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.
The R package ‘Luminescence’ by the R-Luminescence Group provides a collection of various R functions for luminescence dating data analysis.
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or visit our R-Luminescence homepage.
With release of version 0.4.2 part of the analyse_IRSAR.RF() function was rewritten in C++ to increase its perfomance. This inevitably introduced the requirement for the GNU Compiler Collection (gcc) when the R package ‘Luminescence’ is installed from source. Depending on your OS please download and install one of the following:
Windows (32/64bit) - ‘Rtools’ (provided by CRAN)
https://cran.r-project.org/bin/windows/Rtools/
Mac OS X - ‘Xcode’ (provided by Apple)
https://developer.apple.com/xcode/downloads/
For Linux users gcc often comes pre-installed in most distributions. Should gcc be not available, however, we kindly refer to the exhaustive collection of installation guides depending on the linux distribution.
Install any development versions using our RStudio add-in
To install the stable version from CRAN, simply run the following from an R console:
install.packages("Luminescence")
To install the latest development builds directly from GitHub, run
if(!require("devtools"))install.packages("devtools")devtools::install_github("R-Lum/[email protected]")
To install a developer build other than ‘master’, replace the term ‘master’ in the codeline by the name of the wanted developer build.
The R luminescence project is based on and evolves from ideas, contributions and constructive criticism of its users. Help us to maintain and develop the package, to find bugs and create new functions as well as a user-friendly design. Try https://github.com/R-Lum/Luminescence/issues or write us an e-mail if anything crosses your mind or if you want your new self-written function to be to implemented. You are kindly invited to bring forward the package with us!
The package comes without any guarantee!
Please further note that this version is a development version and may change day by day. For stable branches please visit the package on CRAN ‘Luminescence’.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
‘Luminescence’ 0.9.X releases will be the last versions supporting R < 3.5.0.
The behaviour of the base R function sample()
was changed / corrected
(see news on https://r-project.org for details). This function is used
heavily within functions by ‘Luminescence’ (e.g., plot_GrowthCurve()
).
That being said, it means that old data re-analysed by ‘Luminescence’
using R versions >= 3.6.0 will not give the same results. Differences
are small, however, they may significant. If you want to reproduce your
data, we recommend to use one of our Docker
images which include the R version
from the package release date.
convert_Wavelength2Energy()
Smooth and quick emission spectra
conversion from wavelength to energy scalesfit_OSLLifeTimes()
Fit and deconvolution of OSL lifetimes using
off-time measurements, i.e. after the stimulation was switched off.plot_DRCSummary()
Summarise all dose-response curves from your SAR
OSL analysis in one single plot.scale_GammaDose()
Scale the gamma dose rate considering
layer-to-layer variations in soil radioactivity. Contributed by S.
Riedesel and M. Autzen.fit_ThermalQuenching()
Provide an easy option to fit thermal
quenching data and determine the activation energy.apply_CosmicRayRemoval()
RLum.Data.Spectrum
objects and and RLum.Analysis
objects (also
nested in a list)apply_EfficiencyCorrection()
analyse_SAR.CWOSL()
list
), the arguments contrary to what is written in the manual,
the arguments such as signal.integral.min
had not been expanded
properly; no one complained, however, corrected.main
no also supports the input list
in the
self-call mode.analyse_SAR.TL()
RLum.Analysis
objects as inputanalyse_FadingMeasurements()
stats::approx()
;
fixedcalc_Huntley2006()
rhop
) is a sensible non-zero
positive value and, if otherwise, stops with a more meaningful error
message. (Issue #74)read_BIN2R()
0
. For BINX-files >= version 6 such timestamps now get corrected
during the importread_XSYG2R()
approx(..., ties = -2)
); fixed.plot_GrowthCurve()
Error in data.MC[, i] : incorrect number of dimensions
under very particular circumstances (reported by
Alice Versendaal). This was due to unwanted internal object
conversion; fixed.plot_RLum.Data.Spectrum()
convert_Wavelength2Enegy()
(the corresponding code
and documentation have been updated or removed).norm
for normalising the data
to the highest or the lowest count value.bg.spectrum
allow to pass a
background spectrum that can be used for the subtractionplot.type
was already set to single
; fixed.bg.channels
crashed the function. Now it
auto-corrects the wrong values.Luminescence:::.matrix_binning()
, which is more efficient cleaner
than the code used beforeplot.type = 'persp'
if
’xaxis.energy = TRUE`.verify_SingeGrainData()
RLum.Analysis-class
objects did not worked; fixedwrite_RLum2CSV()
compact
which is set TRUE
be
default, and keeps the element output as simple as possible, which
is in particular helpful for RLum.Results
objectsRLum.Results
objects,
before the output was hard to understand.write_RLum2BIN()
NA
); now NA
values are consistently replaced by 000000
(other values are not
possible, otherwise the re-import of such file would fail) (reported
by Alice Versendaal via email, 2019-03-06)get_RLum
list
elements got a new argument class
to
remove unwanted RLum
objects in from list of RLum
objectsRLum.Analysis-class
RLum.Data.Spectrum-class
bin_RLum.Data()
ExampleData.TR_OSL
provides a single fast-pulsing OSL curve that
can be used to test the function fit_OSLLifeTimes()
.Luminescence:::.matrix_binning()
to get the
matrix (and curve) binning consistent; so far used only by the the
bin_RLum.Data()
method for RLum.Data.Spectrum-class
if(is.na(x))
returned
an error if x
was not a vector of length 1)src/Makevars
file removed to prevent unconditional stripping in
response to a recent CRAN request; in return the installation size
of the package increased in size on some platforms.