Package: Luminescence 0.9.26.9000-107

Sebastian Kreutzer

Luminescence: 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.

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 [aut], Rachel K. Smedley [ctb], Claire Christophe [ctb], Antoine Zink [ctb], Julie Durcan [ctb], Georgina E. King [ctb, dtc], Anne Philippe [aut], Guillaume Guerin [ctb], Svenja Riedesel [aut], Martin Autzen [aut], Pierre Guibert [ctb], Dirk Mittelstrass [aut], Harrison J. Gray [aut], Jean-Michel Galharret [aut], Marco Colombo [aut], Markus Fuchs [ths]

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Luminescence.pdf |Luminescence.html✨
Luminescence/json (API)
NEWS

# Install 'Luminescence' in R:
install.packages('Luminescence', repos = c('https://r-lum.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/r-lum/luminescence/issues

Pkgdown site:https://r-lum.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

bayesian-statisticsdata-sciencegeochronologyluminescenceluminescence-datingopen-scienceoslplottingradiofluorescencetlxsygcpp

10.07 score 15 stars 7 packages 176 scripts 1.5k downloads 2 mentions 152 exports 29 dependencies

Last updated 1 days agofrom:48038cf78c. Checks:5 OK, 1 FAILURE, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 31 2025
R-4.5-win-x86_64OKJan 31 2025
R-4.5-mac-x86_64NOTEJan 31 2025
R-4.5-mac-aarch64NOTEJan 31 2025
R-4.5-linux-x86_64OKJan 31 2025
R-4.4-win-x86_64OKJan 31 2025
R-4.4-mac-x86_64NOTEJan 31 2025
R-4.4-mac-aarch64NOTEJan 31 2025
R-4.3-win-x86_64OKJan 31 2025
R-4.3-mac-x86_64NOTEJan 31 2025
R-4.3-mac-aarch64OUTDATEDJan 23 2025

Exports:add_metadata<-analyse_Al2O3C_CrossTalkanalyse_Al2O3C_ITCanalyse_Al2O3C_Measurementanalyse_baSARanalyse_FadingMeasurementanalyse_IRSAR.RFanalyse_pIRIRSequenceanalyse_portableOSLanalyse_SAR.CWOSLAnalyse_SAR.OSLdataanalyse_SAR.TLanalyse_ThermochronometryDataapply_CosmicRayRemovalapply_EfficiencyCorrectionbinbin_RLum.Datacalc_AliquotSizecalc_AverageDosecalc_CentralDosecalc_CobbleDoseRatecalc_CommonDosecalc_CosmicDoseRatecalc_EED_Modelcalc_FadingCorrcalc_FastRatiocalc_FiniteMixturecalc_FuchsLang2001calc_gSGCcalc_gSGC_feldsparcalc_HomogeneityTestcalc_Huntley2006calc_IEUcalc_Lamothe2003calc_MaxDosecalc_MinDosecalc_OSLLxTxDecomposedcalc_OSLLxTxRatiocalc_SourceDoseRatecalc_Statisticscalc_ThermalLifetimecalc_TLLxTxRatiocalc_WodaFuchs2008combine_De_Drconvert_Activity2Concentrationconvert_BIN2CSVconvert_Concentration2DoseRateconvert_CW2pHMiconvert_CW2pLMconvert_CW2pLMiconvert_CW2pPMiconvert_Daybreak2CSVconvert_PSL2CSVconvert_PSL2Risoe.BINfileDataconvert_RLum2Risoe.BINfileDataconvert_Second2Grayconvert_SG2MGconvert_Wavelength2Energyconvert_XSYG2CSVCW2pHMiCW2pLMCW2pLMiCW2pPMiextract_IrradiationTimesextract_ROIfit_CWCurvefit_DoseResponseCurvefit_EmissionSpectrafit_IsothermalHoldingfit_LMCurvefit_OSLLifeTimesfit_SurfaceExposurefit_ThermalQuenchingget_Layoutget_Quoteget_rightAnswerget_Risoe.BINfileDataget_RLumgithub_branchesgithub_commitsgithub_issuesimport_Datainstall_DevelopmentVersionis.RLumis.RLum.Analysisis.RLum.Datais.RLum.Data.Curveis.RLum.Data.Imageis.RLum.Data.Spectrumis.RLum.Resultslength_RLummelt_RLummerge_Risoe.BINfileDatamerge_RLummerge_RLum.Analysismerge_RLum.Data.Curvemerge_RLum.Data.Spectrummerge_RLum.Resultsnames_RLumplot_AbanicoPlotplot_DetPlotplot_DoseResponseCurveplot_DRCSummaryplot_DRTResultsplot_FilterCombinationsplot_GrowthCurveplot_Histogramplot_KDEplot_NRtplot_OSLAgeSummaryplot_RadialPlotplot_Risoe.BINfileDataplot_RLumplot_RLum.Analysisplot_RLum.Data.Curveplot_RLum.Data.Imageplot_RLum.Data.Spectrumplot_RLum.Resultsplot_ROIplot_ViolinPlotPSL2Risoe.BINfileDataread_BIN2Rread_Daybreak2Rread_HeliosOSL2Rread_PSL2Rread_RF2Rread_SPE2Rread_TIFF2Rread_XSYG2Rrename_metadata<-replace_metadata<-replicate_RLumreport_RLumRisoe.BINfileData2RLum.Analysisscale_GammaDoseSecond2Grayset_Risoe.BINfileDataset_RLumshowsmooth_RLumsTevestructure_RLumsubset_SingleGrainDatatemplate_DRACtrim_RLum.Datatune_Datause_DRACverify_SingleGrainDataviewwrite_R2BINwrite_R2TIFFwrite_RLum2CSV

Dependencies:askpassbbmlebdsmatrixcurldata.tabledeldirDEoptimhttrinterpjsonlitelamWlatticeMASSMatrixmatrixStatsmclustmimeminpack.lmmvtnormnumDerivopensslR6RcppRcppArmadilloRcppEigenRcppParallelshapesysXML

S4-class Object Structure in 'Luminescence'

Rendered fromS4classObjects.pdf.asisusingR.rsp::asison Jan 31 2025.

Last update: 2017-09-02
Started: 2017-09-02

Readme and manuals

Help Manual

Help pageTopics
Comprehensive Luminescence Dating Data AnalysisLuminescence-package Luminescence
Safe manipulation of object metadataadd_metadata<- rename_metadata<- replace_metadata<-
Al2O3:C Reader Cross Talk Analysisanalyse_Al2O3C_CrossTalk
Al2O3 Irradiation Time Correction Analysisanalyse_Al2O3C_ITC
Al2O3:C Passive Dosimeter Measurement Analysisanalyse_Al2O3C_Measurement
Bayesian models (baSAR) applied on luminescence dataanalyse_baSAR
Analyse fading measurements and returns the fading rate per decade (g-value)analyse_FadingMeasurement
Analyse IRSAR RF measurementsanalyse_IRSAR.RF
Analyse post-IR IRSL measurement sequencesanalyse_pIRIRSequence
Analyse portable CW-OSL measurementsanalyse_portableOSL
Analyse SAR CW-OSL measurementsanalyse_SAR.CWOSL
Analyse SAR CW-OSL measurements (deprecated)Analyse_SAR.OSLdata
Analyse SAR TL measurementsanalyse_SAR.TL
Analyse Thermochronometry Dataanalyse_ThermochronometryData
Function to remove cosmic rays from an RLum.Data.Spectrum S4 class objectapply_CosmicRayRemoval
Function to apply spectral efficiency correction to RLum.Data.Spectrum S4 class objectsapply_EfficiencyCorrection
as() - RLum-object coercionas
Base data set of dose-rate conversion factorsBaseDataSet.ConversionFactors
Base data set of fractional gamma-dose valuesBaseDataSet.FractionalGammaDose
Base dataset for grain size attenuation data by Guérin et al. (2012)BaseDataSet.GrainSizeAttenuation
Channel binning for RLum.Data S4 class objects.bin_RLum.Data
Estimate the amount of grains on an aliquotcalc_AliquotSize
Calculate the Average Dose and the dose rate dispersioncalc_AverageDose
Apply the central age model (CAM) after Galbraith et al. (1999) to a given De distributioncalc_CentralDose
Calculate dose rate of slices in a spherical cobblecalc_CobbleDoseRate
Apply the (un-)logged common age model after Galbraith et al. (1999) to a given De distributioncalc_CommonDose
Calculate the cosmic dose ratecalc_CosmicDoseRate
Modelling Exponential Exposure Distributioncalc_EED_Model
Fading Correction after Huntley & Lamothe (2001)calc_FadingCorr
Calculate the Fast Ratio for CW-OSL curvescalc_FastRatio
Apply the finite mixture model (FMM) after Galbraith (2005) to a given De distributioncalc_FiniteMixture
Apply the model after Fuchs & Lang (2001) to a given De distributioncalc_FuchsLang2001
Calculate De value based on the gSGC by Li et al., 2015calc_gSGC
Calculate Global Standardised Growth Curve (gSGC) for Feldspar MET-pIRIRcalc_gSGC_feldspar
Apply a simple homogeneity test after Galbraith (2003)calc_HomogeneityTest
Apply the Huntley (2006) modelcalc_Huntley2006
Apply the internal-external-uncertainty (IEU) model after Thomsen et al. (2007) to a given De distributioncalc_IEU
Apply fading correction after Lamothe et al., 2003calc_Lamothe2003
Apply the maximum age model to a given De distributioncalc_MaxDose
Apply the (un-)logged minimum age model (MAM) after Galbraith et al. (1999) to a given De distributioncalc_MinDose
Calculate Lx/Tx ratio for decomposed CW-OSL signal componentscalc_OSLLxTxDecomposed
Calculate 'Lx/Tx' ratio for CW-OSL curvescalc_OSLLxTxRatio
Calculation of the source dose rate via the date of measurementcalc_SourceDoseRate
Function to calculate statistic measurescalc_Statistics
Calculates the Thermal Lifetime using the Arrhenius equationcalc_ThermalLifetime
Calculate the Lx/Tx ratio for a given set of TL curves -beta version-calc_TLLxTxRatio
Obtain the equivalent dose using the approach by Woda and Fuchs 2008calc_WodaFuchs2008
Combine Dose Rate and Equivalent Dose Distributioncombine_De_Dr
Convert Nuclide Activities to Abundance and Vice Versaconvert_Activity2Concentration
Export Risoe BIN-file(s) to CSV-filesconvert_BIN2CSV
Dose-rate conversion functionconvert_Concentration2DoseRate
Transform a CW-OSL curve into a pHM-OSL curve via interpolation under hyperbolic modulation conditionsconvert_CW2pHMi CW2pHMi
Transform a CW-OSL curve into a pLM-OSL curveconvert_CW2pLM CW2pLM
Transform a CW-OSL curve into a pLM-OSL curve via interpolation under linear modulation conditionsconvert_CW2pLMi CW2pLMi
Transform a CW-OSL curve into a pPM-OSL curve via interpolation under parabolic modulation conditionsconvert_CW2pPMi CW2pPMi
Export measurement data produced by a Daybreak luminescence reader to CSV-filesconvert_Daybreak2CSV
Export PSL-file(s) to CSV-filesconvert_PSL2CSV
Convert portable OSL data to a Risoe.BINfileData objectconvert_PSL2Risoe.BINfileData
Converts RLum.Analysis-objects and RLum.Data.Curve-objects to RLum2Risoe.BINfileData-objectsconvert_RLum2Risoe.BINfileData
Converting equivalent dose values from seconds (s) to Gray (Gy)convert_Second2Gray
Converts Single-Grain Data to Multiple-Grain Dataconvert_SG2MG
Emission Spectra Conversion from Wavelength to Energy Scales (Jacobian Conversion)convert_Wavelength2Energy
Export XSYG-file(s) to CSV-filesconvert_XSYG2CSV
Example data for calc_CobbleDoseRate()ExampleData.CobbleData
Example De data sets for the package LuminescenceExampleData.DeValues
Example data for feldspar fading measurementsExampleData.Fading
Example portable OSL curve data for the package LuminescenceExampleData.portableOSL
Example data as RLum.Data.Image objectsExampleData.RLum.Data.Image
Example data for scale_GammaDose()ExampleData.ScaleGammaDose
Example OSL surface exposure dating dataExampleData.SurfaceExposure
Example TR-OSL dataExampleData.TR_OSL
Collection of External Dataextdata
Extract Irradiation Times from an XSYG-fileextract_IrradiationTimes
Extract Pixel Values through Circular Region-of-Interests (ROI) from an Imageextract_ROI
Nonlinear Least Squares Fit for CW-OSL curves -beta version-fit_CWCurve
Fit a dose-response curve for luminescence data (Lx/Tx against dose)fit_DoseResponseCurve
Luminescence Emission Spectra Deconvolutionfit_EmissionSpectra
Fit Isothermal Holding Datafit_IsothermalHolding
Non-linear Least Squares Fit for LM-OSL curvesfit_LMCurve
Fitting and Deconvolution of OSL Lifetime Componentsfit_OSLLifeTimes
Nonlinear Least Squares Fit for OSL surface exposure datafit_SurfaceExposure
Fitting Thermal Quenching Datafit_ThermalQuenching
Collection of layout definitionsget_Layout
Function to return essential quotesget_Quote
Function to get the right answerget_rightAnswer
General accessor function for RLum S4 class objectsget_RLum get_RLum,list-method get_RLum,NULL-method
GitHub APIGitHub-API github_branches github_commits github_issues
Import Luminescence Data into Rimport_Data
Attempts to install the development version of the 'Luminescence' packageinstall_DevelopmentVersion
Length retrieval function for RLum S4 class objectslength_RLum
Melt RLum-class objects into a flat data.framemelt_RLum melt_RLum,list-method
Merge Risoe.BINfileData objects or Risoe BIN-filesmerge_Risoe.BINfileData
General merge function for RLum S4 class objectsmerge_RLum
Name retrieval function for RLum S4 class objectsnames_RLum names_RLum,list-method
Function to create an Abanico Plot.plot_AbanicoPlot
Create De(t) plotplot_DetPlot
Plot a dose-response curve for luminescence data (Lx/Tx against dose)plot_DoseResponseCurve
Create a Dose-Response Curve Summary Plotplot_DRCSummary
Visualise dose recovery test resultsplot_DRTResults
Plot filter combinations along with the (optional) net transmission windowplot_FilterCombinations
Fit and plot a dose-response curve for luminescence data (Lx/Tx against dose)plot_GrowthCurve
Plot a histogram with separate error plotplot_Histogram
Plot kernel density estimate with statisticsplot_KDE
Visualise natural/regenerated signal ratiosplot_NRt
Plot Posterior OSL-Age Summaryplot_OSLAgeSummary
Function to create a Radial Plotplot_RadialPlot
Plot Single Luminescence Curves from a Risoe.BINfileData-class objectplot_Risoe.BINfileData
General plot function for RLum S4 class objectsplot_RLum
Plot function for an RLum.Analysis S4 class objectplot_RLum.Analysis
Plot function for an RLum.Data.Curve S4 class objectplot_RLum.Data.Curve
Plot function for an 'RLum.Data.Image' S4 class objectplot_RLum.Data.Image
Plot function for an RLum.Data.Spectrum S4 class objectplot_RLum.Data.Spectrum
Plot function for an RLum.Results S4 class objectplot_RLum.Results
Create Regions of Interest (ROI) Graphicplot_ROI
Create a violin plotplot_ViolinPlot
Convert portable OSL data to a Risoe.BINfileData objectPSL2Risoe.BINfileData
Import Risø BIN/BINX-files into Rread_BIN2R
Import measurement data produced by a Daybreak TL/OSL reader into Rread_Daybreak2R
Import Luminescence Data from Helios Luminescence Readerread_HeliosOSL2R
Import PSL files to Rread_PSL2R
Import RF-files to Rread_RF2R
Import Princeton Instruments (TM) SPE-file into Rread_SPE2R
Import TIFF Image Data into Rread_TIFF2R
Import XSYG files to Rread_XSYG2R
General replication function for RLum S4 class objectsreplicate_RLum
Create a HTML-report for (RLum) objectsreport_RLum
Convert Risoe.BINfileData object to an RLum.Analysis objectRisoe.BINfileData2RLum.Analysis
Class '"RLum"'replicate_RLum,RLum-method RLum-class
Calculate the gamma dose deposited within a sample taking layer-to-layer variations in radioactivity into account (according to Aitken, 1985)scale_GammaDose
Converting equivalent dose values from seconds (s) to Gray (Gy)Second2Gray
General setter function for Risoe.BINfileData objectsset_Risoe.BINfileData
General setter function for RLum S4 class objectsset_RLum
Smoothing of data for RLum S4-class objectssmooth_RLum smooth_RLum,list-method
sTeve - sophisticated tool for efficient data validation and evaluationsTeve
General structure function for RLum S4 class objectsstructure_RLum structure_RLum,list-method
Simple Subsetting of Single Grain Data from Risø BIN/BINX filessubset_SingleGrainData
Create a DRAC input data template (v1.2)template_DRAC
Trim Channels of RLum.Data-class Objectstrim_RLum.Data
Tune data for experimental purposetune_Data
Use DRAC to calculate dose rate datause_DRAC
Verify single grain data sets and check for invalid grains, i.e. zero-light level grainsverify_SingleGrainData
Convenience data visualisation functionview
Export Risoe.BINfileData into Risø BIN/BINX-filewrite_R2BIN
Export RLum.Data.Image and RLum.Data.Spectrum objects to TIFF Imageswrite_R2TIFF
Export RLum-objects to CSVwrite_RLum2CSV