Luminescence v0.8.6

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by Sebastian Kreutzer View Source

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.

Functions in Luminescence

Name	Description
RLum-class	Class "RLum"
BaseDataSet.CosmicDoseRate	Base data set for cosmic dose rate calculation
ExampleData.SurfaceExposure	Example OSL surface exposure dating data
RLum.Data-class	Class "RLum.Data"
Risoe.BINfileData2RLum.Analysis	Convert Risoe.BINfileData object to an RLum.Analysis object
ExampleData.XSYG	Example data for a SAR OSL measurement and a TL spectrum using a lexsyg reader
RLum.Data.Curve-class	Class "RLum.Data.Curve"
ExampleData.LxTxOSLData	Example Lx and Tx curve data from an artificial OSL measurement
ExampleData.LxTxData	Example Lx/Tx data from CW-OSL SAR measurement
analyse_IRSAR.RF	Analyse IRSAR RF measurements
calc_IEU	Apply the internal-external-uncertainty (IEU) model after Thomsen et al. (2007) to a given De distribution
Second2Gray	Converting equivalent dose values from seconds (s) to gray (Gy)
ExampleData.RLum.Analysis	Example data as RLum.Analysis objects
ExampleData.RLum.Data.Image	Example data as RLum.Data.Image objects
RLum.Analysis-class	Class "RLum.Analysis"
analyse_pIRIRSequence	Analyse post-IR IRSL measurement sequences
ExampleData.portableOSL	Example portable OSL curve data for the package Luminescence
ExampleData.Fading	Example data for feldspar fading measurements
analyse_SAR.CWOSL	Analyse SAR CW-OSL measurements
analyse_SAR.TL	Analyse SAR TL measurements
analyse_portableOSL	Analyse portable CW-OSL measurements
calc_CommonDose	Apply the (un-)logged common age model after Galbraith et al. (1999) to a given De distribution
ExampleData.FittingLM	Example data for fit_LMCurve() in the package Luminescence
calc_CosmicDoseRate	Calculate the cosmic dose rate
RLum.Data.Image-class	Class "RLum.Data.Image"
calc_MinDose	Apply the (un-)logged minimum age model (MAM) after Galbraith et al. (1999) to a given De distribution
calc_Kars2008	Apply the Kars et al. (2008) model (deprecated)
RLum.Results-class	Class "RLum.Results"
calc_TLLxTxRatio	Calculate the Lx/Tx ratio for a given set of TL curves [beta version]
calc_ThermalLifetime	Calculates the Thermal Lifetime using the Arrhenius equation
RLum.Data.Spectrum-class	Class "RLum.Data.Spectrum"
calc_OSLLxTxRatio	Calculate Lx/Tx ratio for CW-OSL curves
convert_RLum2Risoe.BINfileData	Converts RLum.Analysis-objects and RLum.Data.Curve-objects to RLum2Risoe.BINfileData-objects
convert_Activity2Concentration	Convert Nuclide Activities to Concentrations and Vice Versa
analyse_Al2O3C_CrossTalk	Al2O3:C Reader Cross Talk Analysis
apply_EfficiencyCorrection	Function to apply spectral efficiency correction to RLum.Data.Spectrum S4 class objects
Risoe.BINfileData-class	Class "Risoe.BINfileData"
analyse_baSAR	Bayesian models (baSAR) applied on luminescence data
as	as() - RLum-object coercion
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
app_RLum	Run Luminescence shiny apps (wrapper)
analyse_Al2O3C_ITC	Al2O3 Irradiation Time Correction Analysis
convert_BIN2CSV	Export Risoe BIN-file(s) to CSV-files
GitHub-API	GitHub API
Luminescence-package	Comprehensive Luminescence Dating Data Analysis
PSL2Risoe.BINfileData	Convert portable OSL data to an Risoe.BINfileData object
calc_SourceDoseRate	Calculation of the source dose rate via the date of measurement
calc_AverageDose	Calculate the Average Dose and the dose rate dispersion
calc_CentralDose	Apply the central age model (CAM) after Galbraith et al. (1999) to a given De distribution
calc_Statistics	Function to calculate statistic measures
calc_Lamothe2003	Apply fading correction after Lamothe et al., 2003
bin_RLum.Data	Channel binning - method dispatchter
analyse_Al2O3C_Measurement	Al2O3:C Passive Dosimeter Measurement Analysis
analyse_FadingMeasurement	Analyse fading measurements and returns the fading rate per decade (g-value)
calc_MaxDose	Apply the maximum age model to a given De distribution
calc_AliquotSize	Estimate the amount of grains on an aliquot
calc_HomogeneityTest	Apply a simple homogeneity test after Galbraith (2003)
calc_Huntley2006	Apply the Huntley (2006) model
calc_WodaFuchs2008	Obtain the equivalent dose using the approach by Woda and Fuchs 2008
fit_SurfaceExposure	Nonlinear Least Squares Fit for OSL surface exposure data
convert_XSYG2CSV	Export XSYG-file(s) to CSV-files
get_Layout	Collection of layout definitions
fit_CWCurve	Nonlinear Least Squares Fit for CW-OSL curves [beta version]
calc_gSGC	Calculate De value based on the gSGC by Li et al., 2015
install_DevelopmentVersion	Attempts to install the development version of the 'Luminescence' package
length_RLum	General accessor function for RLum S4 class objects
extdata	Collection of External Data
plot_KDE	Plot kernel density estimate with statistics
extract_IrradiationTimes	Extract Irradiation Times from an XSYG-file
merge_RLum.Analysis	Merge function for RLum.Analysis S4 class objects
apply_CosmicRayRemoval	Function to remove cosmic rays from an RLum.Data.Spectrum S4 class object
merge_RLum.Data.Curve	Merge function for RLum.Data.Curve S4 class objects
plot_ViolinPlot	Create a violin plot
get_Risoe.BINfileData	General accessor function for RLum S4 class objects
fit_LMCurve	Nonlinear Least Squares Fit for LM-OSL curves
plot_NRt	Visualise natural/regenerated signal ratios
plot_DetPlot	Create De(t) plot
convert_Daybreak2CSV	Export measurement data produced by a Daybreak luminescence reader to CSV-files
convert_PSL2CSV	Export PSL-file(s) to CSV-files
get_Quote	Function to return essential quotes
get_rightAnswer	Function to get the right answer
get_RLum	General accessor function for RLum S4 class objects
read_BIN2R	Import Risoe BIN-file into R
plot_AbanicoPlot	Function to create an Abanico Plot.
calc_FiniteMixture	Apply the finite mixture model (FMM) after Galbraith (2005) to a given De distribution
plot_FilterCombinations	Plot filter combinations along with the (optional) net transmission window
replicate_RLum	General replication function for RLum S4 class objects
plot_DRTResults	Visualise dose recovery test results
calc_FuchsLang2001	Apply the model after Fuchs & Lang (2001) to a given De distribution.
plot_RLum.Data.Image	Plot function for an RLum.Data.Image S4 class object
sTeve	sTeve - sophisticated tool for efficient data validation and evaluation
plot_RLum.Data.Spectrum	Plot function for an RLum.Data.Spectrum S4 class object
set_RLum	General set function for RLum S4 class objects
merge_RLum	General merge function for RLum S4 class objects
merge_RLum.Results	Merge function for RLum.Results S4-class objects
model_LuminescenceSignals	Model Luminescence Signals (wrapper)
report_RLum	Create a HTML report for (RLum) objects
names_RLum	S4-names function for RLum S4 class objects
plot_GrowthCurve	Fit and plot a growth curve for luminescence data (Lx/Tx against dose)
plot_Histogram	Plot a histogram with separate error plot
plot_RadialPlot	Function to create a Radial Plot
plot_Risoe.BINfileData	Plot single luminescence curves from a BIN file object
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
read_Daybreak2R	Import measurement data produced by a Daybreak TL/OSL reader into R
read_SPE2R	Import Princeton Intruments (TM) SPE-file into R
merge_Risoe.BINfileData	Merge Risoe.BINfileData objects or Risoe BIN-files
methods_RLum	methods_RLum
read_XSYG2R	Import XSYG files to R
tune_Data	Tune data for experimental purpose
use_DRAC	Use DRAC to calculate dose rate data
write_R2BIN	Export Risoe.BINfileData into Risoe BIN-file
verify_SingleGrainData	Verify single grain data sets and check for invalid grains, i.e. zero-light level grains
plot_RLum	General plot function for RLum S4 class objects
read_PSL2R	Import PSL files to R
plot_RLum.Results	Plot function for an RLum.Results S4 class object
set_Risoe.BINfileData	General accessor function for RLum S4 class objects
structure_RLum	General structure function for RLum S4 class objects
smooth_RLum	Smoothing of data
template_DRAC	Create a DRAC input data template (v1.2)
write_RLum2CSV	Export RLum-objects to CSV
ExampleData.Al2O3C	Example Al2O3:C Measurement Data
ExampleData.CW_OSL_Curve	Example CW-OSL curve data for the package Luminescence
ExampleData.BINfileData	Example data from a SAR OSL and SAR TL measurement for the package Luminescence
ExampleData.DeValues	Example De data sets for the package Luminescence
Analyse_SAR.OSLdata	Analyse SAR CW-OSL measurements.
CW2pLMi	Transform a CW-OSL curve into a pLM-OSL curve via interpolation under linear modulation conditions
CW2pPMi	Transform a CW-OSL curve into a pPM-OSL curve via interpolation under parabolic modulation conditions
CW2pHMi	Transform a CW-OSL curve into a pHM-OSL curve via interpolation under hyperbolic modulation conditions
CW2pLM	Transform a CW-OSL curve into a pLM-OSL curve
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Vignettes of Luminescence

Name
HowTo_analyse_Al2O3.Rmd
HowTo_analyse_Al2O3.html.asis
HowTo_analyse_pIRIRMeasurements.Rmd
HowTo_analyse_pIRIRMeasurements.html.asis
S4classObjects.pdf.asis
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Last month downloads

Details

Type	Package
Date	2018-10-05
Contact	Package Developers
License	GPL-3
BugReports	https://github.com/R-Lum/Luminescence/issues
LinkingTo	Rcpp (>= 0.12.15), RcppArmadillo (>= 0.8.300.1.0)
VignetteBuilder	R.rsp
URL	https://CRAN.R-project.org/package=Luminescence
Encoding	UTF-8
Collate	'Analyse_SAR.OSLdata.R' 'CW2pHMi.R' 'CW2pLM.R' 'CW2pLMi.R' 'CW2pPMi.R' 'Luminescence-package.R' 'PSL2Risoe.BINfileData.R' 'RcppExports.R' 'replicate_RLum.R' 'RLum-class.R' 'smooth_RLum.R' 'names_RLum.R' 'structure_RLum.R' 'length_RLum.R' 'set_RLum.R' 'get_RLum.R' 'RLum.Analysis-class.R' 'RLum.Data-class.R' 'bin_RLum.Data.R' 'RLum.Data.Curve-class.R' 'RLum.Data.Image-class.R' 'RLum.Data.Spectrum-class.R' 'RLum.Results-class.R' 'Risoe.BINfileData2RLum.Analysis.R' 'Risoe.BINfileData2RLum.Data.Curve.R' 'set_Risoe.BINfileData.R' 'get_Risoe.BINfileData.R' 'RisoeBINfileData-class.R' 'Second2Gray.R' 'addins_RLum.R' 'analyse_Al2O3C_CrossTalk.R' 'analyse_Al2O3C_ITC.R' 'analyse_Al2O3C_Measurement.R' 'analyse_FadingMeasurement.R' 'analyse_IRSAR.RF.R' 'analyse_SAR.CWOSL.R' 'analyse_SAR.TL.R' 'analyse_baSAR.R' 'analyse_pIRIRSequence.R' 'analyse_portableOSL.R' 'app_RLum.R' 'apply_CosmicRayRemoval.R' 'apply_EfficiencyCorrection.R' 'calc_AliquotSize.R' 'calc_AverageDose.R' 'calc_CentralDose.R' 'calc_CommonDose.R' 'calc_CosmicDoseRate.R' 'calc_FadingCorr.R' 'calc_FastRatio.R' 'calc_FiniteMixture.R' 'calc_FuchsLang2001.R' 'calc_HomogeneityTest.R' 'calc_Huntley2006.R' 'calc_IEU.R' 'calc_Kars2008.R' 'calc_Lamothe2003.R' 'calc_MaxDose.R' 'calc_MinDose.R' 'calc_OSLLxTxRatio.R' 'calc_SourceDoseRate.R' 'calc_Statistics.R' 'calc_TLLxTxRatio.R' 'calc_ThermalLifetime.R' 'calc_WodaFuchs2008.R' 'calc_gSGC.R' 'convert_Activity2Concentration.R' 'convert_BIN2CSV.R' 'convert_Daybreak2CSV.R' 'convert_PSL2CSV.R' 'convert_RLum2Risoe.BINfileData.R' 'convert_XSYG2CSV.R' 'extract_IrradiationTimes.R' 'fit_CWCurve.R' 'fit_LMCurve.R' 'fit_SurfaceExposure.R' 'get_Layout.R' 'get_Quote.R' 'get_rightAnswer.R' 'github.R' 'install_DevelopmentVersion.R' 'internal_as.latex.table.R' 'internals_RLum.R' 'merge_RLum.Analysis.R' 'merge_RLum.Data.Curve.R' 'merge_RLum.R' 'merge_RLum.Results.R' 'merge_Risoe.BINfileData.R' 'methods_DRAC.R' 'methods_RLum.R' 'model_LuminescenceSignals.R' 'plot_AbanicoPlot.R' 'plot_DRTResults.R' 'plot_DetPlot.R' 'plot_FilterCombinations.R' 'plot_GrowthCurve.R' 'plot_Histogram.R' 'plot_KDE.R' 'plot_NRt.R' 'plot_RLum.Analysis.R' 'plot_RLum.Data.Curve.R' 'plot_RLum.Data.Image.R' 'plot_RLum.Data.Spectrum.R' 'plot_RLum.R' 'plot_RLum.Results.R' 'plot_RadialPlot.R' 'plot_Risoe.BINfileData.R' 'plot_ViolinPlot.R' 'read_BIN2R.R' 'read_Daybreak2R.R' 'read_PSL2R.R' 'read_SPE2R.R' 'read_XSYG2R.R' 'report_RLum.R' 'template_DRAC.R' 'tune_Data.R' 'use_DRAC.R' 'utils_DRAC.R' 'verify_SingleGrainData.R' 'write_R2BIN.R' 'write_RLum2CSV.R' 'zzz.R'
RoxygenNote	6.1.0
NeedsCompilation	yes
Packaged	2018-10-04 07:37:23 UTC; kreutzer
Repository	CRAN
Date/Publication	2018-10-05 10:02:17 UTC

imports	bbmle (>= 1.0.20) , data.table (>= 1.10.0) , httr (>= 1.3.0) , matrixStats (>= 0.53.0) , methods , minpack.lm (>= 1.2) , parallel , plotrix (>= 3.7) , raster (>= 2.6-7) , readxl (>= 1.0.0) , shape (>= 1.4.3) , XML (>= 3.98-1.9) , zoo (>= 1.8)
suggests	coda (>= 0.19-1) , devtools (>= 1.13.0) , pander (>= 0.6.1) , plotly (>= 4.7.1) , R.rsp (>= 0.42.0) , rjags (>= 4-6) , RLumModel (>= 0.2.3) , RLumShiny (>= 0.2.0) , rmarkdown (>= 1.8) , rstudioapi (>= 0.7) , testthat (>= 2.0.0)
depends	magrittr (>= 1.5) , R (>= 3.3.0) , utils
linkingto	Rcpp (>= 0.12.15) , RcppArmadillo (>= 0.8.300.1.0)
Contributors	Christoph Schmidt, Manfred Fischer, Markus Fuchs, Michael Dietze, Anne Philippe, Christoph Burow, Margret C. Fuchs, Johannes Friedrich, Norbert Mercier, Rachel K. Smedley, Julie Durcan, Claire Christophe, Antoine Zink, Guillaume Guerin, Georgina E. King