Comprehensive Luminescence Dating Data Analysis

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 0.7.5 (30th June, 2017):

Bugfixes and changes:

     • ‘analyse_SAR.CWOSL()’

         • If the signal integral was wrong, the default value was
           not set correctly (#46).

     • ‘calc_AverageDose()’

         • Update documentation and add produced output,

         • unify data.frame return output arguments (all capital
           letters).

     • ‘calc_FastRatio()’

         • Update slot names, which led to an output error.

     • ‘extract_IrradiationTimes()’

         • The exported BINX-file now works with the Analyst and
           the g-value can be calculated therein (thanks to Geoff
           Duller).

     • ‘plot_FilterCombinations()’

         • Calculate optical density and return it,

         • fix calclation of transmission window,

         • improve plot output.

     • ‘plot_RadialPlot()’

         • Fix error which occasionally occurred if a list of
           ‘data.frame’s are provided (thanks to Christina Neudorf
           for spotting the bug).

     • ‘read_BIN2R()’

         • Improve error messages for corrupted BIN/BINX-files,

         • ensure that the file connection is closed sufficiently.

     • ‘RisoeBINfileData2RLum.Analysis()’

         • The grain selection was not accepted and caused a
           constant error (#45).

     • ‘use_DRAC()’

         • The DRAC URL had changed; fixed.

Miscellaneous:

     • Fix package welcome message.

Changes in version 0.7.4 (31st March, 2017):

Changes in S4-classes and methods:

     • ‘get_RLum’ for ‘RLum.Analysis’-objects now returns an error
       and ‘NULL’ if the ‘record.id’ is not valid.

Bugfixes and changes:

     • ‘analyse_baSAR()’

         • The option to force the dose response curve trough the
           origin was not correctly implemented; fixed.

     • ‘analyse_FadingMeasurement()’

         • The function returned unreliable results since the time
           since irradiation had been doubled. This bug only
           affected Lx/Tx data imported from an XSYG-file.

     • ‘analyse_SAR.TL()’

         • A test code snippet made it into the final package. With
           this the Lx/Tx error was taken as fixed value (10/100)
           from the Lx/Tx value itself. The calculated error was
           not considered; corrected,

         • function returns ‘NA’ for the error if the background
           signals are similar and the error would become 0,

         • new argument ‘integral_input’ added to allow for an
           integral definition based on temperatures and not
           channels.

     • ‘calc_TLLxTxRatio()’

         • Arguments ‘Lx.data.background’ and ‘Tx.data.background’
           are now pre-set to ‘NULL’, i.e. the function does not
           longer check for missing entries.

     • ‘plot_KDE()’

         • Further support for layout options as requested by
           Christopher Luethgens.

     • ‘plot_GrowthCurve)’

         • Rename argument options for argument ‘mode’ to
           ‘'interpolation'’ and ‘'extrapolation'’ instead of
           ‘'regenerative'’ and ‘'additive'’.

         • fix a rather rare bug using the combination
           ‘fit.force_through_origin = FALSE’ and ‘mode =
           "extrapolation"’,

         • the graphical representation for ‘mode =
           "extrapolation"’ was not correct (#38).

     • ‘plot_RLum.Data.Spectrum)’

         • Fixwrong axtick labels for interactive plot option
           (#39),

         • correct manual.

     • ‘plot_RLum.Analysis)’

         • Add support for the argument 'type' of the argument
           'combine = TRUE' is used.

     • ‘read_BIN2R()’

         • Correct minor bug while importing corrupt BIN-files,

         • add support for internet connections,

         • if a directory was provided the functions was trapped in
           an endless loop (#36)

     • ‘write_R2BIN()’

         • Argument 'BL_UNIT' was not correctly exported; fixed,

         • export behaviour for BIN-file version 08 improved.

Miscellaneous:

     • BIN-file example data sets can now be exported without error
       to BIN-files using ‘write_R2BIN()’.

Changes in version 0.7.3 (8th Feburary, 2017):

Bugfixes and changes:

     • ‘Risoe.BINfileData()’

         • Correct for mistakes in the manual.

     • ‘write_R2BIN()’

         • Correct for broken function (introduced with v0.7.0).

Miscellaneous:

     • Correct wrong package date format.

     • Add NEWS again to the package.

Changes in version 0.7.2 (7th February (evening), 2017):

    • The CRAN check on the Solaris machines gave an error while
      performing the (on all other platform sucessful) unit tests.
      Consequently, and to reduce the load for the CRAN resources
      all tests are skipped on CRAN.

    • This version never made it on CRAN!

Changes in version 0.7.1 (6th February (evening), 2017):

    • This release accounts for the CRAN check errors on the
      Solaris machines by preventing the unfortunate overload of
      the C++ function pow() with integer values.

Changes in version 0.7.0 (6th February (morning), 2017):

New functions:

     • ‘analyse_FadingMeasurement()’: Analyse fading measurements
       to calculate g-values and to estimate the density of
       recombination centres.

     • ‘analyse_portableOSL()’: The function analyses CW-OSL curve
       data produced by a SUERC portable OSL reader and produces a
       combined plot of OSL/IRSL signal intensities, OSL/IRSL
       depletion ratios and the IRSL/OSL ratio.

     • ‘calc_Kars2008()’: A function to calculate the expected
       sample specific fraction of saturation following Kars et al.
       (2008) and Huntley (2006).

     • ‘calc_AverageDose()’: Function to calculate the average dose
       and their extrinsic dispersion.

     • ‘convert_BIN2R()’: wrapper function around the functions
       ‘read_BIN2R()’ and ‘write_RLum2CSV()’ to convert a BIN-file
       to CSV-files; so far possible.

     • ‘convert_Daybreak2R()’: wrapper function around the
       functions ‘read_Daybreak2R()’ and ‘write_RLum2CSV()’ to
       convert Daybreak measurement data (TXT-file, DATE-file) to
       CSV-files; so far possible.

     • ‘convert_PSL2R()’: wrapper function around the functions
       ‘read_PSL2R()’ and ‘write_RLum2CSV()’ to convert a PSL-file
       (SUERC portable OSL reader file format) to CSV-files; so far
       possible.

     • ‘convert_XSYG2R()’: wrapper function around the functions
       ‘read_XSYG2R()’ and ‘write_RLum2CSV()’ to convert XSYG-file
       to CSV-files; so far possible.

     • ‘github_branches(), github_commits(), github_issues()’: R
       Interface to the GitHub API v3. These functions can be used
       to query a specific repository hosted on GitHub.

     • ‘install_DevelopmentVersion()’: This function is a
       convenient method for installing the development version of
       the R package 'Luminescence' directly from GitHub.

     • ‘PSL2Risoe.BINfileData()’: Converts an ‘RLum.Analysis’
       object produced by the function ‘read_PSL2R()’ to an
       ‘Risoe.BINfileData’ object.

     • ‘read_PSL2R()’: Imports PSL files produced by a SUERC
       portable OSL reader into R.

     • ‘smooth_RLum()’: wrapper function to call the corresponding
       methods to smooth data based on the function ‘zoo:rollmean’.

     • ‘write_RLum2CSV()’: Exports ‘RLum’-objects to CSV-files to
       improve the compatibility to other software.  Supported are
       only numerical values, i.e., ‘data.frame’, ‘matrix’ and
       ‘numeric’.

New example data:

     • ‘ExampleData.fading’: Example data set for fading
       measurements of the IR50, IR100, IR150 and IR225 feldspar
       signals of sample UNIL/NB123. It further contains regular
       equivalent dose measurement data of the same sample, which
       can be used to apply a fading correction to. These data were
       kindly provided by Georgina King.

Changes in S4-classes and methods:

     • Method ‘get_RLum’ for ‘RLum.Analysis’-objects did not
       respect ‘.pid’, fixed.

     • Method ‘get_RLum’ for ‘list’-objects now accepts lists with
       all kinds of ‘RLum’-objects. Previously, only lists of
       ‘RLum.Analysis’-objects were allowed.

     • ‘plot_RLum’ was not passing the argument ‘sub’, as it was
       fetched by the partial argument matching; fixed.

     • ‘set_RLum’ produced ‘NA’ as originator, if the function
       calling the function ‘set_RLum()’ was called from outside of
       the package using the double colons (e.g.,
       ‘Luminescence::function()’); fixed.

     • ‘smooth_RLum’ add method support for ‘RLum.Data.Curve’,
       ‘RLum.Analysis’ and ‘list’ of this objects implemented.

Bugfixes and changes:

     • ‘analyse_baSARL()’

         • Due to a typo in the manual the ‘method_control’
           parameter ‘variable.names’ was not working if correctly
           typed as written in the manual (in the manual:
           'variables.names', but correct is 'variable.names');
           typo corrected fixed,

         • minor improvements and error corrections.

         • ‘analyse_IRSAR.RF()’

             • Add option for a vertical sliding of the RF_nat
               curve (‘method_control = list(vslide_range =
               'auto')’). This feature has beta status and usage
               for publication work is not recommended yet. By
               default no vertical sliding is applied,

             • allow a parallel processing of MC runs by using the
               argument ‘method_control = list(cores = 'auto')’.

         • ‘analyse_SAR.CWOSL()’

             • Fix wrongly set threshold value for recuperation
               rate (#26),

             • fix a rare bug for the combination 'recyling.ratio =
               NA' and more than one provided recyling point,

             • a check has been implemented to refrain from using
               wrong rejection criteria keywords.

         • ‘calc_AliquotSize()’

             • Console output can now be suppressed via 'verbose =
               TRUE' (#24).

         • ‘calc_CosmicDoseRate()’

             • Console output can now be suppressed via 'verbose =
               TRUE' (#24).

         • ‘calc_FastRatio()’

             • New arguments 'Ch_L2' and 'Ch_L3' to allow the user
               to specify custom values for channels L2 and L3.
               Feature requested by A. Versendaal (#29).

         • ‘calc_FadingCorr()’

             • Fixed a bug where the function would crash when
               providing an ‘RLum.Results’ object for ‘g_value’,

             • new argument ‘interval’ to control the age interval
               for solving the equation via ‘uniroot’.

         • ‘calc_FiniteMixture()’

             • Fixed a bug where certain arguments where not passed
               to `plot_RLum.Results` so that the plot was not as
               customisable as intended.  Thanks to Daniele
               Questiaux for reporting the bug.

         • ‘calc_MaxDose()’

             • Fixed a bug in the console output, which provided
               wrong values for the asymmetric error on gamma (Note
               that the values in the output object were correct!).
               Thankfully reported by Xue Rui.

         • ‘calc_Statistics()’

             • The argument ‘n.MC’ got a new value ‘NULL’ which is
               now used as default. With this the basic statistical
               measures are in accordance with the expectations
               (e.g., the standard deviation is returned by default
               in the conventional way and not calculated using an
               MC simulation).

         • ‘calc_OSLLxTxRatio()’

             • Add argument ‘use_previousBG’ to use the background
               of the Lx-curve to get the net signal of the
               Tx-curve (request #15).

         • ‘fit_CWCurve()’

             • Change order of ‘RLum.Results’ output list elements,

             • rename first element to ‘data’,

             • add element slot 'info'.

         • ‘fit_LWCurve()’

             • Change order of ‘RLum.Results’ output list elements,

             • rename first element to ‘data’,

             • add element slot 'info'.

         • ‘model_LuminescenceSignals()’

             • Update function arguments to account for changes in
               RLumModel version 0.2.0.

         • ‘plot_DetPlot()’

             • Correct negative y-axis, the minimum is now the real
               minimum.

         • ‘plot_GrowthCurve()’

             • Reduce number of confusing warning,

             • add new argument ‘mode’ to select the calculation
               mode of the function.  This allows in particular to
               only fit data without calculating a De or
               calculating a De assuming an additive dose response
               curve,

             • account for the very specifc case that all dose
               points are similar. The function stops with an error
               and returns NULL,

             • under weird circumstances points on the growth curve
               were not plotted correctly; fixed.

         • ‘plot_RadialPlot()’

             • Sometimes the function crashed with an out of bonds
               error if more than one data set was provided; fixed,

             • argument ‘negatives’ caused an error if not set to
               ‘'remove'’ and fix some errors around this option,

             • De-adjustment for negative values optimised for
               large scatter.

         • ‘plot_RLum.Analysis()’

             • The usage of the argument ‘smooth’ led to a crash;
               fixed.

         • ‘plot_RLum.Data.Curve()’

             • Function will not stop anymore if the curve contains
               ‘NA’ values, but if the curve consists of only ‘NA’
               values.

         • ‘plot_RLum.Data.Spectrum()’

             • The interactive plot option was broken with the last
               update of the package 'plotly'; fixed.

         • ‘plot_ViolinPlot()’

             • The function erroneously produced a NA value
               warning; fixed.

         • ‘read_BIN2R()’

             • If BIN-files are automatically imported the function
               skipped non BIN-files without crashing if it is used
               in combination with the argument ‘pattern’,

             • add new argument ‘irgnore.RECTYPE’ to provide a
               solution for broken BIN-files are BIN-files with non
               documented entries. Furthermore the general
               behaviour for such cases had been optimised.

         • ‘read_Daybreak2R()’

             • Add support for DAT-files produced by at 1100 reader
               using the software (TLAPLLIC v.3.2).  Thanks to
               Antoine Zink,

             • minor error corrections and adding example code.

         • ‘template_DRAC()’

             • Fixed a typo in the column names (#28).

         • ‘use_DRAC()’

             • Now supports DRAC v1.2 and the newly introduced CSV
               input template.  Older v1.1 excel sheet input
               templates are still supported, but users are highly
               encouraged to use the new CSV file.

             • Columns in the output tables are now assigned proper
               classes (#27).

Internals:

     • The internal function converting BIN-file curves to
       RLum.Data.Curve() objects had been optimised and, amongst
       others, now uses a function written using Rcpp to create the
       curve matrix.  The conversion now works ca. two times
       faster,

     • add ‘`[<-]`’ method for ‘RLum.Data.Curve’ objects,

     • a hint on how to cite a function is now added automatically
       to every major function manual page,

     • add 'magrittr' to the package dependencies (imports) to
       further support the usage of this amazing pipe operator,

     • thanks to Johannes Friedrich this release introduces regular
       unit tests using the package 'testthat' to improve the code
       quality and stability,

     • add internal helper function ‘.smoothing’; no Rd entry.

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")

0.8.4 by Sebastian Kreutzer, 7 days 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] (<https://orcid.org/0000-0002-0734-2199>), Christoph Burow [aut, trl, dtc] (<https://orcid.org/0000-0002-5023-4046>), Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>), Margret C. Fuchs [aut], Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>), Manfred Fischer [aut, trl], Johannes Friedrich [aut], Norbert Mercier [ctb], Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>), Claire Christophe [ctb], Antoine Zink [ctb], Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>), Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>), Anne Philippe [ctb], Guillaume Guerin [ctb] (<https://orcid.org/0000-0001-6298-5579>), Markus Fuchs [ths]


Documentation:   PDF Manual  


GPL-3 license


Imports bbmle, data.table, 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