Commit before CRAN submission

NEWS

@@ -4,22 +4,22 @@ Changes in version 0.4.5 (10th August, 2015):
 
   Changes S4-objects, methods, classes:
 
-         • With the (internal) switch from inlinedocs to roxygen2 for
-           the package manual compilation, some help page entries for
-           our S4-methods got unintentionally lost. Unfortunately this
-           remained unnoticed until the package was alread on CRAN.
-           This issue has been corrected by picking up some code
+         • With the (internal) switch from inlinedocs to roxygen2 used
+           for the package manual compilation, some help page entries
+           for our S4-methods got unintentionally lost. Unfortunately
+           this remained unnoticed until the package was already on
+           CRAN. This issue has been corrected by picking up some code
            changes we already made for the package version 0.5.0.
            However, this may become confusing in terms of warning
            messages ('deprecated') appearing by using object specific
            'get' or 'set' functions such as ‘get_RLum.Analysis’. The
            function calls are still working, but will be defunct in
            version 0.5.0 and removed in version 0.6.0 or better to say
            become part of more general calls like ‘get_RLum’,
-           ‘set_RLum’ and so on. In fact this switch has already been
-           made, but the 'old' functions are still supported and the
-           warning messages may point on necessary changes in your
-           scripts.  Changes in detail:
+           ‘set_RLum’ and so on.  With this update in fact this switch
+           has already been made, but the 'old' functions are still
+           supported and the warning messages may point on future
+           necessary changes in your scripts.  Changes in detail:
 
              • Depraceted S4-generics: ‘set_RLum.Analyis’,
                ‘set_RLum.Data.Curve’, ‘set_RLum.Data.Image’,

R/calc_IEU.R

@@ -9,15 +9,22 @@
 #' @param data \code{\linkS4class{RLum.Results}} or \link{data.frame}
 #' (\bold{required}): for \code{data.frame}: two columns with De
 #' \code{(data[,1])} and De error \code{(values[,2])}
+#'
 #' @param a \code{\link{numeric}}: slope
+#'
 #' @param b \code{\link{numeric}}: intercept
+#'
 #' @param interval \code{\link{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]
+#'
 #' @param decimal.point \code{\link{numeric}} (with default): number of decimal
 #' points for rounding calculations (e.g. 2)
+#'
 #' @param plot \code{\link{logical}} (with default): plot output
+#'
 #' @param \dots further arguments (\code{trace, verbose}).
+#'
 #' @return Returns a plot (optional) and terminal output. In addition an
 #' \code{\linkS4class{RLum.Results}} object is returned containing the
 #' following element:
@@ -30,18 +37,25 @@
 #'
 #' The output should be accessed using the function
 #' \code{\link{get_RLum}}.
-#' @section Function version: 0.1
+#'
+#' @section Function version: 0.1.0
+#'
 #' @author Rachel Smedley, Geography & Earth Sciences, Aberystwyth University
 #' (United Kingdom) \cr Based on an excel spreadsheet and accompanying macro
 #' written by Kristina Thomsen.
+#'
 #' @seealso \code{\link{plot}}, \code{\link{calc_CommonDose}},
 #' \code{\link{calc_CentralDose}}, \code{\link{calc_FiniteMixture}},
 #' \code{\link{calc_FuchsLang2001}}, \code{\link{calc_MinDose}}
-#' @references Thomsen, K.J., Murray, A.S., Boetter-Jensen, L. & Kinahan, J.,
+#'
+#' @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. & Kinahan, J.,
 #' 2007. Determination of burial dose in incompletely bleached fluvial samples
 #' using single grains of quartz. Radiation Measurements 42, 370-379.
-#' @examples
 #'
+#' @examples
 #'
 #' ## load data
 #' data(ExampleData.DeValues, envir = environment())

R/plot_AbanicoPlot.R

@@ -503,6 +503,13 @@ plot_AbanicoPlot <- function(
     breaks <- "Sturges"
   }
 
+  if ("fun" %in% names(extraArgs)) {
+    fun <- list(...)$fun
+
+  } else {
+    fun <- FALSE
+  }
+
   ## check for negative values
   if(min(De.global) <= 0) {
     stop("[plot_AbanicoPlot] Error: Data contains negative or zero values.")
@@ -3214,6 +3221,10 @@ plot_AbanicoPlot <- function(
       pin = par.old.pin,
       family = par.old.family)
 
+  ##sTeve
+  if(fun){sTeve()}
+
+
   ## create and resturn numeric output
   if(output == TRUE) {
     return(list(xlim = limits.x,

R/zzz.R

@@ -5,7 +5,7 @@
 ##==============================================================================
 ##author: R Luminescence Package Team
 ##organisation:
-##version.: 0.2
+##version.: 0.2.0
 ##date: 2013-11-10
 ##==============================================================================
 # Set namespace .LuminescenceEnv ------------------------------------------
@@ -14,7 +14,7 @@
 # Assign variables to Namespace -------------------------------------------
 ##variable col to define colours in the functions for output
 assign("col",
-       unlist(colors())[c(261,552,51,62,76,151,451,474,654,657,100,513,23,612,129,27,551,393,80)],
+       unlist(colors())[c(261,552,51,62,76,151,451,474,654,657,100,513,23,612,129,27,551,393,80,652,555)],
        pos = ".LuminescenceEnv",
        envir = .LuminescenceEnv)
 

RLum.BuildResults/Luminescence_0.4.5-Functions.csv

@@ -30,7 +30,7 @@
 ","<br /> Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne<br /> (France) Christoph Burow, University of Cologne (Germany)<br />  R Luminescence Package Team"
 "calc_HomogeneityTest","Apply a simple homogeneity test after Galbraith (2003)","<br /> A simple homogeneity test for De estimates<br />","0.2","2015-07-23","17:09:29
 ","<br /> Christoph Burow, University of Cologne (Germany)<br />  R Luminescence Package Team"
-"calc_IEU","Apply the internal-external-uncertainty (IEU) model after Thomsen et al.<br /> (2007) to a given De distribution","<br /> Function to calculate the IEU De for a De data set.<br />","0.1","2015-07-23","17:09:29
+"calc_IEU","Apply the internal-external-uncertainty (IEU) model after Thomsen et al.<br /> (2007) to a given De distribution","<br /> Function to calculate the IEU De for a De data set.<br />","0.1.0","2015-08-09","23:43:58
 ","<br /> Rachel Smedley, Geography & Earth Sciences, Aberystwyth University<br /> (United Kingdom)   Based on an excel spreadsheet and accompanying macro<br /> written by Kristina Thomsen.<br />  R Luminescence Package Team"
 "calc_MaxDose","Apply the maximum age model to a given De distribution","<br /> Function to fit the maximum age model to De data. This is a wrapper function<br /> that calls calc_MinDose() and applies a similiar approach as described in<br /> Olley et al. (2006).<br />","0.3","2015-04-30","11:53:34
 ","<br /> Christoph Burow, University of Cologne (Germany)   Based on a<br /> rewritten S script of Rex Galbraith, 2010  <br />  R Luminescence Package Team"
@@ -87,7 +87,7 @@
 ","<br /> Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne<br /> (France)<br />  R Luminescence Package Team"
 "merge_RLum.Results","General accessor function for RLum S4 class objects","<br /> Function calls object-specific get functions for RLum S4 class objects.<br />","0.1
 ",NA,NA,"<br /> Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne<br /> (France)<br />  R Luminescence Package Team"
-"plot_AbanicoPlot","Function to create an Abanico Plot.","<br /> A plot is produced which allows comprehensive presentation of data precision<br /> and its dispersion around a central value as well as illustration of a<br /> kernel density estimate, histogram and/or dot plot of the dose values.<br />","0.1.2","2015-07-23","17:09:29
+"plot_AbanicoPlot","Function to create an Abanico Plot.","<br /> A plot is produced which allows comprehensive presentation of data precision<br /> and its dispersion around a central value as well as illustration of a<br /> kernel density estimate, histogram and/or dot plot of the dose values.<br />","0.1.2","2015-08-10","00:07:10
 ","<br /> Michael Dietze, GFZ Potsdam (Germany),  Sebastian Kreutzer,<br /> IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)  Inspired by a plot<br /> introduced by Galbraith & Green (1990)<br />  R Luminescence Package Team"
 "plot_DRTResults","Visualise dose recovery test results","<br /> The function provides a standardised plot output for dose recovery test<br /> measurements.<br />","0.1.6","2015-07-23","17:09:29
 ","<br /> Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne<br /> (France), Michael Dietze, GFZ Potsdam (Germany)<br />  R Luminescence Package Team"

RLum.BuildResults/Luminescence_0.4.5-Functions.html

@@ -364,11 +364,11 @@ <h4 align="center"> [version: 0.4.5 ]</h4>
 </td>
 <td class=cellinside><br /> Function to calculate the IEU De for a De data set.<br />
 </td>
-<td class=cellinside>0.1
+<td class=cellinside>0.1.0
 </td>
-<td class=cellinside>2015-07-23
+<td class=cellinside>2015-08-09
 </td>
-<td class=cellinside>17:09:29
+<td class=cellinside>23:43:58
 
 </td>
 <td class=cellinside><br /> Rachel Smedley, Geography & Earth Sciences, Aberystwyth University<br /> (United Kingdom)   Based on an excel spreadsheet and accompanying macro<br /> written by Kristina Thomsen.<br />  R Luminescence Package Team
@@ -984,9 +984,9 @@ <h4 align="center"> [version: 0.4.5 ]</h4>
 </td>
 <td class=cellinside>0.1.2
 </td>
-<td class=cellinside>2015-07-23
+<td class=cellinside>2015-08-10
 </td>
-<td class=cellinside>17:09:29
+<td class=cellinside>00:07:10
 
 </td>
 <td class=cellinside><br /> Michael Dietze, GFZ Potsdam (Germany),  Sebastian Kreutzer,<br /> IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)  Inspired by a plot<br /> introduced by Galbraith & Green (1990)<br />  R Luminescence Package Team

RLum.BuildResults/Luminescence_0.4.5-Functions.tex

@@ -1,5 +1,5 @@
-% latex table generated in R 3.2.1 by xtable 1.7-4 package
-% Sun Aug  9 23:16:59 2015
+% latex table generated in R 3.3.0 by xtable 1.7-4 package
+% Mon Aug 10 00:10:41 2015
 \begin{table}[ht]
 \centering
 \begin{tabular}{rlllllll}
@@ -37,7 +37,7 @@
  & $<$br /$>$ Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne$<$br /$>$ (France) Christoph Burow, University of Cologne (Germany)$<$br /$>$  R Luminescence Package Team \\ 
   16 & calc\_HomogeneityTest & Apply a simple homogeneity test after Galbraith (2003) & $<$br /$>$ A simple homogeneity test for De estimates$<$br /$>$ & 0.2 & 2015-07-23 & 17:09:29
  & $<$br /$>$ Christoph Burow, University of Cologne (Germany)$<$br /$>$  R Luminescence Package Team \\ 
-  17 & calc\_IEU & Apply the internal-external-uncertainty (IEU) model after Thomsen et al.$<$br /$>$ (2007) to a given De distribution & $<$br /$>$ Function to calculate the IEU De for a De data set.$<$br /$>$ & 0.1 & 2015-07-23 & 17:09:29
+  17 & calc\_IEU & Apply the internal-external-uncertainty (IEU) model after Thomsen et al.$<$br /$>$ (2007) to a given De distribution & $<$br /$>$ Function to calculate the IEU De for a De data set.$<$br /$>$ & 0.1.0 & 2015-08-09 & 23:43:58
  & $<$br /$>$ Rachel Smedley, Geography \& Earth Sciences, Aberystwyth University$<$br /$>$ (United Kingdom)   Based on an excel spreadsheet and accompanying macro$<$br /$>$ written by Kristina Thomsen.$<$br /$>$  R Luminescence Package Team \\ 
   18 & calc\_MaxDose & Apply the maximum age model to a given De distribution & $<$br /$>$ Function to fit the maximum age model to De data. This is a wrapper function$<$br /$>$ that calls calc\_MinDose() and applies a similiar approach as described in$<$br /$>$ Olley et al. (2006).$<$br /$>$ & 0.3 & 2015-04-30 & 11:53:34
  & $<$br /$>$ Christoph Burow, University of Cologne (Germany)   Based on a$<$br /$>$ rewritten S script of Rex Galbraith, 2010  $<$br /$>$  R Luminescence Package Team \\ 
@@ -94,7 +94,7 @@
  & $<$br /$>$ Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne$<$br /$>$ (France)$<$br /$>$  R Luminescence Package Team \\ 
   49 & merge\_RLum.Results & General accessor function for RLum S4 class objects & $<$br /$>$ Function calls object-specific get functions for RLum S4 class objects.$<$br /$>$ & 0.1
  &  &  & $<$br /$>$ Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne$<$br /$>$ (France)$<$br /$>$  R Luminescence Package Team \\ 
-  50 & plot\_AbanicoPlot & Function to create an Abanico Plot. & $<$br /$>$ A plot is produced which allows comprehensive presentation of data precision$<$br /$>$ and its dispersion around a central value as well as illustration of a$<$br /$>$ kernel density estimate, histogram and/or dot plot of the dose values.$<$br /$>$ & 0.1.2 & 2015-07-23 & 17:09:29
+  50 & plot\_AbanicoPlot & Function to create an Abanico Plot. & $<$br /$>$ A plot is produced which allows comprehensive presentation of data precision$<$br /$>$ and its dispersion around a central value as well as illustration of a$<$br /$>$ kernel density estimate, histogram and/or dot plot of the dose values.$<$br /$>$ & 0.1.2 & 2015-08-10 & 00:07:10
  & $<$br /$>$ Michael Dietze, GFZ Potsdam (Germany),  Sebastian Kreutzer,$<$br /$>$ IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)  Inspired by a plot$<$br /$>$ introduced by Galbraith \& Green (1990)$<$br /$>$  R Luminescence Package Team \\ 
   51 & plot\_DRTResults & Visualise dose recovery test results & $<$br /$>$ The function provides a standardised plot output for dose recovery test$<$br /$>$ measurements.$<$br /$>$ & 0.1.6 & 2015-07-23 & 17:09:29
  & $<$br /$>$ Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne$<$br /$>$ (France), Michael Dietze, GFZ Potsdam (Germany)$<$br /$>$  R Luminescence Package Team \\ 

inst/NEWS.Rd

@@ -4,16 +4,16 @@
 
   \subsection{Changes S4-objects, methods, classes}{
    \itemize{
-      \item With the (internal) switch from inlinedocs to roxygen2 for the package manual compilation,
+      \item With the (internal) switch from inlinedocs to roxygen2 used for the package manual compilation,
       some help page entries for our S4-methods got unintentionally lost. Unfortunately this
-      remained unnoticed until the package was alread on CRAN. This issue has been corrected
+      remained unnoticed until the package was already on CRAN. This issue has been corrected
       by picking up some code changes we already made for the package version 0.5.0. However,
       this may become confusing in terms of warning messages ('deprecated') appearing by using object specific
       'get' or 'set' functions such as \code{get_RLum.Analysis}. The function calls are still working, but will
       be defunct in version 0.5.0 and removed in version 0.6.0 or better to say become part
-      of more general calls like \code{get_RLum},
-      \code{set_RLum} and so on. In fact this switch has already been made, but the 'old' functions
-      are still supported and the warning messages may point on necessary changes in your scripts.
+      of more general calls like \code{get_RLum}, \code{set_RLum} and so on.
+      With this update in fact this switch has already been made, but the 'old' functions
+      are still supported and the warning messages may point on future necessary changes in your scripts.
       Changes in detail:
 
       \itemize{

man/calc_IEU.Rd

@@ -49,7 +49,7 @@ This function uses the equations of Thomsen et al. (2007).  The parameters a
 and b are estimated from dose-recovery experiments.
 }
 \section{Function version}{
- 0.1 (2015-07-23 17:09:29)
+ 0.1.0 (2015-08-09 23:43:58)
 }
 \examples{
 ## load data
@@ -64,6 +64,9 @@ Rachel Smedley, Geography & Earth Sciences, Aberystwyth University
 written by Kristina Thomsen.
 \cr 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. & Kinahan, J.,
 2007. Determination of burial dose in incompletely bleached fluvial samples
 using single grains of quartz. Radiation Measurements 42, 370-379.

man/plot_AbanicoPlot.Rd

@@ -193,7 +193,7 @@ z-scale to specify where ticks are to be drawn by using the parameter
 \code{zlim}-definition.
 }
 \section{Function version}{
- 0.1.2 (2015-07-23 17:09:29)
+ 0.1.2 (2015-08-10 00:07:10)
 }
 \examples{
 ## store original graphics parameters