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Luminescence

The R package 'Luminescence' by the R-Luminescence Group provides a collection of various R functions for luminescence dating data analysis.

Social media and other resources

Follow us on or visit our R-Luminescence homepage.

Installation

i. Requirements

  • Windows (32/64bit): Rtools (provided by CRAN)
  • macOS: Xcode (provided by Apple)
  • Linux: gcc often comes pre-installed in most distributions.

ii. Install the package

Install any development versions using our RStudio add-in

The plain R way

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/Luminescence@<wanted branch>")

Contribute

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!

Note

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.

License

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.

Funding

  • 2011-2013: The initial version of the package was developed in the framework of the PhD thesis by Sebastian Kreutzer, while he was funded through the DFG programme “Rekonstruktion der Umweltbedingungen des Spätpleistozäns in Mittelsachsen anhand von Löss-Paläobodensequenzen” (GEPRIS id: 46526743)

  • 2014-2018: Cooperation and personal exchange between the developers is gratefully funded by the DFG in the framework of the program “Scientific Networks”. Project title: “RLum.Network: Ein Wissenschaftsnetzwerk zur Analyse von Lumineszenzdaten mit R” (GEPRIS id: 250974974)

  • 05/2014-12/2019: The work of Sebastian Kreutzer as maintainer of the package was supported by LabEx LaScArBx (ANR - n. ANR-10-LABX-52).

  • 01/2020-04/2022: Sebastian Kreutzer as maintainer of the package has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 844457 (CREDit), and could continue maintaining the package.

  • All other authors gratefully received additional funding from various public funding bodies.

Related projects

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Version

Install

install.packages('Luminescence')

Monthly Downloads

1,525

Version

0.9.20

License

GPL-3

Maintainer

Sebastian Kreutzer

Last Published

July 17th, 2022

Functions in Luminescence (0.9.20)

ExampleData.Al2O3C

Example Al2O3:C Measurement Data
BaseDataSet.ConversionFactors

Base data set of dose-rate conversion factors
CW2pHMi

Transform a CW-OSL curve into a pHM-OSL curve via interpolation under hyperbolic modulation conditions
BaseDataSet.CosmicDoseRate

Base data set for cosmic dose rate calculation
BaseDataSet.GrainSizeAttenuation

Base dataset for grain size attenuation data by Guérin et al. (2012)
CW2pLMi

Transform a CW-OSL curve into a pLM-OSL curve via interpolation under linear modulation conditions
CW2pLM

Transform a CW-OSL curve into a pLM-OSL curve
CW2pPMi

Transform a CW-OSL curve into a pPM-OSL curve via interpolation under parabolic modulation conditions
Analyse_SAR.OSLdata

Analyse SAR CW-OSL measurements.
ExampleData.Fading

Example data for feldspar fading measurements
BaseDataSet.FractionalGammaDose

Base data set of fractional gamma-dose values
ExampleData.LxTxOSLData

Example Lx and Tx curve data from an artificial OSL measurement
ExampleData.CobbleData

Example data for calc_CobbleDoseRate()
ExampleData.BINfileData

Example data from a SAR OSL and SAR TL measurement for the package Luminescence
ExampleData.LxTxData

Example Lx/Tx data from CW-OSL SAR measurement
ExampleData.ScaleGammaDose

Example data for scale_GammaDose()
ExampleData.XSYG

Example data for a SAR OSL measurement and a TL spectrum using a lexsyg reader
ExampleData.DeValues

Example De data sets for the package Luminescence
ExampleData.TR_OSL

Example TR-OSL data
ExampleData.RLum.Analysis

Example data as RLum.Analysis objects
ExampleData.portableOSL

Example portable OSL curve data for the package Luminescence
GitHub-API

GitHub API
PSL2Risoe.BINfileData

Convert portable OSL data to an Risoe.BINfileData object
ExampleData.RLum.Data.Image

Example data as RLum.Data.Image objects
Luminescence-package

Comprehensive Luminescence Dating Data Analysis
r-luminescence.org
analyse_Al2O3C_CrossTalk

Al2O3:C Reader Cross Talk Analysis
analyse_Al2O3C_ITC

Al2O3 Irradiation Time Correction Analysis
RLum.Data-class

Class "RLum.Data"
Risoe.BINfileData2RLum.Analysis

Convert Risoe.BINfileData object to an RLum.Analysis object
Second2Gray

Converting equivalent dose values from seconds (s) to Gray (Gy)
RLum.Data.Curve-class

Class "RLum.Data.Curve"
RLum.Data.Image-class

Class "RLum.Data.Image"
ExampleData.SurfaceExposure

Example OSL surface exposure dating data
RLum.Data.Spectrum-class

Class "RLum.Data.Spectrum"
RLum-class

Class "RLum"
ExampleData.CW_OSL_Curve

Example CW-OSL curve data for the package Luminescence
RLum.Analysis-class

Class "RLum.Analysis"
RLum.Results-class

Class "RLum.Results"
ExampleData.FittingLM

Example data for fit_LMCurve() in the package Luminescence
Risoe.BINfileData-class

Class "Risoe.BINfileData"
apply_CosmicRayRemoval

Function to remove cosmic rays from an RLum.Data.Spectrum S4 class object
analyse_Al2O3C_Measurement

Al2O3:C Passive Dosimeter Measurement Analysis
analyse_IRSAR.RF

Analyse IRSAR RF measurements
analyse_pIRIRSequence

Analyse post-IR IRSL measurement sequences
analyse_portableOSL

Analyse portable CW-OSL measurements
analyse_baSAR

Bayesian models (baSAR) applied on luminescence data
analyse_SAR.TL

Analyse SAR TL measurements
analyse_FadingMeasurement

Analyse fading measurements and returns the fading rate per decade (g-value)
apply_EfficiencyCorrection

Function to apply spectral efficiency correction to RLum.Data.Spectrum S4 class objects
calc_CobbleDoseRate

Calculate dose rate of slices in a spherical cobble
calc_CentralDose

Apply the central age model (CAM) after Galbraith et al. (1999) to a given De distribution
analyse_SAR.CWOSL

Analyse SAR CW-OSL measurements
as

as() - RLum-object coercion
bin_RLum.Data

Channel binning - method dispatcher
calc_FadingCorr

Apply a fading correction according to Huntley & Lamothe (2001) for a given g-value and a given tc
calc_FastRatio

Calculate the Fast Ratio for CW-OSL curves
calc_AverageDose

Calculate the Average Dose and the dose rate dispersion
calc_AliquotSize

Estimate the amount of grains on an aliquot
calc_CommonDose

Apply the (un-)logged common age model after Galbraith et al. (1999) to a given De distribution
calc_Lamothe2003

Apply fading correction after Lamothe et al., 2003
calc_CosmicDoseRate

Calculate the cosmic dose rate
calc_MaxDose

Apply the maximum age model to a given De distribution
calc_HomogeneityTest

Apply a simple homogeneity test after Galbraith (2003)
calc_Huntley2006

Apply the Huntley (2006) model
calc_MinDose

Apply the (un-)logged minimum age model (MAM) after Galbraith et al. (1999) to a given De distribution
calc_OSLLxTxDecomposed

Calculate Lx/Tx ratio for decomposed CW-OSL signal components
calc_IEU

Apply the internal-external-uncertainty (IEU) model after Thomsen et al. (2007) to a given De distribution
calc_gSGC

Calculate De value based on the gSGC by Li et al., 2015
calc_gSGC_feldspar

Calculate Global Standardised Growth Curve (gSGC) for Feldspar MET-pIRIR
calc_TLLxTxRatio

Calculate the Lx/Tx ratio for a given set of TL curves -beta version-
calc_Statistics

Function to calculate statistic measures
convert_Activity2Concentration

Convert Nuclide Activities to Concentrations and Vice Versa
convert_BIN2CSV

Export Risoe BIN-file(s) to CSV-files
convert_Concentration2DoseRate

Dose-rate conversion function
combine_De_Dr

Combine Dose Rate and Equivalent Dose Distribution
calc_OSLLxTxRatio

Calculate Lx/Tx ratio for CW-OSL curves
calc_SourceDoseRate

Calculation of the source dose rate via the date of measurement
calc_FiniteMixture

Apply the finite mixture model (FMM) after Galbraith (2005) to a given De distribution
calc_WodaFuchs2008

Obtain the equivalent dose using the approach by Woda and Fuchs 2008
calc_ThermalLifetime

Calculates the Thermal Lifetime using the Arrhenius equation
calc_FuchsLang2001

Apply the model after Fuchs & Lang (2001) to a given De distribution.
convert_XSYG2CSV

Export XSYG-file(s) to CSV-files
convert_Wavelength2Energy

Emission Spectra Conversion from Wavelength to Energy Scales
convert_RLum2Risoe.BINfileData

Converts RLum.Analysis-objects and RLum.Data.Curve-objects to RLum2Risoe.BINfileData-objects
convert_SG2MG

Converts Single-Grain Data to Multiple-Grain Data
fit_OSLLifeTimes

Fitting and Deconvolution of OSL Lifetime Components
fit_SurfaceExposure

Nonlinear Least Squares Fit for OSL surface exposure data
fit_EmissionSpectra

Luminescence Emission Spectra Deconvolution
fit_LMCurve

Nonlinear Least Squares Fit for LM-OSL curves
get_RLum

General accessors function for RLum S4 class objects
get_Quote

Function to return essential quotes
merge_RLum

General merge function for RLum S4 class objects
merge_RLum.Results

Merge function for RLum.Results S4-class objects
install_DevelopmentVersion

Attempts to install the development version of the 'Luminescence' package
length_RLum

General accessor function for RLum S4 class objects
convert_Daybreak2CSV

Export measurement data produced by a Daybreak luminescence reader to CSV-files
calc_Kars2008

Apply the Kars et al. (2008) model (deprecated)
extract_ROI

Extract Pixel Values through Circular Region-of-Interests (ROI) from an Image
convert_PSL2CSV

Export PSL-file(s) to CSV-files
get_rightAnswer

Function to get the right answer
get_Risoe.BINfileData

General accessor function for RLum S4 class objects
merge_RLum.Analysis

Merge function for RLum.Analysis S4 class objects
fit_CWCurve

Nonlinear Least Squares Fit for CW-OSL curves -beta version-
merge_RLum.Data.Curve

Merge function for RLum.Data.Curve S4 class objects
get_Layout

Collection of layout definitions
extract_IrradiationTimes

Extract Irradiation Times from an XSYG-file
fit_ThermalQuenching

Fitting Thermal Quenching Data
extdata

Collection of External Data
methods_RLum

methods_RLum
plot_Histogram

Plot a histogram with separate error plot
plot_GrowthCurve

Fit and plot a growth curve for luminescence data (Lx/Tx against dose)
plot_DRCSummary

Create a Dose-Response Curve Summary Plot
merge_Risoe.BINfileData

Merge Risoe.BINfileData objects or Risoe BIN-files
plot_DetPlot

Create De(t) plot
plot_DRTResults

Visualise dose recovery test results
plot_NRt

Visualise natural/regenerated signal ratios
plot_KDE

Plot kernel density estimate with statistics
plot_OSLAgeSummary

Plot Posterior OSL-Age Summary
plot_RLum.Data.Spectrum

Plot function for an RLum.Data.Spectrum S4 class object
plot_RLum

General plot function for RLum S4 class objects
plot_FilterCombinations

Plot filter combinations along with the (optional) net transmission window
plot_RLum.Analysis

Plot function for an RLum.Analysis S4 class object
plot_RLum.Data.Curve

Plot function for an RLum.Data.Curve S4 class object
plot_AbanicoPlot

Function to create an Abanico Plot.
plot_RLum.Data.Image

Plot function for an RLum.Data.Image S4 class object
names_RLum

S4-names function for RLum S4 class objects
read_TIFF2R

Import TIFF Image Data into R
plot_RLum.Results

Plot function for an RLum.Results S4 class object
read_Daybreak2R

Import measurement data produced by a Daybreak TL/OSL reader into R
plot_Risoe.BINfileData

Plot single luminescence curves from a BIN file object
plot_ViolinPlot

Create a violin plot
plot_RadialPlot

Function to create a Radial Plot
read_SPE2R

Import Princeton Instruments (TM) SPE-file into R
structure_RLum

General structure function for RLum S4 class objects
read_RF2R

Import RF-files to R
smooth_RLum

Smoothing of data
template_DRAC

Create a DRAC input data template (v1.2)
report_RLum

Create a HTML-report for (RLum) objects
replicate_RLum

General replication function for RLum S4 class objects
set_RLum

General set function for RLum S4 class objects
read_PSL2R

Import PSL files to R
set_Risoe.BINfileData

General accessor function for RLum S4 class objects
read_XSYG2R

Import XSYG files to R
tune_Data

Tune data for experimental purpose
sTeve

sTeve - sophisticated tool for efficient data validation and evaluation
read_BIN2R

Import Risø BIN/BINX-files into R
scale_GammaDose

Calculate the gamma dose deposited within a sample taking layer-to-layer variations in radioactivity into account (according to Aitken, 1985)
write_RLum2CSV

Export RLum-objects to CSV
use_DRAC

Use DRAC to calculate dose rate data
plot_ROI

Create Regions of Interest (ROI) Graphic
verify_SingleGrainData

Verify single grain data sets and check for invalid grains, i.e. zero-light level grains
write_R2TIFF

Export RLum.Data.Image and RLum.Data.Spectrum objects to TIFF Images
write_R2BIN

Export Risoe.BINfileData into Risø BIN/BINX-file