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Changelog

Source: NEWS.md

Changes in version 1.1.0 (2025-06-11)

CRAN release: 2025-06-11

New functions

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

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

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

New datasets

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

Breaking changes

Bugfixes and changes

analyse_baSAR()

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

analyse_FadingMeasurement()

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

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

analyse_IRSAR.RF()

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

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

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

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

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

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

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

analyse_pIRIRSequence()

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

analyse_portableOSL()

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

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

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

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

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

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

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

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

analyse_SAR.CWOSL()

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

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

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

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

  • More code optimisation for better readability (#802)

analyse_SAR.TL()

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

calc_AliquotSize()

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

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

calc_AverageDose()

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

calc_FiniteMixture()

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

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

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

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

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

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

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

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

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

calc_Huntley2006()

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

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

  • The function now warns if the number of bootstrap replicates is too low to perform the loess fitting (#721).

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()

  • The function validates its input values more thoroughly (#613).

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

  1. (#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()

  • Fix crash when attempting to plot a frame with non-positive counts (#761).

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()

  • It is now possible to specify different values for the light attenuation coefficient 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()

  • The argument 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()

  • The function uses the most common formats (BINX and XSYG) before trying all others.

merge_RLum.Data.Curve()

  • The function does no longer stops for differing channel resolutions, but it does issue a warning. The user is responsible for the consequences.

plot_DetPlot()

  • The logic for multicore support was incorrect, which resulted in always starting a parallel cluster even when 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()

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()

  • Argument 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()

  • The function now returns a less messy data frame because it encapsulates .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()

  • The function now throws messages instead of warnings for wanted coercions; however, it will be hard on failed coercions that would cause 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()

  • The function crashed if an object originating from read_XSYG2R() contained positions in its info field (#740).

write_R2TIFF()

  • The function now supports the export of more than one image slice.

Internals

  • The internal function 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.

Changes in version 1.0.1 (2025-03-07)

CRAN release: 2025-03-07

Bugfixes

analyse_baSAR()

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

analyse_FadingMeasurement()

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

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

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

analyse_pIRIRSequence()

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

calc_CosmicDoseRate()

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

calc_FadingCorr()

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

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

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

calc_FastRatio()

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

plot_AbanicoPlot()

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

plot_RLum.Analysis()

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

sort_RLum()

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

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

Changes in version 1.0.0 (2025-02-21)

CRAN release: 2025-02-21

New functions

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

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

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

  • 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).

Breaking changes

  • We have dropped our dependency on the readxl package: functions analyse_baSAR() and use_DRAC() now do not accept XLS files anymore but CSV files instead (#237). 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).

Renamed functions and deprecations

New dependencies

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

Bugfixes

analyse_Al2O3C_CrossTalk()

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

analyse_baSAR()

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

analyse_SAR.CWOSL()

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

analyse_FadingMeasurement()

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

analyse_IRSAR.RF()

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

analyse_pIRIRSequence()

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

analyse_SAR.CWOSL()

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

apply_CosmicRayRamoval()

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

calc_AverageDose()

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

calc_CentralDose()

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

calc_FastRatio()

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

calc_FiniteMixture()

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

calc_gSGC()

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

calc_Huntley2006()

  • Some crashes in case of model misspecification have been solved (#538).
  • Some details in the implementation of the function have been optimized, and now it is much faster than before. As part of this, we have changed the default setting of the 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).
  • Fitting the “GOK” model on the unfaded data failed when the “EXP” model we use to find a good starting point failed: in such cases, we try again using the simulated fit (#549; thanks to @SalOehl for reporting and providing data to reproduce the error).
  • The natural/simulated curve was not plotted in the negative quadrant for mode = "extrapolation", which made it harder to see where it extrapolated to (#551; thanks to @SalOehl for reporting).

calc_IEU()

  • The code of this function has been consolidated to avoid duplication and make its debugging easier: this has uncovered a small coding error and also led to some speed up (#429).
  • Some crashes in the function have been solved (#424).

calc_Lamothe2003()

  • We addressed a long-standing issue regarding the calculation of the Ln/Tn error after fading correction, which led to smaller than expected errors (#96).

convert_RLum2Risoe.BINFileData()

  • The function could crash with a incompatible types (from raw to character) error under particular circumstances; fixed.
  • The function would fail in edge cases where different objects are mixed so that certain fields for METADATA are already available but in the wrong format; fixed.

extract_IrradiationTimes()

  • In some circumstances the function failed to update an existing BIN/BINX file due to an incorrect way of subsetting an intermediate data frame of results (#445).
  • The function crashed if the info element startDate was missing in the irradiation curve; fixed.

fit_CWCurve()

  • The function crashed if the computation of the confidence intervals done in confint() failed. This has now been fixed, and in cases of failures we report the error message received from confint() (#509).
  • Argument output.terminal has been renamed to verbose for consistency with other functions.
  • The function has gained the new 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).
  • In case of plot failure the function now is able to recover gracefully and produce an output object (#574).

fit_EmissionSpectra()

  • The function can now return a data frame with the values of all curves plotted, so that it’s much easier to produce alternative plots, by setting option export.plot.data = TRUE within the method_control argument (#569).

fit_LMCurve()

  • The function has gained the new 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).
  • In case of plot failure the function now is able to recover gracefully and produce an output object (#574; thanks to @LumTKO for reporting).

get_RLum()

  • If the 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()

  • The function automatically determines the available import functions and ensures that formats supported by the package are tested and used.
  • A minor change in the code enables the support of 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()

  • If negative values were provided, the function sometimes produced wrong plots for z.log = TRUE (the default); fixed.
  • Support for tcl and tck arguments via ... was removed as they were never used internally.

plot_DetPlot()

  • Option plot.single has been renamed to plot_singlePanels (#351, fixed in #408).

plot_DRTResults()

  • The function crashed if option na.rm was used alongside the preheat option but the data set contained no missing values (#474).

plot_GrowthCurve()

  • The function is now implemented as a wrapper around fit_DoseResponseCurve() and plot_DoseResponseCurve(). There should be no visible user-facing changes (#319).
  • Support new ... 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.
  • Add density_polygon, density_polygon_col, density_rug, box as ... arguments to plot and add respective plot options
  • The function crashed for single grain data that sometimes caused a lot of NaN values during log conversions required for estimating the start parameters. The result was the error object 'b.MC' not found (#374; fixed)
  • For the non-linear choices of 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).
  • We replaced 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).
  • Option output.plotExtended.single has been renamed to plot_singlePanels (#351).
  • The function now supports a list of data frames as input, in which case it calls itself on each element of the list and produces a list of RLum.Results as output (#405).
  • The function reported negative dose values in the MC runs plot when using fit.method = "QDR" and mode = "extrapolation" (#504).
  • Argument NumberIterations.MC has been renamed to n.MC (#546).

plot_RLum.Analysis()

  • Option plot.single has been renamed to plot_singlePanels (#351).

plot_RLum.Data.Curve()

  • Argument 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()

  • The gradient between colours when plot.type = "persp" is now more consistent and doesn’t produce artefacts in the regions of transition between colours (#371).
  • The function would crash if the bin.rows or bin.cols value was set too high or if xlim and ylim were set too tight (#415).

read_BIN2R()

  • The function is now much faster: we have recorded an overall improvement of over 60% on a 46M file, with potentially bigger time savings for larger files (#298).
  • Argument 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).
  • Argument zero_data.rm was not correctly propagated if the input object was provided as a list (#342).
  • The 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).
  • The .RESERVED slot is now kept in sync with the rest of the object when records are dropped from the input BIN/BINX file (#337).
  • The function doesn’t crash anymore when reading a file that contains a record with an unrecognised version after other records with a valid version have been read (#352).
  • The function doesn’t crash anymore when reading a file that contains a ROI record while using fastForward = TRUE (#356).

read_HeliosOSL2R()

  • If the function encounters problems in the provided list of files, it shows a more relaxed handling; throws an error but continues reading.

read_XSYG2R()

  • The new n_records argument now enables to control the number of records to import, which can be useful in case the file is faulty.
  • The function failed to import files when a directory name was provided; this was a regression introduced in v0.9.25 and it has now been fixed.
  • The function truncated the terminal output under certain circumstances; fixed.

scale_GammaDose()

  • Option 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()

  • The function gained a new argument 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.
  • The template contained a couple of minor mistakes that got fixed along with a more strict enforcement of the class of each field, which is now set as an attribute; the change should have no user-visible effect.
  • The function now supports the conversion factors by Cresswell et al. (2018) (Cresswelletal2018). Please ensure that the server supports that option.

trim_RLum.Data()

  • The function has been made more robust against misspecifications of its trim_range argument that could lead to crashes (#460).

use_DRAC()

  • Support for DRAC v1.1 XLS/XLSX files has been dropped, users should use CSV files according to the DRAC v1.2 CSV template.
  • The function gained support for three new ... arguments: version_ignore to ignore the DRAC version check, user and password to access password protected websites.
  • The identifiers submitted to the DRAC server are now better randomized to to guarantee more confidentiality of the data transmitted (#435).

verify_SingleGrainData()

  • Potentially breaking old code!: if 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.
  • The function doesn’t crash anymore when applied to an empty list (#365).
  • Silence the very talkative terminal output even if nothing was removed from a record for cleanup = TRUE.
  • The function now provides better terminal feedback if the selection results in an empty record.
  • Add a new logical argument use_fft that will apply an additional Fast Discrete Fourier Transform (FFT) verification on the data if wanted.

write_R2BIN()

  • The function now supports the verbose argument, which can be used to suppress output to the terminal (#442).