0.4.0_[2014-12-02.164623]

DESCRIPTION

@@ -23,6 +23,6 @@ Description: Package provides a collection of various R functions for Luminescen
 Contact: Package Developer Team <team@r-luminescence.de>
 License: GPL-3
 Depends: R (>= 3.1.1), utils
-Imports: methods, XML, shape, rgl, matrixStats, raster, sp, zoo
+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_MinDose3.R calc_MinDose4.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_MaxDose3.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 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 zzz.R

NAMESPACE

@@ -6,4 +6,5 @@ import(matrixStats)
 import(raster)
 import(sp)
 import(zoo)
+import(bbmle)
 exportPattern("^[[:alpha:]]+")

NEWS

@@ -8,6 +8,13 @@ Changes in version 0.4.0 (XX XXXX, 2014):
            including. Image data in slot ‘data’ are stored as
            ‘RasterBrick’
 
+         • ‘RLum.Results’: homogenised structure for containing the
+           following base items in the slot data: 'summary', 'args' and
+           'call'. Where applicable the 'data' slot contains the
+           original input data.  Depending on the function various
+           further slots are added containing additional (intermediate)
+           data and objects,
+
          • ‘set_RLum.Data.Image()’: Set method for class
            ‘RLum.Data.Image’
 
@@ -22,6 +29,19 @@ Changes in version 0.4.0 (XX XXXX, 2014):
          • ‘analyse_pIRIRSequence()’: Function to analyse post-IR IRSL
            sequence measurements (#133),
 
+         • ‘calc_MinDose()’: the previous ‘calc_MinDose3()’ and
+           ‘calc_MinDose4()’ functions were merged to the new
+           ‘calc_MinDose()’ function, which was rewritten from scratch
+           and now contains both the 3- and 4-parametric Minimum Age
+           Models (introducing the new argument ‘par’).  Detailed
+           changes and bugfixes are listed further below,
+
+         • ‘calc_MaxDose()’: a wrapper function that calls
+           ‘calc_MinDose()’, but transforms the data set similar to the
+           method described in Olley et al. (2006).  Rather than
+           estimating the minimum dose of a De distribution, this
+           function estimates the maximum dose.
+
          • ‘get_Layout()’: Helper function to return a list with layout
            definitions for more homogenous plotting,
 
@@ -37,7 +57,14 @@ Changes in version 0.4.0 (XX XXXX, 2014):
 
          • ‘plot_RLum.Data.Image()’: Plot function for
            ‘RLum.Data.Image’ object.  Function also added to wrapper
-           function ‘plot_RLum’
+           function ‘plot_RLum’,
+
+         • ‘plot_RLum.Results()’: Plot function for ‘RLum.Results’
+           objects.  RLum.Results objects created, e.g. by the age
+           model functions may now be passed to ‘plot_RLum.Results()’
+           to create specific plots that previously were generated by
+           the functions themselves.  Function also added to wrapper
+           function ‘plot_RLum’,
 
          • ‘readSPE2R()’: Add support Princenton Instruments *.SPE
            files (camera and spectrometer measurements). Function
@@ -125,27 +152,209 @@ Changes in version 0.4.0 (XX XXXX, 2014):
          • ‘Analyse_SAR.OSLdata()’:
 
              • Error message implemented for non OSL data sets (#130,
-               Georgina King)
+               Georgina King),
+
+             • Added argument ‘dtype’ to provide further curve
+               limitation options,
+
+             • minor code polishing.
+
+         • ‘calc_AliquotSize()’:
+
+             • new argument ‘plot’ (logical): option to (dis-)allow
+               plotting of the Monte Carlo estimation,
+
+             • argument ‘MC.estimate’ was renamed to ‘MC’,
+
+             • new structure of the returned ‘RLum.Results’ object,
+               containing the elements 'summary', 'args', 'call' and
+               'MC'.
+
+             • plotting now done by ‘plot_RLum.Results()’.
+
+         • ‘calc_CentralDose()’:
+
+             • removed argument ‘sample.id’,
+
+             • removed argument ‘print.iterations’,
+
+             • renamed argument ‘input.data’ to ‘data’,
+
+             • new argument ‘'...'’, which is checked for arguments
+               ‘verbose’ (logical) and ‘trace’ (logical) to (dis-)allow
+               (extended) console output,
+
+             • new structure of the returned ‘RLum.Results’ object,
+               containing the elemennts 'summary', 'data', 'args',
+               'call' and 'profile',
+
+             • fixed a bug that occured for non-dispersed data sets and
+               resulted in a virtually infinite loop using up all
+               available memory,
+
+             • plotting now done by
+
+             • plot_RLum.Results().
+
+         • ‘calc_CommonDose()’:
+
+             • removed argument ‘sample.id’,
+
+             • renamed argument ‘input.data’ to ‘data’,
+
+             • new argument ‘'...'’ (currently not used),
+
+             • new structure of the returned ‘RLum.Results’ object,
+               containing the elements 'summary', 'data', 'args' and
+               'call'.
+
+         • ‘calc_CosmicDoseRate()’:
+
+             • new structure of the returned RLum.Results object,
+               containing the elements 'summary', 'args' and 'call'
+
+         • ‘calc_FiniteMixture()’:
+
+             • removed argument ‘sample.id’,
+
+             • removed argument ‘n.iterations’,
+
+             • removed argument ‘main’,
+
+             • renamed argument ‘input.data’ to ‘data’,
+
+             • new argument ‘plot’ option to (dis-)allow plotting when
+               a vector of length > 1 is provided for ‘n.components’,
+
+             • new argument ‘'...'’, which is checked for arguments
+               ‘verbose’ (logical) and ‘trace’ (logical) to (dis-)allow
+               (extended) console output. ‘main’ may be used to set the
+               title of the plot,
+
+             • new structure of the returned ‘RLum.Results’ object,
+               containing the elements 'summary', 'data', 'args',
+               'call', 'mle', 'BIC', 'llik', 'grain.probability',
+               'components' and 'single.comp',
+
+             • plotting now done by ‘plot_RLum.Results()’.
+
+         • ‘calc_FuchsLang2001()’:
+
+             • removed argument ‘sample.mtext’,
+
+             • removed argument ‘sample.id’,
+
+             • removed argument ‘output.terminal’,
+
+             • renamed argument ‘sample’ to ‘data’,
+
+             • renamed argument ‘output.plot’ to ‘plot’,
+
+             • the argument ‘'...'’ is checked for ‘verbose’ (logical)
+               to (dis-)allow console output,
+
+             • new structure of the returned ‘RLum.Results’ object,
+               containing the elements 'summary', 'data', 'args',
+               'call' and 'usedDeValues',
+
+             • plotting now done by ‘plot_RLum.Results()’.
 
-         • ‘calc_MaxDose3()’ & ‘calc_MaxDose4()’:
+         • ‘calc_HomogeneityTest()’:
 
-             • bootstrap method (recycled) as described in Cunningham &
-               Wallinga (2012) implemented,
+             • removed argument ‘sample.id’,
 
-             • upper and lower plot margins of profile log likelihood
-               plots decreased,
+             • renamed argument ‘input.data’ to ‘data’,
 
-             • function now iteratively adjusts boundaries for gamma,
-               sigma and p0 when one of the estimators reaches the
-               lower or upper boundary,
+             • the argument ‘'...'’ is checked for ‘verbose’ (logical)
+               to (dis-)allow console output,
 
-             • new arguments: ‘boundary.sigma’, ‘boundary.gamma’,
-               ‘init.values’, ‘...’ (‘bs.M’, ‘bs.N’, ‘bs.h’,
-               ‘sigmab.sd’),
+             • new structure of the returned ‘RLum.Results’ object,
+               containing the elements 'summary', 'data', 'args' and
+               'call'.
 
-             • removed/merged arguments: ‘sigma.xlb’, ‘sigma.xub’,
-               ‘gamma.xlb’, ‘gamma.xub’, ‘init.gamma’, ‘init.sigma’,
-               ‘init.p0’, ‘output.indices’
+         • ‘calc_MaxDose3()’:
+
+             • Function renamed to ‘calc_MaxDose()’,
+
+             • this is now just a wrapper function that calls the new
+               ‘calc_MinDose()’ function, but transforms the data set
+               similar to the method described in Olley et al. (2006).
+               For further details please see the changes/bugfixes for
+               the ‘calc_MinDose3()’ / ‘calc_MinDose4()’ functions,
+
+             • plotting now done by ‘plot_RLum.Results()’.
+
+         • ‘calc_MinDose3()’ and ‘calc_MinDose4()’
+
+             • the functions ‘calc_MinDose3()’ and ‘calc_MinDose4()’
+               were merged in the new function ‘calc_MinDose()’,
+
+             • renamed argument ‘input.data’ to ‘data’,
+
+             • renamed argument ‘output.plot’ to ‘plot’,
+
+             • removed arguments ‘sample.id’, ‘gamma.xlb’, ‘gamma.xub’,
+               ‘sigma.xlb’, ‘sigma.xub’, ‘mu.xlb’, ‘mu.xub’,
+               ‘init.gamma’, ‘init.sigma’, ‘init.p0’, ‘init.mu’,
+               ‘ignore.NA’, ‘calc.ProfileLikelihoods’,
+               ‘console.ProfileLikelihoods’, ‘console.extendedOutput’,
+               ‘output.indices’,
+
+             • new argument ‘par’ that accepts a numeric value (either
+               3 or 4) to set whether the 3- or 4-parametric Minimum
+               Age Model should be applied,
+
+             • new argument ‘bootstrap’ (logical) to apply the recycled
+               bootstrap approach of Cunningham & Wallinga (2012),
+
+             • new argument ‘boundaries’ that accepts a named list
+               containing values for the lower and upper boundaries for
+               all parameters,
+
+             • new argument ‘init.values’ that accepts a named list
+               containing the starting values for all parameters,
+
+             • new argument ‘'...'’ that, amongst others, checks for
+               ‘debug’ (logical) and ‘verbose’ (logical) to (dis-)allow
+               (extended) console output. Further allowed arguments are
+               ‘bs.M’, ‘bs.N’, ‘bs.h’ and ‘sigmab.sd’ to set various
+               bootstrap parameters,
+
+             • implemented (recycled) bootstrap method as described in
+               Cunningham & Wallinga (2012),
+
+             • function now iteratively adjusts boundaries for sigma
+               when the estimator reaches the upper boundary,
+
+             • function now tries to estimate reasonable starting
+               values for all parameters,
+
+             • calculation and plotting of the maximum log likelihood
+               functions/profiles are now done using the mle2()
+               function of the 'bbmle' package
+
+             • the optimisation routine was changed from 'nlminb' to
+               'optim' using the 'L-BFGS-B' method,
+
+             • confidence intervals for all parameters are now
+               calculated by the 'confint()' method and exclusively on
+               the 95% confidence level
+
+             • the asymmetric error on gamma (i.e., the minimum dose)
+               is now exclusively determined on the 95% confidence
+               interval of the profile log likelihood function for
+               gamma
+
+             • a symmetric standard error for gamma is automatically
+               derived from the 95% confidence interval of the profile
+               log likelihood function by dividing the length of this
+               interval by 3.92 (see Galbraith & Roberts, 2012).
+
+             • new structure of the returned ‘RLum.Results’ object,
+               containing the elements 'summary', 'data', 'args',
+               'call', 'mle', 'BIC', 'confint', 'profile', 'bootstrap',
+
+             • plotting now done by ‘plot_RLum.Results()’.
 
          • ‘calc_OSLLxTxRatio()’:
 
@@ -163,6 +372,14 @@ Changes in version 0.4.0 (XX XXXX, 2014):
              • argument ‘sigmab’ was listed but was so far not
                implement. Fixed (#166)
 
+         • ‘calc_OSLLxTxRatio()’:
+
+             • support of data without given uncertainties.
+
+         • ‘calc_Statistics()’:
+
+             • support of data with ‘NA’ or zero errors
+
          • ‘calc_TLLxTxRatio()’:
 
              • Lx/Tx ratio wrongly calculated as due to a coding error
@@ -206,7 +423,14 @@ Changes in version 0.4.0 (XX XXXX, 2014):
 
              • rotate-Option added to Abanico Plot,
 
-             • minor modifications of layout definitions.
+             • minor modifications of layout definitions (#124),
+
+             • ‘grid.col’ bug fixed (#149),
+
+             • error message for data with zero or without errors added
+               (#154),
+
+             • support of ‘par(mfcol())’.
 
          • ‘plot_DRTResults()’:
 
@@ -236,7 +460,31 @@ Changes in version 0.4.0 (XX XXXX, 2014):
          • ‘plot_Histogram()’:
 
              • Change default y-axis labelling from 'Counts' to
-               'Frequency'
+               'Frequency',
+
+             • support of ‘par(mfcol())’ (#146),
+
+             • support of data without and ‘NA’-values for error values
+               (#152, #162),
+
+             • implementation of ‘calc_Stats()’-call for extended
+               statistic summary,
+
+             • support of summary keywords "kurtosis" and "skewness"
+
+         • ‘plot_KDE()’:
+
+             • wrong x-axis and y-axis limit calculation fixed (#158),
+
+             • renaming and extension of summary and ‘summary.pos’
+               parameter,
+
+             • plot now longer shows a density error when no error
+               exists (#160),
+
+             • De.stats error fixed (#163),
+
+             • support of ‘par(mfcol())’.
 
          • ‘plot_GrowthCurve()’:
 
@@ -279,7 +527,10 @@ Changes in version 0.4.0 (XX XXXX, 2014):
                single plot modus ‘abline’ is more sufficiently used as
                separat function call,
 
-             • now reset ‘par’ parameters suffciently.
+             • now reset ‘par’ parameters suffciently,
+
+             • add argument ‘combine’ to allow fast combining of curves
+               in single plot window.
 
          • ‘plot_RLum.Data.Curve()’:
 
@@ -323,7 +574,12 @@ Changes in version 0.4.0 (XX XXXX, 2014):
 
              • If the stimulator is infrared light the ‘recordType’
                will be set to ‘IRSL’. This makes the curve types more
-               consistent with the commonly applied nomenclature.
+               consistent with the commonly applied nomenclature,
+
+             • now the function automatically converts time values to
+               temperature values also for spectra data (#121);
+               behavious is triggered with the argument
+               ‘recalculate.TL.curves’
 
   Internals:
 
@@ -332,5 +588,8 @@ Changes in version 0.4.0 (XX XXXX, 2014):
 
          • dependency to package 'Rserve' removed,
 
-         • dependcy to package 'zoo' added (used for running means).
+         • dependcy to package 'zoo' added (used for running means),
+
+         • dependency to package 'bbmle' added (used for maximum
+           likelihood estimations).