0.4.0_[2014-12-16.152224]

R-Lum · Dec 16, 2014 · 2ee57bd · 2ee57bd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: Luminescence
 Type: Package
-Title: Package for Luminescence Dating data analysis [upcoming]
+Title: Package for Luminescence Dating data analysis 
 Version: 0.4.0
-Date: 2014-XX-XX
+Date: 2014-12-19
 Author: Sebastian Kreutzer [aut, trl, cre],
   Michael Dietze [aut],
   Christoph Burow [aut],
@@ -22,7 +22,7 @@ Maintainer: Sebastian Kreutzer <[email protected]>
 Description: Package provides a collection of various R functions for Luminescence Dating data analysis.
 Contact: Package Developer Team <[email protected]>
 License: GPL-3
-Depends: R (>= 3.1.1), utils
+Depends: R (>= 3.1.2), utils
 Imports: methods, XML, shape, rgl, matrixStats, raster, sp, zoo, bbmle
 URL: http://CRAN.R-project.org/package=Luminescence 
-Collate: Analyse_SAR.OSLdata.R analyse_SAR.CWOSL.R analyse_SAR.TL.R analyse_IRSAR.RF.R CW2pLM.R CW2pLMi.R CW2pHMi.R CW2pPMi.R calc_FadingCorr.R calc_FuchsLang2001.R calc_OSLLxTxRatio.R calc_TLLxTxRatio.R Second2Gray.R fit_LMCurve.R fit_CWCurve.R plot_Risoe.BINfileData.R plot_KDE.R plot_GrowthCurve.R plot_Histogram.R plot_RadialPlot.R plot_RLum.R plot_RLum.Analysis.R plot_RLum.Data.Curve.R readBIN2R.R RisoeBINfileData-class.R Risoe.BINfileData2RLum.Analysis.R RLum-class.R RLum.Data-class.R RLum.Data.Curve-class.R RLum.Analysis-class.R RLum.Results-class.R calc_CentralDose.R calc_FiniteMixture.R calc_MinDose.R calc_CommonDose.R calc_CosmicDoseRate.R merge_Risoe.BINfileData.R writeR2BIN.R Risoe.BINfileData2RLum.Data.Curve.R calc_HomogeneityTest.R calc_AliquotSize.R readXSYG2R.R RLum.Data.Spectrum-class.R plot_RLum.Data.Spectrum.R calc_MaxDose.R plot_AbanicoPlot.R plot_DRTResults.R calc_Statistics.R apply_CosmicRayRemoval.R apply_EfficiencyCorrection.R readSPE2R.R RLum.Data.Image-class.R plot_RLum.Data.Image.R get_Layout.R analyse_pIRIRSequence.R merge_RLum.R get_RLum.R merge_RLum.Analysis.R plot_RLum.Results.R zzz.R
+Collate: Analyse_SAR.OSLdata.R analyse_SAR.CWOSL.R analyse_SAR.TL.R analyse_IRSAR.RF.R CW2pLM.R CW2pLMi.R CW2pHMi.R CW2pPMi.R calc_FadingCorr.R calc_FuchsLang2001.R calc_OSLLxTxRatio.R calc_TLLxTxRatio.R Second2Gray.R fit_LMCurve.R fit_CWCurve.R plot_Risoe.BINfileData.R plot_KDE.R plot_GrowthCurve.R plot_Histogram.R plot_RadialPlot.R plot_RLum.R plot_RLum.Analysis.R plot_RLum.Data.Curve.R readBIN2R.R RisoeBINfileData-class.R Risoe.BINfileData2RLum.Analysis.R RLum-class.R RLum.Data-class.R RLum.Data.Curve-class.R RLum.Analysis-class.R RLum.Results-class.R calc_CentralDose.R calc_FiniteMixture.R calc_MinDose.R calc_CommonDose.R calc_CosmicDoseRate.R merge_Risoe.BINfileData.R writeR2BIN.R Risoe.BINfileData2RLum.Data.Curve.R calc_HomogeneityTest.R calc_AliquotSize.R readXSYG2R.R RLum.Data.Spectrum-class.R plot_RLum.Data.Spectrum.R calc_MaxDose.R plot_AbanicoPlot.R plot_DRTResults.R calc_Statistics.R apply_CosmicRayRemoval.R apply_EfficiencyCorrection.R readSPE2R.R RLum.Data.Image-class.R plot_RLum.Data.Image.R get_Layout.R analyse_pIRIRSequence.R merge_RLum.R get_RLum.R merge_RLum.Analysis.R plot_RLum.Results.R calc_SourceDoseRate.R zzz.R
diff --git a/NEWS b/NEWS
@@ -1,6 +1,6 @@
 NEWS for the R Package Luminescence
 
-Changes in version 0.4.0 (XX XXXX, 2014):
+Changes in version 0.4.0 (December 19th, 2014):
 
   New S4-classes, methods:
 
@@ -42,6 +42,10 @@ Changes in version 0.4.0 (XX XXXX, 2014):
            estimating the minimum dose of a De distribution, this
            function estimates the maximum dose.
 
+         • ‘calc_SourceDoseRate()’: calculating the dose rate of the
+           irradiation source at the date of measurement based on:
+           source calibration date, source dose rate, dose rate error.
+
          • ‘get_Layout()’: Helper function to return a list with layout
            definitions for more homogenous plotting,
 
@@ -160,8 +164,11 @@ Changes in version 0.4.0 (XX XXXX, 2014):
              • Error message implemented for non OSL data sets (#130,
                Georgina King),
 
-             • Added argument ‘dtype’ to provide further curve
-               limitation options,
+             • add argument ‘dtype’ to provide further curve limitation
+               options,
+
+             • add argument ‘keep.SEL’ to allow a manual curve
+               selection (advanced users),
 
              • minor code polishing.
 
@@ -447,7 +454,9 @@ Changes in version 0.4.0 (XX XXXX, 2014):
              • bug for small values fixed, rounding to 0 decimals
                replaced by 3 significant digits,
 
-             • parameter ‘at’ to allow user-defined z-tick positions.
+             • parameter ‘at’ to allow user-defined z-tick positions,
+
+             • individual statistical summary order supported (#184).
 
          • ‘plot_DRTResults()’:
 
@@ -492,7 +501,9 @@ Changes in version 0.4.0 (XX XXXX, 2014):
 
              • support of summary keywords "kurtosis" and "skewness",
 
-             • example y-lim bug removed (#177).
+             • example y-lim bug removed (#177),
+
+             • individual statistical summary order supported (#184).
 
          • ‘plot_KDE()’:
 
@@ -509,7 +520,9 @@ Changes in version 0.4.0 (XX XXXX, 2014):
              • support of ‘par(mfcol())’,
 
              • support of error-free data extended (now also for
-               calculation of kde max) (#178).
+               calculation of kde max) (#178),
+
+             • individual statistical summary order supported (#184).
 
          • ‘plot_GrowthCurve()’:
 
@@ -541,6 +554,8 @@ Changes in version 0.4.0 (XX XXXX, 2014):
              • fix ‘'EXP+EXP'’ fit as is was broken, due to a coding
                error,
 
+             • correct for wrong ‘par()’ resetting,
+
              • minor code polishing and adjustment.
 
          • ‘plot_RadialPlot()’:
@@ -550,7 +565,9 @@ Changes in version 0.4.0 (XX XXXX, 2014):
              • rug option added,
 
              • bug for small values fixed, rounding to 0 decimals
-               replaced by 3 significant digits.
+               replaced by 3 significant digits,
+
+             • individual statistical summary order supported (#184).
 
          • ‘plot_RLum.Analysis()’:
 

diff --git a/R/Analyse_SAR.OSLdata.R b/R/Analyse_SAR.OSLdata.R
@@ -9,7 +9,7 @@ Analyse_SAR.OSLdata<- structure(function(#Analyse SAR CW-OSL measurements.
   ## Margret C. Fuchs, AWI Potsdam (Germany), TU Bergakademie Freiberg (Germany)\cr
 
   ##section<<
-  ## version 0.2.14
+  ## version 0.2.15
   # ===========================================================================
 
   input.data,
@@ -45,6 +45,11 @@ Analyse_SAR.OSLdata<- structure(function(#Analyse SAR CW-OSL measurements.
   ### limits the curves to this two data types. By default all values are allowed.
   ### See \link{Risoe.BINfileData-class} for allowed data types. 
 
+  keep.SEL = FALSE,
+  ### \code{\link{logical}} (default): option allowing to use the \code{SEL} element of the 
+  ### \link{Risoe.BINfileData-class} manually. NOTE: In this case any limitation provided by
+  ### \code{run}, \code{set} and \code{dtype} are ignored!
+
   info.measurement = "unkown measurement",
   ### \link{character} (with default): option to provide information about
   ### the measurement on the plot output (e.g. name of the BIN or BINX file).
@@ -118,12 +123,14 @@ if(length(which(sample.data@METADATA["POSITION"]==i))>0){
 
     }
 
+    if(!keep.SEL){
     ##select all OSL data depending on the run and set
     sample.data@METADATA[,"SEL"]<-FALSE
     sample.data@METADATA[sample.data@METADATA[,"LTYPE"]=="OSL" & 
       sample.data@METADATA[,"RUN"]%in%run==TRUE &
       sample.data@METADATA[,"SET"]%in%set==TRUE &
       sample.data@METADATA[,"DTYPE"]%in%dtype==TRUE, "SEL"] <- TRUE
+    }
 
     ##grep all OSL curve IDs 
     OSL.curveID<-sample.data@METADATA[sample.data@METADATA["SEL"]==TRUE &

diff --git a/R/RLum.Results-class.R b/R/RLum.Results-class.R
@@ -3,8 +3,8 @@
 ##//////////////////////////////////////////////////////////////////////////////
 ##==============================================================================
 ##author: Sebastian Kreutzer
-##organisation: IRAMAT-CRP2A, Universite Bordeaux Montaigne/JLU Giessen/Freiberg Instruments
-##version: 0.2.5
+##organisation: IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)
+##version: 0.2.6
 
 ##==============================================================================
 
@@ -193,6 +193,16 @@ setMethod("get_RLum.Results",
 
             }
 
+            ##-------------------------------------------------------------
+            ##calc_SourceDoseRate        
+            if(object@originator == "calc_SourceDoseRate") {
+
+              return(object@data[[1]])
+
+            }
+
+
+
             ##-------------------------------------------------------------
             ##plot_GrowthCurve         
             if(object@originator == "plot_GrowthCurve") {

diff --git a/R/RisoeBINfileData-class.R b/R/RisoeBINfileData-class.R
@@ -87,7 +87,7 @@ setMethod("get_Risoe.BINfileData",
           signature=signature(object = "Risoe.BINfileData"), 
           definition = function(object) {
 
-            cat("[get_Risoe.BINfileData]: No direct access is provided object type. Use the function 'Risoe.BINfileData2RLum.Analysis' for object coercing instead.")
+            cat("[get_Risoe.BINfileData()]: No direct access is provided object type. Use the function 'Risoe.BINfileData2RLum.Analysis' for object coercing instead.")
 
           })##end setMethod
 

diff --git a/R/Second2Gray.R b/R/Second2Gray.R
@@ -4,29 +4,67 @@ Second2Gray <- structure(function(#Converting values from seconds (s) to gray (G
 
   # ===========================================================================
   ##author<<
-  ## Sebastian Kreutzer, JLU Giessen (Germany), 
-  ## Michael Dietze, GFZ Potsdam (Germany),
+  ## Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France),\cr
+  ## Michael Dietze, GFZ Potsdam (Germany),\cr
   ## Margret C. Fuchs, AWI Potsdam (Germany), \cr
 
   ##section<<
-  ## version 0.3
+  ## version 0.4
   # ===========================================================================
 
   values,
-  ### \link{data.frame} (\bold{required}): measured data (\code{values[,1]}) and data error 
-  ### (\code{values [,2]})
+  ### \code{\link{data.frame}} (\bold{required}): input values, structure: 
+  ### data (\code{values[,1]}) and data error (\code{values [,2]}) are required
 
   dose_rate,
-  ### \link{vector} (\bold{required}): dose rate in Gy/s and dose rate error in Gy/s
+  ### \code{\linkS4class{RLum.Results}} or \code{\link{vector}} (\bold{required}): 
+  ### \code{RLum.Results} needs to be orginated from the function \code{\link{calc_SourceDoseRate}},
+  ### for \code{vector}dose rate in Gy/s and dose rate error in Gy/s
 
   method = "gaussian"
   ### \link{character} (with default): method used for error calculation 
   ### (\code{gaussian} or \code{absolute}), see details for further information
 ){ 
 
+  # Integrity tests -----------------------------------------------------------------------------
+
+  ##(1) data.frame or RLum.Data.Curve object?
+  if(is(values, "data.frame") == FALSE){
+
+    stop("[Second2Gray()] 'values' object has to be of type 'data.frame'!")
+
+  }
+
+  ##(2) data.frame or RLum.Data.Curve object?
+  if(is(dose_rate, "numeric") == FALSE & is(dose_rate, "RLum.Results") == FALSE){
+
+    stop("[Second2Gray()] 'dose_rate' object has to be of type 'numeric' or 'RLum.Results'!")
+
+  }
+
+  ##(3) check for right orginator
+  if(is(dose_rate, "RLum.Results")){
+
+    if(dose_rate@originator != "calc_SourceDoseRate"){
+
+      stop("[Second2Gray()]  Wrong originator for dose_rate 'RLum.Results' object.")  
+
+    }else{
+
+     dose_rate <- as.numeric(get_RLum.Results(dose_rate, data.object = "dose.rate"))
+
+
+    }
+
+  }
+
+  # Calculation ---------------------------------------------------------------------------------
+
+
   De.seconds <- values[,1]
   De.error.seconds <- values[,2]
 
+
   De.gray <- NA
   De.error.gray <- NA
 
@@ -42,13 +80,14 @@ Second2Gray <- structure(function(#Converting values from seconds (s) to gray (G
 
   }else{
 
-    stop("[Second2Gray] Error: unknown error calculation method!" )
+    stop("[Second2Gray()] unsupported error calculation method!" )
 
   }
-    
+
   values <- data.frame(De=De.gray, De.error=De.error.gray)
-	return(values)
-
+
+  return(values)
+
   # DOCUMENTATION - INLINEDOC LINES -----------------------------------------
 
   ##details<<
@@ -77,8 +116,26 @@ Second2Gray <- structure(function(#Converting values from seconds (s) to gray (G
 
 }, ex=function(){
 
-  ##(1) for dose taken from the example data help file
+  ##(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, c(0.0438,0.0019))
+
+
+
+
+
+  ##(B) for source dose rate calibration data
+  ## - calculate source dose rate first
+  dose_rate <-  calc_SourceDoseRate(measurement.date = "2014-01-08",
+                                    calib.date <- "2008-03-01",
+                                    calib.dose.rate <- 5.95,
+                                    calib.error <- 0.04)  
+  # read example data
+  data(ExampleData.DeValues, envir = environment())
+
+  # apply Dose_rate to convert De(s) to De(Gy)
+  Second2Gray(ExampleData.DeValues, dose_rate)
 
-})  
+})  
diff --git a/R/analyse_IRSAR.RF.R b/R/analyse_IRSAR.RF.R
@@ -7,7 +7,7 @@ analyse_IRSAR.RF<- structure(function(# Analyse IRSAR RF measurements
   ## Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) \cr
 
   ##section<<
-  ## version 0.2.0
+  ## version 0.2.1
   # ===========================================================================
 
   ##TODO - keep fit.range in mind for De calculation
@@ -673,7 +673,7 @@ if(output.plot==TRUE){
          type="p", 
          pch=20,
          col="grey", 
-         ylab="Residual [a.u.]",
+         ylab="Resid. [a.u.]",
          #lwd=2,
          log="")
 
@@ -682,7 +682,7 @@ if(output.plot==TRUE){
   }else{
     plot(NA,NA,
          xlim=c(0,max(temp.sequence.structure$x.max)),
-         ylab="Residual [a.u.]",
+         ylab="Resid. [a.u.]",
          xlab=xlab, 
          ylim=c(-1,1)
     )    
@@ -769,7 +769,7 @@ if(output.plot==TRUE){
          type="p", 
          pch=20,
          col="grey", 
-         ylab="Residual [a.u.]",
+         ylab="Resid. [a.u.]",
          #lwd=2,
          log="")
 
@@ -787,7 +787,7 @@ if(output.plot==TRUE){
            type="p", 
            pch=20,
            col="grey", 
-           ylab="Residual [a.u.]",
+           ylab="Resid. [a.u.]",
            #lwd=2,
            log="")