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Luminescence-Manual

1. Y k b non poisson rse us Yo Y1 k 0 1 1 k Yo Vi k Value Returns an S4 object of type RLum Results Slot data contains a list with the following structure LxTx table data frame LnLx calc_OSLLxTxRatio 53 LnLx BG TnTx TnTx BG Net_LnLx Net_LnLx Error Net_TnTx Error LxTx LxTx Error calc parameters list sigmab LnTx sigmab TnTx k Function version 0 4 5 2015 03 04 00 19 53 Note The results of this function have been cross checked with the Analyst vers 3 24b Access to the results object via get_RLum Results Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References Duller G 2007 Analyst http www nutech dtu dk english media Andre_Universitetsenheder Nutech Produkter 200g 20services Dosimetri radiation_measurement_instruments tl_ osl_reader Manuals analyst_manual_v3_22b ashx Galbraith R F 2002 A note on the variance of a background corrected OSL count Ancient TL 20 2 49 51 Galbraith R F 2014 A further note on the variance of a background corrected OSL count Ancient TL 31 2 1 3 See Also Analyse_SAR OSLdata plot_GrowthCurve analyse_SAR CWOSL Examples load data data ExampleData LxTxOSLData envir environment calculate Lx Tx ratio results lt calc_OSLLxTxRatio Lx data Tx data signal integral c 1
2. 7 Combine all values and truncate all values for t gt max t The number of values for t lt 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 package RLum object with two additional info elements CW2pHMi x t transformed time values CW2pHMi method used method for the production of the new data points 60 CW2pHMi data frame with four columns x time y t transformed count values x t transformed time values method used method for the production of the new data points Function version 0 2 2 2015 03 04 18 42 57 Note According to Bos amp 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 in terpolate 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 K
3. FIT the asymmetric error range is taken from the standard deviation of the natural signal 8 analyse_IRSAR RF For method SLIDE an beta version of an error estimation based on boostrapping is imple mented however this needs further documentation Value A plot optional and an RLum Results object is returned containing the following elements De values data frame containing De values with error gray dashed lines in the plot and further parameters Corrected De values are only provided for the method SLIDE provided the trend correction is applied fit nls nlsModel object Note The output De values should be accessed using the function get_RLum Results Function version 0 3 1 2015 03 23 13 07 08 Note This function assumes that there is no sensitivity change during the measurements natural vs re generated signal which is in contrast to the findings from Buylaert et al 2012 Please note that method FIT has beta status and was not properly tested yet Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References Buylaert J P Jain M Murray A S Thomsen K J Lapp T 2012 IR RF dating of sand sized K feldspar extracts A test of accuracy Radiation Measurements 44 5 6 560 565 doi 10 1016 j radmeas 2012 06 021 Erfurt G Krbetschek M R 2003 IRSAR A single aliquot regenerative dose dating protocol applied t
4. So far each XSYG file can only contain one lt Sample gt lt Sample gt 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 HE Heating element PMT Photomultiplier tube Interpolation is done using the function approx CASE 1 nrow matrix PMT gt nrow matrix HE Missing temperature values from the heating element are calculated using time values from the PMT measurement CASE 2 nrow matrix PMT lt nrow matrix HE Missing count values from the PMT are calculated using time values from the heating element mea surement 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
5. absolute standard error kdemax maxi mum of the KDE skewness skewness and kurtosis kurtosis summary pos numeric or character with default optional position coordinates or key word 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 In case of coordinate specification y coordinate refers to the right y axis polygon col character or numeric with default colour of the polygon showing the dose dispersion around the central value Only relevant if dispersion is specified order logical Order data in ascending order bw character with default bin width chose a numeric value for manual setting 112 plot_KDE output logical Optional output of numerical plot parameters These can be useful to reproduce similar plots Default is FALSE further arguments and graphical parameters passed to plot Details The function allow passing several plot arguments such as main xlab cex However as the figure is an overlay of two separate plots ylim must be specified in the order c ymin_axisl ymax_axisl ymin_axis2 ymax_axis2 when using the cumulative values plot option Similarly if other than the default colours are desired the argument col must be provided with colours in the following order probability density function De values De error bars s
6. containing objects of class RLum Data protocol Object of class character describing the applied measurement protocol S3Class Object of class character Methods show signature object RLum Analysis set_RLum Analysis signature records list protocol character Construction method for RLum Analysis object The slot protocol is optional and prede fined as UNKNOWN by default get_RLum Analysis signature object RLum Analysis Accessor method for RLum Analysis object The slots record id recordType curveType and RLum type are optional to allow for records limited by their id list index number their record type e g recordType OSL or object type Example curve type e g curveType predefined or curveType measured The selection of a specific RLum type object superimposes the default selection Currently supported objects are RLum Data Curve and RLum Data Spectrum The argument get index TRUE just returns a numeric vector with the index of each element in the RLum Analysis object The argument keep object allowing returns an RLum Analysis object instead of the single elements Default is keep object FALSE RLum Data class 145 get_structure RLum Analysis signature object RLum Analysis get meta structure of object as data frame length_RLum Analysis signature object RLum Analysis returns length of the object i e number of records in
7. given dose 2800 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 200 200 200 240 240 106 plot_GrowthCurve 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_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 rege
8. with DO lt calibration dose rate T 1 2 lt half life of the source nuclide here in days t lt time since source calibration in days log 2 T 1 2 equals the decay constant lambda Information on the date of measurements may be taken from the data s original BIN file using e g BINfile lt readBIN2R and the slot BINfile METADATA DATE Allowed source types and related values Source type T 1 2 Reference 1 Sr 90 28 90 y NNDC Brookhaven National Laboratory 2 Am 214 432 6 y NNDC Brookhaven National Laboratory 3 Co 60 5 274 y NNDC Brookhaven National Laboratory calc_SourceDoseRate 55 Value Returns an S4 object of type RLum Results Slot data contains a list with the following structure dose rate data frame dose rate dose rate error parameters list source type halflife dose rate unit Function version 0 1 2015 03 04 14 33 28 Note H Author s Margret C Fuchs AWI Potsdam Germany Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References NNDC Brookhaven National Laboratory http www nndc bnl gov See Also Second2Gray Examples 1 Simple function usage Basic calculation of the dose rate for a specific date dose rate lt calc_SourceDoseRate measurement date 2012 01 27 calib date 2014 12 19 calib dose rate 0 0438 calib error 0 0019 show results get
9. 0 2 This value represents the expected overdispersion in the data should the sample be well bleached Cunningham amp Walling 2012 p 100 log logical with default fit the un logged three parameter minimum dose model to De data par numeric with default apply the 3 or 4 parametric minimum age model par 3 or par 4 bootstrap init values plot Details numeric with default starting values for gamma sigma p0 and mu Custom values need to be provided in a vector of length three in the form of c gamma sigma po logical with default plot output TRUE FALSE further arguments for bootstrapping bs M bs N bs h sigmab sd See details for their usage Data transformation To estimate the maximum dose population and its standard error the three parameter minimum age model of Galbraith et al 1999 is adapted The measured De values are transformed as fol lows 1 convert De values to natural logs calc_MaxDose 45 2 multiply the logged data to creat a mirror image of the De distribution 3 shift De values along x axis by the smallest x value found to obtain only positive values 4 combine in quadrature the measurement error associated with each De value with a relative error specified by sigmab 5 apply the MAM to these data When all calculations are done the results are then converted as follows 1 subtract the x offset 2 multiply the natural logs by 1 3 take the exponent to obtain the maximu
10. 111 114 116 154 plot_RadialPlot 00 113 plot_Risoe BINfileData 118 740 plot_RLum 63 78 120 122 124 126 128 130 143 147 148 150 plot_RLum Analysis 78 120 121 121 plot_RLum Data Curve 720 122 123 plot_RLum Data Image 1 20 121 124 plot_RLum Data Spectrum 78 120 121 126 plot_RLum Results 720 121 129 plotRGB 125 profile 83 87 profile mle2 48 raster 124 126 133 raw 130 readBin 131 133 readBIN2R 75 17 80 81 92 118 119 130 137 140 141 156 readSPE2R 76 125 132 readXSYG2R 77 78 80 81 134 Risoe BINfileData 81 91 92 131 137 140 143 145 155 156 Risoe BINfileData class 14 15 17 70 118 131 137 Risoe BINfileData2RLum Analysis 740 140 142 143 145 Risoe BINfileData2RLum Data Curve 140 142 RLum 59 62 65 68 90 93 95 120 145 148 150 151 RLum class 143 RLum Analysis 5 9 11 12 14 17 19 75 77 78 90 94 95 120 121 134 136 141 143 144 RLum Analysis class 144 RLum Data 144 146 150 RLum Data class 145 RLum Data Curve 59 60 62 69 81 84 90 94 96 120 121 123 136 142 143 160 145 146 RLum Data Curve class 146 RLum Data Image 76 90 94 95 120 121 124 126 133 RLum Data Image class 147 RLum Data Spectrum 20 22 78 90 94 95 120 121 126 128 132 133 146 RLum Data Spectrum class 149 RLum Results 8 11 13 14 18 19 26 30 33 35 36 38 40 44 46 48 52 55 38 80 81
11. 57 Topic datasets BaseDataSet CosmicDoseRate 23 ExampleData BINfileData 69 ExampleData CW_OSL_Curve 71 ExampleData RLum Analysis 75 ExampleData RLum Data Image 76 ExampleData XSYG 77 Topic dplot Analyse_SAR OSLdata 15 calc_FuchsLang2001 39 fit_CWCurve 81 fit_LMCurve 84 157 plot_DRTResults 103 plot_Risoe BINfileData 118 plot_RLum 120 Topic manip apply_CosmicRayRemoval 19 apply_EfficiencyCorrection 21 calc_SourceDoseRate 54 CW2pHMi 58 CW2pLM 62 CW2pLMi 64 CW2pPMi 66 extract_IrradiationTimes 79 merge_Risoe BINfileData 91 Risoe BINfileData2RLum Analysis 140 Risoe BINfileData2RLum Data Curve 142 Second2Gray 152 sTeve 153 Topic methods RLum Results class 150 Topic models fit_CWCurve 81 fit_LMCurve 84 Topic package Luminescence package 3 Topic plot analyse_pIRIRSequence 9 analyse_SAR CWOSL 12 analyse_SAR TL 17 Topic utilities get_RLum 89 merge_RLum 93 merge_RLum Analysis 94 merge_RLum Data Curve 95 abline 721 analyse_IRSAR RF 5 analyse_pIRIRSequence 9 analyse_SAR CWOSL 10 11 12 16 53 Analyse_SAR OSLdata 14 15 53 analyse_SAR TL 17 58 apply_CosmicRayRemoval 7 19 2 apply_EfficiencyCorrection 21 158 approx 60 135 136 BaseDataSet CosmicDoseRate 23 34 calc_AliquotSize 25 calc_CentralDose 27 31 39 41 43 46 50 calc_CommonDose 29 29 39 41 43 46 50 calc_CosmicDoseRate 31 calc_FadingCorr 35 calc_FiniteMixture 29
12. Data Curve or data frame required RLum Data Curve or data frame with measured curve data of type stimulation time t values 1 and mea sured counts cts values 2 P vector optional stimulation period in seconds If no value is given the opti mal 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 amp 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 f 1 lt 0 P ye 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 lt 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 1m 5 Extrapolate values for t lt min t based on the previously obtained fit parameters The ex trapolation is limited to two values Other values at the beginning of the transformed curve are set to 0 6 Transform values using pLM t t P x CW t 68 CW2pPMi 7 Combine all values and truncate all values for
13. Lab Luminescence Laboratory TU Bergakademie Freiberg Lab Code ZEU SA1 Location Zeuchfeld Zeuchfeld Sandur Saxony Anhalt Germany Material K feldspar 130 200 um Reference 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 readSPE2R to R to pro duce an RLum Data Image object Usage ExampleData RLum Data Image Format Object of class RLum Data Image ExampleData XS YG 77 Version 0 1 Source ExampleData RLum Data Image These data were kindly provided by Regina DeWitt Lab Department of Physics East Carolina University NC USA Lab Code Location Material Reference Image data is a measurement of fluorescent ceiling lights with a cooled Princeton Instruments TM camera fitted on Risoe DA 20 TL OSL reader References Examples load data data ExampleData RLum Data Image envir environment plot data plot_RLum ExampleData
14. Matrix structure Column 1 and 2 time and rev time values Additional columns are used for the components two for each component con taining IO 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 2 16 2015 03 10 16 11 27 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 R42 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 References Bulur E 1996 An Alternative Technique For Optically Stimulated Luminescence OSL Experi ment Radiation Measurements 26 5 701 709 Jain M Murray A S Boetter Jensen L 2003 Characterisation of blue light stimulated lumi nescence components in different quartz samples implications for dose measurement Radiation Measurements 37 4 5 441 449 Kitis G amp 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
15. Run Info option within the Sequence Editor or by editing in R Value Returns a plot Function version 0 4 1 2015 03 04 00 19 53 Note The function has been successfully tested for the Sequence Editor file output version 3 and 4 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Michael Dietze GFZ Potsdam Germany R Luminescence Package Team References Duller G 2007 Analyst pp 1 45 See Also Risoe BINfileData class readBIN2R CW2pLM CW2pLMi CW2pPMi CW2pHMi Examples load data data ExampleData BINfileData envir environment plot all curves from the first position to the desktop pdf file Desktop Curve0utput pdf paper a4 height 11 onefile TRUE tttexample load from bin file BINfile lt file choose BINfileData lt readBIN2R BINfile par mfrow c 4 3 oma c 5 1 0 5 1 plot_Risoe BINfileData CWOSL SAR Data position 1 timtext side 4 BINfile outer TRUE col blue cex 7 dev off 120 plot_RLum plot_RLum General plot function for RLum S4 class objects Description Function calls object specific plot functions for RLum S4 class objects Usage plot_RLum object Arguments object RLum required S4 object of class RLum further arguments and graphical parameters that will be passed to the specific plot functions Details The function provides a generalised access point for plottin
16. conversion from version 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 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References Duller G 2007 Analyst 156 writeR2BIN See Also readBIN2R Risoe BINfileData writeBin Examples uncomment for usage data ExampleData BINfileData envir environment writeR2BIN CWOSL SAR Data file your path output bin Index Topic IO extract_IrradiationTimes 79 merge_Risoe BINfileData 91 readBIN2R 130 readSPE2R 132 readXSYG2R 134 writeR2BIN 154 Topic aplot plot_RLum Analysis 121 plot_RLum Data Curve 123 plot_RLum Data Image 124 plot_RLum Data Spectrum 126 plot_RLum Results 129 Topic Classes Risoe BINfileData class 137 RLum class 143 RLum Analysis class 144 RLum Data class 145 RLum Data Curve class 146 RLum Data Image class 147 RLum Data Spectrum class 149 RLum Results class 150 Topic datagen analyse_IRSAR RF 5 analyse_pIRIRSequence 9 analyse_SAR CWOSL 12 Analyse_SAR OSLdata 15 analyse_SAR TL 17 calc_FadingCorr 35 calc_OSLLxTxRatio 51 calc_TLLxTxRatio
17. kde TRUE hist FALSE dots FALSE y axis TRUE error bars FALSE polygon col bar col line line col line label grid col bw SJ output FALSE 2 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 exclude 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 De fault is TRUE central value numeric User defined central value primarily used for horizontal centering of the z axis 98 centrality dispersion plot ratio rotate mtext summary summary pos legend legend pos stats rug kde hist dots y axis error bars polygon col bar col line plot_AbanicoPlot character or numeric with default measure of centrality used for automat ically centering the plot and drawing the central line Can either be one out of mean median mean weighted and median weighted or one or more numeric values used for the standardisation If more than one value is specified more than one 2 sigma bar will be plotted and the dataset is centered using the median Default is mean weighted character with default measure of dispersion used for drawing the polygon that depic
18. 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 x maz t u y 2xtx P The new count values are then calculated by ctsNEW cts u P and the returned data frame is produced by data frame u ctsNEW Value The function returns the same data type as the input data type with the transformed curve values data frame generic R data structure RLum Data Curve package RLum object CW2pLM 63 Function version 0 4 1 2015 03 04 18 47 17 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 Ra diation Measurements 32 141 145 Further Reading Bulur E 1996 An Alternative Technique For Optically Stimulated Luminescence OSL Ex periment Radiation Measurements 26 701 709 See Also CW2pHMi CW2pLMi CW2pPMi fit_LMCur
19. values transformed lt CW2pLMi ExampleData CW_OSL_Curve plot plot values transformed x values transformed y t log x 2 produce Fig 4 from Bos amp Wallinga 2012 load data data ExampleData CW_OSL_Curve envir environment values lt 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 amp Wallinga 2012 values t lt CW2pLMi values P 1 20 lines values 1 length values t 1 1 1 1 CW2pLMi values P 1 20 2 col red lwd 1 3 text 0 03 4500 LM col red cex 8 values t lt 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 lt CW2pPMi values P 1 10 lines values 1 length values t 11 1 CW2pPMi values P 1 10 21 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 CW2pPMi 67 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 amp Wallinga 2012 Usage CW2pPMi values P Arguments values RLum
20. 1 small empty User specific layout definitions must be provided as a list object of predefined structure see details get_RLum 89 Details The easiest way to create a user specific layout definition is perhaps to create either an empty or a de fault layout object and fill modify the definitions user layout lt get_Layout data empty Value A list object with layout definitions for plot functions Function version 0 1 2015 03 04 00 19 53 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 lt 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 lt 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_RLum General accessor function for RLum S4 class objects Description Function calls object specific get functions for RLum S4 class objects Usage get_RLum object 90 get_RLum Arguments object RLum required S4 object of c
21. 2 background integral c 85 100 get results object get_RLum Results results 54 calc_SourceDoseRate calc_SourceDoseRate Calculation of the source dose rate via the date of measurement Description Calculating the dose rate of the irradiation source via the date of measurement based on source calibration date source dose rate dose rate error The function returns a data frame that provides the input argument dose_rate for the function Second2Gray Usage calc_SourceDoseRate measurement date calib date calib dose rate calib error source type Sr 90 dose rate unit Gy s Arguments measurement date character required date of measurement in Y Y Y Y MM DD calib date character required date of source calibration in YY YY MM DD calib dose rate numeric required dose rate at date of calibration in Gy s or Gy min calib error numeric required error of dose rate at date of calibration Gy s or Gy min source type character with default specify irrdiation source Sr 9 or Co 6 or Am 214 see details for further information dose rate unit character with default specify dose rate unit for input Gy min or Gy s the output is given in Gy s as valid for the function Second2Gray Details Calculation of the source dose rate based on the time elapsed since the last calibration of the irradi ation source Decay parameters assume a Sr 90 beta source dose rate DO x exp log 2 T 1 2 xt
22. 323 get_Layout Ritz C amp Streibig J C 2008 Nonlinear Regression with R R Gentleman K Hornik amp G Parmigiani eds Springer p 150 See Also fit_CWCurve plot nls 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 output plotBG 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 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 re turned If name is provided the respective definition is returned One of the following supported layout definitions is possible default journal
23. Arnold L J amp Roberts R G 2009 Stochastic modelling of multi grain equivalent dose De distri butions Implications for OSL dating of sediment mixtures Quaternary Geochronology 4 204 230 Bailey R M amp Arnold L J 2006 Statistical modelling of single grain quartz De distributions and an assessment of procedures for estimating burial dose Quaternary Science Reviews 25 2475 2502 Cunningham A C amp 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 amp 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 dis tribution Ancient TL 26 3 10 See Also calc_CentralDose calc_CommonDose calc_FiniteMixture calc_FuchsLang2001 calc_MinDose Examples load example data data ExampleData DeValues envir environment apply the maximum dose model calc_MaxDose ExampleData DeValues CA1 sigmab 0 2 par 3 calc_MinDose Apply the un logged minimum age model MAM after Galbraith et al 1999 to a given De distribution Description Function to fit the un logged three or four parameter minimum dose model MAM 3 4 to De data Usage calc_MinDose data sigmab log TRUE par 3 bootstrap FALSE init
24. J amp Roberts R G 2009 Stochastic modelling of multi grain equivalent dose De distri butions Implications for OSL dating of sediment mixtures Quaternary Geochronology 4 204 230 Bailey R M amp Arnold L J 2006 Statistical modelling of single grain quartz De distributions and an assessment of procedures for estimating burial dose Quaternary Science Reviews 25 2475 2502 Cunningham A C amp Wallinga J 2012 Realizing the potential of fluvial archives using robust 50 calc_MinDose OSL chronologies Quaternary Geochronology 12 98 106 Rodnight H Duller G A T Wintle A G amp 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 dis tribution Ancient TL 26 3 10 See Also calc_CentralDose calc_CommonDose calc_FiniteMixture calc_FuchsLang2001 calc_MaxDose Examples Load example data data ExampleData DeValues envir environment 1 Apply the minimum age model with minimum required parameters By default this will apply the un logged 3 parametric MAM calc_MinDose data ExampleData DeValues CA1 sigmab 0 1 2 Re run the model but save results to a variable and turn plotting of the log likelihood profiles off mam lt calc_MinDose data ExampleData DeValues CA1 sigmab 0 1 plot FALSE Show
25. RLum Data Image 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 im ported from a Freiberg Instruments XSYG file using the function readXSYG2R Usage ExampleData XSYG 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 78 ExampleData XS YG 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 TL Spectrum Lab Lab Code Location Material Reference Spectrum Heating References Luminescence Laboratory Giessen no code not specified Coarse grain quartz on steel cups on lexsyg research reader unpublished Luminescence Laboratory Giessen BT753 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 Unpublished data measured to serve as example data for that package Location origin of sample BT75
26. Spectrum set_RLum Data Spectrum signature recordType character curveType character data matri Construction method for RLum Data Spectrum object The slot info is optional and prede fined as empty list by default get_RLum Data Spectrum signature object RLum Data Spectrum info object character Accessor method for RLum Data Spectrum object The argument info object is optional to directly access the info elements If no info element name is provided the raw curve data matrix will be returned 150 RLum Results class Version 0 1 2013 11 23 Note The class should only contain data for a single spectra data set For additional elements the slot info can be used Author s Sebastian Kreutzer JLU Giessen Germany References See Also RLum RLum Data plot_RLum Examples showClass RLum Data Spectrum show example data uncomment for usage data ExampleData XSYG envir environment TL Spectrum RLum Results class Class RLum Results Description Object class contains results data from functions Objects from the Class Objects can be created by calls of the form new RLum Results Slots originator Object of class character containing name of the producing function data Object of class list containing output data S3Class Object of class character RLum Results class 151 Methods validObject signature
27. 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 6 2015 03 04 13 27 28 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 character istics and their relevance in single aliquot regeneration dating protocols Radiation Measurements 41 369 391 See Also plot plot_DRTResults 105 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 lt ExampleData DeValues BT998 7 11 x 2 lt 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
28. are set to 10 dose points numeric optional a numeric vector containg the dose points values Using this argument overwrites dose point values in the signal curves mtext outer character optional option to provide an outer margin mtext plot logical with default enables or disables plot output analyse_SAR CWOSL 13 plot single logical with default or numeric optional single plot output TRUE FALSE to allow for plotting the results in single plot windows If a numerice vector is provided the plots can be selected individually i e plot single c 1 2 3 4 will plot the TL and Lx Tx curves but not the legend 5 or the growth curve 6 7 and 8 belong to rejection criteria plots Requires plot TRUE further arguments that will be passed to the function plot_GrowthCurve Details The function performs an analysis for a standard SAR protocol measurements introduced by Mur ray and Wintle 2000 with CW OSL curves For the calculation of the Lx Tx value the function calc_OSLLxTxRatio is used Working with IRSL data The function was originally designed to work just for OSL curves following the principles of the SAR protocol An IRSL measurement protocol may follow this procedure e g post IR IRSL pro tocol Thomsen et al 2008 Therefore this functions has been enhanced to work with IRSL data however the function is only capable of analysing curves that follow the SAR protocol structure i e to analyse a po
29. call main axes xlab ylab ext interpolate maxpixels alpha colNA stretch plot type contour Uses the function contour plot function from the raster function contour For each raster layer one contour plot is produced Arguments that are passed through the function call main axes xlab ylab xlim ylim col Value Returns a plot Function version 0 1 2015 03 04 00 19 53 Note This function has been created to faciliate the plotting of image data imported by the function readSPE2R However so far the function is not optimized to handle image data gt 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 References 126 plot_RLum Data Spectrum See Also RLum Data Image plot plot_RLum raster 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 xaxis energy FALSE legend text z2 Arguments object
30. containing all calculation tables The output should be accessed using the function get_RLum Results Function version 0 1 2015 03 04 13 18 38 Author s Rachel Smedley Geography amp Earth Sciences Aberystwyth University United Kingdom Based on an excel spreadsheet and accompanying macro written by Kristina Thomsen R Lumines cence Package Team References Thomsen K J Murray A S Boetter Jensen L amp Kinahan J 2007 Determination of burial dose in incompletely bleached fluvial samples using single grains of quartz Radiation Measurements 42 370 379 See Also plot calc_CommonDose calc_CentralDose calc_FiniteMixture calc_FuchsLang2001 calc_MinDose 44 Examples load data calc_MaxDose data ExampleData DeValues envir environment apply the IEU model ieu lt calc_IFU ExampleData DeValues CA1 a 0 2 b 1 9 interval 1 calc_MaxDose Apply the maximum age model to a given De distribution Description Function to fit the maximum age model to De data This is a wrapper function that calls calc_MinDose and applies a similiar approach as described in Olley et al 2006 Usage calc_MaxDose data sigmab log TRUE par 3 bootstrap FALSE init values 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
31. data to csv if temp is a RLum Data Spectrum object write table x get_RLum Data Spectrum temp file your path and filename sep row names FALSE readXSYG2R Import XSYG files to R Description Imports XSYG files produced by a Freiberg Instrument lexsyg reader into R Usage readXSYG2R file recalculate TL curves TRUE import TRUE txtProgressBar TRUE Arguments file character required path and file name of the XSYG file 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 over writes the time vs count TL curve Select FALSE to import the raw data delivered by the lexsyg Works for TL curves and spectra import logical with default if set to FALSE only the XSYG file structure is shown 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 trans lated into an RLum Analysis object General structure XSYG format lt xml lt Sample gt lt Sequence gt lt Record gt readXS YG2R 135 lt Curve name first curve gt lt Curve name curve with data gt x y x1 yl 3 x2 y2 x3 y3 lt Curve gt lt Record gt lt Sequence gt lt Sample gt
32. density TRUE plot TRUE xlab unit s legend pos Arguments object RLum Analysis required input object containing data for protocol analysis sequence structure vector character with default specifies the general sequence structure Al lowed steps are NATURAL REGENERATED In addition any other character is al lowed in the sequence structure such curves will be ignored method character with default setting method applied for the data analysis Possible options are FIT or SLIDE rejection criteria list with default set rejection criteria for see details for more informa tion Currently without usage fit range min integer optional set the minimum channel range for signal fitting and slid ing Usually the entire data set is used for curve fitting but there might be reasons to limit the channels used for fitting Note This option also limits the values used for natural signal calculation fit range max integer optional set maximum channel range for signal fitting and sliding Usually the entire data set is used for curve fitting but there might be reasons to limit the channels used for fitting 6 analyse_IRSAR RF fit trace logical with default trace fitting for debugging use fit MC runs numeric with default set number of Monte Carlo runs for start parameter estimation Note Large values will significantly increase the calculation time slide MC runs integer with default set
33. histogram data ExampleData DeValues envir environment plot_Histogram ExampleData DeValues BT998 xlab De s 2 plot value as histogram with Second to Gray convertion data ExampleData DeValues envir environment De values lt Second2Gray ExampleData DeValues BT998 dose rate c 0 0438 0 0019 method gaussian plot_Histogram De values xlab De Gy ExampleData FittingLM Example data for fit_LMCurve in the package Luminescence Description Lineraly modulated LM measurement data from a quartz sample from Norway including back ground measurement Measurements carried out in the luminescence laboratory at the University of Bayreuth Usage ExampleData FittingLM Format Two objects data frames with two columns time and counts 74 ExampleData LxTxData Source Lab Luminescence Laboratory Bayreuth Lab Code BT900 Location Norway Material 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 LxTxData Example Lx Tx data from CW OSL SAR measurement Description LxTx data from a SAR measure
34. 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 obvi ous that the data is not log normally distributed the mean weighted or not cannot be a valid mea sure 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 ap propriate The proportion of the polar part and the cartesian part of the Abanico Plot can be modfied for dis play reasons plot ratio 0 75 By default the polar part spreads over 75 and leaves 25 for the part that shows the KDE graph The optional parameter layout allows to modify the entire plot more sophisticated Each ele ment 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
35. limits plot_AbanicoPlot data ExampleData DeValues zlim c 100 200 now with adjusted x scale limits plot_AbanicoPlot data ExampleData DeValues xlim c 0 60 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 plot_AbanicoPlot 101 bw 0 01 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 now with user defined central value plot_AbanicoPlot data ExampleData DeValues central value 120 now with weighted median as measure of centrality plot_AbanicoPlot data ExampleData DeValues centrality median weighted now with median quartile range as measure of centrality dispersion plot_AbanicoPlot data ExampleData DeValues centrality median dispersion qr now with user defined green line for minimum age model CAM lt calc_CentralDose ExampleData DeValues plot FALSE plot_AbanicoPlot data ExampleData DeVal
36. lt i lt 8 and A is the decay constant and WO the intial number of trapped electrons for the used equation cf Boetter Jensen et al 2003 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 Ac cording to Lave 1970 the value is calculated as pseudoR 1 RSS TSS where RSS Residual Sum of Squares and TSS Total Sum of Squares Error of fitted component parameters fit_CWCurve 83 The 1 sigma error for the components is calculated using the function confint Due to consid erable 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 infor mation For details on the nonlinear regression in R see Ritz amp Streibig 2008 Value plot table optional the fitted CW OSL curves are returned as plot optional an output table csv with parameters of the fitted components is provided if the output path is set RLum Results object Function version 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 sum mary confint pr
37. mixture International Journal of Radiation Applications and Instrumentation Part D Nuclear Tracks and Radiation Mea surements 17 3 197 206 Galbraith R F amp Laslett G M 1993 Statistical models for mixed fission track ages Nuclear Tracks And Radiation Measurements 21 4 459 470 Galbraith R F 1994 Some Applications of Radial Plots Journal of the American Statistical Association 89 428 1232 1242 Galbraith R F 2010 On plotting OSL equivalent doses Ancient TL 28 1 1 10 Galbraith R F amp 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 See Also plot plot_KDE plot_Histogram Examples load example data data ExampleData DeValues envir environment ExampleData DeValues lt Second2Gray ExampleData DeValues BT998 c 0 0438 0 0019 plot the example data straightforward plot_RadialPlot data ExampleData DeValues now with linear z scale plot_RadialPlot data ExampleData DeValues log z FALSE now with output of the plot parameters plot1 lt plot_RadialPlot data ExampleData DeValues log z FALSE output TRUE plot1 plot1 zlim now with adjusted z scale limits plot_RadialPlot data ExampleData DeValues log z FALSE zlim c 100 200 now the two plots with serious but seasonally changing fun plot_RadialPlot da
38. number of Monte Carlo runs error calculation Note Large values will significantly increase the calculation time slide outlier rm logical with default enable or disable outlier removal Outliers are removed from the natural signal curve only slide trend corr logical with default enable or disable trend correction If TRUE the sliding is applied to a previously trend corrected data set slide show density logical with default enable or disable KDE for MC runs If FALSE the final values are indicated with triangles plot logical with default plot output TRUE or FALSE xlab unit character with default set unit for x axis legend pos character with default useful keywords are bottomright bottom bottomleft left topleft top topright right and center For further details see legend further arguments that will be passed to the plot output Currently supported arguments are main xlab ylab xlim ylim log Details The function performs an IRSAR analysis described for K feldspar samples by Erfurt et al 2003 assuming a negligible sensitivity change of the RF signal General Sequence Structure according to Erfurt et al 2003 Measuring IR RF intensity of the natural dose for a few seconds Dratural Bleach the samples under solar conditions for at least 30 min without changing the geometry Waiting for at least one hour Regeneration of the IR RF signal to at least the natural level Fitting data wi
39. object Description The function provides a standardised plot output for image data of an RLum Data ImageS4 class object mainly using the plot functions provided by the raster package Usage plot_RLum Data Image object par local TRUE plot type plot raster aa Arguments object RLum Data Image required S4 object of class RLum Data Image 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 types Supported types are plot raster plotRGB or contour further arguments and graphical parameters that will be passed to the specific plot functions plot_RLum Data Image 125 Details Details on the plot functions Image is visualised as 2D plot usinng generic plot types provided by other packages Supported plot types plot type plot raster Uses the standard plot function for raster data from the package raster plot For each raster layer in a raster brick one plot is produced Arguments that are passed through the function call main axes xlab ylab xlim ylim col plot type plotRGB Uses the function plotRGB from the raster package Only one image plot is produced as all layers in a brick a combined This plot type is useful to see whether any signal is recorded by the camera Arguments that are passed through the function
40. structure of the RLum Results object mam Show summary table that contains the most relevant results res lt get_RLum Results mam summary res Plot the log likelihood profiles retroactively because before we set plot FALSE plot_RLum Results mam Plot the dose distribution in an abanico plot and draw a line at the minimum dose estimate plot_AbanicoPlot data ExampleData DeValues CA1 main 3 parameter Minimum Age Model line mam polygon col none hist TRUE rug TRUE summary c n mean mean weighted median in ci centrality res de line col red grid col none line label paste round res de 1 UQ B1 round res de_err 1 Gy bw 0 1 ylim c 25 18 calc_OSLLxTxRatio summary pos topleft mtext bquote Parameters 51 sigma b get_RLum mam args sigmab gamma round log res de 1 sigma round res sig 1 gt rho round res p0 2 3 Run the minimum age model with bootstrap NOTE Bootstrapping is computationally intensive which is why the following example is commented out To run the examples just uncomment the code 3 1 run the minimum age model with default values for bootstrapping calc_MinDose data ExampleData DeValues CA1 sigmab 0 15 bootstrap TRUE 3 2 Bootstrap control parameters mam lt calc_MinDose data Ex
41. the EXP fit fails a LIN fit is done instead EXP LIN tries to fit an exponential plus linear function of the form y ax 1 exp 1 c b 9 x The De is calculated by iteration Note In the context of luminescence dating this function has no physical meaning Therefore no DO value is returned EXP EXP tries to fit a double exponential function of the form y al 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 fit 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 108 plot_GrowthCurve 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
42. the chosen fitting method Subtitle information To avoid plotting the subtitle information provide an empty user mtext mtext other subtitle text use mtext nn To plot any Value RLum Results object containing the De De De Error D01 value D02 value De MC and Fit type and the fit object nls object for EXP EXP LIN and EXP EXP In case of a resulting linear fit when using EXP OR LIN alm object is returned The formula Formula is returned as R expression for further evaluation Additionally a plot is returned Function version 1 5 2015 03 04 12 43 39 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Michael Dietze GFZ Potsdam Germany R Luminescence Package Team Examples 1 plot growth curve for a dummy data set and show De value data ExampleData LxTxData envir environment temp lt plot_GrowthCurve LxTxData get_RLum Results temp 1a to access the fitting value try get_RLum Results 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 plot_Histogram 109 plot_Histogram Plot a histogram
43. the object Version 0 1 4 2014 02 26 Note The method get_structure RLum Analysis is currently just avaiblable for objects containing RLum Data Curve Author s Sebastian Kreutzer Freiberg Instruments JLU Giessen Germany References See Also Risoe BINfileData2RLum Analysis Risoe BINfileData RLum Examples showClass RLum Analysis usage of get_RLum Analysis with returining an RLum Analysis object get_RLum Analysis object keep object TRUE RLum Data class Class RLum Data Description Generalized virtual data class for luminescence data Objects from the Class A virtual Class No objects can be created from it Slots S3Class Object of class character Methods No methods defined with class RLum Data in the signature 146 RLum Data Curve class Version 0 1 2013 01 18 Note Just a virtual class Author s Sebastian Kreutzer 2013 Freiberg Instruments JLU Giessen Germany References See Also RLum RLum Data Curve RLum Data Spectrum Examples showClass RLum Data RLum Data Curve class Class RLum Data Curve Description Class for luminescence curve data Objects from the Class Objects can be created by calls of the form new RLum Data Curve Slots recordType Object of class character containing the type of the curve e g TL or OSL curveType Object of class character containi
44. 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 argu ments can be found in the documentations of each merge function object corresponding merge function RLum Results merge_RLum Results Value Return is the same as input objects as provided in the list Function version 0 1 2015 03 04 14 47 38 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 References See Also merge_RLum Results RLum Results 94 merge_RLum Analysis 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 lt calc_CentralDose ExampleData DeValues CA1 tttapply the central dose model 2nd time temp2 lt calc_CentralDose ExampleData DeValues CA1 merge the results and store them in a new object temp merged lt get_RLum Results merge_RLum objects list temp1 temp2 merge_RLum Analysis Merge function for RLum Analysis S4 class objects Description Function allows merging of RLum Analysis objects and adding of allowed objects to an RLum Analysis Usage merge_RLum Analysis objects A
45. to calculate n x y d are assumed to be normally distributed with means Hz Hy Ha and standard deviations Oz Oy Og For the mean grain size random samples are taken first from N uy Cy where y mean grain size and o max grain size min grain size 4 so that 95 of all grains are within the provided the grain size range This effectively takes into account that after sieving the sample there is still a small chance of having grains smaller or larger than the used mesh sizes For each random sample the mean grain size is calculated from which random subsamples are drawn for the Monte Carlo simulation The packing density is assumed to be normally distributed with an empirically determined u 0 65 or provided value and o 0 18 The normal distribution is truncated at d 0 87 as this is ap proximately the maximum packing density that can be achieved in PECC problem The sample diameter has y sample diameter and o 0 2 to take into account variations in sample disc preparation i e applying silicon spray to the disc A lower truncation point at x 0 5 is used which assumes that aliqouts with smaller sample diameters of 0 5 mm are discarded Like wise the normal distribution is truncated at 9 8 mm which is the diameter of the sample disc For each random sample drawn from the normal distributions the amount of grains on the aliquot is calculated By default 10 5 iterations are used but can be reduced increased with MC ite
46. usage plot_RLum Data Spectrum TL Spectrum plot type persp xlim c 310 750 ylim c 0 300 bin rows 10 bin cols 1 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 data single TRUE Arguments data 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 1 2015 03 10 09 43 59 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 R Luminescence Package Team References 130 readBIN2R See Also plot plot_RLum Examples load data data ExampleData DeValues envir environment apply the un logged minimum age model mam lt 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 lt calc_AliquotSize grain size c 100 150 sample dia
47. values plot TRUE multicore FALSE Arguments data RLum Results or data frame required for data frame two columns with De data 1 and De error values 2 calc_MinDose sigmab log par bootstrap init values plot multicore Details Parameters 47 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 amp Walling 2012 p 100 logical with default fit the un logged minimum dose model to De data numeric with default apply the 3 or 4 parametric minimum age model par 3 or par 4 The MAM 3 is used by default logical with default apply the recycled bootstrap approach of Cunningham amp Wallinga 2012 numeric optional a named list with starting values for gamma sigma pO and mu e g list gamma 100 sigma 1 5 p0 0 1 mu 100 If no values are provided reasonable values are tried to be estimated from the data logical with default plot output TRUE FALSE logical with default enable parallel computation of the bootstrap by creating a multicore SNOW cluster Depending on the number of available logical CPU cores this will drastically reduce the computation time Note that this option is highly experimental and not work for all machines TRUE FALSE optional further arguments for bootstrapping bs M bs N bs h sigmab sd See details for
48. vector optional range of sets used for the analysis If no value is given the range of the sets in the sequence is deduced from the Risoe BINfileData ob ject dtype character optional allows to further limit the curves by their data type DTYPE e g dtype c Natural Dose limits the curves to this two data types By default all values are allowed See Risoe BINfileData class for allowed data types keep SEL logical default option allowing to use the SEL element of the Risoe BINfileData class manually NOTE In this case any limitation provided by run set and dtype are ignored info measurement character with default option to provide information about the measurement on the plot output e g name of the BIN or BINX file 16 Analyse_SAR OSLdata log character with default a character string which contains x if the x axis is to Wow be logarithmic y if the y axis is to be logarithmic and xy or yx if both axes are to be logarithmic See plot default output plot logical with default plot output TRUE FALSE output plot single logical with default single plot output TRUE FALSE to allow for plotting the results in single plot windows Requires output plot TRUE cex global numeric with default global scaling factor Details The function works only for standard SAR protocol measurements introduced by Murray and Win tle 2000 with CW OSL curves For the calculation of the Lx Tx
49. with separate error plot Description Function plots a predefined histogram with an accompanying error plot as suggested by Rex Gal braith at the UK LED in Oxford 2010 Usage plot_Histogram data na exclude TRUE mtext cex global breaks se rug normal_curve summary summary pos colour Arguments data na exclude mtext cex global breaks se rug normal_curve summary summary pos colour data frame or RLum Results object required for data frame two columns De data 1 and De error data 2 logical with default excludes NA values from the data set prior to any further operations character optional further sample information mtext numeric with default global scaling factor with default sets breakpoints for histogram Works as in hist logical optional plots standard error points over the histogram default is FALSE logical optional adds rugs to the histogram default is TRUE logical with default adds a normal curve to the histogram Mean and sd are calculated from the input data More see details section character optional adds numerical output to the plot Can be one or more out of n number of samples mean mean De value mean weighted error weighted mean median median of the De values kdemax max imum of the KDE sdrel relative standard deviation in percent sdabs absolute standard deviation serel r
50. 0 1 2015 03 04 00 19 53 Note The function is intended for experimental usage Normally the function Risoe BINfileData2RLum Analysis should be used for the conversion RLum class 143 Author s Sebastian Kreutzer Freiberg Instruments JLU Giessen Germany R Luminescence Package Team References See Also Risoe BINfileData2RLum Analysis set_RLum Data Curve RLum Data Curve RLum Analysis Risoe BINfileData plot_RLum Examples get package example data data ExampleData BINfileData envir environment convert one record Risoe BINfileData2RLum Data Curve CWOSL SAR Data id 1 RLum class Class RLum Description Abstract class for data in the package Luminescence Objects from the Class A virtual Class No objects can be created from it Slots S3Class Object of class character Methods No methods defined with class RLum in the signature Version 0 1 2013 01 18 Note RLum is a virtual class Author s Sebastian Kreutzer 2013 Freiberg Instruments JLU Giessen Germany 144 RLum Analysis class References See Also RLum Data RLum Analysis Examples showClass RLum RLum Analysis class Class RLum Analysis Description Object class containing analysis data for protocol analysis Objects from the Class Objects can be created by calls of the form new RLum Analysis Slots records Object of class list
51. 0 150 sample diameter 1 Calculate the mean packing density of large aliquots calc_AliquotSize grain size c 100 200 sample diameter 8 grains counted c 2525 2312 2880 calc_CentralDose Apply the central age model CAM after Galbraith et al 1999 to a given De distribution Description This function calculates the central dose and dispersion of the De distribution their standard errors and the profile log likelihood function for sigma Usage calc_CentralDose data sigmab plot TRUE Arguments data RLum Results or data frame required for data frame two columns with De data 11 and De error values 2 sigmab numeric with default 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 amp Walling 2012 p 100 plot logical with default plot output further arguments trace verbose 28 calc_CentralDose Details This function uses the equations of Galbraith et al 1999 358 359 The parameter sigma is estimated using the maximum likelihood approach A detailed explanation on maximum likelihood estimation can be found in the appendix of Galbraith amp Laslett 1993 468 470 Value Returns a plot optional and terminal output In addition an RLum Results object is returned containing the following element summary data frame summary of all relevant model results data da
52. 12 p 100 calc_FiniteMixture 37 n components numeric required number of components to be fitted If a vector is pro vided 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 compo nents 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 Pos sible 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
53. 120 160 mtext n 25 now the data set is split into sub groups one is manipulated data 1 lt ExampleData DeValues 1 15 data 2 lt ExampleData DeValues 16 25 1 3 now a common dataset is created from the two subgroups data 3 lt 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 col c steelblue4 orange4 bar col c steelblue3 orange3 polygon col c steelblue1 orange1 pch c 2 6 density c 10 20 angle c 30 50 summary c n in ci create Abanico plot with predefined layout definition plot_AbanicoPlot data ExampleData DeValues plot_AbanicoPlot plot_DRTResults 103 layout journal now with predefined layout definition and further modifications plot_AbanicoPlot data data 3 layout journal col c steelblue4 orange4 bar col adjustcolor c steelblue3 orange3 alpha f 5 polygon col c steelblue3 orange3 for further information on layout definitions see documentation of function get_Layout restore original graphical parameters par par old 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 error rang
54. 3 26 15 Note The input data is not restricted to a special type Author s Michael Dietze GFZ Potsdam Germany Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team See Also hist plot Examples load data data ExampleData DeValues envir environment ExampleData DeValues lt Second2Gray ExampleData DeValues BT998 dose rate c 0 0438 0 0019 plot histogram the easiest way plot_Histogram ExampleData DeValues plot histogram with some more modifications plot_Histogram ExampleData DeValues rug TRUE normal_curve TRUE cex global 0 9 pch 2 colour c grey black blue green summary c n mean sdrel summary pos topleft main Histogram of De values mtext Example data set ylab c expression paste DLe distribution Error xlim c 100 250 ylim c 0 0 1 5 20 plot_KDE 111 plot_KDE Plot kernel density estimate with statistics Description Plot a kernel density estimate of measurement values in combination with the actual values and associated error bars in ascending order Optionally statistical measures such as mean median standard deviation standard error and quartile range can be provided visually and numerically Usage plot_KDE data na exclude TRUE weights FALSE values cumulative TRUE centrality dispersion summary summary pos poly
55. 3 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 readXSYG2R RLum Analysis RLum Data Spectrum plot_RLum plot_RLum Analysis plot_RLum Data Spectrum Examples show data data ExampleData XSYG envir environment Ti 32 SE SS ooo OS ES RSS 1 OSL SARMeasurement OSL SARMeasurement show Sequence Object extract_IrradiationTimes 719 OSL SARMeasurement Sequence Object grep OSL curves and plot the first curve OSLcurve lt get_RLum Analysis OSL SARMeasurement Sequence Object recordType 0SL 1 plot_RLum OSLcurve HH PP SSS SSS SS SS SS SSS SS SS SS SSS SS 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 extract_IrradiationTimes Extract irradiation times from an XSYG file Description Extracts irradiation times dose and times since last irradiation from a Freiberg Instruments XSYG file These information can be further used to update
56. 31 36 41 43 46 S0 calc_FuchsLang2001 29 31 39 39 43 46 S0 calc_HomogeneityTest 41 calc_IEU 42 calc_MaxDose 44 50 calc_MinDose 29 31 39 41 43 45 46 46 calc_OSLLxTxRatio 11 13 14 16 17 51 calc_SourceDoseRate 54 152 calc_Statistics 56 calc_TLLxTxRatio 18 19 57 call 26 28 30 33 38 40 42 43 48 character 5 6 10 12 15 16 18 20 37 52 54 56 79 82 85 88 91 95 98 99 103 104 106 109 111 114 115 118 121 124 126 127 130 132 134 141 152 155 coerce RLum Analysis method RLum Data Curve class 146 coerce RLum Data Image method RLum Data Image class 147 coerce RLum Data Spectrum method RLum Data Spectrum class 149 confint 81 83 85 87 contour 125 128 CW2pHMi 58 63 66 69 119 CW2pLM 60 62 66 69 85 119 CW2pLMi 60 63 64 69 119 CW2pPMi 60 63 66 66 119 data frame 8 10 13 16 18 22 26 30 33 36 38 40 44 46 48 52 56 57 59 60 62 64 67 68 70 72 77 81 83 85 87 97 103 106 109 111 114 131 136 145 147 149 152 density 112 do call 2 ExampleData BINfileData 69 ExampleData CW_OSL_Curve 71 ExampleData DeValues 72 ExampleData FittingLM 73 ExampleData LxTxData 74 INDEX ExampleData LxTxOSLData 75 ExampleData RLum Analysis 75 ExampleData RLum Data Image 76 ExampleData XSYG 77 extract_IrradiationTimes 79 fit_CWCurve 81 88 fit_LMCurve 60 63 66 69 84 84 formula 3 get_Layout 88 get_Ri
57. 35 57 84 91 106 121 126 127 131 140 142 154 legend 6 length_RLum Analysis RLum Analysis class 144 length_RLum Analysis RLum Analysis method RLum Analysis class 144 length_RLum Analysis methods RLum Analysis class 144 list 5 12 16 18 26 28 30 33 35 38 40 42 43 48 49 52 55 57 72 87 88 93 95 121 131 lm 59 60 63 64 67 107 108 logical 6 10 12 13 15 16 20 25 27 29 31 37 40 41 43 44 47 56 80 82 85 91 97 99 103 104 106 107 109 111 112 114 115 121 123 124 126 127 129 130 132 134 J33 Luminescence Luminescence package 3 Luminescence package 3 matrix 38 83 87 147 149 merge_Risoe BINfileData 91 131 140 merge_RLum 93 95 96 merge_RLum Analysis 94 merge_RLum Data Curve 95 merge_RLum Results 93 merge_RLum Results RLum Results class 150 merge_RLum Results list method RLum Results class 150 merge_RLum Results methods RLum Results class 150 mle2 48 mtext 109 nlminb 48 nls 6 8 9 81 83 84 86 88 107 108 numeric 6 10 12 13 16 25 27 29 31 35 37 40 43 44 47 48 52 54 82 85 95 97 99 103 104 107 109 111 114 115 118 140 141 144 persp3d 128 plot 29 40 41 43 82 84 88 104 109 110 112 116 122 126 128 130 plot default 16 18 plot_AbanicoPlot 97 plot_DRTResults 103 plot_GrowthCurve 10 11 13 14 17 19 53 106 plot_Histogram 00 109 116 plot_KDE 100 109
58. 83 84 90 93 97 103 109 111 114 120 121 129 152 RLum Results class 150 rollmedian 7 rowMeans 96 rowSums 96 sd 108 Second2Gray 54 55 152 set_Risoe BINfileData Risoe BINfileData class 137 set_Risoe BINfileData ANY method Risoe BINfileData class 137 INDEX set_RLum Data Image methods RLum Data Image class 147 set_RLum Data Spectrum RLum Data Spectrum class 149 set_RLum Data Spectrum ANY method RLum Data Spectrum class 149 set_RLum Data Spectrum character matrix method RLum Data Spectrum class 149 set_RLum Data Spectrum RLum Data Spectrum method RLum Data Spectrum class 149 set_RLum Data Spectrum methods RLum Data Spectrum class 149 set_RLum Results RLum Results class 150 set_RLum Results ANY list method RLum Results class 150 set_RLum Results RLum Results method RLum Results class 150 show Risoe BINfileData method Risoe BINfileData class 137 show RLum Analysis method RLum Analysis class 144 show RLum Data Curve method RLum Data Curve class 146 set_Risoe BINfileData data frame list method show RLum Data Image method Risoe BINfileData class 137 RLum Data Image class 147 set_Risoe BINfileData Risoe BINfileData methoghow RLum Data Spectrum method Risoe BINfileData class 137 set_RLum Analysis RLum Analysis class 144 set_RLum Analysis list method RLum Analysis class 144 set_RLum Analysis RLum Analysis met
59. Analysis CWOSL SAR Data pos 1 142 Risoe BINfileData2RLum Data Curve Risoe BINfileData2RLum Data Curve Convert an element from a Risoe BINfileData object to an RLum Data Curve object Description The function converts one specified single record from a Risoe BINfileData object to an RLum Data Curve object Usage Risoe BINfileData2RLum Data Curve object id pos run set Arguments object Risoe BINfileData required Risoe BINfileData object id integer required record id in the Risoe BINfileData object of the curve that is to be stored in the RLum Data Curve object If no value for id is provided the record has to be specified by pos set and run pos integer optional record position number in the Risoe BINfileData object of the curve that is to be stored in the RLum Data Curve object If a value for id is provided this argument is ignored run integer optional record run number in the Risoe BINfileData object of the curve that is to be stored in the RLum Data Curve object If a value for id 1s provided this argument is ignored set integer optional record set number in the Risoe BINfileData object of the curve that is to be stored in the RLum Data Curve object If a value for id is provided this argument is ignored Details The function extracts all METADATA from the Risoe BINfileData object and stores them in the RLum Data Curve object Value Returns an RLum Data Curve object Function version
60. Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Margret C Fuchs AWI Potsdam Germany TU Bergakademie Freiberg Germany R Luminescence Package Team References Aitken M J and Smith B W 1988 Optical dating recuperation after bleaching Quaternary Science Reviews 7 387 393 Duller G 2003 Distinguishing quartz and feldspar in single grain luminescence measurements Radiation Measurements 37 2 161 165 Murray A S and Wintle A G 2000 Luminescence dating of quartz using an improved single aliquot regenerative dose protocol Radiation Measurements 32 57 73 See Also calc_OSLLxTxRatio Risoe BINfileData class readBIN2R and for further analysis plot_GrowthCurve Examples load data data ExampleData BINfileData envir environment tHtanalyse data output lt Analyse_SAR OSLdata input data CWOSL SAR Data signal integral c 1 5 background integral c 900 1000 position c 1 1 output plot TRUE combine results relevant for further analysis output SAR lt data frame Dose output LnLxTnTx 1 Dose LxTx output LnLxTnTx E1 11 LxTx LxTx Error output LnLxTnTxL 11 LxTx Error output SAR analyse_SAR TL Analyse SAR TL measurements Description The function performs a SAR TL analysis on a RLum Analysis object including growth curve fitting Usage analyse_SAR TL object object background signal integral min signal integral max se
61. 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 or Risoe BINfileData required Character vector with path and files names e g input objects c path filel bin path file2 bin or Risoe BINfileData objects e g input objects c object1 object2 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 pos
62. Galbraith s radial plot is produced on a logarithmic or a linear scale 114 Usage plot_RadialPlot data na exclude data na exclude negatives log z central value centrality mtext summary summary pos legend legend pos stats rug plot ratio plot_RadialPlot TRUE negatives remove log z TRUE central value centrality mean weighted mtext summary summary pos legend legend pos stats rug FALSE plot ratio bar col y ticks TRUE grid col line line col line label output FALSE Arguments data frame or RLum Results object required for data frame two columns De data 11 and De error data 21 To plot several data sets in one plot the data sets must be provided as list e g list data 1 data 2 logical with default excludes NA values from the data set prior to any further Operations character with default rule for negative values Default is remove i e negative values are removed from the data set logical with default Option to display the z axis in logarithmic scale De fault is TRUE numeric User defined central value primarily used for horizontal centering of the z axis character or numeric with default measure of centrality used for automat ically centering the plot and drawing the central line Can either be one out of mean median mean weighted and median weighted or a numeric value used for the standa
63. L_UNIT integer 03 06 Bleaching unit mJ J secs mins hrs 25 NORMI numeric 03 06 Normalisation factor 1 26 NORM2 numeric 03 06 Normalisation factor 2 27 NORM3 numeric 03 06 Normalisation factor 3 28 BG numeric 03 06 Background level 29 SHIFT integer 03 06 Number of channels to shift data 30 TAG integer 03 06 Tag triggers SEL 31 LTYPE character 03 06 Luminescence type 32 LIGHTSOURCE character 03 06 Light source 33 LPOWER numeric 03 06 Optical stimulation power 34 LIGHTPOWER numeric 06 Optical stimulation power 35 LOW numeric 03 06 Low temperature time wavelength 36 HIGH numeric 03 06 High temperature time wavelength 37 RATE numeric 03 06 Rate heating rate scan rate 38 TEMPERATURE integer 03 06 Sample temperature 39 MEASTEMP integer 06 Measured temperature 40 AN_TEMP numeric 03 06 Annealing temperature 41 AN_TIME numeric 03 06 Annealing time 42 TOLDELAY integer 03 06 TOL delay channels 43 TOLON integer 03 06 TOL on channels 44 TOLOFF integer 03 06 TOL off channels Risoe BINfileData class 139 45 IRR_TIME numeric 03 06 Irradiation time 46 IRR_TYPE integer 03 06 Irradiation type alpha beta or gamma 47 IRR_UNIT integer 03 04 Irradiation unit Gy Rads secs mins hrs 48 IRR _DOSERATE numeric 06 Irradiation dose rate Gy s 49 IRR _DOSERATEERR numeric 06 Irradiation dose rate error Gy s 50 TIMESINCEIRR integer 06 Time since irradiat
64. Lum Data Image frame range txtProgressBar TRUE Arguments file character required spe file name including path e g WIN readSPE2R C Desktop test spe MAC LINUX readSPER User test Desktop test spe 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 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 readSPE2R 133 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 func tion get_RLum Data Spectrum is used meaning that the same
65. 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 calc_AliquotSize 25 calc_AliquotSize Estimate the amount of grains on an aliquot Description Estimate the number of grains on an aliquot Alternatively the packing density of an aliquot is computed Usage calc_AliquotSize grain size sample diameter packing density 0 65 MC TRUE grains counted plot TRUE Arguments grain size numeric required mean grain size microns or a range of grain sizes from which the mean grain size is computed e g c 100 200 sample diameter numeric required diameter mm of the targeted area on the sample carrier packing density numeric with default empirical value for mean packing density If packing density inf a hexagonal structure on an infinite plane with a packing density of 0 906 is assumed MC logical optional if TRUE the function performs a monte carlo simulation for estimating the amount of grains on the sample carrier and assumes random errors in grain size distribution and packing density Requires a vector with min and max grain size for grain size For more information see details grains counted numeric optional grains counted on a sam
66. Package Luminescence March 23 2015 Type Package Title Comprehensive Luminescence Dating Data Analysis Version 0 4 2 Date 2015 03 23 Author Sebastian Kreutzer aut trl cre Michael Dietze aut Christoph Burow aut Margret C Fuchs aut Christoph Schmidt aut Manfred Fischer aut trl Rachel K Smedley aut Markus Fuchs ths Maintainer Sebastian Kreutzer lt sebastian kreutzer u bordeaux montaigne fr gt Description A collection of various R functions for the purpose of Luminescence dating data analy sis This includes amongst others data import export application of age models curve decon volution sequence analysis and plotting of equivalent dose distributions Contact Package Developer Team lt team r luminescence de gt License GPL 3 Depends R gt 3 1 2 utils Imports methods XML shape rgl matrixStats raster sp zoo bbmle data table Repp gt 0 11 4 parallel LinkingTo Rcpp URL http CRAN R project org package Luminescence Collate Analyse_SAR OSLdata R analyse_SAR CWOSL R analyse_SAR TL R analyse_IRSAR RF R CW2pLM R CW2pLMi R CW2pHMi R CW2pPMi R calc_FadingCorr R calc_FuchsLang2001 R calc_OSLLxTxRatio R calc_TLLxTxRatio R Second2Gray R fit_LMCurve R fit_CWCurve R plot_Risoe BINfileData R plot_KDE R plot_GrowthCurve R plot_Histogram R plot_RadialPlot R plot_RLum R plot_RLum Analysis R plot_RLum Data Curve R readBIN2R R RisoeBINfileData class R Risoe BINfileData2RLum Analysi
67. RLum Data Spectrum required S4 object of class RLum Data Spectrum 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 persp3d for a 2D plot contour single or multiple lines along the time or temperature axis or transect along the wavelength axis Note The use of persp3d will produce a dynamic 3D surface plot on the screen 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 bin ning e g bin rows 2 two channels are summed up plot_RLum Data Spectrum 127 bin cols integer with default allow summing up channel counts vertical binning for plotting e g bin cols 2 two channels are summed up rug logical with default enables or disables colour rug Currently only imple mented for plot type multiple lines xaxis energy logical with default enables or disables energy instead of wave
68. 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 writeR2BIN object file version txtProgressBar TRUE writeR2BIN 155 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 writeR2BIN object C Desktop test bin MAC LINUX writeR2BIN User test Desktop test bin version character optional version number for the output file If no value is pro vided the highest version number from the Risoe BINfileData is taken auto matically Note This argument can be used to convert BIN file versions 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 2 5 2015 03 23 12 57 25 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 and output data e g
69. Se wee 93 merge _RLum Analysis o ee ee ee 94 merge_RLum Data Curve ee 95 plot Aba icoPlot veria o ar as Bee ae 97 plot DRTResults lt e 4 6 4 204 2X4 eS BEd doe SEM aE SoG eRe ee araa a 103 plot GrowthCurve ss nee eb eR RO e ew Re eR a oO 106 plot_Histogram io p eero ee Ra E E oe ee 109 plot KDE ins tee es oe SG AAR J Ws hy Boe kde de ce ry a Boh A Ale Reda et Gere ego 111 plot_RadialPlot 2 e e a e a a e k ee 113 plot_Risoe BlNfileData ee ee 118 plot RLM s e e ae ee a4 Eee A Peed obo a e 120 plot_RLum Analysis oaa ee 121 plot_RLum Data Curve pacca e ae e E a a ee 123 plot_RLum Data Image a aoaaa ee 124 plot_RLum Data Spectrum ooa a 126 plot_RLum Results e aE ee 129 a sori p NE AE 130 Te dd SPEZR ici a a a ae Se A RT 132 readXSYG2R orere apanan ee 134 Risoe BlNfileData class ee 137 Risoe BINfileData2RLum Analysis 20 20 0000 0000002000 140 Risoe BINfileData2RLum Data Curve osoa ee 142 RLumsclass 03 4 ea ee OG Re ad Bae Re e da Le e S 143 RLum Analysis class ee 144 RLum Data class ee 145 RLum Data Curve class ee 146 RLum Data Image class 2 ee 147 RLum Data Spectrum class 2 149 RLum Results class ee 150 Second2Gray 26 5 8 Se a A ee a 152 SITO Ada So Hee ste ta arto ees os ae OE cee ey Tecate we ete O daa 153 writeR2BIN aaa aaa ee 154 157 Luminescence package Compr
70. Wallinga J 2012 Realizing the potential of fluvial archives using robust calc_CommonDose 29 OSL chronologies Quaternary Geochronology 12 98 106 Rodnight H Duller G A T Wintle A G amp Tooth S 2006 Assessing the reproducibility and accuracy of optical dating of fluvial deposits Quaternary Geochronology 109 120 Rodnight H 2008 How many equivalent dose values are needed to obtain a reproducible dis tribution Ancient TL 26 3 10 See Also plot calc_CommonDose calc_FiniteMixture calc_FuchsLang2001 calc_MinDose Examples load example data data ExampleData DeValues envir environment apply the central dose model calc_CentralDose ExampleData DeValues CA1 calc_CommonDose Apply the un logged common age model after Galbraith et al 1999 to a given De distribution Description Function to calculate the common dose of a De distribution Usage calc_CommonDose data sigmab log 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 with default 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 amp Walling 2012 p 100 log logical with default fit the un logged common age model to De data currently not used Details Un logged model When log TRUE this funct
71. _Curve Example CW OSL curve data for the package Luminescence Description data frame containing CW OSL curve data time counts Usage data ExampleData CW_OSL_Curve Format Data frame with 1000 observations on the following 2 variables x a numeric vector time ya numeric vector counts Details see source Source ExampleData CW_OSL_Curve Lab Luminescence Laboratory Bayreuth Lab Code BT607 Location Saxony Germany Material Middle grain quartz measured on aluminum cups on a Risoe TL OSL DA 15 reader Reference unpublished data CW_Curve BosWallinga2012 Lab Netherlands Centre for Luminescence Dating NCL Lab Code NCL 2108077 Location Guadalentin Basin Spain Material Coarse grain quartz Reference Bos amp Wallinga 2012 and Baartman et al 2011 References Baartman J E M Veldkamp A Schoorl J M Wallinga J Cammeraat L H 2011 Unravel ling Late Pleistocene and Holocene landscape dynamics The Upper Guadalentin Basin SE Spain 72 ExampleData De Values Geomorphology 125 172 185 Bos A J J amp 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
72. _RLum Results dose rate 2 Usage in combination with another function e g Second2Gray load example data data ExampleData DeValues envir environment use the calculated variable dose rate as input argument to convert De s to De Gy Second2Gray ExampleData DeValues BT998 dose rate 56 calc_Statistics calc_Statistics Function to calculate statistic measures Description This function calculates a number of descriptive statistics for De data most fundamentally using error weighted approaches Usage calc_Statistics data weight calc reciprocal na rm TRUE 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 weight calc character type of weight calculation One out of reciprocal weight is 1 error square weight is l error 2 na rm logical with default indicating whether NA values should be stripped before the computation proceeds Value Returns a list with weighted and unweighted statistic measures Function version 0 1 1 2015 03 04 17 27 01 Author s Michael Dietze GFZ Potsdam Germany R Luminescence Package Team Examples load example data data ExampleData DeValues envir environment show a rough plot of the data to illustrate the non normal distribution plot_KDE Ex
73. able when bootstrap TRUE and spawns n R instances for each core to get MAM estimates for each of the N and M boostrap replicates Note that this option is highly experimental and may or may not work for your machine Also the performance gain increases for larger number of bootstrap replicates Also note that with each additional core and hence R instance and depending on the number of bootstrap replicates the memory usage can significantly increase Make sure that memory is always availabe otherwise there will be a massive perfomance hit 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 mle2 object containing the maximum log likelhood functions for all parameters BIC numeric BIC score confint data frame confidence intervals for all parameters profile profile mle2 the log likelihood profiles calc_MinDose 49 bootstrap list bootstrap results The output should be accessed using the function get_RLum Results Function version 0 4 1 2015 03 18 13 29 54 Note The default starting values for gamma mu sigma and p0 may only be appropriate for some De data sets and may need to be changed for other data This is especially true when the un logged version is applied Also note that all R warning me
74. al aspects of equivalent dose and error calculation and display in OSL dating An overview and some recommendations Quaternary Geochronology 11 1 27 Further reading Arnold L J amp Roberts R G 2009 Stochastic modelling of multi grain equivalent dose De distri butions Implications for OSL dating of sediment mixtures Quaternary Geochronology 4 204 230 Bailey R M amp Arnold L J 2006 Statistical modelling of single grain quartz De distributions and an assessment of procedures for estimating burial dose Quaternary Science Reviews 25 2475 2502 Cunningham A C amp 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 amp 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 dis tribution Ancient TL 26 3 10 calc_CosmicDoseRate 31 See Also calc_CentralDose calc_FiniteMixture calc_FuchsLang2001 calc_MinDose Examples load example data data ExampleData DeValues envir environment apply the common dose model calc_CommonDose ExampleData DeValues CA1 calc_CosmicDoseRate Calculate the cosmic dose rate Description This function calculates the cosmic dose rate taking into account the soft and h
75. ally stimulated luminescence 2 IRSE Infrared stimulated luminescence 3 M IR Infrared monochromator scan 4 M VIS Visible monochromator scan 51 TOL Thermo optical luminescence 6 TRPOSL Time Resolved Pulsed OSL 7 RIR Ramped IRSL 8 RBR Ramped Blue LEDs 9 USER User defined 10 POSL Pulsed OSL 11 SGOSL Single Grain OSL 12 RL Radio Luminescence 13 XRF X ray Fluorescence LTYPES LO 0 Natural 140 Risoe BINfileData2RLum Analysis N dose Bleach Bleach dose Natural Bleach N dose Bleach Dose Background XAO Uh uyn KR information on the LTYPE and DTYPE kindly provided by Risoe DTU Nutech Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France References Risoe DTU 2013 The Sequence Editor User Manual Feb 2013 http www nutech dtu dk See Also plot_Risoe BINfileData readBIN2R writeR2BIN merge_Risoe BINfileData Risoe BINfileData2RLum Analys Risoe BINfileData2RLum Data Curve Examples showClass Risoe BINfileData 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 run set ltype protocol unknown Arguments object Risoe BINfileData required Risoe BINfileData object pos integer require
76. ampleData DeValues ylim c 0 0 08 0 35 centrality c median mean dispersion sd polygon col lightblue create plot with statistical summary below header plot_KDE data ExampleData DeValues summary c n median skewness qr create plot with statistical summary as legend plot_KDE data ExampleData DeValues summary c n mean sdrel seabs summary pos topleft split data set into sub groups one is manipulated and merge again data 1 lt ExampleData DeValues 1 15 data 2 lt ExampleData DeValues 16 25 1 3 data 3 lt list data 1 data 2 create plot with two subsets straightforward plot_KDE data data 3 create plot with two subsets and summary legend at user coordinates plot_KDE data data 3 summary c n median skewness summary pos c 110 0 07 col c blue orange example of how to use the numerical output of the function return plot output to draw a thicker KDE line KDE lt plot_KDE data ExampleData DeValues output TRUE read out coordinates of KDE graph KDE x lt KDE De density 1 x KDE y lt KDE De density 1 y transform y values to right y axis dimensions KDE y lt KDE y max KDE y nrow ExampleData DeValues 1 1 draw the KDE line lines x KDE x y KDE y lwd 3 plot_RadialPlot Function to create a Radial Plot Description A
77. ampleData DeValues BT998 calculate statistics and show output str calc_Statistics ExampleData DeValues BT998 now the same for 10000 normal distributed random numbers with equal errors x lt as data frame cbind rnorm n 10 5 mean 0 sd 1 rep 0 001 10 5 note the congruent results for weighted and unweighted measures str calc_Statistics x calc_TLLxTxRatio 57 calc_TLLxTxRatio Calculate the Lx Tx ratio for a given set of TL curves beta version Description Calculate Lx Tx ratio for a given set of TL curves Usage calc_TLLxTxRatio Lx data signal Lx data background Tx data signal Tx data background signal integral min signal integral max Arguments Lx data signal data frame required TL data x temperature y counts TL signal Lx data background data frame optional TL data x temperature y counts If no data are provided no background subtraction is performed Tx data signal data frame required TL data x temperature y counts TL test signal Tx data background data frame optional TL data x temperature y counts If no data are provided no background subtraction is performed signal integral min integer required channel number for the lower signal integral bound e g signal integral min 100 signal integral max integer required channel number for the upper signal integral bound e g signal integral max 200 Details Value Returns an S4
78. ampleData DeValues CA1 sigmab sd 0 06 plot FALSE sigmab 0 15 bootstrap TRUE bs M 300 bs N 500 bs h 4 Plot the results plot_RLum mam save bootstrap results in a separate variable bs lt get_RLum Results mam bootstrap show structure of the bootstrap results str bs max level 2 give attr FALSE print summary of minimum dose and likelihood pairs summary bs pairs gamma Show polynomial fits of the bootstrap pairs bs poly fits poly three Plot various statistics of the fit using the generic plot par mfcol c 2 2 plot bs poly fits poly three ask FALSE Show the fitted values of the polynomials summary bs poly fits poly three fitted values function calc_OSLLxTxRatio Calculate Lx Tx ratio for CW OSL curves Description Calculate Lx Tx ratios from a given set of CW OSL curves 52 calc_OSLLxTxRatio Usage calc_OSLLxTxRatio Lx data Tx data signal integral background integral background count distribution non poisson sigmab Arguments Lx data data frame required requires a CW OSL shine down curve x time y counts Tx data data frame optional requires a CW OSL shine down curve x time y counts If no input is given the Tx data will be treated as NA and no Lx Tx ratio is calculated signal integral vector required vector with the limits for the signal integral background integral vector
79. an existing BINX file Usage extract_IrradiationTimes file XSYG file BINX recordType c irradiation NA IRSL UVVIS OSL UVVIS TL UVVIS txtProgressBar TRUE Arguments file XSYG character required path and file name of the XSYG file 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 mea surement recordType character with default select relevant curves types from the XSYG file As the XSYG file format comprises much more information than usually needed for routine data analysis and allowed in the BINX file format only the relevant 80 extract_IrradiationTimes curves are selected by using the function get_RLum Analysis The argument recordType works as described for this function Note A wrong selection will causes a function error Please change this argu ment only if you have reasons to do so 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 XS YG file anyway these in formation can be extracted and used for further analysis
80. arameters are then sam pled 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 Ac cording to Lave 1970 the value is calculated as pseudoR 1 RSS TSS where RSS Residual Sum of Squares and TSS Total Sum of Squares Error of fitted component parameters The 1 sigma error for the components is calculated using the function confint Due to consider able calculation time this option is deactived by default In addition the error for the components fit_LMCurve 87 can be estimated by using internal R functions like summary See the nls help page for more infor mation For more details on the nonlinear regression in R see Ritz amp Streibig 2008 Value plot optional various types of plots are returned For details see above table optional an output table csv with the fitted components is provided if the output path is set list object beside the plot and table output a list is returned The list contains a an nls object fit for which generic R functions are provided e g sum mary confint profile For more details see nls b a data frame containing the summarised parameters including the error 0utput table c a matrix containing the values for the component to sum contribution plot component contribution matrix
81. ard component of the cosmic ray flux and allows corrections for geomagnetic latitude altitude above sea level and geomagnetic field changes Usage calc_CosmicDoseRate depth density latitude longitude altitude corr fieldChanges FALSE est age NA half depth FALSE error 10 Arguments depth numeric required depth of overburden m For more than one absorber use c depth_1 depth_2 depth_n density numeric required average overburden density g cm3 For more than one absorber use c density_1 density_2 density_n latitude numeric required latitude decimal degree N positive longitude numeric required longitude decimal degree E positive altitude numeric required altitude m above sea level corr fieldChanges logical with default correct for geomagnetic field changes after Prescott amp Hutton 1994 Apply only when justified by the data est age numeric with default estimated age range ka for geomagnetic field change correction 0 80 ka allowed half depth logical with default How to overcome with varying overburden thickness If TRUE only half the depth is used for calculation Apply only when justified 1 e when a constant sedimentation rate can safely be assumed error numeric with default general error percentage to be implemented on cor rected cosmic dose rate estimate 32 calc_CosmicDoseRate Details This function calculates the total cosmic dose rate consi
82. 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 100 plot_AbanicoPlot Function version 0 1 2 2015 03 04 14 53 26 Author s Michael Dietze GFZ Potsdam Germany Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Inspired by a plot introduced by Galbraith amp Green 1990 R Luminescence Package Team References Galbraith R amp Green P 1990 Estimating the component ages in a finite mixture International Journal of Radiation Applications and Instrumentation Part D Nuclear Tracks and Radiation Mea surements 17 3 pp 197 206 See Also plot_RadialPlot plot_KDE plot_Histogram Examples store original graphics parameters par old lt par no readonly TRUE load example data and recalculate to Gray data ExampleData DeValues envir environment ExampleData DeValues lt Second2Gray ExampleData DeValues BT998 c 0 0438 0 0019 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 lt plot_AbanicoPlot data ExampleData DeValues output TRUE str plot1 plot1 zlim now with adjusted z scale
83. ate the location of individual values numeric User defined plot area ratio i e curvature of the z axis If omitted the default value 4 5 5 5 is used and modified automatically to optimise the z axis curvature The parameter should be decreased when data points are plotted outside the z axis or when the z axis gets too elliptic plot_RadialPlot bar col y ticks grid col line line col line label output Details 115 character or numeric with default colour of the bar showing the 2 sigma range around the central value To disable the bar use none Default is srey logical Option to hide y axis labels Useful for data with small scatter character or numeric with default colour of the grid lines originating at 0 0 and stretching to the z scale To disable grid lines use none Default is grey numeric numeric values of the additional lines to be added character or numeric colour of the additional lines character labels for the additional lines logical Optional output of numerical plot parameters These can be useful to reproduce similar plots Default is FALSE Further plot arguments to pass xlab must be a vector of length 2 specifying the upper and lower x axes labels Details and the theoretical background of the radial plot are given in the cited literature This func tion is based on an S script of Rex Galbraith To reduce the manual adjustments the function has been r
84. ation routine for P i e provide no own value for P Value The function returns the same data type as the input data type with the transformed curve values RLum Data Curve package RLum object with two additional info elements CW2pLMi x t transformed time values CW2pLMi method used method for the production of the new data points Function version 0 3 1 2015 03 04 18 48 02 Note According to Bos amp 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 amp Wallinga J 2012 How to visualize quartz OSL signal components Radiation Mea surements 47 752 758 Further Reading Bulur E 1996 An Alternative Technique For Optically Stimulated Luminescence OSL Ex periment Radiation Measurements 26 701 709 Bulur E 2000 A simple transformation for converting CW OSL curves to LM OSL curves Ra diation Measurements 32 141 145 66 CW2pPMi See Also CW2pLM CW2pHMi CW2pPMi fit_LMCurve RLum Data Curve Examples 1 load CW OSL curve data data ExampleData CW_OSL_Curve envir environment transform values
85. c_FiniteMixture eaea tedo 00002 ee eee cale FuchsLang2001l eG e a ee ee Re eS calc_HomogeneityTest 0 0 00 02 0 0 eee Cal IEU ones ais BS Bee eee EE ee Re eS calc MaxDose y ut ida ao ees ABS we Ged dow ee Se lo eee 4 calc MinDose 0 0000 eee eee eee calc_OSLLxTxRatio 0 00000 0000 2 eee calc_SourceDoseRate 2 2 0 ee ee cale Statistics s c emea Bos w wok A calc TLLxTxRatio s s goia e CW2pHM ca soo aar a a di A EW2pEMi oia a e a da A CW2PEML escoria a BES amp BA e CWZpPMA 2206 68 ae Go ee a a a a ExampleData BINfileData o o ExampleData CW_OSL_CuUrve o o ExampleData DeValues o o ExampleData FitingLM o o ExampleData LxTxData o ExampleData LxTxOSLData o ExampleData RLum Analysis o ExampleData RLum Data Image o ExampleDataXSYG o o extract_IrradiationTimes o oo a a e fit CWCUIVE sea Es w ds ds e a Ee eH A fit TIMICUEVE lt sorrir sae eed SS doers Rat eS ee ee ek om o R topics documented Luminescence package 3 Index pet Layout 22405 o 44s Oe ae PRGAS Sa eee ee dae RA ee bed 88 BEE RM he sis Ge ae Bens he Hs See hy dp gt Beha e e Reale Be i A de Rd Bh ee Repl 89 merge_Risoe BlNfileData e 91 merge RLM 04 a a Sa a Bad BO Seale Abe de aie
86. calculate the cosmic dose rate provided by Prescott amp Hutton 1994 is falsely stated to be valid from the surface to 104 hg cm 2 of standard rock The original expression by Barbouti amp Rastin 1983 only considers the muon flux i e hard component and is by their own definition only valid for depths between 10 104 hg cm 2 Thus for near surface samples i e for depths lt 167 g cm 2 the equation of Prescott amp 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 amp Hutton 1988 give another approximation of Barbouti amp Rastins equation in the form of D 0 21 x exp 0 070 x absorber 0 0005 absorber which is valid for depths between 150 5000 g cm 2 For shallower depths lt 150 g cm22 they provided a graph Fig 1 from which the dose rate can be read As a result this function employs the equation of Prescott amp Hutton 1994 only for depths gt 167 g cm 2 i e only for the hard component of the cosmic ray flux Cosmic dose rate values for depths lt 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 amp Hutton 1988 However these values assume an average overburden density of 2 g cm 3 It is cu
87. ce lt sebastian kreutzer u bordeaux montaigne fr gt Acknowledgement analyse_IRSAR RF 5 Cooperation and personal exchange between the developers is gratefully funded by the DFG SCHM 305 1 3 1 in the framework of the program Scientific Networks Project title Lum Network Ein Wissenschaftsnetzwerk zur Analyse von Lumineszenzdaten mit R 2014 2017 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 pp 11 18 Fuchs M C Kreutzer S Burow C Dietze M Fischer M Schmidt C Fuchs M 2014 Data processing in luminescence dating analysis An exemplary workflow using the R package Lumi nescence Quaternary International pp 1 6 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 pp 1 8 analyse_IRSAR RF Analyse IRSAR RF measurements Description Function to analyse IRSAR RF measurements on K feldspar samples performed using the protocol according to Erfurt et al 2003 Usage analyse_IRSAR RF object sequence structure c NATURAL REGENERATED method FIT rejection criteria fit range min fit range max fit trace FALSE fit MC runs 10 slide MC runs 10 slide outlier rm FALSE slide trend corr FALSE slide show
88. channel see Details Note requires input for values bg 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 output with fitting results output terminaladvanced logical with default enhanced terminal output Requires output terminal TRUE If output terminal FALSE no advanced output is possible output plot logical with default returns a plot of the fitted curves output plotBG 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 Details Fitting function The function for the fitting has the general form y exp 0 5 Imy a a2m xexp x 2 am exp 0 5 Im x xm exp a 2 am where l lt i lt 8 This function and the equations for the conversion to b detrapping probability and nO proportional to initially trapped charge have been taken from Kitis et al 2008 xm Vmax t b 86 fit_LMCurve Im exp 0 5 n0 am 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 ba
89. ck will be returned Version 0 1 2014 07 22 Note The class should only contain data for a set of images For additional elements the slot info can be used Author s Sebastian Kreutzer Universite Bordeaux Montaigne France References See Also RLum RLum Data plot_RLum RLum Data Spectrum class 149 Examples showClass RLum Data Image so far no further example available RLum Data Spectrum class Class RLum Data Spectrum 1 Description Class for luminescence spectra data TL OSL RF Objects from the Class Objects can be created by calls of the form new RLum Data Spectrum Slots recordType Object of class character containing the type of the curve e g TL or OSL curveType Object of class character containing curve type allowed values are measured or predefined data Object of class matrix containing spectrum count values row labels indicating wavelength pixel values column labels temperature or time values info Object of class list containing further meta information objects 1 S3Class Object of class character Extends Class RLum Data directly Methods coerce signature from data frame to RLum Data Spectrum signature from matrix to RLum Data Spectrum Furthermore lossy coercing is possible from RLum Data Spectrum to data frame matrix show signature object RLum Data
90. ckground subtraction y axa t beritcrar derte linear a linear function is fitted using glm and the resulting function is used for background subtraction y axxc 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 output plot TRUE with the pseudo curve based on the pseudo start parameters is provided This may give the oppor tunity to identify appropriate start parameters visually b If start values are provided the function works like a simple n1s fitting approach c If no start parameters are provided and the option fit advanced TRUE is chosen an ad vanced start paramter estimation is applied using a stochastical attempt Therefore the recalculated start parameters a are used to construct a normal distribution The start p
91. d position number of the Risoe BINfileData object for which the curves are stored in the RLum Analysis object If the position is not valid NA is returned run vector numeric optional run number from the measurement to limit the converted data set e g run c 1 48 Risoe BINfileData2RLum Analysis 141 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 Allowed values are IRSL OSL TL RIR RBR and USER protocol character optional sets protocol type for analysis object Value may be used by subsequent analysis functions 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 Function version 0 1 2 2015 03 04 00 19 53 Note The protocol argument of the RLum Analysis object is set to unknown if not stated otherwise Author s Sebastian Kreutzer JLU Giessen Germany R Luminescence Package Team References See Also Risoe BINfileData RLum Analysis readBIN2R Examples load data data ExampleData BINfileData envir environment convert values for position 1 Risoe BINfileData2RLum
92. d spectral resolution Value Returns same object as input RLum Data Spectrum Function version 0 1 2015 03 04 00 19 53 Note Please note that the spectral efficiency data from the camera may not sufficiently correct for spectral efficiency of the entire optical system e g spectrometer camera This function has BETA status Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Johannes Friedrich University of Bayreuth Germany R Luminescence Package Team References See Also RLum Data Spectrum Examples 1 use with your own data uncomment for usage spectral efficiency lt read csv your data Ht your spectrum lt apply_EfficiencyCorrection your spectrum BaseDataSet CosmicDoseRate 23 BaseDataSet CosmicDoseRate Base data set for cosmic dose rate calculation Description Collection of data from various sources needed for cosmic dose rate calculation Usage BaseDataSet CosmicDoseRate Format values cosmic Softcomp data frame containing cosmic dose rates for shallow depths lt 167 g cm 2 obtained using values factor Altitude data frame containing altitude factors for adjusting geomagnetic field change factors Value values par FJH data frame containing values for parameters F J and H read from Fig 2 in Prescott amp Hut Dc D0 x F J xezp altitude 1000 H Version 0 1 Source The following data were car
93. d or qr polygon The line type lty for additional measures of centrality will cycle through the default values 1 2 by default i e KDE line solid further vertical lines dashed dotted dash dotted and so on To change this behaviour specify the desired order of line types e g lty c 1 3 2 5 See examples for some further explanations For details on the calculation of the bin width parameter bw see density Function version 3 5 2015 03 04 13 25 51 Note The plot output is no PD plot cf the discussion of Berger and Galbraith in Ancient TL see references Author s Michael Dietze GFZ Potsdam Germany Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne R Luminescence Package Team See Also density plot Examples read example data set data ExampleData DeValues envir environment ExampleData DeValues lt Second2Gray ExampleData DeValues BT998 c 0 0438 0 0019 create plot straightforward plot_KDE data ExampleData DeValues create plot with logarithmic x axis plot_KDE data ExampleData DeValues log O create plot with user defined labels and axes limits plot_KDE data ExampleData DeValues main Dose distribution xlab Dose s ylab c KDE estimate Cumulative dose value xlim c 100 250 plot_RadialPlot 113 ylim c 0 08 0 30 create plot with centrality lines and distribution polygons plot_KDE data Ex
94. data from a SAR OSL and SAR TL measurement for the pack age Luminescence 70 Description ExampleData BINfileData 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 class Usage ExampleData 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 Source CWOSL SAR Data Lab Luminescence Laboratory Bayreuth Lab Code BT607 Location Saxony Germany Material Middle grain quartz measured on aluminum cups on a Risoe TL OSL DA 15 reader Reference unpublished TL SAR Data Lab Luminescence Laboratory of Cologne Lab Code LP1_5 Location Spain Material Flint Setup Risoe TL OSL DA 20 reader Filter Semrock Brightline HC475 50 N2 unpolished steel discs Reference unpublished Remarks dataset limited to one position References CWOSL SAR Data unpublished data TL SAR Data unpublished data ExampleData CW_OSL_Curve 71 Examples show first 5 elements of the METADATA and DATA elements in the terminal data ExampleData BINfileData envir environment CWOSL SAR Data METADATAL1 5 CWOSL SAR Data DATAL1 5 ExampleData CW_OSL
95. dering both the soft and hard component of the cosmic ray flux Internal calculation steps 1 Calculate total depth of all absorber in hg cm 2 1 hg cm 2 100 g cm 2 absorber depth x density deptha x densitya depth density 2 If half depth TRUE absorber absorber 2 3 Calculate cosmic dose rate at sea level and 55 deg latitude a If absorber is gt 167 g cm 2 only hard component Allkofer et al 1975 apply equation given by Prescott amp Hutton 1994 c f Barbouti amp Rastin 1983 DO C absorber d a absober H exp B x absorber b If absorber is lt 167 g cm 2 soft and hard component derive DO from Fig 1 in Prescott amp Hutton 1988 4 Calculate geomagnetic latitude Prescott amp Stephan 1982 Prescott amp Hutton 1994 A arcsin 0 203 x cos latitude x cos longitude 291 0 979 x 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 amp Stephan 1982 and fitted with 3 degree polynomials for lambda lt 35 degree and a linear fit for lambda gt 35 degree Dc D0 x F J x exp altitude 1000 H 6 Optional Apply correction for geomagnetic field changes in the last 0 80 ka Prescott amp Hutton 1994 Correction and altitude factors are given in Table 1 and Fig 1 in Prescott amp Hutton 1994 Values for altitude factor were fitted
96. during heating not only increase Value Using the option import FALSE A list consisting of two elements is shown 136 readXS YG2R Sample data frame with information on file Sequences 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 4 1 2015 03 21 03 09 47 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 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 lt file choose temp lt readXSYG2R FILE 2 additional examples for pure XML import using the package XML HH uncomment for usage Risoe BINfileData class 137 im
97. e 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 individ ual 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 1 e values is a list Otherwise a given dose for each input data set has to be provided e g given dose c 100 200 If no given dose 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 sa
98. e S4 class objects Description Function allows merging of RLum Data Curve objects in different ways Usage merge_RLum Data Curve object merge method mean method info Arguments object list of RLum Data Curve required list of S4 objects of class RLum Curve merge method character required method for combining of the objects e g mean sum see details for further information and allowed methods Note Elements in slot info will be taken from the first curve in the list method info numeric optional allows to specify how info elements of the input objects are combined e g 1 means that just the elements from the first object are kept 2 keeps only the info elements from the 2 object etc If nothing is provided all elements are combined 96 merge_RLum Data Curve Details This function simply allowing to merge RLum Data Curve objects without touching the objects it self Merging is always applied on the 2nd colum of the data matrix of the object Supported merge operations are RLum Data Curve sum All count values will be summed up using the function rowSums mean The mean over the count values is calculated using the function rowMeans non The row sums of the last objects are subtracted from the first object myn The row sums of the last objects are mutliplied with the first object Values of the first object are divided by row sums of the last objects Value Ret
99. e 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 B for source dose rate calibration data calculate source dose rate first dose rate lt read example data calc_SourceDoseRate measurement date 2012 01 27 calib date lt 2014 12 19 calib dose rate lt 0 0438 calib error lt 0 0019 data ExampleData DeValues envir environment apply dose rate to convert De s to De Gy Second2Gray ExampleData DeValues BT998 dose rate 153 sTeve sTeve sophisticated tool for efficient data validation and evaluation Description This function provides a sophisticated routine for comprehensive luminescence dating data analysis Usage sTeve n_frames 10 t_animation 2 n tree 7 type 154 writeR2BIN Arguments n_frames integer with default n frames t_animation integer with default t animation n tree integer with default How many trees do you want to cut type integer optional Make a decision 1 2 or 3 Details This amazing sophisticated function validates your data seriously Value Validates your data Note This function should not be taken too seriously Author s R Luminescence Team 2012 2013 References See Also plot_KDE Examples no example available writeR2BIN Export
100. e structure the reader is referred to the Risoe website http www nutech dtu dk Value Returns an S4 Risoe BINfileData class object containing two slots METADATA A data frame containing all variables stored in the bin file DATA A list containing a numeric vector of the measured data The ID corresponds to the record ID in METADATA Function version 0 8 1 2015 03 04 12 43 39 Note The function has been successfully tested for BIN format versions 03 04 and 06 The version num ber depends on the used Sequence Editor Other BIN format versions are currently not supported Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Margret C Fuchs AWI Potsdam Germany R Luminescence Package Team References Duller G 2007 Analyst http www nutech dtu dk english media Andre_Universitetsenheder Nutech Produkter 200g 20services Dosimetri radiation_measurement_instruments tl_ osl_reader Manuals analyst_manual_v3_22b ashx See Also writeR2BIN Risoe BINfileData readBin merge_Risoe BINfileData txtProgressBar 132 readSPE2R Examples 1 import Risoe BIN file to R uncomment for usage FILE lt file choose temp lt readBIN2R FILE temp readSPE2R 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 readSPE2R file output object R
101. ed radiation dose in seconds s to the SI unit gray Gy including error prop agation Normally used for equivalent dose data Usage Second2Gray data dose rate method gaussian Arguments data data frame required input values structure data values 1 and data error values 2 are required dose rate RLum Results or vector required RLum Results needs to be orginated from the function calc_SourceDoseRate for vectordose rate in Gy s and dose rate error in Gy s method character with default method used for error calculation gaussian or absolute see details for further information Details Calculation of De values from seconds s to gray Gy De Gy Dels x DoseRate Gy s Provided calculation methods for error calculation gaussian error propagation De error gray dose rate x De error seconds De seconds x dose rate error absolute error propagation De error gray abs dose rate x De error seconds abs De seconds x dose rate error Value Returns a data frame with converted values Function version 0 4 2015 03 04 13 42 29 Note If no or a wrong method is given the execution of the function is stopped sTeve Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Michael Dietze GFZ Potsdam Germany Margret C Fuchs AWI Potsdam Germany R Luminescence Package Team References See Also Examples A for known source dos
102. ediment mixtures a test of single grain optical dating procedures using mix tures of laboratory dosed quartz Radiation Measurements 32 459 465 Galbraith R F 2005 Statistics for Fission Track Analysis Chapman 4 Hall CRC Boca Raton Further reading calc_FuchsLang2001 39 Arnold L J amp Roberts R G 2009 Stochastic modelling of multi grain equivalent dose De distri butions Implications for OSL dating of sediment mixtures Quaternary Geochronology 4 204 230 Cunningham A C amp 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 amp 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 dis tribution 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 compon
103. ee 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 lt 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 results summary export results to csv file uncomment for usage write csv results file c users public results csv 4 calculate cosmic dose rate for 6 samples from the same profile HH and save to csv file calculate cosmic dose rate and save to variable calc_FadingCorr 35 results lt 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 ttexport results to csv
104. efully read from figures in mentioned sources and used for fitting pro cedures The derived expressions are used in the function calc_CosmicDoseRate values cosmic Softcomp Program AGE Reference Gruen 2009 Fit Polynomials in the form of For depths between 40 167 g cm 2 y 2 x 1076 x 0 0008 a 0 2535 For depths lt 40 g cm 2 y 6 x 1078 2 2x 1075 x 0 0025 x 0 2969 values factor Altitude Reference Prescott amp Hutton 1994 Page 499 Figure 1 Fit 2 degree polynomial in the form of 24 BaseDataSet CosmicDoseRate y 0 026 x 2 0 6628 x 1 0435 values par FJH Reference Prescott amp Hutton 1994 Page 500 Figure 2 Fits 3 degree polynomials and linear fits F non linear part A lt 36 5 deg y 7 1077 z 8 1075 x 2 0 0009 x 0 3988 F linear part A gt 36 5 deg y 0 0001 z 0 2347 J non linear part A lt 34 deg y 5 x 1076 x 23 5 x 1075 x 0 0026 x x 0 5177 J linear part A gt 34 deg y 0 0005 x 0 7388 H non linear part A lt 36 deg y 3 10 6 3 5 x 1075 a 0 0031 x x 4 398 H linear part A gt 36 deg y 0 0002 x 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
105. ehensive 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 4 Luminescence package Details Package Luminescence Type Package Version 0 4 2 Date 2015 03 23 License GPL 3 Author s Authors Christoph Burow University of Cologne Germany Michael Dietze GFZ Helmholtz Centre Potsdam Germany Manfred Fischer University of Bayreuth Germany Margret C Fuchs Alfred Wegener Insitute for Polar and Marine Research Potsdam Germany Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne Pessac France Christoph Schmidt University of Bayreuth Germany Rachel K Smedley Aberystwyth University United Kingdom Beta Tester Thomas Kolb University of Bayreuth Germany Supervisor Markus Fuchs Justus Liebig University Giessen Germany Support contact lt developer r luminescence de gt We may further encourage the usage of our support forum For this please visit our project website link below Bug reporting lt bugtracker r luminescence de gt Project website http www r luminescence de Project source code repository https github com R Lum Luminescence Package maintainer Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne Pessac Fran
106. elative standard error seabs abso lute standard error skewness skewness and kurtosis kurtosis Note Keywords kdemax is implemented for consistency reasons however no KDE is shown The bandwidth is calculated according to plot_KDE numeric or character with default optional position coordinates or key word 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 In case of coordinate specification y coordinate refers to the right y axis numeric or character with default optional vector of length 4 which specifies the colours of the following plot items in exactly this order histogram bars rug lines normal distribution curve and standard error points e g c grey black red grey further arguments and graphical parameters passed to plot If y axis labels are provided these must be specified as a vector of length 2 since the plot features two axes e g ylab c axis label 1 axis label 2 Y axes limits ylim must be provided as vector of length four with the first two elements specifying the left axes limits and the latter two elements giving the right axis limits 110 plot_Histogram Details If the normal curve is added the y axis in the histogram will show the probability density Function version 0 4 3 2015 03 04 1
107. ents and save results NOTE The following example is computationally intensive Please un comment the following lines to make the example work FMM lt 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 Results object FMM data object components calc_FuchsLang2001 Apply the model after Fuchs amp Lang 2001 to a given De distribution Description This function applies the method according to Fuchs amp Lang 2001 for heterogeneously bleached samples with a given coefficient of variation threshold 40 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 11 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 calcula tions 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_
108. ernal usage only get_Risoe BINfileData signature object Risoe BINfileData Formal get method for Risoe BINfileData object It does not allow accessing the object directly it is just showing a terminal message 138 Risoe BINfileData class Version 0 4 2014 02 27 Note Internal METADATA object structure Name Data Type V Description L1 ID numeric RLum Unique record ID same ID as in slot DATA 2 SEL logic RLum Record selection not part official BIN format triggered by TAG L3 VERSION raw 03 06 BIN file version number 4 LENGTH integer 03 06 Length of this record 5 PREVIOUS integer 03 06 Length of previous record 6 NPOINTS integer 03 06 Number of data points in the record 7 RUN integer 03 06 Run number 8 SET integer 03 06 Set number 9 POSITION integer 03 06 Position number 10 GRAIN integer 03 04 Grain number L11 GRAINNUMBER integer 06 Grain number 12 CURVENO integer 06 Curve number 13 XCOORD integer 03 06 X position of a single grain 14 YCOORD integer 03 06 Y position of a single grain 15 SAMPLE factor 03 06 Sample name 16 COMMENT factor 03 06 Comment name 17 SYSTEMID integer 03 06 Risoe system id 18 FNAME factor 06 File name bin binx 19 USER facotr 03 06 User name 20 TIME character 03 06 Data collection time hh mm ss 21 DATE factor 03 06 Data collection date ddmmyy 22 DTYPE character 03 06 Data type 23 BL_TIME numeric 03 06 Bleaching time 24 B
109. evant 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 Results Function version 0 4 2015 03 04 13 33 56 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 amp Green P F 1990 Estimating the component ages in a finite mixture Nuclear Tracks and Radiation Measurements 17 197 206 Galbraith R F amp Laslett G M 1993 Statistical models for mixed fission track ages Nuclear Tracks Radiation Measurements 4 459 470 Galbraith R F amp 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 amp Olley J M 2000 Distinguishing dose populations in s
110. ewritten Thanks to Rex Galbraith for useful comments on this function Plotting can be disabled by adding the argument plot FALSE e g to return only numeric plot output Earlier versions of the Radial Plot in this package had the 2 sigma bar drawn onto the z axis How ever this might have caused misunderstanding in that the 2 sigma range may also refer to the z scale which it does not Rather it applies only to the x y coordinate system standardised error vs precision A spread in doses or ages must be drawn as lines originating at zero precision x0 and zero standardised estimate y0 Such a range may be drawn by adding lines to the radial plot line line col line label cf examples Value Returns a plot object Function version 0 5 3 2015 03 04 13 25 19 Author s Michael Dietze GFZ Potsdam Germany Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Based on a rewritten S script of Rex Galbraith 2010 R Luminescence Package Team References Galbraith R F 1988 Graphical Display of Estimates Having Differing Standard Errors Techno metrics 30 3 271 281 116 plot_RadialPlot Galbraith R F 1990 The radial plot Graphical assessment of spread in ages International Jour nal of Radiation Applications and Instrumentation Part D Nuclear Tracks and Radiation Measure ments 17 3 207 214 Galbraith R amp Green P 1990 Estimating the component ages in a finite
111. file uncomment for usage write csv results file c users public results_profile csv calc_FadingCorr Apply a fading correction according to Huntley amp Lamothe 2001 for a given g value Description This function runs the iterations that are needed to calculate the corrected age including the error for a given g value according to Huntley amp Lamothe 2001 Usage calc_FadingCorr g_value tc age faded n MCruns 10000 Arguments g_value vector required g value and error obtained from separate fading measure ments see example tc numeric required time in seconds time between irradiation and the prompt measurement cf Huntely amp Lamothe 2001 age faded numeric vector required uncorrected age with error in ka see example n MCruns integer with default number of Monte Carlo simulation runs for error estima tion Details The error of the fading corrected age is determined using a Monte Carlo simulation approach Solv ing of the equation is realised using uniroot Large values for n MCruns will significantly increase the computation time Value Returns an S4 object of type RLum Results Slot data contains a list with the following struc ture age corr data frame age age error age corr MC numeric Age corr MC contain all possible ages from the Monte Carlo error simulation Function version 0 2 2015 03 21 01 18 50 36 calc_FiniteMixture Note The upper age li
112. 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 82 fit_CWCurve 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 output 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 101 x Ay exp Ai x 1 10 Aj exp r x x where 1
113. 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 8 Lang 2001 temp lt calc_FuchsLang2001 ExampleData DeValues BT998 cvThreshold 5 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 RLum Results or data frame required for data frame two columns with De dataL 1 and De error values 2 log logical with default peform the homogeniety test with un logged data further arguments for internal compatibility only Details For details see Galbraith 2003 42 calc_IEU Value Returns a terminal output In addition an RLum Results object is returned containing the following element summary data frame summary of all relevant model results data data frame original input data args list used arguments call call the function call The output should be accessed using the function get_RLum Results Function version 0 2 2015 03 04 13 31 44 Author s Christoph Burow University of Cologne Germany R Luminescence Package Team References Galbraith R F 2003 A simple homogeneity test for estimates of dose ob
114. g specific RLum objects Depending on the input object the corresponding plot function will be selected Allowed arguments can be found in the documentations of each plot function object corresponding plot function RLum Data Curve plot_RLum Data Curve RLum Data Spectrum plot_RLum Data Spectrum RLum Data Image plot_RLum Data Image RLum Analysis plot_RLum Analysis RLum Results plot_RLum Results Value Returns a plot Function version 0 3 2015 03 04 00 19 53 Note The provided plot output depends on the input object Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References plot_RLum Analysis 121 See Also plot_RLum Data Curve RLum Data Curve plot_RLum Data Spectrum RLum Data Spectrum plot_RLum Data Image RLum Data Image plot_RLum Analysis RLum Analysis plot_RLum Results RLum Results Examples load Example data data ExampleData CW_OSL_Curve envir environment transform data frame to RLum Data Curve object temp lt as ExampleData CW_OSL_Curve RLum Data Curve plot RLum object plot_RLum temp plot_RLum Analysis Plot function for an RLum Analysis S4 class object Description The function provides a standardised plot output for curve data of an RLum Analysis S4 class object Usage plot_RLum Analysis object nrows 3 ncols 2 abline combine FALSE curve transformation plot s
115. gon col order TRUE bw nrd0 output FALSE Arguments data data frame or RLum Results object required for data frame two columns De values 1 and De error values 2 For plotting multiple data sets these must be provided as list e g list dataset1 dataset2 na exclude logical with default exclude NA values from the data set prior to any further operations weights logical with default calculate the KDE with De errors as weights Attention using errors as weights will result in a plot similar to a a probability density plot with all ambiguities related to this plot type values cumulative logical with default show cumulative individual data centrality character measure s of centrality used for plotting vertical lines of the re spective measure Can be one out of mean median mean weighted median weighted and kdemax dispersion character measure of dispersion used for drawing the polygon that depicts the dose distribution One out of sd standard deviation 2sd 2 standard deviations qr quartile range summary character optional adds numerical output to the plot Can be one or more out of n number of samples mean mean De value mean weighted error weighted mean median median of the De values sdrel relative standard deviation in percent sdabs absolute standard deviation serel relative standard error seabs
116. gral min 900 background integral max 1000 log x fit method EXP Analyse_SAR OSLdata 15 show De results get_RLum Results results show LnTnLxTx table get_RLum Results results data object LnLxTnTx table Analyse_SAR OSLdata Analyse SAR CW OSL measurements Description The function analyses SAR CW OSL curve data and provides a summary of the measured data for every position The output of the function is optimised for SAR OSL measurements on quartz Usage Analyse_SAR OSLdata input data signal integral background integral position run set dtype keep SEL FALSE info measurement unkown measurement log output plot FALSE output plot single FALSE cex global 1 Arguments input data Risoe BINfileData class required input data from a Risoe BIN file produced by the function readBIN2R signal integral vector required channels used for the signal integral e g signal integral c 1 2 background integral vector required channels used for the background integral e g background integral c 85 100 position vector optional reader positions that want to be analysed e g position c 1 48 Empty positions are automatically omitted If no value is given all positions are analysed by default run vector optional range of runs used for the analysis If no value is given the range of the runs in the sequence is deduced from the Risoe BINfileData object set
117. hod RLum Analysis class 144 set_RLum Data Curve 143 set_RLum Data Curve RLum Data Curve class 146 set_RLum Data Curve ANY method RLum Data Curve class 146 set_RLum Data Curve character matrix method RLum Data Curve class 146 set_RLum Data Curve RLum Data Curve method RLum Data Curve class 146 set_RLum Data Curve methods RLum Data Curve class 146 set_RLum Data Image RLum Data Image class 147 set_RLum Data Image ANY method RLum Data Image class 147 set_RLum Data Image character matrix method RLum Data Image class 147 set_RLum Data Image RLum Data Image method RLum Data Image class 147 RLum Data Spectrum class 149 show RLum Results method RLum Results class 150 smooth 20 21 smooth spline 20 21 sTeve 153 summary 83 87 txtProgressBar 130 132 155 uniroot 35 36 validObject RLum Results method RLum Results class 150 vector 5 10 15 18 35 52 59 64 67 81 118 126 131 132 140 141 144 152 writeBin 56 writeR2BIN 80 81 92 131 139 140 154 xml 134 136
118. in the Risoe Sequence Editor ltype character with default option to limit the plotted curves by the type of lu minescence stimulation Allowed values IRSL OSL TL RIR RBR corresponds to LM OSL RL All type of curves are plotted by default curve transformation dose_rate temp lab cex global Details Nomenclature character optional allows transforming CW OSL and CW IRSL curves to pseudo LM curves via transformation functions Allowed values are CW2pLM CW2pLMi CW2pHMi and CW2pPMi See details numeric optional dose rate of the irradition source at the measurement date If set the given irradiation dose will be shown in Gy See details character optional option to allow for different temperature units If no value is set deg C is chosen numeric with default global scaling factor further undocumented plot arguments See Risoe BINfileData class curve transformation plot_Risoe BINfileData 119 This argument allows transforming continuous wave CW curves to pseudo linear modulated curves For the transformation the functions of the package are used Currently it is not possible to pass further arguments to the transformation functions The argument works only for 1type OSL and IRSL Irradiation time Plotting the irradiation time s or the given dose Gy requires that the variable IRR_TIME has been set within the BIN file This is normally done by using the
119. ines Accordingly initial values for the four parameters can be specified via init values If no values are provided for init values reasonable starting values are estimated from the input data If the final estimates of gamma mu sigma and p0 are totally off target consider providing custom starting values via init values In contrast to previous versions of this function the boundaries for the individual model parameters can no longer be specified Appropriate boundary are now hard coded and are valid for all input data sets Bootstrap When bootstrap TRUE the function applies the bootstrapping method as described in Wallinga amp Cunningham 2012 By default the minimum age model produces 1000 first level and 3000 second level bootstrap replicates actually the number of second level bootstrap replicates is three times the number of first level replicates unless specified otherwise The uncertainty on sigmab is 0 04 by default These values can be changed by using the arguments bs M first level replicates bs N second level replicates and sigmab sd error on sigmab With bs h the bandwidth of the kernel density estimate can be specified By default h is calculated as h 2 opR V n Multicore support This function supports parallel computing and can be activated by multicore TRUE By default the number of available logical CPU cores is determined automatically but can be changed with cores The multicore support is only avail
120. ingle FALSE Arguments object RLum Analysis required S4 object of class RLum Analysis nrows integer with default sets number of rows for plot output ncols integer with default sets number of columns for plot output abline list optional allows to set similar ablines in each plot This option uses the function do call meaning that every argument in the list has to be provided as list e g abline list list v 120 list v 350 produces two vertical ablines One at 150 and another one at 350 Within the call all arguments supported by abline are fully supported combine logical with default allows to combine all codeRLum Data Curve objects in one single plot Works only for RLum Analysis that comprises a single curve object option is currently only roughly implemented curve transformation character optional allows transforming CW OSL and CW IRSL curves to pseudo LM curves via transformation functions Allowed values are CW2pLM CW2pLMi CW2pHMi and CW2pPMi See details plot single logical with default each curve is plotted in a single window overwrites the settings of norws and ncols 122 plot_RLum Analysis further arguments and graphical parameters will be passed to the plot func tion Supported arguments main mtext log lwd lty type pch col and for combine TRUE also xlim ylim xlab ylab sub legend text legend pos Details The function produces a multiple plot output A file ou
121. ion s 51 TIMETICK numeric 06 Time tick for pulsing s 52 ONTIME integer 06 On time for pulsing in time ticks 53 STIMPERIOD integer 06 Stimulation period on off in time ticks 54 GATE_ENABLED raw 06 PMT signal gating enabled 55 ENABLE_FLAGS raw 03 PMT signal gating enabled 56 GATE_START integer 06 Start gating in time ticks 57 GATE_STOP ingeter 06 Stop gating in time ticks Gateend for version 04 here only G 58 PTENABLED raw 06 Photon time enabled 59 DTENABLED raw 06 PMT dead time correction enabled 60 DEADTIME numeric 06 PMT dead time s 61 MAXLPOWER numeric 06 Stimulation power to 100 percent mW cm 2 62 XRF_ACQTIME numeric 06 XRF acquisition time s 63 XRF_HV numeric 06 XRF X ray high voltage V 64 XRF_ CURR integer 06 XRF X ray current uA 65 XRF_DEADTIMEF numeric 06 XRF dead time fraction 66 SEQUENCE character 03 04 Sequence name V BIN file version RLum means that it does not depend on a specific BIN version Note that the Risoe BINfileData object combines all values from different versions from the BIN file reserved bits are skipped however the function writeR2BIN reset arbitrary reserved bits Invalid values for a specific version are set to NA Furthermore the internal R data types do not necessarily match the required data types for the BIN file data import Data types are converted during data import LTYPES LO TL Thermoluminescence 1 OSL Optic
122. ion calculates the weighted mean of logarithmic De values Each of the estimates is weighted by the inverse square of its relative standard error The weighted mean is then transformed back to the dose scale Galbraith amp Roberts 2012 p 14 30 calc_CommonDose The log transformation is not applicable if the De estimates are close to zero or negative In this case the un logged model can be applied instead log FALSE The weighted mean is then calculated using the un logged estimates of De and their absolute standard error Galbraith amp Roberts 2012 p 14 Value Returns a terminal output In addition an RLum Results object is returned containing the following element summary data frame summary of all relevant model results data data frame original input data args list used arguments call call the function call The output should be accessed using the function get_RLum Results Author s Christoph Burow University of Cologne Germany R Luminescence Package Team References Galbraith R F amp Laslett G M 1993 Statistical models for mixed fission track ages Nuclear Tracks Radiation Measurements 4 459 470 Galbraith R F Roberts R G Laslett G M Yoshida H amp Olley J M 1999 Optical dating of single grains of quartz from Jinmium rock shelter northern Australia Part I experimental de sign and statistical models Archaeometry 41 339 364 Galbraith R F amp Roberts R G 2012 Statistic
123. ition 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 92 merge_Risoe BINfileData 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 Value Returns a file or a Risoe BINfileData object Function version 0 2 2 2015 03 04 12 43 39 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 readBIN2R writeR2BIN Examples merge two objects data ExampleData BINfileData envir environment object1 lt CWOSL SAR Data object2 lt CWOSL SAR Data object new lt merge_Risoe BINfileData c object1 object2 merge_RLum 93 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 Arguments objects list of RLum required list of S4 object of class RLum further arguments that one might want to pass to
124. lass RLum further arguments that one might want to pass to the specific get function 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 each get function object corresponding get function RLum Data Curve get_RLum Data Curve RLum Data Image get_RLum Data Image RLum Data Spectrum get_RLum Data Spectrum RLum Analysis get_RLum Analysis RLum Results get_RLum Results Value Return is the same as input objects as provided in the list Function version 0 1 2015 03 04 14 39 52 Note Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References See Also get_RLum Data Curve RLum Data Curve get_RLum Data Image RLum Data Image get_RLum Data Spectrum RLum Data Spectrum get_RLum Analysis RLum Analysis get_RLum Results RLum Results Examples Example based using data and from the calc_CentralDose function load example data data ExampleData DeValues envir environment tttapply the central dose model 1st time temp1 lt calc_CentralDose ExampleData DeValues CA1 merge_Risoe BINfileData 91 get results and store them in a new object temp get lt get_RLum object temp1 merge_Risoe BINfileData Merge Risoe BINfileData objects or Risoe BIN files
125. leData DeValues 16 25 1 3 now a common dataset is created from the two subgroups data 3 lt list data 1 data 2 now the two data sets are plotted in one plot plot_RadialPlot data data 3 now with some graphical modification plot_RadialPlot data data 3 col c darkblue darkgreen bar col c lightblue lightgreen pch c 2 6 summary c n in ci summary pos sub legend c Sample 1 Sample 2 118 plot_Risoe BINfileData plot_Risoe BINfileData Plot single luminescence curves from a BIN file object Description Plots single luminescence curves from an object returned by the readBIN2R function Usage plot_Risoe BINfileData BINfileData position run set sorter POSITION ltype c IRSL OSL TL RIR RBR RL curve transformation dose_rate temp lab cex global 1 Arguments BINfileData Risoe BINfileData class required requires an S4 object returned by the read BIN2R function position vector optional option to limit the plotted curves by position e g position position c 1 3 5 run vector optional option to limit the plotted curves by run e g run 1 run c 1 3 5 set vector optional option to limit the plotted curves by set e g set 1 set c 1 3 5 sorter character with default the plot output can be ordered by POSITION SET or RUN POSITION SET and RUN are options defined
126. length axis Axis labelling are changed accordingly so far no manual axis labelling is choosen 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 func tion Details Matrix structure cf RLum Data Spectrum e rows x values wavelengths channels xlim xlab e columns y values time temperature ylim ylab e 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 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 e shade default is 0 4 e phi default is 30 e theta default is 30 e expand default is 1 e ticktype default is detailed 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 line
127. ls of statistically important values in the plot One or more out of the following min max median logical Option to add a rug to the KDE part to indicate the location of indi vidual values logical Option to add a KDE plot to the dispersion part default is TRUE logical Option to add a histogram to the dispersion part Only meaningful when not more than one data set is plotted 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 logical Option to hide y axis labels Useful for data with small scatter logical Option to show De errors as error bars on De points Useful in com bination with y axis FALSE bar col none character or numeric with default colour of the polygon showing the dose dispersion around the central value To disable the polygon use none Default is grey80 character or numeric with default colour of the bar showing the 2 sigma range of the dose error around the central value To disable the bar use none Default is grey50 numeric numeric values of the additional lines to be added plot_AbanicoPlot 99 line col character or numeric colour of the 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 n
128. m Data Image class Class RLum Data Image Description Class for luminescence image data TL OSL RF Objects from the Class Objects can be created by calls of the form new RLum Data Image 148 RLum Data Image class Slots recordType Object of class character containing the type of the curve e g OSL image TL image curveType Object of class character containing curve type allowed values are measured or predefined data Object of class RasterBrick containing images raster data info Object of class list containing further meta information objects S3Class Object of class character Extends Class RLum Data directly Methods coerce signature from data frame to RLum Data Image signature from matrix to RLum Data Image Furthermore lossy coercing is possible from RLum Data Image to data frame matrix show signature object RLum Data Image set_RLum Data Image signature recordType character curveType character data RasterBr Construction method for RLum Data Image object The slot info is optional and predefined as empty list by default get_RLum Data Image signature object RLum Data Image info object character Accessor method for RLum Data Image object The argument info object is optional to directly access the info elements If no info element name is provided the raw image data RasterBri
129. m dose estimate in Gy Further documentation Please see calc_MinDose Value Please see calc_MinDose Function version 0 3 2015 03 04 13 31 23 Author s Christoph Burow University of Cologne Germany Based on a rewritten S script of Rex Galbraith 2010 R Luminescence Package Team References Arnold L J Roberts R G Galbraith R F amp DeLong S B 2009 A revised burial dose estima tion procedure for optical dating of young and modern age sediments Quaternary Geochronology 4 306 325 Galbraith R F amp Laslett G M 1993 Statistical models for mixed fission track ages Nuclear Tracks Radiation Measurements 4 459 470 Galbraith R F Roberts R G Laslett G M Yoshida H amp Olley J M 1999 Optical dating of single grains of quartz from Jinmium rock shelter northern Australia Part I experimental de sign and statistical models Archaeometry 41 339 364 Galbraith R F 2005 Statistics for Fission Track Analysis Chapman amp Hall CRC Boca Raton Galbraith R F amp 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 Olley J M Roberts R G Yoshida H Bowler J M 2006 Single grain optical dating of grave infill associated with human burials at Lake Mungo Australia Quaternary Science Reviews 25 2469 2474 46 calc_MinDose Further reading
130. ment for the package Luminescence Usage ExampleData LxTxData Format A data frame with 4 columns Dose LxTx LxTx Error TnTx Source Lab Luminescence Laboratory Bayreuth Lab Code BT607 Location Ostrau Saxony Anhalt Germany Material Middle grain 38 63 um quartz measured on a Risoe TL OSL DA 15 reader References unpublished data ExampleData LxTxOSLData 75 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 Usage ExampleData LxTxOSLData RData Format Two data frames containing time and count values Source Arbitrary OSL measurement References unpublished data Examples load data data ExampleData LxTxOSLData envir environment plot data plot Lx data plot Tx data ExampleData RLum Analysis Example data as RLum Analysis objects Description Collection of different RLum Analysis objects for protocol analysis Usage ExampleData RLum Analysis 76 ExampleData RLum Data Image 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
131. meter 1 plot FALSE plot plot_RLum Results grains readBIN2R 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 readBIN2R file show raw values FALSE n records show record number FALSE txtProgressBar TRUE forced VersionNumber Arguments file character required bin file name including path e g WIN readBIN2R C Desktop test bin MAC LINUX readBIN2R User test Desktop test bin show raw values logical with default shows raw values from BIN file for LTYPE DTYPE and LIGHTSOURCE without translation in characters n records raw optional limits the number of imported records Can be used in com bination with show record number for debugging purposes e g corrupt BIN files show record number logical with default shows record number of the imported record for debug ging usage only txtProgressBar logical with default enables or disables txtProgressBar readBIN2R 131 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 Note The usage is at own risk only supported BIN file versions have been tested 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 fil
132. minescence Package Team References Pych W 2003 A Fast Algorithm for Cosmic Ray Removal from Single Images Astrophysics 116 148 153 http arxiv org pdf astro ph 0311290 pdf origin publication_detail See Also RLum Data Spectrum smooth smooth spline apply_CosmicRayRemoval Examples 1 use with your own data and combine uncomment for usage run two times the default method and smooth with another method your spectrum lt apply_CosmicRayRemoval your spectrum method Pych your spectrum lt apply_CosmicRayRemoval your spectrum method Pych your spectrum lt apply_CosmicRayRemoval your spectrum method smooth apply_EfficiencyCorrection Function to apply spectral efficiency correction to RLum Data Spectrum S4 class objects Description The function allows spectral efficiency corrections for RLum Data Spectrum S4 class objects Usage apply_EfficiencyCorrection object spectral efficiency 22 apply_EfficiencyCorrection Arguments object RLum Data Spectrum required S4 object of class RLum Data Spectrum spectral efficiency data frame required Data set containing wavelengths x column and rela tive spectral response values y column in percentage Details The efficiency correction is based on a spectral response dataset provided by the user Usually the data set for the quantum efficiency is of lower resolution and values are interpolated for the require
133. mit is set to 500 ka Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne R Luminescence Package Team References Huntley D J Lamothe M 2001 Ubiquity of anomalous fading in K feldspars and the measure ment and correction for it in optical dating Canadian Journal of Earth Sciences 38 1093 1106 See Also RLum Results get_RLum Results uniroot Examples results lt calc_FadingCorr g_value c 3 3 0 03 tc 752 age faded c 100 10 n MCruns 100 get_RLum Results results 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 amp Wallinga 20
134. mples mean mean De value mean weighted error weighted mean median median of the De values sdrel relative standard deviation in percent sdabs absolute standard deviation serel relative standard error and seabs absolute standard error 104 plot_DRTResults 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 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 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
135. n the regenera tive curve but here the impact of single outliers on the curve adjustment sliding is considered as negligible The applied outlier removal algorithm consists of three steps a Input data are smoothed using the function rollmedian Value k for the rolling window is fixed to 11 Therefore the natural curve needs to comprise at least of 33 values otherwise outlier removal 1s rejected b To subsequently remove outliers code blocks from the function apply_CosmicRayRemoval were recycled therefore in general the outlier correction works as described by Pych 2003 In contrast here no sigma clipping before constructing the histograms is applied c Outliers are marked in the data set and visualised in the graphical output The subsequent ad justement of both curves natural and regenerative is done without outliers whereas the sliding itself is done with the entire data set Trend correction slide trend corr TRUE This option allows for correcting any linear trend in the natural curve in comparison to the regen erative curve The trend correction is based on regression analysis of the residuals from the slided curve The corrected De is obtained by sliding the trend corrected values again along the regener ative data curve This correction is driven by the idea that the rediduals from the regenerative and the natural curve should be free of any trend as long as they are comparable Error estimation For method
136. native for PDF output uncomment and complete for usage HH pdf file height 15 width 15 results lt analyse_pIRIRSequence object signal integral min 1 signal integral max 2 background integral min 900 background integral max 1000 fit method EXP main Pseudo pIRIR data set based on quartz OSL dev off analyse_SAR CWOSL Analyse SAR CW OSL measurements Description The function performs a SAR CW OSL analysis on an RLum Analysis object including growth curve fitting Usage analyse_SAR CWOSL object signal integral min signal integral max background integral min background integral max rejection criteria dose points mtext outer plot TRUE plot single FALSE 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 rejection criteria list with default provide list and set rejection criteria in percentage for fur ther calculation Allowed arguments are recycling ratio recuperation rate palaeodose error and exceed max regpoint TRUE FALSe g rejection criteria list r Per default all values
137. nerative protocol Usage plot_GrowthCurve sample na rm TRUE fit method EXP fit weights TRUE fit includingRepeatedRegPoints TRUE fit NumberRegPoints fit NumberRegPointsReal fit bounds TRUE NumberIterations MC 100 output plot TRUE output plotExtended TRUE output plotExtended single FALSE cex global 1 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 na rm logical with default excludes NA values from the data set prior to any further operations fit method character with default function used for fitting Possible options are LIN EXP EXP OR LIN EXP LIN or EXP EXP See details 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
138. ng curve type allowed values are measured or predefined data Object of class matrix containing curve x and y data info Object of class list containing further meta information objects S3Class Object of class character Extends Class RLum Data RLum Data Image class 147 Methods coerce signature from data frame to RLum Data Curve signature from matrix to RLum Data Curve Furthermore lossy coercing is possible from RLum Data Curve to data frame matrix show signature object RLum Data Curve set_RLum Data Curve signature recordType character curveType character data matrix Construction method for RLum Data Curve object The slot info is optional and predefined as empty list by default get_RLum Data Curve signature object RLum Data Curve info object character Accessor method for RLum Data Curve object The argument info object is optional to directly access the info elements If no info element name is provided the raw curve data matrix will be returned Version 0 1 2 2013 11 22 Note The class should only contain data for a single curve For additional elements the slot info can be used e g providing additional heating ramp curve Author s Sebastian Kreutzer Freiberg Instruments JLU Giessen Germany References See Also RLum RLum Data plot_RLum Examples showClass RLum Data Curve RLu
139. o the infrared radiofluorescence IR RF of coarse grain K feldspar Ancient TL 21 35 42 Erfurt G 2003 Infrared luminescence of Pb centres in potassium rich feldspars physica status solidi a 200 429 438 Erfurt G Krbetschek M R 2003 Studies on the physics of the infrared radioluminescence of potassium feldspar and on the methodology of its application to sediment dating Radiation Mea surements 37 505 510 Erfurt G Krbetschek M R Bortolot V J Preusser F 2003 A fully automated multi spectral radioluminescence reading system for geochronometry and dosimetry Nuclear Instruments and Methods in Physics Research Section B Beam Interactions with Materials and Atoms 207 487 499 Lapp T Jain M Thomsen K J Murray A S Buylaert J P 2012 New luminescence measure ment facilities in retrospective dosimetry Radiation Measurements 47 803 808 doi 10 1016 j radmeas 2012 02 006 analyse_pIRIRSequence 9 Pych W 2003 A Fast Algorithm for Cosmic Ray Removal from Single Images Astrophysics 116 148 153 http arxiv org pdf astro ph 0311290 pdf origin publication_detail Trautmann T 2000 A study of radioluminescence kinetics of natural feldspar dosimeters experi ments and simulations Journal of Physics D Applied Physics 33 2304 2310 Trautmann T Krbetschek M R Dietrich A Stolz W 1998 Investigations of feldspar radiolu minescence potential for a new dating technique Radiation Meas
140. object RLum Results validates object depending on the originator argument show signature object RLum Results set_RLum Results signature originator character data list Construction method for RLum Results object The slot originator is optional and prede fined as the function that calls the function set_RLum Results get_RLum Results signature object RLum Results data object character accessor method for RLum Results object The argument data object allows directly ac cessing objects delivered within the slot data If no data object is specified a prese lected object is returned The default return object depends on the object originator e g fit_LMCurve merge_RLum Results signature object list list merge method for RLum Results objects The argument object list requires a list of RLum Results objects Merging is done by appending similar elements to the first object of the input list Version 0 2 3 2014 12 16 Note The class is intended to store results from functions to be used by other functions The data in the object should always be accessed by the method get_RLum Results Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France References See Also RLum Examples showClass RLum Results 152 Second2Gray Second2Gray Converting values from seconds s to gray Gy Description Conversion of absorb
141. object of type RLum Results Slot data contains a list with the following structure LxTx table LnLx LnLx BG TnTx TnTx BG Net_LnLx Net_LnLx Error Function version 0 3 2015 03 04 00 19 53 58 CW2pHMi Note This function has still BETA status Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Christoph Schmidt University of Bayreuth Germany R Luminescence Package Team References See Also RLum Results analyse_SAR TL Examples load package example data data ExampleData BINfileData envir environment convert Risoe BINfileData into a curve object temp lt Risoe BINfileData2RLum Analysis TL SAR Data pos 3 Lx data signal lt get_RLum Analysis temp record id 1 Lx data background lt get_RLum Analysis temp record id 2 Tx data signal lt get_RLum Analysis temp record id 3 Tx data background lt get_RLum Analysis temp record id 4 signal integral min lt 210 signal integral max lt 230 output lt calc_TLLxTxRatio Lx data signal Lx data background Tx data signal Tx data background signal integral min signal integral max get_RLum Results output CW2pHMi Transform a CW OSL curve into a pHM OSL curve via interpolation under hyperbolic modulation conditions Description This function transforms a conventionally measured continuous wave CW OSL curve to a pseudo hyperbolic modulated pHM cur
142. of the function analyse_SAR CWOSL Value Plots optional and an RLum Results object is returned containing the following elements De values data frame containing De values De error and further parameters LnLxTnTx values data frame of all calculated Lx Tx values including signal background counts and the dose points rejection criteria data frame with values that might by used as rejection criteria NA is produced if no RO dose point exists The output should be accessed using the function get_RLum Results Function version 0 1 4 2015 03 04 12 43 39 Note Best graphical output can be achieved by using the function pdf with the following options pdf file height 15 width 15 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team analyse_pIRIRSequence 11 References 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 00253 X Thomsen K J Murray A S Jain M Boetter Jensen L 2008 Laboratory fading rates of vari ous luminescence signals from feldspar rich sediment extracts Radiation Measurements 43 1474 1486 doi 10 1016 j radmeas 2008 06 002 See Also analyse_SAR CWOSL calc_OSLLxTxRatio plot_GrowthCurve RLum Analysis RLum Results get_RLum Results Examples NOTE For this example e
143. ofile 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 com ponent 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 con taining IO and nO The last columns cont provide information on the relative component contribution for each time interval including the row sum for this values 0 4 4 2015 03 04 00 19 53 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 R42 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 84 fit_LMCurve 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 amp Streibig J C 2008 Nonlinear Regres
144. one Default is grey bw character with default bin width for KDE choose a numeric value for man ual setting output logical Optional output of numerical plot parameters These can be useful to reproduce similar plots Default is FALSE 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 den sity 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 amp 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 themselfes Since the 2 sigma bar is a polygon
145. 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 readXSYG2R readBIN2R writeR2BIN for data import and export Value An RLum Results object is returned with the following structure Sirr times data frame If a BINX file path and name is set the output will be additionally transferred to a new BINX file with the function name as suffix For the output the path of the input BINX file itself is used Function version 0 1 2015 03 23 12 56 18 Note The produced output object contains still the irradiation steps to keep the output transparent How ever for the BINX file export this steps are removed as the BINX file format description does not allow irradiations as separat sequences steps Know issue The fading correction menu in the Analyst will not work appear with the produced BIN BINX file due to hidden bits which are not reproduced by the function writeR2BIN Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References Duller G 2007 Analyst fit_CWCurve 81 See Also RLum Results Risoe BINfileData readXSYG2R readBIN2R writeR2BIN Examples 1 example for yo
146. ot_RLum Data Curve Plot function for an RLum Data Curve S4 class object Description The function provides a standardised plot output for curve data of an RLum Data Curve S4 class object Usage plot_RLum Data Curve object par local TRUE norm FALSE 204 Arguments object RLum Data Curve required S4 object of class RLum Data Curve par local logical with default use local graphical parameters for plotting e g the plot 1s shown in one column and one row If par local FALSE global parameters are inherited norm logical with default allows curve normalisation to the highest count value further arguments and graphical parameters that will be passed to the plot func tion Details Only single curve data can be plotted with this function Arguments according to plot Value Returns a plot Function version 0 1 5 2015 03 04 00 19 53 Note Not all arguments of plot will be passed Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team 124 plot_RLum Data Image References See Also plot plot_RLum Examples plot curve data load Example data data ExampleData CW_OSL_Curve envir environment transform data frame to RLum Data Curve object temp lt as ExampleData CW_OSL_Curve RLum Data Curve plot RLum Data Curve object plot_RLum Data Curve temp plot_RLum Data Image Plot function for an RLum Data Image 4 class
147. parameters to 0 Lim ited 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 estima tion See details output plot logical with default plot output TRUE FALSE plot_GrowthCurve 107 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 plot ting the results in single plot windows Requires output plot TRUE and output plotExtended TRUE cex global numeric with default global scaling factor Further arguments and graphical parameters to be passed Note Standard ar guments 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 and the EXP OR LIN the nls function with the port algo rithm is used LIN fits a linear function to the data using lm Yy Mxzt N EXP try to fit a function of the form y ax 1 exp x c b Parameters b and c are approximated by a linear fit using Im Note b DO EXP OR LIN works for some cases where an EXP fit fails If
148. ple carrier If a non zero positive integer is provided this function will calculate the packing density of the aliquot If more than one value is provided the mean packing density and its standard deviation is calculated Note that this overrides packing density plot logical with default plot output TRUE FALSE further arguments to pass main xlab MC iter Details This function can be used to either estimate the number of grains on an aliquot or to compute the packing density depending on the the arguments provided The following function is used to estimate the number of grains n n m x mx y x d where x is the radius of the aliquot size microns y is the mean radius of the mineral grains mm and d is the packing density value between 0 and 1 Packing density The default value for packing density is 0 65 which is the mean of empirical values deter mined by Heer et al 2012 and unpublished data from the Cologne luminescence laboratory If packing density inf a maximum density of n V12 0 9068 is used However note 26 calc_AliquotSize that this value is not appropriate as the standard preparation procedure of aliquots resembles a PECC Packing Equal Circles in a Circle problem where the maximum packing density is asymptotic to about 0 87 Monte Carlo simulation The number of grains on an aliquot can be estimated by Monte Carlo simulation when setting MC TRUE Each of the parameters necessary
149. port entire XML file FILE lt file choose temp lt xmlRoot 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 lt get_RLum Analysis OSL SARMeasurement Sequence Object recordType 0SL gt 1 1 3 How to see the structure of an object get_structure RLum Analysis OSL SARMeasurement Sequence Object Risoe BINfileData class Class Risoe BINfileData Description S4 class object for luminescence data in R The object is produced as output of the function readBIN2R Objects from the Class Objects can be created by calls of the form new Risoe BINfileData Slots METADATA Object of class data frame containing the meta information for each curve DATA Object of class list containing numeric vector with count data RESERVED Object of class list containing list of undocumented raw values for internal use only S3Class Object of class character Methods show signature object Risoe BINfileData set_Risoe BINfileData signature METADATA data frame DATA list RESERVED list The Risoe BINfileData is normally produced as output of the function readBIN2R This construction method is intended for int
150. quence structure c PREHEAT SIGNAL BACKGROUND rejection criteria list recycling ratio 10 recuperation rate 10 log 18 analyse_SAR TL Arguments object RLum Analysis required input object containing data for analysis object background currently not used signal integral min integer required requires the channel number for the lower signal integral bound e g signal integral min 100 signal integral max integer required requires the channel number for the upper signal integral bound e g signal integral max 200 sequence structure vector character with default specifies the general sequence structure Three steps are allowed PREHEAT SIGNAL BACKGROUND in addition a param eter EXCLUDE This allows excluding TL curves which are not relevant for the protocol analysis Note None TL are removed by default rejection criteria list with default list containing rejection criteria in percentage for the calcula tion log character with default a character string which contains x if the x axis is to be logarithmic y if the y axis is to be logarithmic and xy or yx if both axes are to be logarithmic See plot default further arguments that will be passed to the function plot_GrowthCurve Details This function performs a SAR TL analysis on a set of curves The SAR procedure in general is given by Murray and Wintle 2000 For the calculation of
151. quired lower bound of the background integral Provide this value as vector for different integration limits for the different IRSL curves 10 analyse_pIRIRSequence background integral max integer required upper bound of the background integral Provide this value as vector for different integration limits for the different IRSL curves dose points numeric optional a numeric vector containing the dose points values Using this argument overwrites dose point values in the signal curves sequence structure vector character with default specifies the general sequence structure Al lowed values are TL and any IR combination e g IR50 pIRIR225 Additionally a parameter EXCLUDE is allowed to exclude curves from the anal ysis Note If a preheat without PMT measurement is used i e preheat as non TL remove the TL step plot logical with default enables or disables plot output plot single logical with default single plot output TRUE FALSE to allow for plotting the results in single plot windows Requires plot TRUE further arguments that will be passed to the function analyse_SAR CWOSL and plot_GrowthCurve Details To allow post IR IRSL protocol Thomsen et al 2008 measurement analysis this function has been written as extended wrapper function for the function analyse_SAR CWOSL facilitating an entire sequence analysis in one run With this its functionality is strictly limited by the functionality
152. r see The results are visualised in a bar and boxplot together with a statistical summary 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 MC list results of the Monte Carlo simulation The output should be accessed using the function get_RLum Results Function version 0 31 2015 03 04 00 19 53 Author s Christoph Burow University of Cologne Germany R Luminescence Package Team calc_CentralDose 27 References Duller G A T 2008 Single grain optical dating of Quaternary sediments why aliquot size matters in luminescence dating Boreas 37 589 612 Heer A J Adamiec G Moska P 2012 How many grains are there on a single aliquot Ancient TL 30 9 16 Further reading Chang H C Wang L C 2010 A simple proof of Thue s Theorem on Circle Packing http arxiv org pdf 1009 4322v1 pdf 2013 09 13 Graham R L Lubachevsky B D Nurmela K J Oestergard P R J 1998 Dense packings of congruent circles in a circle Discrete Mathematics 181 139 154 Huang W Ye T 2011 Global optimization method for finding dense packings of equal circles in a circle European Journal of Operational Research 210 474 481 Examples Estimate the amount of grains on a small aliquot calc_AliquotSize grain size c 10
153. rdisation character additional text below the plot title character optional adds numerical output to the plot Can be one or more out of n number of samples mean mean De value mean weighted error weighted mean median median of the De values sdrel relative standard deviation in percent sdabs absolute standard deviation serel relative standard error seabs absolute standard error kdemax max imum of the KDE skewness skewness and kurtosis kurtosis and in ci percent of samples in confidence interval e g 2 sigma Note Keywords kdemax skewness kurtosis are implemented for consistency reasons however no KDE is shown The bandwidth is calculated according to plot_KDE 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 is only possible if mtext is not used character vector optional legend content to be added to the plot numeric or character with default optional position coordinates or keyword e g topright for the legend to be plotted character additional labels of statistically important values in the plot One max median jm n or more out of the following min logical Option to add a rug to the z scale to indic
154. required vector with the bounds for the background integral background count distribution character with default Sets the count distribution assumed for the error cal culation Possible arguments poisson or non poisson See details for further information sigmab numeric optional 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 e g sigmab c 300 300 Note If only one value is provided this value is taken for both LnTx and TnTx signals Details The integrity of the chosen values for the signal and background integral is checked by the function the signal integral limits have to be lower than the background integral limits If a vector is given as input instead of a data frame an artificial data frame is produced The error calculation is done according to Galbraith 2002 background count distribution This argument allows selecting the distribution assumption that is used for the error calculation Ac cording to Galbraith 2002 2014 the background counts may be overdispersed i e do not follow a poisson distribution which is assumed for the photomultiplier counts In that case might be the normal case it has to be accounted for the overdispersion by estimating o i e the overdispersion value Therefore the relative standard error is calculated as a poisson rse us y Yo i k Yo
155. results can be obtained by using the function get_RLum Data Spectrum on an RLum Data Spectrum object or get_RLum Data Image on an RLum Data Image object Function version 0 1 2015 03 04 12 43 39 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 Universite Bordeaux Montaigne France R Luminescence Package Team References Princeton Instruments 2014 Princeton Instruments SPE 3 0 File Format Specification Version 1 A ftp ftp princetoninstruments com Public Manuals Princeton 20Instruments SPE 203 0 20File 20Format 20Specification pdf Hall C 2012 readSPE m http www mathworks com matlabcentral fileexchange 35940 readspe content readSPE m See Also readBin RLum Data Spectrum raster Examples to run examples uncomment lines and run the code 1 Import data as RLum Data Spectrum object file lt file choose temp lt readSPE2R file temp 2 Import data as RLum Data Image object file lt file choose temp lt readSPE2R file output object RLum Data Image temp 134 readXS YG2R 3 Import data as matrix object file lt file choose temp lt readSPE2R file output object matrix temp 4 Export raw
156. reutzer 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 amp Wallinga J 2012 How to visualize quartz OSL signal components Radiation Mea surements 47 752 758 Further Reading Bulur E 1996 An Alternative Technique For Optically Stimulated Luminescence OSL Ex periment Radiation Measurements 26 701 709 Bulur E 2000 A simple transformation for converting CW OSL curves to LM OSL curves Ra diation 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 CW2pHMi 61 transform values values transformed lt CW2pHMi ExampleData CW_OSL_Curve 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 HBINfileData lt readBIN2R path to BIN file data ExampleData BINfileData envir environment grep first CW OSL curve from ALQ 1 curve ID lt CWOSL SAR Data METADATALCWOSL SAR Data METADATAL LTYPE 0SL amp CWOSL SAR Data METADATAL POSITION J 1 ID curve HIGH lt CWOSL SAR Data METADATALCWOSL SAR Data METADATAL ID curve ID 1 HIGH cu
157. rguments objects list of RLum Analysis required list of S4 objects of class RLum Analysis Furthermore other objects of class RLum can be added see details Details This function simply allowing to merge RLum Analysis objects Additionally other RLum ob jects can be added to an existing RLum Analysis object Supported objects to be added are RLum Data Curve RLum Data Spectrum and RLum Data Image The order in the new RLum Analysis object is the object order provided with the input list Value Return an RLum Analysis object Function version 0 1 2015 03 04 00 19 53 merge_RLum Data Curve 95 Note The information for the slot protocol is taken from the first RLum Analysis object in the input list Therefore at least one object of type RLum Analysis has to be provided Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References See Also merge_RLum RLum Analysis RLum Data Curve RLum Data Spectrum RLum Data Image RLum Examples merge different RLum objects from the example data data ExampleData RLum Analysis envir environment data ExampleData BINfileData envir environment object lt Risoe BINfileData2RLum Analysis CWOSL SAR Data pos 1 curve lt get_RLum object 2 temp merged lt merge_RLum Analysis list curve IRSAR RF Data IRSAR RF Data merge_RLum Data Curve Merge function for RLum Data Curv
158. rrently 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 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 34 calc_CosmicDoseRate 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 An cient TL 27 45 46 Prescott J R Hutton J T 1988 Cosmic ray and gamma ray dosimetry for TL and ESR Nu clear Tracks and Radiation Measurements 14 223 227 Prescott J R Hutton J T 1994 Cosmic ray contributions to dose rates for lumines cence 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 S
159. rve NPOINTS lt CWOSL SAR Data METADATALCWOSL SAR Data METADATAL ID curve ID 1 NPOINTS J combine curve to data set curve lt data frame x seq curve HIGH curve NPOINTS curve HIGH by curve HIGH curve NPOINTS y unlist CWOSL SAR Data DATALcurve ID 1 transform values curve transformed lt CW2pHMi curve plot curve plot curve transformed x curve transformed y t log x 3 produce Fig 4 from Bos amp Wallinga 2012 load data data ExampleData CW_OSL_Curve envir environment values lt CW_Curve BosWallinga2012 tHtopen 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 amp Wallinga 2012 values t lt CW2pLMi values P 1 20 lines values 1 length values t 11 1 CW2pLMi values P 1 20 21 62 CW2pLM col red 1wd 1 3 text 0 03 4500 LM col red cex 8 values t lt CW2pHMi values delta 40 lines values 1 length values t 1 1 CW2pHMi values delta 40 21 col black lwd 1 3 text 0 005 3000 HM cex 8 values t lt 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 modu lated
160. s All frames drawn in one frame 128 plot_RLum Data Spectrum 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 x1im 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 border box lwd bty Value Returns a plot Function version 0 3 5 2015 03 21 10 14 55 Note Not all additional arguments will be passed similarly Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References See Also RLum Data Spectrum plot plot_RLum persp persp3d 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 simple spectrum 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 plot_RLum Results 129 3 plot 3d spectrum uncomment for
161. s R RLum class R RLum Data class R RLum Data Curve class R RLum Analysis class R RLum Results class R calc_CentralDose R calc_FiniteMixture R calc_MinDose R calc_CommonDose R calc_CosmicDoseRate R merge_Risoe BINfileData R writeR2BIN R Risoe BINfileData2RLum Data Curve R calc_HomogeneityTest R 1 calc_AliquotSize R readXS YG2R R RLum Data Spectrum class R plot_RLum Data Spectrum R calc_MaxDose R plot_AbanicoPlot R plot_DRTResults R calc_Statistics R apply_CosmicRayRemoval R apply_EfficiencyCorrection R readSPE2R R RLum Data Image class R plot_RLum Data Image R get_Layout R analyse_pIRIRSequence R merge_RLum R get_RLum R merge_RLum Analysis R plot_RLum Results R calc_SourceDoseRate R merge_RLum Data Curve R calc_IEU R extract_IrradiationTimes R ReppExports R zzz R R topics documented Luminescence package 1 2 eee ee ee analyse IRSAR RF 2 o 200 2200 eee ee eee analyse_pIRIRSequence o o analyse_SAR CWOSL o e e e Analyse_SAR OSLdata o e ee e analyse SARTE ocre E E A apply_CosmicRayRemoval o o apply_EfficiencyCorrectiOd o o o BaseDataSet CosmicDoseRate calc_AliquotSize o o ee ee ee cale CentralDOS oc ee eG SS Bee dow HA Sear G calc_CommonDose 0 0000 eee ee ee ees calc_CosmicDoseRate 0 0000 eee ee ees calc Fading Corr s 5 cae ghd eA ae ae E ee G cal
162. section in Rot tewitz Saxony Germany and for a coarse grain quartz sample from a fluvial deposit in the rock shelter of Cueva Anton Murcia Spain Usage ExampleData DeValues 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 Rotte witz 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 Source BT998 Lab Lab Code Location Material Units Dose Rate Measurement Date CA1 Lab Lab Code Location Material 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 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 r ExampleData FittingLM 73 Units Values are given in Gray Measurement Date 2012 References BT998 Unpublished data CA1 Burow C Kehl M Hilgers A Weniger G C Angelucci D Villaverde V Zapata J and Zilhao J accepted Luminescence dating of fluvial deposits in the rock shelter of Cueva Anton Spain Geochronometria Examples 1 plot values as
163. sed during fitting min 1 max 7 fit_LMCurve 85 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 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 for intensity 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 cex global numeric with default global scaling factor fit trace logical with default traces the fitting process on the terminal fit advanced logical with default enables advanced fitting attempt for automatic start pa rameter recognition Works only if no start parameters are provided Note It may take a while fit calcError logical with default calculate 1 sigma error range of components using con fint bg subtraction character with default specifies method for background subtraction polynomial linear
164. sion 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 Results Examples load data data ExampleData CW_OSL_Curve envir environment fit data fit lt fit_CWCurve values ExampleData CW_OSL_Curve main CW Curve Fit n components max 4 log Mx 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 Usage fit_LMCurve values values bg n components 3 start_values input dataType LM sample_code un nn sample_ID LED power 36 LED wavelength 470 cex global 0 8 fit trace FALSE fit advanced FALSE fit calcError FALSE bg subtraction polynomial output path output terminal TRUE output terminaladvanced TRUE output plot TRUE output plotBG 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 recogni
165. soe BINfileData Risoe BINfileData class 137 get_Risoe BINfileData Risoe BINfileData method Risoe BINfileData class 137 get_Risoe BINfileData methods Risoe BINfileData class 137 get_RLum 89 get_RLum Analysis 80 90 get_RLum Analysis RLum Analysis class 144 get_RLum Analysis RLum Analysis method RLum Analysis class 144 get_RLum Analysis methods RLum Analysis class 144 get_RLum Data Curve 90 get_RLum Data Curve RLum Data Curve class 146 get_RLum Data Curve ANY method RLum Data Curve class 146 get_RLum Data Curve methods RLum Data Curve class 146 get_RLum Data Image 90 133 get_RLum Data Image RLum Data Image class 147 get_RLum Data Image ANY method RLum Data Image class 147 get_RLum Data Image methods RLum Data Image class 147 get_RLum Data Spectrum 90 133 get_RLum Data Spectrum RLum Data Spectrum class 149 get_RLum Data Spectrum ANY method RLum Data Spectrum class 149 get_RLum Data Spectrum methods RLum Data Spectrum class 149 get_RLum Results 8 11 14 18 19 26 28 30 33 36 38 42 43 49 53 84 90 get_RLum Results RLum Results class 150 get_RLum Results RLum Results method RLum Results class 150 INDEX get_structure RLum Analysis RLum Analysis class 144 159 pchisq 42 pdf 122 129 get_structure RLum Analysis RLum Analysis metpbedsp 127 128 RLum Analysis class 144 glm 86 hist 109 110 integer 5 6 9 10 12 18 20
166. ssages are suppressed when running this function If the results seem odd consider re running the model with debug TRUE which provides extended console output and forwards all internal warning messages Author s Christoph Burow University of Cologne Germany Based on a rewritten S script of Rex Galbraith 2010 The bootstrap approach is based on a rewritten MATLAB script of Alastair Cunningham Alastair Cunningham is thanked for his help in implementing and cross checking the code R Luminescence Package Team References Arnold L J Roberts R G Galbraith R F amp DeLong S B 2009 A revised burial dose estima tion procedure for optical dating of young and modern age sediments Quaternary Geochronology 4 306 325 Galbraith R F amp Laslett G M 1993 Statistical models for mixed fission track ages Nuclear Tracks Radiation Measurements 4 459 470 Galbraith R F Roberts R G Laslett G M Yoshida H amp Olley J M 1999 Optical dating of single grains of quartz from Jinmium rock shelter northern Australia Part I experimental de sign and statistical models Archaeometry 41 339 364 Galbraith R F 2005 Statistics for Fission Track Analysis Chapman amp Hall CRC Boca Raton Galbraith R F amp 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 Further reading Arnold L
167. st IR IRSL protocol curve data have to be pre selected by the user to fit the standards of the SAR protocol i e Lx Tx Lx Tx and so on Example Imagine the measurement contains pIRIR50 and pIRIR225 IRSL curves Only one curve type can be analysed at the same time The pIRIRSO curves or the pIRIR225 curves Supported rejection criteria recyling ratio calculated for every repeated regeneration dose point recuperation rate recuperation rate calculated by comparing the Lx Tx values of the zero regen eration point with the Ln Tn value the Lx Tx ratio of the natural signal For methodological background see Aitken and Smith 1988 palaeodose error set the allowed error for the De value which per default should not exceed 10 Value A plot optional and an RLum Results object is returned containing the following elements De values data frame containing De values De error and further parameters LnLxTnTx values data frame of all calculated Lx Tx values including signal background counts and the dose points rejection criteria data frame with values that might by used as rejection criteria NA is produced if no RO dose point exists Formula formula formula that have been used for the growth curve fitting 14 analyse_SAR CWOSL The output should be accessed using the function get_RLum Results Function version 0 5 1 2015 03 09 15 43 53 Note This function must not be mixed up with the function Anal
168. t gt max t The number of values for t lt 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 package RLum object with two additional info elements CW2pPMi x t transformed time values CW2pPMi method used method for the production of the new data points data frame with four columns x time y t transformed count values x t transformed time values method used method for the production of the new data points Function version 0 2 1 2015 03 04 18 48 47 Note According to Bos amp 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 amp Wallinga J 2012 How to visualize quartz OSL signal components Radiation Mea surements 47 752 758 Further Reading Bulur E 1996 An Alternative Technique For Optically Stimulated Luminescence OSL E
169. ta data 3 fun TRUE now with user defined central value in log scale again plot_RadialPlot data ExampleData DeValues central value 150 now with a rug indicating individual De values at the z scale plot_RadialPlot data ExampleData DeValues rug TRUE plot_RadialPlot 117 now with legend colour different points and smaller scale plot_RadialPlot data ExampleData DeValues legend text Sample 1 col tomato4 bar col peachpuff pch R cex 0 8 now without 2 sigma bar y axis grid lines and central value line plot_RadialPlot data ExampleData DeValues bar col none grid col none y ticks FALSE lwd Q now with user defined axes labels plot_RadialPlot data ExampleData DeValues xlab c Data error Data precision ylab Scatter zlab Equivalent dose Gy now with minimum maximum and median value indicated plot_RadialPlot data ExampleData DeValues central value 150 n stats c min max median now with a brief statistical summary plot_RadialPlot data ExampleData DeValues summary c n in ci now with another statistical summary as subheader plot_RadialPlot data ExampleData DeValues summary c mean weighted median summary pos sub now the data set is split into sub groups one is manipulated data 1 lt ExampleData DeValues 1 15 data 2 lt Examp
170. ta frame original input data args list used arguments call call the function call profile data frame the log likelihood profile for sigma The output should be accessed using the function get_RLum Results Function version 1 3 2015 03 04 13 35 16 Author s Christoph Burow University of Cologne Germany Based on a rewritten S script of Rex Galbraith 2010 R Luminescence Package Team References Galbraith R F amp Laslett G M 1993 Statistical models for mixed fission track ages Nuclear Tracks Radiation Measurements 4 459 470 Galbraith R F Roberts R G Laslett G M Yoshida H amp Olley J M 1999 Optical dating of single grains of quartz from Jinmium rock shelter northern Australia Part I experimental de sign and statistical models Archaeometry 41 339 364 Galbraith R F amp 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 Further reading Arnold L J amp Roberts R G 2009 Stochastic modelling of multi grain equivalent dose De distri butions Implications for OSL dating of sediment mixtures Quaternary Geochronology 4 204 230 Bailey R M amp Arnold L J 2006 Statistical modelling of single grain quartz De distributions and an assessment of procedures for estimating burial dose Quaternary Science Reviews 25 2475 2502 Cunningham A C amp
171. tained 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 calc_IEU Apply the internal external uncertainty IEU model after Thomsen et al 2007 to a given De distribution Description Function to calculate the IEU De for a De data set Usage calc_IEU data a b interval decimal point 2 plot TRUE calc_IEU 43 Arguments data RLum Results or data frame required for data frame two columns with De data 11 and De error values 2 a numeric slope b numeric intercept interval numeric fixed interval e g 5 Gy used for iteration of Dbar from the mean to Lowest De used to create Graph IEU Dbar Fixed vs Z decimal point numeric with default number of decimal points for rounding calculations e g 2 plot logical with default plot output further arguments trace verbose Details This function uses the equations of Thomsen et al 2007 The parameters a and b are estimated from dose recovery experiments Value Returns a plot optional and terminal output In addition an RLum Results object is returned containing the following element summary data frame summary of all relevant model results data data frame original input data args list used arguments call call the function call tables list a list of data frames
172. th a stretched exponential function Nn fF WN Calculate the the palaeodose De using the parameters from the fitting Function Used For The Fitting according to Erfurt et al 2003 D do Ag 1 exp A D with D the dose dependent IR RF flux dp the inital IR RF flux Ad the dose dependent change of the IR RF flux A the exponential parameter D the dose and the dispersive factor To obtain the palaeodose De the function is changed to De In D 0 A 9 4 1 A The fitting is done using the port algorithm of the nls function Two methods are supported to obtain the De analyse_IRSAR RF 7 method FIT The principle is described above and follows the orignal suggestions from Erfurt et al 2003 method SLIDE For this method the natural curve is slided along the x axis until congruence with the regenerated curve is reached Instead of fitting this allows to work with the original data without the need of any physical model This approach was introduced for RF curves by Buylaert et al 2012 and Lapp et al 2012 Here the sliding is done by searching for the minimum of the residual squares min RF regy RF naty for k t 0 02 tmar 1 Correction for outliers slide outlier rm TRUE By using method SLIDE and setting the argument slide outlier rm TRUE an automatic outlier removal can be applied to the natural curve Outliers may be observed also o
173. the Lx Tx value the function calc_TLLxTxRatio is used Provided rejection criteria recyling ratio calculated for every repeated regeneration dose point recuperation rate recuperation rate calculated by comparing the Lx Tx values of the zero regen eration point with the Ln Tn value the Lx Tx ratio of the natural signal For methodological background see Aitken and Smith 1988 Value A plot optional and an RLum Results object is returned containing the following elements De values data frame containing De values and further parameters LnLxTnTx values data frame of all calculated Lx Tx values including signal background counts and the dose points rejection criteria data frame with values that might by used as rejection criteria NA is produced if no RO dose point exists note the output should be accessed using the function get_RLum Results apply_CosmicRayRemoval 19 Function version 0 1 4 2015 03 04 00 19 53 Note THIS IS A BETA VERSION None TL curves will be removed from the input object without further warning Author s Sebastian Kreutzer Freiberg Instruments JLU Giessen Germany R Luminescence Package Team References Aitken M J and Smith B W 1988 Optical dating recuperation after bleaching Quaternary Science Reviews 7 387 393 Murray A S and Wintle A G 2000 Luminescence dating of quartz using an improved single aliquot regenerative dose protocol Radiation Measuremen
174. their usage Further arguments are verbose to de activate con sole output logical debug for extended console output logical and cores in teger to manually specify the number of cores to be used when multicore TRUE This model has four parameters gamma minimum dose on the log scale mu mean of the non truncated normal distribution sigma spread in ages above the minimum po proportion of grains at gamma If par 3 default the 3 parametric minimum age model is applied where gamma mu For par 4 the 4 parametric model is applied instead Un logged model In the original version of the three parameter minimum dose model the basic data are the natu ral logarithms of the De estimates and relative standard errors of the De estimates This model will be applied if log TRUE If log FALSE the modified un logged model will be applied instead This has essentially the same form as the original version gamma and sigma are in Gy and gamma becomes the minimum true dose in the population While the original logged version of the mimimum dose model may be appropriate for most sam ples i e De distributions the modified un logged version is specially designed for modern age 48 calc_MinDose and young samples containing negative zero or near zero De estimates Arnold et al 2009 p 323 Initial values amp boundaries The log likelihood calculations use the nlminb function for box constrained optimisation using PORT rout
175. 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 2015 03 04 13 31 55 Note Please consider the requirements and the constraints of this method see Fuchs amp Lang 2001 calc_HomogeneityTest 41 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Christoph Burow University of Cologne Germany R Luminescence Package Team References Fuchs M amp Lang A 2001 OSL dating of coarse grain fluvial quartz using single aliqout proto cols on sediments from NE Peloponnese Greece In Quaternary Science Reviews 20 783 787 Fuchs M amp Wagner G A 2003 Recognition of insufficient bleaching by small aliquots of quartz
176. tput is recommended e g pdf curve transformation This argument allows transforming continuous wave CW curves to pseudo linear modulated curves For the transformation the functions of the package are used Currently it is not possible to pass further arguments to the transformation functions The argument works only for 1type OSL and IRSL Please note The curve transformation within this functions works roughly i e every IRSL or OSL curve is transformed without considerung whether it is measured with the PMT or not However for a fast look it might be helpful Value Returns multiple plots Function version 0 2 0 2015 03 04 19 15 10 Note Not all arguments available for plot will be passed Only plotting of RLum Data Curve and RLum Data Spectrum objects are currently supported Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References See Also plot plot_RLum plot_RLum Data Curve Examples load data data ExampleData BINfileData envir environment convert values for position 1 temp lt Risoe BINfileData2RLum Analysis CWOSL SAR Data pos 1 plot_RLum Data Curve 123 plot all values plot_RLum Analysis temp plot combine TL curves in one plot temp sel lt get_RLum Analysis temp recordType TL keep object TRUE plot_RLum Analysis temp sel combine TRUE norm TRUE main TL combined pl
177. ts 32 57 73 See Also calc_TLLxTxRatio plot_GrowthCurve RLum Analysis RLum Results get_RLum Results Examples load data data ExampleData BINfileData envir environment transform the values from the first position in a RLum Analysis object object lt Risoe BINfileData2RLum Analysis TL SAR Data pos 3 perform analysis analyse_SAR TL object signal integral min signal integral max nn log y fit method EXP OR LIN sequence structure c SIGNAL BACKGROUND 210 220 apply_CosmicRayRemoval Function to remove cosmic rays from an RLum Data Spectrum S4 class object Description The function provides several methods for cosmic ray removal and spectrum smoothing for an RLum Data Spectrum S4 class object 20 apply_CosmicRayRemoval Usage apply_CosmicRayRemoval object method Pych method Pych smoothing 2 silent FALSE plot FALSE Arguments object RLum Data Spectrum required S4 object of class RLum Data Spectrum method character with default Defines method that is applied for cosmic ray re moval Allowed methods are smooth smooth smooth spline smooth spline and Pych default See details for further information method Pych smoothing integer with default Smoothing parameter for cosmic ray removal according to Pych 2003 The value defines how many neighboring values in each frame are used for smoothing e g 2 means that the two previo
178. ts the dose distribution One out of sd standard deviation 2sd 2 standard deviations qr quartile range or cinn confidence interval with nn specifying the level e g ci95 meaning the 95 confidence interval i e data between the quantiles 0 025 and 0 975 default is sd numeric Relative space given to the radial versus the cartesian plot part deault is 0 75 logical Option to turn the plot by 90 degrees character additional text below the plot title character optional adds numerical output to the plot Can be one or more out of n number of samples mean mean De value mean weighted error weighted mean median median of the De values sdrel relative standard deviation in percent sdabs absolute standard deviation serel relative standard error seabs absolute standard error and in ci per cent of samples in confidence interval e g 2 sigma 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 character vector optional legend content to be added to the plot numeric or character with default optional position coordinates or keyword e g topright for the legend to be plotted character additional labe
179. ues 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 Q 8 now without 2 sigma bar polygon grid lines and central value line plot_AbanicoPlot data ExampleData DeValues bar col none polygon col none rid col none y axis FALSE lwd 0 102 now with direct display of De errors without 2 sigma bar plot_AbanicoPlot data ExampleData DeValues bar col none ylab y axis FALSE error bars TRUE now with user defined axes labels plot_AbanicoPlot data ExampleData DeValues xlab c Data error Data precision Kernel density ylab Scatter zlab Equivalent dose Gy now with minimum maximum and median value indicated plot_AbanicoPlot data ExampleData DeValues central value 150 stats c min max n median now with a brief statistical summary plot_AbanicoPlot data ExampleData DeValues summary c n in ci now with another statistical summary as subheader plot_AbanicoPlot data ExampleData DeValues summary c mean weighted median summary pos sub now a plot with two 2 sigma bars for one data set plot_AbanicoPlot data ExampleData DeValues centrality c
180. unts cts values 2 P 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 amp 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 t 1 2x1 P t 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 lt 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 1m 5 Extrapolate values for t lt min t based on the previously obtained fit parameters CW2pLMi 65 6 Transform values using pLM t t PxCW t 7 Combine values and truncate all values for t gt max t The number of values for t lt 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 estim
181. ur own data HH set files and run function He oth Hh tk tk te tt file XSYG lt file choose file BINX lt file choose output lt extract_IrradiationTimes file XSYG file XSYG file BINX file BINX get_RLum Results output HH export results additionally to a CSV file in the same directory as the XSYG file write table x get_RLum Results output file paste0 file BINX _extract_IrradiationTimes csv sep 3 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 pa rameters The fitting procedure uses the nls function with the port algorithm Usage fit_CWCurve values n components max fit failure_threshold 3 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 output 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 fit ting The upper limit is 7 fit failure_threshold vector with default limits the failed fitting attempts
182. urements 29 421 425 Trautmann T Krbetschek M R Dietrich A Stolz W 1999 Feldspar radioluminescence a new dating method and its physical background Journal of Luminescence 85 45 58 Trautmann T Krbetschek M R Stolz W 2000 A systematic study of the radioluminescence properties of single feldspar grains Radiation Measurements 32 685 690 See Also RLum Analysis RLum Results get_RLum Results nls Examples load data data ExampleData RLum Analysis envir environment perform analysis temp lt analyse_IRSAR RF object IRSAR RF Data analyse_pIRIRSequence Analyse post IR IRSL sequences Description The function performs an analysis of post IR IRSL sequences including curve fitting on RLum Analysis objects Usage analyse_pIRIRSequence object signal integral min signal integral max background integral min background integral max dose points sequence structure c TL IR50 pIRIR225 plot TRUE plot single FALSE Arguments object RLum Analysis required input object containing data for analysis signal integral min integer required lower bound of the signal integral Provide this value as vector for different integration limits for the different IRSL curves signal integral max integer required upper bound of the signal integral Provide this value as vector for different integration limits for the different IRSL curves background integral min integer re
183. urn an RLum Data Curve object Function version 0 1 2015 03 04 00 19 53 Note The information from the slot recordType is taken from the first RLum Data Curve object in the input list The slot curveType is filled with the name merged Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References See Also merge_RLum RLum Data Curve plot_AbanicoPlot 97 Examples load example data data ExampleData XSYG envir environment grep first and 3d TL curves TL curves lt get_RLum Analysis OSL SARMeasurement Sequence Object recordType TL UVVIS TL curve 1 lt TL curves 1 TL curve 3 lt TL curves 3 plot single curves plot_RLum TL curve 1 plot_RLum TL curve 3 subtract the 1st curve from the 2nd and plot TL curve merged lt merge_RLum Data Curve list TL curve 3 TL curve 1 merge method plot_RLum TL curve merged 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 of the dose values Usage plot_AbanicoPlot data na exclude TRUE log z TRUE central value centrality mean weighted dispersion sd plot ratio 0 75 rotate FALSE mtext summary summary pos legend legend pos stats rug FALSE
184. us and two following values are used silent logical with default Option to suppress terminal output plot logical with default If TRUE the histograms used for the cosmic ray removal are returned as plot including the used threshold Note A separat plot is returned for each frame Currently only for method Pych a graphical output is provided further arguments and graphical parameters that will be passed to the smooth function Details method Pych This method applies the cosmic ray removal algorithm described by Pych 2003 Some aspects that are different to the publication e For interpolation between neighbouring values the median and not the mean is used The number of breaks to construct the histogram is set to length number of input values 2 For further details see references below method smooth Method uses the function smooth to remove cosmic rays Arguments that can be passed are kind twiceit method smooth spline Method uses the function smooth spline to remove cosmic rays Arguments that can be passed are spar How to combine methods Different methods can be combined by applying the method repeatedly to the dataset see example apply_EfficiencyCorrection 21 Value Returns same object as input RLum Data Spectrum Function version 0 1 3 2015 03 21 10 34 18 Note Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Lu
185. 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 itera tion of k 38 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 rel
186. value the function calc_OSLLxTxRatio is used Provided rejection criteria recyling ratio calculated for every repeated regeneration dose point recuperation recuperation rate calculated by comparing the Lx Tx values of the zero regeneration point with the Ln Tn value the Lx Tx ratio of the natural signal For methodological background see Aitken and Smith 1988 IRSL BOSL the integrated counts signal integral of an IRSL curve are compared to the integrated counts of the first regenerated dose point It is assumed that IRSL curves got the same dose as the first regenerated dose point Note This is not the IR depletation ratio described by Duller 2003 Value A plot optional and list is returned containing the following elements LnLxTnTx data frame of all calculated Lx Tx values including signal background counts and the dose points RejectionCriteria data frame with values that might by used as rejection criteria NA is produced if no RO dose point exists SARParameters data frame of additional measurement parameters obtained from the BIN file e g preheat or read temperature not valid for all types of measurements Function version 0 2 15 2015 03 04 00 19 53 Note Rejection criteria are calculated but not considered during the analysis to discard values The development of this function will not be continued We recommend to use the function analyse SAR CWOSL instead analyse_SAR TL 17
187. ve lm RLum Data Curve The output of the function can be further used for LM OSL fitting CW2pLMi CW2pHMi CW2pPMi fit_LMCurve RLum Data Curve plot_RLum 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 lt CWOSL SAR Data METADATALCWOSL SAR Data METADATAL LTYPE OSL ID produce x and y time and count data for the data set x lt seq CWOSL SAR Data METADATALid OSL 1 HIGH CWOSL SAR Data METADATALid OSLE1 NPOINTS CWOSL SAR Data METADATALid OSL 1 HIGH by CWOSL SAR Data METADATALid OSLL1 HIGH CWOSL SAR Data METADATALid OSL 1 NPOINTS y lt unlist CWOSL SAR Data DATALid OSL 1 values lt data frame x y transform values values transformed lt CW2pLM values plot plot values transformed 64 CW2pLMi 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 de scribed by Bos amp Wallinga 2012 Usage CW2pLMi values P 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 mea sured co
188. ve under hyperbolic modulation conditions using the interpolation procedure described by Bos amp Wallinga 2012 Usage CW2pHMi values delta CW2pHMi 59 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 mea sured counts cts values 2 delta vector optional stimulation rate parameter if no value is given the optimal value is estimated automatically see details Smaller values of delta produce more points in the rising tail of the curve Details The complete procedure of the transformation is described in Bos amp Wallinga 2012 The input data frame consists of two columns time t and count values CW t Internal transformation steps 1 log CW OSL values 2 Calculate t which is the transformed time t t 1 0 log 1 6 t 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 lt 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 1m 5 Extrapolate values for t lt min t based on the previously obtained fit parameters 6 Transform values using pHM t 8 x t 1 8 x t cx CW t P length stimulation period
189. with a 2 degree polynomial The altitude factor is operated on the decimal part of the correction factor De Dex correction Factor 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 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 cm3 calc_CosmicDoseRate 33 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 Results Function version 0 5 2 2015 03 04 00 19 53 Note Despite its universal use the equation to
190. x periment Radiation Measurements 26 701 709 Bulur E 2000 A simple transformation for converting CW OSL curves to LM OSL curves Ra diation Measurements 32 141 145 ExampleData BINfileData 69 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 lt CW2pPMi ExampleData CW_OSL_Curve plot plot values transformed x values transformed y t log x 2 produce Fig 4 from Bos amp Wallinga 2012 load data data ExampleData CW_OSL_Curve envir environment values lt 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 8 Wallinga 2012 values t lt CW2pLMi values P 1 20 lines values 1 length values t 11 1 1 CW2pLMi values P 1 20 2 col red lwd 1 3 text 0 03 4500 LM col red cex 8 values t lt 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 lt CW2pPMi values P 1 10 lines values 1 length values t 11 1 CW2pPMi values P 1 10 2 col blue lwd 1 3 text 0 5 6500 PM col blue cex 8 ExampleData BINfileData Example
191. xisting example data are used These data are non pIRIR data HHH 1 Compile example data set based on existing example data SAR quartz measurement a Load example data data ExampleData BINfileData envir environment b Transform the values from the first position in a RLum Analysis object object lt Risoe BINfileData2RLum Analysis CWOSL SAR Data pos 1 c Grep curves and exclude the last two one TL and one IRSL object lt get_RLum Analysis object record id c 29 30 d Define new sequence structure and set new RLum Analysis object sequence structure lt c 1 2 2 3 4 4 sequence structure lt as vector sapply seq length object 1 by 4 function x sequence structure x object lt sapply 1 length sequence structure function x object sequence structure x object lt set_RLum Analysis records object protocol pIRIR 2 Perform pIRIR analysis for this example with quartz OSL data Note output as single plots to avoid problems with this example results lt analyse_pIRIRSequence object signal integral min 1 signal integral max 2 background integral min 900 background integral max 1000 fit method EXP sequence structure c TL pseudoIRSL1 pseudoIRSL2 main Pseudo pIRIR data set based on quartz OSL plot single TRUE 3 Perform pIRIR analysis for this example with quartz OSL data 12 analyse_SAR CWOSL Alter
192. yse_SAR OSLdata which works with Risoe BINfileData class objects The function currently does only support OSL or IRSL data Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References Aitken M J and Smith B W 1988 Optical dating recuperation after bleaching Quaternary Science Reviews 7 387 393 Duller G 2003 Distinguishing quartz and feldspar in single grain luminescence measurements Radiation Measurements 37 2 161 165 Murray A S and Wintle A G 2000 Luminescence dating of quartz using an improved single aliquot regenerative dose protocol Radiation Measurements 32 57 73 Thomsen K J Murray A S Jain M Boetter Jensen L 2008 Laboratory fading rates of vari ous luminescence signals from feldspar rich sediment extracts Radiation Measurements 43 1474 1486 doi 10 1016 j radmeas 2008 06 002 See Also calc_OSLLxTxRatio plot_GrowthCurve RLum Analysis RLum Results get_RLum Results Examples 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 lt Risoe BINfileData2RLum Analysis CWOSL SAR Data pos 1 perform SAR analysis results lt analyse_SAR CWOSL object signal integral min 1 signal integral max 2 background inte

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