See also the write-up for this release on the REPLAY website.
All import functions will now always append the detector used to
the recordType slot of the RLum.Data.Curve
object generated, for consistency with what has always been done by
read_XSYG2R(). The following functions have been modified
to support this new behaviour:
read_Daybreak2R()read_PSL2R()read_RF2R()read_SPE2()Risoe.BINfileData2RLum.Data.Curve() In most cases, this
is the string “(PMT)” for BIN/BINX, PSL and Daybreak files; in the
remaining cases the string “(NA)” is appended. The following example
files have been updated to reflect these changes:ExampleData.RLum.AnalysisExampleData.portableOSL As a consequence of these
changes, default titles for curve plots will now also contain the
detector string. This may potentially disrupt code that uses strict
equality (==) when selecting curves based on their
recordType (#1275, #1286).Function read_XSYG2R() will now prepend an
underscore to the recordType slot of the
RLum.Data.Curve object generated from an XSYG file for all
objects after the first curve in a record. This will allow an easier way
to differentiate the curves to analyse (for example, “OSL (UVVIS”) from
those that are not useful in the analysis (for example, “_OSL (NA)“)
(#1276).
The @info slot returned by function
read_XSYG2R() no longer contains a name field:
this has been replaced by sequenceName, to differentiate it
from the newly-added recordName (#1239, #1387).
Functions calc_OSLLxTxRatio(),
calc_OSLLxTxDecomposed(), calc_TLLxTxRatio()
and analyse_SAR.TL() return two extra columns,
SN_RATIO_LnLx and SN_RATIO_TnTx, in their
result object. This may disrupt code that relies on column indices
instead of column names (#1281, #1330, #1436).
See this post on the REPLAY website for more information and advice on how to deal with these changes.
normalise_RLum(): This function enables a fast
normalisation of RLum.Data.Curve-class,
RLum.Data.Spectrum-class,
RLum.Data.Image-class and their combination in
RLum.Analysis-class objects. Normalisation was already
possible for plotting (e.g.,
plot_RLum.Data.Curve(…, norm = TRUE)), which uses an
internal function called .normalise_curves() to do the job.
With normalise_RLum() we expose this functionality to
RLum-class objects and enable a convenient normalisation of
values that might come in handy in same cases. Normalised values are
only count values. Currently implemented is normalisation via keywords,
such as "max", "min", "first",
"last", "huot", "intensity".
Additionally, the function supports normalisation to a positive number
(#1250 by @RLumSK,
#1300).
read_BINXLOG2R(): This function enables the
salvaging of log files created by a Risø reader into R as
RLum.Analysis-class. It also allows for exporting these
files into a BIN/BINX format. While the function has been tested on a
few examples, it is important to note that log files are not a
well-defined data format. This function is intended for use in cases
where you have a corrupted BIN/BINX file but a complete log file is
still available. Supported log formats are TL, OSL, and IRSL curves. All
other formats are ignored (#1241 by @RLumSK; thanks to Michael Kenzler for
bringing this to our attention).
Functions github_branches(),
github_commits(), github_issues(),
is.RLum(), is.RLum.Analysis(),
is.RLum.Data(), is.RLum.Data.Curve(),
is.RLum.Data.Image(), is.RLum.Data.Spectrum()
and is.RLum.Results() (deprecated since 1.1.2) have been
removed (#1242).
Function install_DevelopmentVersion() has been
removed as it relied on the now deprecated
devtools::install_github(). Equivalent functionality is
available via pak::pkg_install("R-Lum/Luminescence")
(#1453).
analyse_Al2O3C_CrossTalk()The signal_integral argument was silently ignored
(#1428).
The function now supports the integral_input
argument, which can be set to either "channel" (default)
and "measurement". When the latter is used, the integrals
can be specified in terms of seconds, in which case the function
performs an automatic conversion to channels (#1396).
analyse_Al2O3C_ITC()The function used to output a suppressed error message instead of validating the input ahead of that (#1256).
The signal_integral argument was silently ignored
(#1428).
The function now supports the integral_input
argument, which can be set to either "channel" (default)
and "measurement". When the latter is used, the integrals
can be specified in terms of seconds, in which case the function
performs an automatic conversion to channels (#1396).
analyse_Al2O3C_Measurement()integral_input argument,
which can be set to either "channel" (default) and
"measurement". When the latter is used, the integrals can
be specified in terms of seconds, in which case the function performs an
automatic conversion to channels (#1396).analyse_baSAR()The function has been updated to use
fit_DoseResponseCurve() and
plot_DoseResponseCurve() instead of
plot_GrowthCurve(). This should not have any visible
difference other than the renaming of two arguments:
output.plot has been renamed to plot_drc,
while output.plotExtended has been renamed to
plot_extended. The older names will still work but generate
a deprecation warning (#1244).
Arguments signal.integral,
background.integral, signal.integral.Tx and
background.integral.Tx have been renamed to
signal_integral, background_integral,
signal_integral_Tx and background_integral_Tx,
respectively. The older names will still work but generate a deprecation
warning (#1290).
The function no longer crashes if aliquot_range
specifies non-positive indices or if source_doserate = 0
(#1424, #1426).
analyse_FadingMeasurement()The plots were affected by a bug in
plot_RLum.Analysis(), so that the output was unnecessarily
split over two pages (#1247).
Arguments signal.integral and
background.integral have been renamed to
signal_integral, background_integral,
respectively. The older names will still work but generate a deprecation
warning (#1290).
The function now supports the integral_input
argument, which can be set to either "channel" (default)
and "measurement". When the latter is used, the integrals
can be specified in terms of seconds, in which case the function
performs an automatic conversion to channels (#1396).
analyse_IRSAR.RF()slide$squared_residuals field of the
@data slot in the RLum.Results object returned
by the function is no longer a 1-column matrix, but a plain numeric
vector (#1254).analyse_pIRIRSequence()Arguments signal.integral.min,
signal.integral.max, background.integral.min
and background.integral.max have been replaced by
signal_integral and background_integral: each
of them now defines a vector of channels for the respective integrals.
The older names will still work but generate a deprecation warning
(#1290).
The function crashed if called on an empty list (#1372).
The function now supports the integral_input
argument, which can be set to either "channel" (default)
and "measurement". When the latter is used, the integrals
can be specified in terms of seconds, in which case the function
performs an automatic conversion to channels (#1396).
analyse_portableOSL()Argument signal.integral has been renamed to
signal_integral. The older name will still work but
generates a deprecation warning (#1290).
The function now supports the integral_input
argument, which can be set to either "channel" (default)
and "measurement". When the latter is used, the integrals
can be specified in terms of seconds, in which case the function
performs an automatic conversion to channels (#1396).
analyse_SAR.CWOSL()If mode = "alternate", the dose value is no longer
reset automatically. If the first dose point was > 0, the function
detected a dose-recovery test and automatically reset this dose point to
0. While this is likely convenient in 9 out of 10 cases, it caused
trouble if the mode = "alternate" (passed on to
fit_DoseResponseCurve()) because it modified the first dose
point and this required additional handling afterwards. Please keep in
mind that you have to redefine the recuperation reference in such a
case: this is wanted and not a bug (fixed in commit 9ff29bf).
The order of columns in the rejection.criteria data
frame that is output by the function has been changed so that the
UID column appears now first. This is meant to facilitate
seeing visually to what aliquot each criteria belongs to. While the
UID values are random-looking alphanumeric values, they can
identify univocally an aliquot also after merge operations
(#1172).
A new argument, dose_rate_source, was added to allow
users to specify a value for the source dose rate and display values in
Gy, rather than seconds. Previously, this was only possible by using a
factor with the dose.points argument. However, setting it
manually was particularly inconvenient if the dose points were already
extracted automatically, as it required users to insert dose values
manually regardless of the automated extraction. This argument is also
available in other functions that wrap around
analyse_SAR.CWOSL() (fixed in commit 4fc985d).
The function warns if the most common curve type (which is the one used in the analysis) matches multiple record types, as this may be a sign that the user has forgotten to select the correct set of curves to analyze (#1269).
A new signal-to-noise ratio rejection criterion has been added,
with default threshold of 50 (controllable by setting the
sn.ratio parameter in the rejection.criteria
list to a different value). By default it uses the signal-to-noise value
computed for the natural curve, but a different curve can be specified
via the sn_reference parameter in the
rejection.criteria list (#1284).
Arguments signal.integral.min,
signal.integral.max, background.integral.min
and background.integral.max have been replaced by
signal_integral, background_integral,
signal_integral_Tx and background_integral_Tx:
each of them now defines a vector of channels for the respective
integrals. The older names will still work but generate a deprecation
warning (#1290).
When rejection criteria are set to NA, in the plot
we now only show the value calculated (say, 1.1) instead of incorrectly
showing NAs for both the sign and the threshold (as in
1.1 NA NA) which would look ugly and confusing
(#1318).
The rejection criteria for the highest dose points was not
considered correctly, and in most cases validated to
"FAILED" even for thresholds set to NA or
Inf (fixed in commit 3562bca).
It is now possible to consider value uncertainties in the
computation of some rejection criteria (currently only
recycling.ratio, recuperation.rate and
exceed.max.point) by setting
consider.uncertainties = TRUE in the
rejection.criteria list. This is disabled by default to
preserve existing behaviour (#1325).
The function now supports setting
background_integral = NA, in which case no background
integral is subtracted (#1385; thanks to Annette Kadereit for
reporting).
If the function processes a list of objects, as is the typical scenario, the aliquot number (not the position number) is returned. The aliquot number represents the consecutive number of objects processed.
Add support to control the legend size and the legend symbols via
legend.cex and legend.pch (fixed in commit
9ec687d).
The function now supports the integral_input
argument, which can be set to either "channel" (default)
and "measurement". When the latter is used, the integrals
can be specified in terms of seconds, in which case the function
performs an automatic conversion to channels (#1396).
When OSL.component is specified, the function now
checks that the input object was actually processed by
OSLdecomposed::RLum.OSL_decomposition(), in order to return
a warning message when that is not the case (#1464).
Curves with recordType starting with _
are automatically removed. This allows to analyse an XSYG file directly
without (in many cases) any manual intervention required. This behaviour
can be changed by setting argument
method_control = list(auto_curve_removal = FALSE)
(#1468).
analyse_SAR.TL()Argument signal.integral has been renamed to
signal_integral. The older name will still work but
generate a deprecation warning (#1290).
The integral_input argument now accepts options
“channel” (as before) and “measurement” (instead of “temperature”). This
was done to uniform the choices accepted by the argument throughout the
package. The older name will still work but generates a deprecation
warning (#1396).
apply_EfficiencyCorrection()RLum.Data.Spectrum object (#1402).calc_AverageDose()RLum.Results returned now contains a
$data field to store the input data for consistency with
similar functions, and two columns have been appended to the end of the
$summary field for internal use (#1455).calc_CobbleDoseRate()input has been renamed to object.
The older name will still work but generates a deprecation warning
(#1434).calc_CommonDose()sigmab > 1 when log = FALSE due to
excessively strict input validation (#1343).calc_FiniteMixture()n.components = 1:3, enforcing the usage of
n.components = 2:3 instead. This check, added in v1.1.0,
was unnecessarily stringent and has been reverted (#1458).calc_gSGC()n.MC is set to 0
(#1327).calc_MaxDose()bootstrap = TRUE were
not transformed back to the original scale before being returned to the
user (#1351).calc_MinDose()The function now set non-positive De values to NA
when log = TRUE, which used to lead to a crash when
combined with bootstrap = TRUE (#1313).
The bootstrap results stored in the
@data$bootstrap$pairs$gamma matrix are now correctly
converted to the normal scale for log models. This fixes a regression
introduced in v1.0.0, which caused those values to be stored in the log
scale (#1345).
The function now stores the bootstrap results in the
summary slot when bootstrap = TRUE. Moreover,
summary results are printed to the terminal also when using bootstrap
(#1336; thanks to @feldsparlover and Arindam Biswas for
reporting and to Marijn van der Meij for checking the
implementation).
The function crashed when bootstrapping with
bs.N = 1. Now the bs.N parameter is silently
reset to 2 in that case, although such low values are discouraged as
they may trigger a warning during loess fitting (#1355).
The computation of frequencies of bootstrap replicates has been fixed to be sample-wise, while before it was mistakenly computed as a cumulative sum over all samples. In our tests, the difference in results produced by the two implementations appears to be minimal (#1374).
calc_OSLLxTxDecomposed()SN_RATIO_LnLx and SN_RATIO_TnTx
(containing NA) for consistency with the output produced by
calc_OSLLxTxRatio() (#1330).calc_OSLLxTxRatio()The data frame returned by the function now contains two
additional columns, SN_RATIO_LnLx and
SN_RATIO_TnTx. This is the signal-to-noise ratio for the
respective shine-down curves for Lx and Tx
(#1281).
Arguments signal.integral,
background.integral, signal.integral.Tx and
background.integral.Tx have been renamed to
signal_integral, background_integral,
signal_integral_Tx and background_integral_Tx,
respectively. The older names will still work but generate a deprecation
warning (#1290).
The function can now accept lists for its Lx.data
and Tx.data arguments, in which case it will self-call.
This can simplify using the function, as it’s no longer necessary to
write a loop to process all records (#1299).
The function now supports setting signal_integral to
a chosen set of channels while setting
background_integral = NA. In this case, no background
integral is subtracted and the error calculation and the signal-to-noise
ratio will report NA values (#1375).
The function now supports the integral_input
argument, which can be set to either "channel" (default)
and "measurement". When the latter is used, the integrals
can be specified in terms of time or temperature, in which case the
function performs an automatic conversion to channels (#1396).
calc_TLLxTxRatio()Argument signal.integral has been renamed to
signal_integral. The older name will still work but
generate a deprecation warning (#1290).
The function now supports the integral_input
argument, which can be set to either "channel" (default)
and "measurement". When the latter is used, the integrals
can be specified in terms of temperature, in which case the function
performs an automatic conversion to channels (#1396).
combine_De_Dr()Age_range argument
contained missing values (#1378).convert_CW2pHMi()
and convert_CW2pPMi()correct_PMTLinerarity()The function, introduced in v1.1.2, unintentionally came with a
major flaw, in that it did nothing on a single
RLum.Data.Curve() object (fixed in commit
1d978cf).
If the channel resolution was not changing, the function produced
NaN values even in cases where dead time was not corrected
(fixed in commit 1d978cf).
convert_Concentration2DoseRate()Argument input has been renamed to
object. The older name will still work but generates a
deprecation warning (#1434).
The interpolation of attenuation values has been corrected so that it will not unexpectedly fail if a non-integer value for the grain size is provided, as long as it’s in the valid range (#1444; thanks to Christina Neudorf for reporting).
convert_CW2p*()values has been renamed to
object. The older name will still work but generates a
deprecation warning (#1434).convert_Second2Gray()dose_rate argument is now better validated
(#1439).convert_SG2MG()The function crashed if used on an object resulting from a subset
operation, as it used the rownames (which may no longer correspond to
row indices) to index into the METADATA slot
(#1415).
The function now exits cleanly instead of crashing if more than one input filenames are provided (#1446).
extract_IrradiationTimes()position field in its info object (#1466).fit_CWCurve()values has been renamed to
object. The older name will still work but generates a
deprecation warning (#1434).fit_DoseResponseCurve()The C++ implementation of the GOK function has been tweaked to
avoid some repeated computations in a loop. Given the different ordering
of computations (although mathematically equivalent), there will be
small differences in the numerical output when
fit.method = "GOK" is used (#1277).
The fit message reported is now also stored in the
@info slot of the object returned by the function
(#1362).
The function now consistently returns the material specific
parameter R for OTOR and OTORX
and its uncertainty (fixed in commit 9b4d6bd).
fit_LMCurve()Arguments values and values.bg have
been renamed to object and object.bg,
respectively. The older names will still work but generate a deprecation
warning (#1434).
The function now checks that the number of data points provided is large enough to fit the requested number of components (#1448).
get_RLum()RLum.Analysis object (#1271).merge_RLum.Risoe.BINfileData()input.objects has been renamed to
objects. The older name will still work but generates a
deprecation warning (#1434).merge_RLum.Data.Spectrum()plot_AbanicoPlot()RLum.Results object generated
by calc_AverageDose(), calc_CentralDose(),
calc_MaxDose(), calc_MinDose() or
calc_FiniteMixture(), one or more lines (and corresponding
labels) for the relevant results will be automatically drawn, unless
explicitly suppressed by setting line = NA (#1452).plot_DetPlot()When operating on a list with the default setting of
multicore = TRUE, the function limits the size of the
parallel cluster to the number of list elements to process
(#1258).
Arguments signal.integral.min,
signal.integral.max, background.integral.min
and background.integral.max have been replaced by
signal_integral, background_integral,
signal_integral_Tx and background_integral_Tx:
each of them now defines a vector of channels for the respective
integrals. The older names will still work but generate a deprecation
warning (#1290).
The function now supports the integral_input
argument, which can be set to either "channel" (default)
and "measurement". When the latter is used, the integrals
can be specified in terms of seconds, in which case the function
performs an automatic conversion to channels (#1396).
plot_DRTResults()values has been renamed to
object. The older name will still work but generates a
deprecation warning (#1434).plot_RLum.Analysis()plot_RLum.Data.Curve()cex didn’t account of
the par.local argument, thus affecting curve plots
generated by plot_RLum.Analysis() (#1347).plot_RLum.Data.Spectrum()The norm argument is no longer limited to just
"min" and "max" but now supports all options
provided by normalise_RLum() (#1303).
The function now returns NULL (instead of producing
an empty plot or crashing) whenever the normalisation step replaces all
values with zeroes, which can happen if the normalisation term used is
0, for example when the bg.spectrum argument is used and
norm = "min" (#1305).
Setting log = "z" will produce a warning if the data
contains non-positive values (for example after background subtraction
or normalisation) before setting those values to NA. This
avoids producing infinities or NaN values that would lead to crashes for
some plot types (#1307).
plot_FilterCombinations()The interactive mode did not accept all plotting options from the default (non-interactive) mode (fixed in commit c27a656).
If the function was used on a shiny server, the plot showed only after the app was closed (fixed in commit c27a656).
plot_GrowthCurve()sample has been renamed to
object. The older name will still work but generates a
deprecation warning (#1434).plot_KDE()plot_RadialPlot()If the error column contains zero values, they are reset to the
smallest between the non-zero errors in the dataset and 10-9. This
avoids a crash when using the argument
centrality = "mean.weighted", which is the default for this
function (#1314).
The weighted median used to compute the central values when
centrality = "median.weighted" now uses the precision as
weight (similarly to what is done for the weighted mean), while before
it incorrectly used the error (#1323).
read_BIN2R()The function could crash if called with do.call()
and some particularly odd inputs (#1260).
The function now throws an error instead of returning
NULL when a file with the wrong extension is read
(#1393).
The function will now look for files recursively if the path to a directory is provided (#1393).
read_Daybreak2R()The function struggled with variable header lengths (#1262; thanks to @andrzejbluszcz for reporting).
The function will no longer crash if the data point entries have more than four columns (thanks to @andrzejbluszcz for reporting).
The import of binary .DAT files has been overhauled
and made more correct; moreover, the function accepts both
.DAT and .dat extensions for binary inputs,
and supports DataType=Command records in ASCII files
(#1263, #1266; thanks to @andrzejbluszcz for contributing code
and datasets).
Trying to import multiple files by specifying a directory name failed because the generated path missed a directory separator (#1264).
read_PSL2R()NULL instead of throwing an
error if a directory is provided and no PSL files are found within it
(#1393).read_RF2R()NULL if a list containing elements other than character
strings is provided (#1393).read_SPE2R()NULL if the filename provided does not exist (#1393).read_XSYG2R()Attributes from the record level are now all included in the
@info slot, as long as they do not duplicate the attributes
from the curve level. Hence, those attributes are now available for
filtering (#1239; thanks to @DirkMittelstrass for
reporting).
The function could crash if called with do.call()
and some particularly odd inputs (#1260).
remove_RLum()NULL records when an
invalid record.id was specified, which in turn could cause
a crash when displaying the object to the terminal (#1380).report_RLum()do.call() and
some particularly odd inputs (#1260).subset_SingleGrainData()The internal function .normalise_curve() received
support to normalise by the minimum value ("min"), the
first value ("first"), the channel length
("intensity") or a positive number (e.g, 2.2). These new
settings are automatically available to
plot_RLum.Analysis() and the
plot_RLum.Data.*() functions (#1250, #1300).
All the read_*() functions now process and validate
the file argument through the same internal helper
function. This allows them to support single and multiple files, URLs
and directory paths (#1393).
The package no longer depends on RcppArmadillo. This
has no visible impact to the user other than a small reduction in the
package size (#1254).
The show method for an RLum.Analysis-class object
would fail if the record slot contained NULL elements
(fixed in commit f1846c5c).
The package has now reached 100% coverage! The test-coverage workflow action has been updated so that any decrease in coverage will be marked as a failure (#548).
See also the write-up for this release on the REPLAY website.
This package version requires R >= 4.4
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).
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()"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()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()calc_CosmicDoseRate()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()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()calc_Huntley()calc_OSLLxTxRatio()Lx.data and Tx.data arguments are now
better validated (#1178).calc_SourceDoseRate()calc_Statistics()calc_Statistics()
(#1160).combine_De_Dr()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()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()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()graphics::arrows() when datasets having wildly different
distributions are plotted (#1184).plot_Histogram()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 at the bottom of the plot is no longer added when the
boxplot is not plotted because values.cumulative = FALSE
(#1110).
The plot title and subtitle now respect the cex
option (#1112).
The function now better validates its input arguments (#1158).
plot_RadialPlot()The function avoids some possible overprinting at the extremes of the z-axis labels and draws lines at the extremes of the ellipse (#1013).
The appearance of the y-axis ticks has been improved in the case when the y-axis is particularly narrow (#1060).
If summary.pos contains multiple valid positions,
use the first one rather than generating warnings and not showing the
summary (#1093).
The functionality of the stats argument had
regressed in version 1.1.1, and now has been restored (#1106).
The function better validates the zlim argument, to
avoid crashes on misspecified axis limits if log.z = TRUE
(#1140).
The function now always returns invisibly the list of plot
parameters, independently of the value of the output
argument. This change made that argument redundant, so it was removed.
This should have no impact on users; if specified, it will be ignored
(#1142).
The function stops with an error instead of crashing if the input contains only 1 data point (#1150).
The function reports a message instead of throwing a warning when
adding a line with negative value if log.z = TRUE (#1164,
#1168).
The summary text and line labels now scale better at high
cex values (#1170).
The function no lonver crashes if central.value is a
non-positive value when log.z = TRUE (#1173).
Some graphical artifacts related to the 2-sigma bar, which would
appear for extreme settings of the central.value argument
have been fixed (#1194).
plot_RLum.Analysis()Setting records_max to a value larger than the
number of curves no longer generates spurious legend entries
(#1017).
The function now supports plotting of
RLum.Data.Image objects contained in its records
(#1028).
plot_RLum.Data.Image()The function now supports the ... argument
mtext (#1031).
The positioning of axis ticks and labels in raster and contour plots of low-resolution images has been improved, and pixel numbering starts consistently from 1 (#1191).
The function gained support for the arguments digits
and scientific. Moreover, it is possible to specify
multiple plot titles in main. Thanks to @Zink-Antoine for the
contribution (#1197).
plot_RLum.Data.Spectrum()The function doesn’t crash anymore if bg.spectrum is
used and ylim specifies an interval that doesn’t contain
any background channels (#1019).
The function doesn’t crash anymore if the value of
frames given is too large when
plot.type = "multiple.lines" (#1021).
The legend text now scales better at high cex values
(#1068).
The function now makes better use of the plot area by setting smaller margins and reducing the spacing between axis elements (#1070).
read_PSL2R()pattern argument to refine the
list of files to read when a directory path is specified (#1099).read_SPE2R()frame.range is
misspecified (#1138).subset.Risoe.BINfileData().RESERVED slot (if
present) to keep only the elements selected (#1089).verify_SingleGrainData()RLum.Analysis-class
objects. Now a warning and NULL is returned.The ExampleData.portableOSL file has been updated
with surface coordinates (#1095).
Documentation for all example data (including synthetic datasets) is now more easily findable from RStudio (#1166; thanks to @DirkMittelstrass for reporting).
See also the write-up for this release on the REPLAY website.
correct_PMTLinearity(): A helper function to correct
luminescence signals measured with a PMT for count linearity
(#920).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).
add_metadata<-()NULL
value instead of silently ignoring it (#946).analyse_Al2O3C_ITC()analyse_Al2O3C_Measurement()cross_talk_argument
as a numeric vector of length 3, as was already documented (#930).analyse_SAR.CWOSL()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()calc_Huntley2006()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()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()fit_CWCurve()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()log = "x" is specified and the lowest value is set to
0 threw the correct warning but actually did nothing
(38e4324).fit_OSLLifeTimes()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()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() (9ba54e65).
The legend positioning can now be controlled via the
... argument legend.pos (#959).
plot_DRCSummary()plot_DRTResults()Points didn’t scale correctly at non-default cex
values (#879).
Option summary = "weighted$median" is now officially
supported (#905).
plot_Histogram()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()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()cex
settings (#854).plot_RLum.Data.Curve()interactive
that enables interactive plotting of curves using
plotly::plot_ly(). It requires the suggested package
'plotly' to be installed (e4746eaa).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()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()correct_PMTLinearity()
(#920).smooth_RLum()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()trim_range argument exceeded the number of channels
available (#871).use_DRAC()See also the write-up for this release on the REPLAY website.
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 2024 (#677). The code implementation follows the
Python reference by jll2 with
an addition for an allowed offset parameter 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 where 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.