Tue Aug 9 00:09:12 CEST 2011

Author: "tony"
Date: 2011-08-09 00:09:12 +0200 (Tue, 09 Aug 2011)
New Revision: 286

Added:
   pkg/gsDesignExplorer-dev/
   pkg/gsDesignExplorer-dev/trunk/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/DESCRIPTION
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/NAMESPACE
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/gsDesignGUI.R
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/gsdLaunch.R
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/gsDesignExplorer.vpj
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/gsDesignExplorer.vpw
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/inst/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/inst/doc/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/inst/doc/gsDesignExplorer.pdf
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/inst/unitTests/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/inst/unitTests/Makefile
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/man/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/man/gsDesignGUI.Rd
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/CMakeLists.txt
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/GsRList.cpp
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/GsRList.h
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/Makefile
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/Makefile.win
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/Rcpp.cpp
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/Rcpp.hpp
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/gsDesignGUI.cpp
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/gsDesignGUI.h
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/gsDesignTips.cpp
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/gsdesign.cpp
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/gsdesign.h
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/gsdesign.ui
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images.qrc
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/splash/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/splash/gsDesignSplash.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/splash/gsDesignSplash.xcf
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/splash/gsdSplash.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/designDefault.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/designDelete.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/designExecute.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/designExport.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/designLoad.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/designNew.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/edit.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/fileOpen.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/fileSave.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/help.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/home.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/images/toolbar/plotExport.png
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/main.cpp
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/src/mkdef.sh
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/tests/
   pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/tests/doRUnit.R
Modified:
   /
   pkg/
   pkg/gsDesign/
   pkg/gsDesign/R/
   pkg/gsDesign/inst/
   pkg/gsDesign/inst/NewTests/
   pkg/gsDesign/inst/doc/
   pkg/gsDesign/inst/unitTests/
   pkg/gsDesign/man/
   pkg/gsDesign/src/
   pkg/gsDesign/tex/
   pkg/gsDesign/tex/Sections/
   pkg/gsDesign/tex/figs/
   pkg/gsDesign/tex/tmphelp/
   pkg/gsDesign/tex/tmphelp/Rd/
   pkg/gsDesign/tex/tmphelp/tex/
   pkg/gsDesignExplorer/
   pkg/gsDesignGUI/
   pkg/gsDesignGUI/R/
   pkg/gsDesignGUI/inst/
   pkg/gsDesignGUI/inst/doc/
   pkg/gsDesignGUI/inst/unitTests/
   pkg/gsDesignGUI/man/
   pkg/gsDesignGUI/src/
   pkg/gsDesignGUI/src/explorergui/
   pkg/gsDesignGUI/tests/
   pkg/gsDesignGUIReview/
   pkg/gsDesignGUIReview/osx/
   www/
Log:
Removing old gsDesignGUI directory


Property changes on: 
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/R
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/inst
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/inst/NewTests
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/inst/doc
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/inst/unitTests
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/man
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/src
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/tex
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/tex/Sections
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/tex/figs
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/tex/tmphelp
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/tex/tmphelp/Rd
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesign/tex/tmphelp/tex
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesignExplorer
___________________________________________________________________
Modified: svn:ignore
   - *.vpwhist
*.vtg

   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesignExplorer-dev
___________________________________________________________________
Added: svn:ignore
   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesignExplorer-dev/trunk
___________________________________________________________________
Added: svn:ignore
   + explorergui-build
*.vpwhist
*.vtg



Property changes on: pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer
___________________________________________________________________
Added: svn:ignore
   + explorergui-build
*.vpwhist
*.vtg


Added: pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/DESCRIPTION
===================================================================

--- pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/DESCRIPTION	                        (rev 0)
+++ pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/DESCRIPTION	2011-08-08 22:09:12 UTC (rev 286)
@@ -0,0 +1,9 @@
+Package: gsDesignExplorer
+Version: 1.0-2
+Title: Group Sequential Design GUI
+Author: REvolution Computing
+Maintainer: REvolution Computing <packages at revolution-computing.com>
+Description: Graphical user interface for the gsDesign package.
+Depends: R (>= 2.6.2), gsDesign (>= 2.2-8)
+License: GPL-3
+Copyright: Copyright 2009 Merck Research Laboratories and REvolution Computing


Property changes on: pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/DESCRIPTION
___________________________________________________________________
Added: svn:eol-style
   + native

Added: pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/NAMESPACE
===================================================================
--- pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/NAMESPACE	                        (rev 0)
+++ pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/NAMESPACE	2011-08-08 22:09:12 UTC (rev 286)
@@ -0,0 +1,10 @@
+useDynLib(libgsDesignExplorer, .registration=TRUE)
+
+export(gsDesignExplorer)
+export(runDesign)
+export(gsDesignPrint)
+export(exportDesign)
+export(exportDesignToRScript)
+export(QtDesignToRList)
+export(parseMathText)
+export(openGSDesignGUIManual)


Property changes on: pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/NAMESPACE
___________________________________________________________________
Added: svn:eol-style
   + native


Property changes on: pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R
___________________________________________________________________
Added: svn:ignore
   + explorergui-build
*.vpwhist
*.vtg


Added: pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/gsDesignGUI.R
===================================================================
--- pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/gsDesignGUI.R	                        (rev 0)
+++ pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/gsDesignGUI.R	2011-08-08 22:09:12 UTC (rev 286)
@@ -0,0 +1,677 @@
+## Copyright (C) 2009 Merck Research Laboratories and REvolution Computing, Inc.
+##
+##	This file is part of gsDesignExplorer.
+##
+##  gsDesignExplorer is free software: you can redistribute it and/or modify
+##  it under the terms of the GNU General Public License as published by
+##  the Free Software Foundation, either version 3 of the License, or
+##  (at your option) any later version.
+
+##  gsDesignExplorer is distributed in the hope that it will be useful,
+##  but WITHOUT ANY WARRANTY; without even the implied warranty of
+##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##  GNU General Public License for more details.
+
+##  You should have received a copy of the GNU General Public License
+##  along with gsDesignExplorer.  If not, see <http://www.gnu.org/licenses/>.
+##################################################################################
+#  gsDesignGUI Functions
+#
+#  Exported Functions:
+#
+#  Hidden Functions
+#    QtDesignToRList
+#    gsDesignToQt
+#    gsDesignPrint
+#    gsDesignPlot
+#    runDesign
+#    launchGSDesignGUI
+#    exportDesign
+#    exportDesignToRScript
+#    parseMathText
+#
+#  Author(s): William Constantine, REvolution Computing
+#             Lee Edlefsen, REvolution Computing
+#
+#  Reviewer(s):
+#
+#  Version: 1.0-0
+#
+##################################################################################
+
+###
+# PRIMARY FUNCTIONS
+###
+
+"runDesign" <- function(designListRaw, plotPath=file.path(tempdir(), "gsDesignPlot.png"), plotBackground="white")
+{
+   # create design script
+   design <- exportDesignToRScript(designListRaw, file=NULL, append=FALSE, writeHeader=FALSE, gsDesignGUIVersion=NULL, writePlot=FALSE)
+
+   # evaluate the design
+   eval(parse(text=design$designScript))
+
+   # store design object
+   gsDesignObject <- get(design$designName)
+
+   # define local functions
+   nextEven <- function(x) ceiling(x/2) * 2
+
+   # form output to send back to Qt
+   #
+   # text : print of current design (string scalar)
+   # plot : path to plot file (string scalar)
+   # fixedSampleSize : fixed sample size (integer scalar)
+   # fixedEvents : fixed number of events (integer scalar)
+   # analysisMaxnIPlan : planned final sample size, used in analysis mode only (integer scalar)
+   # analysisNI : sample size required at each analysis to achieve desired timing and beta for the output value of delta (numeric vector, length=k)
+   list(
+     text=gsDesignPrint(gsDesignObject),
+     plot=gsDesignPlot(gsDesignObject, design$designList, plotPath=plotPath, plotBackground=plotBackground),
+     fixedSampleSize=as.integer(nextEven(fixedDesign$sampleSize)),
+     fixedEvents=as.integer(ceiling(fixedDesign$events)),
+     analysisMaxnIPlan=if (gsDesignObject$n.fix != 1) ceiling(gsDesignObject$n.I[gsDesignObject$k]) else gsDesignObject$n.I[gsDesignObject$k],
+     analysisNI=gsDesignObject$n.I
+   )
+}
+
+"gsDesignPrint" <- function(gsDesignObject)
+{
+  paste(capture.output(print(gsDesignObject)), collapse="\n")
+}
+
+"gsDesignPlot" <- function(gsDesignObject, designList, plotPath=file.path(tempdir(), "gsDesignPlot.png"), plotBackground="white", createRScript=FALSE)
+{
+
+  ###
+  # Qt->R map
+  ###
+
+  isAnalysisMode <- designList$dnModeCombo == "Analysis"
+
+  ## plot type
+  supportedTypes <- c("Boundaries", "Power", "Treatment Effect", "Conditional Power", "Spending Function","Expected Sample Size","B-Values")
+  plottype <- match(designList$opTypeCombo, supportedTypes)
+  plotName <- supportedTypes[plottype]
+
+  # if treatment effect has been chosen and the endpoint is survival, remap the plottype to 8
+  if (designList$sampleSizeTab == "Time to Event" && plotName == "Treatment Effect")
+  {
+     plottype <- 8
+  }
+
+  # main
+  main <- designList$opTitleLine
+
+  # abscissa label
+  xlab <- designList$opXLabelLine
+
+  # ordinate label
+  ylab <- designList$opYLabelLeftLine
+
+  # line and point properties
+  col <- c(designList$opLine1ColorCombo, designList$opLine2ColorCombo)
+  lty <- c(designList$opLine1TypeCombo, designList$opLine2TypeCombo)
+  lwd <- c(designList$opLine1WidthSpin, designList$opLine2WidthSpin)
+  dgt <- c(designList$opLine1SymDigitsSpin, designList$opLine2SymDigitsSpin)
+
+  # map basic or ggplot2 style
+  base <- !(length(grep("high quality", tolower(designList$opPlotRenderCombo))) > 0)
+
+  # parse from the file name the format of the exported plot
+  exportFormat <- strsplit(basename(plotPath), "[.]")[[1]]
+  exportFormat <- tolower(exportFormat[length(exportFormat)])
+  exportFormat <- match.arg(exportFormat, c("bmp","png","pdf","jpg","jpeg","tiff"))
+
+  "labelStr" <- function(x)
+  {
+    if (length(x) == 1)
+    {
+      gsub("^\\[1\\] ", "", capture.output(print(x)))
+    }
+    else
+    {
+      paste("c(", paste(unlist(lapply(x, labelStr)), collapse=", "), ")", sep="")
+    }
+  }
+
+  "argStr" <- function(x, collapse=",\n  ")
+  {
+     paste(paste(deparse(substitute(x)), "=", labelStr(x), collapse="", sep=""), collapse, sep="")
+  }
+
+  # define script gsDesign object name
+  gsDesignObjectScriptName <- if (isAnalysisMode) paste(designList$dnNameCombo, ".analysis", sep="") else designList$dnNameCombo
+
+  "plotStr" <- paste(
+    "# ", plotName, " Plot\n",
+    "plot(",
+     gsDesignObjectScriptName, ",\n  ",
+     argStr(plottype),
+     argStr(base),
+     if (nchar(main)) argStr(main),
+     if (nchar(xlab)) argStr(xlab),
+     if (nchar(ylab)) argStr(ylab),
+     argStr(col),
+     argStr(lwd),
+     argStr(lty),
+     argStr(dgt, collapse=""),
+     ")", sep="")
+
+  if (createRScript)
+  {
+    return(plotStr)
+  }
+
+  if (!base)
+  {
+    "plotStr" <- paste("print(", plotStr, ")", sep="")
+  }
+
+  # export graph to file
+  # bg choices typically are "white" or "transparent"
+  switch(exportFormat,
+    "png" = png(file=plotPath, bg=plotBackground),
+    "bmp" = bmp(file=plotPath, bg=plotBackground),
+    "pdf" = pdf(file=plotPath, bg=plotBackground),
+    "jpg" = jpeg(file=plotPath, bg=plotBackground),
+    "jpeg" = jpeg(file=plotPath, bg=plotBackground),
+    "tiff" = tiff(file=plotPath, bg=plotBackground),
+    png(file=plotPath, bg="transparent")
+  )
+
+  # issue plot commands
+  eval(parse(text=gsub(paste("plot\\(", gsDesignObjectScriptName, sep=""), "plot(gsDesignObject", plotStr)))
+
+  dev.off()
+
+  plotPath
+}
+
+"exportDesign" <- function(designListRaw, file=NULL, append=FALSE, writeHeader=FALSE, gsDesignGUIVersion=NULL, writePlot=TRUE)
+{
+  # parse from the file name the format of the exported plot
+  exportFormat <- strsplit(basename(file), "[.]")[[1]]
+  exportFormat <- tolower(exportFormat[length(exportFormat)])
+  exportFormat <- match.arg(exportFormat, c("r","tex","rtf","rnw"))
+
+  # export design to file
+  switch(exportFormat,
+    "r" = exportDesignToRScript(designListRaw, file=file, append=append, writeHeader=writeHeader, gsDesignGUIVersion=gsDesignGUIVersion, writePlot=writePlot),
+    "tex" = stop("LaTeX export currently not supported"),
+    "rtf" = stop("Rich Text Format export currently not supported"),
+    "rnw" = stop("Sweave export currently not supported"),
+     exportDesignToRScript(designListRaw, file=file, append=append, writeHeader=writeHeader, gsDesignGUIVersion=gsDesignGUIVersion)
+  )
+}
+
+"exportDesignToRScript" <- function(designListRaw, file=NULL, append=FALSE, writeHeader=FALSE, gsDesignGUIVersion=NULL, writePlot=TRUE)
+{
+   # define local functions
+   "ifelse1" <- function (test, x, y, ...)
+   {
+     if (test)
+         x
+     else if (missing(..1))
+         y
+     else ifelse1(y, ...)
+   }
+
+   # define local functions
+   catString <- function(oldstr, var, value) c(oldstr, paste(var, "<-", value))
+   formCatVector <- function(...) paste("c(", paste(..., sep=", "), ")", sep="")
+
+   # convert raw design list (names = keys, values = flattened strings from the Qt QMap)
+   # to a named list of R objects (values = strings, vectors, matrices, etc.)
+   designList <- QtDesignToRList(designListRaw)
+
+   # initialize variables
+   if (writeHeader)
+   {
+     designScript <- paste("# This R script was created via an export of a group sequential design\n",
+       "# developed in gsDesign Explorer",
+       if (!is.null(gsDesignGUIVersion)) paste(" version ",  gsDesignGUIVersion, sep="") else "",
+       " on ", date(), sep="")
+   }
+   else
+   {
+     designScript <- ""
+   }
+
+   ###
+   # Qt -> R mapping
+   ###
+
+   designScript <- c(designScript, paste("\n###\n# Design : ", designList$dnNameCombo, "\n# Description : ",
+     designList$dnDescCombo, "\n###\n"))
+
+   # number of intervals
+   designScript <- catString(designScript, "k", designList$eptIntervalsSpin + 1)
+
+   # test type
+   isTwoSidedWithFutility <- designList$sflTestCombo == "2-sided with futility"
+   isBetaSpending <- designList$sflLBSCombo == "Beta-spending"
+   isHypothesisSpending <- designList$sflLBSCombo == "H0 spending"
+   isBinding <- designList$sflLBTCombo == "Binding"
+   isNonBinding <- designList$sflLBTCombo == "Non-binding"
+
+   test.type <- which(c(
+     designList$sflTestCombo == "1-sided",
+     designList$sflTestCombo == "2-sided symmetric",
+     isTwoSidedWithFutility && isBetaSpending && isBinding,
+     isTwoSidedWithFutility && isBetaSpending && isNonBinding,
+     isTwoSidedWithFutility && isHypothesisSpending && isBinding,
+     isTwoSidedWithFutility && isHypothesisSpending && isNonBinding))[1]
+
+   designScript <- catString(designScript, "test.type", test.type)
+
+   # Type I Error
+   alpha <- designList$eptErrorDSpin / 100.0
+   designScript <- catString(designScript, "alpha", alpha)
+
+   # Type II Error
+   beta <- 1.0 - designList$eptPowerDSpin / 100.0
+   designScript <- catString(designScript, "beta", beta)
+
+   # sample size for fixed design with no interim
+   isSurvival <- designList$sampleSizeTab == "Time to Event"
+   isBinomial <- designList$sampleSizeTab == "Binomial"
+   isUserInput <- designList$sampleSizeTab == "User Input"
+   isAnalysisMode <- designList$dnModeCombo == "Analysis"
+
+   if (isBinomial)
+   {
+     designScript <- catString(designScript, "p1", designList$ssBinControlDSpin)
+     designScript <- catString(designScript, "p2", designList$ssBinExpDSpin)
+     designScript <- catString(designScript, "delta0", designList$ssBinDeltaDSpin)
+     designScript <- catString(designScript, "delta1", "p1 - p2")
+   }
+
+   if (isSurvival)
+   {
+      designScript <- catString(designScript, paste(designList$dnNameCombo, "Survival", sep=""),
+        paste("nSurvival(",
+            "lambda1=", designList$ssTECtrlDSpin,
+            ", lambda2=", designList$ssTEExpDSpin,
+            ", eta=", designList$ssTEDropoutDSpin,
+            ", Ts=", designList$ssTEAccrualDSpin + designList$ssTEFollowDSpin,
+            ", Tr=", designList$ssTEAccrualDSpin,
+            ", ratio=", designList$ssTERatioDSpin,
+            ", alpha=", alpha,
+            ", beta=", beta,
+            ", sided=1",
+            ", type=\"", ifelse(designList$ssTEHypCombo == "Risk Ratio", "rr", "rd"), "\"",
+            ", entry=\"", ifelse(designList$ssTEAccrualCombo == "Uniform", "unif", "expo"), "\"",
+            ", gamma=", designList$ssTEGammaDSpin, ")", sep=""))
+       designScript <- catString(designScript, "n.fix", paste(designList$dnNameCombo, "Survival$nEvents", sep=""))
+   }
+   else
+   {
+      designScript <- catString(designScript, "n.fix",
+       switch(designList$sampleSizeTab,
+       "User Input" =  designList$ssUserFixedSpin,
+       "Binomial" = paste("nBinomial(",
+                        "p1=p1, p2=p2",
+                        ", alpha=", alpha,
+                        ", beta=", beta,
+                        ", delta0=delta0",
+                        ", ratio=", designList$ssBinRatioDSpin, ")", sep="")))
+   }
+
+   # relative timing of interim analyses
+   timing <- designList$eptTimingTable
+   designScript <- catString(designScript, "timing", paste("c(", paste(timing, collapse=", "), ")", sep=""))
+
+   # upper spending function
+   designScript <- catString(designScript, "sfu",
+     switch(designList$sfuParamToolBox,
+            "ParameterFree" = switch(designList$sfu0PCombo,
+                                "Pocock" = "sfLDPocock",
+                                "sfLDOF"),
+            "OneParameter" = switch(designList$sfu1PCombo,
+                                "Power" = "sfPower",
+                                "Exponential" = "sfExponential",
+                                "sfHSD"),
+            "TwoParameter" = switch(designList$sfu2PFunCombo,
+                                "Logistic" = "sfLogistic",
+                                "Normal" = "sfNormal",
+                                "Cauchy" = "sfCauchy",
+                                "Extreme Value" = "sfExtremeValue",
+                                "Extreme Value (2)" = "sfExtremeValue2",
+                                "Beta Distribution" = "sfBetaDist"),
+            "ThreeParameter" = "sfTDist",
+            "PiecewiseLinear" = "sfLinear",
+            "sfHSD"))
+
+   designScript <- catString(designScript, "sfupar",
+     switch(designList$sfuParamToolBox,
+            "ParameterFree" = -8,
+            "OneParameter" = designList$sfu1PDSpin,
+            "TwoParameter" = ifelse1(designList$sfu2PTab == "Points",
+                                formCatVector(designList$sfu2PPt1XDSpin, designList$sfu2PPt2XDSpin, designList$sfu2PPt1YDSpin, designList$sfu2PPt2YDSpin),
+                                formCatVector(designList$sfu2PLMIntDSpin, designList$sfu2PLMSlpDSpin)),
+            "ThreeParameter" = ifelse1(designList$sfu3PTab == "Points",
+                                formCatVector(designList$sfu3PPt1XDSpin, designList$sfu3PPt2XDSpin, designList$sfu3PPt1YDSpin, designList$sfu3PPt2YDSpin, designList$sfu3PPtsDfDSpin),
+                                formCatVector(designList$sfu3PLMIntDSpin, designList$sfu3PLMSlpDSpin, designList$sfu3PLMDfDSpin)),
+            "PiecewiseLinear" = formCatVector(designList$sfuPieceTableX[1], designList$sfuPieceTableX[2], designList$sfuPieceTableY[1], designList$sfuPieceTableY[2]),
+            -8))
+
+   # lower spending function
+   designScript <- catString(designScript, "sfl",
+     switch(designList$sflParamToolBox,
+            "ParameterFree" = switch(designList$sfl0PCombo,
+                                "Pocock" = "sfLDPocock",
+                                "sfLDOF"),
+            "OneParameter" = switch(designList$sfl1PCombo,
+                                "Power" = "sfPower",
+                                "Exponential" = "sfExponential",
+                                "sfHSD"),
+            "TwoParameter" = switch(designList$sfl2PFunCombo,
+                                "Logistic" = "sfLogistic",
+                                "Normal" = "sfNormal",
+                                "Cauchy" = "sfCauchy",
+                                "Extreme Value" = "sfExtremeValue",
+                                "Extreme Value (2)" = "sfExtremeValue2",
+                                "Beta Distribution" = "sfBetaDist"),
+            "ThreeParameter" = "sfTDist",
+            "PiecewiseLinear" = "sfLinear",
+            "sfHSD"))
+
+   designScript <- catString(designScript, "sflpar",
+     switch(designList$sflParamToolBox,
+            "ParameterFree" = -8,
+            "OneParameter" = designList$sfl1PDSpin,
+            "TwoParameter" = ifelse1(designList$sfl2PTab == "Points",
+                                formCatVector(designList$sfl2PPt1XDSpin, designList$sfl2PPt2XDSpin, designList$sfl2PPt1YDSpin, designList$sfl2PPt2YDSpin),
+                                formCatVector(designList$sfl2PLMIntDSpin, designList$sfl2PLMSlpDSpin)),
+            "ThreeParameter" = ifelse1(designList$sfl3PTab == "Points",
+                                formCatVector(designList$sfl3PPt1XDSpin, designList$sfl3PPt2XDSpin, designList$sfl3PPt1YDSpin, designList$sfl3PPt2YDSpin, designList$sfl3PPtsDfDSpin),
+                                formCatVector(designList$sfl3PLMIntDSpin, designList$sfl3PLMSlpDSpin, designList$sfl3PLMDfDSpin)),
+            "PiecewiseLinear" = formCatVector(designList$sflPieceTableX[1], designList$sflPieceTableX[2], designList$sflPieceTableY[1], designList$sflPieceTableY[2]),
+            -8))
+
+   # set sample size endpoint type
+   if (isSurvival)
+   {
+     designScript <- catString(designScript, "endpoint", "\"tte\"")
+   }
+
+   if (isBinomial)
+   {
+     designScript <- catString(designScript, "endpoint", "\"binomial\"")
+   }
+
+   if (isUserInput)
+   {
+     designScript <- catString(designScript, "endpoint", "\"user\"")
+   }
+
+   # calculate the design
+   if (isSurvival)
+   {
+      designScript <- catString(designScript, designList$dnNameCombo,
+        paste("gsDesign(k=k, test.type=test.type, alpha=alpha, beta=beta, n.fix=n.fix, timing=timing, sfu=sfu, sfupar=sfupar, sfl=sfl, sflpar=sflpar, ",
+        "endpoint=endpoint, ",
+        "nFixSurv=",
+          paste(designList$dnNameCombo, "Survival$n", sep=""), ")", sep=""))
+   }
+   else if (isBinomial)
+   {
+      designScript <- catString(designScript, designList$dnNameCombo,
+        paste("gsDesign(k=k, test.type=test.type, alpha=alpha, beta=beta, n.fix=n.fix, timing=timing, sfu=sfu, sfupar=sfupar, sfl=sfl, sflpar=sflpar, ",
+        "endpoint=endpoint, delta0=delta0, delta1=delta1)", sep=""))
+   }
+   else
+   {
+      designScript <- catString(designScript, designList$dnNameCombo,
+        paste("gsDesign(k=k, test.type=test.type, alpha=alpha, beta=beta, n.fix=n.fix, timing=timing, sfu=sfu, sfupar=sfupar, sfl=sfl, sflpar=sflpar",
+        ", endpoint=endpoint",
+        ")", sep=""))
+   }
+
+   # add fixed design information
+   if (isSurvival)
+   {
+     designScript <- catString(designScript, "fixedDesign",
+       paste("list(events = ", paste(designList$dnNameCombo, "Survival$nEvents", sep=""),
+                   ", sampleSize = ", paste(designList$dnNameCombo, "Survival$n", sep=""), ")", sep=""))
+   }
+
+   if (isBinomial)
+   {
+     designScript <- catString(designScript, "fixedDesign", "list(events = 0, sampleSize = n.fix)")
+   }
+
+   if (isUserInput)
+   {
+     designScript <- catString(designScript, "fixedDesign", paste("list(events = ", designList$ssUserFixedSpin, ", sampleSize = 0)", sep=""))
+   }
+
+   if (isAnalysisMode)
+   {
+      designScript <- c(designScript, "\n# Analysis")
+      designScript <- catString(designScript, "maxn.IPlan", paste(designList$dnNameCombo, "$n.I[", designList$dnNameCombo, "$k]", sep=""))
+
+      designScript <- catString(designScript, paste(designList$dnNameCombo, "analysis", sep="."),
+        paste("gsDesign(k=", designList$anlMaxSampleSizeSpin,
+        ", test.type=test.type, alpha=alpha, beta=beta, sfu=sfu, sfupar=sfupar, sfl=sfl, sflpar=sflpar, ",
+           paste("delta=", designList$dnNameCombo, "$delta, ", sep=""),
+           "maxn.IPlan=maxn.IPlan, ",
+           paste("n.I=c(", paste(designList$anlSampleSizeTable[1:designList$anlMaxSampleSizeSpin], collapse=", "), ")", sep=""),
+           ")", sep=""))
+   }
+
+   # write the current design to file
+   if (!is.null(file))
+   {
+     if (append && (!file.exists(file) || (file.access(file, mode=2) != 0)))
+     {
+        stop("Append mode: file ", file, " does not exist or is not writable")
+     }
+
+     write(designScript, file=file, append=append, sep="\n") #, ncol=3)
+
+     if (writePlot)
+     {
+        plotStr <- paste("\n", gsDesignPlot(NULL, designList, createRScript=TRUE), sep="")
+        write(plotStr, file=file, append=TRUE, sep="\n")
+     }
+
+   }
+
+   # return name of design to display in text/plot outputs
+   designName <- if (isAnalysisMode) paste(designList$dnNameCombo, "analysis", sep=".") else designList$dnNameCombo
+
+   list(designList=designList, designScript=designScript, designName=designName)
+}
+
+###
+# CONVERSION FUNCTIONS
+###
+
+"QtDesignToRList" <- function(designListRaw)
+{
+  # converts a raw design list (names = keys, values = flattened strings from a Qt QMap)
+  # to a named list of R objects containing unflattened data converted to the corresponding data type
+  # (e.g., strings, vectors, matrices, etc.)
+
+  designDF <- t(data.frame(designListRaw))
+  factors <- rep("NA", nrow(designDF))
+  nms <- row.names(designDF)
+  factors[grep("Tab[.](string|index)", nms)] <- "QTabWidget"
+  factors[grep("Table[XY]*[.](nrow|ncol|data)", nms)] <- "QTableWidget"
+  factors[grep("Spin$", nms)] <- "QSpinBox"
+  factors[grep("DSpin$", nms)] <- "QDoubleSpinBox"
+  factors[grep("Combo[.](index|string)", nms)] <- "QComboBox"
+  factors[grep("ToolBox[.](index|string)", nms)] <- "QToolBox"
+  factors[grep("Radio$", nms)] <- "QRadioButton"
+  factors[grep("Line$", nms)] <- "QLineEdit"
+
+  objectNames <- gsub("[.].*$","", row.names(designDF))
+
+  z <- data.frame(designDF, factors, objectNames, stringsAsFactors=FALSE)
+  names(z) <- c("Value", "Class", "objectName")
+
+  # group data by objectName
+  z <- split(z, z$objectName)
+
+  lapply(z, function(designDF)
+  {
+     xclass <- as.vector(designDF$Class[1])
+     objectName <- as.vector(designDF$objectName[1])
+
+     if (xclass == "QTableWidget")
+     {
+       designDF.nrow <- as.integer(designDF[paste(objectName, "nrow", sep="."), "Value"])
+       designDF.ncol <- as.integer(designDF[paste(objectName, "ncol", sep="."), "Value"])
+       designDF.data <- as.numeric(strsplit(designDF[paste(objectName, "data", sep="."), "Value"], ",")[[1]])
+
+       return(if (designDF.nrow == 1 || designDF.ncol == 1) designDF.data else matrix(designDF.data, nrow=designDF.nrow, ncol=designDF.ncol, byrow=FALSE))
+     }
+
+     if (xclass == "QDoubleSpinBox")
+     {
+       return(as.numeric(designDF$Value[1]))
+     }
+
+     if (xclass == "QSpinBox")
+     {
+       return(as.integer(designDF$Value[1]))
+     }
+
+     if (xclass == "QComboBox")
+     {
+       return(designDF[paste(objectName, "string", sep="."),]$Value)
+     }
+
+     if (xclass == "QRadioButton")
+     {
+       return(designDF$Value[1] == "1")
+     }
+
+     if (xclass == "QLineEdit")
+     {
+       return(parseMathText(designDF$Value[1]))
+     }
+
+     if (xclass == "QTabWidget")
+     {
+       return(designDF[paste(objectName, "string", sep="."), ]$Value)
+     }
+
+     if (xclass == "QToolBox")
+     {
+       return(gsub("[0-9]$", "", designDF[paste(objectName, "string", sep="."), ]$Value))
+     }
+
+  })
+}
+
+"parseMathText" <- function(x)
+{
+  # Converts mt() entries in a string to expression entries.
+  #
+  # > x <- "mt(Lambda), the lazy dog (mt(hat(theta)/delta)) is basking in the mt(widetilde(xy)) sun mt(32*degree)"
+  # > parseMathText(x)
+  # expression(paste(Lambda, ", the lazy dog (", hat(theta)/delta, ") is basking in the ", widetilde(xy), " sun ", 32 * degree, sep = ""))
+  # > plot(1:5, xlab=parseMathText(x))
+
+  if (!is.character(x) || length(x) > 1)
+  {
+    stop("Input must be a single character string")
+  }
+
+  # if there are no math tokens in the string
+  # then return the original string
+  token <- "mt\\("
+
+  if (!length(grep(token, x)))
+  {
+    return(x)
+  }
+
+  # prepend and append blank math text calls to input string to
+  # force deterministic end conditions
+  x <- paste("mt()", x, "mt()", sep="")
+
+  # define local functions
+  "rightParenReplace" <- function(x)
+  {
+    # Finds the matching right parenthesis to a previous 'mt(' split.
+    # Once found, that ")" character is replaced by the proper text
+    # needed to form the end of the current expression.
+    # This function also will catch syntax errors in that, if the user
+    # is missing a closing right parenthesis, an error will be thrown.
+    #
+    # Input:
+    #   x : a character string previously split using the token "mt\\("
+    #
+    # Output:
+    #   A character string with replaced tokens for the matching right brace
+
+    # intialize variables
+    # i : looping index from 1 .. nchar(x)
+    # count : a counter.
+    # index : to contain the index of the matching right parenthesis once found in the current string
+    i <- count <- 1
+    index <- NULL
+
+    # break string into a vector of single characters
+    z <- strsplit(x, "")[[1]]
+
+    # search through the character vector from left to right.
+    # if a "(" is encountered, increment count by 1.
+    # if a ")" is encountered, decrement count by 1.
+    # if the count is 0, it means we have isolated the matching parenthesis. store the index and break.
+    while (i <= length(z))
+    {
+      count <- count + switch(z[i], "(" = 1, ")" = -1, 0)
+
+      if (count == 0)
+      {
+        index <- i
+        break
+      }
+
+      i <- i + 1
+    }
+
+    # ensure that we found a matching right parenthesis
+    if (is.null(index))
+    {
+       stop("Syntax error: missing matching right parenthesis")
+    }
+
+    # replace the matching right parenthesis with the proper text needed to form the overall expression
+    z[index] <- if (index > 1) ", \"" else "\""
+
+    # collapse the vector of strings back into a single character of strings and return
+    paste(z, collapse="")
+  }
+
+  # split the original string into a vector of strings split by the starting token
+  mt <- unlist(lapply(strsplit(x,token)[[1]], function(x) if (nchar(x)) x))
+  y <- unlist(lapply(mt, rightParenReplace))
+  empty <- grep("^\\)$", y)
+  if (length(empty)) y <- y[-empty]
+
+  # form overall expression as a string
+  z <- paste("expression(paste(", gsub(", \"$", "", paste(y, collapse="\", ", sep="")), "))", sep="", collapse="")
+  z <- gsub("\"\",","", z)
+  z <- gsub(", \"\")", ")", z)
+
+  # return the evaluated string, resulting in an expression
+  eval(parse(text=z))
+}
+
+###
+# OPEN PDF MANUAL
+###
+
+"openGSDesignGUIManual" <- function()
+{
+  # returns an invisible error string containing path to the file.
+  # if there is a problem, RShowDoc() throws an error
+  RShowDoc("gsDesignExplorer", package="gsDesignExplorer", type="pdf")
+}
+


Property changes on: pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/gsDesignGUI.R
___________________________________________________________________
Added: svn:eol-style
   + native

Added: pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/gsdLaunch.R
===================================================================
--- pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/gsdLaunch.R	                        (rev 0)
+++ pkg/gsDesignExplorer-dev/trunk/gsDesignExplorer/R/gsdLaunch.R	2011-08-08 22:09:12 UTC (rev 286)
@@ -0,0 +1,34 @@
+## Copyright (C) 2009 Merck Research Laboratories and REvolution Computing, Inc.
+##
+##	This file is part of gsDesignExplorer.
+##
+##  gsDesignExplorer is free software: you can redistribute it and/or modify
+##  it under the terms of the GNU General Public License as published by
+##  the Free Software Foundation, either version 3 of the License, or
+##  (at your option) any later version.
+
+##  gsDesignExplorer is distributed in the hope that it will be useful,
+##  but WITHOUT ANY WARRANTY; without even the implied warranty of
+##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##  GNU General Public License for more details.
+
+##  You should have received a copy of the GNU General Public License
+##  along with gsDesignExplorer.  If not, see <http://www.gnu.org/licenses/>.
+
+"gsDesignExplorer" <- function( exitOnClose = FALSE )
+{
+  if ( exitOnClose )
+  {
+    on.exit( quit( "no" ) )
+  }
+# initialize variables
+	curdir <- getwd()
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/gsdesign -r 286
