
method_control for consistency with all other functions in
the package (#411).analyse_pIRIRSequence()plot.single has been renamed to
plot_singlePanels (#351, fixed in #408).RLum.Results object now also contains a
column for the grain (#553).sequence.structure
argument contains at least one IR step (#579).analyse_SAR.CWOSL()plot.single has been renamed to
plot_singlePanels (#351).apply_CosmicRayRamoval()smooth_RLum that can be passed as new argument for
method.calc_AverageDose()calc_CentralDose()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).sigma < 1e-16, as
allowing sigma to become zero leads to infinities and buggy
behaviour (#304).calc_FastRatio()calc_FiniteMixture()dose.scale and pdf.scale were
not used and have been removed (#566).calc_gSGC()calc_Huntley2006()rprime vector that
is used in the calculation of the natural dose response and the field
saturation, so that more points are concentrated in the bulk of the
distribution: this previously depended incorrectly on the number of
Monte Carlo iterations requested, so this change brings an additional
speed boost. The default setting can be overridden via the
rprime argument (#258).mode = "extrapolation", which made it harder to see
where it extrapolated to (#551; thanks to @SalOehl for reporting).calc_IEU()calc_Lamothe2003()Ln/Tn error after fading correction, which led to smaller
than expected errors (#96).convert_RLum2Risoe.BINFileData()incompatible types (from raw to character) error under
particular circumstances; fixed.METADATA are already
available but in the wrong format; fixed.extract_IrradiationTimes()startDate was
missing in the irradiation curve; fixed.fit_CWCurve()confint() failed. This has now been fixed, and in
cases of failures we report the error message received from
confint() (#509).output.terminal has been renamed to
verbose for consistency with other functions.method_control
argument, which can be used to control the saving of the component
contribution matrix in the RLum.Results object it returns. This is now
disabled by default: to restore the previous behaviour, add
method_control = list(export.comp.contrib.matrix = TRUE) to
the function call (#573).fit_EmissionSpectra()export.plot.data = TRUE within the
method_control argument (#569).fit_LMCurve()method_control
argument, which can be used to control the saving of the component
contribution matrix in the RLum.Results object it returns. This is now
disabled by default: to restore the previous behaviour, add
method_control = list(export.comp.contrib.matrix = TRUE) to
the function call (#573).get_RLum()subset option was used on info elements of an
RLum.Analysis object, it would return wrong results if the
info element was not present in all records; fixed.import_Data()character vectors of length > 1 as input (e.g.,
different file names). Furthermore, the function received more testing
against a mixture of input formats. Therefore you can provide many
different files formats and the function will try to import them all in
one go.plot_AbanicoPlot()z.log = TRUE (the default); fixed.tcl and tck arguments via
... was removed as they were never used internally.plot_DetPlot()plot.single has been renamed to
plot_singlePanels (#351, fixed in #408).plot_DRTResults()na.rm was used alongside
the preheat option but the data set contained no missing
values (#474).plot_GrowthCurve()fit_DoseResponseCurve() and
plot_DoseResponseCurve(). There should be no visible
user-facing changes (#319).... arguments for plotting (implementation
in plot_DoseResponseCurve()) for legend (turn
on/off legend) and reg_points_pch for fine grained control
over the point shape.density_polygon, density_polygon_col,
density_rug, box as ... arguments
to plot and add respective plot optionsNaN values during log conversions required for
estimating the start parameters. The result was the error
object 'b.MC' not found (#374; fixed)fit.method
("EXP+LIN", "EXP+EXP", "GOK" and
"LambertW"), the function could get stuck in an endless
loop when the number of parameters was larger than or equal to the
number of data points. This is now checked, and in those cases the
method is changed to "LIN" (#381).nls() with minpack.lm::nlsLM()
as it’s more robust and can find a fit in cases where nls()
would fail. Please keep in mind that it does not mean that fit results
in those cases make any sense, it just helps to avoid uncontained events
in the R session (addresses #381).output.plotExtended.single has been renamed to
plot_singlePanels (#351).RLum.Results as output (#405).fit.method = "QDR" and
mode = "extrapolation" (#504).NumberIterations.MC has been renamed to
n.MC (#546).plot_RLum.Analysis()plot.single has been renamed to
plot_singlePanels (#351).plot_RLum.Data.Curve()norm is now better validated so that
specifying an incorrect value returns an error instead of silently
skipping curve normalisation (#250).plot_RLum.Data.Spectrum()plot.type = "persp"
is now more consistent and doesn’t produce artefacts in the regions of
transition between colours (#371).bin.rows or
bin.cols value was set too high or if xlim and
ylim were set too tight (#415).read_BIN2R()n.records is now better supported for BIN
files v3 and v4 and doesn’t lead to a crash when used in conjunction
with the fastForward option (#343).zero_data.rm was not correctly propagated if
the input object was provided as a list (#342).METADATA fields that are not actually read from the
BINX file in case of a ROI record are now set to NA rather
than being assigned the value from the previous record (#336)..RESERVED slot is now kept in sync with the rest of
the object when records are dropped from the input BIN/BINX file
(#337).fastForward = TRUE (#356).read_HeliosOSL2R()read_XSYG2R()n_records argument now enables to control the
number of records to import, which can be useful in case the file is
faulty.scale_GammaDose()plot_single has been renamed to
plot_singlePanels and was changed so that
plot_singlePanels = TRUE will produce one plot per panel,
for consistency with other functions (#351).template_DRAC()file_input that
enables the creating of a DRAC template based on an existing DRAC CSV
file. This way, already available DRAC files can be conveniently
modified without having to call use_DRAC() first.Cresswelletal2018). Please ensure that the
server supports that option.trim_RLum.Data()trim_range argument that could lead to crashes
(#460).use_DRAC()...
arguments: version_ignore to ignore the DRAC version check,
user and password to access password protected
websites.verify_SingleGrainData()cleanup = TRUE the result was not consistent and produced a
mixture of RLum.Results and
RLum.Analysis/Risoe.BINFileData objects in
particular when run over a list, this was not what stated in the manual.
Now the function indeed cleans up the object, hence if a list of
RLum.Analysis objects is provided, the result is a cleaned
list of that object. If the clean-up ends up removing everything, the
result is NULL.cleanup = TRUE.use_fft that will apply an
additional Fast Discrete Fourier Transform (FFT) verification on the
data if wanted.write_R2BIN()verbose argument, which
can be used to suppress output to the terminal (#442).These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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