Comprehensive Luminescence Dating Data Analysis [upcoming]

A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.


News

NEWS for the R Package Luminescence

Changes in version 0.8.6 (October 5th, 2018):

Bugfixes and changes:

     • ‘analyse_Al2O3C_Measurement()’

         • The argument ‘signal_integral’ was not treated
           correctly; fixed,

         • Set threshold for wrong stimulation power detection from
           0.01 to 0.05, otherwise it fires to oftern in false
           positive cases.

     • ‘analyse_SAR.CWOSL())’

         • The function crashed for only noise like data yielding
           negative Lx/Tx values (reported by Dirk Mittelstraß);
           fixed,

         • In the output ‘data.frame’ containg the De values, the
           column 'RC.Status' was of type ‘factor’, but should have
           been of type ‘character’; fixed.

     • ‘analyse_pIRIRMeasurement()’

         • If measurements did not contain TL curves, the function
           showed a confusing warnings message; fixed.

     • ‘plot_DetPlot()’

         • Function does not break anymore if ‘signal.integral.min
           == signal.integral.max’ (reported by Andrea Junge).

     • ‘plot_KDE()’

         • The function could not handle ‘Inf’ values (#71) as
           reported by Dirk Mittelstraß; fixed.

         • The function could not handle ‘data.frames’ with more
           than 2 columns and ‘NA’ values in the unused columns
           (reported by Dirk Mittelstraß). Now the function takes
           only the first two columns.

     • ‘plot_GrowthCurve()’

         • The function crashed due to problems with the start
           parameter estimation for negative Lx/Tx values (reported
           by Dirk Mittelstaß); fixed.

     • ‘plot_RadialPlot()’

         • The function now uses only the first two columns from a
           ‘data.frame’, regardless its size.

     • ‘report_RLum()’

         • Add new argument ‘show_report’ to allow file creation
           only without getting the RStudio viewer involved.

Changes in version 0.8.5 (June 8th, 2018):

Bugfixes and changes:

     • ‘analyse_Al2O3C_Measurement()’

         • The cross-talk value was erroneously substracted the
           dose point values instead from the final De, the effect
           is small, but still, it was not correct; fixed,

         • add new argument ‘calculate_TL_dose’ which allows to
           experimentally calculate the apparent dose based on the
           TL curves. This feature may help in certain cases to
           cross-check the results obtained with the GSL,

         • the manual was not complete and the reference wrong,
           fixed.

     • ‘analyse_baSAR()’

         • Add support for ‘RLum.Analysis’-objects as input,

         • correct odd message informing about removed aliquots
           that had been never removed,

         • add new argument ‘distribution_plot’ to allow a manual
           selection of the frequentist distribution plot output.

     • ‘analyse_SAR.CWOSL()’

         • A newly introduced typo caused a function crash; fixed.

     • ‘bin.RLum.Data.Curve()’

         • The method was not passing the argument ‘bin_size’
           properly; fixed.

Changes in version 0.8.4 (April 20th, 2018):

Bugfixes and changes:

     • The previous package versions did not pass the CRAN tests on
       the Solaris platform; fixed.

Changes in version 0.8.3 (April 20th, 2018):

Bugfixes and changes:

     • ‘analyse_SAR.CWOSL()’

         • The function crashed if the ‘plot_GrowthCurve()’
           returned ‘NULL’; fixed,

         • ff the dose-response curve was not fitted, but ‘plot’
           was set to ‘TRUE’ no plot was returned (even no empty
           plot); fixed,

         • if all curves were IRSL curves, the function crashed
           while trying to plot the IRSL curve for the IRSL test.
           Now only the last IRSL curve is plotted. This does not
           make really sense since probably the user did not
           measure quartz, however, this solution fixes the problem
           and does not break other users code.

     • ‘analyse_FiniteMixture()’

         • For wrong user input and not well understood
           assumptions, the function crashed uncontrolled; fixed.

     • ‘analyse_pIRIRSequence()’

         • Fixed unwanted functions crashes for very odd datasets
           (e.g., ‘Inf’ values).

     • ‘convert_RLum2Risoe.BINfileData()’

         • The record type was not correclty extracted, fixed,

         • the conversion now keeps the original position numbers
           instead of assigning new.

     • ‘plot_GrowthCurve()’

         • If number of regeneration points was reduced for
           plotting and fitting, an unwanted warning message
           appeared due to a coding error,

         • if the D0 values is precisely 0.0000, the fit probably
           went wrong, in such cases now another attempt is made,

         • if a value for Lx/Tx is 0 now the value is set to
           ‘.Machine$double.eps’, instead of 0.001,

         • the formula output for ‘EXP+EXP’ was not correct, fixed.

     • ‘src_create_RLumDataCurve_matrix()’

         • Until today, you probably did not know that this
           function exists at all. This function is written in C++,
           working in the back and helps to create
           ‘RLum.Data.Curve’-objects out of BIN/BINX-files.
           Recently we became aware of non-conform BIN/BINX-files,
           circulating in the wild. For such files the TL curves
           were not created correctly, more important, the user did
           not know why. Now the function throws out a message, at
           least.

Changes in version 0.8.2 (March 10th, 2018):

Internals:

     • Package size significantly reduced by excluding the
       XSYG-file used for buildung the vignette.

Changes in version 0.8.1 (March 9th, 2018):

New functions:

     • ‘calc_Huntley2006()’

         • A function to calculate the expected sample specific
           fraction of saturation based on the model of Huntley
           (2006) using the approach as implemented in Kars et al.
           (2008) or Guralnik et al. (2015). This function
           supersedes the formerly released function
           'calc_Kars2008()'. The new function is identical to
           'calc_Kars2008()' when 'fit.method = "EXP"' (the
           default) is used, but also allows fitting a
           general-order kinetic function after Guralnik et al.
           (2015) ('fit.method = "GOK"').

Bugfixes and changes:

     • ‘calc_Kars2008()’

         • This function is now deprecated and will eventually be
           removed in an upcoming version of the 'Luminescence'
           package. Older scripts using this function will still
           work, but it is highly recommended to use the newly
           introduced function 'calc_Huntley2006()'.

     • ‘calc_MinDose()’

         • Previously, the function globally disabled warning
           messages via 'options(warn = -1)' due to the overly
           verbose output of functions in the 'bbmle' package.
           Globally disabling warning messages may prevent the
           display of unexpected warnings, however, and in
           rmarkdown files it wouldn't work anyway. This behaviour
           was replaced with explicit calls to 'suppressWarnings()'
           for particular functions. (#66)

         • Fixed a bug where the function tried to calculate the
           log of infinite (Inf, -Inf) values, which produced 'NaN'
           warnings.

     • ‘get_RLum()’

         • The argument ‘subset’ was broken and not working
           anymore, similar to the S3-method ‘subset’ dispatching
           to ‘get_RLum’ for ‘RLum.Analysis’-objects.  Both issues
           have been fixed.

     • ‘plot_DRTResults()’

         • If ‘boxplot = TRUE’ and ‘give.dose = NULL’ the plot
           still showed the abline at 1 including the +/- 10 %
           error range. Now, the abline is only showed if a numeric
           value is provided for ‘give.dose’, ‘NULL’ plots no
           abline.

     • ‘plot_GrowthCurve()’

         • Now allows fitting of the general-order kinetics
           function after Guralnik et al. (2015). Use ‘"GOK"’ as
           input for argument ‘fit.method’.

     • ‘template_DRAC()’

         • New argument ‘preset’ to allow the selection of
           pre-defined templates for various configurations (e.g.,
           ‘'quartz_coarse'’) for quartz coarse grain data. The
           templates bring pre-filled values to speed up the
           workflow, however, they do not free the researcher from
           cross-checking these values.

Internals:

     • Lower required dependent package versions to get the package
       passed on CRAN.

     • Further compress example data ... it was not yet the
       optimum.

     • Further compress 'vignettes'.

Changes in version 0.8.0 (Feburary 9th, 2018):

New functions:

     • ‘analyse_Al2O3C_ITC()’: Function to analyse data determined
       to correct irradiation times as suggested by Kreutzer et
       al., 2018

     • ‘analyse_Al2O3C_CrossTalk()’: Function to analyse data to
       analyse crosstalk measurements as shown in Kreutzer et al.,
       2018

     • ‘analyse_Al2O3C_Measurement()’: Function to analyse Al2O3:C
       data as shown by Kreutzer et al., 2018

     • ‘convert_Activity2Concentration()’: converts nuclide
       activity data (Bq/kg) to concentrations (ppm or %) and vice
       versa

     • ‘convert_RLum2Risoe.BINfileData()’: Function to convert
       ‘RLum.Analysis’ and ‘RLum.Data.Curve’ objects to
       ‘Risoe.BINfileData’, which can be exported to BIN/BINX-files
       using the function ‘write_R2BIN()’.

     • ‘calc_WodaFuchs2008()’: Function to obtain the equivalent
       dose using the approach proposed by Woda and Fuchs, 2008.

     • ‘fit_SurfaceExposure()’: Function to fit eq. 1 in Sohbati et
       al. (2012a) to OSL surface exposure data and derive
       estimates of its parameters (i.a., the age). Alternatively,
       eq. 12 in Sohbati et al. (2012b) can be fitted, which also
       considers the dose rate.

     • ‘calc_Lamothe2003()’: Function to support the fading
       correction suggested by Lamothe et al., 2003. As input the
       function accepts ‘data.frame’ output from the functions
       ‘analyse_SAR.CWOSL()’ and ‘analyse_pIRIRSequence)’.

New example data:

     • ‘ExampleData.SurfaceExposure’: A set of synthetic OSL
       surface exposure dating data to demonstrate the
       fit_SurfaceExposure() functionality. See
       ?ExampleData.SurfaceExposure for details.

     • ‘ExampleData.Al2O3C’: Al2O3:C chips measurement data to
       supplement the newly implemented functions to analyse
       Al2O3:C data.

S4-classes and methods:

     • The ‘RLum.Analysis’ show method failed for
       ‘RLum.Data.Spectrum’ objects; fixed.

     • Method for ‘get_RLum’ with signature ‘NULL’ added. Now it
       returns ‘NULL’.

     • The coercion from ‘list’ to ‘RLum.Results’ using ‘as()’ did
       not work; fixed.

     • Method ‘get_RLum’ for ‘RLum.Analysis’ returned a confusing
       error if what was provided via 'subset' was not a logical
       expression; fixed.

     • ‘structure_RLum()’ and ‘names_RLum()’ each got a method to
       deal with a list of ‘RLum’ objects.

Bugfixes and changes:

     • ‘analyse_SAR.CWOSL()’

         • The function gained a new argument ‘'onlyLxTxTable'’. If
           set to ‘TRUE’ only the Lx/Tx table is returned
           (including regeneration point sorting).

     • ‘analyse_IRSAR.RF()’

         • Multicore processing now also supports Windows (#47)

         • Fixed a bug where manually specifying the number of CPU
           cores via 'method.control = list(cores = x)' was not
           respected,

         • mixing of curves (e.g., regenerated first, natural
           second) led to a crash of the function, even the
           structure was correctly specified; fixed (#61),

         • the function will not break anymore uncontrolled of both
           RF curves are of similar extension on the x-axis.

     • ‘analyse_pIRIRSequence()’

         • If the number of records did not match the sequence
           structure the function crashed with a confusing error
           message. Now it shows an error and returns ‘NULL’,

         • make the argument ‘main’ more powerful if the input is a
           list,

         • add missing items to the manual.

     • ‘calc_HomogeneityTest()’

         • The calculation was wrong for the option ‘log = TRUE’
           (the default); fixed (#63).

     • ‘calc_Kars2008()’

         • In some cases the calculated LxTx values of the
           simulated natural dose-response curve were slightly
           underestimated and its maximum value differed from the
           individually calculated nN(ss) value. The approach to
           calculate the natural DRC was changed and now yields a
           maximum LxTx value indistinguishable from nN(ss).

         • Numeric output in the plot should now always be inside
           the plotting frame.

         • The number of digits for the numeric output in the plot
           was slightly adjusted.

     • ‘plot_FilterCombinations()’

         • Add interactive mode (‘interactive = TRUE’),

         • correct wrong visualisation of transmission windows for
           long or short pass filters,

         • fix legend error if only one filter was provided (due to
           a recent matrix behaviour change).

     • ‘plot_GrowthCurve()’

         • The function now turns ‘Inf’ into ‘NA’,

         • the argument ‘na.rm’ is defunct and should not be used
           anymore,

         • minor code modifications to handle special cases such as
           input values with a ‘data.frame’ with no error column,

         • extent examples by for test data set by Berger & Huntley
           (1989),

         • remove one more confusion warning if the fit did not
           work.

     • ‘plot_Historgram()’

         • The forwarded argument ‘breaks’ was not treated
           correctly (#54); fixed.

     • ‘plot_RLum()’

         • The function now supports plotting even of highly nested
           lists of `RLum-objects`.

     • ‘plot_RLum.Analysis()’

         • The option `col` was not working as expected if `black`
           was provided; fixed,

         • setting ‘ylim’ caused a function break (#65); fixed.

     • ‘read_BIN2R()’

         • The function unexpectedly dropped are warning for an
           unused connection; fixed,

         • if a file link was provided and the argument ‘pattern’
           was set and error was shown; fixed.

     • ‘read_Daybreak2R()’

         • The functions did not work anymore on ASCII files;
           fixed!

     • ‘read_XSYG2R()’

         • Argument ‘verbose’ added for more consistency with other
           functions,

         • the functions now supports the import form files via the
           internet,

         • minor modifications to support minimal examples without
           'recordType',

         • give the XSYG-file import a 50% performance boost,

         • set option `XML_PARSE_HUGE` to allow parsing of larger
           nodes within the XSYG-file,

         • the metadata entries ‘curveType’ and ‘parentID’ appeared
           duplicated, fixed.

     • ‘read_SPE2R()’

         • Add support for internet connections,

         • fix unclear file extension recognition.

     • ‘write_R2BIN()’

         • The BIN-file export to version 04 failed in very rare
           cases for ‘NA’ values in the byte position ‘SEQUENCE’;
           fixed,

         • the compatibility mode was extended, now limiting the
           maxmium number of points for one curve to 9,999 (if the
           option is chosen). This improves the compatibility with
           older versions of the Analyst.

Internals:

     • Add new vignette 'Analyse Al2O3:C Measurements'

     • Add new vignette 'Analyse post-IR IRSL Measurements'

Internals:

     • Start supporting RStudio add-ins for more advanced users.

     • Add fitting test data set by Berger & Huntley (1989) as
       external data.

     • The internal documentation now uses 'markdown'.

     • Internal function `.unlist_RLum()` allows to get rid of
       nested lists.

     • Required R version increased to 3.4.0 (patchlevel 0).

     • Cleanup help index and hide internal functions and methods.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("Luminescence")

0.9.0.110 by Sebastian Kreutzer, a day ago


https://CRAN.R-project.org/package=Luminescence


Report a bug at https://github.com/R-Lum/Luminescence/issues


Browse source code at https://github.com/cran/Luminescence


Authors: Sebastian Kreutzer [aut, trl, cre, dtc] , Christoph Burow [aut, trl, dtc] , Michael Dietze [aut] , Margret C. Fuchs [aut] , Christoph Schmidt [aut] , Manfred Fischer [aut, trl] , Johannes Friedrich [aut] , Norbert Mercier [ctb] , Rachel K. Smedley [ctb] , Claire Christophe [ctb] , Antoine Zink [ctb] , Julie Durcan [ctb] , Georgina E. King [ctb, dtc] , Anne Philippe [ctb] , Guillaume Guerin [ctb] , Svenja Riedesel [ctb] , Martin Autzen [ctb] , Markus Fuchs [ths]


Documentation:   PDF Manual  


GPL-3 license


Imports bbmle, data.table, DEoptim, httr, matrixStats, methods, minpack.lm, plotrix, raster, readxl, shape, parallel, XML, zoo

Depends on utils, magrittr

Suggests RLumShiny, RLumModel, plotly, rmarkdown, rstudioapi, rjags, coda, pander, testthat, devtools, R.rsp

Linking to Rcpp, RcppArmadillo


Imported by BayLum, RLumShiny, TLdating.

Depended on by RLumModel.


See at CRAN