# Comprehensive Luminescence Dating Data Analysis

## Documentation for package ‘Luminescence’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C E F G I L M N P R S T U V W

Luminescence-package | Comprehensive Luminescence Dating Data Analysis

## -- A --

add_metadata<- | Safe manipulation of object metadata
analyse_Al2O3C_CrossTalk | Al2O3:C Reader Cross Talk Analysis
analyse_Al2O3C_ITC | Al2O3 Irradiation Time Correction Analysis
analyse_Al2O3C_Measurement | Al2O3:C Passive Dosimeter Measurement Analysis
analyse_baSAR | Bayesian models (baSAR) applied on luminescence data
analyse_FadingMeasurement | Analyse fading measurements and returns the fading rate per decade (g-value)
analyse_IRSAR.RF | Analyse IRSAR RF measurements
analyse_pIRIRSequence | Analyse post-IR IRSL measurement sequences
analyse_portableOSL | Analyse portable CW-OSL measurements
analyse_SAR.CWOSL | Analyse SAR CW-OSL measurements
Analyse_SAR.OSLdata | Analyse SAR CW-OSL measurements (deprecated)
analyse_SAR.TL | Analyse SAR TL measurements
apply_CosmicRayRemoval | Function to remove cosmic rays from an RLum.Data.Spectrum S4 class object
apply_Crosstalk | Apply crosstalk
apply_EfficiencyCorrection | Function to apply spectral efficiency correction to RLum.Data.Spectrum S4 class objects
as | as() - RLum-object coercion

## -- B --

BaseDataSet.ConversionFactors | Base data set of dose-rate conversion factors
BaseDataSet.FractionalGammaDose | Base data set of fractional gamma-dose values
BaseDataSet.GrainSizeAttenuation | Base dataset for grain size attenuation data by Guérin et al. (2012)
bin_RLum.Data | Channel binning for RLum.Data S4 class objects.

## -- C --

calc_AliquotSize | Estimate the amount of grains on an aliquot
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_CobbleDoseRate | Calculate dose rate of slices in a spherical cobble
calc_CommonDose | Apply the (un-)logged common age model after Galbraith et al. (1999) to a given De distribution
calc_CosmicDoseRate | Calculate the cosmic dose rate
calc_EED_Model | Modelling Exponential Exposure Distribution
calc_FadingCorr | Fading Correction after Huntley & Lamothe (2001)
calc_FastRatio | Calculate the Fast Ratio for CW-OSL curves
calc_FiniteMixture | Apply the finite mixture model (FMM) after Galbraith (2005) to a given De distribution
calc_FuchsLang2001 | Apply the model after Fuchs & Lang (2001) 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_HomogeneityTest | Apply a simple homogeneity test after Galbraith (2003)
calc_Huntley2006 | Apply the Huntley (2006) model
calc_IEU | Apply the internal-external-uncertainty (IEU) model after Thomsen et al. (2007) to a given De distribution
calc_Lamothe2003 | Apply fading correction after Lamothe et al., 2003
calc_MaxDose | Apply the maximum age model to a given De distribution
calc_MinDose | Apply the (un-)logged minimum age model (MAM) after Galbraith et al. (1999) to a given De distribution
calc_MoransI | Calculate Moran's I
calc_OSLLxTxDecomposed | Calculate Lx/Tx ratio for decomposed CW-OSL signal components
calc_OSLLxTxRatio | Calculate 'Lx/Tx' ratio for CW-OSL curves
calc_SourceDoseRate | Calculation of the source dose rate via the date of measurement
calc_Statistics | Function to calculate statistic measures
calc_ThermalLifetime | Calculates the Thermal Lifetime using the Arrhenius equation
calc_TLLxTxRatio | Calculate the Lx/Tx ratio for a given set of TL curves -beta version-
calc_WodaFuchs2008 | Obtain the equivalent dose using the approach by Woda and Fuchs 2008
combine_De_Dr | Combine Dose Rate and Equivalent Dose Distribution
convert_Activity2Concentration | Convert Nuclide Activities to Abundance and Vice Versa
convert_BIN2CSV | Export Risoe BIN-file(s) to CSV-files
convert_Concentration2DoseRate | Dose-rate conversion function
convert_CW2pHMi | Transform a CW-OSL curve into a pHM-OSL curve via interpolation under hyperbolic modulation conditions
convert_CW2pLM | Transform a CW-OSL curve into a pLM-OSL curve
convert_CW2pLMi | Transform a CW-OSL curve into a pLM-OSL curve via interpolation under linear modulation conditions
convert_CW2pPMi | Transform a CW-OSL curve into a pPM-OSL curve via interpolation under parabolic modulation conditions
convert_Daybreak2CSV | Export measurement data produced by a Daybreak luminescence reader to CSV-files
convert_PSL2CSV | Export PSL-file(s) to CSV-files
convert_PSL2Risoe.BINfileData | Convert portable OSL data to a Risoe.BINfileData object
convert_RLum2Risoe.BINfileData | Converts RLum.Analysis and RLum.Data.Curve objects to RLum2Risoe.BINfileData objects
convert_Second2Gray | Converting equivalent dose values from seconds (s) to Gray (Gy)
convert_SG2MG | Converts Single-Grain Data to Multiple-Grain Data
convert_Wavelength2Energy | Emission Spectra Conversion from Wavelength to Energy Scales (Jacobian Conversion)
convert_XSYG2CSV | Export XSYG-file(s) to CSV-files
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
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

## -- E --

ExampleData.CobbleData | Example data for calc_CobbleDoseRate()
ExampleData.DeValues | Example De data sets for the package Luminescence
ExampleData.Fading | Example data for feldspar fading measurements
ExampleData.portableOSL | Example portable OSL curve data for the package Luminescence
ExampleData.RLum.Data.Image | Example data as RLum.Data.Image objects
ExampleData.ScaleGammaDose | Example data for scale_GammaDose()
ExampleData.SurfaceExposure | Example OSL surface exposure dating data
ExampleData.TR_OSL | Example TR-OSL data
extdata | Collection of External Data
extract_IrradiationTimes | Extract Irradiation Times from an XSYG-file
extract_ROI | Extract Pixel Values through Circular Region-of-Interests (ROI) from an Image

## -- F --

fit_CWCurve | Nonlinear Least Squares Fit for CW-OSL curves -beta version-
fit_DoseResponseCurve | Fit a dose-response curve for luminescence data (Lx/Tx against dose)
fit_EmissionSpectra | Luminescence Emission Spectra Deconvolution
fit_LMCurve | Non-linear Least Squares Fit for LM-OSL curves
fit_OSLLifeTimes | Fitting and Deconvolution of OSL Lifetime Components
fit_SurfaceExposure | Nonlinear Least Squares Fit for OSL surface exposure data
fit_ThermalQuenching | Fitting Thermal Quenching Data

## -- G --

get_Layout | Collection of layout definitions
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
get_RLum-method | General accessor function for RLum S4 class objects
GitHub-API | GitHub API
github_branches | GitHub API
github_commits | GitHub API
github_issues | GitHub API

## -- I --

import_Data | Import Luminescence Data into R
install_DevelopmentVersion | Attempts to install the development version of the 'Luminescence' package

## -- L --

length_RLum | Length retrieval function for RLum S4 class objects
Luminescence | Comprehensive Luminescence Dating Data Analysis

## -- M --

melt_RLum | Melt RLum-class objects into a flat data.frame
melt_RLum-method | Melt RLum-class objects into a flat data.frame
merge_Risoe.BINfileData | Merge Risoe.BINfileData objects or Risoe BIN-files
merge_RLum | General merge function for RLum S4 class objects

## -- N --

names_RLum | Name retrieval function for RLum S4 class objects
names_RLum-method | Name retrieval function for RLum S4 class objects

## -- P --

plot_AbanicoPlot | Function to create an Abanico Plot.
plot_DetPlot | Create De(t) plot
plot_DoseResponseCurve | Plot a dose-response curve for luminescence data (Lx/Tx against dose)
plot_DRCSummary | Create a Dose-Response Curve Summary Plot
plot_DRTResults | Visualise dose recovery test results
plot_FilterCombinations | Plot filter combinations along with the (optional) net transmission window
plot_GrowthCurve | Fit and plot a dose-response curve for luminescence data (Lx/Tx against dose)
plot_Histogram | Plot a histogram with separate error plot
plot_KDE | Plot kernel density estimate with statistics
plot_MoranScatterplot | Moran Scatter Plot: Visualizing Spatial Dependency
plot_NRt | Visualise natural/regenerated signal ratios
plot_OSLAgeSummary | Plot Posterior OSL-Age Summary
plot_RadialPlot | Function to create a Radial Plot
plot_Risoe.BINfileData | Plot Single Luminescence Curves from a Risoe.BINfileData-class object
plot_RLum | General plot function for RLum S4 class objects
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_RLum.Data.Image | Plot function for an 'RLum.Data.Image' S4 class object
plot_RLum.Data.Spectrum | Plot function for an RLum.Data.Spectrum S4 class object
plot_RLum.Results | Plot function for an RLum.Results S4 class object
plot_ROI | Create Regions of Interest (ROI) Graphic
plot_SingleGrainDisc | Plot a disc with its values
plot_ViolinPlot | Create a violin plot
PSL2Risoe.BINfileData | Convert portable OSL data to a Risoe.BINfileData object

## -- R --

read_BIN2R | Import Risø BIN/BINX-files into R
read_Daybreak2R | Import measurement data produced by a Daybreak TL/OSL reader into R
read_HeliosOSL2R | Import Luminescence Data from Helios Luminescence Reader
read_PSL2R | Import PSL files to R
read_RF2R | Import RF-files to R
read_SPE2R | Import Princeton Instruments (TM) SPE-file into R
read_TIFF2R | Import TIFF Image Data into R
read_XSYG2R | Import XSYG files to R
rename_metadata<- | Safe manipulation of object metadata
replace_metadata<- | Safe manipulation of object metadata
replicate_RLum | General replication function for RLum S4 class objects
replicate_RLum-method | Class '"RLum"'
report_RLum | Create a HTML-report for (RLum) objects
Risoe.BINfileData2RLum.Analysis | Convert Risoe.BINfileData object to an RLum.Analysis object
RLum-class | Class '"RLum"'

## -- S --

scale_GammaDose | Calculate the gamma dose deposited within a sample taking layer-to-layer variations in radioactivity into account (according to Aitken, 1985)
Second2Gray | Converting equivalent dose values from seconds (s) to Gray (Gy)
set_Risoe.BINfileData | General setter function for Risoe.BINfileData objects
set_RLum | General setter function for RLum S4 class objects
smooth_RLum | Smoothing of data for RLum S4-class objects
smooth_RLum-method | Smoothing of data for RLum S4-class objects
sort_RLum | Sort data for RLum S4-class objects
sTeve | sTeve - sophisticated tool for efficient data validation and evaluation
structure_RLum | General structure function for RLum S4 class objects
structure_RLum-method | General structure function for RLum S4 class objects
subset_SingleGrainData | Simple Subsetting of Single Grain Data from Risø BIN/BINX files

## -- T --

template_DRAC | Create a DRAC input data template (v1.2)
trim_RLum.Data | Trim Channels of RLum.Data-class Objects
tune_Data | Tune data for experimental purpose

## -- U --

use_DRAC | Use DRAC to calculate dose rate data

## -- V --

verify_SingleGrainData | Verify single grain data sets and check for invalid grains, i.e. zero-light level grains
view | Convenience data visualisation function

## -- W --

write_R2BIN | Export Risoe.BINfileData into Risø BIN/BINX-file
write_R2TIFF | Export RLum.Data.Image and RLum.Data.Spectrum objects to TIFF Images
write_RLum2CSV | Export RLum-objects to CSV