Luminescence Manual
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Package ‘Luminescence’ January 22, 2018 Type Package Title Comprehensive Luminescence Dating Data Analysis [upcoming] Version 0.8.0 Date 2018-01-22 Author 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 [ctb], Rachel K. Smedley [ctb], Claire Christophe [ctb], Antoine Zink [ctb], Julie Durcan [ctb], Georgina King [ctb, dtc], Anne Philippe [ctb], Guillaume Guerin [ctb], Markus Fuchs [ths] Maintainer Sebastian KreutzerDescription 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. Contact Package Developers License GPL-3 BugReports https://github.com/R-Lum/Luminescence/issues Depends R (>= 3.4.0), utils, magrittr (>= 1.5) LinkingTo Rcpp (>= 0.12.12), RcppArmadillo (>= 0.7.960.1.2) Imports bbmle (>= 1.0.19), data.table (>= 1.10.0), httr (>= 1.3.1), matrixStats (>= 0.52.2), methods, minpack.lm (>= 1.2-1), plotrix (>= 3.6-6), raster (>= 2.5-8), readxl (>= 1.0.0), shape (>= 1.4.3), parallel, XML (>= 3.98-1.9), zoo (>= 1.8-0) 1 2 Suggests RLumShiny (>= 0.2.0), RLumModel (>= 0.2.1), plotly (>= 4.7.1), rmarkdown (>= 1.6), rstudioapi (>= 0.7), rjags (>= 4-6), coda (>= 0.19-1), pander (>= 0.6.1), testthat (>= 1.0.2), devtools (>= 1.13.3), R.rsp (>= 0.41.0) 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_IEU.R' 'calc_Kars2008.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' R topics documented: 3 '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 6.0.1 NeedsCompilation yes R topics documented: Luminescence-package . . . . . analyse_Al2O3C_CrossTalk . . analyse_Al2O3C_ITC . . . . . analyse_Al2O3C_Measurement analyse_baSAR . . . . . . . . . analyse_FadingMeasurement . . analyse_IRSAR.RF . . . . . . . analyse_pIRIRSequence . . . . analyse_portableOSL . . . . . . analyse_SAR.CWOSL . . . . . Analyse_SAR.OSLdata . . . . . analyse_SAR.TL . . . . . . . . apply_CosmicRayRemoval . . . apply_EfficiencyCorrection . . . app_RLum . . . . . . . . . . . as . . . . . . . . . . . . . . . . BaseDataSet.CosmicDoseRate . bin_RLum.Data . . . . . . . . . calc_AliquotSize . . . . . . . . calc_AverageDose . . . . . . . calc_CentralDose . . . . . . . . calc_CommonDose . . . . . . . calc_CosmicDoseRate . . . . . calc_FadingCorr . . . . . . . . calc_FastRatio . . . . . . . . . . calc_FiniteMixture . . . . . . . calc_FuchsLang2001 . . . . . . calc_gSGC . . . . . . . . . . . calc_HomogeneityTest . . . . . calc_IEU . . . . . . . . . . . . calc_Kars2008 . . . . . . . . . calc_MaxDose . . . . . . . . . calc_MinDose . . . . . . . . . . calc_OSLLxTxRatio . . . . . . calc_SourceDoseRate . . . . . . calc_Statistics . . . . . . . . . . calc_ThermalLifetime . . . . . . calc_TLLxTxRatio . . . . . . . calc_WodaFuchs2008 . . . . . . convert_Activity2Concentration convert_BIN2CSV . . . . . . . convert_Daybreak2CSV . . . . convert_PSL2CSV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 7 9 11 13 20 23 30 33 34 38 41 43 45 46 47 48 50 52 54 57 59 61 65 68 70 73 75 77 78 80 84 87 92 96 98 100 102 104 106 108 109 110 R topics documented: 4 convert_RLum2Risoe.BINfileData convert_XSYG2CSV . . . . . . . CW2pHMi . . . . . . . . . . . . CW2pLM . . . . . . . . . . . . . CW2pLMi . . . . . . . . . . . . . CW2pPMi . . . . . . . . . . . . . ExampleData.Al2O3C . . . . . . ExampleData.BINfileData . . . . ExampleData.CW_OSL_Curve . . ExampleData.DeValues . . . . . . ExampleData.Fading . . . . . . . ExampleData.FittingLM . . . . . ExampleData.LxTxData . . . . . ExampleData.LxTxOSLData . . . ExampleData.portableOSL . . . . ExampleData.RLum.Analysis . . ExampleData.RLum.Data.Image . ExampleData.SurfaceExposure . . ExampleData.XSYG . . . . . . . extdata . . . . . . . . . . . . . . . extract_IrradiationTimes . . . . . fit_CWCurve . . . . . . . . . . . fit_LMCurve . . . . . . . . . . . fit_SurfaceExposure . . . . . . . . get_Layout . . . . . . . . . . . . get_Quote . . . . . . . . . . . . . get_rightAnswer . . . . . . . . . get_Risoe.BINfileData . . . . . . get_RLum . . . . . . . . . . . . . GitHub-API . . . . . . . . . . . . install_DevelopmentVersion . . . length_RLum . . . . . . . . . . . merge_Risoe.BINfileData . . . . . merge_RLum . . . . . . . . . . . model_LuminescenceSignals . . . names_RLum . . . . . . . . . . . plot_AbanicoPlot . . . . . . . . . plot_DetPlot . . . . . . . . . . . . plot_DRTResults . . . . . . . . . plot_FilterCombinations . . . . . plot_GrowthCurve . . . . . . . . plot_Histogram . . . . . . . . . . plot_KDE . . . . . . . . . . . . . plot_NRt . . . . . . . . . . . . . plot_RadialPlot . . . . . . . . . . plot_Risoe.BINfileData . . . . . . plot_RLum . . . . . . . . . . . . plot_RLum.Analysis . . . . . . . plot_RLum.Data.Curve . . . . . . plot_RLum.Data.Image . . . . . . plot_RLum.Data.Spectrum . . . . plot_RLum.Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 112 113 117 119 121 124 125 126 127 128 130 131 131 132 132 133 134 137 139 140 142 145 149 153 154 155 156 157 158 160 161 162 163 165 167 168 175 178 181 184 188 191 194 196 201 203 205 207 208 210 214 Luminescence-package 5 plot_ViolinPlot . . . . . . . . . . . PSL2Risoe.BINfileData . . . . . . . read_BIN2R . . . . . . . . . . . . . read_Daybreak2R . . . . . . . . . . read_PSL2R . . . . . . . . . . . . . read_SPE2R . . . . . . . . . . . . . read_XSYG2R . . . . . . . . . . . replicate_RLum . . . . . . . . . . . report_RLum . . . . . . . . . . . . Risoe.BINfileData2RLum.Analysis RLum-class . . . . . . . . . . . . . Second2Gray . . . . . . . . . . . . set_Risoe.BINfileData . . . . . . . set_RLum . . . . . . . . . . . . . . smooth_RLum . . . . . . . . . . . sTeve . . . . . . . . . . . . . . . . structure_RLum . . . . . . . . . . . template_DRAC . . . . . . . . . . . tune_Data . . . . . . . . . . . . . . use_DRAC . . . . . . . . . . . . . verify_SingleGrainData . . . . . . . write_R2BIN . . . . . . . . . . . . write_RLum2CSV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 217 218 220 222 223 225 228 229 232 234 236 238 239 240 242 243 244 245 247 249 252 254 256 Luminescence-package Comprehensive Luminescence Dating Data Analysis Description 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. Details Package: Type: Version: Date: License: Luminescence Package 0.8.0 2017-XX-XX GPL-3 Author(s) Full list of authors and contributors (alphabetic order) Christoph Burow University of Cologne, Germany* 6 Luminescence-package Claire Christophe Michael Dietze Julie Durcan Manfred Fischer Margret C. Fuchs Johannes Friedrich Guillaume Guérin Georgina King Sebastian Kreutzer Norbert Mercier Anne Philippe Christoph Schmidt Rachel K. Smedley Antoine Zink IRAMAT-CRP2A, Université Bordeaux Montaigne, France GFZ Helmholtz Centre Potsdam, Germany University of Oxford, United Kingdom University of Bayreuth, Germany Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz-Institute Freiberg for Resource Technology, Fre University of Bayreuth, Germany IRAMAT-CRP2A, Université Bordeaux Montaigne, France Institute of Geological Sciences, University of Bern, Switzerland IRAMAT-CRP2A, Université Bordeaux Montaigne, France IRAMAT-CRP2A, Université Bordeaux Montaigne, France Universite de Nantes and ANJA INRIA, Rennes, France University of Bayreuth, Germany Aberystwyth University, United Kingdom C2RMF, Palais du Louvre, Paris, France Supervisor of the initial version in 2012 Markus Fuchs, Justus-Liebig-University Giessen, Germany Support contact We may further encourage the usage of our support forum. For this please visit our project website (link below). Bug reporting • or • https://github.com/R-Lum/Luminescence/issues Project website • http://www.r-luminescence.org Project source code repository • https://github.com/R-Lum/Luminescence Related package projects • https://cran.r-project.org/package=RLumShiny • http://shiny.r-luminescence.org • https://cran.r-project.org/package=RLumModel • http://model.r-luminescence.org Package maintainer Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne, Pessac, France, Acknowledgement Cooperation and personal exchange between the developers is gratefully funded by the DFG (SCHM 3051/3-1) in the framework of the program "Scientific Networks". Project title: "RLum.Network: Ein Wissenschaftsnetzwerk zur Analyse von Lumineszenzdaten mit R" (2014-2018) analyse_Al2O3C_CrossTalk 7 References Dietze, M., Kreutzer, S., Fuchs, M.C., Burow, C., Fischer, M., Schmidt, C., 2013. A practical guide to the R package Luminescence. Ancient TL, 31, 11-18. Dietze, M., Kreutzer, S., Burow, C., Fuchs, M.C., Fischer, M., Schmidt, C., 2016. The abanico plot: visualising chronometric data with individual standard errors. Quaternary Geochronology 31, 1-7. http://dx.doi.org/10.1016/j.quageo.2015.09.003 Fuchs, M.C., Kreutzer, S., Burow, C., Dietze, M., Fischer, M., Schmidt, C., Fuchs, M., 2015. Data processing in luminescence dating analysis: An exemplary workflow using the R package ’Luminescence’. Quaternary International, 362,8-13. http://dx.doi.org/10.1016/j.quaint.2014.06.034 Kreutzer, S., Schmidt, C., Fuchs, M.C., Dietze, M., Fischer, M., Fuchs, M., 2012. Introducing an R package for luminescence dating analysis. Ancient TL, 30, 1-8. Smedley, R.K., 2015. A new R function for the Internal External Uncertainty (IEU) model. Ancient TL 33, 16-21. analyse_Al2O3C_CrossTalk Al2O3:C Reader Cross Talk Analysis Description The function provides the analysis of cross-talk measurements on a FI lexsyg SMART reader using Al2O3:C pellets Usage analyse_Al2O3C_CrossTalk(object, signal_integral = NULL, dose_points = c(0, 4), recordType = c("OSL (UVVIS)"), irradiation_time_correction = NULL, method_control = NULL, plot = TRUE, ...) Arguments object RLum.Analysis (required): measurement input signal_integral numeric (optional): signal integral, used for the signal and the background. If nothing is provided the full range is used dose_points numeric (with default): vector with dose points, if dose points are repeated, only the general pattern needs to be provided. Default values follow the suggestions made by Kreutzer et al., 2017 recordType character (with default): input curve selection, which is passed to function get_RLum. To deactivate the automatic selection set the argument to NULL irradiation_time_correction numeric or RLum.Results (optional): information on the used irradiation time correction obained by another experiements. method_control list (optional): optional parameters to control the calculation. See details for further explanations plot logical (with default): enable/disable plot output ... further arguments that can be passed to the plot output 8 analyse_Al2O3C_CrossTalk Value Function returns results numerically and graphically: ———————————– [ NUMERICAL OUTPUT ] ———————————– RLum.Results-object slot: @data Element $data $data_full $fit $col.seq Type data.frame data.frame lm numeric Description summed apparent dose table full apparent dose table the linear model obtained from fitting the used colour vector slot: @info The original function call ———————— [ PLOT OUTPUT ] ———————— • An overview of the obtained apparent dose values Function version 0.1.2 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). analyse_Al2O3C_CrossTalk(): Al2O3:C Reader Cross Talk Analysis. Function version 0.1.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References TODO See Also analyse_Al2O3C_ITC analyse_Al2O3C_ITC 9 Examples ##load data data(ExampleData.Al2O3C, envir = environment()) ##run analysis analyse_Al2O3C_CrossTalk(data_CrossTalk) analyse_Al2O3C_ITC Al2O3 Irradiation Time Correction Analysis Description The function provides a very particular analysis to correct the irradiation time while irradiating Al2O3:C pellets in a luminescence reader. Usage analyse_Al2O3C_ITC(object, signal_integral = NULL, dose_points = c(2, 4, 8, 12, 16), recordType = c("OSL (UVVIS)"), method_control = NULL, verbose = TRUE, plot = TRUE, ...) Arguments object RLum.Analysis or list (required): results obtained from the measurement. Alternatively a list of ’RLum.Analysis’ objects can be provided to allow an automatic analysis. signal_integral numeric (optional): signal integral, used for the signal and the background. If nothing is provided the full range is used. Argument can be provided as list. dose_points numeric (with default): vector with dose points, if dose points are repeated, only the general pattern needs to be provided. Default values follow the suggestions made by Kreutzer et al., 2017. Argument can be provided as list. recordType character (with default): input curve selection, which is passed to function get_RLum. To deactivate the automatic selection set the argument to NULL method_control list (optional): optional parameters to control the calculation. See details for further explanations verbose logical (with default): enable/disable verbose mode plot logical (with default): enable/disable plot output ... further arguments that can be passed to the plot output Details Background: Due to their high dose sensitivity Al2O3:C pellets are usually irradiated for only a very short duration or under the closed beta-source within a luminescence reader. However, due to its high dose sensitivity, during the movement towards the beta-source, the pellet already receives and non-negligible dose. Based on measurements following a protocol suggested by Kreutzer et al., XXXX, a dose response curve is constructed and the intersection (absolute value) with the time axis is taken as real irradiation time. 10 analyse_Al2O3C_ITC method_control To keep the generic argument list as clear as possible, arguments to allow a deeper control of the method are all preset with meaningful default parameters and can be handled using the argument method_control only, e.g., method_control = list(fit.method = "LIN"). Supported arguments are: ARGUMENT mode fit.method FUNCTION plot_GrowthCurve plot_GrowthCurve DESCRIPTION as in plot_GrowthCurve; sets the mode used for fitting as in plot_GrowthCurve; sets the function applied for fitting Value Function returns results numerically and graphically: ———————————– [ NUMERICAL OUTPUT ] ———————————– RLum.Results-object slot: @data Element $data $table $table_mean $fit Type data.frame data.frame data.frame lm or nls Description correction value and error table used for plotting table used for fitting the fitting as returned by the function plot_GrowthCurve slot: @info The original function call ———————— [ PLOT OUTPUT ] ———————— • A dose response curve with the marked correction values Function version 0.1.1 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). analyse_Al2O3C_ITC(): Al2O3 Irradiation Time Correction Analysis. Function version 0.1.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team analyse_Al2O3C_Measurement 11 References TODO See Also plot_GrowthCurve Examples ##load data data(ExampleData.Al2O3C, envir = environment()) ##run analysis analyse_Al2O3C_ITC(data_ITC) analyse_Al2O3C_Measurement Al2O3:C Passive Dosimeter Measurement Analysis Description The function provides the analysis routines for measurements on a FI lexsyg SMART reader using Al2O3:C pellets according to Kreutzer et al., XXXX Usage analyse_Al2O3C_Measurement(object, signal_integral = NULL, dose_points = c(0, 4), recordType = c("OSL (UVVIS)", "TL (UVVIS)"), irradiation_time_correction = NULL, cross_talk_correction = NULL, travel_dosimeter = NULL, test_parameters = NULL, verbose = TRUE, plot = TRUE, ...) Arguments object RLum.Analysis (required): measurement input signal_integral numeric (optional): signal integral, used for the signal and the background. If nothing is provided the full range is used dose_points recordType numeric (with default): vector with dose points, if dose points are repeated, only the general pattern needs to be provided. Default values follow the suggestions made by Kreutzer et al., XXXX character (with default): input curve selection, which is passed to function get_RLum. To deactivate the automatic selection set the argument to NULL irradiation_time_correction numeric or RLum.Results (optional): information on the used irradiation time correction obained by another experiements. I a numeric is provided it has to be of length two: mean, standard error 12 analyse_Al2O3C_Measurement cross_talk_correction numeric or RLum.Results (optional): information on the used irradiation time correction obained by another experiements. If a numeric vector is provided it has to be of length three: mean, 2.5 % quantile, 97.5 % quantile. travel_dosimeter numeric (optional): specify the position of the travel dosimeter (so far measured a the same time). The dose of travel dosimeter will be subtracted from all other values. test_parameters list (with default): set test parameters. Supported parameters are: TL_peak_shift All input: numeric values, NA and NULL (s. Details) verbose logical (with default): enable/disable verbose mode plot logical (with default): enable/disable plot output, if object is of type list, a numeric vector can be provided to limit the plot output to certain aliquots ... further arguments that can be passed to the plot output Details Working with a travel dosimeter ##ADD INFORMATION ON HOW IT WORKS WITH THE TRAVEL DOSIMETERS Test parameters TL_peak_shift numeric (default: 15): Checks whether the TL peak shift is bigger > 15 K, indicating a problem with the thermal contact of the chip. stimulation_power numeric (default: 0.01): So far available, information on the delievered optical stimulation are compared. Compared are the information from the first curves with all others. If the ratio differs more from unity than the defined by the threshold, a warning is returned. Value Function returns results numerically and graphically: ———————————– [ NUMERICAL OUTPUT ] ———————————– RLum.Results-object slot: @data Element $data $data_table test_parameters data_TDcorrected Type data.frame data.frame data.frame data.frame slot: @info The original function call ———————— Description the estimated equivalent dose full dose and signal table results with test paramaters travel dosimeter corrected results (only if TD was provided) analyse_baSAR 13 [ PLOT OUTPUT ] ———————— • OSL and TL curves, combined on two plots. Function version 0.1.8 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). analyse_Al2O3C_Measurement(): Al2O3:C Passive Dosimeter Measurement Analysis. Function version 0.1.8. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References TODO See Also analyse_Al2O3C_ITC Examples ##load data data(ExampleData.Al2O3C, envir = environment()) ##run analysis analyse_Al2O3C_Measurement(data_CrossTalk) analyse_baSAR Bayesian models (baSAR) applied on luminescence data Description This function allows the application of Bayesian models on luminescence data, measured with the single-aliquot regenerative-dose (SAR, Murray and Wintle, 2000) protocol. In particular, it follows the idea proposed by Combes et al., 2015 of using an hierarchical model for estimating a central equivalent dose from a set of luminescence measurements. This function is (I) the adaption of this approach for the R environment and (II) an extension and a technical refinement of the published code. 14 analyse_baSAR Usage analyse_baSAR(object, XLS_file = NULL, aliquot_range = NULL, source_doserate = NULL, signal.integral, signal.integral.Tx = NULL, background.integral, background.integral.Tx = NULL, sigmab = 0, sig0 = 0.025, distribution = "cauchy", baSAR_model = NULL, n.MCMC = 1e+05, fit.method = "EXP", fit.force_through_origin = TRUE, fit.includingRepeatedRegPoints = TRUE, method_control = list(), digits = 3L, plot = TRUE, plot_reduced = TRUE, plot.single = FALSE, verbose = TRUE, ...) Arguments object Risoe.BINfileData, RLum.Results, character or list (required): input object used for the Bayesian analysis. If a character is provided the function assumes a file connection and tries to import a BIN-file using the provided path. If a list is provided the list can only contain either Risoe.BINfileData objects or characters providing a file connection. Mixing of both types is not allowed. If an RLum.Results is provided the function directly starts with the Bayesian Analysis (see details) XLS_file character (optional): XLS_file with data for the analysis. This file must contain 3 columns: the name of the file, the disc position and the grain position (the last being 0 for multi-grain measurements). Alternatively a data.frame of similar structure can be provided. aliquot_range numeric (optional): allows to limit the range of the aliquots used for the analysis. This argument has only an effect if the argument XLS_file is used or the input is the previous output (i.e. is RLum.Results). In this case the new selection will add the aliquots to the removed aliquots table. source_doserate numeric (required): source dose rate of beta-source used for the measuremnt and its uncertainty in Gy/s, e.g., source_doserate = c(0.12, 0.04). Paramater can be provided as list, for the case that more than one BIN-file is provided, e.g., source_doserate = list(c(0.04, 0.004), c(0.05, 0.004)). signal.integral vector (required): vector with the limits for the signal integral used for the calculation, e.g., signal.integral = c(1:5). Ignored if object is an RLum.Results object. The parameter can be provided as list, see source_doserate. signal.integral.Tx vector (optional): vector with the limits for the signal integral for the Tx curve. I f nothing is provided the value from signal.integral is used and it is ignored if object is an RLum.Results object. The parameter can be provided as list, see source_doserate. background.integral vector (required): vector with the bounds for the background integral. Ignored if object is an RLum.Results object. The parameter can be provided as list, see source_doserate. background.integral.Tx vector (optional): vector with the limits for the background integral for the Tx curve. If nothing is provided the value from background.integral is used. Ignored if object is an RLum.Results object. The parameter can be provided as list, see source_doserate. analyse_baSAR 15 sigmab numeric (with default): option to set a manual value for the overdispersion (for LnTx and TnTx), used for the Lx/Tx error calculation. The value should be provided as absolute squared count values, cf. calc_OSLLxTxRatio. The parameter can be provided as list, see source_doserate. sig0 numeric (with default): allow adding an extra component of error to the final Lx/Tx error value (e.g., instrumental errror, see details is calc_OSLLxTxRatio). The parameter can be provided as list, see source_doserate. distribution character (with default): type of distribution that is used during Bayesian calculations for determining the Central dose and overdispersion values. Allowed inputs are "cauchy", "normal" and "log_normal". baSAR_model character (optional): option to provide an own modified or new model for the Bayesian calculation (see details). If an own model is provided the argument distribution is ignored and set to 'user_defined' n.MCMC integer (with default): number of iterations for the Markov chain Monte Carlo (MCMC) simulations fit.method character (with default): fit method used for fitting the growth curve using the function plot_GrowthCurve. Here supported methods: EXP, EXP+LIN and LIN fit.force_through_origin logical (with default): force fitting through origin fit.includingRepeatedRegPoints logical (with default): includes the recycling point (assumed to be measured during the last cycle) method_control list (optional): named list of control parameters that can be directly passed to the Bayesian analysis, e.g., method_control = list(n.chains = 4). See details for further information digits integer (with default): round output to the number of given digits plot logical (with default): enables or disables plot output plot_reduced logical (with default): enables or disables the advanced plot output plot.single logical (with default): enables or disables single plots or plots arranged by analyse_baSAR verbose logical (with default): enables or disables verbose mode ... parameters that can be passed to the function calc_OSLLxTxRatio (almost full support), readxl::read_excel (full support), read_BIN2R (n.records, position, duplicated.rm), see details. Details Internally the function consists of two parts: (I) The Bayesian core for the Bayesian calculations and applying the hierchical model and (II) a data pre-processing part. The Bayesian core can be run independently, if the input data are sufficient (see below). The data pre-processing part was implemented to simplify the analysis for the user as all needed data pre-processing is done by the function, i.e. in theory it is enough to provide a BIN/BINX-file with the SAR measurement data. For the Bayesian analysis for each aliquot the following information are needed from the SAR analysis. LxTx, the LxTx error and the dose values for all regeneration points. How the systematic error contribution is calculated? Standard errors (so far) provided with the source dose rate are considered as systematic uncertainties and added to final central dose by: 16 analyse_baSAR systematic.error = 1/n SE(central.dose.f inal) = p X SE(source.doserate) SE(central.dose)2 + systematic.error2 Please note that this approach is rather rough and can only be valid if the source dose rate errors, in case different readers had been used, are similar. In cases where more than one source dose rate is provided a warning is given. Input / output scenarios Various inputs are allowed for this function. Unfortunately this makes the function handling rather complex, but at the same time very powerful. Available scenarios: (1) - object is BIN-file or link to a BIN-file Finally it does not matter how the information of the BIN/BINX file are provided. The function supports (a) either a path to a file or directory or a list of file names or paths or (b) a Risoe.BINfileData object or a list of these objects. The latter one can be produced by using the function read_BIN2R, but this function is called automatically if only a filename and/or a path is provided. In both cases it will become the data that can be used for the analysis. [XLS_file = NULL] If no XLS file (or data frame with the same format) is provided the functions runs an automatic process that consists of the following steps: 1. Select all valid aliquots using the function verify_SingleGrainData 2. Calculate Lx/Tx values using the function calc_OSLLxTxRatio 3. Calculate De values using the function plot_GrowthCurve These proceeded data are subsequently used in for the Bayesian analysis [XLS_file != NULL] If an XLS-file is provided or a data.frame providing similar information the pre-processing steps consists of the following steps: 1. Calculate Lx/Tx values using the function calc_OSLLxTxRatio 2. Calculate De values using the function plot_GrowthCurve Means, the XLS file should contain a selection of the BIN-file names and the aliquots selected for the further analysis. This allows a manual selection of input data, as the automatic selection by verify_SingleGrainData might be not totally sufficient. (2) - object RLum.Results object If an RLum.Results object is provided as input and(!) this object was previously created by the function analyse_baSAR() itself, the pre-processing part is skipped and the function starts directly the Bayesian analysis. This option is very powerful as it allows to change parameters for the Bayesian analysis without the need to repeat the data pre-processing. If furthermore the argument aliquot_range is set, aliquots can be manually excluded based on previous runs. method_control These are arguments that can be passed directly to the Bayesian calculation core, supported arguments are: Parameter Type Descritpion analyse_baSAR lower_centralD upper_centralD n.chains inits thin variable.names 17 numeric numeric integer list numeric character sets the lower bound for the expected De range. Change it only if you know what you are sets the upper bound for the expected De range. Change it only if you know what you are sets number of parallel chains for the model (default = 3) (cf. rjags::jags.model) option to set initialisation values (cf. rjags::jags.model) thinning interval for monitoring the Bayesian process (cf. rjags::jags.model) set the variables to be monitored during the MCMC run, default: ’central_D’, ’sigma_D User defined models The function provides the option to modify and to define own models that can be used for the Bayesian calculation. In the case the user wants to modify a model, a new model can be piped into the funtion via the argument baSAR_model as character. The model has to be provided in the JAGS dialect of the BUGS language (cf. rjags::jags.model) and parameter names given with the pre-defined names have to be respected, otherwise the function will break. FAQ Q: How can I set the seed for the random number generator (RNG)? A: Use the argument method_control, e.g., for three MCMC chains (as it is the default): method_control = list( inits = list( list(.RNG.name = "base::Wichmann-Hill", .RNG.seed = 1), list(.RNG.name = "base::Wichmann-Hill", .RNG.seed = 2), list(.RNG.name = "base::Wichmann-Hill", .RNG.seed = 3) )) This sets a reproducible set for every chain separately. Q: How can I modify the output plots? A: You can’t, but you can use the function output to create own, modified plots. Q: Can I change the boundaries for the central_D? A: Yes, we made it possible, but we DO NOT recommend it, except you know what you are doing! Example: method_control = list(lower_centralD = 10)) Q: The lines in the baSAR-model appear to be in a wrong logical order? A: This is correct and allowed (cf. JAGS manual) Additional arguments support via the ... argument This list summarizes the additional arguments that can be passed to the internally used functions. Supported argument threshold sheet col_names col_types skip n.records duplicated.rm pattern position Corresponding function verify_SingleGrainData readxl::read_excel readxl::read_excel readxl::read_excel readxl::read_excel read_BIN2R read_BIN2R read_BIN2R read_BIN2R Default 30 1 TRUE NULL 0 NULL TRUE TRUE NULL **Short description ** change rejection threshold for curve select XLS-sheet for import first row in XLS-file is header limit import to specific columns number of rows to be skipped durin limit records during BIN-file impor remove duplicated records in the BI select BIN-file by name pattern limit import to a specific position 18 analyse_baSAR background.count.distribution fit.weights fit.bounds NumberIterations.MC output.plot output.plotExtended calc_OSLLxTxRatio plot_GrowthCurve plot_GrowthCurve plot_GrowthCurve plot_GrowthCurve plot_GrowthCurve "non-poisson" TRUE TRUE 100 TRUE TRUE set assumed count distribution enables / disables fit weights enables / disables fit bounds number of MC runs for error calcul enables / disables dose response cu enables / disables extended dose res Value Function returns results numerically and graphically: ———————————– [ NUMERICAL OUTPUT ] ———————————– RLum.Results-object slot: @data Element $summary $mcmc $models $input_object $removed_aliquots Type data.frame mcmc character data.frame data.frame Description statistical summary, including the central dose object including raw output of rjags::rjags implemented models used in the baSAR-model core summarising table (same format as the XLS-file) including, e.g., Lx/Tx values table with removed aliquots (e.g., NaN, or Inf Lx/Tx values). If nothing was remov slot: @info The original function call ———————— [ PLOT OUTPUT ] ———————— • (A) Ln/Tn curves with set integration limits, • (B) trace plots are returned by the baSAR-model, showing the convergence of the parameters (trace) and the resulting kernel density plots. If plot_reduced = FALSE for every(!) dose a trace and a density plot is returned (this may take a long time), • (C) dose plots showing the dose for every aliquot as boxplots and the marked HPD in within. If boxes are coloured ’orange’ or ’red’ the aliquot itself should be checked, • (D) the dose response curve resulting from the monitoring of the Bayesian modelling are provided along with the Lx/Tx values and the HPD. Note: The amount for curves displayed is limited to 1000 (random choice) for performance reasons, • (E) the final plot is the De distribution as calculated using the conventional approach and the central dose with the HPDs marked within. Please note: If distribution was set to log_normal the central dose is given as geometric mean! Function version 0.1.29 (2018-01-21 17:22:38) analyse_baSAR 19 How to cite Mercier, N., Kreutzer, S. (2018). analyse_baSAR(): Bayesian models (baSAR) applied on luminescence data. Function version 0.1.29. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note If you provide more than one BIN-file, it is strongly recommanded to provide a list with the same number of elements for the following parameters: source_doserate, signal.integral, signal.integral.Tx, background.integral, background.integral.Tx, sigmab, sig0. Example for two BIN-files: source_doserate = list(c(0.04, 0.006), c(0.05, 0.006)) The function is currently limited to work with standard Risoe BIN-files only! Author(s) Norbert Mercier, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) The underlying Bayesian model based on a contribution by Combes et al., 2015. R Luminescence Package Team References Combes, B., Philippe, A., Lanos, P., Mercier, N., Tribolo, C., Guerin, G., Guibert, P., Lahaye, C., 2015. A Bayesian central equivalent dose model for optically stimulated luminescence dating. Quaternary Geochronology 28, 62-70. doi:10.1016/j.quageo.2015.04.001 Mercier, N., Kreutzer, S., Christophe, C., Guerin, G., Guibert, P., Lahaye, C., Lanos, P., Philippe, A., Tribolo, C., 2016. Bayesian statistics in luminescence dating: The ’baSAR’-model and its implementation in the R package ’Luminescence’. Ancient TL 34, 14-21. Further reading Gelman, A., Carlin, J.B., Stern, H.S., Dunson, D.B., Vehtari, A., Rubin, D.B., 2013. Bayesian Data Analysis, Third Edition. CRC Press. Murray, A.S., Wintle, A.G., 2000. Luminescence dating of quartz using an improved single-aliquot regenerative-dose protocol. Radiation Measurements 32, 57-73. doi:10.1016/S1350-4487(99)00253X Plummer, M., 2017. JAGS Version 4.3.0 user manual. https://sourceforge.net/projects/mcmcjags/files/Manuals/4.x/jags_user_manual.pdf/download See Also read_BIN2R, calc_OSLLxTxRatio, plot_GrowthCurve, readxl::read_excel, verify_SingleGrainData, rjags::jags.model, rjags::coda.samples, boxplot.default Examples ##(1) load package test data set data(ExampleData.BINfileData, envir = environment()) ##(2) selecting relevant curves, and limit dataset 20 analyse_FadingMeasurement CWOSL.SAR.Data <- subset( CWOSL.SAR.Data, subset = POSITION%in%c(1:3) & LTYPE == "OSL") ## Not run: ##(3) run analysis ##please not that the here selected parameters are ##choosen for performance, not for reliability results <- analyse_baSAR( object = CWOSL.SAR.Data, source_doserate = c(0.04, 0.001), signal.integral = c(1:2), background.integral = c(80:100), fit.method = "LIN", plot = FALSE, n.MCMC = 200 ) print(results) ##XLS_file template ##copy and paste this the code below in the terminal ##you can further use the function write.csv() to export the example XLS_file 36.5 deg.): y = −0.0001 ∗ x + 0.2347 50 bin_RLum.Data J (non-linear part, λ < 34 deg.): y = 5 ∗ 10− 6 ∗ x3 − 5 ∗ 10− 5 ∗ x2 + 0.0026 ∗ x + 0.5177 J (linear part, λ > 34 deg.): y = 0.0005 ∗ x + 0.7388 H (non-linear part, λ < 36 deg.): y = −3 ∗ 10− 6 ∗ x3 − 5 ∗ 10− 5 ∗ x2 − 0.0031 ∗ x + 4.398 H (linear part, λ > 36 deg.): y = 0.0002 ∗ x + 4.0914 References Gruen, R., 2009. The "AGE" program for the calculation of luminescence age estimates. Ancient TL, 27, pp. 45-46. Prescott, J.R., Hutton, J.T., 1988. Cosmic ray and gamma ray dosimetry for TL and ESR. Nuclear Tracks and Radiation Measurements, 14, pp. 223-227. Prescott, J.R., Hutton, J.T., 1994. Cosmic ray contributions to dose rates for luminescence and ESR dating: large depths and long-term time variations. Radiation Measurements, 23, pp. 497-500. Examples ##load data data(BaseDataSet.CosmicDoseRate) bin_RLum.Data Channel binning - method dispatchter Description Function calls the object-specific bin functions for RLum.Data S4 class objects. Usage bin_RLum.Data(object, ...) Arguments object RLum.Data (required): S4 object of class RLum.Data ... further arguments passed to the specifc class method bin_RLum.Data 51 Details The function provides a generalised access point for specific RLum.Data objects. Depending on the input object, the corresponding function will be selected. Allowed arguments can be found in the documentations of the corresponding RLum.Data class. Value An object of the same type as the input object is provided Function version 0.1.0 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). bin_RLum.Data(): Channel binning - method dispatchter. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note Currenlty only RLum.Data objects of class RLum.Data.Curve are supported! Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also RLum.Data.Curve Examples ##load example data data(ExampleData.CW_OSL_Curve, envir = environment()) ##create RLum.Data.Curve object from this example curve 167 g/cm^2 (only hard-component; Allkofer et al. 1975): apply equation given by Prescott & Hutton (1994) (c.f. Barbouti & Rastin 1983) D0 = C/(((absorber + d)α + a) ∗ (absober + H)) ∗ exp(−B ∗ absorber) b) If absorber is < 167 g/cm^2 (soft- and hard-component): derive D0 from Fig. 1 in Prescott & Hutton (1988). (4) Calculate geomagnetic latitude (Prescott & Stephan 1982, Prescott & Hutton 1994) λ = arcsin(0.203 ∗ cos(latitude) ∗ cos(longitude − 291) + 0.979 ∗ sin(latitude)) (5) Apply correction for geomagnetic latitude and altitude above sea-level. Values for F, J and H were read from Fig. 3 shown in Prescott & Stephan (1982) and fitted with 3-degree polynomials for lambda < 35 degree and a linear fit for lambda > 35 degree. Dc = D0 ∗ (F + J ∗ exp((altitude/1000)/H)) (6) Optional: Apply correction for geomagnetic field changes in the last 0-80 ka (Prescott & Hutton 1994). Correction and altitude factors are given in Table 1 and Fig. 1 in Prescott & Hutton (1994). Values for altitude factor were fitted with a 2-degree polynomial. The altitude factor is operated on the decimal part of the correction factor. Dc0 = Dc ∗ correctionF actor Usage of depth and density (1) If only one value for depth and density is provided, the cosmic dose rate is calculated for exactly one sample and one absorber as overburden (i.e. depth*density). (2) In some cases it might be useful to calculate the cosmic dose rate for a sample that is overlain by more than one absorber, e.g. in a profile with soil layers of different thickness and a distinct difference in density. This can be calculated by providing a matching number of values for depth and density (e.g. depth = c(1, 2), density = c(1.7, 2.4)) (3) Another possibility is to calculate the cosmic dose rate for more than one sample of the same profile. This is done by providing more than one values for depth and only one for density. For example, depth = c(1, 2, 3) and density = 1.7 will calculate the cosmic dose rate for three samples in 1, 2 and 3 m depth in a sediment of density 1.7 g/cm^3. calc_CosmicDoseRate 63 Value Returns a terminal output. In addition an RLum.Results-object is returned containing the following element: summary data.frame summary of all relevant calculation results. args list used arguments call call the function call The output should be accessed using the function get_RLum Function version 0.5.2 (2018-01-21 17:22:38) How to cite Burow, C. (2018). calc_CosmicDoseRate(): Calculate the cosmic dose rate. Function version 0.5.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note Despite its universal use the equation to calculate the cosmic dose rate provided by Prescott & Hutton (1994) is falsely stated to be valid from the surface to 10^4 hg/cm^2 of standard rock. The original expression by Barbouti & Rastin (1983) only considers the muon flux (i.e. hard-component) and is by their own definition only valid for depths between 10-10^4 hg/cm^2. Thus, for near-surface samples (i.e. for depths < 167 g/cm^2) the equation of Prescott & Hutton (1994) underestimates the total cosmic dose rate, as it neglects the influence of the soft-component of the cosmic ray flux. For samples at zero depth and at sea-level the underestimation can be as large as ~0.1 Gy/ka. In a previous article, Prescott & Hutton (1988) give another approximation of Barbouti & Rastins equation in the form of D = 0.21 ∗ exp(−0.070 ∗ absorber + 0.0005 ∗ absorber2 ) which is valid for depths between 150-5000 g/cm^2. For shallower depths (< 150 g/cm^2) they provided a graph (Fig. 1) from which the dose rate can be read. As a result, this function employs the equation of Prescott & Hutton (1994) only for depths > 167 g/cm^2, i.e. only for the hard-component of the cosmic ray flux. Cosmic dose rate values for depths < 167 g/cm^2 were obtained from the "AGE" programm (Gruen 2009) and fitted with a 6-degree polynomial curve (and hence reproduces the graph shown in Prescott & Hutton 1988). However, these values assume an average overburden density of 2 g/cm^3. It is currently not possible to obtain more precise cosmic dose rate values for near-surface samples as there is no equation known to the author of this function at the time of writing. Author(s) Christoph Burow, University of Cologne (Germany) R Luminescence Package Team 64 calc_CosmicDoseRate References Allkofer, O.C., Carstensen, K., Dau, W.D., Jokisch, H., 1975. Letter to the editor. The absolute cosmic ray flux at sea level. Journal of Physics G: Nuclear and Particle Physics 1, L51-L52. Barbouti, A.I., Rastin, B.C., 1983. A study of the absolute intensity of muons at sea level and under various thicknesses of absorber. Journal of Physics G: Nuclear and Particle Physics 9, 1577-1595. Crookes, J.N., Rastin, B.C., 1972. An investigation of the absolute intensity of muons at sea-level. Nuclear Physics B 39, 493-508. Gruen, R., 2009. The "AGE" program for the calculation of luminescence age estimates. Ancient TL 27, 45-46. Prescott, J.R., Hutton, J.T., 1988. Cosmic ray and gamma ray dosimetry for TL and ESR. Nuclear Tracks and Radiation Measurements 14, 223-227. Prescott, J.R., Hutton, J.T., 1994. Cosmic ray contributions to dose rates for luminescence and ESR dating: large depths and long-term time variations. Radiation Measurements 23, 497-500. Prescott, J.R., Stephan, L.G., 1982. The contribution of cosmic radiation to the environmental dose for thermoluminescence dating. Latitude, altitude and depth dependences. PACT 6, 17-25. See Also BaseDataSet.CosmicDoseRate Examples ##(1) calculate cosmic dose rate (one absorber) calc_CosmicDoseRate(depth = 2.78, density = 1.7, latitude = 38.06451, longitude = 1.49646, altitude = 364, error = 10) ##(2a) calculate cosmic dose rate (two absorber) calc_CosmicDoseRate(depth = c(5.0, 2.78), density = c(2.65, 1.7), latitude = 38.06451, longitude = 1.49646, altitude = 364, error = 10) ##(2b) calculate cosmic dose rate (two absorber) and ##correct for geomagnetic field changes calc_CosmicDoseRate(depth = c(5.0, 2.78), density = c(2.65, 1.7), latitude = 12.04332, longitude = 4.43243, altitude = 364, corr.fieldChanges = TRUE, est.age = 67, error = 15) ##(3) calculate cosmic dose rate and export results to .csv file #calculate cosmic dose rate and save to variable results<- calc_CosmicDoseRate(depth = 2.78, density = 1.7, latitude = 38.06451, longitude = 1.49646, altitude = 364, error = 10) # the results can be accessed by get_RLum(results, "summary") #export results to .csv file - uncomment for usage #write.csv(results, file = "c:/users/public/results.csv") calc_FadingCorr 65 ##(4) calculate cosmic dose rate for 6 samples from the same profile ## and save to .csv file #calculate cosmic dose rate and save to variable results<- calc_CosmicDoseRate(depth = c(0.1, 0.5 , 2.1, 2.7, 4.2, 6.3), density = 1.7, latitude = 38.06451, longitude = 1.49646, altitude = 364, error = 10) #export results to .csv file - uncomment for usage #write.csv(results, file = "c:/users/public/results_profile.csv") calc_FadingCorr Apply a fading correction according to Huntley & Lamothe (2001) for a given g-value and a given tc Description This function solves the equation used for correcting the fading affected age including the error for a given g-value according to Huntley & Lamothe (2001). Usage calc_FadingCorr(age.faded, g_value, tc = NULL, tc.g_value = tc, n.MC = 10000, seed = NULL, interval = c(0.01, 500), txtProgressBar = TRUE, verbose = TRUE) Arguments age.faded g_value numeric vector (required): uncorrected age with error in ka (see example) vector (required): g-value and error obtained from separate fading measurements (see example). Alternatively an RLum.Results object can be provided produced by the function analyse_FadingMeasurement, in this case tc is set automatically tc numeric (required): time in seconds between irradiation and the prompt measurement (cf. Huntley & Lamothe 2001). Argument will be ignored if g_value was an RLum.Results object tc.g_value numeric (with default): the time in seconds between irradiation and the prompt measurement used for estimating the g-value. If the g-value was normalised to, e.g., 2 days, this time in seconds (i.e., 172800) should be given here. If nothing is provided the time is set to tc, which is usual case for g-values obtained using the SAR method and g-values that had been not normalised to 2 days. n.MC integer (with default): number of Monte Carlo simulation runs for error estimation. If n.MC = 'auto' is used the function tries to find a ’stable’ error for the age. Note: This may take a while! seed integer (optional): sets the seed for the random number generator in R using set.seed interval numeric (with default): a vector containing the end-points (age interval) of the interval to be searched for the root in ’ka’. This argument is passed to the function stats::uniroot used for solving the equation. txtProgressBar logical (with default): enables or disables txtProgressBar verbose logical (with default): enables or disables terminal output 66 calc_FadingCorr Details As the g-value sligthly depends on the time between irradiation and the prompt measurement, this is tc, always a tc value needs to be provided. If the g-value was normalised to a distinct time or evaluated with a different tc value (e.g., external irradiation), also the tc value for the g-value needs to be provided (argument tc.g_value and then the g-value is recalcualted to tc of the measurement used for estimating the age applying the following equation: κtc = κtc.g /(1 − κtc.g ∗ log(tc/tc.g)) where κtc.g = g/100/log(10) with log the natural logarithm. The error of the fading-corrected age is determined using a Monte Carlo simulation approach. Solving of the equation is realised using uniroot. Large values for n.MC will significantly increase the computation time. n.MC = ’auto’ The error estimation based on a stochastic process, i.e. for a small number of MC runs the calculated error varies considerably every time the function is called, even with the same input values. The argument option n.MC = 'auto' tries to find a stable value for the standard error, i.e. the standard deviation of values calculated during the MC runs (age.corr.MC), within a given precision (2 digits) by increasing the number of MC runs stepwise and calculating the corresponding error. If the determined error does not differ from the 9 values calculated previously within a precision of (here) 3 digits the calculation is stopped as it is assumed that the error is stable. Please note that (a) the duration depends on the input values as well as on the provided computation ressources and it may take a while, (b) the length (size) of the output vector age.corr.MC, where all the single values produced during the MC runs are stored, equals the number of MC runs (here termed observations). To avoid an endless loop the calculation is stopped if the number of observations exceeds 10^7. This limitation can be overwritten by setting the number of MC runs manually, e.g. n.MC = 10000001. Note: For this case the function is not checking whether the calculated error is stable. seed This option allows to recreate previously calculated results by setting the seed for the R random number generator (see set.seed for details). This option should not be mixed up with the option n.MC = ’auto’. The results may appear similar, but they are not comparable! FAQ Q: Which tc value is expected? A: tc is the time in seconds between irradiation and the prompt measurement applied during your De measurement. However, this tc might differ from the tc used for estimating the g-value. In the case of an SAR measurement tc should be similar, however, if it differs, you have to provide this tc value (the one used for estimating the g-value) using the argument tc.g_value. calc_FadingCorr 67 Value Returns an S4 object of type RLum.Results. Slot: @data Object age.corr age.corr.MC Type data.frame numeric Comment Corrected age MC simulation results with all possible ages from that simulation Slot: @info Object info Type character Comment the original function call Function version 0.4.2 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). calc_FadingCorr(): Apply a fading correction according to Huntley & Lamothe (2001) for a given g-value and a given tc. Function version 0.4.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note Special thanks to Sebastien Huot for his support and clarification via e-mail. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References Huntley, D.J., Lamothe, M., 2001. Ubiquity of anomalous fading in K-feldspars and the measurement and correction for it in optical dating. Canadian Journal of Earth Sciences, 38, 1093-1106. See Also RLum.Results, get_RLum, uniroot Examples ##run the examples given in the appendix of Huntley and Lamothe, 2001 ##(1) faded age: 100 a results <- calc_FadingCorr( 68 calc_FastRatio age.faded = c(0.1,0), g_value = c(5.0, 1.0), tc = 2592000, tc.g_value = 172800, n.MC = 100) ##(2) faded age: 1 ka results <- calc_FadingCorr( age.faded = c(1,0), g_value = c(5.0, 1.0), tc = 2592000, tc.g_value = 172800, n.MC = 100) ##(3) faded age: 10.0 ka results <- calc_FadingCorr( age.faded = c(10,0), g_value = c(5.0, 1.0), tc = 2592000, tc.g_value = 172800, n.MC = 100) ##access the last output get_RLum(results) calc_FastRatio Calculate the Fast Ratio for CW-OSL curves Description Function to calculate the fast ratio of quartz CW-OSL single grain or single aliquot curves after Durcan & Duller (2011). Usage calc_FastRatio(object, stimulation.power = 30.6, wavelength = 470, sigmaF = 2.6e-17, sigmaM = 4.28e-18, Ch_L1 = 1, Ch_L2 = NULL, Ch_L3 = NULL, x = 1, x2 = 0.1, dead.channels = c(0, 0), fitCW.sigma = FALSE, fitCW.curve = FALSE, plot = TRUE, ...) Arguments object RLum.Analysis, RLum.Data.Curve or data.frame (required): x, y data of measured values (time and counts). stimulation.power numeric (with default): Stimulation power in mW/cm^2 wavelength numeric (with default): Stimulation wavelength in nm sigmaF numeric (with default): Photoionisation cross-section (cm^2) of the fast component. Default value after Durcan & Duller (2011). sigmaM numeric (with default): Photoionisation cross-section (cm^2) of the medium component. Default value after Durcan & Duller (2011). calc_FastRatio 69 Ch_L1 numeric (with default): An integer specifying the channel for L1. Ch_L2 numeric (optional): An integer specifying the channel for L2. Ch_L3 numeric (optional): A vector of length 2 with integer values specifying the start and end channels for L3 (e.g., c(40, 50)). x numeric (with default): % of signal remaining from the fast component. Used to define the location of L2 and L3 (start). x2 numeric (with default): % of signal remaining from the medium component. Used to define the location of L3 (end). dead.channels numeric (with default): Vector of length 2 in the form of c(x, y). Channels that do not contain OSL data, i.e. at the start or end of measurement. fitCW.sigma logical (optional): fit CW-OSL curve using fit_CWCurve to calculate sigmaF and sigmaM (experimental). fitCW.curve logical (optional): fit CW-OSL curve using fit_CWCurve and derive the counts of L2 and L3 from the fitted OSL curve (experimental). plot logical (with default): plot output (TRUE/FALSE) ... available options: verbose (logical). Further arguments passed to fit_CWCurve. Details This function follows the equations of Durcan & Duller (2011). The energy required to reduce the fast and medium quartz OSL components to x and x2 % respectively using eq. 3 to determine channels L2 and L3 (start and end). The fast ratio is then calculated from: (L1 − L3)/(L2 − L3). Value Returns a plot (optional) and an S4 object of type RLum.Results. The slot data contains a list with the following elements: summary data.frame summary of all relevant results data the original input data fit RLum.Results object if either fitCW.sigma or fitCW.curve is TRUE args list of used arguments call [call] the function call Function version 0.1.1 (2018-01-21 17:22:38) How to cite King, G., Durcan, J., Burow, C. (2018). calc_FastRatio(): Calculate the Fast Ratio for CW-OSL curves. Function version 0.1.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Georgina King, University of Cologne (Germany) Julie A. Durcan, University of Oxford (United Kingdom) Christoph Burow, University of Cologne (Germany) R Luminescence Package Team 70 calc_FiniteMixture References Durcan, J.A. & Duller, G.A.T., 2011. The fast ratio: A rapid measure for testing the dominance of the fast component in the initial OSL signal from quartz. Radiation Measurements 46, 1065-1072. Madsen, A.T., Duller, G.A.T., Donnelly, J.P., Roberts, H.M. & Wintle, A.G., 2009. A chronology of hurricane landfalls at Little Sippewissett Marsh, Massachusetts, USA, using optical dating. Geomorphology 109, 36-45. Further reading Steffen, D., Preusser, F. & Schlunegger, 2009. OSL quartz age underestimation due to unstable signal components. Quaternary Geochronology 4, 353-362. See Also fit_CWCurve, get_RLum, RLum.Analysis, RLum.Results, RLum.Data.Curve Examples # load example CW-OSL curve data("ExampleData.CW_OSL_Curve") # calculate the fast ratio w/o further adjustments res <- calc_FastRatio(ExampleData.CW_OSL_Curve) # show the summary table get_RLum(res) calc_FiniteMixture Apply the finite mixture model (FMM) after Galbraith (2005) to a given De distribution Description This function fits a k-component mixture to a De distribution with differing known standard errors. Parameters (doses and mixing proportions) are estimated by maximum likelihood assuming that the log dose estimates are from a mixture of normal distributions. Usage calc_FiniteMixture(data, sigmab, n.components, grain.probability = FALSE, dose.scale, pdf.weight = TRUE, pdf.sigma = "sigmab", pdf.colors = "gray", pdf.scale, plot.proportions = TRUE, plot = TRUE, ...) Arguments data RLum.Results or data.frame (required): for data.frame: two columns with De (data[,1]) and De error (values[,2]) sigmab numeric (required): spread in De values given as a fraction (e.g. 0.2). This value represents the expected overdispersion in the data should the sample be well-bleached (Cunningham & Wallinga 2012, p. 100). calc_FiniteMixture 71 n.components numeric (required): number of components to be fitted. If a vector is provided (e.g. c(2:8)) the finite mixtures for 2, 3 ... 8 components are calculated and a plot and a statistical evaluation of the model performance (BIC score and maximum log-likelihood) is provided. grain.probability logical (with default): prints the estimated probabilities of which component each grain is in dose.scale numeric: manually set the scaling of the y-axis of the first plot with a vector in the form of c(min, max) pdf.weight logical (with default): weight the probability density functions by the components proportion (applies only when a vector is provided for n.components) pdf.sigma character (with default): if "sigmab" the components normal distributions are plotted with a common standard deviation (i.e. sigmab) as assumed by the FFM. Alternatively, "se" takes the standard error of each component for the sigma parameter of the normal distribution pdf.colors character (with default): color coding of the components in the the plot. Possible options are "gray", "colors" and "none" pdf.scale numeric: manually set the max density value for proper scaling of the x-axis of the first plot plot.proportions logical (with default): plot barplot showing the proportions of components plot logical (with default): plot output ... further arguments to pass. See details for their usage. Details This model uses the maximum likelihood and Bayesian Information Criterion (BIC) approaches. Indications of overfitting are: • increasing BIC • repeated dose estimates • covariance matrix not positive definite • covariance matrix produces NaNs • convergence problems Plot If a vector (c(k.min:k.max)) is provided for n.components a plot is generated showing the the k components equivalent doses as normal distributions. By default pdf.weight is set to FALSE, so that the area under each normal distribution is always 1. If TRUE, the probability density functions are weighted by the components proportion for each iteration of k components, so the sum of areas of each component equals 1. While the density values are on the same scale when no weights are used, the y-axis are individually scaled if the probability density are weighted by the components proportion. The standard deviation (sigma) of the normal distributions is by default determined by a common sigmab (see pdf.sigma). For pdf.sigma = "se" the standard error of each component is taken instead. The stacked barplot shows the proportion of each component (in per cent) calculated by the FFM. The last plot shows the achieved BIC scores and maximum log-likelihood estimates for each iteration of k. 72 calc_FiniteMixture Value Returns a plot (optional) and terminal output. In addition an RLum.Results object is returned containing the following elements: .$summary data.frame summary of all relevant model results. .$data data.frame original input data .$args list used arguments .$call call the function call .$mle covariance matrices of the log likelhoods .$BIC BIC score .$llik maximum log likelihood .$grain.probability probabilities of a grain belonging to a component .$components matrix estimates of the de, de error and proportion for each component .$single.comp data.frame single componente FFM estimate If a vector for n.components is provided (e.g. c(2:8)), mle and grain.probability are lists containing matrices of the results for each iteration of the model. The output should be accessed using the function get_RLum Function version 0.4 (2018-01-21 17:22:38) How to cite Burow, C. (2018). calc_FiniteMixture(): Apply the finite mixture model (FMM) after Galbraith (2005) to a given De distribution. Function version 0.4. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Christoph Burow, University of Cologne (Germany) Based on a rewritten S script of Rex Galbraith, 2006. R Luminescence Package Team References Galbraith, R.F. & Green, P.F., 1990. Estimating the component ages in a finite mixture. Nuclear Tracks and Radiation Measurements 17, 197-206. Galbraith, R.F. & Laslett, G.M., 1993. Statistical models for mixed fission track ages. Nuclear Tracks Radiation Measurements 4, 459-470. Galbraith, R.F. & Roberts, R.G., 2012. Statistical aspects of equivalent dose and error calculation and display in OSL dating: An overview and some recommendations. Quaternary Geochronology 11, 1-27. Roberts, R.G., Galbraith, R.F., Yoshida, H., Laslett, G.M. & Olley, J.M., 2000. Distinguishing dose populations in sediment mixtures: a test of single-grain optical dating procedures using mixtures of laboratory-dosed quartz. Radiation Measurements 32, 459-465. calc_FuchsLang2001 73 Galbraith, R.F., 2005. Statistics for Fission Track Analysis, Chapman & Hall/CRC, Boca Raton. Further reading Arnold, L.J. & Roberts, R.G., 2009. Stochastic modelling of multi-grain equivalent dose (De) distributions: Implications for OSL dating of sediment mixtures. Quaternary Geochronology 4, 204-230. Cunningham, A.C. & Wallinga, J., 2012. Realizing the potential of fluvial archives using robust OSL chronologies. Quaternary Geochronology 12, 98-106. Rodnight, H., Duller, G.A.T., Wintle, A.G. & Tooth, S., 2006. Assessing the reproducibility and accuracy of optical dating of fluvial deposits. Quaternary Geochronology 1, 109-120. Rodnight, H. 2008. How many equivalent dose values are needed to obtain a reproducible distribution?. Ancient TL 26, 3-10. See Also calc_CentralDose, calc_CommonDose, calc_FuchsLang2001, calc_MinDose Examples ## load example data data(ExampleData.DeValues, envir = environment()) ## (1) apply the finite mixture model ## NOTE: the data set is not suitable for the finite mixture model, ## which is why a very small sigmab is necessary calc_FiniteMixture(ExampleData.DeValues$CA1, sigmab = 0.2, n.components = 2, grain.probability = TRUE) ## (2) repeat the finite mixture model for 2, 3 and 4 maximum number of fitted ## components and save results ## NOTE: The following example is computationally intensive. Please un-comment ## the following lines to make the example work. FMM<- calc_FiniteMixture(ExampleData.DeValues$CA1, sigmab = 0.2, n.components = c(2:4), pdf.weight = TRUE, dose.scale = c(0, 100)) ## show structure of the results FMM ## show the results on equivalent dose, standard error and proportion of ## fitted components get_RLum(object = FMM, data.object = "components") calc_FuchsLang2001 Apply the model after Fuchs & Lang (2001) to a given De distribution. Description This function applies the method according to Fuchs & Lang (2001) for heterogeneously bleached samples with a given coefficient of variation threshold. 74 calc_FuchsLang2001 Usage calc_FuchsLang2001(data, cvThreshold = 5, startDeValue = 1, plot = TRUE, ...) Arguments data RLum.Results or data.frame (required): for data.frame: two columns with De (data[,1]) and De error (values[,2]) cvThreshold numeric (with default): coefficient of variation in percent, as threshold for the method, e.g. cvThreshold = 3. See details . startDeValue numeric (with default): number of the first aliquot that is used for the calculations plot logical (with default): plot output TRUE/FALSE ... further arguments and graphical parameters passed to plot Details Used values If the coefficient of variation (c[v]) of the first two values is larger than the threshold c[v_threshold], the first value is skipped. Use the startDeValue argument to define a start value for calculation (e.g. 2nd or 3rd value). Basic steps of the approach 1. Estimate natural relative variation of the sample using a dose recovery test 2. Sort the input values ascendingly 3. Calculate a running mean, starting with the lowermost two values and add values iteratively. 4. Stop if the calculated c[v] exceeds the specified cvThreshold Value Returns a plot (optional) and terminal output. In addition an RLum.Results object is returned containing the following elements: summary data.frame summary of all relevant model results. data data.frame original input data args list used arguments call call the function call usedDeValues data.frame containing the used values for the calculation Function version 0.4.1 (2018-01-21 17:22:38) How to cite Kreutzer, S., Burow, C. (2018). calc_FuchsLang2001(): Apply the model after Fuchs & Lang (2001) to a given De distribution.. Function version 0.4.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence calc_gSGC 75 Note Please consider the requirements and the constraints of this method (see Fuchs & Lang, 2001) Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) Christoph Burow, University of Cologne (Germany) R Luminescence Package Team References Fuchs, M. & Lang, A., 2001. OSL dating of coarse-grain fluvial quartz using single-aliqout protocols on sediments from NE Peloponnese, Greece. In: Quaternary Science Reviews 20, 783-787. Fuchs, M. & Wagner, G.A., 2003. Recognition of insufficient bleaching by small aliquots of quartz for reconstructing soil erosion in Greece. Quaternary Science Reviews 22, 1161-1167. See Also plot, calc_MinDose, calc_FiniteMixture, calc_CentralDose, calc_CommonDose, RLum.Results Examples ## load example data data(ExampleData.DeValues, envir = environment()) ## calculate De according to Fuchs & Lang (2001) temp<- calc_FuchsLang2001(ExampleData.DeValues$BT998, cvThreshold = 5) calc_gSGC Calculate De value based on the gSGC by Li et al., 2015 Description Function returns De value and De value error using the global standardised growth curve (gSGC) assumption proposed by Li et al., 2015 for OSL dating of sedimentary quartz Usage calc_gSGC(data, gSGC.type = "0-250", gSGC.parameters, n.MC = 100, verbose = TRUE, plot = TRUE, ...) Arguments data data.frame (required): input data of providing the following columns: ’LnTn’, ’LnTn.error’, Lr1Tr1’, ’Lr1Tr1.error’, ’Dr1’ Note: column names are not required. The function expect the input data in the given order gSGC.type character (with default): define the function parameters that should be used for the iteration procedure: Li et al., 2015 (Table 2) presented function parameters for two dose ranges: "0-450" and "0-250" 76 calc_gSGC gSGC.parameters list (optional): option to provide own function parameters used for fitting as named list. Nomenclature follows Li et al., 2015, i.e. list(A,A.error,D0,D0.error,c,c.error,Y0 range requires a vector for the range the function is considered as valid, e.g. range = c(0,250) Using this option overwrites the default parameter list of the gSGC, meaning the argument gSGC.type will be without effect n.MC integer (with default): number of Monte Carlo simulation runs for error estimation, see details. verbose logical: enable or disable terminal output plot logical: enable or disable graphical feedback as plot ... parameters will be passed to the plot output Details The error of the De value is determined using a Monte Carlo simulation approach. Solving of the equation is realised using uniroot. Large values for n.MC will significantly increase the computation time. Value Returns an S4 object of type RLum.Results. @data $ De.value (data.frame) .. $ De .. $ De.error .. $ Eta $ De.MC (list) contains the matricies from the error estimation. $ uniroot (list) contains the uniroot outputs of the De estimations @info ‘$ call“ (call) the original function call Function version 0.1.1 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). calc_gSGC(): Calculate De value based on the gSGC by Li et al., 2015. Function version 0.1.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montagine (France) R Luminescence Package Team calc_HomogeneityTest 77 References Li, B., Roberts, R.G., Jacobs, Z., Li, S.-H., 2015. Potential of establishing a ’global standardised growth curve’ (gSGC) for optical dating of quartz from sediments. Quaternary Geochronology 27, 94-104. doi:10.1016/j.quageo.2015.02.011 See Also RLum.Results, get_RLum, uniroot Examples results <- calc_gSGC(data = data.frame( LnTn = 2.361, LnTn.error = 0.087, Lr1Tr1 = 2.744, Lr1Tr1.error = 0.091, Dr1 = 34.4)) get_RLum(results, data.object = "De") calc_HomogeneityTest Apply a simple homogeneity test after Galbraith (2003) Description A simple homogeneity test for De estimates Usage calc_HomogeneityTest(data, log = TRUE, ...) Arguments data log ... RLum.Results or data.frame (required): for data.frame: two columns with De (data[,1]) and De error (values[,2]) logical (with default): perform the homogeneity test with (un-)logged data further arguments (for internal compatibility only). Details For details see Galbraith (2003). Value Returns a terminal output. In addition an RLum.Results-object is returned containing the following elements: summary data args call data.frame summary of all relevant model results. data.frame original input data list used arguments call the function call The output should be accessed using the function get_RLum 78 calc_IEU Function version 0.3.0 (2018-01-21 17:22:38) How to cite Burow, C., Kreutzer, S. (2018). calc_HomogeneityTest(): Apply a simple homogeneity test after Galbraith (2003). Function version 0.3.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Christoph Burow, University of Cologne (Germany), Sebastian Kreutzer, IRAMAT-CRP2A, Université Bordeaux Montaigne (France) R Luminescence Package Team References Galbraith, R.F., 2003. A simple homogeneity test for estimates of dose obtained using OSL. Ancient TL 21, 75-77. See Also pchisq Examples ## load example data data(ExampleData.DeValues, envir = environment()) ## apply the homogeneity test calc_HomogeneityTest(ExampleData.DeValues$BT998) ## using the data presented by Galbraith (2003) df max(t) NOTE: The number of values for t’ < min(t) depends on the stimulation rate parameter delta. To avoid the production of too many artificial data at the raising tail of the determined pHM curve, it is recommended to use the automatic estimation routine for delta, i.e. provide no value for delta. Value The function returns the same data type as the input data type with the transformed curve values. RLum.Data.Curve $CW2pHMi.x.t $CW2pHMi.method : transformed time values : used method for the production of the new data points data.frame $x $y.t $x.t $method : : : : time transformed count values transformed time values used method for the production of the new data points CW2pHMi 115 Function version 0.2.2 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). CW2pHMi(): Transform a CW-OSL curve into a pHM-OSL curve via interpolation under hyperbolic modulation conditions. Function version 0.2.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.Rproject.org/package=Luminescence Note According to Bos & Wallinga (2012), the number of extrapolated points should be limited to avoid artificial intensity data. If delta is provided manually and more than two points are extrapolated, a warning message is returned. The function approx may produce some Inf and NaN data. The function tries to manually interpolate these values by calculating the mean using the adjacent channels. If two invalid values are succeeding, the values are removed and no further interpolation is attempted. In every case a warning message is shown. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) Based on comments and suggestions from: Adrie J.J. Bos, Delft University of Technology, The Netherlands R Luminescence Package Team References Bos, A.J.J. & Wallinga, J., 2012. How to visualize quartz OSL signal components. Radiation Measurements, 47, 752-758. Further Reading Bulur, E., 1996. An Alternative Technique For Optically Stimulated Luminescence (OSL) Experiment. Radiation Measurements, 26, 701-709. Bulur, E., 2000. A simple transformation for converting CW-OSL curves to LM-OSL curves. Radiation Measurements, 32, 141-145. See Also CW2pLM, CW2pLMi, CW2pPMi, fit_LMCurve, lm, RLum.Data.Curve Examples ##(1) - simple transformation ##load CW-OSL curve data data(ExampleData.CW_OSL_Curve, envir = environment()) ##transform values values.transformed<-CW2pHMi(ExampleData.CW_OSL_Curve) 116 CW2pHMi ##plot plot(values.transformed$x, values.transformed$y.t, log = "x") ##(2) - load CW-OSL curve from BIN-file and plot transformed values ##load BINfile #BINfileData<-readBIN2R("[path to BIN-file]") data(ExampleData.BINfileData, envir = environment()) ##grep first CW-OSL curve from ALQ 1 curve.ID<-CWOSL.SAR.Data@METADATA[CWOSL.SAR.Data@METADATA[,"LTYPE"]=="OSL" & CWOSL.SAR.Data@METADATA[,"POSITION"]==1 ,"ID"] curve.HIGH<-CWOSL.SAR.Data@METADATA[CWOSL.SAR.Data@METADATA[,"ID"]==curve.ID[1] ,"HIGH"] curve.NPOINTS<-CWOSL.SAR.Data@METADATA[CWOSL.SAR.Data@METADATA[,"ID"]==curve.ID[1] ,"NPOINTS"] ##combine curve to data set curve<-data.frame(x = seq(curve.HIGH/curve.NPOINTS,curve.HIGH, by = curve.HIGH/curve.NPOINTS), y=unlist(CWOSL.SAR.Data@DATA[curve.ID[1]])) ##transform values curve.transformed <- CW2pHMi(curve) ##plot curve plot(curve.transformed$x, curve.transformed$y.t, log = "x") ##(3) - produce Fig. 4 from Bos & Wallinga (2012) ##load data data(ExampleData.CW_OSL_Curve, envir = environment()) values <- CW_Curve.BosWallinga2012 ##open plot area plot(NA, NA, xlim=c(0.001,10), ylim=c(0,8000), ylab="pseudo OSL (cts/0.01 s)", xlab="t [s]", log="x", main="Fig. 4 - Bos & Wallinga (2012)") values.t<-CW2pLMi(values, P=1/20) lines(values[1:length(values.t[,1]),1],CW2pLMi(values, P=1/20)[,2], col="red" ,lwd=1.3) text(0.03,4500,"LM", col="red" ,cex=.8) values.t<-CW2pHMi(values, delta=40) CW2pLM 117 lines(values[1:length(values.t[,1]),1],CW2pHMi(values, delta=40)[,2], col="black", lwd=1.3) text(0.005,3000,"HM", cex=.8) values.t<-CW2pPMi(values, P=1/10) lines(values[1:length(values.t[,1]),1],CW2pPMi(values, P=1/10)[,2], col="blue", lwd=1.3) text(0.5,6500,"PM", col="blue" ,cex=.8) CW2pLM Transform a CW-OSL curve into a pLM-OSL curve Description Transforms a conventionally measured continuous-wave (CW) curve into a pseudo linearly modulated (pLM) curve using the equations given in Bulur (2000). Usage CW2pLM(values) Arguments values RLum.Data.Curve or data.frame (required): RLum.Data.Curve data object. Alternatively, a data.frame of the measured curve data of type stimulation time (t) (values[,1]) and measured counts (cts) (values[,2]) can be provided. Details According to Bulur (2000) the curve data are transformed by introducing two new parameters P (stimulation period) and u (transformed time): P = 2 ∗ max(t) p u = (2 ∗ t ∗ P ) The new count values are then calculated by ctsN EW = cts(u/P ) and the returned data.frame is produced by: data.frame(u,ctsNEW) The output of the function can be further used for LM-OSL fitting. Value The function returns the same data type as the input data type with the transformed curve values (data.frame or RLum.Data.Curve). Function version 0.4.1 (2018-01-21 17:22:38) 118 CW2pLM How to cite Kreutzer, S. (2018). CW2pLM(): Transform a CW-OSL curve into a pLM-OSL curve. Function version 0.4.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note The transformation is recommended for curves recorded with a channel resolution of at least 0.05 s/channel. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References Bulur, E., 2000. A simple transformation for converting CW-OSL curves to LM-OSL curves. Radiation Measurements, 32, 141-145. Further Reading Bulur, E., 1996. An Alternative Technique For Optically Stimulated Luminescence (OSL) Experiment. Radiation Measurements, 26, 701-709. See Also CW2pHMi, CW2pLMi, CW2pPMi, fit_LMCurve, lm, RLum.Data.Curve Examples ##read curve from CWOSL.SAR.Data transform curve and plot values data(ExampleData.BINfileData, envir = environment()) ##read id for the 1st OSL curve id.OSL <- CWOSL.SAR.Data@METADATA[CWOSL.SAR.Data@METADATA[,"LTYPE"] == "OSL","ID"] ##produce x and y (time and count data for the data set) x<-seq(CWOSL.SAR.Data@METADATA[id.OSL[1],"HIGH"]/CWOSL.SAR.Data@METADATA[id.OSL[1],"NPOINTS"], CWOSL.SAR.Data@METADATA[id.OSL[1],"HIGH"], by = CWOSL.SAR.Data@METADATA[id.OSL[1],"HIGH"]/CWOSL.SAR.Data@METADATA[id.OSL[1],"NPOINTS"]) y <- unlist(CWOSL.SAR.Data@DATA[id.OSL[1]]) values <- data.frame(x,y) ##transform values values.transformed <- CW2pLM(values) ##plot plot(values.transformed) CW2pLMi 119 CW2pLMi Transform a CW-OSL curve into a pLM-OSL curve via interpolation under linear modulation conditions Description Transforms a conventionally measured continuous-wave (CW) OSL-curve into a pseudo linearly modulated (pLM) curve under linear modulation conditions using the interpolation procedure described by Bos & Wallinga (2012). Usage CW2pLMi(values, P) Arguments values P RLum.Data.Curve or data.frame (required): RLum.Data.Curve or data.frame with measured curve data of type stimulation time (t) (values[,1]) and measured counts (cts) (values[,2]) vector (optional): stimulation time in seconds. If no value is given the optimal value is estimated automatically (see details). Greater values of P produce more points in the rising tail of the curve. Details The complete procedure of the transformation is given in Bos & Wallinga (2012). The input data.frame consists of two columns: time (t) and count values (CW(t)) Nomenclature • P = stimulation time (s) • 1/P = stimulation rate (1/s) Internal transformation steps (1) log(CW-OSL) values (2) Calculate t’ which is the transformed time: t0 = 1/2 ∗ 1/P ∗ t2 (3) Interpolate CW(t’), i.e. use the log(CW(t)) to obtain the count values for the transformed time (t’). Values beyond min(t) and max(t) produce NA values. (4) Select all values for t’ < min(t), i.e. values beyond the time resolution of t. Select the first two values of the transformed data set which contain no NA values and use these values for a linear fit using lm. (5) Extrapolate values for t’ < min(t) based on the previously obtained fit parameters. (6) Transform values using pLM (t) = t/P ∗ CW (t0 ) (7) Combine values and truncate all values for t’ > max(t) NOTE: The number of values for t’ < min(t) depends on the stimulation period (P) and therefore on the stimulation rate 1/P. To avoid the production of too many artificial data at the raising tail of the determined pLM curves it is recommended to use the automatic estimation routine for P, i.e. provide no own value for P. 120 CW2pLMi Value The function returns the same data type as the input data type with the transformed curve values. RLum.Data.Curve $CW2pLMi.x.t $CW2pLMi.method : transformed time values : used method for the production of the new data points Function version 0.3.1 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). CW2pLMi(): Transform a CW-OSL curve into a pLM-OSL curve via interpolation under linear modulation conditions. Function version 0.3.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note According to Bos & Wallinga (2012) the number of extrapolated points should be limited to avoid artificial intensity data. If P is provided manually and more than two points are extrapolated, a warning message is returned. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne Based on comments and suggestions from: Adrie J.J. Bos, Delft University of Technology, The Netherlands R Luminescence Package Team References Bos, A.J.J. & Wallinga, J., 2012. How to visualize quartz OSL signal components. Radiation Measurements, 47, 752-758. Further Reading Bulur, E., 1996. An Alternative Technique For Optically Stimulated Luminescence (OSL) Experiment. Radiation Measurements, 26, 701-709. Bulur, E., 2000. A simple transformation for converting CW-OSL curves to LM-OSL curves. Radiation Measurements, 32, 141-145. See Also CW2pLM, CW2pHMi, CW2pPMi, fit_LMCurve, RLum.Data.Curve Examples ##(1) ##load CW-OSL curve data data(ExampleData.CW_OSL_Curve, envir = environment()) CW2pPMi 121 ##transform values values.transformed <- CW2pLMi(ExampleData.CW_OSL_Curve) ##plot plot(values.transformed$x, values.transformed$y.t, log = "x") ##(2) - produce Fig. 4 from Bos & Wallinga (2012) ##load data data(ExampleData.CW_OSL_Curve, envir = environment()) values <- CW_Curve.BosWallinga2012 ##open plot area plot(NA, NA, xlim = c(0.001,10), ylim = c(0,8000), ylab = "pseudo OSL (cts/0.01 s)", xlab = "t [s]", log = "x", main = "Fig. 4 - Bos & Wallinga (2012)") values.t <- CW2pLMi(values, P = 1/20) lines(values[1:length(values.t[,1]),1],CW2pLMi(values, P = 1/20)[,2], col = "red", lwd = 1.3) text(0.03,4500,"LM", col = "red", cex = .8) values.t <- CW2pHMi(values, delta = 40) lines(values[1:length(values.t[,1]),1],CW2pHMi(values, delta = 40)[,2], col = "black", lwd = 1.3) text(0.005,3000,"HM", cex =.8) values.t <- CW2pPMi(values, P = 1/10) lines(values[1:length(values.t[,1]),1], CW2pPMi(values, P = 1/10)[,2], col = "blue", lwd = 1.3) text(0.5,6500,"PM", col = "blue", cex = .8) CW2pPMi Transform a CW-OSL curve into a pPM-OSL curve via interpolation under parabolic modulation conditions Description Transforms a conventionally measured continuous-wave (CW) OSL-curve into a pseudo parabolic modulated (pPM) curve under parabolic modulation conditions using the interpolation procedure described by Bos & Wallinga (2012). Usage CW2pPMi(values, P) 122 CW2pPMi Arguments values RLum.Data.Curve or data.frame (required): RLum.Data.Curve or data.frame with measured curve data of type stimulation time (t) (values[,1]) and measured counts (cts) (values[,2]) P vector (optional): stimulation period in seconds. If no value is given, the optimal value is estimated automatically (see details). Greater values of P produce more points in the rising tail of the curve. Details The complete procedure of the transformation is given in Bos & Wallinga (2012). The input data.frame consists of two columns: time (t) and count values (CW(t)) Nomenclature • P = stimulation time (s) • 1/P = stimulation rate (1/s) Internal transformation steps (1) log(CW-OSL) values (2) Calculate t’ which is the transformed time: t0 = (1/3) ∗ (1/P 2 )t3 (3) Interpolate CW(t’), i.e. use the log(CW(t)) to obtain the count values for the transformed time (t’). Values beyond min(t) and max(t) produce NA values. (4) Select all values for t’ < min(t), i.e. values beyond the time resolution of t. Select the first two values of the transformed data set which contain no NA values and use these values for a linear fit using lm. (5) Extrapolate values for t’ < min(t) based on the previously obtained fit parameters. The extrapolation is limited to two values. Other values at the beginning of the transformed curve are set to 0. (6) Transform values using pLM (t) = t2 /P 2 ∗ CW (t0 ) (7) Combine all values and truncate all values for t’ > max(t) NOTE: The number of values for t’ < min(t) depends on the stimulation period P. To avoid the production of too many artificial data at the raising tail of the determined pPM curve, it is recommended to use the automatic estimation routine for P, i.e. provide no value for P. Value The function returns the same data type as the input data type with the transformed curve values. RLum.Data.Curve $CW2pPMi.x.t $CW2pPMi.method : transformed time values : used method for the production of the new data points data.frame $x : time CW2pPMi 123 $y.t $x.t $method : transformed count values : transformed time values : used method for the production of the new data points Function version 0.2.1 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). CW2pPMi(): Transform a CW-OSL curve into a pPM-OSL curve via interpolation under parabolic modulation conditions. Function version 0.2.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note According to Bos & Wallinga (2012), the number of extrapolated points should be limited to avoid artificial intensity data. If P is provided manually, not more than two points are extrapolated. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) Based on comments and suggestions from: Adrie J.J. Bos, Delft University of Technology, The Netherlands R Luminescence Package Team References Bos, A.J.J. & Wallinga, J., 2012. How to visualize quartz OSL signal components. Radiation Measurements, 47, 752-758. Further Reading Bulur, E., 1996. An Alternative Technique For Optically Stimulated Luminescence (OSL) Experiment. Radiation Measurements, 26, 701-709. Bulur, E., 2000. A simple transformation for converting CW-OSL curves to LM-OSL curves. Radiation Measurements, 32, 141-145. See Also CW2pLM, CW2pLMi, CW2pHMi, fit_LMCurve, RLum.Data.Curve Examples ##(1) ##load CW-OSL curve data data(ExampleData.CW_OSL_Curve, envir = environment()) ##transform values values.transformed <- CW2pPMi(ExampleData.CW_OSL_Curve) ##plot 124 ExampleData.Al2O3C plot(values.transformed$x,values.transformed$y.t, log = "x") ##(2) - produce Fig. 4 from Bos & Wallinga (2012) ##load data data(ExampleData.CW_OSL_Curve, envir = environment()) values <- CW_Curve.BosWallinga2012 ##open plot area plot(NA, NA, xlim = c(0.001,10), ylim = c(0,8000), ylab = "pseudo OSL (cts/0.01 s)", xlab = "t [s]", log = "x", main = "Fig. 4 - Bos & Wallinga (2012)") values.t <- CW2pLMi(values, P = 1/20) lines(values[1:length(values.t[,1]),1],CW2pLMi(values, P = 1/20)[,2], col = "red",lwd = 1.3) text(0.03,4500,"LM", col = "red", cex = .8) values.t <- CW2pHMi(values, delta = 40) lines(values[1:length(values.t[,1]),1], CW2pHMi(values, delta = 40)[,2], col = "black", lwd = 1.3) text(0.005,3000,"HM", cex = .8) values.t <- CW2pPMi(values, P = 1/10) lines(values[1:length(values.t[,1]),1], CW2pPMi(values, P = 1/10)[,2], col = "blue", lwd = 1.3) text(0.5,6500,"PM", col = "blue", cex = .8) ExampleData.Al2O3C Example Al2O3:C Measurement Data Description Measurement data obtained from measuring Al2O3:C chips at the IRAMAT-CRP2A, Université Bordeaux Montainge in 2017 on a Freiberg Instruments lexsyg SMART reader. The example data used in particular to allow test of the functions developed in framework of the work by Kreutzer et al., 2018. Format Two datasets comprising RLum.Analysis data imported using the function read_XSYG2R data_ITC: Measurement data to determine the irradiation time correction, the data can be analysed with the function analyse_Al2O3C_ITC data_CrossTalk: Measurement data obtained while estimating the irradiation cross-talk of the reader used for the experiments. The data can be analysed either with the function analyse_Al2O3C_CrossTalk or analyse_Al2O3C_Measurement ExampleData.BINfileData 125 Note From both datasets unneeded curves have been removed and the number of aliquots have been reduced to a required minimum to keep the file size small, but still being able to run the corresponding functions. References Kreutzer et al., 2018 (TODO) See Also analyse_Al2O3C_ITC, analyse_Al2O3C_CrossTalk, analyse_Al2O3C_Measurement Examples ##(1) curves data(ExampleData.Al2O3C, envir = environment()) plot_RLum(data_ITC[1:2]) ExampleData.BINfileData Example data from a SAR OSL and SAR TL measurement for the package Luminescence Description Example data from a SAR OSL and TL measurement for package Luminescence directly extracted from a Risoe BIN-file and provided in an object of type Risoe.BINfileData Format CWOSL.SAR.Data: SAR OSL measurement data TL.SAR.Data: SAR TL measurement data Each class object contains two slots: (a) METADATA is a data.frame with all metadata stored in the BIN file of the measurements and (b) DATA contains a list of vectors of the measured data (usually count values). Version 0.1 Note Please note that this example data cannot be exported to a BIN-file using the function writeR2BIN as it was generated and implemented in the package long time ago. In the meantime the BIN-file format changed. Source CWOSL.SAR.Data 126 ExampleData.CW_OSL_Curve Lab: Lab-Code: Location: Material: Reference: Luminescence Laboratory Bayreuth BT607 Saxony/Germany Middle grain quartz measured on aluminum cups on a Risoe TL/OSL DA-15 reader unpublished TL.SAR.Data Lab: Lab-Code: Location: Material: Setup: Reference: Remarks: Luminescence Laboratory of Cologne LP1_5 Spain Flint Risoe TL/OSL DA-20 reader (Filter: Semrock Brightline, HC475/50, N2, unpolished steel discs) unpublished dataset limited to one position References CWOSL.SAR.Data: unpublished data TL.SAR.Data: unpublished data Examples ## show first 5 elements of the METADATA and DATA elements in the terminal data(ExampleData.BINfileData, envir = environment()) CWOSL.SAR.Data@METADATA[1:5,] CWOSL.SAR.Data@DATA[1:5] ExampleData.CW_OSL_Curve Example CW-OSL curve data for the package Luminescence Description data.frame containing CW-OSL curve data (time, counts) Format Data frame with 1000 observations on the following 2 variables: list("x") a numeric vector, time list("y") a numeric vector, counts Source ExampleData.CW_OSL_Curve Lab: Lab-Code: Location: Material: Reference: Luminescence Laboratory Bayreuth BT607 Saxony/Germany Middle grain quartz measured on aluminum cups on a Risoe TL/OSL DA-15 reader. unpublished data ExampleData.DeValues 127 CW_Curve.BosWallinga2012 Lab: Lab-Code: Location: Material: Reference: Netherlands Centre for Luminescence Dating (NCL) NCL-2108077 Guadalentin Basin, Spain Coarse grain quartz Bos & Wallinga (2012) and Baartman et al. (2011) References Baartman, J.E.M., Veldkamp, A., Schoorl, J.M., Wallinga, J., Cammeraat, L.H., 2011. Unravelling Late Pleistocene and Holocene landscape dynamics: The Upper Guadalentin Basin, SE Spain. Geomorphology, 125, 172-185. Bos, A.J.J. & Wallinga, J., 2012. How to visualize quartz OSL signal components. Radiation Measurements, 47, 752-758. Examples data(ExampleData.CW_OSL_Curve, envir = environment()) plot(ExampleData.CW_OSL_Curve) ExampleData.DeValues Example De data sets for the package Luminescence Description Equivalent dose (De) values measured for a fine grain quartz sample from a loess section in Rottewitz (Saxony/Germany) and for a coarse grain quartz sample from a fluvial deposit in the rock shelter of Cueva Anton (Murcia/Spain). Format A list with two elements, each containing a two column data.frame: $BT998: De and De error values for a fine grain quartz sample from a loess section in Rottewitz. $CA1: Single grain De and De error values for a coarse grain quartz sample from a fluvial deposit in the rock shelter of Cueva Anton References BT998 Unpublished data CA1 Burow, C., Kehl, M., Hilgers, A., Weniger, G.-C., Angelucci, D., Villaverde, V., Zapata, J. and Zilhao, J. (2015). Luminescence dating of fluvial deposits in the rock shelter of Cueva Anton, Spain. Geochronometria 52, 107-125. BT998 128 ExampleData.Fading Lab: Lab-Code: Location: Material: Units: Dose Rate: Measurement Date: Luminescence Laboratory Bayreuth BT998 Rottewitz (Saxony/Germany) Fine grain quartz measured on aluminum discs on a Risoe TL/OSL DA-15 reader Values are given in seconds Dose rate of the beta-source at measurement ca. 0.0438 Gy/s +/- 0.0019 Gy/s 2012-01-27 CA1 Lab: Lab-Code: Location: Material: Units: Measurement Date: Cologne Luminescence Laboratory (CLL) C-L2941 Cueva Anton (Murcia/Spain) Coarse grain quartz (200-250 microns) measured on single grain discs on a Risoe TL/OSL DA-20 re Values are given in Gray 2012 Examples ##(1) plot values as histogram data(ExampleData.DeValues, envir = environment()) plot_Histogram(ExampleData.DeValues$BT998, xlab = "De [s]") ##(2) plot values as histogram (with second to gray conversion) data(ExampleData.DeValues, envir = environment()) De.values <- Second2Gray(ExampleData.DeValues$BT998, dose.rate = c(0.0438, 0.0019)) plot_Histogram(De.values, xlab = "De [Gy]") ExampleData.Fading Example data for feldspar fading measurements Description Example data set for fading measurements of the IR50, IR100, IR150 and IR225 feldspar signals of sample UNIL/NB123. It further contains regular equivalent dose measurement data of the same sample, which can be used to apply a fading correction to. Format A list with two elements, each containing a further list of data.frames containing the data on the fading and equivalent dose measurements: $fading.data: A named list of data.frames, each having three named columns (LxTx, LxTx.error, timeSinceIr ..$IR50: Fading data of the IR50 signal. ..$IR100: Fading data of the IR100 signal. ..$IR150: Fading data of the IR150 signal. ExampleData.Fading 129 ..$IR225: Fading data of the IR225 signal. $equivalentDose.data: A named of data.frames, each having three named columns (dose, LxTx, LxTx.error). ..$IR50: Equivalent dose measurement data of the IR50 signal. ..$IR100: Equivalent dose measurement data of the IR100 signal. ..$IR150: Equivalent dose measurement data of the IR150 signal. ..$IR225: Equivalent dose measurement data of the IR225 signal. Source These data were kindly provided by Georgina King. Detailed information on the sample UNIL/NB123 can be found in the reference given below. The raw data can be found in the accompanying supplementary information. References King, G.E., Herman, F., Lambert, R., Valla, P.G., Guralnik, B., 2016. Multi-OSL-thermochronometry of feldspar. Quaternary Geochronology 33, 76-87. doi:10.1016/j.quageo.2016.01.004 Details Lab: Lab-Code: Location: Material: Units: Lab Dose Rate: Environmental Dose Rate: University of Lausanne UNIL/NB123 Namche Barwa (eastern Himalaya) Coarse grained (180-212 microns) potassium feldspar Values are given in seconds Dose rate of the beta-source at measurement ca. 0.1335 +/- 0.004 Gy/s 7.00 +/- 0.92 Gy/ka (includes internal dose rate) Examples ## Load example data data("ExampleData.Fading", envir = environment()) ## Get fading measurement data of the IR50 signal IR50_fading <- ExampleData.Fading$fading.data$IR50 head(IR50_fading) ## Determine g-value and rho' for the IR50 signal IR50_fading.res <- analyse_FadingMeasurement(IR50_fading) ## Show g-value and rho' results gval <- get_RLum(IR50_fading.res) rhop <- get_RLum(IR50_fading.res, "rho_prime") gval rhop ## Get LxTx values of the IR50 DE measurement IR50_De.LxTx <- ExampleData.Fading$equivalentDose.data$IR50 ## Calculate the De of the IR50 signal IR50_De <- plot_GrowthCurve(IR50_De.LxTx, mode = "interpolation", 130 ExampleData.FittingLM fit.method = "EXP") ## Extract the calculated De and its error IR50_De.res <- get_RLum(IR50_De) De <- c(IR50_De.res$De, IR50_De.res$De.Error) ## Apply fading correction (age conversion greatly simplified) IR50_Age <- De / 7.00 IR50_Age.corr <- calc_FadingCorr(IR50_Age, g_value = IR50_fading.res) ExampleData.FittingLM Example data for fit_LMCurve() in the package Luminescence Description Lineraly modulated (LM) measurement data from a quartz sample from Norway including background measurement. Measurements carried out in the luminescence laboratory at the University of Bayreuth. Format Two objects (data.frames) with two columns (time and counts). Source Lab: Lab-Code: Location: Material: Luminescence Laboratory Bayreuth BT900 Norway Beach deposit, coarse grain quartz measured on aluminum discs on a Risoe TL/OSL DA-15 reader References Fuchs, M., Kreutzer, S., Fischer, M., Sauer, D., Soerensen, R., 2012. OSL and IRSL dating of raised beach sand deposits along the southeastern coast of Norway. Quaternary Geochronology, 10, 195-200. Examples ##show LM data data(ExampleData.FittingLM, envir = environment()) plot(values.curve,log="x") ExampleData.LxTxOSLData ExampleData.LxTxData 131 Example Lx/Tx data from CW-OSL SAR measurement Description LxTx data from a SAR measurement for the package Luminescence. Format A data.frame with 4 columns (Dose, LxTx, LxTx.Error, TnTx). Source Lab: Lab-Code: Location: Material: Luminescence Laboratory Bayreuth BT607 Ostrau (Saxony-Anhalt/Germany) Middle grain (38-63 µm) quartz measured on a Risoe TL/OSL DA-15 reader. References unpublished data Examples ## plot Lx/Tx data vs dose [s] data(ExampleData.LxTxData, envir = environment()) plot(LxTxData$Dose,LxTxData$LxTx) ExampleData.LxTxOSLData Example Lx and Tx curve data from an artificial OSL measurement Description Lx and Tx data of continous wave (CW-) OSL signal curves. Format Two data.frames containing time and count values. Source Arbitrary OSL measurement. 132 ExampleData.RLum.Analysis References unpublished data Examples ##load data data(ExampleData.LxTxOSLData, envir = environment()) ##plot data plot(Lx.data) plot(Tx.data) ExampleData.portableOSL Example portable OSL curve data for the package Luminescence Description A list of RLum.Analysis objects, each containing the same number of RLum.Data.Curve objects representing individual OSL, IRSL and dark count measurements of a sample. Source ExampleData.portableOSL Lab: Lab-Code: Location: Material: Reference: Cologne Luminescence Laboratory Nievenheim/Germany Fine grain quartz unpublished data Examples data(ExampleData.portableOSL, envir = environment()) plot_RLum(ExampleData.portableOSL) ExampleData.RLum.Analysis Example data as RLum.Analysis objects Description Collection of different RLum.Analysis objects for protocol analysis. ExampleData.RLum.Data.Image 133 Format IRSAR.RF.Data: IRSAR.RF.Data on coarse grain feldspar Each object contains data needed for the given protocol analysis. Version 0.1 Source IRSAR.RF.Data These data were kindly provided by Tobias Lauer and Matthias Krbetschek. Lab: Lab-Code: Location: Material: Reference: Luminescence Laboratory TU Bergakademie Freiberg ZEU/SA1 Zeuchfeld (Zeuchfeld Sandur; Saxony-Anhalt/Germany) K-feldspar (130-200 µm) Kreutzer et al. (2014) References IRSAR.RF.Data Kreutzer, S., Lauer, T., Meszner, S., Krbetschek, M.R., Faust, D., Fuchs, M., 2014. Chronology of the Quaternary profile Zeuchfeld in Saxony-Anhalt / Germany - a preliminary luminescence dating study. Zeitschrift fuer Geomorphologie 58, 5-26. doi: 10.1127/0372-8854/2012/S-00112 Examples ##load data data(ExampleData.RLum.Analysis, envir = environment()) ##plot data plot_RLum(IRSAR.RF.Data) ExampleData.RLum.Data.Image Example data as RLum.Data.Image objects Description Measurement of Princton Instruments camera imported with the function read_SPE2R to R to produce an RLum.Data.Image object. Format Object of class RLum.Data.Image Version 0.1 134 ExampleData.SurfaceExposure Source ExampleData.RLum.Data.Image These data were kindly provided by Regina DeWitt. Lab.: Lab-Code: Location: Material: Reference: Department of Physics, East-Carolina University, NC, USA - Image data is a measurement of fluorescent ceiling lights with a cooled Princeton Instruments (TM) camera fitted on Risoe DA-20 TL/OSL reader. Examples ##load data data(ExampleData.RLum.Data.Image, envir = environment()) ##plot data plot_RLum(ExampleData.RLum.Data.Image) ExampleData.SurfaceExposure Example OSL surface exposure dating data Description A set of synthetic OSL surface exposure dating data to demonstrate the fit_SurfaceExposure functionality. See examples to reproduce the data interactively. Format A list with 4 elements: Element $sample_1 $sample_2 $set_1 $set_2 Content A data.frame with 3 columns (depth, intensity, error) A data.frame with 3 columns (depth, intensity, error) A list of 4 data.frames, each representing a sample with different ages A list of 5 data.frames, each representing a sample with different ages Details $sample_1 mu 0.9 sigmaphi 5e-10 age 10000 ExampleData.SurfaceExposure 135 $sample_2 mu 0.9 sigmaphi 5e-10 age 10000 Dose rate 2.5 D0 40 $set_1 mu 0.9 sigmaphi 5e-10 ages 1e3, 1e4, 1e5, 1e6 $set_2 mu 0.9 sigmaphi 5e-10 ages 1e2, 1e3, 1e4, 1e5, 1e6 Dose rate 1.0 D0 40 Source See examples for the code used to create the data sets. References Unpublished synthetic data Examples ## ExampleData.SurfaceExposure$sample_1 sigmaphi <- 5e-10 age <- 10000 mu <- 0.9 x <- seq(0, 10, 0.1) fun <- exp(-sigmaphi * age * 365.25*24*3600 * exp(-mu * x)) set.seed(666) synth_1 <- data.frame(depth = x, intensity = jitter(fun, 1, 0.1), error = runif(length(x), 0.01, 0.2)) ## VALIDATE sample_1 fit_SurfaceExposure(synth_1, mu = mu, sigmaphi = sigmaphi) ## ExampleData.SurfaceExposure$sample_2 sigmaphi <- 5e-10 age <- 10000 mu <- 0.9 x <- seq(0, 10, 0.1) Ddot <- 2.5 / 1000 / 365.25 / 24 / 60 / 60 # 2.5 Gy/ka in Seconds D0 <- 40 fun <- (sigmaphi * exp(-mu * x) * 136 ExampleData.SurfaceExposure exp(-(age * 365.25*24*3600) * (sigmaphi * exp(-mu * x) + Ddot/D0)) + Ddot/D0) / (sigmaphi * exp(-mu * x) + Ddot/D0) set.seed(666) synth_2 <- data.frame(depth = x, intensity = jitter(fun, 1, 0.1), error = runif(length(x), 0.01, 0.2)) ## VALIDATE sample_2 fit_SurfaceExposure(synth_2, mu = mu, sigmaphi = sigmaphi, Ddot = 2.5, D0 = D0) ## ExampleData.SurfaceExposure$set_1 sigmaphi <- 5e-10 mu <- 0.9 x <- seq(0, 15, 0.2) age <- c(1e3, 1e4, 1e5, 1e6) set.seed(666) synth_3 <- vector("list", length = length(age)) for (i in 1:length(age)) { fun <- exp(-sigmaphi * age[i] * 365.25*24*3600 * exp(-mu * x)) synth_3[[i]] <- data.frame(depth = x, intensity = jitter(fun, 1, 0.05)) } ## VALIDATE set_1 fit_SurfaceExposure(synth_3, age = age, sigmaphi = sigmaphi) ## ExampleData.SurfaceExposure$set_2 sigmaphi <- 5e-10 mu <- 0.9 x <- seq(0, 15, 0.2) age <- c(1e2, 1e3, 1e4, 1e5, 1e6) Ddot <- 1.0 / 1000 / 365.25 / 24 / 60 / 60 # 2.0 Gy/ka in Seconds D0 <- 40 set.seed(666) synth_4 <- vector("list", length = length(age)) for (i in 1:length(age)) { fun <- (sigmaphi * exp(-mu * x) * exp(-(age[i] * 365.25*24*3600) * (sigmaphi * exp(-mu * x) + Ddot/D0)) + Ddot/D0) / (sigmaphi * exp(-mu * x) + Ddot/D0) } synth_4[[i]] <- data.frame(depth = x, intensity = jitter(fun, 1, 0.05)) ExampleData.XSYG 137 ## VALIDATE set_2 fit_SurfaceExposure(synth_4, age = age, sigmaphi = sigmaphi, D0 = D0, Ddot = 1.0) ## Not run: ExampleData.SurfaceExposure <- list( sample_1 = synth_1, sample_2 = synth_2, set_1 = synth_3, set_2 = synth_4 ) ## End(Not run) ExampleData.XSYG Example data for a SAR OSL measurement and a TL spectrum using a lexsyg reader Description Example data from a SAR OSL measurement and a TL spectrum for package Luminescence imported from a Freiberg Instruments XSYG file using the function read_XSYG2R. Format OSL.SARMeasurement: SAR OSL measurement data The data contain two elements: (a) $Sequence.Header is a data.frame with metadata from the measurement,(b) Sequence.Object contains an RLum.Analysis object for further analysis. TL.Spectrum: TL spectrum data RLum.Data.Spectrum object for further analysis. The spectrum was cleaned from cosmic-rays using the function apply_CosmicRayRemoval. Note that no quantum efficiency calibration was performed. Version 0.1 Source OSL.SARMeasurement Lab: Lab-Code: Location: Material: Reference: Luminescence Laboratory Giessen no code not specified Coarse grain quartz on steel cups on lexsyg research reader unpublished TL.Spectrum Lab: Lab-Code: Luminescence Laboratory Giessen BT753 138 ExampleData.XSYG Location: Material: Reference: Spectrum: Heating: Dolni Vestonice/Czech Republic Fine grain polymineral on steel cups on lexsyg rearch reader Fuchs et al., 2013 Integration time 19 s, channel time 20 s 1 K/s, up to 500 deg. C References Unpublished data measured to serve as example data for that package. Location origin of sample BT753 is given here: Fuchs, M., Kreutzer, S., Rousseau, D.D., Antoine, P., Hatte, C., Lagroix, F., Moine, O., Gauthier, C., Svoboda, J., Lisa, L., 2013. The loess sequence of Dolni Vestonice, Czech Republic: A new OSL-based chronology of the Last Climatic Cycle. Boreas, 42, 664–677. See Also read_XSYG2R, RLum.Analysis, RLum.Data.Spectrum, plot_RLum, plot_RLum.Analysis, plot_RLum.Data.Spectrum Examples ##show data data(ExampleData.XSYG, envir = environment()) ## ========================================= ##(1) OSL.SARMeasurement OSL.SARMeasurement ##show $Sequence.Object OSL.SARMeasurement$Sequence.Object ##grep OSL curves and plot the first curve OSLcurve <- get_RLum(OSL.SARMeasurement$Sequence.Object, recordType="OSL")[[1]] plot_RLum(OSLcurve) ## ========================================= ##(2) TL.Spectrum TL.Spectrum ##plot simple spectrum (2D) plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="contour", xlim = c(310,750), ylim = c(0,300), bin.rows=10, bin.cols = 1) ##plot 3d spectrum (uncomment for usage) # plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="persp", # xlim = c(310,750), ylim = c(0,300), bin.rows=10, # bin.cols = 1) extdata extdata 139 Collection of External Data Description Description and listing of data provided in the folder data/extdata Details The R package Luminescence includes a number of raw data files, which are mostly used in the example sections of appropriate functions. They are also used internally for testing corresponding functions using the testthat package (see files in tests/testthat/) to ensure their operational reliability. Accessibility If the R package Luminescence is installed correctly the preferred way to access and use these data from within R is as follows: system.file("extdata/ ", package = "Luminescence") Individual file descriptions »Daybreak_TestFile.DAT/.txt« Type: raw measurement data Device: Daybreak OSL/TL reader Measurement date: unknown Location: unknown Provided by: unknown Related R function(s): read_Daybreak2R() Reference: unknown »DorNie_0016.psl« Type: raw measurement data Device: SUERC portable OSL reader Measurement date: 19/05/2016 Location: Dormagen-Nievenheim, Germany Provided by: Christoph Burow (University of Cologne) Related R function(s): read_PSL2R() Reference: unpublished Additional information: Sample measured at an archaeological site near Dormagen-Nievenheim (Germany) during a practical course on Luminesence dating in 2016. »QNL84_2_bleached.txt, QNL84_2_unbleached.txt« Type: Test data for exponential fits Reference: Berger, G.W., Huntley, D.J., 1989. Test data for exponential fits. Ancient TL 7, 43-46. »STRB87_1_bleached.txt, STRB87_1_unbleached.txt« Type: Test data for exponential fits Reference: Berger, G.W., Huntley, D.J., 1989. Test data for exponential fits. Ancient TL 7, 43-46. 140 extract_IrradiationTimes extract_IrradiationTimes Extract Irradiation Times from an XSYG-file Description Extracts irradiation times, dose and times since last irradiation, from a Freiberg Instruments XSYGfile. These information can be further used to update an existing BINX-file. Usage extract_IrradiationTimes(object, file.BINX, recordType = c("irradiation (NA)", "IRSL (UVVIS)", "OSL (UVVIS)", "TL (UVVIS)"), compatibility.mode = TRUE, txtProgressBar = TRUE) Arguments object character, RLum.Analysis or list (required): path and file name of the XSYG file or an RLum.Analysis produced by the function read_XSYG2R; alternatively a list of RLum.Analysis can be provided. Note: If an RLum.Analysis is used, any input for the arguments file.BINX and recordType will be ignored! file.BINX character (optional): path and file name of an existing BINX-file. If a file name is provided the file will be updated with the information from the XSYG file in the same folder as the original BINX-file. Note: The XSYG and the BINX-file have to be originate from the same measurement! recordType character (with default): select relevant curves types from the XSYG file or RLum.Analysis object. As the XSYG-file format comprises much more information than usually needed for routine data analysis and allowed in the BINXfile format, only the relevant curves are selected by using the function get_RLum. The argument recordType works as described for this function. Note: A wrong selection will causes a function error. Please change this argument only if you have reasons to do so. compatibility.mode logical (with default): this option is parsed only if a BIN/BINX file is produced and it will reset all position values to a max. value of 48, cf.write_R2BIN txtProgressBar logical (with default): enables TRUE or disables FALSE the progression bars during import and export Details The function was written to compensate missing information in the BINX-file output of Freiberg Instruments lexsyg readers. As all information are available within the XSYG-file anyway, these information can be extracted and used for further analysis or/and to stored in a new BINX-file, which can be further used by other software, e.g., Analyst (Geoff Duller). Typical application example: g-value estimation from fading measurements using the Analyst or any other self written script. Beside the some simple data transformation steps the function applies the functions read_XSYG2R, read_BIN2R, write_R2BIN for data import and export. extract_IrradiationTimes 141 Value An RLum.Results object is returned with the following structure: .. $irr.times (data.frame) If a BINX-file path and name is set, the output will be additionally transferred into a new BINX-file with the function name as suffix. For the output the path of the input BINX-file itself is used. Note that this will not work if the input object is a file path to an XSYG-file, instead of a link to only one file. In this case the argument input for file.BINX is ignored. In the self call mode (input is a list of RLum.Analysis objects a list of RLum.Results is returned. Function version 0.3.1 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). extract_IrradiationTimes(): Extract Irradiation Times from an XSYG-file. Function version 0.3.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note The produced output object contains still the irradiation steps to keep the output transparent. However, for the BINX-file export this steps are removed as the BINX-file format description does not allow irradiations as separat sequences steps. BINX-file ’Time Since Irradiation’ value differs from the table output? The way the value ’Time Since Irradiation’ is defined differs. In the BINX-file the ’Time Since Irradiation’ is calculated as the ’Time Since Irradiation’ plus the ’Irradiation Time’. The table output returns only the real ’Time Since Irradiation’, i.e. time between the end of the irradiation and the next step. Negative values for TIMESINCELAS.STEP? Yes, this is possible and no bug, as in the XSYG-file multiple curves are stored for one step. Example: TL step may comprise three curves: • (a) counts vs. time, • (b) measured temperature vs. time and • (c) predefined temperature vs. time. Three curves, but they are all belonging to one TL measurement step, but with regard to the time stamps this could produce negative values as the important function (read_XSYG2R) do not change the order of entries for one step towards a correct time order. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References Duller, G.A.T., 2015. The Analyst software package for luminescence data: overview and recent improvements. Ancient TL 33, 35-42. 142 fit_CWCurve See Also RLum.Analysis, RLum.Results, Risoe.BINfileData, read_XSYG2R, read_BIN2R, write_R2BIN Examples ## (1) - example for your own data ## ## set files and run function # # file.XSYG <- file.choose() # file.BINX <- file.choose() # # output <- extract_IrradiationTimes(file.XSYG = file.XSYG, file.BINX = file.BINX) # get_RLum(output) # ## export results additionally to a CSV.file in the same directory as the XSYG-file # write.table(x = get_RLum(output), # file = paste0(file.BINX,"_extract_IrradiationTimes.csv"), # sep = ";", # row.names = FALSE) fit_CWCurve Nonlinear Least Squares Fit for CW-OSL curves [beta version] Description The function determines the weighted least-squares estimates of the component parameters of a CW-OSL signal for a given maximum number of components and returns various component parameters. The fitting procedure uses the nls function with the port algorithm. Usage fit_CWCurve(values, n.components.max, fit.failure_threshold = 5, fit.method = "port", fit.trace = FALSE, fit.calcError = FALSE, LED.power = 36, LED.wavelength = 470, cex.global = 0.6, sample_code = "Default", output.path, output.terminal = TRUE, output.terminalAdvanced = TRUE, plot = TRUE, ...) Arguments values RLum.Data.Curve or data.frame (required): x, y data of measured values (time and counts). See examples. n.components.max vector (optional): maximum number of components that are to be used for fitting. The upper limit is 7. fit.failure_threshold vector (with default): limits the failed fitting attempts. fit_CWCurve 143 fit.method character (with default): select fit method, allowed values: 'port' and 'LM'. 'port' uses the ’port’ routine usint the funtion nls 'LM' utilises the function nlsLM from the package minpack.lm and with that the Levenberg-Marquardt algorithm. fit.trace logical (with default): traces the fitting process on the terminal. fit.calcError logical (with default): calculate 1-sigma error range of components using confint LED.power numeric (with default): LED power (max.) used for intensity ramping in mW/cm^2. Note: The value is used for the calculation of the absolute photoionisation cross section. LED.wavelength numeric (with default): LED wavelength used for stimulation in nm. Note: The value is used for the calculation of the absolute photoionisation cross section. cex.global numeric (with default): global scaling factor. sample_code character (optional): sample code used for the plot and the optional output table (mtext). output.path character (optional): output path for table output containing the results of the fit. The file name is set automatically. If the file already exists in the directory, the values are appended. output.terminal logical (with default): terminal ouput with fitting results. output.terminalAdvanced logical (with default): enhanced terminal output. Requires output.terminal = TRUE. If output.terminal = FALSE no advanced output is possible. plot logical (with default): returns a plot of the fitted curves. ... further arguments and graphical parameters passed to plot. Details Fitting function The function for the CW-OSL fitting has the general form: y = I01 ∗ λ1 ∗ exp(−λ1 ∗ x)+, . . . , +I0i ∗ λi ∗ exp(−λi ∗ x) where 0 < i < 8 and λ is the decay constant and I0 the intial number of trapped electrons. (for the used equation cf. Boetter-Jensen et al., 2003, Eq. 2.31) Start values Start values are estimated automatically by fitting a linear function to the logarithmized input data set. Currently, there is no option to manually provide start parameters. Goodness of fit The goodness of the fit is given as pseudoR^2 value (pseudo coefficient of determination). According to Lave (1970), the value is calculated as: pseudoR2 = 1 − RSS/T SS where RSS = Residual Sum of Squares and T SS = T otal Sum of Squares 144 fit_CWCurve Error of fitted component parameters The 1-sigma error for the components is calculated using the function confint. Due to considerable calculation time, this option is deactived by default. In addition, the error for the components can be estimated by using internal R functions like summary. See the nls help page for more information. For details on the nonlinear regression in R, see Ritz & Streibig (2008). Value plot (optional) the fitted CW-OSL curves are returned as plot. table (optional) an output table (*.csv) with parameters of the fitted components is provided if the output.path is set. RLum.Results Beside the plot and table output options, an RLum.Results object is returned. fit: an nls object ($fit) for which generic R functions are provided, e.g. summary, confint, profile. For more details, see nls. output.table: a data.frame containing the summarised parameters including the error component.contribution.matrix: matrix containing the values for the component to sum contribution plot ($component.contribution.matrix). Matrix structure: Column 1 and 2: time and rev(time) values Additional columns are used for the components, two for each component, containing I0 and n0. The last columns cont. provide information on the relative component contribution for each time interval including the row sum for this values. object beside the plot and table output options, an RLum.Results object is returned. fit: an nls object ($fit) for which generic R functions are provided, e.g. summary, confint, profile. For more details, see nls. output.table: a data.frame containing the summarised parameters including the error component.contribution.matrix: matrix containing the values for the component to sum contribution plot ($component.contribution.matrix). Matrix structure: Column 1 and 2: time and rev(time) values Additional columns are used for the components, two for each component, containing I0 and n0. The last columns cont. provide information on the relative component contribution for each time interval including the row sum for this values. Function version 0.5.2 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). fit_CWCurve(): Nonlinear Least Squares Fit for CW-OSL curves [beta version]. Function version 0.5.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence fit_LMCurve 145 Note Beta version - This function has not been properly tested yet and should therefore not be used for publication purposes! The pseudo-R^2 may not be the best parameter to describe the goodness of the fit. The trade off between the n.components and the pseudo-R^2 value is currently not considered. The function does not ensure that the fitting procedure has reached a global minimum rather than a local minimum! Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References Boetter-Jensen, L., McKeever, S.W.S., Wintle, A.G., 2003. Optically Stimulated Luminescence Dosimetry. Elsevier Science B.V. Lave, C.A.T., 1970. The Demand for Urban Mass Transportation. The Review of Economics and Statistics, 52 (3), 320-323. Ritz, C. & Streibig, J.C., 2008. Nonlinear Regression with R. In: R. Gentleman, K. Hornik, G. Parmigiani, eds., Springer, p. 150. See Also fit_LMCurve, plot,nls, RLum.Data.Curve, RLum.Results, get_RLum, minpack.lm::nlsLM Examples ##load data data(ExampleData.CW_OSL_Curve, envir = environment()) ##fit data fit <- fit_CWCurve(values = ExampleData.CW_OSL_Curve, main = "CW Curve Fit", n.components.max = 4, log = "x") fit_LMCurve Nonlinear Least Squares Fit for LM-OSL curves Description The function determines weighted nonlinear least-squares estimates of the component parameters of an LM-OSL curve (Bulur 1996) for a given number of components and returns various component parameters. The fitting procedure uses the function nls with the port algorithm. 146 fit_LMCurve Usage fit_LMCurve(values, values.bg, n.components = 3, start_values, input.dataType = "LM", fit.method = "port", sample_code = "", sample_ID = "", LED.power = 36, LED.wavelength = 470, fit.trace = FALSE, fit.advanced = FALSE, fit.calcError = FALSE, bg.subtraction = "polynomial", verbose = TRUE, plot = TRUE, plot.BG = FALSE, ...) Arguments values RLum.Data.Curve or data.frame (required): x,y data of measured values (time and counts). See examples. values.bg RLum.Data.Curve or data.frame (optional): x,y data of measured values (time and counts) for background subtraction. n.components integer (with default): fixed number of components that are to be recognised during fitting (min = 1, max = 7). start_values data.frame (optional): start parameters for lm and xm data for the fit. If no start values are given, an automatic start value estimation is attempted (see details). input.dataType character (with default): alter the plot output depending on the input data: "LM" or "pLM" (pseudo-LM). See: CW2pLM fit.method character (with default): select fit method, allowed values: 'port' and 'LM'. 'port' uses the ’port’ routine usint the funtion nls 'LM' utilises the function nlsLM from the package minpack.lm and with that the Levenberg-Marquardt algorithm. sample_code character (optional): sample code used for the plot and the optional output table (mtext). sample_ID character (optional): additional identifier used as column header for the table output. LED.power numeric (with default): LED power (max.) used forintensity ramping in mW/cm^2. Note: This value is used for the calculation of the absolute photoionisation cross section. LED.wavelength numeric (with default): LED wavelength in nm used for stimulation. Note: This value is used for the calculation of the absolute photoionisation cross section. fit.trace logical (with default): traces the fitting process on the terminal. fit.advanced logical (with default): enables advanced fitting attempt for automatic start parameter recognition. Works only if no start parameters are provided. Note: It may take a while and it is not compatible with fit.method = "LM". fit.calcError logical (with default): calculate 1-sigma error range of components using confint. bg.subtraction character (with default): specifies method for background subtraction (polynomial, linear, channel, see Details). Note: requires input for values.bg. verbose logical (with default): terminal output with fitting results. plot logical (with default): returns a plot of the fitted curves. plot.BG logical (with default): returns a plot of the background values with the fit used for the background subtraction. ... Further arguments that may be passed to the plot output, e.g. xlab, xlab, main, log. fit_LMCurve 147 Details Fitting function The function for the fitting has the general form: y = (exp(0.5)∗Im1 ∗x/xm1 )∗exp(−x2 /(2∗xm21 ))+, . . . , +exp(0.5)∗Imi ∗x/xmi )∗exp(−x2 /(2∗xm2i )) where 1 < i < 8 This function and the equations for the conversion to b (detrapping probability) and n0 (proportional to initially trapped charge) have been taken from Kitis et al. (2008): xmi = p max(t)/bi Imi = exp(−0.5)n0/xmi Background subtraction Three methods for background subtraction are provided for a given background signal (values.bg). • polynomial: default method. A polynomial function is fitted using glm and the resulting function is used for background subtraction: y = a ∗ x4 + b ∗ x3 + c ∗ x2 + d ∗ x + e • linear: a linear function is fitted using glm and the resulting function is used for background subtraction: y =a∗x+b • channel: the measured background signal is subtracted channelwise from the measured signal. Start values The choice of the initial parameters for the nls-fitting is a crucial point and the fitting procedure may mainly fail due to ill chosen start parameters. Here, three options are provided: (a) If no start values (start_values) are provided by the user, a cheap guess is made by using the detrapping values found by Jain et al. (2003) for quartz for a maximum of 7 components. Based on these values, the pseudo start parameters xm and Im are recalculated for the given data set. In all cases, the fitting starts with the ultra-fast component and (depending on n.components) steps through the following values. If no fit could be achieved, an error plot (for plot = TRUE) with the pseudo curve (based on the pseudo start parameters) is provided. This may give the opportunity to identify appropriate start parameters visually. (b) If start values are provided, the function works like a simple nls fitting approach. (c) If no start parameters are provided and the option fit.advanced = TRUE is chosen, an advanced start paramter estimation is applied using a stochastical attempt. Therefore, the recalculated start parameters (a) are used to construct a normal distribution. The start parameters are then sampled randomly from this distribution. A maximum of 100 attempts will be made. Note: This process may be time consuming. Goodness of fit The goodness of the fit is given by a pseudoR^2 value (pseudo coefficient of determination). According to Lave (1970), the value is calculated as: pseudoR2 = 1 − RSS/T SS 148 fit_LMCurve where RSS = Residual Sum of Squares and T SS = T otal Sum of Squares Error of fitted component parameters The 1-sigma error for the components is calculated using the function confint. Due to considerable calculation time, this option is deactived by default. In addition, the error for the components can be estimated by using internal R functions like summary. See the nls help page for more information. For more details on the nonlinear regression in R, see Ritz & Streibig (2008). Value Various types of plots are returned. For details see above. Furthermore an RLum.Results object is returned with the following structure: @data: .. $data : data.frame with fitting results .. $fit : nls (nls object) .. $component.contribution.matrix : list component distribution matrix info: .. $call : call the original function call Matrix structure for the distribution matrix: Column 1 and 2: time and rev(time) values Additional columns are used for the components, two for each component, containing I0 and n0. The last columns cont. provide information on the relative component contribution for each time interval including the row sum for this values. Function version 0.3.2 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). fit_LMCurve(): Nonlinear Least Squares Fit for LM-OSL curves. Function version 0.3.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note The pseudo-R^2 may not be the best parameter to describe the goodness of the fit. The trade off between the n.components and the pseudo-R^2 value currently remains unconsidered. The function does not ensure that the fitting procedure has reached a global minimum rather than a local minimum! In any case of doubt, the use of manual start values is highly recommended. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team fit_SurfaceExposure 149 References Bulur, E., 1996. An Alternative Technique For Optically Stimulated Luminescence (OSL) Experiment. Radiation Measurements, 26, 5, 701-709. Jain, M., Murray, A.S., Boetter-Jensen, L., 2003. Characterisation of blue-light stimulated luminescence components in different quartz samples: implications for dose measurement. Radiation Measurements, 37 (4-5), 441-449. Kitis, G. & Pagonis, V., 2008. Computerized curve deconvolution analysis for LM-OSL. Radiation Measurements, 43, 737-741. Lave, C.A.T., 1970. The Demand for Urban Mass Transportation. The Review of Economics and Statistics, 52 (3), 320-323. Ritz, C. & Streibig, J.C., 2008. Nonlinear Regression with R. R. Gentleman, K. Hornik, & G. Parmigiani, eds., Springer, p. 150. See Also fit_CWCurve, plot, nls, minpack.lm::nlsLM, get_RLum Examples ##(1) fit LM data without background subtraction data(ExampleData.FittingLM, envir = environment()) fit_LMCurve(values = values.curve, n.components = 3, log = "x") ##(2) fit LM data with background subtraction and export as JPEG ## -alter file path for your preferred system ##jpeg(file = "~/Desktop/Fit_Output\%03d.jpg", quality = 100, ## height = 3000, width = 3000, res = 300) data(ExampleData.FittingLM, envir = environment()) fit_LMCurve(values = values.curve, values.bg = values.curveBG, n.components = 2, log = "x", plot.BG = TRUE) ##dev.off() ##(3) fit LM data with manual start parameters data(ExampleData.FittingLM, envir = environment()) fit_LMCurve(values = values.curve, values.bg = values.curveBG, n.components = 3, log = "x", start_values = data.frame(Im = c(170,25,400), xm = c(56,200,1500))) fit_SurfaceExposure Nonlinear Least Squares Fit for OSL surface exposure data Description This function determines the (weighted) least-squares estimates of the parameters of either eq. 1 in Sohbati et al. (2012a) or eq. 12 in Sohbati et al. (2012b) for a given OSL surface exposure data set (BETA). 150 fit_SurfaceExposure Usage fit_SurfaceExposure(data, sigmaphi = NULL, mu = NULL, age = NULL, Ddot = NULL, D0 = NULL, weights = FALSE, plot = TRUE, legend = TRUE, error_bars = TRUE, coord_flip = FALSE, ...) Arguments data data.frame or list (required): Measured OSL surface exposure data with the following structure: (optional) | depth (a.u.)| intensity | error | | [ ,1] | [ ,2] | [ ,3] | |-------------|-----------|-------| [1, ]| ~~~~ | ~~~~ | ~~~~ | [2, ]| ~~~~ | ~~~~ | ~~~~ | ... | ... | ... | ... | [x, ]| ~~~~ | ~~~~ | ~~~~ | Alternatively, a list of data.frames can be provided, where each data.frame has the same structure as shown above, with the exception that they must not include the optional error column. Providing a list as input automatically activates the global fitting procedure (see details). sigmaphi numeric (optional): A numeric value for sigmaphi, i.e. the charge detrapping rate. Example: sigmaphi = 5e-10 mu numeric (optional): A numeric value for mu, i.e. the light attenuation coefficient. Example: mu = 0.9 age numeric (optional): The age (a) of the sample, if known. If data is a list of x samples, then age must be a numeric vector of length x. Example: age = 10000, or age = c(1e4, 1e5, 1e6). Ddot numeric (optional): A numeric value for the environmental dose rate (Gy/ka). For this argument to be considered a value for D0 must also be provided; otherwise it will be ignored. D0 numeric (optional): A numeric value for the characteristic saturation dose (Gy). For this argument to be considered a value for Ddot must also be provided; otherwise it will be ignored. weights logical (optional): If TRUE the fit will be weighted by the inverse square of the error. Requires data to be a data.frame with three columns. plot logical (optional): Show or hide the plot. legend logical (optional): Show or hide the equation inside the plot. error_bars logical (optional): Show or hide error bars (only applies if errors were provided). coord_flip logical (optional): Flip the coordinate system. ... Further parameters passed to plot. Custom parameters include: • • • • verbose (logical): show or hide console output line_col: Color of the fitted line line_lty: Type of the fitted line (see lty in ?par) line_lwd: Line width of the fitted line (see lwd in ?par) fit_SurfaceExposure 151 Details Weighted fitting If weights = TRUE the function will use the inverse square of the error (1/σ 2 ) as weights during fitting using minpack.lm::nlsLM. Naturally, for this to take effect individual errors must be provided in the third column of the data.frame for data. Weighted fitting is not supported if data is a list of multiple data.frames, i.e., it is not available for global fitting. Dose rate If any of the arguments Ddot or D0 is at its default value (NULL), this function will fit eq. 1 in Sohbati et al. (2012a) to the data. If the effect of dose rate (i.e., signal saturation) needs to be considered, numeric values for the dose rate (Ddot) (in Gy/ka) and the characteristic saturation dose (D0) (in Gy) must be provided. The function will then fit eq. 12 in Sohbati et al. (2012b) to the data. NOTE: Currently, this function does not consider the variability of the dose rate with sample depth (x)! In the original equation the dose rate D is an arbitrary function of x (term D(x)), but here D is assumed constant. Global fitting If data is list of multiple data.frames, each representing a separate sample, the function automatically performs a global fit to the data. This may be useful to better constrain the parameters sigmaphi or mu and requires that known ages for each sample is provided (e.g., age = c(100, 1000) if data is a list with two samples). Value Function returns results numerically and graphically: ———————————– [ NUMERICAL OUTPUT ] ———————————– RLum.Results-object slot: @data Element $summary $data $fit $args $call Type data.frame data.frame nls character call Description summary of the fitting results the original input data the fitting object produced by minpack.lm::nlsLM arguments of the call the original function call slot: @info Currently unused. ———————— [ PLOT OUTPUT ] ———————— A scatter plot of the provided depth-intensity OSL surface exposure data with the fitted model. Function version 0.1.0 (2018-01-21 17:22:38) 152 fit_SurfaceExposure How to cite Burow, C. (2018). fit_SurfaceExposure(): Nonlinear Least Squares Fit for OSL surface exposure data. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note This function has BETA status. If possible, results should be cross-checked. Author(s) Christoph Burow, University of Cologne (Germany) R Luminescence Package Team References Sohbati, R., Murray, A.S., Chapot, M.S., Jain, M., Pederson, J., 2012a. Optically stimulated luminescence (OSL) as a chronometer for surface exposure dating. Journal of Geophysical Research 117, B09202. doi:10.1029/2012JB009383 Sohbati, R., Jain, M., Murray, A.S., 2012b. Surface exposure dating of non-terrestial bodies using optically stimulated luminescence: A new method. Icarus 221, 160-166. See Also ExampleData.SurfaceExposure, minpack.lm::nlsLM Examples ## Load example data data("ExampleData.SurfaceExposure") ## Example 1 - Single sample # Known parameters: 10000 a, mu = 0.9, sigmaphi = 5e-10 sample_1 <- ExampleData.SurfaceExposure$sample_1 head(sample_1) results <- fit_SurfaceExposure(sample_1, mu = 0.9, sigmaphi = 5e-10) get_RLum(results) ## Example 2 - Single sample and considering dose rate # Known parameters: 10000 a, mu = 0.9, sigmaphi = 5e-10, # dose rate = 2.5 Gy/ka, D0 = 40 Gy sample_2 <- ExampleData.SurfaceExposure$sample_2 head(sample_2) results <- fit_SurfaceExposure(sample_2, mu = 0.9, sigmaphi = 5e-10, Ddot = 2.5, D0 = 40) get_RLum(results) ## Example 3 - Multiple samples (global fit) to better constrain 'mu' # Known parameters: ages = 1e3, 1e4, 1e5, 1e6 a, mu = 0.9, sigmaphi = 5e-10 set_1 <- ExampleData.SurfaceExposure$set_1 str(set_1, max.level = 2) get_Layout 153 results <- fit_SurfaceExposure(set_1, age = c(1e3, 1e4, 1e5, 1e6), sigmaphi = 5e-10) get_RLum(results) ## Example 4 - Multiple samples (global fit) and considering dose rate # Known parameters: ages = 1e2, 1e3, 1e4, 1e5, 1e6 a, mu = 0.9, sigmaphi = 5e-10, # dose rate = 1.0 Ga/ka, D0 = 40 Gy set_2 <- ExampleData.SurfaceExposure$set_2 str(set_2, max.level = 2) results <- fit_SurfaceExposure(set_2, age = c(1e2, 1e3, 1e4, 1e5, 1e6), sigmaphi = 5e-10, Ddot = 1, D0 = 40) get_RLum(results) get_Layout Collection of layout definitions Description This helper function returns a list with layout definitions for homogeneous plotting. Usage get_Layout(layout) Arguments layout character or list object (required): name of the layout definition to be returned. If name is provided the respective definition is returned. One of the following supported layout definitions is possible: "default", "journal.1", "small", "empty". User-specific layout definitions must be provided as a list object of predefined structure, see details. Details The easiest way to create a user-specific layout definition is perhaps to create either an empty or a default layout object and fill/modify the definitions (user.layout <- get_Layout(data = "empty")). Value A list object with layout definitions for plot functions. Function version 0.1 (2018-01-21 17:22:38) How to cite Dietze, M. (2018). get_Layout(): Collection of layout definitions. Function version 0.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence 154 get_Quote Author(s) Michael Dietze, GFZ Potsdam (Germany) R Luminescence Package Team Examples ## read example data set data(ExampleData.DeValues, envir = environment()) ## show structure of the default layout definition layout.default <- get_Layout(layout = "default") str(layout.default) ## show colour definitions for Abanico plot, only layout.default$abanico$colour ## set Abanico plot title colour to orange layout.default$abanico$colour$main <- "orange" ## create Abanico plot with modofied layout definition plot_AbanicoPlot(data = ExampleData.DeValues, layout = layout.default) ## create Abanico plot with predefined layout "journal" plot_AbanicoPlot(data = ExampleData.DeValues, layout = "journal") get_Quote Function to return essential quotes Description This function returns one of the collected essential quotes in the growing library. If called without any parameters, a random quote is returned. Usage get_Quote(ID, separated = FALSE) Arguments ID character (optional): qoute ID to be returned. separated logical (with default): return result in separated form. Value Returns a character with quote and respective (false) author. Function version 0.1.2 (2018-01-21 17:22:38) get_rightAnswer 155 How to cite Dietze, M. (2018). get_Quote(): Function to return essential quotes. Function version 0.1.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Michael Dietze, GFZ Potsdam (Germany) R Luminescence Package Team Examples ## ask for an arbitrary qoute get_Quote() get_rightAnswer Function to get the right answer Description This function returns just the right answer Usage get_rightAnswer(...) Arguments ... you can pass an infinite number of further arguments Value Returns the right answer Function version 0.1.0 (2018-01-21 17:22:38) How to cite NA, NA, , (2018). get_rightAnswer(): Function to get the right answer. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) inspired by R.G. R Luminescence Package Team 156 get_Risoe.BINfileData Examples ## you really want to know? get_rightAnswer() get_Risoe.BINfileData General accessor function for RLum S4 class objects Description Function calls object-specific get functions for RisoeBINfileData S4 class objects. Usage get_Risoe.BINfileData(object, ...) Arguments object Risoe.BINfileData (required): S4 object of class RLum ... further arguments that one might want to pass to the specific get function Details The function provides a generalised access point for specific Risoe.BINfileData objects. Depending on the input object, the corresponding get function will be selected. Allowed arguments can be found in the documentations of the corresponding Risoe.BINfileData class. Value Return is the same as input objects as provided in the list Function version 0.1.0 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). get_Risoe.BINfileData(): General accessor function for RLum S4 class objects. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also Risoe.BINfileData get_RLum 157 get_RLum General accessor function for RLum S4 class objects Description Function calls object-specific get functions for RLum S4 class objects. Method to handle NULL if the user calls get_RLum Usage get_RLum(object, ...) ## S4 method for signature 'list' get_RLum(object, null.rm = FALSE, ...) ## S4 method for signature '`NULL`' get_RLum(object, ...) Arguments object ... null.rm RLum (required): S4 object of class RLum or an object of type list containing only objects of type RLum further arguments that will be passed to the object specific methods. For furter details on the supported arguments please see the class documentation: RLum.Data.Curve, RLum.Data.Spectrum, RLum.Data.Image, RLum.Analysis and RLum.Results logical (with default): option to get rid of empty and NULL objects Details The function provides a generalised access point for specific RLum objects. Depending on the input object, the corresponding get function will be selected. Allowed arguments can be found in the documentations of the corresponding RLum class. Value Return is the same as input objects as provided in the list. Methods (by class) • list: Returns a list of RLum objects that had been passed to get_RLum • NULL: Returns NULL Function version 0.3.2 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). get_RLum(): General accessor function for RLum S4 class objects. Function version 0.3.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence 158 GitHub-API Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also RLum.Data.Curve, RLum.Data.Image, RLum.Data.Spectrum, RLum.Analysis, RLum.Results Examples ##Example based using data and from the calc_CentralDose() function ##load example data data(ExampleData.DeValues, envir = environment()) ##apply the central dose model 1st time temp1 <- calc_CentralDose(ExampleData.DeValues$CA1) ##get results and store them in a new object temp.get <- get_RLum(object = temp1) GitHub-API GitHub API Description R Interface to the GitHub API v3. Usage github_commits(user = "r-lum", repo = "luminescence", branch = "master", n = 5) github_branches(user = "r-lum", repo = "luminescence") github_issues(user = "r-lum", repo = "luminescence", verbose = TRUE) Arguments user character (with default): GitHub user name (defaults to ’r-lum’). repo character (with default): name of a GitHub repository (defaults to ’luminescence’). branch character (with default): branch of a GitHub repository (defaults to ’master’). n integer (with default): number of commits returned (defaults to 5). verbose logical (with default): print the output to the console (defaults to TRUE). GitHub-API 159 Details These functions can be used to query a specific repository hosted on GitHub. github_commits lists the most recent n commits of a specific branch of a repository. github_branches can be used to list all current branches of a repository and returns the corresponding SHA hash as well as an installation command to install the branch in R via the ’devtools’ package. github_issues lists all open issues for a repository in valid YAML. Value github_commits: data.frame with columns: [ ,1] [ ,2] [ ,3] [ ,4] SHA AUTHOR DATE MESSAGE github_branches: data.frame with columns: [ ,1] [ ,2] [ ,3] BRANCH SHA INSTALL github_commits: Nested list with n elements. Each commit element is a list with elements: [[1]] [[2]] [[3]] [[4]] [[5]] [[6]] [[7]] [[8]] NUMBER TITLE BODY CREATED UPDATED CREATOR URL STATUS [[1]: R:[1 [[2]: R:[2 [[3]: R:[3 [[4]: R:[4 [[5]: R:[5 [[6]: R:[6 [[7]: R:[7 [[8]: R:[8 Function version 0.1.0 How to cite Burow, C. (2018). GitHub-API(): GitHub API. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescen 160 install_DevelopmentVersion Author(s) Christoph Burow, University of Cologne (Germany) R Luminescence Package Team References GitHub Developer API v3. https://developer.github.com/v3/, last accessed: 10/01/2017. Examples ## Not run: github_branches(user = "r-lum", repo = "luminescence") github_issues(user = "r-lum", repo = "luminescence") github_commits(user = "r-lum", repo = "luminescence", branch = "master", n = 10) ## End(Not run) install_DevelopmentVersion Attempts to install the development version of the ’Luminescence’ package Description This function is a convenient method for installing the development version of the R package ’Luminescence’ directly from GitHub. Usage install_DevelopmentVersion(force_install = FALSE) Arguments force_install logical (optional): If FALSE (the default) the function produces and prints the required code to the console for the user to run manually afterwards. When TRUE and all requirements are fulfilled (see details) this function attempts to install the package itself. Details This function uses Luminescence::github_branches to check which development branches of the R package ’Luminescence’ are currently available on GitHub. The user is then prompted to choose one of the branches to be installed. It further checks whether the R package ’devtools’ is currently installed and available on the system. Finally, it prints R code to the console that the user can copy and paste to the R console in order to install the desired development version of the package. If force_install=TRUE the functions checks if ’devtools’ is available and then attempts to install the chosen development branch via devtools::install_github. length_RLum 161 Value This function requires user input at the command prompt to choose the desired development branch to be installed. The required R code to install the package is then printed to the console. Examples ## Not run: install_DevelopmentVersion() ## End(Not run) length_RLum General accessor function for RLum S4 class objects Description Function calls object-specific get functions for RLum S4 class objects. Usage length_RLum(object) Arguments object RLum (required): S4 object of class RLum Details The function provides a generalised access point for specific RLum objects. Depending on the input object, the corresponding get function will be selected. Allowed arguments can be found in the documentations of the corresponding RLum class. Value Return is the same as input objects as provided in the list. Function version 0.1.0 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). length_RLum(): General accessor function for RLum S4 class objects. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team 162 merge_Risoe.BINfileData See Also RLum.Data.Curve, RLum.Data.Image, RLum.Data.Spectrum, RLum.Analysis, RLum.Results merge_Risoe.BINfileData Merge Risoe.BINfileData objects or Risoe BIN-files Description Function allows merging Risoe BIN/BINX files or Risoe.BINfileData objects. Usage merge_Risoe.BINfileData(input.objects, output.file, keep.position.number = FALSE, position.number.append.gap = 0) Arguments input.objects character with Risoe.BINfileData objects (required): Character vector with path and files names (e.g. input.objects = c("path/file1.bin", "path/file2.bin") or Risoe.BINfileData objects (e.g. input.objects = c(object1, object2)). Alternatively a list is supported. output.file character (optional): File output path and name. If no value is given, a Risoe.BINfileData is returned instead of a file. keep.position.number logical (with default): Allows keeping the original position numbers of the input objects. Otherwise the position numbers are recalculated. position.number.append.gap integer (with default): Set the position number gap between merged BIN-file sets, if the option keep.position.number = FALSE is used. See details for further information. Details The function allows merging different measurements to one file or one object. The record IDs are recalculated for the new object. Other values are kept for each object. The number of input objects is not limited. position.number.append.gap option If the option keep.position.number = FALSE is used, the position numbers of the new data set are recalculated by adding the highest position number of the previous data set to the each position number of the next data set. For example: The highest position number is 48, then this number will be added to all other position numbers of the next data set (e.g. 1 + 48 = 49) However, there might be cases where an additional addend (summand) is needed before the next position starts. Example: • Position number set (A): 1,3,5,7 • Position number set (B): 1,3,5,7 With no additional summand the new position numbers would be: 1,3,5,7,8,9,10,11. That might be unwanted. Using the argument position.number.append.gap = 1 it will become: 1,3,5,7,9,11,13,15,17. merge_RLum 163 Value Returns a file or a Risoe.BINfileData object. Function version 0.2.7 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). merge_Risoe.BINfileData(): Merge Risoe.BINfileData objects or Risoe BINfiles. Function version 0.2.7. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note The validity of the output objects is not further checked. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References Duller, G., 2007. Analyst. See Also Risoe.BINfileData, read_BIN2R, write_R2BIN Examples ##merge two objects data(ExampleData.BINfileData, envir = environment()) object1 <- CWOSL.SAR.Data object2 <- CWOSL.SAR.Data object.new <- merge_Risoe.BINfileData(c(object1, object2)) merge_RLum General merge function for RLum S4 class objects Description Function calls object-specific merge functions for RLum S4 class objects. Usage merge_RLum(objects, ...) 164 merge_RLum Arguments objects list of RLum (required): list of S4 object of class RLum ... further arguments that one might want to pass to the specific merge function Details The function provides a generalised access point for merge specific RLum objects. Depending on the input object, the corresponding merge function will be selected. Allowed arguments can be found in the documentations of each merge function. Empty list elements (NULL) are automatically removed from the input list. object RLum.Data.Curve RLum.Analysis RLum.Results : : : corresponding merge function merge_RLum.Data.Curve merge_RLum.Analysis merge_RLum.Results Value Return is the same as input objects as provided in the list. Function version 0.1.2 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). merge_RLum(): General merge function for RLum S4 class objects. Function version 0.1.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note So far not for every RLum object a merging function exists. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also RLum.Data.Curve, RLum.Data.Image, RLum.Data.Spectrum, RLum.Analysis, RLum.Results Examples ##Example based using data and from the calc_CentralDose() function ##load example data data(ExampleData.DeValues, envir = environment()) ##apply the central dose model 1st time model_LuminescenceSignals 165 temp1 <- calc_CentralDose(ExampleData.DeValues$CA1) ##apply the central dose model 2nd time temp2 <- calc_CentralDose(ExampleData.DeValues$CA1) ##merge the results and store them in a new object temp.merged <- get_RLum(merge_RLum(objects = list(temp1, temp2))) model_LuminescenceSignals Model Luminescence Signals (wrapper) Description Wrapper for the function RLumModel::model_LuminescenceSignals from the package RLumModel::RLumModelpackage. For the further details and examples please see the manual of this package. Usage model_LuminescenceSignals(model, sequence, lab.dose_rate = 1, simulate_sample_history = FALSE, plot = TRUE, verbose = TRUE, show_structure = FALSE, own_parameters = NULL, own_state_parameters = NULL, own_start_temperature = NULL, ...) Arguments model character (required): set model to be used. Available models are: "Bailey2001", "Bailey2002", "Bailey2004", "Pagonis2007", "Pagonis2008", "Friedrich2017", "Friedrich2018" and for own models "customized" (or "customised"). Note: When model = "customized" is set, the argument ’own_parameters’ has to be set. sequence list (required): set sequence to model as list or as *.seq file from the Riso sequence editor. To simulate SAR measurements there is an extra option to set the sequence list (cf. details). lab.dose_rate numeric (with default): laboratory dose rate in XXX Gy/s for calculating seconds into Gray in the *.seq file. simulate_sample_history logical (with default): FALSE (with default): simulation begins at laboratory conditions, TRUE: simulations begins at crystallization (all levels 0) process plot logical (with default): Enables or disables plot output verbose logical (with default): Verbose mode on/off show_structure logical (with default): Shows the structure of the result. Recommended to show record.id to analyse concentrations. own_parameters list (with default): This argument allows the user to submit own parameter sets. The list has to contain the following items: • N: Concentration of electron- and hole traps [cm^(-3)] • E: Electron/Hole trap depth [eV 166 model_LuminescenceSignals • s: Frequency factor [s^(-1)] • A: Conduction band to electron trap and valence band to hole trap transition probability [s^(-1) * cm^(3)]. CAUTION: Not every publication uses the same definition of parameter A and B! See vignette "RLumModel Usage with own parameter sets" for further details • B: Conduction band to hole centre transition probability [s^(-1) * cm^(3)]. • Th: Photo-eviction constant or photoionisation cross section, respectively • E_th: Thermal assistence energy [eV] • k_B: Boltzman constant 8.617e-05 [eV/K] • W: activation energy 0.64 [eV] (for UV) • K: 2.8e7 (dimensionless constant) • model: "customized" • R (optional): Ionisation rate (pair production rate) equivalent to 1 Gy/s [s^(1) * cm^(-3)] For further details see Bailey 2001, Wintle 1975, vignette "RLumModel - Using own parameter sets" and example 3. own_state_parameters numeric (with default): Some publications (e.g. Pagonis 2009) offer state parameters. With this argument the user can submit this state parameters. For further details see vignette ""RLumModel - Using own parameter sets" and example 3. own_start_temperature numeric (with default): Parameter to control the start temperature (in deg. C) of a simulation. This parameter takes effect only when ’model = "customized"’ is choosen. ... further arguments and graphical parameters passed to plot.default. See details for further information. Function version 0.1.3 (2018-01-21 17:22:38) How to cite Friedrich, J., Kreutzer, S. (2018). model_LuminescenceSignals(): Model Luminescence Signals (wrapper). Function version 0.1.3. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Johannes Friedrich, University of Bayreuth (Germany) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaige (France) R Luminescence Package Team names_RLum 167 names_RLum S4-names function for RLum S4 class objects Description Function calls object-specific names functions for RLum S4 class objects. Usage names_RLum(object) Arguments object RLum (required): S4 object of class RLum Details The function provides a generalised access point for specific RLum objects. Depending on the input object, the corresponding ’names’ function will be selected. Allowed arguments can be found in the documentations of the corresponding RLum class. Value Returns a character Function version 0.1.0 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). names_RLum(): S4-names function for RLum S4 class objects. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also RLum.Data.Curve, RLum.Data.Image, RLum.Data.Spectrum, RLum.Analysis, RLum.Results 168 plot_AbanicoPlot plot_AbanicoPlot Function to create an Abanico Plot. Description A plot is produced which allows comprehensive presentation of data precision and its dispersion around a central value as well as illustration of a kernel density estimate, histogram and/or dot plot of the dose values. Usage plot_AbanicoPlot(data, na.rm = TRUE, log.z = TRUE, z.0 = "mean.weighted", dispersion = "qr", plot.ratio = 0.75, rotate = FALSE, mtext, summary, summary.pos, summary.method = "MCM", legend, legend.pos, stats, rug = FALSE, kde = TRUE, hist = FALSE, dots = FALSE, boxplot = FALSE, y.axis = TRUE, error.bars = FALSE, bar, bar.col, polygon.col, line, line.col, line.lty, line.label, grid.col, frame = 1, bw = "SJ", output = TRUE, interactive = FALSE, ...) Arguments data data.frame or RLum.Results object (required): for data.frame two columns: De (data[,1]) and De error (data[,2]). To plot several data sets in one plot the data sets must be provided as list, e.g. list(data.1, data.2). na.rm logical (with default): exclude NA values from the data set prior to any further operations. log.z logical (with default): Option to display the z-axis in logarithmic scale. Default is TRUE. z.0 character or numeric: User-defined central value, used for centering of data. One out of "mean", "mean.weighted" and "median" or a numeric value (not its logarithm). Default is "mean.weighted". dispersion character (with default): measure of dispersion, used for drawing the scatter polygon. One out of • • • • • "qr" (quartile range), "pnn" (symmetric percentile range with nn the lower percentile, e.g. "p05" depicting the range between 5 and 95 "sd" (standard deviation) and "2sd" (2 standard deviations), The default is "qr". Note that "sd" and "2sd" are only meaningful in combination with "z.0 = 'mean'" because the unweighted mean is used to center the polygon. plot.ratio numeric: Relative space, given to the radial versus the cartesian plot part, default is 0.75. rotate logical: Option to turn the plot by 90 degrees. mtext character: additional text below the plot title. summary character (optional): add statistic measures of centrality and dispersion to the plot. Can be one or more of several keywords. See details for available keywords. Results differ depending on the log-option for the z-scale (see details). plot_AbanicoPlot 169 summary.pos numeric or character (with default): optional position coordinates or keyword (e.g. "topright") for the statistical summary. Alternatively, the keyword "sub" may be specified to place the summary below the plot header. However, this latter option in only possible if mtext is not used. summary.method character (with default): keyword indicating the method used to calculate the statistic summary. One out of • "unweighted", • "weighted" and • "MCM". See calc_Statistics for details. legend character vector (optional): legend content to be added to the plot. legend.pos numeric or character (with default): optional position coordinates or keyword (e.g. "topright") for the legend to be plotted. stats character: additional labels of statistically important values in the plot. One or more out of the following: • "min", • "max", • "median". rug logical: Option to add a rug to the KDE part, to indicate the location of individual values. kde logical: Option to add a KDE plot to the dispersion part, default is TRUE. hist logical: Option to add a histogram to the dispersion part. Only meaningful when not more than one data set is plotted. dots logical: Option to add a dot plot to the dispersion part. If number of dots exceeds space in the dispersion part, a square indicates this. boxplot logical: Option to add a boxplot to the dispersion part, default is FALSE. y.axis logical: Option to hide y-axis labels. Useful for data with small scatter. error.bars logical: Option to show De-errors as error bars on De-points. Useful in combination with y.axis = FALSE, bar.col = "none". bar numeric (with default): option to add one or more dispersion bars (i.e., bar showing the 2-sigma range) centered at the defined values. By default a bar is drawn according to "z.0". To omit the bar set "bar = FALSE". bar.col character or numeric (with default): colour of the dispersion bar. Default is "grey60". polygon.col character or numeric (with default): colour of the polygon showing the data scatter. Sometimes this polygon may be omitted for clarity. To disable it use FALSE or polygon = FALSE. Default is "grey80". line numeric: numeric values of the additional lines to be added. line.col character or numeric: colour of the additional lines. line.lty integer: line type of additional lines line.label character: labels for the additional lines. grid.col character or numeric (with default): colour of the grid lines (originating at [0,0] and strechting to the z-scale). To disable grid lines use FALSE. Default is "grey". frame numeric (with default): option to modify the plot frame type. Can be one out of 170 plot_AbanicoPlot • • • • 0 (no frame), 1 (frame originates at 0,0 and runs along min/max isochrons), 2 (frame embraces the 2-sigma bar), 3 (frame embraces the entire plot as a rectangle). Default is 1. bw character (with default): bin-width for KDE, choose a numeric value for manual setting. output logical: Optional output of numerical plot parameters. These can be useful to reproduce similar plots. Default is TRUE. interactive logical (with default): create an interactive abanico plot (requires the ’plotly’ package) ... Further plot arguments to pass. xlab must be a vector of length 2, specifying the upper and lower x-axes labels. Details The Abanico Plot is a combination of the classic Radial Plot (plot_RadialPlot) and a kernel density estimate plot (e.g plot_KDE). It allows straightforward visualisation of data precision, error scatter around a user-defined central value and the combined distribution of the values, on the actual scale of the measured data (e.g. seconds, equivalent dose, years). The principle of the plot is shown in Galbraith & Green (1990). The function authors are thankful for the thoughtprovocing figure in this article. The semi circle (z-axis) of the classic Radial Plot is bent to a straight line here, which actually is the basis for combining this polar (radial) part of the plot with any other cartesian visualisation method (KDE, histogram, PDF and so on). Note that the plot allows dispaying two measures of distribution. One is the 2-sigma bar, which illustrates the spread in value errors, and the other is the polygon, which stretches over both parts of the Abanico Plot (polar and cartesian) and illustrates the actual spread in the values themselves. Since the 2-sigma-bar is a polygon, it can be (and is) filled with shaded lines. To change density (lines per inch, default is 15) and angle (default is 45 degrees) of the shading lines, specify these parameters. See ?polygon() for further help. The Abanico Plot supports other than the weighted mean as measure of centrality. When it is obvious that the data is not (log-)normally distributed, the mean (weighted or not) cannot be a valid measure of centrality and hence central dose. Accordingly, the median and the weighted median can be chosen as well to represent a proper measure of centrality (e.g. centrality = "median.weighted"). Also user-defined numeric values (e.g. from the central age model) can be used if this appears appropriate. The proportion of the polar part and the cartesian part of the Abanico Plot can be modfied for display reasons (plot.ratio = 0.75). By default, the polar part spreads over 75 % and leaves 25 % for the part that shows the KDE graph. A statistic summary, i.e. a collection of statistic measures of centrality and dispersion (and further measures) can be added by specifying one or more of the following keywords: • "n" (number of samples) • "mean" (mean De value) • "median" (median of the De values) • "sd.rel" (relative standard deviation in percent) • "sd.abs" (absolute standard deviation) plot_AbanicoPlot 171 • "se.rel" (relative standard error) • "se.abs" (absolute standard error) • "in.2s" (percent of samples in 2-sigma range) • "kurtosis" (kurtosis) • "skewness" (skewness) Note that the input data for the statistic summary is sent to the function calc_Statistics() depending on the log-option for the z-scale. If "log.z = TRUE", the summary is based on the logarithms of the input data. If "log.z = FALSE" the linearly scaled data is used. Note as well, that "calc_Statistics()" calculates these statistic measures in three different ways: unweighted, weighted and MCM-based (i.e., based on Monte Carlo Methods). By default, the MCM-based version is used. If you wish to use another method, indicate this with the appropriate keyword using the argument summary.method. The optional parameter layout allows to modify the entire plot more sophisticated. Each element of the plot can be addressed and its properties can be defined. This includes font type, size and decoration, colours and sizes of all plot items. To infer the definition of a specific layout style cf. get_Layout() or type eg. for the layout type "journal" get_Layout("journal"). A layout type can be modified by the user by assigning new values to the list object. It is possible for the z-scale to specify where ticks are to be drawn by using the parameter at, e.g. at = seq(80, 200, 20), cf. function documentation of axis. Specifying tick positions manually overrides a zlim-definition. Value returns a plot object and, optionally, a list with plot calculus data. Function version 0.1.10 (2018-01-21 17:22:38) How to cite Dietze, M., Kreutzer, S. (2018). plot_AbanicoPlot(): Function to create an Abanico Plot.. Function version 0.1.10. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Michael Dietze, GFZ Potsdam (Germany) Sebastian Kreutzer, RAMAT-CRP2A, Universite Bordeaux Montaigne (France) Inspired by a plot introduced by Galbraith & Green (1990) R Luminescence Package Team References Galbraith, R. & Green, P., 1990. Estimating the component ages in a finite mixture. International Journal of Radiation Applications and Instrumentation. Part D. Nuclear Tracks and Radiation Measurements, 17 (3), 197-206. Dietze, M., Kreutzer, S., Burow, C., Fuchs, M.C., Fischer, M., Schmidt, C., 2015. The abanico plot: visualising chronometric data with individual standard errors. Quaternary Geochronology. doi:10.1016/j.quageo.2015.09.003 172 plot_AbanicoPlot See Also plot_RadialPlot, plot_KDE, plot_Histogram Examples ## load example data and recalculate to Gray data(ExampleData.DeValues, envir = environment()) ExampleData.DeValues <- ExampleData.DeValues$CA1 ## plot the example data straightforward plot_AbanicoPlot(data = ExampleData.DeValues) ## now with linear z-scale plot_AbanicoPlot(data = ExampleData.DeValues, log.z = FALSE) ## now with output of the plot parameters plot1 <- plot_AbanicoPlot(data = ExampleData.DeValues, output = TRUE) str(plot1) plot1$zlim ## now with adjusted z-scale limits plot_AbanicoPlot(data = ExampleData.DeValues, zlim = c(10, 200)) ## now with adjusted x-scale limits plot_AbanicoPlot(data = ExampleData.DeValues, xlim = c(0, 20)) ## now with rug to indicate individual values in KDE part plot_AbanicoPlot(data = ExampleData.DeValues, rug = TRUE) ## now with a smaller bandwidth for the KDE plot plot_AbanicoPlot(data = ExampleData.DeValues, bw = 0.04) ## now with a histogram instead of the KDE plot plot_AbanicoPlot(data = ExampleData.DeValues, hist = TRUE, kde = FALSE) ## now with a KDE plot and histogram with manual number of bins plot_AbanicoPlot(data = ExampleData.DeValues, hist = TRUE, breaks = 20) ## now with a KDE plot and a dot plot plot_AbanicoPlot(data = ExampleData.DeValues, dots = TRUE) ## now with user-defined plot ratio plot_AbanicoPlot(data = ExampleData.DeValues, plot.ratio = 0.5) plot_AbanicoPlot ## now with user-defined central value plot_AbanicoPlot(data = ExampleData.DeValues, z.0 = 70) ## now with median as central value plot_AbanicoPlot(data = ExampleData.DeValues, z.0 = "median") ## now with the 17-83 percentile range as definition of scatter plot_AbanicoPlot(data = ExampleData.DeValues, z.0 = "median", dispersion = "p17") ## now with user-defined green line for minimum age model CAM <- calc_CentralDose(ExampleData.DeValues, plot = FALSE) plot_AbanicoPlot(data = ExampleData.DeValues, line = CAM, line.col = "darkgreen", line.label = "CAM") ## now create plot with legend, colour, different points and smaller scale plot_AbanicoPlot(data = ExampleData.DeValues, legend = "Sample 1", col = "tomato4", bar.col = "peachpuff", pch = "R", cex = 0.8) ## now without 2-sigma bar, polygon, grid lines and central value line plot_AbanicoPlot(data = ExampleData.DeValues, bar.col = FALSE, polygon.col = FALSE, grid.col = FALSE, y.axis = FALSE, lwd = 0) ## now with direct display of De errors, without 2-sigma bar plot_AbanicoPlot(data = ExampleData.DeValues, bar.col = FALSE, ylab = "", y.axis = FALSE, error.bars = TRUE) ## now with user-defined axes labels plot_AbanicoPlot(data = ExampleData.DeValues, xlab = c("Data error (%)", "Data precision"), ylab = "Scatter", zlab = "Equivalent dose [Gy]") ## now with minimum, maximum and median value indicated plot_AbanicoPlot(data = ExampleData.DeValues, stats = c("min", "max", "median")) ## now with a brief statistical summary as subheader 173 174 plot_AbanicoPlot plot_AbanicoPlot(data = ExampleData.DeValues, summary = c("n", "in.2s")) ## now with another statistical summary plot_AbanicoPlot(data = ExampleData.DeValues, summary = c("mean.weighted", "median"), summary.pos = "topleft") ## now a plot with two 2-sigma bars for one data set plot_AbanicoPlot(data = ExampleData.DeValues, bar = c(30, 100)) ## now the data set is split into sub-groups, one is manipulated data.1 <- ExampleData.DeValues[1:30,] data.2 <- ExampleData.DeValues[31:62,] * 1.3 ## now a common dataset is created from the two subgroups data.3 <- list(data.1, data.2) ## now the two data sets are plotted in one plot plot_AbanicoPlot(data = data.3) ## now with some graphical modification plot_AbanicoPlot(data = data.3, z.0 = "median", col = c("steelblue4", "orange4"), bar.col = c("steelblue3", "orange3"), polygon.col = c("steelblue1", "orange1"), pch = c(2, 6), angle = c(30, 50), summary = c("n", "in.2s", "median")) ## create Abanico plot with predefined layout definition plot_AbanicoPlot(data = ExampleData.DeValues, layout = "journal") ## now with predefined layout definition and further modifications plot_AbanicoPlot(data = data.3, z.0 = "median", layout = "journal", col = c("steelblue4", "orange4"), bar.col = adjustcolor(c("steelblue3", "orange3"), alpha.f = 0.5), polygon.col = c("steelblue3", "orange3")) ## for further information on layout definitions see documentation ## of function get_Layout() ## now with manually added plot content ## create empty plot with numeric output AP <- plot_AbanicoPlot(data = ExampleData.DeValues, pch = NA, output = TRUE) ## identify data in 2 sigma range in_2sigma <- AP$data[[1]]$data.in.2s plot_DetPlot 175 ## restore function-internal plot parameters par(AP$par) ## add points inside 2-sigma range points(x = AP$data[[1]]$precision[in_2sigma], y = AP$data[[1]]$std.estimate.plot[in_2sigma], pch = 16) ## add points outside 2-sigma range points(x = AP$data[[1]]$precision[!in_2sigma], y = AP$data[[1]]$std.estimate.plot[!in_2sigma], pch = 1) plot_DetPlot Create De(t) plot Description Plots the equivalent dose (De) in dependency of the chosen signal integral (cf. Bailey et al., 2003). The function is simply passing several arguments to the function plot and the used analysis functions and runs it in a loop. Example: legend.pos for legend position, legend for legend text. Usage plot_DetPlot(object, signal.integral.min, signal.integral.max, background.integral.min, background.integral.max, method = "shift", signal_integral.seq = NULL, analyse_function = "analyse_SAR.CWOSL", analyse_function.control = list(), n.channels = NULL, show_ShineDownCurve = TRUE, respect_RC.Status = FALSE, verbose = TRUE, ...) Arguments object RLum.Analysis (required): input object containing data for analysis signal.integral.min integer (required): lower bound of the signal integral. signal.integral.max integer (required): upper bound of the signal integral. background.integral.min integer (required): lower bound of the background integral. background.integral.max integer (required): upper bound of the background integral. method character (with default): method applied for constructing the De(t) plot. • shift (the default): the chosen signal integral is shifted the shine down curve, • expansion: the chosen signal integral is expanded each time by its length signal_integral.seq numeric (optional): argument to provide an own signal integral sequence for constructing the De(t) plot 176 plot_DetPlot analyse_function character (with default): name of the analyse function to be called. Supported functions are: 'analyse_SAR.CWOSL', 'analyse_pIRIRSequence' analyse_function.control list (optional): arguments to be passed to the supported analyse functions ('analyse_SAR.CWOSL', 'analyse_pIRIRSequence') n.channels integer (optional): number of channels used for the De(t) plot. If nothing is provided all De-values are calculated and plotted until the start of the background integral. show_ShineDownCurve logical (with default): enables or disables shine down curve in the plot output respect_RC.Status logical (with default): remove De-values with ’FAILED’ RC.Status from the plot (cf. analyse_SAR.CWOSL and analyse_pIRIRSequence) verbose logical (with default): enables or disables terminal feedback ... further arguments and graphical parameters passed to plot.default, analyse_SAR.CWOSL and analyse_pIRIRSequence. See details for further information. Details method The original method presented by Baiely et al., 2003 shifted the signal integrals and slightly extended them accounting for changes in the counting statistics. Example: c(1:3, 3:5, 5:7). However, here also another method is provided allowing to expand the signal integral by consectutively expaning the integral by its chosen length. Example: c(1:3, 1:5, 1:7) Note that in both cases the integral limits are overlap. The finally applied limits are part of the function output. Value A plot and an RLum.Results object with the produced De values @data: Object De.values signal_integral.seq Type data.frame numeric Description table with De values integral sequence used for the calculation @info: Object call Type call Description the original function call Function version 0.1.1 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). plot_DetPlot(): Create De(t) plot. Function version 0.1.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: plot_DetPlot 177 Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.Rproject.org/package=Luminescence Note The entire analysis is based on the used analysis functions, namely analyse_SAR.CWOSL and analyse_pIRIRSequence. However, the integrity checks of this function are not that thoughtful as in these functions itself. It means, that every sequence should be checked carefully before running long calculations using serveral hundreds of channels. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References Bailey, R.M., Singarayer, J.S., Ward, S., Stokes, S., 2003. Identification of partial resetting using De as a function of illumination time. Radiation Measurements 37, 511-518. doi:10.1016/S13504487(03)00063-5 See Also plot, analyse_SAR.CWOSL, analyse_pIRIRSequence Examples ## Not run: ##load data ##ExampleData.BINfileData contains two BINfileData objects ##CWOSL.SAR.Data and TL.SAR.Data data(ExampleData.BINfileData, envir = environment()) ##transform the values from the first position in a RLum.Analysis object object <- Risoe.BINfileData2RLum.Analysis(CWOSL.SAR.Data, pos=1) plot_DetPlot(object, signal.integral.min = 1, signal.integral.max = 3, background.integral.min = 900, background.integral.max = 1000, n.channels = 5, ) ## End(Not run) 178 plot_DRTResults plot_DRTResults Visualise dose recovery test results Description The function provides a standardised plot output for dose recovery test measurements. Usage plot_DRTResults(values, given.dose = NULL, error.range = 10, preheat, boxplot = FALSE, mtext, summary, summary.pos, legend, legend.pos, par.local = TRUE, na.rm = FALSE, ...) Arguments values RLum.Results or data.frame (required): input values containing at least De and De error. To plot more than one data set in one figure, a list of the individual data sets must be provided (e.g. list(dataset.1, dataset.2)). given.dose numeric (optional): given dose used for the dose recovery test to normalise data. If only one given dose is provided this given dose is valid for all input data sets (i.e., values is a list). Oherwise a given dose for each input data set has to be provided (e.g., given.dose = c(100,200)). If given.dose in NULL the values are plotted without normalisation (might be useful for preheat plateau tests). Note: Unit has to be the same as from the input values (e.g., Seconds or Gray). error.range numeric: symmetric error range in percent will be shown as dashed lines in the plot. Set error.range to 0 to void plotting of error ranges. preheat numeric: optional vector of preheat temperatures to be used for grouping the De values. If specified, the temperatures are assigned to the x-axis. boxplot logical: optionally plot values, that are grouped by preheat temperature as boxplots. Only possible when preheat vector is specified. mtext character: additional text below the plot title. summary character (optional): adds numerical output to the plot. Can be one or more out of: • • • • • • • • "n" (number of samples), "mean" (mean De value), "weighted$mean" (error-weighted mean), "median" (median of the De values), "sd.rel" (relative standard deviation in percent), "sd.abs" (absolute standard deviation), "se.rel" (relative standard error) and "se.abs" (absolute standard error) and all other measures returned by the function calc_Statistics. summary.pos numeric or character (with default): optional position coordinates or keyword (e.g. "topright") for the statistical summary. Alternatively, the keyword "sub" may be specified to place the summary below the plot header. However, this latter option in only possible if mtext is not used. legend character vector (optional): legend content to be added to the plot. plot_DRTResults 179 legend.pos numeric or character (with default): optional position coordinates or keyword (e.g. "topright") for the legend to be plotted. par.local logical (with default): use local graphical parameters for plotting, e.g. the plot is shown in one column and one row. If par.local = FALSE, global parameters are inherited, i.e. parameters provided via par() work na.rm logical: indicating wether NA values are removed before plotting from the input data set ... further arguments and graphical parameters passed to plot. Details Procedure to test the accuracy of a measurement protocol to reliably determine the dose of a specific sample. Here, the natural signal is erased and a known laboratory dose administered which is treated as unknown. Then the De measurement is carried out and the degree of congruence between administered and recovered dose is a measure of the protocol’s accuracy for this sample. In the plot the normalised De is shown on the y-axis, i.e. obtained De/Given Dose. Value A plot is returned. Function version 0.1.11 (2018-01-21 17:22:38) How to cite Kreutzer, S., Dietze, M. (2018). plot_DRTResults(): Visualise dose recovery test results. Function version 0.1.11. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note Further data and plot arguments can be added by using the appropiate R commands. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) Michael Dietze, GFZ Potsdam (Germany) R Luminescence Package Team References Wintle, A.G., Murray, A.S., 2006. A review of quartz optically stimulated luminescence characteristics and their relevance in single-aliquot regeneration dating protocols. Radiation Measurements, 41, 369-391. See Also plot 180 plot_DRTResults Examples ## read example data set and misapply them for this plot type data(ExampleData.DeValues, envir = environment()) ## plot values plot_DRTResults(values = ExampleData.DeValues$BT998[7:11,], given.dose = 2800, mtext = "Example data") ## plot values with legend plot_DRTResults(values = ExampleData.DeValues$BT998[7:11,], given.dose = 2800, legend = "Test data set") ## create and plot two subsets with randomised values x.1 <- ExampleData.DeValues$BT998[7:11,] x.2 <- ExampleData.DeValues$BT998[7:11,] * c(runif(5, 0.9, 1.1), 1) plot_DRTResults(values = list(x.1, x.2), given.dose = 2800) ## some more user-defined plot parameters plot_DRTResults(values = list(x.1, x.2), given.dose = 2800, pch = c(2, 5), col = c("orange", "blue"), xlim = c(0, 8), ylim = c(0.85, 1.15), xlab = "Sample aliquot") ## plot the data with user-defined statistical measures as legend plot_DRTResults(values = list(x.1, x.2), given.dose = 2800, summary = c("n", "mean.weighted", "sd")) ## plot the data with user-defined statistical measures as sub-header plot_DRTResults(values = list(x.1, x.2), given.dose = 2800, summary = c("n", "mean.weighted", "sd"), summary.pos = "sub") ## plot the data grouped by preheat temperatures plot_DRTResults(values = ExampleData.DeValues$BT998[7:11,], given.dose = 2800, preheat = c(200, 200, 200, 240, 240)) ## read example data set and misapply them for this plot type data(ExampleData.DeValues, envir = environment()) ## plot values plot_DRTResults(values = ExampleData.DeValues$BT998[7:11,], given.dose = 2800, mtext = "Example data") ## plot two data sets grouped by preheat temperatures plot_DRTResults(values = list(x.1, x.2), given.dose = 2800, preheat = c(200, 200, 200, 240, 240)) plot_FilterCombinations 181 ## plot the data grouped by preheat temperatures as boxplots plot_DRTResults(values = ExampleData.DeValues$BT998[7:11,], given.dose = 2800, preheat = c(200, 200, 200, 240, 240), boxplot = TRUE) plot_FilterCombinations Plot filter combinations along with the (optional) net transmission window Description The function allows to plot transmission windows for different filters. Missing data for specific wavelenghts are automatically interpolated for the given filter data using the function approx. With that a standardised output is reached and a net transmission window can be shown. Usage plot_FilterCombinations(filters, wavelength_range = 200:1000, show_net_transmission = TRUE, interactive = FALSE, plot = TRUE, ...) Arguments filters list (required): a named list of filter data for each filter to be shown. The filter data itself should be either provided as data.frame or matrix. (for more options s. Details) wavelength_range numeric (with default): wavelength range used for the interpolation show_net_transmission logical (with default): show net transmission window as polygon. interactive logical (with default): enable/disable interactive plot plot logical (with default): enables or disables the plot output ... further arguments that can be passed to control the plot output. Suppored are main, xlab, ylab, xlim, ylim, type, lty, lwd. For non common plotting parameters see the details section. Details Calculations Net transmission window The net transmission window of two filters is approximated by Tf inal = T1 ∗ T2 Optical density OD = −log(T ) 182 plot_FilterCombinations Total optical density ODtotal = OD1 + OD2 Please consider using own calculations for more precise values. How to provide input data? CASE 1 The function expects that all filter values are either of type matrix or data.frame with two columns. The first columens contains the wavelength, the second the relative transmission (but not in percentage, i.e. the maximum transmission can be only become 1). In this case only the transmission window is show as provided. Changes in filter thickness and relection factor are not considered. CASE 2 The filter data itself are provided as list element containing a matrix or data.frame and additional information on the thickness of the filter, e.g., list(filter1 = list(filter_matrix, d = 2)). The given filter data are always considered as standard input and the filter thickness value is taken into account by T ransmission = T ransmission( d) with d given in the same dimension as the original filter data. CASE 3 Same as CASE 2 but additionally a reflection factor P is provided, e.g., list(filter1 = list(filter_matrix, d = 2, The final transmission becomes: T ransmission = T ransmission( d) ∗ P Advanced plotting parameters The following further non-common plotting parameters can be passed to the function: Argument legend legend.pos legend.text net_transmission.col net_transmission.col_lines net_transmission.density grid Datatype logical character character col col numeric list Description enable/disable legend change legend position (graphics::legend) same as the argument legend in (graphics::legend) colour of net transmission window polygon colour of net transmission window polygon lines specify line density in the transmission polygon full list of arguments that can be passd to the function graphics::grid For further modifications standard additional R plot functions are recommend, e.g., the legend can be fully customised by disabling the standard legend and use the function graphics::legend instead. Value Returns an S4 object of type RLum.Results. @data Object Type Description plot_FilterCombinations 183 net_transmission_window OD_total filter_matrix matrix matrix matrix the resulting net transmission window the total optical density the filter matrix used for plotting @info Object call Type Description call the original function call Function version 0.3.1 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). plot_FilterCombinations(): Plot filter combinations along with the (optional) net transmission window. Function version 0.3.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montagine (France) R Luminescence Package Team See Also RLum.Results, approx Examples ## (For legal reasons no real filter data are provided) ## Create filter sets filter1 <- density(rnorm(100, mean = 450, sd = 20)) filter1 <- matrix(c(filter1$x, filter1$y/max(filter1$y)), ncol = 2) filter2 <- matrix(c(200:799,rep(c(0,0.8,0),each = 200)), ncol = 2) ## Example 1 (standard) plot_FilterCombinations(filters = list(filter1, filter2)) ## Example 2 (with d and P value and name for filter 2) results <- plot_FilterCombinations( filters = list(filter_1 = filter1, Rectangle = list(filter2, d = 2, P = 0.6))) results ## Example 3 show optical density plot(results$OD_total) ## Not run: ##Example 4 ##show the filters using the interactive mode plot_FilterCombinations(filters = list(filter1, filter2), interactive = TRUE) 184 plot_GrowthCurve ## End(Not run) plot_GrowthCurve Fit and plot a growth curve for luminescence data (Lx/Tx against dose) Description A dose response curve is produced for luminescence measurements using a regenerative or additive protocol. The function supports interpolation and extraxpolation to calculate the equivalent dose. Usage plot_GrowthCurve(sample, na.rm = TRUE, mode = "interpolation", fit.method = "EXP", fit.force_through_origin = FALSE, fit.weights = TRUE, fit.includingRepeatedRegPoints = TRUE, fit.NumberRegPoints = NULL, fit.NumberRegPointsReal = NULL, fit.bounds = TRUE, NumberIterations.MC = 100, output.plot = TRUE, output.plotExtended = TRUE, output.plotExtended.single = FALSE, cex.global = 1, txtProgressBar = TRUE, verbose = TRUE, ...) Arguments sample data.frame (required): data frame with three columns for x=Dose,y=LxTx,z=LxTx.Error, y1=TnTx. The column for the test dose response is optional, but requires ’TnTx’ as column name if used. For exponential fits at least three dose points (including the natural) should be provided. na.rm logical (with default): excludes NA values from the data set prior to any further operations. mode character (with default): selects calculation mode of the function. • "interpolation" (default) calculates the De by interpolation, • "extrapolation" calculates the De by extrapolation and • "alternate" calculates no De and just fits the data points. Please note that for option "regenrative" the first point is considered as natural dose fit.method character (with default): function used for fitting. Possible options are: • • • • • • LIN, QDR, EXP, EXP OR LIN, EXP+LIN or EXP+EXP. See details. fit.force_through_origin logical (with default) allow to force the fitted function through the origin. For method = "EXP+EXP" the function will go to the origin in either case, so this option will have no effect. plot_GrowthCurve 185 fit.weights logical (with default): option whether the fitting is done with or without weights. See details. fit.includingRepeatedRegPoints logical (with default): includes repeated points for fitting (TRUE/FALSE). fit.NumberRegPoints integer (optional): set number of regeneration points manually. By default the number of all (!) regeneration points is used automatically. fit.NumberRegPointsReal integer (optional): if the number of regeneration points is provided manually, the value of the real, regeneration points = all points (repeated points) including reg 0, has to be inserted. fit.bounds logical (with default): set lower fit bounds for all fitting parameters to 0. Limited for the use with the fit methods EXP, EXP+LIN and EXP OR LIN. Argument to be inserted for experimental application only! NumberIterations.MC integer (with default): number of Monte Carlo simulations for error estimation. See details. output.plot logical (with default): plot output (TRUE/FALSE). output.plotExtended logical (with default): If’ TRUE, 3 plots on one plot area are provided: 1. growth curve, 2. histogram from Monte Carlo error simulation and 3. a test dose response plot. If FALSE, just the growth curve will be plotted. Requires: output.plot = TRUE. output.plotExtended.single logical (with default): single plot output (TRUE/FALSE) to allow for plotting the results in single plot windows. Requires output.plot = TRUE and output.plotExtended = TRUE. cex.global numeric (with default): global scaling factor. txtProgressBar logical (with default): enables or disables txtProgressBar. If verbose = FALSE also no txtProgressBar is shown. verbose logical (with default): enables or disables terminal feedback. ... Further arguments and graphical parameters to be passed. Note: Standard arguments will only be passed to the growth curve plot. Supported: xlim, ylim, main, xlab, ylab Details Fitting methods For all options (except for the LIN, QDR and the EXP OR LIN), the minpack.lm::nlsLM function with the LM (Levenberg-Marquardt algorithm) algorithm is used. Note: For historical reasons for the Monte Carlo simulations partly the function nls using the port algorithm. The solution is found by transforming the function or using uniroot. LIN: fits a linear function to the data using lm: y =m∗x+n QDR: fits a linear function to the data using lm: y = a + b ∗ x + c ∗ x2 186 plot_GrowthCurve EXP: try to fit a function of the form y = a ∗ (1 − exp(−(x + c)/b)) Parameters b and c are approximated by a linear fit using lm. Note: b = D0 EXP OR LIN: works for some cases where an EXP fit fails. If the EXP fit fails, a LIN fit is done instead. EXP+LIN: tries to fit an exponential plus linear function of the form: y = a ∗ (1 − exp(−(x + c)/b) + (g ∗ x)) The De is calculated by iteration. Note: In the context of luminescence dating, this function has no physical meaning. Therefore, no D0 value is returned. EXP+EXP: tries to fit a double exponential function of the form y = (a1 ∗ (1 − exp(−(x)/b1))) + (a2 ∗ (1 − exp(−(x)/b2))) This fitting procedure is not robust against wrong start parameters and should be further improved. Fit weighting If the option fit.weights = TRUE is chosen, weights are calculated using provided signal errors (Lx/Tx error): f it.weights = 1/error/(sum(1/error)) Error estimation using Monte Carlo simulation Error estimation is done using a Monte Carlo (MC) simulation approach. A set of Lx/Tx values is constructed by randomly drawing curve data from samled from normal distributions. The normal distribution is defined by the input values (mean = value, sd = value.error). Then, a growth curve fit is attempted for each dataset resulting in a new distribution of single De values. The sd of this distribution is becomes then the error of the De. With increasing iterations, the error value becomes more stable. Note: It may take some calculation time with increasing MC runs, especially for the composed functions (EXP+LIN and EXP+EXP). Each error estimation is done with the function of the chosen fitting method. Subtitle information To avoid plotting the subtitle information, provide an empty user mtext mtext = "". To plot any other subtitle text, use mtext. Value Along with a plot (so far wanted) an RLum.Results object is returned containing, the slot data contains the following elements: DATA.OBJECT ..$De : ..$De.MC : ..$Fit : ..$Formula : ..$call : TYPE data.frame numeric nls or lm expression call DESCRIPTION Table with De values Table with De values from MC runs object from the fitting for EXP, EXP+LIN and EXP+EXP. In case of a resulting linear fit wh Fitting formula as R expression The original function call plot_GrowthCurve 187 Function version 1.9.10 (2018-01-21 17:22:38) How to cite Kreutzer, S., Dietze, M. (2018). plot_GrowthCurve(): Fit and plot a growth curve for luminescence data (Lx/Tx against dose). Function version 1.9.10. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) Michael Dietze, GFZ Potsdam (Germany) R Luminescence Package Team References Berger, G.W., Huntley, D.J., 1989. Test data for exponential fits. Ancient TL 7, 43-46. See Also nls, RLum.Results, get_RLum, minpack.lm::nlsLM, lm, uniroot Examples ##(1) plot growth curve for a dummy data.set and show De value data(ExampleData.LxTxData, envir = environment()) temp <- plot_GrowthCurve(LxTxData) get_RLum(temp) ##(1a) to access the fitting value try get_RLum(temp, data.object = "Fit") ##(2) plot the growth curve only - uncomment to use ##pdf(file = "~/Desktop/Growth_Curve_Dummy.pdf", paper = "special") plot_GrowthCurve(LxTxData) ##dev.off() ##(3) plot growth curve with pdf output - uncomment to use, single output ##pdf(file = "~/Desktop/Growth_Curve_Dummy.pdf", paper = "special") plot_GrowthCurve(LxTxData, output.plotExtended.single = TRUE) ##dev.off() ##(4) plot resulting function for given intervall x x <- seq(1,10000, by = 100) plot( x = x, y = eval(temp$Formula), type = "l" ) ##(5) plot using the 'extrapolation' mode LxTxData[1,2:3] <- c(0.5, 0.001) 188 plot_Histogram print(plot_GrowthCurve(LxTxData,mode = "extrapolation")) ##(6) plot using the 'alternate' mode LxTxData[1,2:3] <- c(0.5, 0.001) print(plot_GrowthCurve(LxTxData,mode = "alternate")) ##(7) import and fit test data set by Berger & Huntley 1989 QNL84_2_unbleached ca. 200 MByte and thus plotting of such data is extremely slow. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also RLum.Data.Image, plot, plot_RLum, raster::raster 210 plot_RLum.Data.Spectrum Examples ##load data data(ExampleData.RLum.Data.Image, envir = environment()) ##plot data plot_RLum.Data.Image(ExampleData.RLum.Data.Image) plot_RLum.Data.Spectrum Plot function for an RLum.Data.Spectrum S4 class object Description The function provides a standardised plot output for spectrum data of an RLum.Data.Spectrum S4 class object Usage plot_RLum.Data.Spectrum(object, par.local = TRUE, plot.type = "contour", optical.wavelength.colours = TRUE, bg.channels, bin.rows = 1, bin.cols = 1, rug = TRUE, limit_counts = NULL, xaxis.energy = FALSE, legend.text, ...) Arguments object RLum.Data.Spectrum or matrix (required): S4 object of class RLum.Data.Spectrum or a matrix containing count values of the spectrum. Please note that in case of a matrix rownames and colnames are set automatically if not provided. par.local logical (with default): use local graphical parameters for plotting, e.g. the plot is shown in one column and one row. If par.local = FALSE global parameters are inherited. plot.type character (with default): plot type, for 3D-plot use persp, or interactive, for a 2D-plot contour, single or multiple.lines (along the time or temperature axis) or transect (along the wavelength axis) optical.wavelength.colours logical (with default): use optical wavelength colour palette. Note: For this, the spectrum range is limited: c(350,750). Own colours can be set with the argument col. bg.channels vector (optional): defines channel for background subtraction If a vector is provided the mean of the channels is used for subtraction. Note: Background subtraction is applied prior to channel binning bin.rows integer (with defaul): allow summing-up wavelength channels (horizontal binning), e.g. bin.rows = 2 two channels are summed up bin.cols integer (with default): allow summing-up channel counts (vertical binning) for plotting, e.g. bin.cols = 2 two channels are summed up plot_RLum.Data.Spectrum 211 rug logical (with default): enables or disables colour rug. Currently only implemented for plot type multiple.lines and single limit_counts numeric (optional): value to limit all count values to this value, i.e. all count values above this threshold will be replaced by this threshold. This is helpful especially in case of TL-spectra. xaxis.energy logical (with default): enables or disables energy instead of wavelength axis. Note: This option means not only simnply redrawing the axis, instead the spectrum in terms of intensity is recalculated, s. details. legend.text character (with default): possiblity to provide own legend text. This argument is only considered for plot types providing a legend, e.g. plot.type="transect" ... further arguments and graphical parameters that will be passed to the plot function. Details Matrix structure (cf. RLum.Data.Spectrum) • rows (x-values): wavelengths/channels (xlim, xlab) • columns (y-values): time/temperature (ylim, ylab) • cells (z-values): count values (zlim, zlab) Note: This nomenclature is valid for all plot types of this function! Nomenclature for value limiting • xlim: Limits values along the wavelength axis • ylim: Limits values along the time/temperature axis • zlim: Limits values along the count value axis Energy axis re-calculation If the argument xaxis.energy = TRUE is chosen, instead intensity vs. wavelength the spectrum is plotted as intensiyt vs. energy. Therefore the entire spectrum is re-recaluated (e.g., Appendix 4 in Blasse and Grabmeier, 1994): The intensity of the spectrum (z-values) is re-calcualted using the following equation: φE = φλ ∗ λ2 /(hc) with φE the intensity per interval of energy E (eV), φλ the intensity per interval of wavelength λ (nm) and h (eV/s) the Planck constant and c (m/s) the velocity of light. For transforming the wavelength axis (x-values) the equation E = hc/λ is used. For further details please see the cited the literature. Details on the plot functions Spectrum is visualised as 3D or 2D plot. Both plot types are based on internal R plot functions. plot.type = "persp" Arguments that will be passed to persp: 212 plot_RLum.Data.Spectrum • shade: default is 0.4 • phi: default is 15 • theta: default is -30 • expand: default is 1 • ticktype: default is detailed, r: default is 10 Note: Further parameters can be adjusted via par. For example to set the background transparent and reduce the thickness of the lines use: par(bg = NA, lwd = 0.7) previous the function call. plot.type = "single" Per frame a single curve is returned. Frames are time or temperature steps. plot.type = "multiple.lines" All frames plotted in one frame. plot.type = "transect" Depending on the selected wavelength/channel range a transect over the time/temperature (y-axis) will be plotted along the wavelength/channels (x-axis). If the range contains more than one channel, values (z-values) are summed up. To select a transect use the xlim argument, e.g. xlim = c(300,310) plot along the summed up count values of channel 300 to 310. Further arguments that will be passed (depending on the plot type) xlab, ylab, zlab, xlim, ylim, zlim, main, mtext, pch, type ("single", "multiple.lines", "interactive"), col, border, box lwd, bty, showscale ("interactive") Value Returns a plot. Function version 0.5.3 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). plot_RLum.Data.Spectrum(): Plot function for an RLum.Data.Spectrum S4 class object. Function version 0.5.3. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note Not all additional arguments (...) will be passed similarly! Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References Blasse, G., Grabmaier, B.C., 1994. Luminescent Materials. Springer. plot_RLum.Data.Spectrum See Also RLum.Data.Spectrum, plot, plot_RLum, persp, plotly::plot_ly, contour Examples ##load example data data(ExampleData.XSYG, envir = environment()) ##(1)plot simple spectrum (2D) - contour plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="contour", xlim = c(310,750), ylim = c(0,300), bin.rows=10, bin.cols = 1) ##(2) plot spectrum (3D) plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="persp", xlim = c(310,750), ylim = c(0,100), bin.rows=10, bin.cols = 1) ##(3) plot multiple lines (2D) - multiple.lines (with ylim) plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="multiple.lines", xlim = c(310,750), ylim = c(0,100), bin.rows=10, bin.cols = 1) ## Not run: ##(4) interactive plot using the package plotly ("surface") plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="interactive", xlim = c(310,750), ylim = c(0,300), bin.rows=10, bin.cols = 1) ##(5) interactive plot using the package plotly ("contour") plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="interactive", xlim = c(310,750), ylim = c(0,300), bin.rows=10, bin.cols = 1, type = "contour", showscale = TRUE) ##(6) interactive plot using the package plotly ("heatmap") plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="interactive", xlim = c(310,750), ylim = c(0,300), bin.rows=10, bin.cols = 1, type = "heatmap", showscale = TRUE) ##(7) alternative using the package fields fields::image.plot(get_RLum(TL.Spectrum)) contour(get_RLum(TL.Spectrum), add = TRUE) 213 214 plot_RLum.Results ## End(Not run) plot_RLum.Results Plot function for an RLum.Results S4 class object Description The function provides a standardised plot output for data of an RLum.Results S4 class object Usage plot_RLum.Results(object, single = TRUE, ...) Arguments object RLum.Results (required): S4 object of class RLum.Results single logical (with default): single plot output (TRUE/FALSE) to allow for plotting the results in as few plot windows as possible. ... further arguments and graphical parameters will be passed to the plot function. Details The function produces a multiple plot output. A file output is recommended (e.g., pdf). Value Returns multiple plots. Function version 0.2.1 (2018-01-21 17:22:38) How to cite Burow, C., Kreutzer, S. (2018). plot_RLum.Results(): Plot function for an RLum.Results S4 class object. Function version 0.2.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note Not all arguments available for plot will be passed! Only plotting of RLum.Results objects are supported. Author(s) Christoph Burow, University of Cologne (Germany) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team plot_ViolinPlot 215 See Also plot, plot_RLum Examples ###load data data(ExampleData.DeValues, envir = environment()) # apply the un-logged minimum age model mam <- calc_MinDose(data = ExampleData.DeValues$CA1, sigmab = 0.2, log = TRUE, plot = FALSE) ##plot plot_RLum.Results(mam) # estimate the number of grains on an aliquot grains<- calc_AliquotSize(grain.size = c(100,150), sample.diameter = 1, plot = FALSE, MC.iter = 100) ##plot plot_RLum.Results(grains) plot_ViolinPlot Create a violin plot Description Draws a kernal densiy plot in combination with a boxplot in its middle. The shape of the violin is constructed using a mirrored density curve. This plot is especially designed for cases where the individual errors are zero or to small to be visualised. The idea for this plot is based on the the ’volcano plot’ in the ggplot2 package by Hadely Wickham and Winston Chang. The general idea for the Violin Plot seems to be introduced by Hintze and Nelson (1998). Usage plot_ViolinPlot(data, boxplot = TRUE, rug = TRUE, summary = NULL, summary.pos = "sub", na.rm = TRUE, ...) Arguments data numeric or RLum.Results (required): input data for plotting. Alternatively a data.frame or a matrix can be provided, but only the first column will be considered by the function boxplot logical (with default): enable or disable boxplot rug logical (with default): enable or disable rug summary character (optional): add statistic measures of centrality and dispersion to the plot. Can be one or more of several keywords. See details for available keywords. 216 plot_ViolinPlot summary.pos numeric or character (with default): optional position keywords (cf., legend) for the statistical summary. Alternatively, the keyword "sub" may be specified to place the summary below the plot header. However, this latter option in only possible if mtext is not used. na.rm logical (with default): exclude NA values from the data set prior to any further operations. ... further arguments and graphical parameters passed to plot.default, stats::density and boxplot. See details for further information Details The function is passing several arguments to the function plot, stats::density, graphics::boxplot: Supported arguments are: xlim, main, xlab, ylab, col.violin, col.boxplot, mtext, cex, mtext Valid summary keywords 'n', 'mean', 'median', 'sd.abs', 'sd.rel', 'se.abs', 'se.rel'. 'skewness', 'kurtosis' Function version 0.1.4 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). plot_ViolinPlot(): Create a violin plot. Function version 0.1.4. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.Rproject.org/package=Luminescence Note Although the code for this function was developed independently and just the idea for the plot was based on the ’ggplot2’ package plot type ’volcano’, it should be mentioned that, beyond this, two other R packages exist providing a possibility to produces this kind of plot, namely: ’vioplot’ and ’violinmplot’ (see References for details). Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References Daniel Adler (2005). vioplot: A violin plot is a combination of a box plot and a kernel density plot. R package version 0.2 http://CRAN.R-project.org/package=violplot Hintze, J.L., Nelson, R.D., 1998. A Box Plot-Density Trace Synergism. The American Statistician 52, 181-184. Raphael W. Majeed (2012). violinmplot: Combination of violin plot with mean and standard deviation. R package version 0.2.1. http://CRAN.R-project.org/package=violinmplot Wickham. H (2009). ggplot2: elegant graphics for data analysis. Springer New York. See Also stats::density, plot, boxplot, rug, calc_Statistics PSL2Risoe.BINfileData 217 Examples ## read example data set data(ExampleData.DeValues, envir = environment()) ExampleData.DeValues <- Second2Gray(ExampleData.DeValues$BT998, c(0.0438,0.0019)) ## create plot straightforward plot_ViolinPlot(data = ExampleData.DeValues) PSL2Risoe.BINfileData Convert portable OSL data to an Risoe.BINfileData object Description Converts an RLum.Analysis object produced by the function read_PSL2R() to an Risoe.BINfileData object (BETA). Usage PSL2Risoe.BINfileData(object, ...) Arguments object RLum.Analysis (required): RLum.Analysis object produced by read_PSL2R ... currently not used. Details This function converts an RLum.Analysis object that was produced by the read_PSL2R function to an Risoe.BINfileData. The Risoe.BINfileData can be used to write a Risoe BIN file via write_R2BIN. Value Returns an S4 Risoe.BINfileData object that can be used to write a BIN file using write_R2BIN. Function version 0.0.1 (2018-01-21 17:22:38) How to cite Burow, C. (2018). PSL2Risoe.BINfileData(): Convert portable OSL data to an Risoe.BINfileData object. Function version 0.0.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Christoph Burow, University of Cologne (Germany) R Luminescence Package Team 218 read_BIN2R See Also RLum.Analysis, RLum.Data.Curve, Risoe.BINfileData Examples # (1) load and plot example data set data("ExampleData.portableOSL", envir = environment()) plot_RLum(ExampleData.portableOSL) # (2) merge all RLum.Analysis objects into one merged <- merge_RLum(ExampleData.portableOSL) merged # (3) convert to RisoeBINfile object bin <- PSL2Risoe.BINfileData(merged) bin # (4) write Risoe BIN file ## Not run: write_R2BIN(bin, "~/portableOSL.binx") ## End(Not run) read_BIN2R Import Risoe BIN-file into R Description Import a *.bin or a *.binx file produced by a Risoe DA15 and DA20 TL/OSL reader into R. Usage read_BIN2R(file, show.raw.values = FALSE, position = NULL, n.records = NULL, zero_data.rm = TRUE, duplicated.rm = FALSE, fastForward = FALSE, show.record.number = FALSE, txtProgressBar = TRUE, forced.VersionNumber = NULL, ignore.RECTYPE = FALSE, pattern = NULL, verbose = TRUE, ...) Arguments file show.raw.values character or list (required): path and file name of the BIN/BINX file (URLs are supported). If input is a list it should comprise only characters representing each valid path and BIN/BINX-file names. Alternatively the input character can be just a directory (path), in this case the the function tries to detect and import all BIN/BINX files found in the directory. logical (with default): shows raw values from BIN file for LTYPE, DTYPE and LIGHTSOURCE without translation in characters. Can be provided as list if file is a list. read_BIN2R 219 position numeric (optional): imports only the selected position. Note: the import performance will not benefit by any selection made here. Can be provided as list if file is a list. n.records raw (optional): limits the number of imported records. Can be used in combination with show.record.number for debugging purposes, e.g. corrupt BIN-files. Can be provided as list if file is a list. zero_data.rm logical (with default): remove erroneous data with no count values. As such data are usally not needed for the subsequent data analysis they will be removed by default. Can be provided as list if file is a list. duplicated.rm logical (with default): remove duplicated entries if TRUE. This may happen due to an erroneous produced BIN/BINX-file. This option compares only predeccessor and successor. Can be provided as list if file is a list. fastForward logical (with default): if TRUE for a more efficient data processing only a list of RLum.Analysis objects is returned instead of a Risoe.BINfileData object. Can be provided as list if file is a list. show.record.number logical (with default): shows record number of the imported record, for debugging usage only. Can be provided as list if file is a list. txtProgressBar logical (with default): enables or disables txtProgressBar. forced.VersionNumber integer (optional): allows to cheat the version number check in the function by own values for cases where the BIN-file version is not supported. Can be provided as list if file is a list. Note: The usage is at own risk, only supported BIN-file versions have been tested. ignore.RECTYPE logical (with default): this argument allows to ignore values in the byte ’RECTYPE’ (BIN-file version 08), in case there are not documented or faulty set. In this case the corrupted records are skipped. pattern character (optional): argument that is used if only a path is provided. The argument will than be passed to the function list.files used internally to construct a list of wanted files verbose logical (with default): enables or disables verbose mode ... further arguments that will be passed to the function Risoe.BINfileData2RLum.Analysis. Please note that any matching argument automatically sets fastForward = TRUE Details The binary data file is parsed byte by byte following the data structure published in the Appendices of the Analyst manual p. 42. For the general BIN-file structure, the reader is referred to the Risoe website: http://www.nutech. dtu.dk/ Value Returns an S4 Risoe.BINfileData object containing two slots: METADATA DATA A data.frame containing all variables stored in the bin-file. A list containing a numeric vector of the measured data. The ID corresponds to the record ID in METADATA. If fastForward = TRUE a list of RLum.Analysis object is returned. The internal coercing is done using the function Risoe.BINfileData2RLum.Analysis 220 read_Daybreak2R Function version 0.15.7 (2018-01-21 17:22:38) How to cite Kreutzer, S., Fuchs, M.C. (2018). read_BIN2R(): Import Risoe BIN-file into R. Function version 0.15.7. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note The function works for BIN/BINX-format versions 03, 04, 06, 07 and 08. The version number depends on the used Sequence Editor. ROI data sets introduced with BIN-file version 8 are not supported and skipped durint import. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) Margret C. Fuchs, HZDR Freiberg, (Germany) R Luminescence Package Team References DTU Nutech, 2016. The Squence Editor, Users Manual, February, 2016. http://www.nutech. dtu.dk/english/products-and-services/radiation-instruments/tl_osl_reader/manuals See Also write_R2BIN, Risoe.BINfileData, base::readBin, merge_Risoe.BINfileData, RLum.Analysis utils::txtProgressBar, list.files Examples ##(1) import Risoe BIN-file to R (uncomment for usage) #FILE <- file.choose() #temp <- read_BIN2R(FILE) #temp read_Daybreak2R Import measurement data produced by a Daybreak TL/OSL reader into R Description Import a TXT-file (ASCII file) or a DAT-file (binary file) produced by a Daybreak reader into R. The import of the DAT-files is limited to the file format described for the software TLAPLLIC v.3.2 used for a Daybreak, model 1100. read_Daybreak2R 221 Usage read_Daybreak2R(file, raw = FALSE, verbose = TRUE, txtProgressBar = TRUE) Arguments file character or list (required): path and file name of the file to be imported. Alternatively a list of file names can be provided or just the path a folder containing measurement data. Please note that the specific, common, file extension (txt) is likely leading to function failures during import when just a path is provided. raw logical (with default): if the input is a DAT-file (binary) a data.table::data.table instead of the RLum.Analysis object can be returned for debugging purposes. verbose logical (with default): enables or disables terminal feedback txtProgressBar logical (with default): enables or disables txtProgressBar. Value A list of RLum.Analysis objects (each per position) is provided. Function version 0.3.1 (2018-01-21 17:22:38) How to cite Kreutzer, S., Zink, A. (2018). read_Daybreak2R(): Import measurement data produced by a Daybreak TL/OSL reader into R. Function version 0.3.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note [BETA VERSION] This function still needs to be tested properly. In particular the function has underwent only very rough rests using a few files. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) Anotine Zink, C2RMF, Palais du Louvre, Paris (France) The ASCII-file import is based on a suggestion by Willian Amidon and Andrew Louis Gorin R Luminescence Package Team See Also RLum.Analysis, RLum.Data.Curve, data.table::data.table Examples ## Not run: file <- file.choose() temp <- read_Daybreak2R(file) ## End(Not run) 222 read_PSL2R read_PSL2R Import PSL files to R Description Imports PSL files produced by a SUERC portable OSL reader into R (BETA). Usage read_PSL2R(file, drop_bg = FALSE, as_decay_curve = TRUE, smooth = FALSE, merge = FALSE, ...) Arguments file character (required): path and file name of the PSL file. If input is a vector it should comprise only characters representing valid paths and PSL file names. Alternatively the input character can be just a directory (path). In this case the the function tries to detect and import all PSL files found in the directory. drop_bg logical (with default): TRUE to automatically remove all non-OSL/IRSL curves. as_decay_curve logical (with default): Portable OSL Reader curves are often given as cumulative light sum curves. Use TRUE (default) to convert the curves to the more usual decay form. smooth logical (with default): TRUE to apply Tukey’s Running Median Smoothing for OSL and IRSL decay curves. Smoothing is encouraged if you see random signal drops within the decay curves related to hardware errors. merge logical (with default): TRUE to merge all RLum.Analysis objects. Only applicable if multiple files are imported. ... currently not used. Details This function provides an import routine for the SUERC portable OSL Reader PSL format. PSL files are just plain text and can be viewed with any text editor. Due to the formatting of PSL files this import function relies heavily on regular expression to find and extract all relevant information. See note. Value Returns an S4 RLum.Analysis object containing RLum.Data.Curve objects for each curve. Function version 0.0.1 (2018-01-21 17:22:38) How to cite Burow, C. (2018). read_PSL2R(): Import PSL files to R. Function version 0.0.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.Rproject.org/package=Luminescence read_SPE2R 223 Note Because this function relies heavily on regular expressions to parse PSL files it is currently only in beta status. If the routine fails to import a specific PSL file please report to christoph.burow@unikoeln.de so the function can be updated. Author(s) Christoph Burow, University of Cologne (Germany) R Luminescence Package Team See Also RLum.Analysis, RLum.Data.Curve, RLum.Data.Curve Examples # (1) Import PSL file to R file <- system.file("extdata", "DorNie_0016.psl", package = "Luminescence") psl <- read_PSL2R(file, drop_bg = FALSE, as_decay_curve = TRUE, smooth = TRUE, merge = FALSE) print(str(psl, max.level = 3)) plot(psl, combine = TRUE) read_SPE2R Import Princeton Intruments (TM) SPE-file into R Description Function imports Princeton Instruments (TM) SPE-files into R environment and provides RLum objects as output. Usage read_SPE2R(file, output.object = "RLum.Data.Image", frame.range, txtProgressBar = TRUE, verbose = TRUE) Arguments file character (required): spe-file name (including path), e.g. • [WIN]: read_SPE2R("C:/Desktop/test.spe") • [MAC/LINUX]: readSPER("/User/test/Desktop/test.spe"). Additionally internet connections are supported. output.object character (with default): set RLum output object. Allowed types are "RLum.Data.Spectrum", "RLum.Data.Image" or "matrix" frame.range vector (optional): limit frame range, e.g. select first 100 frames by frame.range = c(1,100) txtProgressBar logical (with default): enables or disables txtProgressBar. verbose logical (with default): enables or disables verbose mode 224 read_SPE2R Details Function provides an import routine for the Princton Instruments SPE format. Import functionality is based on the file format description provided by Princton Instruments and a MatLab script written by Carl Hall (s. references). Value Depending on the chosen option the functions returns three different type of objects: output.object RLum.Data.Spectrum An object of type RLum.Data.Spectrum is returned. Row sums are used to integrate all counts over one channel. RLum.Data.Image An object of type RLum.Data.Image is returned. Due to performace reasons the import is aborted for files containing more than 100 frames. This limitation can be overwritten manually by using the argument frame.frange. matrix Returns a matrix of the form: Rows = Channels, columns = Frames. For the transformation the function get_RLum is used, meaning that the same results can be obtained by using the function get_RLum on an RLum.Data.Spectrum or RLum.Data.Image object. Function version 0.1.2 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). read_SPE2R(): Import Princeton Intruments (TM) SPE-file into R. Function version 0.1.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note The function does not test whether the input data are spectra or pictures for spatial resolved analysis! The function has been successfully tested for SPE format versions 2.x. Currently not all information provided by the SPE format are supported. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Université Bordeaux Montaigne (France) R Luminescence Package Team References Princeton Instruments, 2014. Princeton Instruments SPE 3.0 File Format Specification, Version 1.A (for document URL please use an internet search machine) Hall, C., 2012: readSPE.m. http://www.mathworks.com/matlabcentral/fileexchange/35940-readspe/ content/readSPE.m read_XSYG2R 225 See Also readBin, RLum.Data.Spectrum, raster::raster Examples ## to run examples uncomment lines and run the code ##(1) Import data as RLum.Data.Spectrum object #file <- file.choose() #temp <- read_SPE2R(file) #temp ##(2) Import data as RLum.Data.Image object #file <- file.choose() #temp <- read_SPE2R(file, output.object = "RLum.Data.Image") #temp ##(3) Import data as matrix object #file <- file.choose() #temp <- read_SPE2R(file, output.object = "matrix") #temp ##(4) Export raw data to csv, if temp is a RLum.Data.Spectrum object # write.table(x = get_RLum(temp), # file = "[your path and filename]", # sep = ";", row.names = FALSE) read_XSYG2R Import XSYG files to R Description Imports XSYG files produced by a Freiberg Instrument lexsyg reader into R. Usage read_XSYG2R(file, recalculate.TL.curves = TRUE, fastForward = FALSE, import = TRUE, pattern = ".xsyg", verbose = TRUE, txtProgressBar = TRUE) Arguments file character or list (required): path and file name of the XSYG file. If input is a list it should comprise only characters representing each valid path and xsyg-file names. Alternatively the input character can be just a directory (path), in this case the the function tries to detect and import all xsyg files found in the directory. 226 read_XSYG2R recalculate.TL.curves logical (with default): if set to TRUE, TL curves are returned as temperature against count values (see details for more information) Note: The option overwrites the time vs. count TL curve. Select FALSE to import the raw data delivered by the lexsyg. Works for TL curves and spectra. fastForward logical (with default): if TRUE for a more efficient data processing only a list of RLum.Analysis objects is returned. import logical (with default): if set to FALSE, only the XSYG file structure is shown. pattern regex (with default): optional regular expression if file is a link to a folder, to select just specific XSYG-files verbose logical (with default): enable or disable verbose mode. If verbose is FALSE the txtProgressBar is also switched off txtProgressBar logical (with default): enables TRUE or disables FALSE the progression bar during import Details How does the import function work? The function uses the xml package to parse the file structure. Each sequence is subsequently translated into an RLum.Analysis object. General structure XSYG format So far, each XSYG file can only contain one x0 , y0 ; x1 , y1 ; x2 , y2 ; x3 , y3 , but multiple sequences. Each record may comprise several curves. TL curve recalculation On the FI lexsyg device TL curves are recorded as time against count values. Temperature values are monitored on the heating plate and stored in a separate curve (time vs. temperature). If the option recalculate.TL.curves = TRUE is chosen, the time values for each TL curve are replaced by temperature values. Practically, this means combining two matrices (Time vs. Counts and Time vs. Temperature) with different row numbers by their time values. Three cases are considered: 1. HE: Heating element 2. PMT: Photomultiplier tube 3. Interpolation is done using the function approx CASE (1): nrow(matrix(PMT)) > nrow(matrix(HE)) Missing temperature values from the heating element are calculated using time values from the PMT measurement. read_XSYG2R 227 CASE (2): nrow(matrix(PMT)) < nrow(matrix(HE)) Missing count values from the PMT are calculated using time values from the heating element measurement. CASE (3): nrow(matrix(PMT)) == nrow(matrix(HE)) A new matrix is produced using temperature values from the heating element and count values from the PMT. Note: Please note that due to the recalculation of the temperature values based on values delivered by the heating element, it may happen that mutiple count values exists for each temperature value and temperature values may also decrease during heating, not only increase. Advanced file import To allow for a more efficient usage of the function, instead of single path to a file just a directory can be passed as input. In this particular case the function tries to extract all XSYG-files found in the directory and import them all. Using this option internally the function constructs as list of the XSYG-files found in the directory. Please note no recursive detection is supported as this may lead to endless loops. Value Using the option import = FALSE A list consisting of two elements is shown: • data.frame with information on file. • data.frame with information on the sequences stored in the XSYG file. Using the option import = TRUE (default) A list is provided, the list elements contain: Sequence.Header data.frame with information on the sequence. Sequence.Object RLum.Analysis containing the curves. Function version 0.6.5 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). read_XSYG2R(): Import XSYG files to R. Function version 0.6.5. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note This function is a beta version as the XSYG file format is not yet fully specified. Thus, further file operations (merge, export, write) should be done using the functions provided with the package xml. So far, no image data import is provided! Corresponding values in the XSXG file are skipped. 228 replicate_RLum Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References Grehl, S., Kreutzer, S., Hoehne, M., 2013. Documentation of the XSYG file format. Unpublished Technical Note. Freiberg, Germany Further reading XML: http://en.wikipedia.org/wiki/XML See Also xml, RLum.Analysis, RLum.Data.Curve, approx Examples ##(1) import XSYG file to R (uncomment for usage) #FILE <- file.choose() #temp <- read_XSYG2R(FILE) ##(2) additional examples for pure XML import using the package XML ## (uncomment for usage) ##import entire XML file #FILE <- file.choose() #temp <- XML::xmlRoot(XML::xmlTreeParse(FILE)) ##search for specific subnodes with curves containing 'OSL' #getNodeSet(temp, "//Sample/Sequence/Record[@recordType = 'OSL']/Curve") ##(2) How to extract single curves ... after import data(ExampleData.XSYG, envir = environment()) ##grep one OSL curves and plot the first curve OSLcurve <- get_RLum(OSL.SARMeasurement$Sequence.Object, recordType="OSL")[[1]] ##(3) How to see the structure of an object? structure_RLum(OSL.SARMeasurement$Sequence.Object) replicate_RLum General replication function for RLum S4 class objects Description Function replicates RLum S4 class objects and returns a list for this objects Usage replicate_RLum(object, times = NULL) report_RLum 229 Arguments object RLum (required): an RLum object times integer (optional): number for times each element is repeated element Value Returns a list of the object to be repeated Function version 0.1.0 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). replicate_RLum(): General replication function for RLum S4 class objects. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also RLum report_RLum Create a HTML report for (RLum) objects Description This function creates a HTML report for a given object, listing its complete structure and content. The object itself is saved as a serialised .Rds file. The report file serves both as a convenient way of browsing through objects with complex data structures as well as a mean of properly documenting and saving objects. Usage report_RLum(object, file = tempfile(), title = "RLum.Report", compact = TRUE, timestamp = TRUE, launch.browser = FALSE, css.file = NULL, quiet = TRUE, clean = TRUE, ...) 230 report_RLum Arguments object (required): The object to be reported on, preferably of any RLum-class. file character (with default): A character string naming the output file. If no filename is provided a temporary file is created. title character (with default): A character string specifying the title of the document. compact logical (with default): When TRUE the following report components are hidden: @.pid, @.uid, 'Object structure', 'Session Info' and only the first and last 5 rows of long matrices and data frames are shown. See details. timestamp logical (with default): TRUE to add a timestamp to the filename (suffix). launch.browser logical (with default): TRUE to open the HTML file in the system’s default web browser after it has been rendered. css.file character (optional): Path to a CSS file to change the default styling of the HTML document. quiet logical (with default): TRUE to supress printing of the pandoc command line. clean logical (with default): TRUE to clean intermediate files created during rendering. ... further arguments passed to or from other methods and to control the document’s structure (see details). Details The HTML report is created with rmarkdown::render and has the following structure: Section Header Object content Object structure File Session Info Plots Description A summary of general characteristics of the object A comprehensive list of the complete structure and content of the provided object. Summary of the objects structure given as a table Information on the saved RDS file Captured output from sessionInfo() (optional) For RLum-class objects a variable number of plots The structure of the report can be controlled individually by providing one or more of the following arguments (all logical): Argument header main structure rds session plot Description Hide or show general information on the object Hide or show the object’s content Hide or show object’s structure Hide or show information on the saved RDS file Hide or show the session info Hide or show the plots (depending on object) Note that these arguments have higher precedence than compact. Further options that can be provided via the ... argument: Argument short_table theme Description If TRUE only show the first and last 5 rows of lang tables. Specifies the Bootstrap theme to use for the report. Valid themes include "default", "cerulean", "journal", report_RLum highlight css 231 Specifies the syntax highlighting style. Supported styles include "default", "tango", "pygments", "kate", "m TRUE or FALSE to enable/disable custom CSS styling The following arguments can be used to customise the report via CSS (Cascading Style Sheets): Argument font_family headings_size content_color Description Define the font family of the HTML document (default: arial) Size of the to
tags used to define HTML headings (default: 166%). Color of the object’s content (default: #a72925). Note that these arguments must all be of class character and follow standard CSS syntax. For exhaustive CSS styling you can provide a custom CSS file for argument css.file. CSS styling can be turned of using css = FALSE. Value Writes a HTML and .Rds file. Function version 0.1.0 (2018-01-21 17:22:38) How to cite Burow, C. (2018). report_RLum(): Create a HTML report for (RLum) objects. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note This function requires the R packages ’rmarkdown’, ’pander’ and ’rstudioapi’. Author(s) Christoph Burow, University of Cologne (Germany) R Luminescence Package Team See Also rmarkdown::render, pander::pander_return, pander::openFileInOS, rstudioapi::viewer, browseURL Examples ## Not run: ## Example: RLum.Results ---# load example data data("ExampleData.DeValues") 232 Risoe.BINfileData2RLum.Analysis # apply the MAM-3 age model and save results mam <- calc_MinDose(ExampleData.DeValues$CA1, sigmab = 0.2) # create the HTML report report_RLum(object = mam, file = "~/CA1_MAM.Rmd", timestamp = FALSE, title = "MAM-3 for sample CA1") # when creating a report the input file is automatically saved to a # .Rds file (see saveRDS()). mam_report <- readRDS("~/CA1_MAM.Rds") all.equal(mam, mam_report) ## Example: Temporary file & Viewer/Browser ---# (a) # Specifying a filename is not necessarily required. If no filename is provided, # the report is rendered in a temporary file. If you use the RStudio IDE, the # temporary report is shown in the interactive Viewer pane. report_RLum(object = mam) # (b) # Additionally, you can view the HTML report in your system's default web browser. report_RLum(object = mam, launch.browser = TRUE) ## Example: RLum.Analysis ---data("ExampleData.RLum.Analysis") # create the HTML report (note that specifying a file # extension is not necessary) report_RLum(object = IRSAR.RF.Data, file = "~/IRSAR_RF") ## Example: RLum.Data.Curve ---data.curve <- get_RLum(IRSAR.RF.Data)[[1]] # create the HTML report report_RLum(object = data.curve, file = "~/Data_Curve") ## Example: Any other object ---x <- list(x = 1:10, y = runif(10, -5, 5), z = data.frame(a = LETTERS[1:20], b = dnorm(0:9)), NA) report_RLum(object = x, file = "~/arbitray_list") ## End(Not run) Risoe.BINfileData2RLum.Analysis 233 Risoe.BINfileData2RLum.Analysis Convert Risoe.BINfileData object to an RLum.Analysis object Description Converts values from one specific position of a Risoe.BINfileData S4-class object to an RLum.Analysis object. Usage Risoe.BINfileData2RLum.Analysis(object, pos = NULL, grain = NULL, run = NULL, set = NULL, ltype = NULL, dtype = NULL, protocol = "unknown", keep.empty = TRUE, txtProgressBar = FALSE) Arguments object Risoe.BINfileData (required): Risoe.BINfileData object pos numeric (optional): position number of the Risoe.BINfileData object for which the curves are stored in the RLum.Analysis object. If length(position)>1 a list of RLum.Analysis objects is returned. If nothing is provided every position will be converted. If the position is not valid NA is returned. grain vector, numeric (optional): grain number from the measurement to limit the converted data set (e.g., grain = c(1:48)). Please be aware that this option may lead to unwanted effects, as the output is strictly limited to the choosen grain number for all position numbers run vector, numeric (optional): run number from the measurement to limit the converted data set (e.g., run = c(1:48)). set vector, numeric (optional): set number from the measurement to limit the converted data set (e.g., set = c(1:48)). ltype vector, character (optional): curve type to limit the converted data. Commonly allowed values are: IRSL, OSL, TL, RIR, RBR and USER (see also Risoe.BINfileData) dtype vector, character (optional): data type to limit the converted data. Commonly allowed values are listed in Risoe.BINfileData protocol character (optional): sets protocol type for analysis object. Value may be used by subsequent analysis functions. keep.empty logical (with default): If TRUE (default) an RLum.Analysis object is returned even if it does not contain any records. Set to FALSE to discard all empty objects. txtProgressBar logical (with default): enables or disables txtProgressBar. Details The RLum.Analysis object requires a set of curves for specific further protocol analyses. However, the Risoe.BINfileData usually contains a set of curves for different aliquots and different protocol types that may be mixed up. Therefore, a conversion is needed. Value Returns an RLum.Analysis object. 234 RLum-class Function version 0.4.2 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). Risoe.BINfileData2RLum.Analysis(): Convert Risoe.BINfileData object to an RLum.Analysis object. Function version 0.4.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note The protocol argument of the RLum.Analysis object is set to ’unknown’ if not stated otherwise. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also Risoe.BINfileData, RLum.Analysis, read_BIN2R Examples ##load data data(ExampleData.BINfileData, envir = environment()) ##convert values for position 1 Risoe.BINfileData2RLum.Analysis(CWOSL.SAR.Data, pos = 1) RLum-class Class "RLum" Description Abstract class for data in the package Luminescence Sublasses are: Usage ## S4 method for signature 'RLum' replicate_RLum(object, times = NULL) Arguments object RLum (required): an object of class RLum times integer (optional): number for times each element is repeated element RLum-class 235 Details RLum-class | |—-RLum.Data |—-|– RLum.Data.Curve |—-|– RLum.Data.Spectrum |—-|– RLum.Data.Image |—-RLum.Analysis |—-RLum.Results Methods (by generic) • replicate_RLum: Replication method RLum-objects Slots originator Object of class character containing the name of the producing function for the object. Set automatically by using the function set_RLum. info Object of class list for additional information on the object itself .uid Object of class character for a unique object identifier. This id is usually calculated using the internal function create_UID() if the funtion set_RLum is called. .pid Object of class character for a parent id. This allows nesting RLum-objects at will. The parent id can be the uid of another object. Objects from the Class A virtual Class: No objects can be created from it. Class version 0.4.0 How to cite Kreutzer, S. (2018). RLum-class(): Class ’RLum’. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note RLum is a virtual class. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Université Bordeaux Montaigne (France) See Also RLum.Data, RLum.Data.Curve, RLum.Data.Spectrum, RLum.Data.Image, RLum.Analysis, RLum.Results, methods_RLum 236 Second2Gray Examples showClass("RLum") Second2Gray Converting equivalent dose values from seconds (s) to gray (Gy) Description Conversion of absorbed radiation dose in seconds (s) to the SI unit gray (Gy) including error propagation. Normally used for equivalent dose data. Usage Second2Gray(data, dose.rate, error.propagation = "omit") Arguments data data.frame (required): input values, structure: data (values[,1]) and data error (values [,2]) are required dose.rate RLum.Results, data.frame or numeric (required): RLum.Results needs to be orginated from the function calc_SourceDoseRate, for vector dose rate in Gy/s and dose rate error in Gy/s error.propagation character (with default): error propagation method used for error calculation (omit, gaussian or absolute), see details for further information Details Calculation of De values from seconds (s) to gray (Gy) De[Gy] = De[s] ∗ DoseRate[Gy/s]) Provided calculation error propagation methods for error calculation (with ’se’ as the standard error and ’DR’ of the dose rate of the beta-source): (1) omit (default) se(De)[Gy] = se(De)[s] ∗ DR[Gy/s] In this case the standard error of the dose rate of the beta-source is treated as systematic (i.e. nonrandom), it error propagation is omitted. However, the error must be considered during calculation of the final age. (cf. Aitken, 1985, pp. 242). This approach can be seen as method (2) (gaussian) for the case the (random) standard error of the beta-source calibration is 0. Which particular method is requested depends on the situation and cannot be prescriptive. (2) gaussian error propagation se(De)[Gy] = p ((DR[Gy/s] ∗ se(De)[s])2 + (De[s] ∗ se(DR)[Gy/s])2 ) Second2Gray 237 Applicable under the assumption that errors of De and se are uncorrelated. (3) absolute error propagation se(De)[Gy] = abs(DR[Gy/s] ∗ se(De)[s]) + abs(De[s] ∗ se(DR)[Gy/s]) Applicable under the assumption that errors of De and se are not uncorrelated. Value Returns a data.frame with converted values. Function version 0.6.0 (2018-01-21 17:22:38) How to cite Kreutzer, S., Dietze, M., Fuchs, M.C. (2018). Second2Gray(): Converting equivalent dose values from seconds (s) to gray (Gy). Function version 0.6.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note If no or a wrong error propagation method is given, the execution of the function is stopped. Furthermore, if a data.frame is provided for the dose rate values is has to be of the same length as the data frame provided with the argument data Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) Michael Dietze, GFZ Potsdam (Germany) Margret C. Fuchs, HZDR, Helmholtz-Institute Freiberg for Resource Technology (Germany) R Luminescence Package Team References Aitken, M.J., 1985. Thermoluminescence dating. Academic Press. See Also calc_SourceDoseRate Examples ##(A) for known source dose rate at date of measurement ## - load De data from the example data help file data(ExampleData.DeValues, envir = environment()) ## - convert De(s) to De(Gy) Second2Gray(ExampleData.DeValues$BT998, c(0.0438,0.0019)) 238 set_Risoe.BINfileData ##(B) for source dose rate calibration data ## - calculate source dose rate first dose.rate <- calc_SourceDoseRate(measurement.date = "2012-01-27", calib.date = "2014-12-19", calib.dose.rate = 0.0438, calib.error = 0.0019) # read example data data(ExampleData.DeValues, envir = environment()) # apply dose.rate to convert De(s) to De(Gy) Second2Gray(ExampleData.DeValues$BT998, dose.rate) set_Risoe.BINfileData General accessor function for RLum S4 class objects Description Function calls object-specific get functions for RisoeBINfileData S4 class objects. Usage set_Risoe.BINfileData(METADATA = data.frame(), DATA = list(), .RESERVED = list()) Arguments METADATA x DATA x .RESERVED x Details The function provides a generalised access point for specific Risoe.BINfileData objects. Depending on the input object, the corresponding get function will be selected. Allowed arguments can be found in the documentations of the corresponding Risoe.BINfileData class. Value Return is the same as input objects as provided in the list. Function version 0.1 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). set_Risoe.BINfileData(): General accessor function for RLum S4 class objects. Function version 0.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence set_RLum 239 Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also Risoe.BINfileData set_RLum General set function for RLum S4 class objects Description Function calls object-specific set functions for RLum S4 class objects. Usage set_RLum(class, originator, .uid = create_UID(), .pid = NA_character_, ...) Arguments class RLum (required): name of the S4 class to create originator character (automatic): contains the name of the calling function (the function that produces this object); can be set manually. .uid character (automatic): sets an unique ID for this object using the internal C++ function create_UID. .pid character (with default): option to provide a parent id for nesting at will. ... further arguments that one might want to pass to the specific set method Details The function provides a generalised access point for specific RLum objects. Depending on the given class, the corresponding method to create an object from this class will be selected. Allowed additional arguments can be found in the documentations of the corresponding RLum class: • RLum.Data.Curve, • RLum.Data.Image, • RLum.Data.Spectrum, • RLum.Analysis, • RLum.Results Value Returns an object of the specified class. Function version 0.3.0 (2018-01-21 17:22:38) 240 smooth_RLum How to cite Kreutzer, S. (2018). set_RLum(): General set function for RLum S4 class objects. Function version 0.3.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also RLum.Data.Curve, RLum.Data.Image, RLum.Data.Spectrum, RLum.Analysis, RLum.Results Examples ##produce empty objects from each class set_RLum(class = "RLum.Data.Curve") set_RLum(class = "RLum.Data.Spectrum") set_RLum(class = "RLum.Data.Spectrum") set_RLum(class = "RLum.Analysis") set_RLum(class = "RLum.Results") ##produce a curve object with arbitrary curve values object <- set_RLum( class = "RLum.Data.Curve", curveType = "arbitrary", recordType = "OSL", data = matrix(c(1:100,exp(-c(1:100))),ncol = 2)) ##plot this curve object plot_RLum(object) smooth_RLum Smoothing of data Description Function calls the object-specific smooth functions for provided RLum S4-class objects. Usage smooth_RLum(object, ...) ## S4 method for signature 'list' smooth_RLum(object, ...) Arguments object ... RLum (required): S4 object of class RLum further arguments passed to the specifc class method smooth_RLum 241 Details The function provides a generalised access point for specific RLum objects. Depending on the input object, the corresponding function will be selected. Allowed arguments can be found in the documentations of the corresponding RLum class. The smoothing is based on an internal function called .smoothing. Value An object of the same type as the input object is provided Methods (by class) • list: Returns a list of RLum objects that had been passed to smooth_RLum Function version 0.1.0 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). smooth_RLum(): Smoothing of data. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.Rproject.org/package=Luminescence Note Currenlty only RLum objects of class RLum.Data.Curve and RLum.Analysis (with curve data) are supported! Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also RLum.Data.Curve, RLum.Analysis Examples ##load example data data(ExampleData.CW_OSL_Curve, envir = environment()) ##create RLum.Data.Curve object from this example curve
= Θ With Θ an arbitray, user defined, threshold. Values above the threshold indicating curves comprising a signal. Note: the absolute difference of E(X) and V ar(x) instead of the ratio was chosen as both terms can become 0 which would result in 0 or Inf, if the ratio is calculated. Value The function returns ———————————– [ NUMERICAL OUTPUT ] ———————————– RLum.Results-object slot:****@data Element $unique_pairs $selection_id $selection_full Type data.frame numeric data.frame Description the unique position and grain pairs the selection as record ID implemented models used in the baSAR-model core slot:****@info The original function call Output variation For cleanup = TRUE the same object as the input is returned, but cleaned up (invalid curves were removed). This means: Either an Risoe.BINfileData or an RLum.Analysis object is returned in such cases. An Risoe.BINfileData object can be exported to a BIN-file by using the function write_R2BIN. Function version 0.2.0 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). verify_SingleGrainData(): Verify single grain data sets and check for invalid grains, i.e. zero-light level grains. Function version 0.2.0. In: Kreutzer, S., Burow, C., Dietze, M., verify_SingleGrainData 251 Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note This function can work with Risoe.BINfileData objects or RLum.Analysis objects (or a list of it). However, the function is highly optimised for Risoe.BINfileData objects as it make sense to remove identify invalid grains before the conversion to an RLum.Analysis object. The function checking for invalid curves works rather robust and it is likely that Reg0 curves within a SAR cycle are removed as well. Therefore it is strongly recommended to use the argument cleanup = TRUE carefully. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also Risoe.BINfileData, RLum.Analysis, write_R2BIN, read_BIN2R Examples ##01 - basic example I ##just show how to apply the function data(ExampleData.XSYG, envir = environment()) ##verify and get data.frame out of it verify_SingleGrainData(OSL.SARMeasurement$Sequence.Object)$selection_full ##02 - basic example II data(ExampleData.BINfileData, envir = environment()) id <- verify_SingleGrainData(object = CWOSL.SAR.Data, cleanup_level = "aliquot")$selection_id ## Not run: ##03 - advanced example I ##importing and exporting a BIN-file ##select and import file file <- file.choose() object <- read_BIN2R(file) ##remove invalid aliquots(!) object <- verify_SingleGrainData(object, cleanup = TRUE) ##export to new BIN-file write_R2BIN(object, paste0(dirname(file),"/", basename(file), "_CLEANED.BIN")) ## End(Not run) 252 write_R2BIN write_R2BIN Export Risoe.BINfileData into Risoe BIN-file Description Exports a Risoe.BINfileData object in a *.bin or *.binx file that can be opened by the Analyst software or other Risoe software. Usage write_R2BIN(object, file, version, compatibility.mode = FALSE, txtProgressBar = TRUE) Arguments object Risoe.BINfileData (required): input object to be stored in a bin file. file character (required): file name and path of the output file • [WIN]: write_R2BIN(object, "C:/Desktop/test.bin") • [MAC/LINUX]: write_R2BIN("/User/test/Desktop/test.bin") version character (optional): version number for the output file. If no value is provided the highest version number from the Risoe.BINfileData is taken automatically. Note: This argument can be used to convert BIN-file versions. compatibility.mode logical (with default): this option recalculates the position values if necessary and set the max. value to 48. The old position number is appended as comment (e.g., ’OP: 70). This option accounts for potential compatibility problems with the Analyst software. It further limits the maximum number of points per curve to 9,999. If a curve contains more data the curve data got binned using the smallest possible bin width. txtProgressBar logical (with default): enables or disables txtProgressBar. Details The structure of the exported binary data follows the data structure published in the Appendices of the Analyst manual p. 42. If LTYPE, DTYPE and LIGHTSOURCE are not of type character, no transformation into numeric values is done. Value Write a binary file. Function version 0.4.4 (2018-01-21 17:22:38) write_R2BIN 253 How to cite Kreutzer, S. (2018). write_R2BIN(): Export Risoe.BINfileData into Risoe BIN-file. Function version 0.4.4. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence Note The function just roughly checks the data structures. The validity of the output data depends on the user. The validity of the file path is not further checked. BIN-file conversions using the argument version may be a lossy conversion, depending on the chosen input andoutput data (e.g., conversion from version 08 to 07 to 06 to 04 or 03). Warning Although the coding was done carefully it seems that the BIN/BINX-files produced by Risoe DA 15/20 TL/OSL readers slightly differ on the byte level. No obvious differences are observed in the METADATA, however, the BIN/BINX-file may not fully compatible, at least not similar to the once directly produced by the Risoe readers! ROI definitions (introduced in BIN-file version 8) are not supported! There are furthermore ignored by the function read_BIN2R. Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team References DTU Nutech, 2016. The Squence Editor, Users Manual, February, 2016. http://www.nutech. dtu.dk/english/products-and-services/radiation-instruments/tl_osl_reader/manuals See Also read_BIN2R, Risoe.BINfileData, writeBin Examples ##uncomment for usage ##data(ExampleData.BINfileData, envir = environment()) ##write_R2BIN(CWOSL.SAR.Data, file="[your path]/output.bin") 254 write_RLum2CSV write_RLum2CSV Export RLum-objects to CSV Description This function exports RLum-objects to CSV-files using the R function utils::write.table. All RLumobjects are supported, but the export is lossy, i.e. the pure numerical values are exported only. Information that cannot be coerced to a data.frame or a matrix are discarded as well as metadata. Usage write_RLum2CSV(object, path = NULL, prefix = "", export = TRUE, ...) Arguments object RLum or a list of RLum objects (required): objects to be written path character (optional): character string naming folder for the output to be written. If nothing is provided path will be set to the working directory. Note: this argument is ignored if the the argument export is set to FALSE. prefix character (with default): optional prefix to name the files. This prefix is valid for all written files export logical (with default): enable or disable the file export. If set to FALSE nothing is written to the file connection, but a list comprising objects of type data.frame and matrix is returned instead ... further arguments that will be passed to the function utils::write.table. All arguments except the argument file are supported Details However, in combination with the implemented import functions, nearly every supported import data format can be exported to CSV-files, this gives a great deal of freedom in terms of compatibility with other tools. Input is a list of objects If the input is a list of objects all explicit function arguments can be provided as list. Value The function returns either a CSV-file (or many of them) or for the option export == FALSE a list comprising objects of type data.frame and matrix Function version 0.1.1 (2018-01-21 17:22:38) How to cite Kreutzer, S. (2018). write_RLum2CSV(): Export RLum-objects to CSV. Function version 0.1.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence write_RLum2CSV Author(s) Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) R Luminescence Package Team See Also RLum.Analysis, RLum.Data, RLum.Results, utils::write.table Examples ##transform values to a list data(ExampleData.BINfileData, envir = environment()) object <- Risoe.BINfileData2RLum.Analysis(CWOSL.SAR.Data)[[1]] write_RLum2CSV(object, export = FALSE) ## Not run: ##export data to CSV-files in the working directory; ##BE CAREFUL, this example creates many files on your file system data(ExampleData.BINfileData, envir = environment()) object <- Risoe.BINfileData2RLum.Analysis(CWOSL.SAR.Data)[[1]] write_RLum2CSV(object, export = FALSE) ## End(Not run) 255 Index calc_Kars2008, 80 calc_OSLLxTxRatio, 92 calc_Statistics, 98 calc_ThermalLifetime, 100 calc_TLLxTxRatio, 102 fit_SurfaceExposure, 149 plot_FilterCombinations, 181 verify_SingleGrainData, 249 ∗Topic datasets BaseDataSet.CosmicDoseRate, 48 ExampleData.Al2O3C, 124 ExampleData.BINfileData, 125 ExampleData.CW_OSL_Curve, 126 ExampleData.DeValues, 127 ExampleData.Fading, 128 ExampleData.portableOSL, 132 ExampleData.RLum.Analysis, 132 ExampleData.RLum.Data.Image, 133 ExampleData.SurfaceExposure, 134 ExampleData.XSYG, 137 extdata, 139 ∗Topic dplot Analyse_SAR.OSLdata, 38 calc_FuchsLang2001, 73 fit_CWCurve, 142 fit_LMCurve, 145 plot_DRTResults, 178 plot_Risoe.BINfileData, 201 plot_RLum, 203 ∗Topic manip apply_CosmicRayRemoval, 43 apply_EfficiencyCorrection, 45 calc_SourceDoseRate, 96 CW2pHMi, 113 CW2pLM, 117 CW2pLMi, 119 CW2pPMi, 121 extract_IrradiationTimes, 140 merge_Risoe.BINfileData, 162 Risoe.BINfileData2RLum.Analysis, 233 Second2Gray, 236 sTeve, 242 ∗Topic IO convert_Activity2Concentration, 106 convert_BIN2CSV, 108 convert_Daybreak2CSV, 109 convert_PSL2CSV, 110 convert_RLum2Risoe.BINfileData, 111 convert_XSYG2CSV, 112 extract_IrradiationTimes, 140 merge_Risoe.BINfileData, 162 PSL2Risoe.BINfileData, 217 read_BIN2R, 218 read_Daybreak2R, 220 read_PSL2R, 222 read_SPE2R, 223 read_XSYG2R, 225 write_R2BIN, 252 write_RLum2CSV, 254 ∗Topic aplot plot_FilterCombinations, 181 plot_RLum.Analysis, 205 plot_RLum.Data.Curve, 207 plot_RLum.Data.Image, 208 plot_RLum.Data.Spectrum, 210 plot_RLum.Results, 214 ∗Topic classes RLum-class, 234 ∗Topic datagen analyse_Al2O3C_CrossTalk, 7 analyse_Al2O3C_ITC, 9 analyse_Al2O3C_Measurement, 11 analyse_baSAR, 13 analyse_FadingMeasurement, 20 analyse_IRSAR.RF, 23 analyse_pIRIRSequence, 30 analyse_portableOSL, 33 analyse_SAR.CWOSL, 34 Analyse_SAR.OSLdata, 38 analyse_SAR.TL, 41 calc_AverageDose, 54 calc_FadingCorr, 65 calc_gSGC, 75 256 INDEX tune_Data, 245 verify_SingleGrainData, 249 ∗Topic models fit_CWCurve, 142 fit_LMCurve, 145 ∗Topic package Luminescence-package, 5 ∗Topic plot analyse_pIRIRSequence, 30 analyse_portableOSL, 33 analyse_SAR.CWOSL, 34 analyse_SAR.TL, 41 ∗Topic utilities bin_RLum.Data, 50 get_Risoe.BINfileData, 156 get_RLum, 157 length_RLum, 161 merge_RLum, 163 names_RLum, 167 replicate_RLum, 228 set_Risoe.BINfileData, 238 set_RLum, 239 smooth_RLum, 240 structure_RLum, 243 abline, 205 analyse_Al2O3C_CrossTalk, 7, 124, 125 analyse_Al2O3C_ITC, 8, 9, 13, 124, 125 analyse_Al2O3C_Measurement, 11, 124, 125 analyse_baSAR, 13 analyse_FadingMeasurement, 20, 22, 65, 82 analyse_IRSAR.RF, 23 analyse_pIRIRSequence, 30, 40, 176, 177 analyse_portableOSL, 33 analyse_SAR.CWOSL, 30–32, 34, 40, 95, 176, 177 Analyse_SAR.OSLdata, 37, 38, 95 analyse_SAR.TL, 41, 104 app_RLum, 46 apply_CosmicRayRemoval, 43, 45 apply_EfficiencyCorrection, 45 approx, 115, 181, 183, 226, 228 array, 101 as, 47 as.data.frame, 244 base::readBin, 220 BaseDataSet.CosmicDoseRate, 48, 64 bibentry, 247 bin_RLum.Data, 50 boxplot, 216 boxplot.default, 19 browseURL, 231 257 calc_AliquotSize, 52 calc_AverageDose, 54 calc_CentralDose, 57, 61, 73, 75, 80, 86, 91, 105 calc_CommonDose, 59, 59, 73, 75, 80, 86, 91 calc_CosmicDoseRate, 61 calc_FadingCorr, 21, 65 calc_FastRatio, 68 calc_FiniteMixture, 59, 61, 70, 75, 80, 86, 91 calc_FuchsLang2001, 59, 61, 73, 73, 80, 86, 91, 105 calc_gSGC, 75 calc_HomogeneityTest, 77 calc_IEU, 78 calc_Kars2008, 80 calc_MaxDose, 84, 91 calc_MinDose, 59, 61, 73, 75, 80, 85, 86, 87 calc_OSLLxTxRatio, 15, 16, 18, 19, 23, 32, 35, 37, 39, 40, 92 calc_SourceDoseRate, 96, 236, 237 calc_Statistics, 98, 169, 178, 192, 216 calc_ThermalLifetime, 100 calc_TLLxTxRatio, 42, 43, 102 calc_WodaFuchs2008, 104 call, 31, 53, 58, 60, 63, 72, 74, 76, 77, 79, 89, 148, 183, 247 character, 7, 9, 11, 14, 15, 17, 21, 24, 25, 30, 35, 38, 39, 41, 43, 47, 55, 67, 71, 75, 93, 96, 99, 100, 106, 108–110, 112, 140, 143, 146, 153, 154, 158, 162, 165, 167–170, 175, 176, 178, 179, 184, 189, 191, 192, 194, 197, 198, 201, 202, 205, 208, 210, 211, 215, 216, 218, 219, 221–223, 225, 230, 231, 233, 235, 236, 239, 247, 249, 252, 254 confint, 143, 144, 146, 148 contour, 213 convert_Activity2Concentration, 106 convert_BIN2CSV, 108 convert_Daybreak2CSV, 109 convert_PSL2CSV, 110 convert_RLum2Risoe.BINfileData, 111 convert_XSYG2CSV, 112 CW2pHMi, 113, 118, 120, 123, 203 CW2pLM, 115, 117, 120, 123, 146, 203 CW2pLMi, 115, 118, 119, 123, 203 CW2pPMi, 115, 118, 120, 121, 203 data.frame, 21, 31, 36, 39, 42, 45, 47, 53, 54, 57–60, 63, 67–70, 72, 74–77, 79–82, 84, 87, 89, 93, 99, 103, 105, 106, 258 108–110, 112, 114, 117, 119, 122, 125, 127–129, 131, 134, 137, 142, 144, 146, 148, 150, 159, 168, 178, 181, 184, 189, 191, 194, 197, 215, 219, 227, 236, 237, 246, 247, 254 data.table::data.table, 221 Date, 96 density, 192, 193 devtools::install_github, 160 ExampleData.Al2O3C, 124 ExampleData.BINfileData, 125 ExampleData.CW_OSL_Curve, 126 ExampleData.DeValues, 127 ExampleData.Fading, 128 ExampleData.FittingLM, 130 ExampleData.LxTxData, 131 ExampleData.LxTxOSLData, 131 ExampleData.portableOSL, 132 ExampleData.RLum.Analysis, 132 ExampleData.RLum.Data.Image, 133 ExampleData.SurfaceExposure, 134, 152 ExampleData.XSYG, 137 expression, 186 extdata, 139 extract_IrradiationTimes, 23, 140 fit_CWCurve, 69, 70, 142, 149 fit_LMCurve, 115, 118, 120, 123, 145, 145 fit_SurfaceExposure, 134, 149 formula, 36 get_Layout, 153 get_Quote, 154 get_rightAnswer, 155 get_Risoe.BINfileData, 156 get_RLum, 7, 9, 11, 28, 29, 31, 32, 36, 37, 42, 43, 53, 58, 60, 63, 67, 70, 72, 77, 79, 89, 95, 97, 102, 140, 145, 149, 157, 157, 187, 205, 224, 247 get_RLum,list-method (get_RLum), 157 get_RLum,NULL-method (get_RLum), 157 GitHub-API, 158 github_branches (GitHub-API), 158 github_commits (GitHub-API), 158 github_issues (GitHub-API), 158 glm, 147 graphics::boxplot, 216 graphics::grid, 182 graphics::hist, 55, 56 graphics::legend, 24, 182 graphics::matplot, 102 hist, 189, 190 INDEX install_DevelopmentVersion, 160 integer, 15, 17, 21, 25, 30, 35, 41, 43, 44, 54, 55, 65, 76, 93, 96, 99, 103, 146, 158, 162, 169, 175, 176, 185, 194, 205, 210, 219, 229, 234, 242, 244 legend, 194, 216 length_RLum, 161 list, 7, 9, 12, 14, 15, 17, 21, 24, 27, 30, 31, 35, 36, 39, 41, 47, 48, 53, 55, 58, 60, 63, 69, 72, 74, 76, 77, 79, 89, 94, 97, 100, 103, 111, 127, 128, 134, 140, 148, 150, 151, 153, 157, 159, 164, 165, 176, 181, 194, 203, 205, 218, 219, 221, 225, 229, 235, 244, 247, 254 list.files, 219, 220 lm, 114, 115, 118, 119, 122, 185–187 logical, 7, 9, 12, 15, 21, 24, 25, 30, 33, 35, 39, 44, 52, 54, 55, 57, 59, 61, 65, 69, 71, 74, 76, 77, 79, 81, 85, 87, 93, 99, 100, 105, 106, 140, 143, 146, 150, 154, 157, 158, 160, 162, 165, 168–170, 176, 178, 179, 181, 184, 185, 189, 191, 192, 194, 197, 198, 205, 207, 208, 210, 211, 214–216, 218, 219, 221–223, 226, 230, 233, 244, 247, 249, 252, 254 Luminescence (Luminescence-package), 5 Luminescence-package, 5 Luminescence::github_branches, 160 matrix, 47, 72, 101, 108–110, 112, 144, 181, 194, 210, 215, 254 merge_Risoe.BINfileData, 162, 220 merge_RLum, 163 methods::as, 48 methods::language, 28 methods_RLum, 235 minpack.lm::nlsLM, 26, 29, 82, 145, 149, 151, 152, 185, 187 mle2, 89 model_LuminescenceSignals, 165 mtext, 189 names_RLum, 167 nlminb, 88 nls, 25, 27, 29, 142–149, 185–187 numeric, 7, 9, 11, 12, 14, 15, 17, 24–26, 30, 35, 39, 41, 43, 52, 54, 55, 57, 59, 61, 65, 67–71, 74, 79, 81, 82, 85, 87, 89, 93, 96, 99–101, 105, 143, 146, 150, 165, 166, 168, 169, 175, 178, 179, INDEX 259 181, 185, 189, 192, 197, 198, 202, 211, 215, 216, 219, 233, 236, 246, 249 pander::openFileInOS, 231 pander::pander_return, 231 par, 194 parallel::mclapply, 29 pchisq, 78 pdf, 205, 214 persp, 211, 213 plot, 59, 74, 75, 80, 81, 143, 145, 149, 150, 175, 177, 179, 189, 190, 192–195, 199, 206–209, 213–216 plot.default, 41, 100, 166, 176, 216 plot_AbanicoPlot, 99, 168 plot_DetPlot, 175 plot_DRTResults, 178 plot_FilterCombinations, 181 plot_GrowthCurve, 10, 11, 15, 16, 18, 19, 30, 32, 35, 37, 40, 41, 43, 81, 82, 95, 184 plot_Histogram, 172, 188, 199 plot_KDE, 172, 191, 199, 242 plot_NRt, 194 plot_RadialPlot, 172, 196 plot_Risoe.BINfileData, 201 plot_RLum, 97, 138, 203, 206, 208, 209, 213, 215 plot_RLum.Analysis, 138, 204, 205 plot_RLum.Data.Curve, 204, 206, 207 plot_RLum.Data.Image, 204, 208 plot_RLum.Data.Spectrum, 138, 204, 210 plot_RLum.Results, 204, 214 plot_ViolinPlot, 215 plotly::plot_ly, 213 profile, 144 profile.mle2, 89 PSL2Risoe.BINfileData, 217 raster, 208, 209 raster::contour, 209 raster::plot, 209 raster::plotRGB, 209 raster::raster, 209, 225 raw, 219 read.table, 56 read_BIN2R, 15–17, 19, 23, 38, 40, 108, 140, 142, 163, 201, 203, 218, 234, 251, 253 read_Daybreak2R, 109, 110, 220 read_PSL2R, 33, 110, 111, 217, 222 read_SPE2R, 133, 209, 223 read_XSYG2R, 23, 112, 113, 124, 137, 138, 140–142, 225 readBin, 225 readxl::read_excel, 15, 17, 19 regex, 226 replicate_RLum, 228 replicate_RLum,RLum-method (RLum-class), 234 report_RLum, 229 Risoe.BINfileData, 14, 16, 37–40, 111, 112, 125, 142, 156, 162, 163, 201–203, 217–220, 233, 234, 238, 239, 249–253 Risoe.BINfileData2RLum.Analysis, 219, 232 rjags::coda.samples, 19 rjags::jags.model, 17, 19 rjags::rjags, 18 RLum, 47, 157, 161, 164, 167, 203, 229, 234, 239–241, 243, 254 RLum-class, 234 RLum.Analysis, 7, 9, 11, 21, 24, 29, 30, 32–37, 41, 43, 47, 68, 70, 108, 110–113, 124, 132, 137, 138, 140–142, 157, 158, 162, 164, 167, 175, 194, 195, 204, 205, 217–223, 226–228, 233–235, 239–241, 243, 249–251, 255 RLum.Data, 50, 51, 108, 110, 111, 113, 235, 255 RLum.Data.Curve, 34, 47, 51, 68, 70, 93, 95, 103, 111, 112, 114, 115, 117–120, 122, 123, 132, 142, 145, 146, 157, 158, 162, 164, 167, 194, 204, 205, 207, 218, 221–223, 228, 235, 239–241, 243 RLum.Data.Image, 48, 133, 157, 158, 162, 164, 167, 204, 208, 209, 224, 235, 239, 240, 243 RLum.Data.Spectrum, 43–46, 48, 137, 138, 157, 158, 162, 164, 167, 204, 210, 211, 213, 224, 225, 235, 239, 240, 243 RLum.Results, 7, 11, 12, 14, 16, 22, 29, 31–33, 36, 37, 42, 43, 48, 53, 54, 57–60, 63, 65, 67, 69, 70, 72, 74–77, 79, 82, 84, 87, 89, 94, 97, 99, 101, 103–105, 108, 110, 111, 113, 141, 142, 144, 145, 157, 158, 162, 164, 167, 168, 176, 178, 182, 183, 187, 189, 191, 197, 204, 214, 215, 235, 236, 239, 240, 243, 247, 255 260 RLumModel::model_LuminescenceSignals, 165 RLumModel::RLumModel-package, 165 RLumShiny::app_RLum, 46 RLumShiny::RLumShiny-package, 46 rmarkdown::render, 230, 231 rollmean, 194 rstudioapi::viewer, 231 rug, 216 sd, 186 Second2Gray, 96, 97, 236 set.seed, 65, 66 set_Risoe.BINfileData, 238 set_RLum, 235, 239 shiny::runApp, 47 smooth, 43–45 smooth.spline, 43–45, 194 smooth_RLum, 240, 241 smooth_RLum,list-method (smooth_RLum), 240 stats::approx, 45 stats::density, 216 stats::lm, 21, 22 stats::nls, 21 stats::rnorm, 102 stats::uniroot, 65 sTeve, 242 structure_RLum, 243 summary, 144, 148 template_DRAC, 244 tune_Data, 245 txtProgressBar, 65, 219, 221, 223, 233, 252 uniroot, 66, 67, 76, 77, 185, 187 use_DRAC, 106, 247 utils::txtProgressBar, 220 utils::write.table, 108, 110, 111, 113, 254, 255 vector, 14, 21, 24, 30, 33, 38, 41, 65, 93, 114, 119, 122, 142, 201, 210, 219, 223, 233 verify_SingleGrainData, 16, 17, 19, 249 write_R2BIN, 111, 112, 140, 142, 163, 217, 220, 250, 251, 252 write_RLum2CSV, 108–113, 254 writeBin, 253 xml, 226–228 zoo::rollmean, 207 INDEX
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