Prepare CRAN submission

NEWS

@@ -9,7 +9,7 @@ Changes in version 0.8.0 (Feburary 9th,2018):
            al., 2018
 
          • ‘analyse_Al2O3C_CrossTalk()’: Function to analyse data to
-           analyse cross talk measurments as shown in Kreutzer et al.,
+           analyse crosstalk measurements as shown in Kreutzer et al.,
            2018
 
          • ‘analyse_Al2O3C_Measurement()’: Function to analyse Al2O3:C
@@ -84,7 +84,7 @@ Changes in version 0.8.0 (Feburary 9th,2018):
                respected,
 
              • mixing of curves (e.g., regenerated first, natural
-               second) led to a crash of the function, even the new
+               second) led to a crash of the function, even the
                structure was correctly specified; fixed (#61),
 
              • the function will not break anymore uncontrolled of both
@@ -109,7 +109,7 @@ Changes in version 0.8.0 (Feburary 9th,2018):
          • ‘calc_Kars2008()’
 
              • In some cases the calculated LxTx values of the
-               simulated natural dose response curve were slightly
+               simulated natural dose-response curve were slightly
                underestimated and its maximum value differed from the
                individually calculated nN(ss) value. The approach to
                calculate the natural DRC was changed and now yields a
@@ -166,7 +166,7 @@ Changes in version 0.8.0 (Feburary 9th,2018):
 
          • ‘read_BIN2R()’
 
-             • The function unexpectetly dropped are warning for an
+             • The function unexpectedly dropped are warning for an
                unused connection; fixed,
 
              • if a file link was provided and the argument ‘pattern’
@@ -208,10 +208,10 @@ Changes in version 0.8.0 (Feburary 9th,2018):
                cases for ‘NA’ values in the byte position ‘SEQUENCE’;
                fixed,
 
-             • the compatibility mode was extended to limit the maxium
-               number of points for one curve to 9,999 (if the option
-               is chosen). This gives more compatibility with older
-               versions of the Analyst.
+             • the compatibility mode was extended, now limiting the
+               maxmium number of points for one curve to 9,999 (if the
+               option is chosen). This improves the compatibility with
+               older versions of the Analyst.
 
   Internals:
 

R/RcppExports.R

@@ -2,18 +2,18 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 create_UID <- function() {
-    .Call(`_Luminescence_create_UID`)
+    .Call('_Luminescence_create_UID', PACKAGE = 'Luminescence')
 }
 
 src_analyse_IRSARRF_SRS <- function(values_regenerated_limited, values_natural_limited, vslide_range, n_MC, trace = FALSE) {
-    .Call(`_Luminescence_analyse_IRSARRF_SRS`, values_regenerated_limited, values_natural_limited, vslide_range, n_MC, trace)
+    .Call('_Luminescence_analyse_IRSARRF_SRS', PACKAGE = 'Luminescence', values_regenerated_limited, values_natural_limited, vslide_range, n_MC, trace)
 }
 
 src_create_RLumDataCurve_matrix <- function(DATA, VERSION, NPOINTS, LTYPE, LOW, HIGH, AN_TEMP, TOLDELAY, TOLON, TOLOFF) {
-    .Call(`_Luminescence_create_RLumDataCurve_matrix`, DATA, VERSION, NPOINTS, LTYPE, LOW, HIGH, AN_TEMP, TOLDELAY, TOLON, TOLOFF)
+    .Call('_Luminescence_create_RLumDataCurve_matrix', PACKAGE = 'Luminescence', DATA, VERSION, NPOINTS, LTYPE, LOW, HIGH, AN_TEMP, TOLDELAY, TOLON, TOLOFF)
 }
 
 src_get_XSYG_curve_values <- function(s) {
-    .Call(`_Luminescence_src_get_XSYG_curve_values`, s)
+    .Call('_Luminescence_src_get_XSYG_curve_values', PACKAGE = 'Luminescence', s)
 }
 

RLum.BuildResults/Luminescence_0.8.0-Functions.csv

@@ -8,13 +8,13 @@
 "analyse_Al2O3C_Measurement","Al2O3:C Passive Dosimeter Measurement Analysis","The function provides the analysis routines for measurements on a FI lexsyg SMART reader using Al2O3:C pellets according to Kreutzer et al., XXXX","0.1.8","2018-02-08","13:28:31
 ","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)<br />  R Luminescence Package Team","Kreutzer, S. (2018). analyse_Al2O3C_Measurement(): Al2O3:C Passive Dosimeter Measurement Analysis. Function version 0.1.8. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
-"analyse_baSAR","Bayesian models (baSAR) applied on luminescence data","This function allows the application of Bayesian models on luminescence data, measured with the single-aliquot regenerative-dose (SAR, Murray and Wintle, 2000) protocol. In particular, it follows the idea proposed by Combes et al., 2015 of using an hierarchical model for estimating a central equivalent dose from a set of luminescence measurements. This function is (I) the adaption of this approach for the R environment and (II) an extension and a technical refinement of the published code.","0.1.29","2018-01-21","17:22:38
+"analyse_baSAR","Bayesian models (baSAR) applied on luminescence data","This function allows the application of Bayesian models on luminescence data, measured with the single-aliquot regenerative-dose (SAR, Murray and Wintle, 2000) protocol. In particular, it follows the idea proposed by Combes et al., 2015 of using an hierarchical model for estimating a central equivalent dose from a set of luminescence measurements. This function is (I) the adaption of this approach for the R environment and (II) an extension and a technical refinement of the published code.","0.1.29","2018-02-08","18:09:55
 ","Norbert Mercier, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)  <br /> Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)  <br /> The underlying Bayesian model based on a contribution by Combes et al., 2015.<br />  R Luminescence Package Team","Mercier, N., Kreutzer, S. (2018). analyse_baSAR(): Bayesian models (baSAR) applied on luminescence data. Function version 0.1.29. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
 "analyse_FadingMeasurement","Analyse fading measurements and returns the fading rate per decade (g-value)","The function analysis fading measurements and returns a fading rate including an error estimation. The function is not limited to standard fading measurements, as can be seen, e.g., Huntley and Lamothe 2001. Additionally, the density of recombination centres (rho') is estimated after Kars et al. 2008.","0.1.5","2018-01-21","17:22:38
 ","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)  <br /> Christoph Burow, University of Cologne (Germany)<br />  R Luminescence Package Team","Kreutzer, S., Burow, C. (2018). analyse_FadingMeasurement(): Analyse fading measurements and returns the fading rate per decade (g-value). Function version 0.1.5. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
-"analyse_IRSAR.RF","Analyse IRSAR RF measurements","Function to analyse IRSAR RF measurements on K-feldspar samples, performed using the protocol according to Erfurt et al. (2003) and beyond.","0.7.5","2018-01-21","17:22:38
+"analyse_IRSAR.RF","Analyse IRSAR RF measurements","Function to analyse IRSAR RF measurements on K-feldspar samples, performed using the protocol according to Erfurt et al. (2003) and beyond.","0.7.5","2018-02-08","18:55:30
 ","Sebastian Kreutzer, IRAMAT-CRP2A, Université Bordeaux Montaigne (France)<br />  R Luminescence Package Team","Kreutzer, S. (2018). analyse_IRSAR.RF(): Analyse IRSAR RF measurements. Function version 0.7.5. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
 "analyse_pIRIRSequence","Analyse post-IR IRSL measurement sequences","The function performs an analysis of post-IR IRSL sequences including curve fitting on  RLum.Analysis  objects.","0.2.4","2018-01-28","19:53:33
@@ -38,7 +38,7 @@
 "apply_CosmicRayRemoval","Function to remove cosmic rays from an RLum.Data.Spectrum S4 class object","The function provides several methods for cosmic ray removal and spectrum smoothing for an RLum.Data.Spectrum S4 class object","0.2.1","2018-01-21","17:22:38
 ","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne<br /> (France)<br />  R Luminescence Package Team","Kreutzer, S. (2018). apply_CosmicRayRemoval(): Function to remove cosmic rays from an RLum.Data.Spectrum S4 class object. Function version 0.2.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
-"apply_EfficiencyCorrection","Function to apply spectral efficiency correction to RLum.Data.Spectrum S4<br /> class objects","The function allows spectral efficiency corrections for RLum.Data.Spectrum S4 class objects","0.1.1","2018-01-21","17:22:38
+"apply_EfficiencyCorrection","Function to apply spectral efficiency correction to RLum.Data.Spectrum S4<br /> class objects","The function allows spectral efficiency corrections for RLum.Data.Spectrum S4 class objects","0.1.1","2018-02-08","18:09:55
 ","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France) <br /> Johannes Friedrich, University of Bayreuth (Germany)<br />  R Luminescence Package Team","Kreutzer, S., Friedrich, J. (2018). apply_EfficiencyCorrection(): Function to apply spectral efficiency correction to RLum.Data.Spectrum S4 class objects. Function version 0.1.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
 "as","as() - RLum-object coercion","for  [RLum.Analysis-class]   for  [RLum.Data.Curve-class]   for  [RLum.Data.Image-class]   for  [RLum.Data.Spectrum-class]   for  [RLum.Results-class]",NA,NA,NA,NA,NA
@@ -103,14 +103,14 @@
 "calc_Statistics","Function to calculate statistic measures","This function calculates a number of descriptive statistics for estimates with a given standard error (SE), most fundamentally using error-weighted approaches.","0.1.7","2018-01-21","17:22:38
 ","Michael Dietze, GFZ Potsdam (Germany)<br />  R Luminescence Package Team","Dietze, M. (2018). calc_Statistics(): Function to calculate statistic measures. Function version 0.1.7. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
-"calc_ThermalLifetime","Calculates the Thermal Lifetime using the Arrhenius equation","The function calculates the thermal lifetime of charges for given E (in eV), s (in 1/s) and T (in deg. C.) parameters. The function can be used in two operational modes:","0.1.0","2018-01-21","17:22:38
+"calc_ThermalLifetime","Calculates the Thermal Lifetime using the Arrhenius equation","The function calculates the thermal lifetime of charges for given E (in eV), s (in 1/s) and T (in deg. C.) parameters. The function can be used in two operational modes:","0.1.0","2018-02-08","18:09:55
 ","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)<br />  R Luminescence Package Team","Kreutzer, S. (2018). calc_ThermalLifetime(): Calculates the Thermal Lifetime using the Arrhenius equation. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
 "calc_TLLxTxRatio","Calculate the Lx/Tx ratio for a given set of TL curves  [beta version]","Calculate Lx/Tx ratio for a given set of TL curves.","0.3.2","2018-01-21","17:22:38
 ","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)  <br /> Christoph Schmidt, University of Bayreuth (Germany)<br />  R Luminescence Package Team","Kreutzer, S., Schmidt, C. (2018). calc_TLLxTxRatio(): Calculate the Lx/Tx ratio for a given set of TL curves [beta version]. Function version 0.3.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
-"calc_WodaFuchs2008","Obtain the equivalent dose using the approach of Woda and Fuchs 2008","The function generates a histogram-like reorganisation of the data, to assess counts per bin. The log-transformed counts per bin are used to calculate the second derivative of the data (i.e., the curcature of the curve) and to find the central value of the bin hosting the distribution maximum. A normal distribution model is fitted to the counts per bin data to estimate the dose distribution parameters. The uncertainty of the model is estimated based on all input equivalent doses smaller that the modelled central value.","0.2.0","2018-01-21","17:22:38
-","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France), <br /> Michael Dietze, GFZ Potsdam (Germany)<br />  R Luminescence Package Team","Kreutzer, S., Dietze, M. (2018). calc_WodaFuchs2008(): Obtain the equivalent dose using the approach of Woda and Fuchs 2008. Function version 0.2.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
+"calc_WodaFuchs2008","Obtain the equivalent dose using the approach by Woda and Fuchs 2008","The function generates a histogram-like reorganisation of the data, to assess counts per bin. The log-transformed counts per bin are used to calculate the second derivative of the data (i.e., the curvature of the curve) and to find the central value of the bin hosting the distribution maximum. A normal distribution model is fitted to the counts per bin data to estimate the dose distribution parameters. The uncertainty of the model is estimated based on all input equivalent doses smaller that of the modelled central value.","0.2.0","2018-02-08","14:24:10
+","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France), <br /> Michael Dietze, GFZ Potsdam (Germany)<br />  R Luminescence Package Team","Kreutzer, S., Dietze, M. (2018). calc_WodaFuchs2008(): Obtain the equivalent dose using the approach by Woda and Fuchs 2008. Function version 0.2.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
 "convert_Activity2Concentration","Convert Nuclide Activities to Concentrations and Vice Versa","The function performs the conversion of the specific activities into concentrations and vice versa for the nuclides U-238, Th-232 and K-40 to harmonise the measurement unit with the required data input unit of potential analytical tools for, e.g. dose rate calculation or related functions such as  use_DRAC .","0.1.0","2018-01-21","17:22:38
 ","Margret C. Fuchs, Helmholtz-Institut Freiberg for Resource Technology (Germany)<br />  R Luminescence Package Team","Fuchs, M.C. (2018). convert_Activity2Concentration(): Convert Nuclide Activities to Concentrations and Vice Versa. Function version 0.1.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
@@ -196,7 +196,7 @@
 "merge_RLum.Analysis","Merge function for RLum.Analysis S4 class objects","Function allows merging of RLum.Analysis objects and adding of allowed objects to an RLum.Analysis.","0.2.0","2018-01-21","17:22:38
 ","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)<br />  R Luminescence Package Team","Kreutzer, S. (2018). merge_RLum.Analysis(): Merge function for RLum.Analysis S4 class objects. Function version 0.2.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
-"merge_RLum.Data.Curve","Merge function for RLum.Data.Curve S4 class objects","Function allows merging of RLum.Data.Curve objects in different ways","0.2.0","2018-01-21","17:22:38
+"merge_RLum.Data.Curve","Merge function for RLum.Data.Curve S4 class objects","Function allows merging of RLum.Data.Curve objects in different ways","0.2.0","2018-02-08","18:09:55
 ","Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)<br />  R Luminescence Package Team","Kreutzer, S. (2018). merge_RLum.Data.Curve(): Merge function for RLum.Data.Curve S4 class objects. Function version 0.2.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.0. https://CRAN.R-project.org/package=Luminescence
 "
 "merge_RLum","General merge function for RLum S4 class objects","Function calls object-specific merge functions for RLum S4 class objects.","0.1.2","2018-01-21","17:22:38