0.4.3_[2015-04-16.114824]

Author: tzerk

DESCRIPTION

@@ -2,7 +2,7 @@ Package: Luminescence
 Type: Package
 Title: Comprehensive Luminescence Dating Data Analysis
 Version: 0.4.3
-Date: 2015-XX-XX [upcoming]
+Date: 2015-04-17
 Author: Sebastian Kreutzer [aut, trl, cre],
   Michael Dietze [aut],
   Christoph Burow [aut],

NEWS

@@ -1,6 +1,6 @@
 NEWS for the R Package Luminescence
 
-Changes in version 0.4.3 (XXth, 2015):
+Changes in version 0.4.3 (17th, 2015):
 
   Bugfixes and changes:
 
@@ -67,14 +67,51 @@ Changes in version 0.4.3 (XXth, 2015):
              • argument 'breaks' removed from the argument list,
                however, supported via the ‘'...'’ argument.
 
+         • ‘plot_GrowthCurve()’
+
+             • Error estimation using the Monte Carlo runs for the
+               fitting function ‘fit.method = "EXP+LIN"’ and
+               ‘fit.method = "EXP+EXP"’ results in false values, as the
+               Monte Carlo simulation was fed by mistake with wrong
+               input variables (introduced in version 0.4.2 with the
+               uniroot function) ... fixed,
+
+             • the function brook if the uniroot algorithm was not able
+               to find a solution within the given ranges, fixed. De
+               will become NA instead and the function continues.
+
+         • ‘plot_RLum.Data.Spectrum()’
+
+             • Colour handing changed towards a more logical behaviour
+               for ‘plot.type = 'single'’.  The color now changes only
+               the colour of the points and the argument ‘rug’ is now
+               recognised also by this plot type. Automatic wavelength
+               colouring for points for in this plot type has been
+               removed.
+
+             • same changes are made for ‘plot.type =
+               'multiple.lines'’,
+
+             • instead of just plotting a new x-axis when the argument
+               ‘xaxis.energy = TRUE’ is used, the spectrum (intensity)
+               is now proper re-calculated (#192),
+
+             • minor code polishing.
+
          • ‘plot_RLum.Anaysis()’
 
              • Setting the argument ‘combine = TRUE’ for 'OSL' and
                'IRSL' caused an error related to the missing argument
                'curve.transformation'; corrected.,
 
              • colour handling for setting ‘combine = TRUE’ improved.
-               It now works as for ‘plot.default’.
+               It now works as for ‘plot.default’,
+
+             • support for ‘xlim’ and ‘ylim’ in the non-combined mode,
+
+             • combine mode (‘combine = TRUE’) is no more limited to an
+               input object of similar curves. Now the plot function
+               tries to combine curves of similar type automatically.
 
          • ‘readBIN2R()’
 

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 0.3.1
+  ## version 0.3.2
   # ===========================================================================
 
   ##TODO - keep fit.range in mind for De calculation
@@ -19,6 +19,7 @@ analyse_IRSAR.RF<- structure(function(# Analyse IRSAR RF measurements
   ###   also on the regenerated curve? At least there should be a clever check.
   ### - currently no feedback on the outlier removal are given
   ### - CHECK ERROR CALCULATION!
+  ### - RETURN values are not sufficiently described.
 
   object,
   ### \code{\linkS4class{RLum.Analysis}} (\bold{required}):
@@ -618,6 +619,7 @@ else if(method == "SLIDE"){
   values.residuals <- temp.sliding[[3]]
   temp.trend.fit <- temp.sliding[[4]]
   values.natural.limited.full <- temp.sliding[[5]]
+  Trend.slope <- temp.sliding[[4]][2]
 
 
   # MC runs for error calculation ---------------------------------------------------------------
@@ -1069,6 +1071,7 @@ if(plot==TRUE){
   if(!exists("De.error.lower")){De.error.lower  <- NA}
   if(!exists("De.error.upper")){De.error.upper  <- NA}
   if(!exists("De.status")){De.status  <- NA}
+  if(!exists("Trend.slope")){Trend.slope  <- NA}
   if(!exists("fit")){fit  <- NA}
 
 
@@ -1080,6 +1083,7 @@ if(plot==TRUE){
                           De.error.lower = De.error.lower,
                           De.error.upper = De.error.upper,
                           De.status = De.status,
+                          Trend.slope =  Trend.slope,
                           row.names=NULL)
 
   newRLumResults.analyse_IRSAR.RF <- set_RLum.Results(

R/calc_Statistics.R

@@ -30,7 +30,7 @@ calc_Statistics <- structure(function(# Function to calculate statistic measures
   ## Check input data
   if(is(data, "RLum.Results") == FALSE &
        is(data, "data.frame") == FALSE) {
-    stop(paste("[calc_Statistics()] Error: Input data format is neither",
+    stop(paste("[calc_Statistics()] Input data format is neither",
                "'data.frame' nor 'RLum.Results'"))
   } else {
     if(is(data, "RLum.Results") == TRUE) {
@@ -61,7 +61,7 @@ calc_Statistics <- structure(function(# Function to calculate statistic measures
   } else if(weight.calc == "square") {
     S.weights <- 1 / data[,2]^2
   } else {
-    stop ("[calc_Statistics] Error: Weight calculation type not supported!")
+    stop ("[calc_Statistics()] Weight calculation type not supported!")
   }
 
   S.weights <- S.weights / sum(S.weights)