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 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.