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Package `Luminescence`

1. S3 method for class list x S3 method for class matrix x S3 method for class matrix x S3 method for class merge x y we RLum Results RLum Data Curve RLum Analysis RLum Data Curve RLum Data Spectrum RLum S3 method for class RLum Analysis unlist x recursive S3 method for class x y S3 method for class x7 y S3 method for class Xx y S3 method for class x y S3 method for class x y z drop TRUE TRUE RLum Data Curve RLum Data Curve RLum Data Curve RLum Data Curve RLum Data Curve methods_RLum methods_RLum 121 S3 method for class RLum Data Spectrum x y z drop TRUE S3 method for class RLum Data Image x y z drop TRUE S3 method for class RLum Analysis x i drop FALSE HH S3 method for class RLum Results x i drop TRUE S3 method for class RLum Analysis x Cil S3 method for class RLum Results x Cil S3 method for class RLum Analysis x i S3 method for class RLum Results x i Arguments x y object row names optional recursive Z drop i Details RLum required input opject integer optional the row index of the matrix data frame further arguments that can be passed to the method RLum required input opject logical with default enables or disables row names as da
2. decrease error by 10 use DRAC plot_AbanicoPlot data increase sample size by 200 207 tune_Data x decrease error 0 1 summary c n mean plot_AbanicoPlot data tune_Data x increase data 2 summary c n mean use_DRAC Use DRAC to calculate dose rate data Description The function provides an interface from R to DRAC An R object or a pre formatted XLS XLSX file is passed to the DRAC website and the results are re imported into R Usage use_DRAC file name Arguments file character spreadsheet to be passed to the DRAC website for calculation Can also be a DRAC template object obtained from template_DRAC name character Optional user name submitted to DRAC If omitted a random name will be generated Further arguments Value Returns an RLum Results object containing the following elements DRAC list a named list containing the following elements in slot data highlights data frame summary of 25 most important input output fields header character HTTP header from the DRAC server response labels data frame descriptive headers of all input output fields content data frame complete DRAC input output table input data frame DRAC input table output data frame DRAC output table data character or list path to the input spreadsheet or a DRAC template call call the function call args list used arguments The output should be accessed using the function get_R
3. error weighted relative standard error seabs absolute standard error seabs weighted error weighted absolute standard error kurtosis kurtosis and skewness skewness 138 Function version 0 4 4 2015 11 29 17 27 48 Note The input data is not restricted to a special type Author s Michael Dietze GEZ 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 D e distribution Standard error xlim c 100 250 ylim c 0 0 1 5 20 plot_Histogram plot KDE 139 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 statis
4. now with output of the plot parameters 148 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 data 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 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 stats c min max median now with a brief statistical summary plot_RadialPlot data ExampleData DeVa
5. plot values with legend plot_DRTResults values ExampleData DeValues BT998 7 11 given dose 2800 legend Test data set 132 plot_GrowthCurve 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 HH some more user defined plot parameters plot_DRTResults values list x 1 x 2 given dose 2800 pch c 2 5 col c orange blue xlim c 0 8 ylim c 0 85 1 15 xlab Sample aliquot plot the data with user defined statistical measures as legend plot_DRTResults values list x 1 x 2 given dose 2800 summary c n mean weighted sd plot the data with user defined statistical measures as sub header plot_DRTResults values list x 1 x 2 given dose 2800 summary c n mean weighted sd summary pos sub plot the data grouped by preheat temperatures plot_DRTResults values ExampleData DeValues BT998 7 11 given dose 2800 preheat c 200 200 200 240 240 read example data set and misapply them for this plot type data ExampleData DeValues envir environment plot values plot_DRTResults values ExampleData DeValues BT998 7 11 given dose 2800 mtext Example data plot two data sets grouped by preheat temperatures plot_DRTR
6. 32 calc_AliquotSize 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 sample 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 VJ12 0 9068 is used However note t
7. 0 2 0 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 07 BIN file version number 4 LENGTH integer 03 07 Length of this record 5 PREVIOUS integer 03 07 Length of previous record 6 NPOINTS integer 03 07 Number of data points in the record 7 RUN integer 03 07 Run number 8 SET integer 03 07 Set number 9 POSITION integer 03 07 Position number 10 GRAIN integer 03 04 Grain number LL11 GRAINNUMBER integer 06 07 Grain number 12 CURVENO integer 06 07 Curve number 13 XCOORD integer 03 07 X position of a single grain 14 YCOORD integer 03 07 Y position of a single grain 15 SAMPLE factor 03 07 Sample name 16 COMMENT factor 03 07 Comment name 17 SYSTEMID integer 03 07 Risoe system id 18 FNAME factor 06 07 File name bin binx 19 USER facotr 03 07 User name 20 TIME character 03 07 Data collection time hh mm ss 21 DATE factor 03 07 Data collection date ddmmyy 22 DTYPE character 03 07 Data type 23 BL_TIME numeric 03 07 Bleaching time 24 BL_UNIT integer 03 07 Bleaching unit mJ J secs mins hrs 25 NORMI numeric 03 07 Normalisation factor 1 26 NORM2 numeric 03 07 Normalisation factor 2 27 NORM3 numeric 03 07 Normalisation factor 3 28 BG numeric 03 07 Background level 29 SH
8. 2 additional examples for pure XML import using the package XML HH uncomment for usage import entire XML file FILE lt file choose temp lt XML xmlRoot XML xmlTreeParse FILE search for specific subnodes with curves containing OSL getNodeSet temp Sample Sequence Record recordType OSL Curve 2 How to extract single curves after import data ExampleData XSYG envir environment grep one OSL curves and plot the first curve OSLcurve lt get_RLum OSL SARMeasurement Sequence Object recordType 0SL C 1J replicate_RLum 175 3 How to see the structure of an object structure_RLum OSL SARMeasurement Sequence Object replicate_RLum General replication function for RLum S4 class objects Description Function replicates RLum S4 class objects and returns a list for this objects Usage replicate_RLum object times NULL Arguments object an object of class RLum required times integer optional number for times each element is repeated element Value Returns a list of the object to be repeated Function version 0 1 0 2015 11 29 17 27 48 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team See Also RLum 176 Risoe BINfileData class Risoe BINfileData class Class Risoe BINfileData Description S4 class object for luminescence data in R The object is produced as output of
9. Examples load data data ExampleData RLum Analysis envir environment perform analysis temp lt analyse_IRSAR RF object IRSAR RF Data show De results and test paramter results get_RLum temp data object De values get_RLum temp data object test_parameter 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 NULL sequence structure c TL IR50 pIRIR225 plot TRUE plot single FALSE Arguments object RLum Analysis required or list of RLum Analysis objects input object containing data for analysis If a list is provided the functions tries to iteratre over the list 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 required lower bound of the background integral Provide this value as vector for different integration limits for the different IRSL curves background integral max integer
10. be orginated from the function calc_SourceDoseRate for vector dose rate in Gy s and dose rate error in Gy s error propagation character with default error propagation method used for error calculation omit gaussian or absolute see details for further information Details Calculation of De values from seconds s to gray Gy De Gy Dels x DoseRate Gy s Provided calculation error propagation methods for error calculation with se as the standard error and DR of the dose rate of the beta source 1 omit default se De Gy se De s x DR Gy s In this case the standard error of the dose rate of the beta source is treated as systematic i e non random it error propagation is omitted However the error must be considered during calculation of the final age cf Aitken 1985 pp 242 This approach can be seen as method 2 gaussian for the case the random standard error of the beta source calibration is 0 Which particular method is requested depends on the situation and cannot be prescriptive 2 gaussian error propagation se De Gy Y DR Gy s se De s De s se DR Gy s Applicable under the assumption that errors of De and se are uncorrelated 3 absolute error propagation se De Gy abs DR Gy s x se De s abs Dels x se DR Gy s Applicable under the assumption that errors of De and se are not uncorrelated Value Returns a data frame with converted valu
11. Arguments object show_RLum get_RLum length_RLum names_RLum an object of class RLum Data Curve required class set_RLum character required name of the RLum class to create originator set_RLum character automatic contains the name of the calling function the function that produces this object can be set manually recordType set_RLum character optional record type e g OSL curveType set_RLum character optional curve type e g predefined or measured data set_RLum matrix required raw curve data If data itself is a RLum Data Curve object this can be used to re construct the object s Details info set_RLum list optional info elements info object get_RLum character optional name of the wanted info element Value set_RLum Returns an RLum Data Curve object RLum Data Curve class 189 get_RLum 1 A matrix with the curve values or 2 only the info object if info object was set length_RLum Number of channels in the curve row number of the matrix names_RLum Names of the info elements slot info Methods by generic e show Show structure of RLum Data Curve object e set_RLum Construction method for RLum Data Curve object The slot info is optional and predefined as empty list by default e get_RLum Accessor method for RLum Data Curve object The argument info object is op tional to directly access the info elements If no info element name is provided the raw curve dat
12. 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 160 plot_RLum Data Spectrum zlim Limits values along the count value axis Energy axis re calculation If the argument xaxis energy TRUE is chosen instead intensity vs wavelength the spectrum is plotted as intensiyt vs energy Therefore the entire spectrum is re recaluated e g Appendix 4 in Blasse and Grabmeier 1994 The intensity of the spectrum z values is re calcualted using the following equation bp px A hc with dp the intensity per interval of energy E eV the intensity per interval of wavelength A nm and h eV s the Planck constant and c m s the velocity of light For transforming the wavelength axis x values the equation E hc A 1s used For further details please see the cited the literature Details on the plot functions Spectrum is visualised as 3D or 2D plot Both plot types are based on internal R plot functions plot type persp Arguments that will be passed to persp e shade default is 0 4 e phi default is 15 e theta default is 30 e expand default is 1 e ticktype def
13. 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 is 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 This function can be used stand alone but is the base function for Risoe BINfileData2RLum Analysis Value Returns an RLum Data Curve object Function version 0 2 1 2015 12 06 23 16 02 Note Due to changes in the BIN file version 3 to version 4 format the recalculation of TL curves might be not overall correct for cases where the TL measurement is combined with a preheat Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Christoph Burow Universtiy of
14. S4 object of class RLum further arguments that one might want to pass to the specific get function Details The function provides a generalised access point for specific Risoe BINfileData objects Depending on the input object the corresponding get function will be selected Allowed arguments can be found in the documentations of the corresponding Risoe BINfileData class Value Return is the same as input objects as provided in the list Function version 0 1 0 2015 11 29 17 27 48 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team get_RLum 109 See Also Risoe BINfileData 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 S4 method for signature list get_RLum object null rm FALSE Arguments object RLum required S4 object of class RLum or an object of type list containing only objects of type RLum null rm logical with default option to get rid of empty and NULL objects further arguments that will be passed to the object specific methods For furter details on the supported arguments please see the class documentation RLum Data Curve RLum Data Spectrum RLum Data Image RLum Analysis and RLum Results Details The function provides a generalised access point for specific RLum objects Depending on the i
15. ia sop a a os Beye we ee A Ge io A i 69 Calo TEEXTEXRAGO 000 a ho i Roa A A A EA ee Ge ats TI CW2PHMI re o be ee ee e eee a 73 CW2PpEM aa ndak ds SE a A dd EE tk bak d 76 CW2pEMi es ar e Ma wee a ta rs e a da 78 CW2DPPM a dic slo scat ae o a a A UA a Bo eo A de ple 8l ExampleData BINfileData e 85 ExampleData CW_OSL_Curve 2 ee 86 ExampleData DeValles o c o 2 lt lt ses 87 ExampleData FitingLM 2 0 0 20 00 0020 0 0000 88 ExampleData LxTxData 2 2 0 0 00000000 0000002000 89 ExampleData LxTxOSLData e 90 ExampleData RLum Analysis 0000000222 ee eee 91 ExampleData RLum Data IMage 0 000 000 00000 92 ExampleData XSYG 0 0 2 0 0 0000000000000 020000 93 extract_IrradiationTimes 0 a 95 fit CW GCUIRVE 625 4 ara eee MG oe A Ge aa ie trae wide Bas SS we dle BAe 2 deed 97 fit IUMCURVE men be cl owe he eee hee ea we be ee de bb hee oe eS 101 Pet_Layoul segs REN SARE RAS EES ERE eS Ree A 105 get QUIE e pessu Pav ae Shs a bake Ee OA a See RES a CA OEE RS RIS 106 petshtAmswer s csoc sereset irete Pas cd tee be a 107 get_Risoe BINfileData 2 2 e 108 pet RM 24 405 e hee ae eis AB ee Beda Ss BS Se OLAS Bho EE Se N 109 length RLum 2 ee 110 merge_Risoe BINfileData ee 111 Merge RLUM sia 4 2044 a e a 4d e eH Ee EAS 113 merge_RLum Analysis e 114 merge_RLum Data Curve sc
16. lt 2 input Depth m lt 2 2 input errDepth m lt 0 22 input Overburden density g cm 3 lt 1 8 input errOverburden density g cm 3 lt 0 1 input Latitude decimal degrees lt 30 0000 input Longitude decimal degrees lt 70 0000 input Altitude m lt 150 input De Gy lt 20 input errDe Gy lt 0 2 use DRAC Not run output lt use_DRAC input End Not run tune_Data Tune data for experimental purpose 206 tune_Data Description The error can be reduced and sample size increased for specific purpose Usage tune_Data data decrease error 0 increase data 0 Arguments data data frame required input values structure data values 11 and data error values 2 are required decrease error numeric factor by which the error is decreased ranges between 0 and 1 increase data numeric factor by which the error is decreased ranges between 0 and inf Value Returns a data frame with tuned values Function version 0 5 0 2015 11 29 17 27 48 Note You should not use this function to improve your poor data set Author s Michael Dietze GFZ Potsdam Germany R Luminescence Package Team References See Also Examples load example data set data ExampleData DeValues envir environment x lt ExampleData DeValues CA1 plot original data plot_AbanicoPlot data x summary c n mean
17. 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 46 calc_FiniteMixture 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 uses the maximum likelihood and Bayesian Information Cri
18. 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 Function version 0 1 2015 11 29 17 27 48 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 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 38 calc_CosmicDoseRate 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 Realizi
19. Function calls object specific get functions for RisoeBINfileData S4 class objects Usage set_Risoe BINfileData METADATA DATA RESERVED Arguments METADATA xX DATA X RESERVED X Details The function provides a generalised access point for specific Risoe BINfileData objects Depending on the input object the corresponding get function will be selected Allowed arguments can be found in the documentations of the corresponding Risoe BINfileData class Value Return is the same as input objects as provided in the list Function version 0 1 2015 11 29 17 27 48 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team See Also Risoe BINfileData set_RLum 201 set_RLum General set function for RLum S4 class objects Description Function calls object specific set functions for RLum S4 class objects Usage set_RLum class originator Arguments class RLum required name of the S4 class to create originator character automatic contains the name of the calling function the function that produces this object can be set manually further arguments that one might want to pass to the specific set method Details The function provides a generalised access point for specific RLum objects Depending on the given class the corresponding method to create an object from this class will be selected Allowed additional arguments can be found in the documenta
20. IRAMAT CRP2A Universite Bordeaux Montaigne R Luminescence Package Team calc_FiniteMixture 45 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 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 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 4 Arguments data RLum Results or data frame required for data frame two columns with De dataL 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 2012 p 100 n components numeric required
21. 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 58 calc_MinDose 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 values plot TRU
22. analyse_SAR TL 22 72 apply_CosmicRayRemoval 24 26 apply_EfficiencyCorrection 26 approx 74 172 174 as 28 29 as data frame 121 204 as data frame RLum Data Curve methods_RLum 118 as data frame RLum Data Spectrum methods_RLum 118 as list RLum Analysis methods_RLum 118 as list RLum Data Curve methods_RLum 118 as list RLum Results methods_RLum 118 as matrix RLum Data Curve methods_RLum 118 213 as matrix RLum Data Spectrum methods_RLum 118 BaseDataSet CosmicDoseRate 29 42 boxplot 164 165 brick 791 calc_AliquotSize 31 calc_CentralDose 34 38 48 50 55 58 62 calc_CommonDose 36 36 48 50 55 58 62 calc_CosmicDoseRate 38 calc_FadingCorr 43 calc_FiniteMixture 36 38 45 50 55 58 62 calc_FuchsLang2001 36 38 48 49 55 58 62 calc_gSGC 51 calc_HomogeneityTest 52 calc_IEU 54 calc_MaxDose 55 62 calc_MinDose 36 38 48 50 55 56 58 58 calc_OSLLxTxRatio 14 16 18 20 21 64 calc_SourceDoseRate 67 198 199 calc_Statistics 69 165 calc_TLLxTxRatio 23 24 71 call 13 33 35 37 40 47 50 53 54 60 207 character 7 13 16 20 22 23 25 28 46 51 64 67 70 95 98 101 102 105 107 111 16 121 125 130 133 137 139 140 142 145 146 150 153 157 159 164 166 168 169 171 180 183 185 186 188 191 193 195 198 201 207 209 210 confint 98 100 102 103 contour 157 161 CW2pHMi 73 78 80 84 151 CW2pLM 75 76
23. 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 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 function 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 64 calc_OSLLxTxRatio calc_OSLLxTxRatio Calculate Lx Tx ratio for CW OSL curves Description Calculate Lx Tx ratios from a given set of CW OSL curves assuming late light background subtrac tion Usage calc_OSLLxTxRatio Lx data Tx data signal integral signal integral Tx NULL background integral background integral Tx NULL background count distribution non poisson sigmab Arguments Lx data RLum Data Curve or data frame required requires a CW OSL shine down curve x time y counts Tx data RLum Data Curve or 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
24. 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 bootstrap list bootstrap results The output should be accessed using the function get_RLum calc_MinDose 61 Function version 0 4 1 2015 11 29 17 27 48 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 1s applied Also note that all R warning messages are suppressed when running this function If the re
25. value to 48 The old position number is appended as comment e g OP 70 This option accounts for potential compatibility problems with the Analyst software txtProgressBar logical with default enables or disables txtProgressBar 210 write_R2BIN 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 3 2 2015 12 06 23 16 02 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 conversion from version 07 to 06 to 04 or 03 Warning Although the coding was done carefully it seems that the BIN BINX files produced by Risoe DA 15 20 TL OSL readers slightly differ on the byte level No obvious differences are observed in the METADATA however the BIN BINX file may not fully compatible at least not similar to the once directly produced by the Risoe readers Implementation of support for version 07 could so far not properly tested Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team Refer
26. 1 plot simple spectrum 2D contour plot_RLum Data Spectrum TL Spectrum plot type contour xlim c 310 750 ylim c 0 300 bin rows 10 bin cols 1 2 plot spectrum 3D plot_RLum Data Spectrum TL Spectrum 162 plot_RLum Results plot type persp xlim c 310 750 ylim c 0 100 bin rows 10 bin cols 1 3 plot multiple lines 2D multiple lines with ylim plot_RLum Data Spectrum TL Spectrum plot type multiple lines xlim c 310 750 ylim c 0 100 bin rows 10 bin cols 1 Not run 4 plot real 3d spectrum using rgl plot_RLum Data Spectrum TL Spectrum plot type persp3d xlim c 310 750 ylim c 0 300 bin rows 10 bin cols 1 End Not run plot_RLum Results Plot function for an RLum Results S4 class object Description The function provides a standardised plot output for data of an RLum Results S4 class object Usage plot_RLum Results object single TRUE Arguments object RLum Results required S4 object of class RLum Results single logical with default single plot output TRUE FALSE to allow for plotting the results in as few plot windows as possible further arguments and graphical parameters will be passed to the plot function Details The function produces a multiple plot output A file output is recommended e g pdf Value Returns multiple plots plot_RLum Results 163 Function version 0 2 1 2015 12 05 15 52
27. 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 dose points numeric optional option set dose points manually analyse_SAR TL 23 log character with default a character string which contains x 1f 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 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 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 fol
28. 48 Note This function has been created to faciliate the plotting of image data imported by the function read_SPE2R 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 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 plot_RLum Data Spectrum 159 Arguments object 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 o
29. Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Margret C Fuchs HZDR Freiberg 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 write_R2BIN Risoe BINfileData readBin merge_Risoe BINfileData RLum Analysis txtProgressBar Examples 1 import Risoe BIN file to R uncomment for usage FILE lt file choose temp lt read_BIN2R FILE temp 168 read_Daybreak2R read_Daybreak2R Import Daybreak ASCH dato into R Description Import a txt ASCII file produced by a Daybreak reader into R Usage read_Daybreak2R file verbose TRUE txtProgressBar TRUE Arguments file character or list required path and file name of the file to be imported Alternatively a list of file names can be provided or just the path a folder contain ing measurement data Please note that the specific common file extension txt 1s likely leading to function failures during import when just a path is provided verbose logical with default enables or disables terminal feedback txtProgressBar logical with default enables or disables txtProgressBar Value A list of RLum Analysis objects each per position is provided Function version 0 2 0 20
30. 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 84 CW2pPMi 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 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 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
31. Cologne Germany R Luminescence Package Team References See Also Risoe BINfileData2RLum Analysis set_RLum RLum Data Curve RLum Analysis Risoe BINfileData plot_RLum RLum class 183 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 Usage S4 method for signature RLum replicate_RLum object times NULL Arguments object an object of class RLum required times integer optional number for times each element is repeated element Methods by generic e replicate_RLum Replication method RLum objects Slots originator Object of class character containing the name of the producing function for the object Set automatically by using the function set_RLum uid Object of class character containing a unique object identifier md5 hash calculated using the internal function create_UID This id is calculated everytime and object is created Objects from the Class A virtual Class No objects can be created from it Class version 0 3 0 Note RLum is a virtual class 184 RLum Analysis class Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France See Also RLum Data RLum Analysis Examples showClass RLum RLum Analysis cla
32. 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 60 A 9 4 1 A The fitting is done using the port algorithm of the nls function 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 squared residuals method control To keep the generic argument list as clear as possible arguments to control the methods for De estimation are all preset with meaningful default parameters and can be handled using the argument method control only e g method control list trace TRUE Supported arguments are ARGUMENT METHOD DESCRIPTION trace FIT SLIDE asin nls shows sum of squared residuals maxiter FIT as in nls warnOnly FIT as in nls minFactor FIT as in nls correct_onset SLIDE The logical argument literally spoken shifts the curves along the x axis by the first channel show_density SLIDE logical with default enables or disables KDE plots for MC run results If the distribution n MC SLIDE integer wiht default This controls the number of MC runs within the sliding assesing t
33. 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 34 calc_CentralDose Examples HH Estimate the amount of grains on a small aliquot calc_AliquotSize grain size c 100 150 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 log TRUE plot TRUE Arguments data RLum Results or data frame required for data frame two columns with De dataL 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 central age model to De data plot logical with default plot output further arguments trace verbose Details This function uses the equation
34. RLum Analysis methods_RLum 118 plot RLum Data Curve methods_RLum 118 plot RLum Data Image methods_RLum 118 215 plot RLum Data Spectrum methods_RLum 118 plot RLum Results methods_RLum 118 plot_AbanicoPlot 123 plot_DRTResults 129 plot_GrowthCurve 3 14 16 18 21 23 24 66 132 plot_Histogram 126 136 147 plot_KDE 26 139 147 203 plot_NRt 142 plot_RadialPlot 26 144 plot_Risoe BINfileData 149 179 plot_RLum 68 78 94 151 154 156 158 161 163 182 190 192 194 197 plot_RLum Analysis 94 152 153 plot_RLum Data Curve 152 154 155 plot_RLum Data Image 152 156 plot_RLum Data Spectrum 94 152 158 plot_RLum Results 752 162 plot_ViolinPlot 164 plotRGB 157 profile 99 100 profile mle2 60 raster 156 158 170 raw 166 read_BIN2R 19 21 96 97 112 149 151 165 176 179 181 210 read_Daybreak2R 168 184 read_SPE2R 92 158 169 190 192 read_XSYG2R 93 97 171 184 190 194 readBin 167 170 readBIN2R read_BIN2R 165 readSPE2R read_SPE2R 169 readXSYG2R read_XSYG2R 171 regex 172 rep RLum methods_RLum 118 replicate_RLum 175 replicate_RLum RLum method RLum class 183 Risoe BINfileData 97 108 109 111 112 167 176 180 182 186 200 209 210 Risoe BINfileData class 18 21 85 149 166 167 176 Risoe BINfileData2RLum Analysis 166 167 179 180 182 186 190 Risoe BINfileData2RLum Data Curve 179 181 181 190 216
35. RLum S4 class objects Usage names_RLum object Arguments object RLum required S4 object of class RLum Details The function provides a generalised access point for specific RLum objects Depending on the input object the corresponding names function will be selected Allowed argu ments can be found in the documentations of the corresponding RLum class Value Returns a character plot_AbanicoPlot 123 Function version 0 1 0 2015 11 29 17 27 48 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team See Also RLum Data Curve RLum Data Image RLum Data Spectrum RLum Analysis RLum Results plot_AbanicoPlot Function to create an Abanico Plot Description A plot is produced which allows comprehensive presentation of data precision and its dispersion around a central value as well as illustration of a kernel density estimate histogram and or dot plot of the dose values Usage plot_AbanicoPlot data na rm TRUE log z TRUE z 0 mean weighted dispersion qr plot ratio 0 75 rotate FALSE mtext summary summary pos legend legend pos stats rug FALSE kde TRUE hist FALSE dots FALSE y axis TRUE error bars FALSE bar bar col polygon col line line col line label grid col frame 1 bw SJ output FALSE Arguments data data frame or RLum Results object required for data frame two colum
36. 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 histogram data ExampleData DeValues envir environment plot_Histogram ExampleData DeValues BT998 xlab De s 2 plot values as histogram with second to gray conversion data ExampleData DeValues envir environment De values lt Second2Gray ExampleData DeValues BT998 dose rate c 0 0438 0 0019 plot_Histogram De values xlab De Gy ExampleData FittingLM Example data for fit_LMCurve in the package Luminescence ExampleData LxTxData 89 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 Format Two objects data frames with two columns time and counts 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 1
37. and plot TL curve merged lt merge_RLum Data Curve list TL curve 3 TL curve 1 merge method plot_RLum TL curve merged merge_RLum Results Merge function for RLum Results S4 class objects Description Function merges objects of class RLum Results The slots in the objects are combined depending on the object type e g for data frame and matrix rows are appended Usage merge_RLum Results objects 118 methods_RLum Arguments objects list required a list of RLum Results objects methods_RLum methods _RLum Description Methods for S3 generics implemented for the package Luminescence This document summarises all implemented S3 generics The name of the function is given before the first dot after the dot the name of the object that is supported by this method is given e g plot RLum Data Curve can be called by plot object where object is the RLum Data Curve object Usage S3 method for class RLum Results plot x y S3 method for class RLum Analysis plot x y S3 method for class RLum Data Curve plot x y S3 method for class RLum Data Spectrum plot x y S3 method for class RLum Data Image plot x y S3 method for class Risoe BINfileData plot x y S3 method for class RLum Results hist x S3 method for class RLum Data Image hist x S3 method for class RLum Data Curve hist x S3 m
38. 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 Value Returns same object as input RLum Data Spectrum 26 apply_EfficiencyCorrection Function version 0 1 3 2015 11 29 17 27 48 Note Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence 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 spectru
39. as input objects as provided in the list Function version 0 1 2015 11 29 17 27 48 merge_Risoe BINfileData 111 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team See Also RLum Data Curve RLum Data Image RLum Data Spectrum RLum Analysis RLum Results merge_Risoe BINfileData Merge Risoe BINfileData objects or Risoe BIN files Description Function allows merging Risoe BIN BINX files or Risoe BINfileData objects Usage merge_Risoe BINfileData input objects output file keep position number FALSE position number append gap 0 Arguments input objects character 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 Th
40. 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 iter 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 Function version 0 31 2015 11 29 17 27 48 Author s Christoph Burow University of Cologne Germany R Luminescence Package Team 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
41. 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 A Statistic summary i e a collection of statistic measures of centrality and dispersion and fur ther measures can be added by specifying one or more of the following keywords n number of samples mean mean De value mean weighted error weighted mean median me dian of the De values sdrel relative standard deviation in percent sdrel weighted error weighted relative standard deviation in percent sdabs absolute standard deviation sdabs weighted 126 plot_AbanicoPlot error weighted absolute standard deviation serel relative standard error serel weighted error weighted relative standard error seabs absolute standard error seabs weighted error weighted absolute standard error in 2s percent of samples in 2 sigma range kurtosis kurtosis and skewness skewness The optional parameter layout allows to m
42. class are automatically created by e g read_XSYG2R Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France See Also RLum RLum Data plot_RLum Examples showClass RLum Data Spectrum show example data data ExampleData XSYG envir environment TL Spectrum show data matrix get_RLum TL Spectrum plot spectrum Not run plot_RLum TL Spectrum End Not run RLum Results class 195 RLum Results class Class RLum Results Description Object class contains results data from functions e g analyse_SAR CWOSL Usage S4 method for signature RLum Results show object S4 method for signature RLum Results set_RLum class originator data list S4 method for signature RLum Results get_RLum object data object drop TRUE S4 method for signature RLum Results length_RLum object S4 method for signature RLum Results names_RLum object Arguments object get_RLum RLum Results required an object of class RLum Results to be evaluated class set_RLum character required name of the RLum class to create originator set_RLum character automatic contains the name of the calling function the function that produces this object can be set manually data set_RLum list optional a list containing the data to be stored in the object data object get_RLum character or numeric name or index of the data slot to be returned dro
43. default option to provide information about the measurement on the plot output e g name of the BIN or BINX file 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 further arguments that will be passed to the function calc_OSLLxTxRatio sup ported background count distribution and sigmab and can be used to adjust the plot Supported mtext log 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 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 optio
44. default traces the fitting process on the terminal fit calcError logical with default calculate 1 sigma error range of components using confint LED power numeric with default LED power max used for intensity ramping in mW cm 2 Note The value is used for the calculation of the absolute photoionisation cross section LED wavelength numeric with default LED wavelength used for stimulation in nm Note The value is used for the calculation of the absolute photoionisation cross section cex global numeric with default global scaling factor sample_code character optional sample code used for the plot and the optional output table mtext output path character optional output path for table output containing the results of the fit The file name is set automatically If the file already exists in the directory the values are appended output terminal logical with default terminal ouput with fitting results output terminalAdvanced logical with default enhanced terminal output Requires output terminal TRUE If output terminal FALSE no advanced output is possible plot logical with default returns a plot of the fitted curves further arguments and graphical parameters passed to plot Details Fitting function The function for the CW OSL fitting has the general form y 101 x Ay exp Ai x 2 10 Aj exp A x x where 0 lt i lt 8 and A is the decay constant and WO the inti
45. dispersion bars i e bar showing the 2 sigma range centered at the defined values By default a bar is drawn according to z 0 To omit the bar set bar FALSE character or numeric with default colour of the dispersion bar Default is grey60 character or numeric with default colour of the polygon showing the data scatter Sometimes this polygon may be omitted for clarity To disable it use FALSE or polygon FALSE Default is grey80 numeric numeric values of the additional lines to be added character or numeric colour of the additional lines plot_AbanicoPlot 125 line label character labels for the additional lines grid col character or numeric with default colour of the grid lines originating at 0 0 and strechting to the z scale To disable grid lines use FALSE Default is srey frame numeric with default option to modify the plot frame type Can be one out of no frame 1 frame originates at 0 0 and runs along min max isochrons 2 frame embraces the 2 sigma bar 3 frame embraces the entire plot as a rect angle Default is 1 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 Aban
46. elements info object get_RLum character name of the info object to returned Value set_RLum Returns an object from class RLum Data Image get_RLum 1 Returns the data object brick 2 only the info object if info object was set names_RLum Returns the names of the info elements Methods by generic e show Show structure of RLum Data Image object e set_RLum Construction method for RLum Data Image object The slot info is optional and predefined as empty list by default e get_RLum Accessor method for RLum Data Image object The argument info object is op tional to directly access the info elements If no info element name is provided the raw image data RasterBrick will be returned e names_RLum Returns the names info elements coming along with this curve object 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 pre defined data Object of class brick containing images raster data info Object of class list containing further meta information objects 192 RLum Data Spectrum class Objects from the Class Objects can be created by calls of the form set_RLum RLum Data Image Class version 0 3 0 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 IRA
47. 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 62 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 Q 1 plot FALSE Show structure of the RLum Results object mam Show summar
48. in this object names_RLum Returns the names of the record types recordType in this object Methods by generic show Show structure of RLum Analysis object set_RLum Construction method for RLum Analysis objects get_RLum 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 structure_RLum Method to show the structure of an RLum Analysis object length_RLum Returns the length of the object i e number of stored records names_RLum Returns the names of the RLum Data objects objects same as shown with the show method Slots protocol Object of class character describing the applied measurement protocol records Object of class list containing objects of class RLum Data Objects from the Class Objects can be created by calls of the form set_RLum RLum Analysis Class version 0 3 0 Note The method structure_RLum is currently just avaiblable for objects containing RLum Data Curve Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France See Also Risoe BINfil
49. last value measurement date and predicts from that the the source source dose rate for the number of days re quested means the multiple orignal input will be replaced However the function do not change entries for the calibration dates but mix them up Therefore it is not recommended to use this option when multiple calibration dates calib date are provided Author s Margret C Fuchs HZDR Helmholtz Institute Freiberg for Resource Technology 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 get_RLum plot_RLum calc_Statistics 69 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_RLum 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 3 source rate prediction and plotting dose rate lt calc_SourceDoseRate measurement date 2012 01 27 calib date 2014 12 19 calib dose rate 0 0438 calib er
50. list should be of similar length as the list provided with the argument object otherwise the function will create an own list of the requested lenght Function output will be just one single RLum Results object Please be careful when using this option It may allow a fast an efficient data analysis but the function may also break with an unclear error message due to wrong input data 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 post 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 recycling 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 a
51. 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 Details Parameters 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 p 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 and young samples containing negative zero or near zero De estimates Arnold et al 2009 p 323 Initial values boundaries The log likelihood calculations use the nlminb function for box constrained optimisation using PORT routines Accordingly initial values for the four parameters can be sp
52. pPM curve under parabolic modulation conditions using the interpolation procedure described by Bos amp Wallinga 2012 82 CW2pPMi Usage CW2pPMi 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 11 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 t 1 3 1 PP 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 v
53. read_XSYG2R Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France See Also RLum RLum Data plot_RLum merge_RLum Examples showClass RLum Data Curve set empty curve object set_RLum class RLum Data Curve RLum Data Image class Class RLum Data Image Description Class for representing luminescence image data TL OSL RF Such data are for example produced by the function read_SPE2R Usage HH S4 method for signature RLum Data Image show object S4 method for signature RLum Data Image set_RLum class originator recordType Image curveType NA_character_ data raster brick raster raster matrix info listQ S4 method for signature RLum Data Image get_RLum object info object HH S4 method for signature RLum Data Image names_RLum object RLum Data Image class 191 Arguments object show_RLum get_RLum names_RLum an object of class RLum Data Image class set_RLum character name of the RLum class to create originator set_RLum character automatic contains the name of the calling function the function that produces this object can be set manually recordType set_RLum character record type e g OSL curveType set_RLum character curve type e g predefined or measured data set_RLum matrix raw curve data If data is of type RLum Data Image this can be used to re construct the object info set_RLum list info
54. signal integral signal integral Tx vector optional vector with the limits for the signal integral for the Tx curve If nothing is provided the value from signal integral is used background integral vector required vector with the bounds for the background integral background integral Tx vector optional vector with the limits for the background integral for the Tx curve If nothing is provided the value from background integral is used 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 calc_OSLLxTxRatio 65 according to Galbraith 2002 sigmab The default value of sigmab is calculated assuming the background is constant and would not applicable when the b
55. text use mtext Value Along with a plot so far wanted an RLum Results object is returned containing the slot data contains the following elements DATA OBJECT TYPE DESCRIPTION De data frame Table with De values De MC numeric Table with De values from MC runs Fit nls or 1m object from the fitting for EXP EXP LIN and EXP EXP In case of a resulting linear fit when Formula expression Fitting formula as R expression call call The original function call 136 plot_Histogram Function version 1 8 1 2015 12 06 23 16 02 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Michael Dietze GFZ Potsdam Germany R Luminescence Package Team See Also nls RLum Results get_RLum nlsLM 1m uniroot 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 temp 1a to access the fitting value try get_RLum temp data object Fit 2 plot the growth curve only uncomment to use pdf file Desktop Growth_Curve_Dummy pdf paper special plot_GrowthCurve LxTxData tHidev 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 tHidev off plot_Histogram Plot a histogram with sepa
56. 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 Ifn MCruns auto is used the function tries to find a stable error for the age Note This may take a while seed integer optional sets the seed for the random number generator in R using set seed txtProgressBar logical with default enables or disables txtProgressBar 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 n MCruns auto The error estimation based on a stochastic process i e for a small number of MC runs the calculated error varies considerably every time the function is called even with the same input values The argument option n MCruns auto tries to find a stable value for the standard error i e the standard deviation of values calculated during the MC runs age corr MC within a given precision 2 digits by increasing the number of MC runs stepwise and calculating the corresponding error 44 calc_FadingCorr If the determined error does not differ from the 9 values calculated previously within a precision of here 3 digits the calculation is stop
57. 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 RLum Data Curve objects in one single plot 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 154 plot_RLum Analysis plot single logical with default global par settings are considered normally this should end in one plot per page further arguments and graphical parameters will be passed to the plot function Supported arguments main can be provided as vector for combine TRUE mtext log 1wd 1ty type pch col norm ylim xlab and for combine TRUE also xlim ylab sub legend text legend pos typical plus outside legend col Details The function produces a multiple plot output A file output 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 fun
58. 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 50 calc_FuchsLang2001 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 11 29 17 27 48 Note Please consider the requirements and the constraints of this method see Fuchs amp Lang 2001 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Christoph Burow University of Cologne Germany R Luminescence Package Team References Fuchs M 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 for reconstructing soil erosion in Greece Quaternary Science Reviews 2
59. 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 11 and mea sured counts 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 6 Transform values using pLM t t Px CW 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 th
60. 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 fastForward logical with default if TRUE for a more efficient data processing only a list of RLum Analysis objects is returned import logical with default if set to FALSE only the XSYG file structure is shown 172 read_XSYG2R pattern regex with default optional regular expression if file is a link to a folder to select just specific XSYG files 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 lt Curve name first curve gt lt Curve name curve with data gt x yO x1 yl 3 x2 y2 x3 y3 lt Curve gt lt Record gt lt Sequence gt lt Sample gt 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 ti
61. values values bg n components 3 start_values input dataType LM fit method port sample_code sample_ID LED power 36 LED wavelength 470 fit trace FALSE fit advanced FALSE fit calcError FALSE bg subtraction polynomial verbose TRUE plot TRUE plot BG FALSE Arguments values RLum Data Curve or data frame required x y data of measured values time and counts See examples values bg RLum Data Curve or data frame optional x y data of measured values time and counts for background subtraction n components integer with default fixed number of components that are to be recognised during fitting min 1 max 7 start_values data frame optional start parameters for lm and xm data for the fit If no start values are given an automatic start value estimation is attempted see details input dataType character with default alter the plot output depending on the input data LM or pLM pseudo LM See CW2pLM fit method character with default select fit method allowed values port and LM port uses the port routine usint the funtion nls LM utilises the function n1sLM from the package minpack 1m and with that the Levenberg Marquardt algorithm 102 fit LMCurve 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
62. 15 12 05 15 52 49 Note BETA VERSION This function version still needs to be properly tested Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Based on a suggestion by Willian Amidon and Andrew Louis Gorin R Luminescence Package Team References See Also RLum Analysis RLum Data Curve read_SPE2R 169 Examples This function has no example yet read_SPE2R Import Princeton Intruments TM SPE file into R Description Function imports Princeton Instruments TM SPE files into R environment and provides RLum objects as output Usage read_SPE2R file output object RLum Data Image frame range txtProgressBar TRUE Arguments file character required spe file name including path e g WIN read_SPE2R C Desktop test spe MAC LINUX readSPER User test Desktop test spe 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 1s based on the file format description provided by Princton Instruments and a MatLab script written by Carl Hall s references Value Depending on the chose
63. 2 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 amp Lang 2001 temp lt calc_FuchsLang2001 ExampleData DeValues BT998 cvThreshold 5 calc_gSGC 51 calc_gSGC Calculate De value based on the gSGC by Li et al 2015 Description Function returns De value and De value error using the global standardised growth curve gSGC assumption proposed by Li et al 2015 for OSL dating of sedimentary quartz Usage calc_gSGC data gSGC type 0 250 gSGC parameters n MC 100 verbose TRUE plot TRUE Arguments data data frame required input data of providing the following columns LnTn LnTn error Lr1Tr1 Lr1Trl error Dr1 Note column names are not re quired The function expect the input data in the given order gSGC type character with default define the function parameters that should be used for the iteration procedure Li et al 2015 Table 2 presented function parameters for two dose ranges 0 450 and 0 250 gSGC parameters list optional option to provide own function parameters used for fitting as named list Nomenclature follows Li et al 2015 i e list A A error D0 D0 error c c error Y0 Y range requires a vector for the range the function is considered as valid e g range c 250 Usi
64. 49 Note Not all arguments available for plot will be passed Only plotting of RLum Results objects are supported Author s Christoph Burow University of Cologne Germany Sebastian Kreutzer IRAMAT CRP2A Uni versite Bordeaux Montaigne France R Luminescence Package Team References 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 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 diameter 1 plot FALSE plot plot_RLum Results grains 164 plot_ViolinPlot plot_ViolinPlot Create a violin plot Description Draws a kernal densiy plot in combination with a boxplot in its middle The shape of the violin is constructed using a mirrored density curve This plot is especially designed for cases where the individual errors are zero or to small to be visualised The idea for this plot is based on the the volcano plot in the ggplot2 package by Hadely Wickham and Winston Chang The general idea for the Violin Plot seems to be introduced by Hintze and Nelson 1998 Usage plot_ViolinPlot data boxplot TRUE rug TRUE summary NULL summary pos sub na rm FALSE Arguments data numeric or RLum Results object r
65. 80 84 101 151 CW2pLMi 75 78 78 84 151 CW2pPMi 75 78 80 81 151 data frame 10 13 17 20 21 23 27 28 33 37 40 45 47 49 51 53 54 56 58 60 64 70 71 73 77 79 82 55 87 93 98 101 117 123 130 133 137 139 142 145 164 167 173 185 198 206 207 Date 67 density 140 164 165 dim RLum Data Curve methods_RLum 118 214 dim RLum Data Spectrum methods_RLum 118 do call 53 ExampleData BINfileData 85 ExampleData CW_OSL_Curve 86 ExampleData DeValues 87 ExampleData FittingLM 88 ExampleData LxTxData 89 ExampleData LxTx0OSLData 90 ExampleData RLum Analysis 91 ExampleData RLum Data Image 92 ExampleData XSYG 93 expression 135 extract_IrradiationTimes 95 fit_CWCurve 97 105 fit_LMCurve 75 78 80 84 100 101 formula 18 get_Layout 105 get_Quote 106 get_rightAnswer 107 get_Risoe BINfileData 108 INDEX hist 137 138 hist RLum Analysis methods_RLum 118 hist RLum Data Curve methods_RLum 118 hist RLum Data Image methods_RLum 118 hist RLum Results methods_RLum 118 integer 8 12 15 16 22 25 43 51 67 70 71 101 111 121 133 142 153 159 166 175 182 183 202 204 legend 7 142 164 length Risoe BINfileData methods_RLum 118 length RLum Analysis methods_RLum 118 length RLum Data Curve methods_RLum 118 length RLum Results methods_RLum 118 length_RLum 110 length_RLum RLum Analysis method RLum Analysis class 1
66. 84 length_RLum RLum Data Curve method RLum Data Curve class 188 length_RLum RLum Results method RLum Results class 195 get_Risoe BINfileData Risoe BINfileData methodist 7 10 12 13 15 17 20 22 28 29 33 Risoe BINfileData class 176 get_RLum 10 11 13 14 18 23 24 33 35 37 40 45 47 52 54 60 66 68 95 100 105 109 109 136 153 170 207 get_RLum list method get_RLum 109 get_RLum RLum Analysis method RLum Analysis class 184 get_RLum RLum Data Curve method RLum Data Curve class 188 get_RLum RLum Data Image method RLum Data Image class 190 get_RLum RLum Data Spectrum method RLum Data Spectrum class 192 get_RLum RLum Results method RLum Results class 195 get_RLum Analysis get_RLum 109 get_RLum Data Curve get_RLum 109 get_RLum Data Image get_RLum 109 get_RLum Data Spectrum get_RLum 109 get_RLum Results get_RLum 109 get_structure RLum Analysis structure_RLum 203 glm 102 103 35 37 40 44 47 50 51 53 54 60 65 68 71 87 105 109 113 114 116 118 142 152 153 166 168 171 175 185 186 188 191 193 196 204 207 lm 73 75 78 79 82 134 136 logical 7 8 13 16 20 25 32 34 36 39 43 46 49 51 53 54 56 58 59 70 95 98 102 107 109 111 121 123 125 130 133 134 137 139 140 142 145 146 153 155 157 159 162 164 166 168 169 171 172 180 185 195 204 209 Luminescence Luminescence packa
67. 95 200 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 measurement for the package Luminescence Format A data frame with 4 columns Dose LxTx LxTx Error TnTx 90 ExampleData LxTxOSLData 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 Examples plot Lx Tx data vs dose s data ExampleData LxTxData envir environment plot LxTxData Dose LxTxData LxTx ExampleData LxTxOSLData Example Lx and Tx curve data from an artificial OSL measurement Description Lx and Tx data of continous wave CW OSL signal curves Format Two data frames containing time and count values Source Arbitrary OSL measurement References unpublished data ExampleData RLum Analysis 91 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 Format IRSAR RF Data IRSAR RF Data on coarse grain feldspar Each object contains data needed for the given pr
68. AL 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 Usage apply_CosmicRayRemoval object method Pych method Pych smoothing 2 silent FALSE plot FALSE apply_CosmicRayRemoval 25 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 previous 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
69. Differing Standard Errors Techno metrics 30 3 271 281 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 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
70. E to allow for plotting the results in single plot windows If a numerice vec tor is provided the plots can be selected individually ie 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 or calc_OSLLxTxRatio supported background count distribution and sigmab Please note that if you consider to use the early light subtraction method you should provide your own sigmab value 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 func tion calc_OSLLxTxRatio is used For changing the way the Lx Tx error is calculated use the argument background count distribution and sigmab which will be passed to the function calc_OSLLxTxRatio Argument object is of type list analyse_SAR CWOSL 17 If the argument object is of type list containing only RLum Analysis objects the function re calls itself as often as elements are in the list This is usefull if an entire measurement wanted to be analysed without writing separate for loops To gain in full control of the parameters e g dose points for every aliquot corresponding to one RLum Analysis object in the list in this case the arguments can be provided as list This
71. E multicore FALSE 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 Walling 2012 p 100 log logical with default fit the un logged minimum dose model to De data par numeric with default apply the 3 or 4 parametric minimum age model par 3 or par 4 The MAM 3 is used by default bootstrap logical with default apply the recycled bootstrap approach of Cunningham amp Wallinga 2012 calc_MinDose 59 init values numeric optional a named list with starting values for gamma sigma p0 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 plot logical with default plot output TRUE FALSE multicore 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 their usage Further arguments are verbose to de activate con sole
72. 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 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 DATA 1 5 ExampleData CW_OSL_Curve Example CW OSL curve data for the package Luminescence Description data frame containing CW OSL curve data time counts Format Data frame with 1000 observations on the following 2 variables list x a numeric vector time list y a numeric vector counts Source ExampleData CW_OSL_Curve Lab 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 ExampleData De Values 87 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 Geomorphology 125 172 185 Bos A J J amp Wallinga J 2012 How to v
73. IFT integer 03 07 Number of channels to shift data 30 TAG integer 03 07 Tag triggers SEL 31 LTYPE character 03 07 Luminescence type 32 LIGHTSOURCE character 03 07 Light source 33 LPOWER numeric 03 07 Optical stimulation power 34 LIGHTPOWER numeric 06 07 Optical stimulation power 35 LOW numeric 03 07 Low temperature time wavelength 36 HIGH numeric 03 07 High temperature time wavelength 37 RATE numeric 03 07 Rate heating rate scan rate 38 TEMPERATURE integer 03 07 Sample temperature 39 MEASTEMP integer 06 07 Measured temperature 40 AN_TEMP numeric 03 07 Annealing temperature 178 Risoe BINfileData class 41 AN_TIME numeric 03 07 Annealing time 42 TOLDELAY integer 03 07 TOL delay channels 43 TOLON integer 03 07 TOL opn channels 44 TOLOFF integer 03 07 TOL off channels 45 IRR_TIME numeric 03 07 Irradiation time 46 IRR_TYPE integer 03 07 Irradiation type alpha beta or gamma 47 IRR_UNIT integer 03 04 Irradiation unit Gy Rads secs mins hrs 48 IRR _DOSERATE numeric 06 07 Irradiation dose rate Gy s 49 IRR _DOSERATEERR numeric 06 07 Irradiation dose rate error Gy s 50 TIMESINCEIRR integer 06 07 Time since irradiation s 51 TIMETICK numeric 06 07 Time tick for pulsing s 52 ONTIME integer 06 07 On time for pulsing in time ticks 53 STIMPERIOD integer 06 07 Stimulation period on off in time ticks 54 GATE_ENABLED raw 06 07 PMT signal gatin
74. Lum 208 use DRAC Function version 0 1 0 2015 12 05 15 52 49 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Michael Dietze GEZ Potsdam Germany Christoph Burow University of Cologne Germany R Luminescence Package Team References Durcan J A King G E Duller G A T 2015 DRAC Dose Rate and Age Calculator for trapped charge dating Quaternary Geochronology 28 54 61 doi 10 1016 j quageo 2015 03 012 Examples 1 Method using the DRAC spreadsheet file lt PATH TO DRAC_Input_and_Output_Template xlsx tt send the actual IO template spreadsheet to DRAC Not run use_DRAC file file End Not run 2 Method using an R template object Create a template input lt template_DRAC Fill the template with values input Project ID lt DRAC Example input Sample ID lt Quartz input Conversion factors lt AdamiecAitken1998 input ExternalU ppm lt 3 4 input errExternal U ppm lt 0 51 input External Th ppm lt 14 47 input errExternal Th ppm lt 1 69 input External K lt 1 2 input errExternal K lt 0 14 input Calculate external Rb from K conc lt N input Calculate internal Rb from K conc lt N input Scale gammadoserate at shallow depths lt N input Grain size min microns lt 90 input Grain size max microns lt 125 input Water cont
75. MAT CRP2A Universite Bordeaux Montaigne France See Also RLum RLum Data plot_RLum read_SPE2R Examples showClass RLum Data Image create empty RLum Data Image object set_RLum class RLum Data Image RLum Data Spectrum class Class RLum Data Spectrum Description Class for representing luminescence spectra data TL OSL RF Usage S4 method for signature RLum Data Spectrum show object S4 method for signature RLum Data Spectrum set_RLum class originator recordType Spectrum curveType NA_character_ data matrix info listQ S4 method for signature RLum Data Spectrum RLum Data Spectrum class 193 get_RLum object info object S4 method for signature RLum Data Spectrum names_RLum object Arguments object show_RLum get_RLum names_RLum an object of class RLum Data Spectrum class set_RLum character automatic name of the RLum class to create originator character automatic contains the name of the calling function the function that produces this object can be set manually recordType set_RLum character record type e g OSL curveType set_RLum character curve type e g predefined or measured data set_RLum matrix raw curve data If data is of type RLum Data Spectrum this can be used to re construct the object info set_RLum list info elements info object get_RLum character optional the name of the info object to be c
76. Nuclear and Particle Physics 9 1577 1595 Crookes J N Rastin B C 1972 An investigation of the absolute intensity of muons at sea level Nuclear Physics B 39 493 508 Gruen R 2009 The AGE program for the calculation of luminescence age estimates 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 42 calc_CosmicDoseRate 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 See Also BaseDataSet CosmicDoseRate Examples 1 calculate cosmic dose rate one absorber calc_CosmicDoseRate depth 2 78 density 1 7 latitude 38 06451 longitude 1 49646 altitude 364 error 10 2a calculate cosmic dose rate two absorber calc_CosmicDoseRate depth c 5 0 2 78 density c 2 65 1 7 latitude 38 06451 longitude 1 49646 altitude 364 error 10 2b calculate cosmic dose rate two absorber and correct for geomagnetic field changes calc_CosmicDoseRate depth c 5 0 2 78 density c 2 65 1 7 latitude 12 04332 longitude 4 43243 altitude 364 corr f
77. OSL curve into a pLM OSL curve CW2pLM 77 Description Transforms a conventionally measured continuous wave CW curve into a pseudo linearly modu lated 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 2x tx 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 list list data frame generic R data structure list list RLum Data Curve package RLum object Function version 0 4 1 2015 11 29 17 27 48 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 78 CW2pLMi References Bulur E 2000 A simple transformation for converting CW OSL curves to LM OSL curves Ra diation Measurements 32 141 145 Further Readi
78. Package Luminescence December 7 2015 Type Package Title Comprehensive Luminescence Dating Data Analysis Version 0 5 1 Date 2015 12 07 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 analysis This includes amongst others data import export application of age models curve deconvolution 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 2 2 utils LinkingTo Rcpp RecppArmadillo gt 0 6 200 2 0 Imports bbmle gt 1 0 17 data table gt 1 9 6 digest gt 0 6 8 httr gt 1 0 0 matrixStats gt 0 15 0 methods Repp gt 0 12 2 minpack Im gt 1 2 0 raster gt 2 4 18 readxl gt 0 1 0 shape gt 1 4 2 parallel XML gt 3 98 1 3 zoo gt 1 7 12 Suggests rel gt 0 95 1201 URL http CRAN R project org package Luminescence Collate Analyse_SAR OSLdata R CW2pHMi R CW2pLM R CW2pLMi R CW2pPMi R Luminescence package R internals_RLum R replicate_RLum R RLum class R names_RLum R 1 R topics documen
79. RLum 28 74 77 80 83 109 110 113 115 221 122 152 175 183 180 187 190 192 194 197 201 203 RLum class 183 RLum Analysis 7 11 12 14 15 17 18 22 24 28 91 93 95 97 109 111 114 115 123 142 143 152 153 167 168 172 174 180 182 184 186 190 201 204 RLum Analysis class 184 RLum Data 184 186 190 192 194 RLum Data class 187 RLum Data Curve 64 66 71 73 75 77 80 82 84 98 100 101 109 111 114 117 123 143 152 153 155 168 174 182 186 188 201 204 RLum Data Curve class 188 RLum Data Image 92 109 111 114 115 123 152 157 138 170 191 201 204 RLum Data Image class 190 RLum Data Spectrum 25 27 93 94 109 111 114 115 123 152 159 161 169 170 187 193 201 204 RLum Data Spectrum class 192 RLum Results 10 11 13 14 17 18 23 24 29 33 37 40 44 45 47 49 54 56 58 60 65 68 70 72 96 97 99 100 109 111 113 114 117 118 123 130 136 137 139 145 152 162 164 195 196 198 201 204 207 RLum Results class 195 rollmean 42 row names RLum Data Spectrum methods_RLum 118 rowMeans 1 16 rowSums 1 6 rug 165 sd 135 Second2Gray 67 68 197 set seed 43 44 set_Risoe BINfileData 200 set_Risoe BINfileData data frame list method Risoe BINfileData class 176 set_RLum 182 183 201 set_RLum RLum Analysis method RLum Analysis class 184 INDEX set_RLum RLum Data Curve method RLum Data Cur
80. The De is calculated by iteration Note In the context of luminescence dating this function has no physical meaning Therefore no plot_GrowthCurve 135 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 02 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 veights 1 error sum 1 error Error estimation using Monte Carlo simulation Error estimation is done using a Monte Carlo MC simulation approach A set of Lx Tx values is constructed by randomly drawing curve data from samled from normal distributions The normal distribution is defined by the input values mean value sd value error Then a growth curve fit is attempted for each dataset resulting in a new distribution of single De values The sd of this distribution is becomes then the error of the De With increasing iterations the error value becomes more stable Note It may take some calculation time with increasing MC runs especially for the composed functions EXP LIN and EXP EXP Each error estimation is done with the function of the chosen fitting method Subtitle information To avoid plotting the subtitle information provide an empty user mtext mtext To plot any other subtitle
81. ULL duplicated rm FALSE fastForward FALSE show record number FALSE txtProgressBar TRUE forced VersionNumber NULL Arguments file character or list required path and file name of the BIN BINX file If input is a list it should comprise only characters representing each valid path and BIN BINX file names Alternatively the input character can be just a directory path in this case the the function tries to detect and import all BIN BINX files found in the directory show raw values logical with default shows raw values from BIN file for LTYPE DTYPE and LIGHTSOURCE without translation in characters position numeric optional imports only the selected position Note the import perfor mance will not benefit by any selection made here 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 duplicated rm logical with default remove duplicated entries if TRUE This may happen due to an erroneous produced BIN BINX file This option compares only pre deccessor and successor fastForward logical with default if TRUE for a more efficient data processing only a list of RLum Analysis objects is returned instead of a Risoe BINfileData class object show record number logical with default shows record number of the imported record for debug ging usage only txtProgressBar logical with defa
82. 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 arm ymazx t b 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 background subtraction y axait bea cexa dxxte fit LMCurve 103 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 plot TRUE with the pseu
83. a matrix will be returned e length_RLum Returns the length of the curve object which is the maximum of the value time temperature of the curve corresponding to the stimulation length e names_RLum Returns the names info elements coming along with this curve object 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 pre defined data Object of class matrix containing curve x and y data data can also be of type RLum Data Curve to change object values without deconstructing the object For example set_RLum class RLum Data Curve dat would just change the recordType Missing arguements the value is taken from the input object in data which is already an RLum Data Curve object in this example info Object of class list containing further meta information objects Create objects from this Class Objects can be created by calls of the form set_RLum class RLum Data Curve Class version 0 3 0 190 RLum Data Image class 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 Objects from the class RLum Data Curve are produced by other functions partyl within RLum Analysis objects namely Risoe BINfileData2RLum Data Curve Risoe BINfileData2RLum Analysis
84. a METADATAL POSITION 1 ID curve HIGH lt CWOSL SAR Data METADATALCWOSL SAR Data METADATAL ID J curve ID 1 HIGH curve NPOINTS lt CWOSL SAR Data METADATALCWOSL SAR Data METADATAL ID curve ID 1 76 CW2pLM NPOINTS 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 8 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 01 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 21 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
85. ackground varies as e g as observed for the early light substraction method 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 Vi k Yo Yi k b non poisson rselus y Yo Yi k 02 1 1 k Yo Y k Please note that when using the early background subtraction method in combination with the non poisson distribution argument the corresponding Lx Tx error may considerably increase due to a high sigmab value Please check whether this is valid for your data set and if necessary consider to provide an own sigmab value using the corresponding argument sigmab Value Returns an S4 object of type RLum Results Slot data contains a list with the following structure LxTx table data frame LnLx LnLx BG TnTx TnTx BG Net_LnLx Net_LnLx Error Net_TnTx Error LxTx LxTx Error calc parameters list sigmab LnTx sigmab TnTx k call original function call 66 calc_OSLLxTxRat
86. al number of trapped electrons for the used equation cf Boetter Jensen et al 2003 fit CWCurve 99 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 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 optional the fitted CW OSL curves are returned as plot table optional an output table csv with parameters of the fitted components is provided if the output path is set list list RLum Results beside the plot and table output options an RLum Results object is returned fit an nls object fit for which generic R functions are provided e g sum mary confint profile For more details see nls output table a data frame contain
87. alc_gSGC data data frame LnTn 2 361 LnTn error 0 087 Lr1Tr1 2 744 Lr1iTr1 error 0 091 Dr1 34 4 get_RLum results data object De calc_HomogeneityTest Apply a simple homogeneity test after Galbraith 2003 Description A simple homogeneity test for De estimates Usage calc_HomogeneityTest data log TRUE calc_Homogeneity Test 53 Arguments data RLum Results or data frame required for data frame two columns with De data 11 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 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 Function version 0 2 2015 11 29 17 27 48 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 obtained using OSL Ancient TL 21 75 77 See Also pchisq Examples load example data data ExampleData DeValues envir environment apply the homogeneity test calc_HomogeneityTest ExampleData DeValu
88. alled Value set_RLum An object from the class RLum Data Spectrum get_RLum 1 A matrix with the spectrum values or 2 only the info object if info object was set names_RLum The names of the info objects Methods by generic show Show structure of RLum Data Spectrum object set_RLum Construction method for RLum Data Spectrum object The slot info is optional and predefined as empty list by default get_RLum 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 names_RLum Returns the names info elements coming along with this curve object 194 RLum Data Spectrum class 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 pre defined data Object of class matrix containing spectrum count values Row labels indicate wave length pixel values column labels are temperature or time values info Object of class list containing further meta information objects Objects from the Class Objects can be created by calls of the form set_RLum RLum Data Spectrum Class version 0 3 0 Note The class should only contain data for a single spectra data set For additional elements the slot info can be used Objects from this
89. alue used for the standardisation mtext character additional text below the plot title summary character optional add statistic measures of centrality and dispersion to the summary pos plot Can be one or more of several keywords See details for available key words 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 legend character vector optional legend content to be added to the plot legend pos numeric or character with default optional position coordinates or keyword e g topright for the legend to be plotted stats character additional labels of statistically important values in the plot One or more out of the following min max median rug logical Option to add a rug to the z scale to indicate the location of individual values plot ratio 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 146 plot_RadialPlot bar col character or numeric with default colour of the bar showing the 2 sigma range around the cen
90. alues Other values at the beginning of the transformed curve are set to 0 6 Transform values using pLM t t P x CW t 7 Combine all values and truncate all values for t gt max t CW2pPMi 83 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 list list 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 list list 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 11 29 17 27 48 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
91. ample data for that package Location origin of sample BT753 is given here Fuchs M Kreutzer S Rousseau D D Antoine P Hatte C Lagroix F Moine O Gauthier C Svoboda J Lisa L 2013 The loess sequence of Dolni Vestonice Czech Republic A new OSL based chronology of the Last Climatic Cycle Boreas 42 664 677 See Also read_XSYG2R RLum Analysis RLum Data Spectrum plot_RLum plot_RLum Analysis plot_RLum Data Spectrum Examples show data data ExampleData XSYG envir environment gt SS SSS SS SS SS SSS SS SS SS SSS SS SS SSS SS SS 1 OSL SARMeasurement OSL SARMeasurement show Sequence Object OSL SARMeasurement Sequence Object grep OSL curves and plot the first curve OSLcurve lt get_RLum OSL SARMeasurement Sequence Object recordType 0SL 1 plot_RLum OSLcurve HH _ _ _ _ IO 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 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 extract_IrradiationTimes 95 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
92. ampleData DeValues layout journal get_Quote Function to return essential quotes Description This function returns one of the collected essential quotes in the growing library If called without any parameters a random quote is returned get_rightAnswer Usage get_Quote ID author separated FALSE Arguments ID character qoute ID to be returned author character all quotes by specified author separated logical return result in separated form Value Returns a character with quote and respective false author Function version 0 1 1 2015 11 29 17 27 48 Author s Michael Dietze GFZ Potsdam Germany R Luminescence Package Team Examples ask for an arbitrary qoute get_Quote 107 get_rightAnswer Function to get the right answer Description This function returns just the right answer Usage get_rightAnswer Arguments you can pass an infinite number of further arguments Value Returns the right answer 108 get_Risoe BINfileData Function version 0 1 0 2015 11 29 17 27 48 Author s inspired by R G R Luminescence Package Team Examples you really want to know get_rightAnswer get_Risoe BINfileData General accessor function for RLum S4 class objects Description Function calls object specific get functions for RisoeBINfileData S4 class objects Usage get_Risoe BINfileData object Arguments object Risoe BINfileData required
93. 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 write_R2BIN or if 1t appears it stops with a floating point error Negative values for TIMESINCELAS STEP Yes this is possible and no bug as in the XSYG file multiple curves are stored for one step Example A TL step may comprise three curves a counts vs time b measured temperature vs time and c predefined temperature vs time Three curves but they are all belonging to one TL measurement step but with regard to the time stamps this could produce negative values as the important function read_XSYG2R do not change the order of entries for one step towards a correct time order Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team fit CWCurve 97 References Duller G 2007 Analyst See Also RLum Analysis RLum Results Risoe BINfileData read_XSYG2R read_BIN2R write_R2BIN Examples 1 example for your own data set files and run function file XSYG lt file choose file BINX lt file choose output lt extract_IrradiationTimes file XSYG file XSYG file BINX file BINX get_RLum output export results additionally to a CSV file in
94. ass oa a 187 RLum Data Curve class a 188 RLum Data Image class ee 190 RLum Data Spectrum class ee 192 RLum Results class ee 195 Second2 Gray 2 445 x deep e ee a O e As ds 197 set_Risoe BlNfileData eces edu p risake nuny 200 Set RLON e eea ea is ia Bk ts bas 201 STEVE tani s wed wits aw a AA e ER eee 202 structure RLum 2 a 203 template_DRAC 2 ee 204 tne WD ata aese s u ke oom ee ee a eee Ge ee Bs ee Re ee ees 205 use_DRAC 2 a e 207 Wilte R2BIN voi 64 8 Sd ee he Bw He eS o eS 209 212 Luminescence package Comprehensive Luminescence Dating Data Analysis Description A collection of various R functions for the purpose of Luminescence dating data analysis This includes amongst others data import export application of age models curve deconvolution sequence analysis and plotting of equivalent dose distributions Luminescence package 5 Details Package Luminescence Type Package Version 0 5 1 Date 2015 12 07 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 Helmholtz Zentrum Dresden Rossendorf Helmholtz Institute Freiberg for Resource Technology Freibe Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France France Christoph Schmidt University of Bayreuth Germany Rachel K Smed
95. ault enables TRUE or disables FALSE the progression bar during MC runs plot logical with default plot output TRUE or FALSE further arguments that will be passed to the plot output Currently supported ar guments are main xlab ylab xlim ylim log legend pos passes argument to x y in legend 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 1 Measuring IR RF intensity of the natural dose for a few seconds RF at 2 Bleach the samples under solar conditions for at least 30 min without changing the geometry 3 Waiting for at least one hour 8 analyse _IRSAR RF 4 Regeneration of the IR RF signal to at least the natural level measuring RFreg 5 Fitting data with a stretched exponential function 6 Calculate the the palaeodose De using the parameters from the fitting Actually two methods are supported to obtain the De method FIT and method SLIDE method FIT The principle is described above and follows the original suggestions by Erfurt et al 2003 For the fitting the mean count value of the RF_nat curve is used Function used for the fitting according to Erfurt et al 2003 D do Ad 1 exp A D with D the dose dependent IR RF flux o the inital IR RF flux Ad the dose dependent change of the
96. ault is detailed r default is 10 Note Further parameters can be adjusted via par For example to set the background transparent and reduce the thickness of the lines use par bg NA lwd 0 7 previous the function call plot type single Per frame a single curve is returned Frames are time or temperature steps plot type multiple lines All frames plotted in one frame plot type transect plot_RLum Data Spectrum 161 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 col border box 1wd bty Value Returns a plot Function version 0 4 2 2015 11 29 17 27 48 Note Not all additional arguments will be passed similarly Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References Blasse G Grabmaier B C 1994 Luminescent Materials Springer See Also RLum Data Spectrum plot plot_RLum persp persp3d contour Examples load example data data ExampleData XSYG envir environment
97. ax integer required channel number for the upper signal integral bound e g signal integral max 200 Details Value Returns an S4 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 72 calc_TLLxTxRatio Function version 0 3 0 2015 11 29 17 27 48 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 temp record id 1 Lx data background lt get_RLum temp record id 2 Tx data signal lt get_RLum temp record id 3 Tx data background lt get_RLum 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 output CW2pHMi 73 CW2pHMi Transform a CW OSL curve into a pHM OSL curve via interpolation under hyperbolic modulation conditions Descriptio
98. calc_AliquotSize 31 H non linear part A lt 36 deg y 3 1076 5 1075 x 0 0031 x x 4 398 H linear part 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 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 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
99. cated function validates your data seriously Value Validates your data structure_RLum 203 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 structure_RLum General structure function for RLum S4 class objects Description Function calls object specific get functions for RLum S4 class objects Usage structure_RLum object Arguments object RLum required S4 object of class RLum Details The function provides a generalised access point for specific RLum objects Depending on the input object the corresponding structure function will be selected Allowed arguments can be found in the documentations of the corresponding RLum class Value Returns a data frame with structure of the object Function version 0 1 0 2015 11 29 17 27 48 204 template DRAC Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team See Also RLum Data Curve RLum Data Image RLum Data Spectrum RLum Analysis RLum Results template_DRAC Create a DRAC input data template v1 1 Description This function returns a DRAC input template v1 1 to be used in conjunction with the use_DRACQ function Usage template_DRAC nrow 1 notification TRUE Arguments nrow integer with default specifies the number of rows of the template i
100. class objects Description Function calls object specific plot functions for RLum S4 class objects Usage plot_RLum object 152 plot_RLum Arguments object RLum required S4 object of class RLum Optional a list containing objects of class RLum can be provided In this case the function tries to plot every object in this list according to 1ts RLum class further arguments and graphical parameters that will be passed to the specific plot functions The only argument that is supported directly is main setting the plot title In contrast to the normal behaviour main can be here provided as list and the arguments in the list will dispatched to the plots if the object is of type list as well Details The function provides a generalised access point for plotting 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 4 2 2015 12 05 15 52 49 Note The provided plot output depends on the input object Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team Refer
101. ctions 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 9 2015 12 05 15 52 49 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 plot_RLum Data Curve 155 Examples load data data ExampleData BINfileData envir environment convert values for position 1 temp lt Risoe BINfileData2RLum Analysis CWOSL SAR Data pos 1 plot all values plot_RLum Analysis temp plot combine TL curves in one plot temp sel lt get_RLum temp recordType TL drop FALSE plot_RLum Analysis temp sel combine TRUE norm TRUE main TL combined plot_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 Arguments object RLum Data Curve required S4 object of class RLum Data Curve par local logical with default use local graphical parameters for plotting
102. cyCorrection 26 calc_SourceDoseRate 67 CW2pHMi 73 CW2pLM 76 CW2pLMi 78 CW2pPMi 81 extract_IrradiationTimes 95 merge_Risoe BINfileData 111 Risoe BINfileData2RLum Analysis 180 Risoe BINfileData2RLum Data Curve 181 Second2Gray 197 sTeve 202 tune_Data 205 Topic methods RLum Analysis class 184 RLum Results class 195 Topic models fit_CWCurve 97 fit_LMCurve 101 Topic package Luminescence package 4 Topic plot analyse_pIRIRSequence 12 analyse_SAR CWOSL 15 analyse_SAR TL 22 INDEX Topic utilities get_Risoe BINfileData 108 get_RLum 109 length_RLum 110 merge_RLum 113 merge_RLum Analysis 114 merge_RLum Data Curve 115 names_RLum 122 replicate_RLum 175 set_Risoe BINfileData 200 set_RLum 201 structure_RLum 203 x RLum Data Curve methods_RLum 118 RLum Data Curve methods_RLum 118 RLum Data Curve methods_RLum 118 RLum Data Curve methods_RLum 118 RLum Analysis methods_RLum 118 RLum Data Curve methods_RLum 118 RLum Data Image methods_RLum 118 RLum Data Spectrum methods_RLum 118 RLum Results methods_RLum 118 CL RLum Analysis methods_RLum 118 CC RLum Results methods_RLum 118 RLum Analysis methods_RLum 118 RLum Results methods_RLum 118 mi ps m TA oe LA ps abline 153 analyse_IRSAR RF 6 analyse_pIRIRSequence 12 2 analyse_SAR CWOSL 13 14 15 21 66 195 Analyse_SAR OSLdata 18 19 66
103. d logical indicating wether NA values are removed before plotting from the input data set further arguments and graphical parameters passed to plot plot_DRTResults 131 Details Procedure to test the accuracy of a measurement protocol to reliably determine the dose of a specific sample Here the natural signal is erased and a known laboratory dose administered which is treated as unknown Then the De measurement is carried out and the degree of congruence between administered and recovered dose is a measure of the protocol s accuracy for this sample In the plot the normalised De is shown on the y axis i e obtained De Given Dose Value A plot is returned Function version 0 1 8 2015 11 29 17 27 48 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 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
104. data args list used arguments call call the function call mle covariance matrices of the log likelhoods BIC BIC score llik maximum log likelihood grain probability probabilities of a grain belonging to a component components matrix estimates of the de de error and proportion for each component single comp data frame single componente FFM estimate If a vector for n components is provided e g c 2 8 mle and grain probability are lists containing matrices of the results for each iteration of the model The output should be accessed using the function get_RLum Function version 0 4 2015 11 29 17 27 48 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 sediment mixtures a test of single grain optical dating procedures u
105. ded 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 txtProgressBar logical with default enables or disables txtProgressBar If verbose FALSE also no txtProgressBar is shown verbose logical with default enables or disables terminal feedback Further arguments and graphical parameters to be passed Note Standard 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 QDR and the EXP OR LIN the nlsLM function with the LM Levenberg Marquardt algorithm algorithm is used Note For historical reasons for the Monte Carlo simulations partly the function nls using the port algorithm The solution is found by transforming the function or using uniroot LIN fits a linear function to the data using Im Y MxX N QDR fits a linear function to the data using Im y a bxa cxa EXP try to fit a function of the form y ax 1 exp 1 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 the EXP fit fails a LIN fit is done instead EXP LIN tries to fit an exponential plus linear function of the form y a 1 exp a c b g x
106. dies 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 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 Measurements 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 nls nlsLM 12 analyse_pIRIRSequence
107. do curve based on the pseudo start parameters is provided This may give the opportunity to identify appropriate start parameters visually b If start values are provided the function works like a simple 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 parameters 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 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 Streibig 2008 104 fit LMCurve Value Various types of plots are returned For details see above Furthermore an RLum Results
108. e the number of data sets you want to submit notification logical with default show or hide the notification Value A list Author s Christoph Burow University of Cologne Germany References Durcan J A King G E Duller G A T 2015 DRAC Dose Rate and Age Calculator for trapped charge dating Quaternary Geochronology 28 54 61 doi 10 1016 j quageo 2015 03 012 See Also as data frame list tune_Data 205 Examples create a new DRAC input input input lt template_DRAC show content of the input print input print input Project ID print input 4 1 Example DRAC Quartz example note that you only have to assign new values where they are different to the default values input Project ID lt DRAC Example input Sample ID lt Quartz input Conversion factors lt AdamiecAitken1998 input ExternalU ppm lt 3 4 input errExternal U ppm lt 0 51 input External Th ppm lt 14 47 input errExternal Th ppm lt 1 69 input External K lt 1 2 input errExternal K lt 0 14 input Calculate external Rb from K conc lt N input Calculate internal Rb from K conc lt N input Scale gammadoserate at shallow depths lt N input Grain size min microns lt 90 input Grain size max microns lt 125 input Water content wet weight dry weight dry weight lt 5 input errWater content
109. e 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 absorber 0 0005 absorber which is valid for depths between 150 5000 g cm 2 For shallower depths lt 150 g cm 2 they provided a graph Fig 1 from which the dose rate can be read As a result this function employs the equation of Prescott 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 currently not possible to obtain more precise cosmic dose rate values for near surface samples as there is no equation known to the author of this function at the time of writing Author s Christoph Burow University of Cologne Germany R Luminescence Package Team 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 L32 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
110. e data to illustrate the non normal distribution plot_KDE ExampleData 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 71 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 RLum Data Curve or data frame required TL data x temperature y counts TL signal Lx data background RLum Data Curve or data frame optional TL data x temperature y counts If no data are provided no background subtraction is performed Tx data signal RLum Data Curve or data frame required TL data x temperature y counts TL test signal Tx data background RLum Data Curve or 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 m
111. e g the plot is 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 156 plot_RLum Data Image Function version 0 1 6 2015 12 05 15 52 49 Note Not all arguments of plot will be passed Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team 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 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 plot_RLum Data Image 157 Arguments object RLum Data Image required S4 object of class RLum Data Image par local logical with defau
112. e one or more of several keywords See details for available key words 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 140 plot KDE bw character with default bin width chose a numeric value for manual setting 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 sd or qr polygon The line type 1ty for add
113. e p e e a a e e A a ee 115 merge_RLum Results a E ee 117 methods REUNY i ee kok aas waoe a be oe wae 118 names RLum 0 eee ea ee 122 plot AbanicoPlot je 4 ri ek BO Ae ok AS ee SD al doe a a 123 plot_DRTResults ee 129 plot_GrowthCurve secr seek RA HR A ee Re ee we A 132 Index Luminescence package plot_Histogram oe si e euw eR EEE HED we Eee 136 plot RDE cui hee Gre ae a ee BS ia BLE e 139 plot NRt 2 24 4 244046 OX be Ga Dee eA Ee ede EN DDS EW ee EES 142 plot RadialPlot eey be ee ee ee OS EE RE a 144 plot_Risoe BlNfileData e 149 plot REUN oe eead ad bis bb baw Hae PGA ee eden 151 plot_RLum Analysis aa e 153 plot_RLum Data Curve a y a ee 155 plot_RLum Data Image e 156 plot_RLum Data Spectrum ooa ee 158 plot_RLum Results e 162 plot ViolinPl t 200 a A Rec a DE a da 164 read BINBR oc ii RAR SASSER EEE A o ee S 165 read DaybreakoR siria a A ee ek Ree aes 168 read SPEQR 2 45 4 Stee a OA EOE a we EOS ROE S OR EES OS 169 tead XSYGQRo p eiea Nese es ek hho be oe bee Se EEE SS 171 replicate RLUM lt s 6 4 4 6 ce oR aa eR e Sh we SOR RE Ae et ee hho 175 Risoe BINfileData class nooo a a 176 Risoe BINfileData2RLum Analysis o a 180 Risoe BINfileData2RLum Data Curve o ooa a 181 REumeclass o ee e ii ie Re AS a nd F 183 RLum Ana lysis C lasS 2 0 peo RS pee di a ae a 184 RLum Data cl
114. e 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 112 merge_Risoe BINfileData number of the next data set For example The highest position number is 48 then this number will be added to all other position numbers of the next data set e g 1 48 49 However there might be cases where an additional addend summand is needed before the next position starts Example Position number set A 1 3 5 7 Position number set B 1 3 5 7 With no additional summand the new position numbers would be 1 3 5 7 8 9 10 11 That might be unwanted Using the argument position number append gap 1 it will become 1 3 5 7 9 11 13 15 17 Value Returns a file or a Risoe BINfileData object Function version 0 2 4 2015 11 29 17 27 48 Note The validity of the output objects is not further checked Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References Duller G 2007 Analyst See Also Risoe BINfileData read_BIN2R write_R2BIN Examples merge two objects data ExampleData BINfileData envir environment object1 lt CWOSL SAR Data ob
115. e stimulation rate 1 P To avoid the production of too many artificial data at the raising tail of the determined pLM curves it is recommended to use the automatic estimation routine for P i e provide no own value for P 80 CW2pLMi Value The function returns the same data type as the input data type with the transformed curve values list list 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 11 29 17 27 48 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 S
116. eData2RLum Analysis Risoe BINfileData RLum RLum Data class Examples showClass RLum Analysis set empty object set_RLum class RLum Analysis use example data load data data ExampleData RLum Analysis envir environment show curves in object get_RLum IRSAR RF Data show only the first object but by keeping the object get_RLum IRSAR RF Data record id 1 drop FALSE 187 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 Class version 0 2 1 Note Just a virtual class Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France See Also RLum RLum Data Curve RLum Data Spectrum Examples showClass RLum Data 188 RLum Data Curve class RLum Data Curve class Class RLum Data Curve Description Class for representing luminescence curve data Usage S4 method for signature RLum Data Curve show object S4 method for signature RLum Data Curve set_RLum class originator recordType NA_character_ curveType NA_character_ data matrix 0 ncol 2 info list S4 method for signature RLum Data Curve get_RLum object info object S4 method for signature RLum Data Curve length_RLum object S4 method for signature RLum Data Curve names_RLum object
117. ecified via init values 60 calc_MinDose 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 pO 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 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 opg vn 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 available when bootstrap TRUE and spawns n R instances
118. ee Also CW2pLM CW2pHMi CW2pPMi fit_LMCurve RLum Data Curve Examples H 1 CW2pPMi 81 load CW OSL curve data data ExampleData CW_OSL_Curve envir environment transform values 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 8 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 8 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 Description Transforms a conventionally measured continuous wave CW OSL curve into a pseudo parabolic modulated
119. elf Merging is always applied on the 2nd colum of the data matrix of the object Supported merge operations are RLum Data Curve 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 ngn The row sums of the last objects are mutliplied with the first object ye Values of the first object are divided by row sums of the last objects Value Return an RLum Data Curve object S3 generic support This function fully operational via S3 generics merge Function version 0 1 1 2015 12 05 15 52 49 merge_RLum Results 117 Note The information from the slot record Type 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 Examples load example data data ExampleData XSYG envir environment grep first and 3d TL curves TL curves lt get_RLum 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
120. ences 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 plot_RLum Analysis 153 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 subset nrows ncols abline combine FALSE curve transformation plot single FALSE Arguments object RLum Analysis required S4 object of class RLum Analysis subset named list optional subsets elements for plotting The arguments in the named list will be directly passed to the function get_RLum e g subset list curveType measu nrows integer optional sets number of rows for plot output if nothing is set the function tries to find a value ncols integer optional sets number of columns for plot output if nothing is set the function tries to find a value 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
121. ences Duller G 2007 Analyst See Also read_BIN2R Risoe BINfileData writeBin write_R2BIN 211 Examples uncomment for usage data ExampleData BINfileData envir environment write_R2BIN CWOSL SAR Data file your path output bin Index Topic IO extract_IrradiationTimes 95 merge_Risoe BINfileData 111 read_BIN2R 165 read_Daybreak2R 168 read_SPE2R 169 read_XSYG2R 171 write_R2BIN 209 Topic aplot plot_RLum Analysis 153 plot_RLum Data Curve 155 plot_RLum Data Image 156 plot_RLum Data Spectrum 158 plot_RLum Results 162 Topic Classes Risoe BINfileData class 176 RLum class 183 RLum Analysis class 184 RLum Data class 187 RLum Data Curve class 188 RLum Data Image class 190 RLum Data Spectrum class 192 RLum Results class 195 Topic datagen analyse_IRSAR RF 6 analyse_pIRIRSequence 12 analyse_SAR CWOSL 15 Analyse_SAR OSLdata 19 analyse_SAR TL 22 calc_FadingCorr 43 calc_gSGC 51 calc_OSLLxTxRatio 64 calc_TLLxTxRatio 71 Topic datasets BaseDataSet CosmicDoseRate 29 ExampleData BINfileData 85 ExampleData CW_OSL_Curve 86 ExampleData DeValues 87 ExampleData RLum Analysis 91 212 ExampleData RLum Data Image 92 ExampleData XSYG 93 Topic dplot Analyse_SAR OSLdata 19 calc_FuchsLang2001 49 fit_CWCurve 97 fit_LMCurve 101 plot_DRTResults 129 plot_Risoe BINfileData 149 plot_RLum 151 Topic manip apply_CosmicRayRemoval 24 apply_Efficien
122. ences Aberystwyth University United Kingdom Based on an excel spreadsheet and accompanying macro written by Kristina Thomsen R Luminescence Package Team References Smedley R K 2015 A new R function for the Internal External Uncertainty IEU model Ancient TL 33 16 21 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 Examples load data 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 56 calc_MaxDose Arguments data RLum Results or data frame required for data frame two columns with De data 11 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 bleac
123. ent wet weight dry weight dry weight lt 5 write_R2BIN 209 input errWater content lt 2 input Depth m lt 2 2 input errDepth m lt 0 22 input Overburden density g cm 3 lt 1 8 input errOverburden density g cm 3 lt 0 1 input Latitude decimal degrees lt 30 0000 input Longitude decimal degrees lt 70 0000 input Altitude m lt 150 input De Gy lt 20 input errDe Gy lt 0 2 use DRAC Not run output lt use_DRAC input End Not run write_R2BIN Export Risoe BINfileData into Risoe BIN file Description Exports a Risoe BINfileData object in a bin or binx file that can be opened by the Analyst software or other Risoe software Usage write_R2BIN object file version compatibility mode FALSE txtProgressBar TRUE Arguments object Risoe BINfileData required input object to be stored in a bin file file character required file name and path of the output file WIN write_R2BIN object C Desktop test bin MAC LINUX write_R2BIN User test Desktop test bin version character optional version number for the output file If no value is 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 compatibility mode logical with default this option recalculates the position values if necessary and set the max
124. equired input data for plotting Alterna tively a data frame or a matrix can be provided but only the first column will be considered by the function boxplot logical with default enable or disable boxplot rug logical with default enable or disable rug summary character optional add statistic measures of centrality and dispersion to the plot Can be one or more of several keywords See details for available key words summary pos numeric or character with default optional position keywords cf legend for the statistical summary Alternatively the keyword sub may be specified to place the summary below the plot header However this latter option in only possible if mtext is not used na rm logical with default exclude NA values from the data set prior to any further Operations further arguments and graphical parameters passed to plot default density and boxplot See details for further information Details The function is passing several arguments to the function plot density boxplot Supported arguments are xlim main xlab ylab col violin col boxplot mtext cex mtext Valid summary keywords n mean median sd abs sd rel se abs se rel skewness kurtosis read_BIN2R 165 Function version 0 1 0 2015 12 05 15 52 49 Note Although the code for this function was developed independently and just the idea for the plot was based on t
125. erences 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 Curve 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 116 Arguments object merge method method info Details merge_RLum Data Curve list of RLum Data Curve required list of S4 objects of class RLum Curve 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 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 This function simply allowing to merge RLum Data Curve objects without touching the objects it s
126. ermoluminescence 1 OSL Optically stimulated luminescence 2 IRSE Infrared stimulated luminescence 3 M IR Infrared monochromator scan 4 M VIS Visible monochromator scan 5 TOL Thermo optical luminescence 6 TRPOSL Time Resolved Pulsed OSL Risoe BINfileData class 179 7 RIR Ramped IRSL 8 RBR Ramped Blue LEDs 9 USER User defined 0 POSL Pulsed OSL 1 SGOSL Single Grain OSL 2 RL Radio Luminescence 3 XRF X ray Fluorescence DTYPE values Natural N dose Bleach Bleach dose Natural Bleach N dose Bleach Dose Background agure UAUA UNEO LIGHTSOURCE values Non Lamp IR diodes IR Laser Calibration LED Blue Diodes White lite Green laser single grain IR laser single grain agun e NYA NN YuynxR CO information on the BIN BINX file format are kindly provided by Risoe DTU Nutech Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References Risoe DTU 2013 The Sequence Editor User Manual Feb 2013 and Risoe DTU 2015 The Sequence Editor User Manual March 2015 http www nutech dtu dk See Also plot_Risoe BINfileData read_BIN2R write_R2BIN merge_Risoe BINfileData Risoe BINfileData2RLum Analysi Risoe BINfileData2RLum Data Curve 180 Risoe BINfileData2RLum Analysis Examples showClass Risoe BINfileData Risoe BINfileData2RLum Analysis Convert Risoe BINfileData objec
127. ernally the function constructs as list of the XSYG files found in the directory Please note no recursive detection is supported as this may lead to endless loops Value Using the option import FALSE A list consisting of two elements is shown 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 5 4 2015 12 06 23 16 02 174 read_XSYG2R 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 read_XSYG2R FILE
128. es Second2Gray 199 Function version 0 6 0 2015 11 29 17 27 48 Note If no or a wrong error propagation method is given the execution of the function is stopped Fur thermore if a data frame is provided for the dose rate values is has to be of the same length as the data frame provided with the argument data Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Michael Dietze GFZ Potsdam Germany Margret C Fuchs HZDR Helmholtz Institute Freiberg for Resource Technology Germany R Luminescence Package Team References Aitken M J 1985 Thermoluminescence dating Academic Press See Also calc_SourceDoseRate Examples A for known source dose rate at date of measurement load De data from the example data help file data ExampleData DeValues envir environment convert De s to De Gy Second2Gray ExampleData DeValues BT998 c 0 0438 0 0019 B for source dose rate calibration data calculate source dose rate first dose rate lt calc_SourceDoseRate measurement date 2012 01 27 calib date 2014 12 19 calib dose rate 0 0438 calib error 0 0019 read example data data ExampleData DeValues envir environment apply dose rate to convert De s to De Gy Second2Gray ExampleData DeValues BT998 dose rate 200 set_Risoe BINfileData set_Risoe BINfileData General accessor function for RLum S4 class objects Description
129. es BT998 54 calc_IEU 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 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 containing all calculation tables The output should be accessed using the function get_RLum calc_MaxDose 55 Function version 0 1 0 2015 11 29 17 27 48 Author s Rachel Smedley Geography amp Earth Sci
130. es are succeeding the values are removed and no further interpolation is attempted In every case a warning message is shown Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France CW2pHMi 75 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 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 BINfileData 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 8 CWOSL SAR Dat
131. esults values list x 1 x 2 given dose 2800 preheat c 200 200 200 240 240 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 plot_GrowthCurve 133 Description A dose response curve is produced for luminescence measurements using a regenerative protocol Usage plot_GrowthCurve sample na rm TRUE fit method EXP fit force_through_origin FALSE 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 txtProgressBar TRUE verbose TRUE Arguments sample data frame required data frame with three columns for x Dose y LxTx z LxTx Error y 1 TnTx The column for the test dose response is optional but requires Tn Tx 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 fit fit fit fit fit fit QDR EXP EXP OR LIN EXP LIN or EXP EXP See details force_through_origin logical with default al
132. ethod for class RLum Analysis hist x S3 method for class RLum Results methods_RLum 119 summary object S3 method for class RLum Analysis summary object S3 method for class RLum Data Image summary object S3 method for class RLum Data Curve summary object S3 method for class RLum Results length x S3 method for class RLum Analysis length x S3 method for class RLum Data Curve length x HH S3 method for class Risoe BINfileData length x HH S3 method for class RLum Data Curve dim x S3 method for class RLum Data Spectrum dim x S3 method for class RLum rep x S3 method for class RLum Data Curve names x S3 method for class RLum Data Spectrum names x HH S3 method for class RLum Data Image names x S3 method for class RLum Analysis names x HH S3 method for class RLum Results names x S3 method for class Risoe BINfileData 120 names x S3 method for class RLum Data Spectrum row names x S3 method for class RLum Data Curve as data frame x row names NULL optional FALSE e S3 method for class RLum Data Spectrum as data frame x row names NULL as as as as as optional FALSE S3 method for class list x S3 method for class list x
133. file These information can be further used to update an existing BINX file Usage extract_IrradiationTimes object file BINX recordType c irradiation NA IRSL UVVIS OSL UVVIS TL CUVVIS compatibility mode TRUE txtProgressBar TRUE Arguments object character required or RLum Analysis object path and file name of the XSYG file or an RLum Analysis produced by the function read_XSYG2R Note If an RLum Analysis is used any input for the arguments file BINX and recordType will be ignored file BINX character optional path and file name of an existing BINX file If a file name is provided the file will be updated with the information from the XSYG file in the same folder as the original BINX file Note The XSYG and the BINX file have to be originate from the same mea surement recordType character with default select relevant curves types from the XSYG file or RLum Analysis object As the XSYG file format comprises much more infor mation than usually needed for routine data analysis and allowed in the BINX file format only the relevant curves are selected by using the function get_RLum The argument recordType works as described for this function Note A wrong selection will causes a function error Please change this argu ment only if you have reasons to do so compatibility mode logical with default this option is parsed only if a BIN BINX file is produced and it will reset all positio
134. g enabled 55 ENABLE_FLAGS raw 06 07 PMT signal gating enabled 56 GATE_START integer 06 07 Start gating in time ticks 57 GATE_STOP ingeter 06 07 Stop gating in time ticks Gateend for version 04 here only GATI 58 PTENABLED raw 06 07 Photon time enabled 59 DTENABLED raw 06 07 PMT dead time correction enabled 60 _DEADTIME numeric 06 07 PMT dead time s 61 MAXLPOWER numeric 06 07 Stimulation power to 100 percent mW cm 2 62 XRF_ACQTIME numeric 06 07 XRF acquisition time s 63 XRF_HV numeric 06 07 XRF X ray high voltage V 64 XRF_ CURR integer 06 07 XRF X ray current uA 65 XRF_DEADTIMEF numeric 06 07 XRF dead time fraction 66 SEQUENCE character 03 04 Sequence name 67 DETECTOR_ID raw 07 Detector ID 68 LOWERFILTER_ID integer 07 Lower filter ID in reader 69 UPPERFILTER_ID integer 07 Uper filter ID in reader 70 ENOISEFACTOR numeric 07 Excess noise filter usage unknown 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 write_R2BIN 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 LTYPE values 0 TL Th
135. ge 4 Luminescence package 4 matrix 28 47 99 100 117 142 164 188 189 191 193 194 merge RLum methods_RLum 118 merge_Risoe BINfileData 111 167 179 merge_RLum 113 115 117 190 197 merge_RLum Analysis 114 merge_RLum Data Curve 115 merge_RLum Results 117 INDEX methods_RLum 118 mle2 60 mtext 137 names Risoe BINfileData methods_RLum 118 names RLum Analysis methods_RLum 118 names RLum Data Curve methods_RLum 118 names RLum Data Image methods_RLum 118 names RLum Data Spectrum methods_RLum 118 names RLum Results methods_RLum 118 names_RLum 122 names_RLum RLum Analysis method RLum Analysis class 184 names_RLum RLum Data Curve method RLum Data Curve class 188 names_RLum RLum Data Image method RLum Data Image class 190 names_RLum RLum Data Spectrum method RLum Data Spectrum class 192 names_RLum RLum Results method RLum Results class 195 nlminb 59 nls 8 10 11 97 101 103 105 134 136 n1sLM 10 11 100 105 134 136 numeric 7 9 10 13 16 20 22 31 32 34 36 39 43 45 46 49 54 56 58 60 64 67 98 102 116 123 125 130 134 137 139 145 146 150 164 166 180 185 195 198 206 par 142 pchisq 53 pdf 154 162 persp 160 161 persp3d 159 161 plot 36 49 50 55 98 100 105 130 131 137 138 140 142 143 147 154 158 161 163 165 plot default 23 164 plot Risoe BINfileData methods_RLum 118 plot
136. ge 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 read_XSYG2R 171 temp lt read_SPE2R file temp 2 Import data as RLum Data Image object file lt file choose temp lt read_SPE2R file output object RLum Data Image temp 3 Import data as matrix object file lt file choose temp lt read_SPE2R file output object matrix temp 4 Export raw data to csv if temp is a RLum Data Spectrum object write table x get_RLum temp file your path and filename sep row names FALSE read_XSYG2R Import XSYG files to R Description Imports XSYG files produced by a Freiberg Instrument lexsyg reader into R Usage read_XSYG2R file recalculate TL curves TRUE fastForward FALSE import TRUE pattern xsyg txtProgressBar TRUE Arguments file character or list required path and file name of the XSYG file If input is a list it should comprise only characters representing each valid path and xsyg file names Alternatively the input character can be just a directory path in this case the the function tries to detect and import all xsyg files found in the directory recalculate TL curves logical with default if set to TRUE TL curves are returned as temperature against count
137. gnal curves pos lt seq 1 9 2 curves lt allCurves pos plot a standard NR t plot plot_NRt curves re plot with rolling mean data smoothing plot_NRt curves smooth rmean k 10 re plot with a logarithmic x axis ngn plot_NRt curves log x smooth rmean k 5 144 re plot with custom axes ranges plot_NRt curves smooth rmean k 5 xlim c 0 1 5 ylim c 0 4 1 6 legend pos bottomleft re plot with smoothing spline on log scale plot_NRt curves smooth spline log x legend pos top EXAMPLE 2 you may also use this function to check whether all TD curves follow the same shape making it a TnTx t plot posTD lt seq 2 14 2 curves lt allCurves posTD plot_NRt curves main TnTx t Plot smooth rmean k 20 ylab TD natural TD regenerated xlim c 0 20 legend FALSE EXAMPLE 3 extract data from all positions data lt lapply 1 24 FUN function pos plot_RadialPlot Risoe BINfileData2RLum Analysis CWOSL SAR Data pos pos ltype OSL get individual curve data from each aliquot aliquot lt lapply data get_RLum set graphical parameters par mfrow c 2 2 create NR t plots for all aliquots for i in 1 length aliquot plot_NRt aliquot LiJ pos main paste Aliquot i smooth rmean k 20 xlim c 10 cex 0 6 legend pos bot
138. h curves will be ignored during the analysis RF_nat lim vector with default set minimum and maximum channel range for natural signal fitting and sliding If only one value is provided this will be treated as minimum value and the maximum l mit will be added automatically RF_reg lim vector with default set minimum and maximum channel range for regener ated signal fitting and sliding If only one value is provided this will be treated as minimum value and the maximum limit will be added automatically method character with default setting method applied for the data analysis Possible options are FIT or SLIDE method control list optional parameters to control the method that can be passed to the choosen method These are for 1 method FIT trace maxiter warnOnly minFactor and for 2 method SLIDE correct_onset show_density See details test_parameter list with default set test parameter Supported parameters are curves_ratio residuals_slope only formethod SLIDE curves_bounds dynamic_ratio lambda beta and delta phi All input numeric values NA and NULL s De tails see Details for further information n MC numeric with default set number of Monte Carlo runs for start parameter estimation method FIT or error estimation method SLIDE Note Large values will significantly increase the computation time txtProgressBar logical with def
139. hallow depths lt 167 g cm 2 obtained using the values factor Altitude data frame containing altitude factors for adjusting geomagnetic field change factors Values w values par FJH data frame containing values for parameters F J and H read from Fig 2 in Prescott amp Hutton Dc D0 x F x exp altitude 1000 H Version 0 1 Source The following data were carefully read from figures in mentioned sources and used for fitting pro cedures The derived expressions are used in the function calc_CosmicDoseRate 30 BaseDataSet 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 0 0008 x 0 2535 For depths lt 40 g cm 2 y 6 1078 2 2 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 y 0 026 x x 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 x 1077 z 8 1075 x x 0 0009 x x 0 3988 F linear part A gt 36 5 deg y 0 0001 x x 0 2347 J non linear part 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
140. hat 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 to calculate n x y d are assumed to be normally distributed with means Hz Hy Ha and standard deviations oz Oy Oq For the mean grain size random samples are taken first from N uy oy where py mean grain size and oy 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 calc_AliquotSize 33 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
141. he analyse_IRSAR RF 9 Error estimation For method FIT the asymmetric error range is obtained by using the 2 5 lower and the 97 5 upper quantiles of the RF curve for calculating the De error range For method SLIDE the error is obtained by bootstrapping the residuals of the slided curve to construct new natural curves for a Monte Carlo simulation The error is returned in two ways a the standard deviation of the herewith obtained De from the MC runs and b the confidence interval using the 2 5 lower and the 97 5 upper quantiles The results of the MC runs are returned with the function output Test parameters The argument test_parameter allows to pass some thresholds for several test parameters which will be evaluated during the function run If a threshold is set and it will be exceeded the test parameter status will be set to FAILED Intentionally this parameter is not termed rejection criteria as not all test parameters are evaluated for both methods and some parameters are calculated by not evaluated by default Common for all parameters are the allowed argument options NA and NULL If the parameter is set to NA the value is calculated but the result will not be evaluated means it has no effect on the status OK or FAILED of the parameter Setting the parameter to NULL disables the parameter entirely and the parameter will be also removed from the function output This might be useful in case
142. he ggplot2 package plot type volcano it should be mentioned that beyond this two other R packages exist providing a possibility to produces this kind of plot namely vioplot and violinmplot see References for details Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References Daniel Adler 2005 vioplot A violin plot is a combination of a box plot and a kernel density plot R package version 0 2 http CRAN R project org package violplot Hintze J L Nelson R D 1998 A Box Plot Density Trace Synergism The American Statistician 52 181 184 Raphael W Majeed 2012 violinmplot Combination of violin plot with mean and standard devi ation R package version 0 2 1 http CRAN R project org package violinmplot Wickham H 2009 ggplot2 elegant graphics for data analysis Springer New York See Also density plot boxplot rug calc_Statistics 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_ViolinPlot data ExampleData DeValues read_BIN2R Import Risoe BIN file into R Description Import a bin or a binx file produced by a Risoe DA15 and DA20 TL OSL reader into R 166 read_BIN2R Usage read_BIN2R file show raw values FALSE position NULL n records N
143. hed 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 logical with default apply the recycled bootstrap approach of Cunningham amp Wallinga 2012 init values 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 pQ plot logical with default plot output TRUE FALSE further arguments for bootstrapping bs M bs N bs h sigmab sd See details for their usage Details 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 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 maximum dose estimate in Gy Further docume
144. http dx doi org 10 1016 j quageo 2015 09 003 Fuchs M C Kreutzer S Burow C Dietze M Fischer M Schmidt C Fuchs M 2015 Data processing in luminescence dating analysis An exemplary workflow using the R package Lumi nescence Quaternary International 362 8 13 http dx doi org 10 1016 j quaint 2014 06 034 Kreutzer S Schmidt C Fuchs M C Dietze M Fischer M Fuchs M 2012 Introducing an R package for luminescence dating analysis Ancient TL 30 1 8 Smedley R K 2015 A new R function for the Internal External Uncertainty IEU model Ancient TL 33 16 21 analyse_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 and beyond Usage analyse_IRSAR RF object sequence structure c NATURAL REGENERATED RF_nat lim RF_reg lim method FIT method control test_parameter n MC 10 txtProgressBar TRUE plot TRUE analyse_IRSAR RF 7 Arguments object RLum Analysis required input object containing data for protocol analysis The function expects to find at least two curves in the RLum Analysis object 1 RF_nat 2 RF_reg 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 suc
145. ico Plot is a combination of the classic Radial Plot plot_RadialPlot and a kernel density estimate plot e g plot_KDE It allows straightforward visualisation of data precision error scatter around a user defined central value and the combined distribution of the values on the actual scale of the measured data e g seconds equivalent dose years The principle of the plot is shown in Galbraith 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 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
146. icoPlot data ExampleData DeValues stats c min max median n now with a brief statistical summary as subheader plot_AbanicoPlot data ExampleData DeValues plot_DRTResults summary c n in 2s now with another statistical summary plot_AbanicoPlot data ExampleData DeValues summary c mean weighted median summary pos topleft now a plot with two 2 sigma bars for one data set plot_AbanicoPlot data ExampleData DeValues bar c 30 100 now the data set is split into sub groups one is manipulated data 1 lt ExampleData DeValues 1 30 data 2 lt ExampleData DeValues 31 62 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 z 0 median col c steelblue4 orange4 bar col c steelblue3 orange3 polygon col c steelblue1 orange1 pch c 2 6 angle c 30 50 summary c n in 2s median create Abanico plot with predefined layout definition plot_AbanicoPlot data ExampleData DeValues layout journal now with predefined layout definition and further modifications plot_AbanicoPlot data data 3 z 0 median layout journal col c steelblue4 orange4 bar col adjustcol
147. ieldChanges 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 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 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 calc_FadingCorr 43 ttexport results to csv file uncomment for usage write csv results file c users public results_profile csv calc_FadingCorr Apply a fading correction according to Huntley 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 seed txtProgressBar TRUE Arguments g_value vector required g value and error obtained from separate fading measure ments see example tc numeric required time in seconds
148. ing 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 100 object Function version fit CWCurve 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 profile For more details see nls output table a data frame containing the summarised parameters including the error component contribution matrix matrix containing the values for the 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 5 1 2015 11 29 17 27 48 Note Beta version This function has not been properly tested yet and should therefore not be used for publication purposes The pseudo R 2
149. io Function version 0 6 0 2015 11 29 17 27 48 Note The results of this function have been cross checked with the Analyst vers 3 24b Access to the results object via get_RLum Caution If you are using early light subtraction EBG please either provide your own sigmab value or use background count distribution poisson Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team See Also RLum Data Curve Analyse_SAR OSLdata plot_GrowthCurve analyse_SAR CWOSL 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 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 background integral c 85 100 get results object get_RLum results calc_SourceDoseRate 67 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
150. ion c 1 3 5 run vector optional option to limit the plotted curves by run e g run 1 run c 1 3 5 150 set sorter ltype plot_Risoe BINfileData vector optional option to limit the plotted curves by set e g set 1 set c 1 3 5 character with default the plot output can be ordered by POSITION SET or RUN POSITION SET and RUN are options defined in the Risoe Sequence Editor 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 This argument allows transforming continuous wave CW curves to pseudo linear modulated curves For the transformatio
151. ision 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 A statistic summary i e a collection of statistic measures of centrality and dispersion and fur ther measures can be added by specifying one or more of the following keywords n number of samples mean mean De value mean weighted error weighted mean median me dian of the De values sdrel relative standard deviation in percent sdrel weighted error weighted relative standard deviation in percent sdabs absolute standard deviation sdabs weighted error weighted absolute standard deviation serel relative standard error serel weighted error weighted relative standard error seabs absolute standard error seabs weighted error weighted absolute standard error in 2s percent of samples in 2 sigma range kurtosis kurtosis and skewness skewness Value Returns a plot object plot_RadialPlot 147 Function version 0 5 3 2015 11 29 17 27 48 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
152. isualize quartz OSL signal components Radiation Measurements 47 752 758 Examples data ExampleData CW_OSL_Curve envir environment plot ExampleData CW_OSL_Curve ExampleData DeValues Example De data sets for the package Luminescence Description Equivalent dose De values measured for a fine grain quartz sample from a loess section in Rot tewitz Saxony Germany and for a coarse grain quartz sample from a fluvial deposit in the rock shelter of Cueva Anton Murcia Spain Format A list with two elements each containing a two column data frame BT998 De and De error values for a fine grain quartz sample from a loess section in 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 Luminescence Laboratory Bayreuth Lab Code BT998 Location Rottewitz Saxony Germany Material Fine grain quartz measured on aluminum discs on a Risoe TL OSL DA 15 reader 88 ExampleData FittingLM Units Values are given in seconds Dose Rate Dose rate of the beta source at measurement ca 0 0438 Gy s 0 0019 Gy s Measurement Date 2012 01 27 CA1 Lab Cologne Luminescence Laboratory CLL Lab Code C L2941 Location Cueva Anton Murcia Spain Material Coarse grain quartz 200 250 microns measured on single grain discs on a Risoe TL OSL DA 20 reade Units Values are given in Gray Measurement Date 2012
153. itional 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 A Statistic summary i e a collection of statistic measures of centrality and dispersion and fur ther measures can be added by specifying one or more of the following keywords n number of samples mean mean De value mean weighted error weighted mean median me dian of the De values sdrel relative standard deviation in percent sdrel weighted error weighted relative standard deviation in percent sdabs absolute standard deviation sdabs weighted error weighted absolute standard deviation serel relative standard error serel weighted error weighted relative standard error seabs absolute standard error seabs weighted error weighted absolute standard error in 2s percent of samples in 2 sigma range kurtosis kurtosis and skewness skewness Function version 3 5 2015 11 29 17 27 48 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 Kreutze
154. ject2 lt CWOSL SAR Data object new lt merge_Risoe BINfileData c object1 object2 merge_RLum 113 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 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 Empty list elements NULL are automatically removed from the input list object corresponding merge function RLum Results merge_RLum Value Return is the same as input objects as provided in the list Function version 0 1 2 2015 11 29 17 27 48 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 114 merge_RLum Analysis See Also RLum Data Curve RLum Data Image RLum Data Spectrum RLum Analysis RLum Results Examples Example based using data and from the calc_CentralDose function load example data data ExampleData DeValues envir environment apply the central do
155. ley Aberystwyth University United Kingdom Beta Tester Thomas Kolb University of Bayreuth Germany Supervisor Markus Fuchs Justus Liebig University Giessen Germany Support contact lt developers 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 Related package projects http cran r project org package RLumShiny 6 analyse _IRSAR RF http shiny r luminescence de Package maintainer Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne Pessac France lt sebastian kreutzer u bordeaux montaigne fr gt Acknowledgement 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 11 18 Dietze M Kreutzer S Burow C Fuchs M C Fischer M Schmidt C 2016 The abanico plot visualising chronometric data with individual standard errors Quaternary Geochronology 31 12 18
156. line to each curve see smooth spline k integer with default integer width of the rolling window legend logical with default show or hide the plot legend legend pos character with default keyword specifying the position of the legend see legend further parameters passed to plot also see par plot_NRt 143 Details This function accepts the individual curve data in many different formats If data is a list each element of the list must contain a two column data frame or matrix containing the XY data of the curves time and counts Alternatively the elements can be objects of class RLum Data Curve Input values can also be provided as a data frame or matrix where the first column contains the time values and each following column contains the counts of each curve Value Returns a plot and RLum Analysis object Author s Christoph Burow University of Cologne Germany References Steffen D Preusser F Schlunegger F 2009 OSL quartz underestimation due to unstable signal components Quaternary Geochronology 4 353 362 See Also plot Examples load example data data ExampleData BINfileData envir environment EXAMPLE 1 convert Risoe BINfileData object to RLum Analysis object data lt Risoe BINfileData2RLum Analysis object CWOSL SAR Data pos 8 ltype OSL extract all OSL curves allCurves lt get_RLum data keep only the natural and regenerated si
157. low to force the fitted function through the origin For method EXP EXP the function will go to the origin in either case so this option will have no effect weights logical with default option whether the fitting is done with or without weights See details includingRepeatedRegPoints logical with default includes repeated points for fitting TRUE FALSE NumberRegPoints integer optional set number of regeneration points manually By default the number of all regeneration points is used automatically 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 bounds logical with default set lower fit bounds for all fitting 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 out integer with default number of Monte Carlo simulations for error estima tion See details put plot logical with default plot output TRUE FALSE 134 plot_GrowthCurve 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 plotExten
158. lowing 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 Function version 0 1 4 2015 11 29 17 27 48 Note THIS IS A BETA VERSION None TL curves will be removed from the input object without further warning Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team 24 apply_CosmicRayRemoval 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 Measurements 32 57 73 See Also calc_TLLxTxRatio plot_GrowthCurve RLum Analysis RLum Results get_RLum 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 log y fit method EXP OR LIN sequence structure c SIGN
159. lt 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 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 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 158 plot_RLum Data Spectrum Function version 0 1 2015 11 29 17 27
160. lues summary c n in 2s plot_RadialPlot plot_Risoe BINfileData 149 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 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_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 2s summary pos sub legend c Sample 1 Sample 2 plot_Risoe BINfileData Plot single luminescence curves from a BIN file object Description Plots single luminescence curves from an object returned by the read_BIN2R 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 1 posit
161. m 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 apply_EfficiencyCorrection 27 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 required spectral resolution Value Returns same object as input RLum Data Spectrum Function version 0 1 2015 11 29 17 27 48 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 L
162. m pIRIR analysis for this example with quartz OSL data Alternative for PDF output uncomment and complete for usage Not run 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 End Not run 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 NULL mtext outer plot TRUE plot single FALSE Arguments object RLum Analysis required input object containing data for analysis alterna tively a list of RLum Analysis objects can be provided signal integral min integer required lower bound of the signal integral Can be a list of integers if object is of type list If the input is vector e g c 1 2 the 2nd value will be interpreted as the minimum signal integral for the Tx curve 16 analyse_SAR CWOSL signal integral max integer required upper bound of the signal integral Can be a list of integers if object is of type list If the input is vector e g c 1 2 the 2nd value will be interp
163. 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 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 Regression with R In R Gentleman K Hornik G Parmigiani eds Springer p 150 See Also fit_LMCurve plot nls RLum Data Curve RLum Results get_RLum nlsLM fit LMCurve 101 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 mer 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
164. me 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 read_XSYG2R 173 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 during heating not only increase Advanced file import To allow for a more efficient usage of the function instead of single path to a file just a directory can be passed as input In this particular case the function tries to extract all XSYG files found in the directory and import them all Using this option int
165. 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 predict NULL Arguments measurement date character or Date required date of measurement in Y Y Y Y MM DD Ex ceptionally if no value is provided the date will be set to today The argument can be provided as vector calib date character or Date 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 predict integer with default option allowing to predicit the dose rate of the source over time in days set by the provided value Starting date is the value set with measurement date e g calc_SourceDoseRate predict 100 cal culates the source dose rate for the next 100 days Details Calculation of the source dose rate based on the time ela
166. n This function transforms a conventionally measured continuous wave CW OSL curve to a pseudo hyperbolic modulated pHM curve under hyperbolic modulation conditions using the interpolation procedure described by Bos amp Wallinga 2012 Usage CW2pHMi values delta 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 Y t 1 6 x log 1 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 pa
167. n 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 3 320 323 Ritz C amp Streibig J C 2008 Nonlinear Regression with R R Gentleman K Hornik amp G Parmigiani eds Springer p 150 get_Layout 105 See Also fit_CWCurve plot nls nlsLM get_RLum Examples 1 fit LM data without background subtraction data ExampleData FittingLM envir environment fit_LMCurve values values curve n components 3 log x 2 fit LM data with background subtraction and export as JPEG alter file path for your preferred system jpeg file Desktop Fit_Output 03d jpg quality 100 height 3000 width 3000 res 300 data ExampleData FittingLM envir environment fit_LMCurve values values curve values bg values curveBG n components 2 log x plot BG TRUE tHidev 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 homoge
168. n 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 Run Info option within the Sequence Editor or by editing in R Value Returns a plot Function version 0 4 1 2015 11 29 17 27 48 plot_RLum 151 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 read_BIN2R 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 CurveOutput pdf paper a4 height 11 onefile TRUE example load from bin file BINfile lt file choose BINfileData lt read_BIN2R BINfile par mfrow c 4 3 oma c 5 1 0 5 1 plot_Risoe BINfileData CWOSL SAR Data position 1 mtext side 4 BINfile outer TRUE col blue cex 7 dev of f plot_RLum General plot function for RLum S4
169. n 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 170 read_SPE2R RLum Data Image An object of type RLum Data Image is returned Due to performace reasons the import is aborted for files containing more than 100 frames This limitation can be overwritten manually by using the argument frame frange matrix Returns a matrix of the form Rows Channels columns Frames For the transformation the function get_RLum is used meaning that the same results can be obtained by using the function get_RLum on an RLum Data Spectrum or RLum Data Image object Function version 0 1 0 2015 12 06 23 16 02 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 2 Instruments SPE 2 3 0 20File 20Format 20Specification pdf Hall C 2012 readSPE m http www mathworks com matlabcentral fileexchan
170. n values to a max value of 48 cf write_R2BIN txtProgressBar logical with default enables TRUE or disables FALSE the progression bars during import and export 96 extract_IrradiationTimes 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 or and to stored in a new BINX file which can be further used by other software e g Analyst Geoff Duller Typical application example g value estimation from fading measurements using the Analyst or any other self written script Beside the some simple data transformation steps the function applies the functions read_XSYG2R read_BIN2R write_R2BIN for data import and export 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 Note that this will not work if the input object is a file path to an XSYG file In this case the argument input is ignored Function version 0 2 1 2015 12 05 15 52 49 Note The produced output object contains still the irradiation steps to keep the output transparent How ever for the BINX file export this steps
171. nal 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 Analyse_SAR OSLdata 21 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 17 2015 11 29 17 27 48 Note Rejection criteria are calculated but not considered during the analysis to discard values The analysis of IRSL data is not directly supported You may want to consider using the func tions analyse_SAR CWOSL or analyse_pIRIRSequence instead The development of this function will not be continued We recommend to use the function analyse SAR CWOSL or instead Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Margret C Fuchs HZDR 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 p
172. nd 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 18 analyse_SAR CWOSL Formula formula formula that have been used for the growth curve fitting The output should be accessed using the function get_RLum Function version 0 7 1 2015 12 05 15 52 49 Note This function must not be mixed up with the function Analyse_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 do
173. neous 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 1 small empty User specific layout definitions must be provided as a list object of predefined structure see details 106 get_Quote 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 11 29 17 27 48 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 Ex
174. ng Bulur E 1996 An Alternative Technique For Optically Stimulated Luminescence OSL Ex periment Radiation Measurements 26 701 709 See Also CW2pHMi CW2pLMi CW2pPMi fit_LMCurve 1m 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 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 CW2pLMi 79 Usage CW2pLMi
175. ng matrix call language class the orignal function call The output De values should be accessed using the function get_RLum Function version 0 5 1 2015 12 05 15 52 49 Note THIS FUNCTION HAS BETA STATUS analyse_IRSAR RF 11 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 Furthermore In course of ongoing research this function has been almost fully re written but further thought ful tests are still pending However as a lot new package functionality was introduced with the changes made for this function and to allow a part of such tests the re newed code was made part of the current package 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 to 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 Stu
176. ng 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_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 hard 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 calc_CosmicDoseRate 39 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 l
177. ng this option overwrites the default parameter list of the gSGC meaning the argument gSGC type will be without effect n MC integer with default number of Monte Carlo simulation runs for error esti mation s details verbose logical enable or disable terminal output plot logical enable or disable graphical feedback as plot parameters will be passed to the plot output Details The error of the De value is determined using a Monte Carlo simulation approach Solving of the equation is realised using uniroot Large values for n MC will significantly increase the computa tion time Value Returns an S4 object of type RLum Results Slot data contains a list with the following structure De value data frame De De error 52 calc_HomogeneityTest Eta De MC list contains the matricies from the error estimation uniroot list contains the uniroot outputs of the De estimations call call the original function call Function version 0 1 0 2015 12 05 15 52 49 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montagine France R Luminescence Package Team References Li B Roberts R G Jacobs Z Li S H 2015 Potential of establishing a global standardised growth curve gSGC for optical dating of quartz from sediments Quaternary Geochronology 27 94 104 doi 10 1016 j quageo 2015 02 011 See Also RLum Results get_RLum uniroot Examples results lt c
178. nput object the corresponding get function will be selected Allowed arguments can be found in the documentations of the corresponding RLum class Value Return is the same as input objects as provided in the list Methods by class e list Returns a list of RLum objects that had been passed to get_RLum Function version 0 3 0 2015 12 06 23 16 02 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team 110 length_RLum See Also RLum Data Curve RLum Data Image RLum Data Spectrum RLum Analysis RLum Results Examples Example based using data and from the calc_CentralDose function load example data data ExampleData DeValues envir environment apply the central dose model 1st time temp1 lt calc_CentralDose ExampleData DeValues CA1 get results and store them in a new object temp get lt get_RLum object temp1 length_RLum General accessor function for RLum S4 class objects Description Function calls object specific get functions for RLum S4 class objects Usage length_RLum object Arguments object RLum required S4 object of class RLum Details The function provides a generalised access point for specific RLum objects Depending on the input object the corresponding get function will be selected Allowed arguments can be found in the documentations of the corresponding RLum class Value Return is the same
179. ns De data 1 and De error data 2 To plot several data sets in one plot the data sets must be provided as list e g list data 1 data 2 na rm logical with default exclude NA values from the data set prior to any further operations log z logical with default Option to display the z axis in logarithmic scale De fault is TRUE z 0 character or numeric User defined central value used for centering of data One out of mean mean weighted and median or a numeric value not its logarithm Default is mean weighted dispersion plot ratio rotate mtext summary summary pos legend legend pos stats rug kde hist dots y axis error bars bar bar col polygon col line line col plot_AbanicoPlot character with default measure of dispersion used for drawing the scat ter polygon One out of qr quartile range pnn symmetric percentile range with nn the lower percentile e g p05 depicting the range between 5 and 95 sd standard deviation and 2sd 2 standard deviations default is qr Note that sd and 2sd are only meaningful in combination with z 0 mean because the unweighted mean is used to center the polygon 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 add s
180. nt 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 read_BIN2R 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 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 20 Analyse_SAR OSLdata 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
181. ntation Please see calc_MinDose Value Please see calc_MinDose calc_MaxDose 57 Function version 0 3 2015 11 29 17 27 48 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 Further reading Arnold L J amp Roberts R G 2009
182. o plot_RadialPlot plot_KDE plot_Histogram Examples load example data and recalculate to Gray data ExampleData DeValues envir environment plot_AbanicoPlot 127 ExampleData DeValues lt ExampleData DeValues CA1 plot the example data straightforward plot_AbanicoPlot data ExampleData DeValues now with linear z scale plot_AbanicoPlot data ExampleData DeValues log z FALSE now with output of the plot parameters plot1 lt plot_AbanicoPlot data ExampleData DeValues output TRUE str plot1 plot1 zlim now with adjusted z scale limits plot_AbanicoPlot data ExampleData DeValues zlim c 10 200 now with adjusted x scale limits plot_AbanicoPlot data ExampleData DeValues xlim c 0 20 now with rug to indicate individual values in KDE part plot_AbanicoPlot data ExampleData DeValues rug TRUE now with a smaller bandwidth for the KDE plot plot_AbanicoPlot data ExampleData DeValues bw 0 04 now with a histogram instead of the KDE plot plot_AbanicoPlot data ExampleData DeValues hist TRUE kde FALSE now with a KDE plot and histogram with manual number of bins plot_AbanicoPlot data ExampleData DeValues hist TRUE breaks 20 now with a KDE plot and a dot plot plot_AbanicoPlot data ExampleData DeValues dots TRUE now with user defined plot ratio plot_AbanicoPlot data ExampleData DeValues plot ratio 0 5 now with
183. object is returned with the following structure data fit nls nls object Soutput table data frame with fitting results component contribution matrix list component distribution matrix call call the original function call Matrix structure for the distribution matrix Column 1 and 2 time and rev time values Additional columns are used for the components two for each component containing 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 Function version 0 3 0 2015 12 05 15 52 49 Note The pseudo R 2 may not be the best parameter to describe the goodness of the fit The trade off between the n components and the pseudo R 2 value currently remains unconsidered The function does not ensure that the fitting procedure has reached a global minimum rather than a local minimum In any case of doubt the use of manual start values is highly recommended Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team 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 Radiatio
184. odify the entire plot more sophisticated Each element of the plot can be addressed and its properties can be defined This includes font type size and decoration colours and sizes of all plot items To infer the definition of a specific layout style cf get_Layout or type eg for the layout type journal get_Layout journal A layout type can be modified by the user by assigning new values to the list object It is possible for the z scale to specify where ticks are to be drawn by using the parameter at e g at seq 80 200 20 cf function documentation of axis Specifying tick positions manually overrides a zlim definition Value returns a plot object and optionally a list with plot calculus data Function version 0 1 7 2015 12 05 15 52 49 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 3 197 206 Dietze M Kreutzer S Burow C Fuchs M C Fischer M Schmidt C 2015 The abanico plot visualising chronometric data with individual standard errors Quaternary Geochronology doi 10 1016 j quageo 2015 09 003 See Als
185. of coordinate specification y coordinate refers to the right y axis colour 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 or hist 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 Details If the normal curve is added the y axis in the histogram will show the probability density A statistic summary 1 e a collection of statistic measures of centrality and dispersion and fur ther measures can be added by specifying one or more of the following keywords n number of samples mean mean De value mean weighted error weighted mean median me dian of the De values sdrel relative standard deviation in percent sdrel weighted error weighted relative standard deviation in percent sdabs absolute standard deviation sdabs weighted error weighted absolute standard deviation serel relative standard error serel weighted
186. olinPlot R read_BIN2R R read_Daybreak2R R read_SPE2R R read_XSYG2R R template_DRAC R tune_Data R use_DRAC R write_R2BIN R zzz R RoxygenNote 5 0 1 NeedsCompilation yes Repository CRAN Date Publication 2015 12 07 23 03 25 R topics documented Luminescence package ee 4 analyse IRSAR RE o 4 5 at Be RE ae BES a Re REE EAS 6 analyse_pIRIRSequence 2 2 0 0 00 ee 12 analyse_SAR CWOSL 0 0 ee ee ee 15 Analyse_SAR OSLdata paok a eoa ee 19 analyse SARTE 4 4 6S a a A E a e e a a a eS 22 apply_CosmicRayRemoval a 24 apply_EfficiencyCorrection ooo ee 26 AS A A A O in ee E ee Es 28 BaseDataSet CosmicDoseRate 2 0 a a a 29 R topics documented 3 calc_AliquotSize ee ee ee ee e 31 CaleCentialDos cs pe s o aa ds ee we oe EOS HOR se Oe Bod 34 calc_CommonDose 2 e a E a S n E E E e E E Aa 36 calc_CosmicDoseRate gt e owa cadut erwe ee a e a a a e e d 38 cale FadmeCort vieiras pd one 43 calc_FiniteMixture aoa a 45 calc_FuchsLang2001 aa ee 49 cale oSGO eur e ate a e bee A A a ee ea 51 calc_HomogeneityTest gt o oc scce 0 02 00 0000 0000000000004 52 calc IEU neri reut da mae AA A A AA eed 54 Calo MAXxDOSE e 200 a a AN kaon a a a ee ee oe Qe nd a es 59 Calc MinDose s seo aa maad e a RE ee eR A a a a eA i 58 Cale OSLEXTXRatio 4 e Oe A A ae ee e 64 calc_SourceDoseRate redni e weak ed anka paa ee aR 67 calc Statistics
187. ongitude 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 i 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 Details This function calculates the total cosmic dose rate considering 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 density deptha x densitya depth x densityn 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 x absober H x exp B x absorber b If absorber is lt 167 g cm 2 sof
188. or c steelblue3 orange3 alpha f 5 polygon col c steelblue3 orange3 for further information on layout definitions see documentation of function get_Layout 129 plot_DRTResults Visualise dose recovery test results 130 Description plot_DRTResults The function provides a standardised plot output for dose recovery test measurements Usage plot_DRTResults values given dose error range 10 preheat boxplot FALSE mtext summary summary pos legend legend pos par local TRUE na rm FALSE Arguments values RLum Results or data frame required input values containing at least De given dose error range preheat boxplot mtext summary summary pos legend legend pos par local na rm 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 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 numeric symmetric error range in percent will be sh
189. otocol analysis Version 0 1 Source IRSAR REData These data were kindly provided by Tobias Lauer and Matthias Krbetschek Lab Luminescence Laboratory TU Bergakademie Freiberg Lab Code ZEU SA1 Location Zeuchfeld Zeuchfeld Sandur Saxony Anhalt Germany Material K feldspar 130 200 jum 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 92 ExampleData RLum Data Image Examples load data data ExampleData RLum Analysis envir environment plot data plot_RLum IRSAR RF Data ExampleData RLum Data Image Example data as RLum Data Image objects Description Measurement of Princton Instruments camera imported with the function read_SPE2R to R to pro duce an RLum Data Image object Format Object of class RLum Data Image 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 Examples load data data E
190. ow for different sets of parameters for every single input element For further information see analyse_SAR CWOSL Value Plots optional and an RLum Results object is returned containing the following elements DATA OBJECT TYPE De values data frame LnLxTnTx table data frame rejection criteria data frame Formula list call call DESCRIPTION Table with De values with the LnLxTnTx values rejection criteria Function used for fitting of the dose response curve the original function call The output should be accessed using the function get_RLum Function version 0 2 0 2015 11 29 17 27 48 Note Best graphical output can be achieved by using the function pdf with the following options pdf file height 15 width 15 14 analyse_pIRIRSequence Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team 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 Result
191. own as dashed lines in the plot Set error range to 0 to void plotting of error ranges numeric optional vector of preheat temperatures to be used for grouping the De values If specified the temperatures are assigned to the x axis logical optionally plot values that are grouped by preheat temperature as boxplots Only possible when preheat vector is specified 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 and seabs absolute standard error 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 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 inherite
192. p get_RLum logical with default coerce to the next possible layer which are data objects drop FALSE keeps the original RLum Results Value set_RLum Returns an object from the class RLum Results get_RLum 196 RLum Results class Returns 1 Data object from the specified slot 2 list of data objects from the slots if data object is vector or 3 an RLum Results for drop FALSE length_RLum Returns the number of data elements in the RLum Results object names_RLum Returns the names of the data elements in the object Methods by generic show Show structure of RLum Results object set_RLum Construction method for an RLum Results object get_RLum Accessor method for RLum Results object The argument data object allows di rectly accessing objects delivered within the slot data The default return object depends on the object originator e g fit_LMCurve If nothing is specified always the first data object will be returned Note Detailed specification should be made in combination with the originator slot in the receiving function if results are pipped length_RLum Returns the length of the object i e number of stored data objects names_RLum Returns the names data objects Slots data Object of class list containing output data Objects from the Class Objects can be created by calls of the form new RLum Results Class version 0 4 0 Note The class is intended to s
193. ped as it is assumed that the error is stable Please note that a the duration depends on the input values as well as on the provided computation ressources and it may take a while b the length size of the output vector age corr MC where all the single values produced during the MC runs are stored equals the number of MC runs here termed observations To avoid an endless loop the calculation is stopped if the number of observations exceeds 1017 This limitation can be overwritten by setting the number of MC runs manually e g n MCruns 10000001 Note For this case the function is not checking whether the calculated error is stable seed This option allows to recreate previously calculated results by setting the seed for the R random number generator see set seed for details This option should not be mixed up with the option n MCruns auto The results may appear similar but they are not comparable 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 faded age faded error g value g value error tc n MCruns observations seed age corr MC numeric Age corr MC contain all possible ages from the Monte Carlo error simulation Function version 0 3 0 2015 12 06 23 16 02 Note The upper age limit is set to 500 ka Author s Sebastian Kreutzer
194. psed 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 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 readBIN2RO and the slot BINfile METADATA DATE Allowed source types and related values 68 calc_SourceDoseRate 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 Value Returns an S4 object of type RLum Results Slot data contains a list with the following struc ture dose rate data frame dose rate dose rate error date corresponding measurement date parameters list source type halflife dose rate unit call the original function call The output should be accessed using the function get_RLum A plot method of the output is provided via plot_RLum Function version 0 3 0 2015 11 29 17 27 48 Note Please be careful when using the option predict especially when a multiple set for measurement date and calib date is provided For the source dose rate prediction the function takes the
195. r IRAMAT CRP2A Universite Bordeaux Montaigne R Luminescence Package Team See Also density plot plot KDE 141 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 x 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 ylim c 0 08 0 30 create plot with centrality lines and distribution polygons plot_KDE data ExampleData DeValues ylim c 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 subse
196. r analysis object Value may be used by subsequent analysis functions txtProgressBar logical with default enables or disables txtProgressBar Details The RLum Analysis object requires a set of curves for specific further protocol analyses However the Risoe BINfileData usually contains a set of curves for different aliquots and different protocol types that may be mixed up Therefore a conversion is needed Risoe BINfileData2RLum Data Curve 181 Value Returns an RLum Analysis object Function version 0 2 2 2015 12 05 15 52 49 Note The protocol argument of the RLum Analysis object is set to unknown if not stated otherwise Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team References See Also Risoe BINfileData Risoe BINfileData2RLum Data Curve RLum Analysis read_BIN2R Examples load data data ExampleData BINfileData envir environment convert values for position 1 Risoe BINfileData2RLum Analysis CWOSL SAR Data pos 1 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 182 Risoe BINfileData2RLum Data Curve Arguments object Risoe BINfileData required
197. r 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 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 and single xaxis energy logical with default enables or disables energy instead of wavelength axis Note This option means not only simnply redrawing the axis insteadly the spectrum in terms of intensity is recalculated s details legend text character with default possiblity to provide own legend text This argument is only considered for plot types providing a legend e g plot type transect further arguments and graphical parameters that will be passed to the plot func tion Details
198. rameters 74 CW2pHMi 6 Transform values using pHM t 6 t 1 6x t cxCW t c 1 8x P 9 P P length stimulation period 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 list list 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 list list 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 11 29 17 27 48 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 valu
199. rate 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 rm TRUE mtext cex global se rug normal_curve summary summary pos colour plot_Histogram 137 Arguments data data frame or RLum Results object required for data frame two columns De dataL 1 and De error data 2 na rm logical with default excludes NA values from the data set prior to any further Operations mtext character optional further sample information mtext cex global numeric with default global scaling factor se logical optional plots standard error points over the histogram default is FALSE rug logical optional adds rugs to the histogram default is TRUE normal_curve logical with default adds a normal curve to the histogram Mean and sd are calculated from the input data More see details section summary character optional add statistic measures of centrality and dispersion to the plot Can be one or more of several keywords See details for available key words 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
200. required upper bound of the background integral Provide this value as vector for different integration limits for the different IRSL curves analyse_pIRIRSequence 13 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 analyses this function has been written as extended wrapper function for the function analyse_SAR CWOSL facilitating an en tire sequence analysis in one run With this its functionality is strictly limited by the functionality of the function analyse_SAR CWOSL If the input is a list If the input is a list of RLum Analysis objects every argument can be provided as list to al l
201. reted as the maximum signal integral for the Tx curve background integral min integer required lower bound of the background integral Can be a list of integers if object is of type list If the input is vector e g c 1 2 the 2nd value will be interpreted as the minimum background integral for the Tx curve background integral max integer required upper bound of the background integral Can be a list of integers if object is of type list If the input is vector e g c 1 2 the 2nd value will be interpreted as the maximum background integral for the Tx curve rejection criteria list with default provide a named list and set rejection criteria in percentage for further calculation Can be a list in a list if object is of type list Allowed arguments are recycling ratio recuperation rate palaeodose error and exceed max regpoint TRUE FALSE Example rejection criteria list recycling rati Per default all numericla values 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 Can be a list of numeric vectors if object is of type list mtext outer character optional option to provide an outer margin mtext Can be a list of characters if object is of type list plot logical with default enables or disables plot output plot single logical with default or numeric optional single plot output TRUE FALS
202. ror 0 0019 predict 1000 plot_RLum dose rate 4 export output to a LaTeX table example using the package xtable Not run xtable xtable get_RLum dose rate End Not run 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 square digits NULL na rm TRUE 70 Arguments data weight calc digits na rm Value calc_Statistics data frame or RLum Results object required for data frame two columns De data 1 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 character type of weight calculation One out of reciprocal weight is 1 error square weight is l error 2 Default is square integer with default round numbers to the specified digits If digits 1s set to NULL nothing is rounded logical with default indicating whether NA values should be stripped before the computation proceeds Returns a list with weighted and unweighted statistic measures Function version 0 1 4 2015 12 05 15 52 49 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 th
203. rotocol Radiation Measurements 32 57 73 See Also calc_OSLLxTxRatio Risoe BINfileData class read_BIN2R 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 22 analyse_SAR TL 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 1 LxTx LxTx Error output LnLxTnTxL 1 1 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 sequence structure c PREHEAT SIGNAL BACKGROUND rejection criteria list recycling ratio 10 recuperation rate 10 dose points log 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
204. s get_RLum Examples NOTE For this example existing 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 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 class 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 analyse_SAR CWOSL 15 signal integral max 2 background integral min background integral max fit method EXP sequence structure c TL pseudoIRSL1 pseudoIRSL2 main Pseudo pIRIR data set based on quartz OSL plot single TRUE 900 1000 3 Perfor
205. s of Galbraith amp Roberts 2012 The parameters delta and sigma are estimated by numerically solving eq 15 and 16 Their standard errors are approximated using eq 17 In addition the profile log likelihood function for sigma is calculated using eq 18 and presented as a plot Numerical values of the maximum likelihood approach are only presented in the plot and not in the console A detailed explanation on maximum likelihood estimation can be found in the appendix of Galbraith amp Laslett 1993 468 470 and Galbraith amp Roberts 2012 15 calc_CentralDose 35 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 profile data frame the log likelihood profile for sigma The output should be accessed using the function get_RLum Function version 1 3 1 2015 11 29 17 27 48 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 Jinmi
206. s where a particular parameter asks for long computation times Currently supported parameters are curves_ratio numeric default 1 001 The ratio of RF a over RF e in the range of RF q of is calculated and should not exceed the threshold value intersection_ratio numeric default NA Calculated as absolute difference from 1 of the ratio of the integral of the normalised RF curves This value indicates intersection of the RF curves and should be close to O if the curves have a similar shape residuals_slope numeric default NA only for method SLIDE A linear function is fitted on the residuals after sliding The corresponding slope can be used to discard values as a high positive negative slope may indicate that both curves are fundamentally different and the method cannot be applied at all Per default the value of this parameter is calcu lated but not evaluated curves_bounds numeric default max RFreg ounts This measure uses the maximum time x value of the regenerated curve The maximum time x value of the natural curve cannot be larger than this value However although this is not recom 10 analyse _IRSAR RF mended the value can be changed or disabled dynamic_ratio numeric default NA The dynamic ratio of the regenerated curve is calculated as ratio of the minimum and maximum count values lambda beta and delta phi numeric default NA method SLIDE The stretched exponential func
207. se model 1st time temp1 lt calc_CentralDose ExampleData DeValues CA1 apply 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 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 Arguments 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 merge_RLum Data Curve 115 Value Return an RLum Analysis object Function version 0 1 2015 12 05 15 52 49 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 Ref
208. se 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 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 Analyse_SAR OSLdata 19 signal integral min signal integral max background integral min 900 background integral max 1000 log x fit method EXP od mm a show De results get_RLum results show LnTnLxTx table get_RLum 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 measureme
209. sing mix tures of laboratory dosed quartz Radiation Measurements 32 459 465 48 calc_FiniteMixture Galbraith R F 2005 Statistics for Fission Track Analysis Chapman amp Hall CRC Boca Raton 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 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 CAl1 sigmab 0 2 n components 2 grain probability TRUE 2 repeat the finite mixture model for 2 3 and 4 maximum number of fitted components and save results NOTE The following example is computa
210. ss Class RLum Analysis Description Object class to represent analysis data for protocol analysis i e all curves spectra etc from one measurements Objects from this class are produced by e g read_XSYG2R read_Daybreak2R Usage HH S4 method for signature RLum Analysis show object S4 method for signature RLum Analysis set_RLum class originator protocol NA_character_ records list HH S4 method for signature RLum Analysis get_RLum object record id NULL recordType NULL curveType NULL RLum type NULL protocol UNKNOWN get index NULL drop TRUE recursive TRUE S4 method for signature RLum Analysis structure_RLum object S4 method for signature RLum Analysis length_RLum object HH S4 method for signature RLum Analysis names_RLum object RLum Analysis class 185 Arguments object show_RLum get_RLum names_RLum length_RLum structure_RLum an object of class RLum Analysis required class set_RLum character required name of the RLum class to be created originator set_RLum character automatic contains the name of the calling function the function that produces this object can be set manually protocol set_RLum character optional sets protocol type for analysis object Value may be used by subsequent analysis functions records set_RLum list required list of RLum Analysis objects set_RLum Returns an RLum Analysis object record id get_RL
211. sults 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 J amp Roberts R G 2009 Stochastic modelling of multi
212. t 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 40 calc_CosmicDoseRate 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 E 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 with a 2 degree polynomial The altitude factor is operated on the decimal part of the correction factor De Dex correctionF actor Usage of depth and density 1 If only one value for depth and density is provided the cosmic dose rate is calculated for exactly one sample and one absorber as overburden i e depth density 2 In some cases it might be useful to calculate the cosmic dose rate for a sample that is overlain by more than one absorber e g in a profile with soil layers of different thickness and a distinct difference in density This can be calculated by providing a matching number of values for dep
213. 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 ExampleData BINfileData 85 ExampleData BINfileData Example data from a SAR OSL and SAR TL measurement for the pack age Luminescence Description Example data from a SAR OSL and TL measurement for package Luminescence directly extracted from a Risoe BIN file and provided in an object of type Risoe BINfileData class Format CWOSL SAR Data SAR OSL measurement data TL SAR Data SAR TL measurement data Each class object contains two slots a METADATA is a data frame with all metadata stored in the BIN file of the measurements and b DATA contains a list of vectors of the measured data usually count values Version 0 1 Note Please note that this example data cannot be exported to a BIN file using the function writeR2BIN as it was generated and implemented in the package long time ago In the meantime the BIN file format changed Source CWOSL SAR Data 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 86 ExampleData CW_OSL_ Curve
214. t to an RLum Analysis object Description Converts values from one specific position of a Risoe BINfileData S4 class object to an RLum Analysis object Internally the function uses the function Risoe BINfileData2RLum Data Curve to recal culate the curves Usage Risoe BINfileData2RLum Analysis object pos grain run set ltype protocol unknown txtProgressBar FALSE Arguments object Risoe BINfileData required Risoe BINfileData object pos numeric optional position number of the Risoe BINfileData object for which the curves are stored in the RLum Analysis object If length position gt 1 a list of RLum Analysis objects is returned If nothing is provided every posi tion will be converted If the position is not valid NA is returned grain vector numeric optional grain number from the measurement to limit the converted data set e g grain c 1 48 Please be aware that this option may lead to unwanted effects as the output is strictly limited to the choosen grain number for all position numbers run vector numeric optional run number from the measurement to limit the converted data set e g run c 1 48 set vector numeric optional set number from the measurement to limit the converted data set e g set c 1 48 ltype vector character optional curve type to limit the converted data Allowed values are IRSL OSL TL RIR RBR and USER protocol character optional sets protocol type fo
215. ta frame logical with default logical If TRUE setting row names and converting col umn names to syntactic names see make names is optional see as data frame logical with default enables or disables further subsetting unlist integer optional the column index of the matrix data frame logical with default keep object structure or drop it character optional name of the wanted record type or data object The term S3 generics sounds complicated however it just means that something has been imple mented in the package to increase the usability for users new in R and who are not familiar with the underlying RLum object structure of the package The practical outcome is that operations and functions presented in standard books on R can be used without knowing the specifica of the R package Luminescence For examples see the example section 122 names_RLum Note methods_RLum are not really new functions everything given here are mostly just surrogates for existing functions in the package Examples load example data data ExampleData RLum Analysis envir environment combine curve is various ways curvel lt IRSAR RF Data 1 curve2 lt IRSAR RF Data 1 curvel curve2 curvel curve2 curvel curve2 curvel curve2 access curves IRSAR RF Data RF names_RLum S4 names function for RLum S4 class objects Description Function calls object specific names functions for
216. ta 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 calc_CommonDose 37 Details Un logged model When log TRUE this function 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 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
217. tatistic measures of centrality and dispersion to the plot Can be one or more of several keywords See details for available key words 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 labels of statistically important values in the plot One n n non 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 numeric with default option to add one or more
218. ted structure_RLum R length_RLum R set_RLum R get_RLum R RLum Analysis class R RLum Data class R RLum Data Curve class R RLum Data Image class R RLum Data Spectrum class R RLum Results class R ReppExports R Risoe BINfileData2RLum Analysis R Risoe BINfileData2RLum Data Curve R set_Risoe BINfileData R get_Risoe BINfileData R RisoeBINfileData class R Second2Gray R analyse_IRSAR RE R analyse_SAR CWOSL R analyse_SAR TL R analyse_pIRIRSequence R apply_CosmicRayRemoval R apply_EfficiencyCorrection R calc_AliquotSize R calc_CentralDose R calc_CommonDose R calc_CosmicDoseRate R calc_FadingCorr R calc_FiniteMixture R calc_FuchsLang2001 R calc_HomogeneityTest R calc_IEU R calc_MaxDose R calc_MinDose R calc_OSLLxTxRatio R calc_SourceDoseRate R calc_Statistics R calc_TLLxTxRatio R calc_gSGC R extract_IrradiationTimes R fit_CWCurve R fit_LMCurve R get_Layout R get_Quote R get_rightAnswer R internal_as latex table R merge_RLum Analysis R merge_RLum Data Curve R merge_RLum R merge_RLum Results R merge_Risoe BINfileData R methods_DRAC R methods_RLum R plot_AbanicoPlot R plot_DRTResults R plot_GrowthCurve R plot_Histogram R plot_KDE R plot_NRt R plot_RLum Analysis R plot_RLum Data Curve R plot_RLum Data Image R plot_RLum Data Spectrum R plot_RLum R plot_RLum Results R plot_RadialPlot R plot_Risoe BINfileData R plot_Vi
219. terion 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 calc_FiniteMixture 47 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
220. th 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 cm 3 Value Returns a terminal output In addition an RLum Results object is returned containing the following element summary data frame summary of all relevant calculation results args list used arguments call call the function call The output should be accessed using the function get_RLum Function version 0 5 2 2015 11 29 17 27 48 calc_CosmicDoseRate 41 Note Despite its universal use the equation to calculate the cosmic dose rate provided by Prescott amp Hutton 1994 is falsely stated to be valid from the surface to 1044 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 b
221. the function read_BIN2R Usage S4 method for signature Risoe BINfileData show object HH S4 method for signature data frame list set_Risoe BINfileData METADATA DATA RESERVED S4 method for signature Risoe BINfileData get_Risoe BINfileData object Arguments object an object of class Risoe BINfileData 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 other arguments that might be passed Methods by generic e show Show structure of RLum and Risoe BINfile class objects e set_Risoe BINfileData The Risoe BINfileData is normally produced as output of the func tion read_BIN2R This construction method is intended for internal usage only e get_Risoe BINfileData Formal get method for Risoe BINfileData object It does not allow accessing the object directly it is just showing a terminal message 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 Objects from the Class Objects can be created by calls of the form new Risoe BINfileData Risoe BINfileData class 177 Function version
222. the same directory as the XSYG file write table x get_RLum output file paste0 file BINX _extract_IrradiationTimes csv sep 5 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 5 fit method port fit trace FALSE fit calcError FALSE LED power 36 LED wavelength 470 cex global 0 6 sample_code Default output path output terminal TRUE output terminalAdvanced TRUE plot TRUE 98 fit CWCurve 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 fit method character with default select fit method allowed values port and LM port uses the port routine usint the funtion nls LM utilises the function n1sLM from the package minpack 1m and with that the Levenberg Marquardt algorithm fit trace logical with
223. 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 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 and it is not compatible with fit method LM 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 channel see Details Note requires input for values bg verbose logical with default terminal output with fitting results plot logical with default returns a plot of the fitted curves plot BG logical with default returns a plot of the background values with the fit used for the background subtraction Further arguments that may be passed to the plot output e g xlab xlab main log Details Fitting function The function for the fitting has the general form y exp 0 5 Imy a am xexp x 2 am exp 0 5 Im x xm exp
224. tical measures such as mean median standard deviation standard error and quartile range can be provided visually and numerically Usage plot_KDE data na rm TRUE weights FALSE values cumulative TRUE centrality dispersion summary summary pos polygon 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 rm 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 add statistic measures of centrality and dispersion to the plot Can b
225. tion suggested by Erfurt et al 2003 describing the decay of the RF signal comprises several parameters that might be useful to evaluate the shape of the curves For method FIT this parameter is obtained during the fitting for method SLIDE a rather rough estimation is made using the function nlsLM and the equation given above Note As this procedure requests more computation time setting of one of these three parameters to NULL also prevents a calculation of the remaining two Value A plot optional and an RLum Results object is returned The slot data contains the following elements De values data frame table with De and corresponding values 6 DE numeric the obtained equivalent dose DE ERROR numeric only method SLIDE standard deviation obtained from MC runs 6 DE LOWER numeric 2 5 quantile for De values obtained by MC runs 6 DE UPPER numeric 97 5 quantile for De values obtained by MC runs 6 DE STATUS character test parameter status RF_NAT LIM charcter used RF_nat curve limits RF_REG LIM character used RF_reg curve limits POSITION integer optional position of the curves DATE character optional measurement date SEQUENCE_NAME character optional sequence name 6 UID character unique data set ID test_parameter data frame table test parameters fit nls nlsModel object slide list data from the sliding process including the slidi
226. tionally 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 object FMM data object components calc_FuchsLang2001 49 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 Usage calc_FuchsLang2001 data cvThreshold 5 startDeValue 1 plot TRUE 25 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_threshold the first value is skipped Use the startDeValue argument
227. tions of the corresponding RLum class RLum Data Curve RLum Data Image RLum Data Spectrum RLum Analysis and RLum Results Value Returns an object of the specified class Function version 0 2 0 2015 12 06 23 16 02 Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France R Luminescence Package Team See Also RLum Data Curve RLum Data Image RLum Data Spectrum RLum Analysis RLum Results 202 sTeve Examples produce empty objects from each class set_RLum class RLum Data Curve set_RLum class RLum Data Spectrum set_RLum class RLum Data Spectrum set_RLum class RLum Analysis set_RLum class RLum Results produce a curve object with arbitrary curve values object lt set_RLum class RLum Data Curve curveType arbitrary recordType OSL data matrix c 1 100 exp c 1 100 ncol 2 plot this curve object plot_RLum object 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 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 sophisti
228. tomleft reset graphical parameters par mfrow c 1 1 plot_RadialPlot Function to create a Radial Plot plot_RadialPlot 145 Description A Galbraith s radial plot is produced on a logarithmic or a linear scale Usage plot_RadialPlot data na rm 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 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 na rm logical with default excludes NA values from the data set prior to any further operations negatives character with default rule for negative values Default is remove i e negative values are removed from the data set log z logical with default Option to display the z axis in logarithmic scale De central value fault is TRUE numeric User defined central value primarily used for horizontal centering of the z axis centrality 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 v
229. tore results from functions to be used by other functions The data in the object should always be accessed by the method get_RLum Author s Sebastian Kreutzer IRAMAT CRP2A Universite Bordeaux Montaigne France Second2Gray 197 See Also RLum plot_RLum merge_RLum Examples showClass RLum Results create an empty object from this class set_RLum class RLum Results use another function to show how it works 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 object dose rate get results get_RLum dose rate get parameters used for the calcualtion from the same object get_RLum dose rate data object parameters alternatively objects can be accessed using S3 generics such as dose rate parameters Second2Gray Converting equivalent dose values from seconds s to gray Gy Description Conversion of absorbed radiation dose in seconds s to the SI unit gray Gy including error prop agation Normally used for equivalent dose data Usage Second2Gray data dose rate error propagation omit 198 Second2Gray Arguments data data frame required input values structure data values 11 and data error values 2 are required dose rate RLum Results or data frame or numeric required RLum Results needs to
230. tral value To disable the bar use none Default is grey n p y ticks logical Option to hide y axis labels Useful for data with small scatter grid col 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 line numeric numeric values of the additional lines to be added line col character or numeric colour of the additional lines line label character labels for the additional lines 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 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 rewritten 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 prec
231. ts 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 142 plot_NRt 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_NRt Visualise natural regenerated signal ratios Description This function creates a Natural Regenerated signal vs time NR t plot as shown in Steffen et al 2009 Usage plot_NRt data log FALSE smooth c none spline rmean k 3 legend TRUE legend pos topright Arguments data a list data frame matrix or RLum Analysis object required X Y data of measured values time and counts See details on individual data structure log character optional logarithmic axes c x y xy smooth character optional apply data smoothing Use rmean to calculate the rolling where k determines the width of the rolling window see rollmean spline applies a smoothing sp
232. ult enables or disables txtProgressBar forced VersionNumber integer optional allows to cheat the version number check in the function by own values for cases where the BIN file version is not supported Note The usage is at own risk only supported BIN file versions have been tested further arguments that will be passed to the function Risoe BINfileData2RLum Analysis Please note that any matching argument automatically sets fastForward TRUE Details The binary data file is parsed byte by byte following the data structure published in the Appendices of the Analyst manual p 42 For the general BIN file structure the reader is referred to the Risoe website http www nutech dtu dk read_BIN2R 167 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 If fastForward TRUE a list of RLum Analysis object is returned The internal coercing is done using the function Risoe BINfileData2RLum Analysis Function version 0 12 0 2015 12 06 23 16 02 Note The function works for BIN BINX format versions 03 04 06 and 07 The version number depends on the used Sequence Editor Potential other BIN BINX format versions are currently not supported The implementation of version 07 support could not been tested so far
233. um numeric or logical optional IDs of specific records If of type logical the entire id range is assuemd and TRUE and FALSE indicates the selec tion recordType get_RLum character optional record type e g OSL Can be also a vector for multiple matching e g recordType c OSL IRSL curveType get_RLum character optional curve type e g predefined or measured RLum type get_RLum character optional RLum object type Defaults to RLum Data Curve and RLum Data Spectrum get index get_RLum logical optional return a numeric vector with the index of each element in the RLum Analysis object drop get_RLum logical with default coerce to the next possible layer which are RLum Data objects drop FALSE keeps the original RLum Analysis recursive get_RLum logical with default if TRUE the default and the result of the gt get_RLum request is a single object this object will be unlisted means only the object itself and no list containing exactly one object is returned Mostly this makes things easier however if this method is used within a loop this might undesired Value get_RLum Returns 1 list of RLum Data objects or 2 Single RLum Data object if only one object is contained and recursive FALSE or 3 RLum Analysis ojects for drop FALSE structure_RLum Returns data frame showing the structure length_RLum 186 RLum Analysis class Returns the number records
234. um 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 Wallinga J 2012 Realizing the potential of fluvial archives using robust OSL chronologies Quaternary Geochronology 12 98 106 36 calc_CommonDose 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 plot calc_CommonDose calc_FiniteMixture calc_FuchsLang2001 calc_MinDose Examples load example data data ExampleData DeValues envir environment tHapply the central dose model calc_CentralDose ExampleDa
235. uminescence 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 HH your spectrum lt apply_EfficiencyCorrection your spectrum 28 as as as RLum object coercion Description for RLum Analysis for RLum Data Curve for RLum Data Image for RLum Data Spectrum for RLum Results Arguments from RLum or list data frame matrix required object to be coerced from to character required class name to be coerced to Details RLum Analysis from to list list Given that the list consits of RLum Analysis objects RLum Data Curve from list data frame matrix RLum Data Image from data frame matrix RLum Data Spectrum from to list data frame matrix to data frame matrix to BaseDataSet CosmicDoseRate 29 data frame data frame matrix matrix RLum Results from to list list Given that the list consits of RLum Results objects Note Due to the complex structure of the RLum objects itself a coercing to standard R data structures will be always loosely See Also as BaseDataSet CosmicDoseRate Base data set for cosmic dose rate calculation Description Collection of data from various sources needed for cosmic dose rate calculation Format values cosmic Softcomp data frame containing cosmic dose rates for s
236. user defined central value plot_AbanicoPlot data ExampleData DeValues z 0 70 now with median as central value 128 plot_AbanicoPlot plot_AbanicoPlot data ExampleData DeValues z 0 median now with the 17 83 percentile range as definition of scatter plot_AbanicoPlot data ExampleData DeValues z 0 median dispersion p17 now with user defined green line for minimum age model CAM lt calc_CentralDose ExampleData DeValues plot FALSE plot_AbanicoPlot data ExampleData DeValues line CAM line col darkgreen line label CAM now create plot with legend colour different points and smaller scale plot_AbanicoPlot data ExampleData DeValues legend Sample 1 col tomato4 bar col peachpuff pch R cex Q 8 now without 2 sigma bar polygon grid lines and central value line plot_AbanicoPlot data ExampleData DeValues bar col FALSE polygon col FALSE grid col FALSE y axis FALSE lwd 0 now with direct display of De errors without 2 sigma bar plot_AbanicoPlot data ExampleData DeValues bar col FALSE ylab y axis FALSE error bars TRUE now with user defined axes labels plot_AbanicoPlot data ExampleData DeValues xlab c Data error Data precision ylab Scatter zlab Equivalent dose Gy now with minimum maximum and median value indicated plot_Aban
237. ve class 188 set_RLum RLum Data Image method RLum Data Image class 190 set_RLum RLum Data Spectrum method RLum Data Spectrum class 192 set_RLum RLum Results method RLum Results class 195 show Risoe BINfileData method Risoe BINfileData class 176 show RLum Analysis method RLum Analysis class 184 show RLum Data Curve method RLum Data Curve class 188 show RLum Data Image method RLum Data Image class 190 show RLum Data Spectrum method RLum Data Spectrum class 192 show RLum Results method RLum Results class 195 smooth 25 26 smooth spline 25 26 142 sTeve 202 structure_RLum 786 203 structure_RLum RLum Analysis method RLum Analysis class 184 summary 99 100 103 summary RLum Analysis methods_RLum 118 summary RLum Data Curve methods_RLum 118 summary RLum Data Image methods_RLum 118 summary RLum Results methods_RLum 118 template_DRAC 204 tune_Data 205 txtProgressBar 43 166 169 180 209 uniroot 43 45 51 52 134 unlist RLum Analysis methods_RLum 118 use_DRAC 207 vector 7 13 19 22 43 64 73 79 82 98 149 150 159 167 169 180 write_R2BIN 95 97 112 167 178 179 209 writeBin 2 0 writeR2BIN write_R2BIN 209 INDEX xml 172 174 217
238. xampleData RLum Data Image envir environment ExampleData XSYG 93 plot data plot_RLum ExampleData 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 read_XSYG2R Format OSL SARMeasurement SAR OSL measurement data The data contain two elements a Sequence Header is a data frame with metadata from the measurement b Sequence Object contains an RLum Analysis object for further analysis TL Spectrum TL spectrum data RLum Data Spectrum object for further analysis The spectrum was cleaned from cosmic rays using the function apply_CosmicRayRemoval Note that no quantum efficiency calibration was performed Version 0 1 Source OSL SARMeasurement Lab Luminescence Laboratory Giessen Lab Code no code Location not specified Material Coarse grain quartz on steel cups on lexsyg research reader Reference unpublished TL Spectrum Lab Luminescence Laboratory Giessen Lab Code BT753 Location Dolni Vestonice Czech Republic Material Fine grain polymineral on steel cups on lexsyg rearch reader 94 ExampleData XS YG Reference Fuchs et al 2013 Spectrum Integration time 19 s channel time 20 s Heating 1 K s up to 500 deg C References Unpublished data measured to serve as ex
239. y table that contains the most relevant results res lt get_RLum 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 calc_MinDose 63 grid col none line label paste0 round res de 1 UQQB1 round res de_err 1 Gy bw 0 1 ylim c 25 18 summary pos topleft mtext bquote Parameters sigma b get_RLum mam args sigmab gamma round log res de 1 sigma round res sig 1 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 ExampleData DeValues CA1 sigmab sd 0 06 plot FALSE sigmab 0 15

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