r-gregmisc-users — Discussion list for R gregmisc packages (gplot, gmodels, gdata, gtools)

[R-gregmisc-users] SF.net SVN: r-gregmisc:[1801] trunk/gdata/tests/unitTests/runit.unknown.R

[<wa...@us...>]

Revision: 1801
          http://sourceforge.net/p/r-gregmisc/code/1801
Author:   warnes
Date:     2014-04-05 21:08:41 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Apply same changes to NAToUnknown that were previously applied to
unknownToNA for POSIXlt.

Modified Paths:
--------------
    trunk/gdata/tests/unitTests/runit.unknown.R

Modified: trunk/gdata/tests/unitTests/runit.unknown.R
===================================================================
--- trunk/gdata/tests/unitTests/runit.unknown.R	2014-04-05 18:41:50 UTC (rev 1800)
+++ trunk/gdata/tests/unitTests/runit.unknown.R	2014-04-05 21:08:41 UTC (rev 1801)
@@ -478,9 +478,59 @@
 
   ## Date-time classes
   checkIdentical(NAToUnknown(xDate, unknown=dateUnk), xDateUnk)
-  checkIdentical(NAToUnknown(xPOSIXlt, unknown=POSIXltUnk), xPOSIXltUnk)
   checkIdentical(NAToUnknown(xPOSIXct, unknown=POSIXctUnk), xPOSIXctUnk)
 
+
+  ####
+  ## Per Brian Ripley on 2014-01-15:
+  ##
+  ## On platforms where POSIXlt has a gmtoff component, it does not need to be set.  So
+  ##
+  ## > z$gmtoff
+  ## [1] 3600   NA
+  ## > xPOSIXltUnk$gmtoff
+  ## [1] 3600 3600
+  ##
+  ## (or sometimes 0, not NA).
+  ##
+  ## So although identical() correctly reports that they differ, this
+  ## is allowed for optional components.
+  ##
+  ## It would also be wrong to use identical() to compare isdst
+  ## components: isdst = -1 means unknown.
+  ##
+  ## Replaced:
+  ##   checkIdentical(NAToUnknown(xPOSIXlt, unknown=POSIXltUnk), xPOSIXltUnk)
+  ## With:
+  tmp_NAToUnknown <- NAToUnknown(xPOSIXlt, unknown=POSIXltUnk)
+  tmp_xPOSIXltUnk   <- xPOSIXltUnk
+  ##
+  tmp_NAToUnknown$gmtoff <- NULL  # Remove $gmtoff to avoid comparison
+  tmp_xPOSIXltUnk$gmtoff   <- NULL
+  ##
+  isdst.unknown <- unique(
+      c(which(is.na(tmp_NAToUnknown$isdst) |
+              tmp_NAToUnknown$isdst==-1
+              )
+        )
+      ,
+      c(which(is.na(tmp_xPOSIXltUnk$isdst) |
+              tmp_xPOSIXltUnk$isdst==-1
+              )
+        )
+
+      )
+  ##
+  checkIdentical(tmp_NAToUnknown$isdst[!isdst.unknown],
+                 tmp_xPOSIXltUnk$isds[!isdst.unknown])
+  ##
+  tmp_NAToUnknown$isdst <- NULL   # Remove $isdst to avoid comparison
+  tmp_xPOSIXltUnk$isdst   <- NULL    # by checkIdentical
+  ##
+  checkIdentical(tmp_NAToUnknown, tmp_xPOSIXltUnk)
+  ####
+
+
   ## --- lists and data.frames ---
 
   ## with vector of single unknown values

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1800] trunk/gdata/inst/NEWS

[<wa...@us...>]

Revision: 1800
          http://sourceforge.net/p/r-gregmisc/code/1800
Author:   warnes
Date:     2014-04-05 18:41:50 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Update NEWS with latest changes

Modified Paths:
--------------
    trunk/gdata/inst/NEWS

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2014-04-05 18:38:23 UTC (rev 1799)
+++ trunk/gdata/inst/NEWS	2014-04-05 18:41:50 UTC (rev 1800)
@@ -12,6 +12,8 @@
 
 - Unit tests and vignettes now follow R standard practice.
 
+- Minor changes to clean up R CMD check warnings.
+
 Changes in 2.13.2 (2013-06-28)
 ------------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1799] trunk/gdata/R/nobs.R

[<wa...@us...>]

Revision: 1799
          http://sourceforge.net/p/r-gregmisc/code/1799
Author:   warnes
Date:     2014-04-05 18:38:23 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Call stats::nobs instead of stats:::nobs.default within
gdata::nobs.default.  This avoids R CMD check warning.

Modified Paths:
--------------
    trunk/gdata/R/nobs.R

Modified: trunk/gdata/R/nobs.R
===================================================================
--- trunk/gdata/R/nobs.R	2014-04-05 18:22:16 UTC (rev 1798)
+++ trunk/gdata/R/nobs.R	2014-04-05 18:38:23 UTC (rev 1799)
@@ -11,10 +11,10 @@
     if(is.numeric(object) || is.logical(object))
       sum( !is.na(object) )
     else
-      stats:::nobs.default(object, ...)
+      stats::nobs(object, ...)
   }
-    
 
+
 nobs.data.frame <- function(object, ...)
   sapply(object, nobs.default)
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1798] trunk/gdata/tests/unitTests/runit.unknown.R

[<wa...@us...>]

Revision: 1798
          http://sourceforge.net/p/r-gregmisc/code/1798
Author:   warnes
Date:     2014-04-05 18:22:16 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Don't compare optional POSIXlt field.   Explicitly compare POSIXlt, with special handling of '-1' unknown value.

Modified Paths:
--------------
    trunk/gdata/tests/unitTests/runit.unknown.R

Modified: trunk/gdata/tests/unitTests/runit.unknown.R
===================================================================
--- trunk/gdata/tests/unitTests/runit.unknown.R	2014-04-05 18:19:49 UTC (rev 1797)
+++ trunk/gdata/tests/unitTests/runit.unknown.R	2014-04-05 18:22:16 UTC (rev 1798)
@@ -331,9 +331,58 @@
 
   ## Date-time classes
   checkIdentical(unknownToNA(xDateUnk, unknown=dateUnk), xDate)
-  checkIdentical(unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXlt)
   checkIdentical(unknownToNA(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXct)
 
+  ####
+  ## Per Brian Ripley on 2014-01-15:
+  ##
+  ## On platforms where POSIXlt has a gmtoff component, it does not need to be set.  So
+  ##
+  ## > z$gmtoff
+  ## [1] 3600   NA
+  ## > xPOSIXltUnk$gmtoff
+  ## [1] 3600 3600
+  ##
+  ## (or sometimes 0, not NA).
+  ##
+  ## So although identical() correctly reports that they differ, this
+  ## is allowed for optional components.
+  ##
+  ## It would also be wrong to use identical() to compare isdst
+  ## components: isdst = -1 means unknown.
+  ##
+  ## Replaced:
+  ##   checkIdentical(unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXlt)
+  ## With:
+  tmp_unknownToNA <- unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk)
+  tmp_xPOSIXlt   <- xPOSIXlt
+  ##
+  tmp_unknownToNA$gmtoff <- NULL  # Remove $gmtoff to avoid comparison
+  tmp_xPOSIXlt$gmtoff   <- NULL
+  ##
+  isdst.unknown <- unique(
+      c(which(is.na(tmp_unknownToNA$isdst) |
+              tmp_unknownToNA$isdst==-1
+              )
+        )
+      ,
+      c(which(is.na(tmp_xPOSIXlt$isdst) |
+              tmp_xPOSIXlt$isdst==-1
+              )
+        )
+
+      )
+  ##
+  checkIdentical(tmp_unknownToNA$isdst[!isdst.unknown],
+                 tmp_xPOSIXlt$isds[!isdst.unknown])
+  ##
+  tmp_unknownToNA$isdst <- NULL   # Remove $isdst to avoid comparison
+  tmp_xPOSIXlt$isdst   <- NULL    # by checkIdentical
+  ##
+  checkIdentical(tmp_unknownToNA, tmp_xPOSIXlt)
+  ####
+
+
   ## --- lists and data.frames ---
 
   ## with vector of single unknown values

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1797] trunk/gdata/R

[<wa...@us...>]

Revision: 1797
          http://sourceforge.net/p/r-gregmisc/code/1797
Author:   warnes
Date:     2014-04-05 18:19:49 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Don't use gdata:::<foo> prefix to access gdata function <foo>

Modified Paths:
--------------
    trunk/gdata/R/mapLevels.R
    trunk/gdata/R/unknown.R

Modified: trunk/gdata/R/mapLevels.R
===================================================================
--- trunk/gdata/R/mapLevels.R	2014-04-05 17:01:31 UTC (rev 1796)
+++ trunk/gdata/R/mapLevels.R	2014-04-05 18:19:49 UTC (rev 1797)
@@ -99,7 +99,7 @@
 
 print.levelsMap <- function(x, ...)
 {
-  x <- gdata:::.unlistLevelsMap(x)
+  x <- .unlistLevelsMap(x)
   print(x, ...)
 }
 
@@ -159,7 +159,7 @@
 as.levelsMap <- function(x, check=TRUE, ...)
 {
   if(check)
-    gdata:::.checkLevelsMap(x, method="raw")
+    .checkLevelsMap(x, method="raw")
   class(x) <- "levelsMap"
   unique(x, ...)
 }
@@ -167,7 +167,7 @@
 as.listLevelsMap <- function(x, check=TRUE)
 {
   if(check)
-    gdata:::.checkListLevelsMap(x, method="raw")
+    .checkListLevelsMap(x, method="raw")
   class(x) <- "listLevelsMap"
   x
 }
@@ -203,7 +203,7 @@
   if(!is.list(x) || any(!sapply(x, FUN=is.levelsMap)))
     stop(sprintf("'%s' must be %s a list of %s", xLab, also,
                  dQuote("levelsMap")))
-  lapply(x, FUN=gdata:::.checkLevelsMap, method=method)
+  lapply(x, FUN=.checkLevelsMap, method=method)
 }
 
 ### }}}
@@ -221,12 +221,12 @@
 c.listLevelsMap <- function(..., sort=TRUE, recursive=FALSE)
 {
   x <- list(...)
-  lapply(x, FUN=gdata:::.checkListLevelsMap, method="class")
+  lapply(x, FUN=.checkListLevelsMap, method="class")
   x <- unlist(x, recursive=FALSE)
   if(!recursive) {
     class(x) <- "listLevelsMap"
   } else {
-    if(any(!sapply(x, FUN=gdata:::.isCharacterMap)))
+    if(any(!sapply(x, FUN=.isCharacterMap)))
       stop(sprintf("can not combine integer %s", dQuote("levelsMaps")))
     if(!is.null(names(x))) names(x) <- NULL
     x <- unlist(x, recursive=FALSE)
@@ -252,7 +252,7 @@
 unique.levelsMap <- function(x, incomparables=FALSE, ...)
 {
   ## Find duplicates
-  y <- gdata:::.unlistLevelsMap(x, ind=TRUE)
+  y <- .unlistLevelsMap(x, ind=TRUE)
   ## Duplicates for values and names combinations
   test <- duplicated(cbind(y[[1]], names(y[[1]])),
                      incomparables=incomparables, ...)
@@ -296,7 +296,7 @@
   if(any(!(class(x) %in% classX)))
     stop(sprintf("'x' must be either: %s", paste(dQuote(classX), collapse=", ")))
 
-  gdata:::.checkLevelsMap(x=value, method="class")
+  .checkLevelsMap(x=value, method="class")
 
   ## --- Mapping levels in x ---
 

Modified: trunk/gdata/R/unknown.R
===================================================================
--- trunk/gdata/R/unknown.R	2014-04-05 17:01:31 UTC (rev 1796)
+++ trunk/gdata/R/unknown.R	2014-04-05 18:19:49 UTC (rev 1797)
@@ -40,7 +40,7 @@
 }
 
 isUnknown.list <- function(x, unknown=NA, ...) {
-  unknown <- gdata:::.unknownList(x=x, unknown=unknown)
+  unknown <- .unknownList(x=x, unknown=unknown)
   x <- mapply(FUN="isUnknown", x=x, unknown=unknown, ..., SIMPLIFY=FALSE)
   x
 }
@@ -90,7 +90,7 @@
 
 unknownToNA.list <- function(x, unknown, warning=FALSE, ...)
 {
-  unknown <- gdata:::.unknownList(x=x, unknown=unknown)
+  unknown <- .unknownList(x=x, unknown=unknown)
   x <- mapply(FUN="unknownToNA", x=x, unknown=unknown, warning=warning,
               SIMPLIFY=FALSE)
   return(x)
@@ -148,7 +148,7 @@
 
 NAToUnknown.list <- function(x, unknown, force=FALSE, call.=FALSE, ...)
 {
-  unknown <- gdata:::.unknownList(x=x, unknown=unknown)
+  unknown <- .unknownList(x=x, unknown=unknown)
   x <- mapply(FUN="NAToUnknown", x=x, unknown=unknown, force=force,
               call.=call., SIMPLIFY=FALSE)
   x

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1796] trunk/gdata/DESCRIPTION

[<wa...@us...>]

Revision: 1796
          http://sourceforge.net/p/r-gregmisc/code/1796
Author:   warnes
Date:     2014-04-05 17:01:31 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Fix syntax error in DESCRIPTION file.

Modified Paths:
--------------
    trunk/gdata/DESCRIPTION

Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION	2014-04-05 17:00:53 UTC (rev 1795)
+++ trunk/gdata/DESCRIPTION	2014-04-05 17:01:31 UTC (rev 1796)
@@ -12,4 +12,4 @@
 Maintainer: Gregory R. Warnes <gr...@wa...>
 License: GPL-2
 NeedsCompilation: no
-Recommends: RUnit
+Suggests: RUnit

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1795] trunk/gdata/tests/runRUnitTests.R

[<wa...@us...>]

Revision: 1795
          http://sourceforge.net/p/r-gregmisc/code/1795
Author:   warnes
Date:     2014-04-05 17:00:53 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Package name needs to be defined outside of if test.

Modified Paths:
--------------
    trunk/gdata/tests/runRUnitTests.R

Modified: trunk/gdata/tests/runRUnitTests.R
===================================================================
--- trunk/gdata/tests/runRUnitTests.R	2014-04-05 17:00:14 UTC (rev 1794)
+++ trunk/gdata/tests/runRUnitTests.R	2014-04-05 17:00:53 UTC (rev 1795)
@@ -36,28 +36,28 @@
 ## make
 ## make all
 
+PKG  <- 'gdata'
+
 if(require("RUnit", quietly=TRUE))
 {
 
-    pkg  <- 'gdata'
-
     path <- normalizePath("unitTests")
 
     cat("\nRunning unit tests\n")
-    print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+    print(list(pkg=PKG, getwd=getwd(), pathToUnitTests=path))
 
-    library(package=pkg, character.only=TRUE)
+    library(package=PKG, character.only=TRUE)
 
     testFileRegexp <- "^runit.+\\.[rR]$"
 
     ## Debugging echo
     cat("\nRunning RUnit tests\n")
-    print(list(pkg=pkg,
+    print(list(pkg=PKG,
                getwd=getwd(),
                pathToRUnitTests=path))
 
     ## Define tests
-    testSuite <- defineTestSuite(name=paste(pkg, "RUnit testing"),
+    testSuite <- defineTestSuite(name=paste(PKG, "RUnit testing"),
                                  dirs=path,
                                  testFileRegexp=testFileRegexp
                                  )
@@ -68,7 +68,7 @@
     if(file.access(path, 02) != 0)
         {
             ## cannot write to path -> use writable one
-            tdir <- tempfile(paste(pkg, "RUnitTests", sep="_"))
+            tdir <- tempfile(paste(PKG, "RUnitTests", sep="_"))
             dir.create(tdir)
             pathReport <- file.path(tdir, "report")
         }
@@ -103,7 +103,7 @@
 } else {
 
     cat("R package 'RUnit' cannot be loaded - no unit tests run\n",
-        "for package", pkg,"\n")
+        "for package", PKG,"\n")
 
 }
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1794] trunk/gdata/vignettes/Rnews.sty

[<wa...@us...>]

Revision: 1794
          http://sourceforge.net/p/r-gregmisc/code/1794
Author:   warnes
Date:     2014-04-05 17:00:14 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Style file needed

Added Paths:
-----------
    trunk/gdata/vignettes/Rnews.sty

Copied: trunk/gdata/vignettes/Rnews.sty (from rev 1786, trunk/gdata/inst/doc/Rnews.sty)
===================================================================
--- trunk/gdata/vignettes/Rnews.sty	                        (rev 0)
+++ trunk/gdata/vignettes/Rnews.sty	2014-04-05 17:00:14 UTC (rev 1794)
@@ -0,0 +1,204 @@
+%%
+%% This is file `Rnews.sty',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% Rnews.dtx  (with options: `package')
+%% 
+%% IMPORTANT NOTICE:
+%% 
+%% For the copyright see the source file.
+%% 
+%% Any modified versions of this file must be renamed
+%% with new filenames distinct from Rnews.sty.
+%% 
+%% For distribution of the original source see the terms
+%% for copying and modification in the file Rnews.dtx.
+%% 
+%% This generated file may be distributed as long as the
+%% original source files, as listed above, are part of the
+%% same distribution. (The sources need not necessarily be
+%% in the same archive or directory.)
+\def\fileversion{v0.3.6}
+\def\filename{Rnews}
+\def\filedate{2002/06/02}
+\def\docdate {2001/10/31}
+%%
+%% Package `Rnews' to use with LaTeX2e
+%% Copyright (C) 2001--2002 by the R Core Development Team
+%% Please report errors to KH or FL
+%%
+%% -*- LaTeX -*-
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\ProvidesPackage{\filename}[\filedate\space\fileversion\space
+                        Rnews package]
+\typeout{Package: `\filename\space\fileversion \@spaces <\filedate>'}
+\typeout{English documentation as of <\docdate>}
+\RequirePackage{ifthen}
+\newboolean{Rnews@driver}
+\DeclareOption{driver}{\setboolean{Rnews@driver}{true}}
+\DeclareOption*{\PackageWarning{\filename}{Unknown option
+    `\CurrentOption'}}
+\ProcessOptions\relax
+\ifthenelse{\boolean{Rnews@driver}}{}{
+\RequirePackage{multicol,graphicx,color,fancyhdr,hyperref}
+\newcommand{\volume}[1]{\def\Rnews@volume{#1}}
+\newcommand{\volnumber}[1]{\def\Rnews@number{#1}}
+\renewcommand{\date}[1]{\def\Rnews@date{#1}}
+\setcounter{secnumdepth}{-1}
+\renewcommand{\author}[1]{\def\Rnews@author{#1}}
+\renewcommand{\title}[1]{\def\Rnews@title{#1}}
+\newcommand{\subtitle}[1]{\def\Rnews@subtitle{#1}}
+\newenvironment{article}{%
+  \author{}\title{}\subtitle{}}{\end{multicols}}
+\renewcommand{\maketitle}{
+  \begin{multicols}{2}[\chapter{\Rnews@title}\refstepcounter{chapter}][3cm]
+    \ifx\empty\Rnews@subtitle\else\noindent\textbf{\Rnews@subtitle}
+    \par\nobreak\addvspace{\baselineskip}\fi
+    \ifx\empty\Rnews@author\else\noindent\textit{\Rnews@author}
+    \par\nobreak\addvspace{\baselineskip}\fi
+    \@afterindentfalse\@nobreaktrue\@afterheading}
+\renewcommand\chapter{\secdef\Rnews@chapter\@schapter}
+\providecommand{\nohyphens}{%
+  \hyphenpenalty=10000\exhyphenpenalty=10000\relax}
+\newcommand{\Rnews@chapter}{%
+  \renewcommand{\@seccntformat}[1]{}%
+  \@startsection{chapter}{0}{0mm}{%
+    -2\baselineskip \@plus -\baselineskip \@minus -.2ex}{\p@}{%
+    \normalfont\Huge\bfseries\raggedright}}
+\renewcommand*\l@chapter{\@dottedtocline{0}{0pt}{1em}}
+\def\@schapter#1{\section*#1}
+\renewenvironment{figure}[1][]{%
+  \def\@captype{figure}
+  \noindent
+  \begin{minipage}{\columnwidth}}{%
+  \end{minipage}\par\addvspace{\baselineskip}}
+\renewcommand{\theequation}{\@arabic\c@equation}
+\def\equation{%
+  \let\refstepcounter\H@refstepcounter
+  \H@equation
+  \def\newname{\arabic{chapter}.\theequation}%
+  \let\theHequation\newname%
+  \hyper@makecurrent{equation}%
+  \Hy@raisedlink{\hyper@anchorstart{\@currentHref}}%
+  \let\refstepcounter\new@refstepcounter}%
+\def\endequation{\Hy@raisedlink{\hyper@anchorend}\H@endequation}
+\renewcommand{\thefigure}{\@arabic\c@figure}
+\renewcommand{\thetable}{\@arabic\c@table}
+\renewcommand{\contentsname}{Contents of this issue:}
+\renewcommand\tableofcontents{%
+  \section*{\contentsname
+    \@mkboth{%
+      \MakeUppercase\contentsname}{\MakeUppercase\contentsname}}%
+  \@starttoc{toc}}
+\renewcommand{\titlepage}{%
+  \noindent
+  \rule{\textwidth}{1pt}\\[-.8\baselineskip]
+  \rule{\textwidth}{.5pt}
+  \begin{center}
+    \includegraphics[height=2cm]{Rlogo}\hspace{7mm}
+    \fontsize{2cm}{2cm}\selectfont
+    News
+  \end{center}
+  The Newsletter of the R Project\hfill
+  Volume \Rnews@volume/\Rnews@number, \Rnews@date\\[-.5\baselineskip]
+  \rule{\textwidth}{.5pt}\\[-.8\baselineskip]
+  \rule{\textwidth}{1pt}
+  \vspace{1cm}
+  \fancyhf{}
+  \fancyhead[L]{Vol.~\Rnews@volume/\Rnews@number, \Rnews@date}
+  \fancyhead[R]{\thepage}
+  \fancyfoot[L]{R News}
+  \fancyfoot[R]{ISSN 1609-3631}
+  \thispagestyle{empty}
+  \begin{bottombox}
+    \begin{multicols}{2}
+      \setcounter{tocdepth}{0}
+      \tableofcontents
+      \setcounter{tocdepth}{2}
+    \end{multicols}
+  \end{bottombox}}
+\setlength{\textheight}{250mm}
+\setlength{\topmargin}{-10mm}
+\setlength{\textwidth}{17cm}
+\setlength{\oddsidemargin}{-6mm}
+\setlength{\columnseprule}{.1pt}
+\setlength{\columnsep}{20pt}
+\RequirePackage{ae,mathpple}
+\RequirePackage[T1]{fontenc}
+\renewcommand{\rmdefault}{ppl}
+\renewcommand{\sfdefault}{aess}
+\renewcommand{\ttdefault}{aett}
+\definecolor{Red}{rgb}{0.7,0,0}
+\definecolor{Blue}{rgb}{0,0,0.8}
+\definecolor{hellgrau}{rgb}{0.55,0.55,0.55}
+\newcommand{\R}{R}
+\newcommand{\address}[1]{\addvspace{\baselineskip}\noindent\emph{#1}}
+\newcommand{\email}[1]{\href{mailto:#1}{\normalfont\texttt{#1}}}
+\newsavebox{\Rnews@box}
+\newlength{\Rnews@len}
+\newenvironment{bottombox}{%
+  \begin{figure*}[b]
+    \begin{center}
+      \noindent
+      \begin{lrbox}{\Rnews@box}
+        \begin{minipage}{0.99\textwidth}}{%
+        \end{minipage}
+      \end{lrbox}
+      \addtolength{\Rnews@len}{\fboxsep}
+      \addtolength{\Rnews@len}{\fboxrule}
+      \hspace*{-\Rnews@len}\fbox{\usebox{\Rnews@box}}
+    \end{center}
+  \end{figure*}}
+\RequirePackage{verbatim}
+\def\boxedverbatim{%
+  \def\verbatim@processline{%
+    {\setbox0=\hbox{\the\verbatim@line}%
+    \hsize=\wd0 \the\verbatim@line\par}}%
+  \@minipagetrue
+  \@tempswatrue
+  \setbox0=\vbox
+  \bgroup\small\verbatim
+}
+\def\endboxedverbatim{%
+  \endverbatim
+  \unskip\setbox0=\lastbox
+  \egroup
+  \fbox{\box0}
+}
+\pagestyle{fancy}
+} % \ifthenelse{\boolean{Rnews@driver}}
+\newcommand\code{\bgroup\@codex}
+\def\@codex#1{{\normalfont\ttfamily\hyphenchar\font=-1 #1}\egroup}
+\newcommand{\kbd}[1]{{\normalfont\texttt{#1}}}
+\newcommand{\key}[1]{{\normalfont\texttt{\uppercase{#1}}}}
+\newcommand\samp{`\bgroup\@noligs\@sampx}
+\def\@sampx#1{{\normalfont\texttt{#1}}\egroup'}
+\newcommand{\var}[1]{{\normalfont\textsl{#1}}}
+\let\env=\code
+\newcommand{\file}[1]{{`\normalfont\textsf{#1}'}}
+\let\command=\code
+\let\option=\samp
+\newcommand{\dfn}[1]{{\normalfont\textsl{#1}}}
+\newcommand{\acronym}[1]{{\normalfont\textsc{\lowercase{#1}}}}
+\newcommand{\strong}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\let\pkg=\strong
+\RequirePackage{alltt}
+\newenvironment{example}{\begin{alltt}}{\end{alltt}}
+\newenvironment{smallexample}{\begin{alltt}\small}{\end{alltt}}
+\newenvironment{display}{\list{}{}\item\relax}{\endlist}
+\newenvironment{smallverbatim}{\small\verbatim}{\endverbatim}
+\providecommand{\operatorname}[1]{%
+  \mathop{\operator@font#1}\nolimits}
+\renewcommand{\P}{%
+  \mathop{\operator@font I\hspace{-1.5pt}P\hspace{.13pt}}}
+\newcommand{\E}{%
+  \mathop{\operator@font I\hspace{-1.5pt}E\hspace{.13pt}}}
+\newcommand{\VAR}{\operatorname{var}}
+\newcommand{\COV}{\operatorname{cov}}
+\newcommand{\COR}{\operatorname{cor}}
+\RequirePackage{amsfonts}
+\endinput
+%%
+%% End of file `Rnews.sty'.

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1793] trunk/gdata

[<wa...@us...>]

Revision: 1793
          http://sourceforge.net/p/r-gregmisc/code/1793
Author:   warnes
Date:     2014-04-05 16:59:43 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
The issue Brian pointed out was an error in the isUnknown() code, not an error in the unit tests!

Modified Paths:
--------------
    trunk/gdata/R/unknown.R
    trunk/gdata/tests/unitTests/runit.unknown.R

Modified: trunk/gdata/R/unknown.R
===================================================================
--- trunk/gdata/R/unknown.R	2014-04-05 15:55:48 UTC (rev 1792)
+++ trunk/gdata/R/unknown.R	2014-04-05 16:59:43 UTC (rev 1793)
@@ -29,7 +29,14 @@
   } else {
     unknown <- as.character(x=unknown, ...)
   }
-  isUnknown.default(x=as.character(x), unknown=unknown)
+
+  if(is.list(x) && !inherits(x=x, what="POSIXlt")) {
+    x <- lapply(x, FUN=as.character, ...)
+  } else {
+    x <- as.character(x=x, ...)
+  }
+
+  isUnknown.default(x=as.character(x), unknown=as.character(unknown))
 }
 
 isUnknown.list <- function(x, unknown=NA, ...) {

Modified: trunk/gdata/tests/unitTests/runit.unknown.R
===================================================================
--- trunk/gdata/tests/unitTests/runit.unknown.R	2014-04-05 15:55:48 UTC (rev 1792)
+++ trunk/gdata/tests/unitTests/runit.unknown.R	2014-04-05 16:59:43 UTC (rev 1793)
@@ -249,42 +249,7 @@
   ## Date-time classes
   checkIdentical(isUnknown(xDateUnk, unknown=dateUnk), xDateTest)
   checkIdentical(isUnknown(xDate1Unk, unknown=dateUnk), xDate1Test)
-
-  ####
-  ## Per Brian Ripley on 2014-01-15:
-  ##
-  ## On platforms where POSIXlt has a gmtoff component, it does not
-  ## need to be set.  So
-  ##
-  ## > z$gmtoff
-  ## [1] 3600   NA
-  ## > xPOSIXltUnk$gmtoff
-  ## [1] 3600 3600
-  ##
-  ## (or sometimes 0, not NA).
-  ##
-  ## So although identical() correctly reports that they differ, this
-  ## is allowed for optional components.
-  ##
-  ## It would also be wrong to use identical() to compare isdst
-  ## components: isdst = -1 means unknown.
-  ##
-  ## Replaced:
-  ##    checkIdentical(isUnknown(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXltTest)
-  ## With:
-  tmp_isUnknown <- isUnknown(xPOSIXltUnk, unknown=POSIXltUnk)
-  tmp_xPOSIXltTest   <- xPOSIXlt
-
-  tmp_isUnknown$gmtoff    <- NULL  # Remove $gmtoff to avoid comparison
-  tmp_xPOSIXltTest$gmtoff <- NULL
-
-  tmp_isUnknownisdst     <- NULL   # Remove $isdst to avoid comparison
-  tmp_xPOSIXltTest$isdst <- NULL
-
-  checkIdentical(tmp_isUnknown, tmp_xPOSIXltTest)
-  ##
-  ####
-
+  checkIdentical(isUnknown(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXltTest)
   checkIdentical(isUnknown(xPOSIXlt1Unk, unknown=POSIXltUnk), xPOSIXlt1Test)
   checkIdentical(isUnknown(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXctTest)
   checkIdentical(isUnknown(xPOSIXct1Unk, unknown=POSIXctUnk), xPOSIXct1Test)
@@ -366,41 +331,9 @@
 
   ## Date-time classes
   checkIdentical(unknownToNA(xDateUnk, unknown=dateUnk), xDate)
+  checkIdentical(unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXlt)
   checkIdentical(unknownToNA(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXct)
 
-  ####
-  ## Per Brian Ripley on 2014-01-15:
-  ##
-  ## On platforms where POSIXlt has a gmtoff component, it does not need to be set.  So
-  ##
-  ## > z$gmtoff
-  ## [1] 3600   NA
-  ## > xPOSIXltUnk$gmtoff
-  ## [1] 3600 3600
-  ##
-  ## (or sometimes 0, not NA).
-  ##
-  ## So although identical() correctly reports that they differ, this
-  ## is allowed for optional components.
-  ##
-  ## It would also be wrong to use identical() to compare isdst
-  ## components: isdst = -1 means unknown.
-  ##
-  ## Replaced:
-  ##   checkIdentical(unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXlt)
-  ## With:
-  tmp_unknownToNA <- unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk)
-  tmp_xPOSIXlt   <- xPOSIXlt
-
-  tmp_unknownToNA$gmtoff <- NULL  # Remove $gmtoff to avoid comparison
-  tmp_xPOSIXlt$gmtoff   <- NULL
-
-  tmp_unknownToNA$isdst <- NULL   # Remove $isdst to avoid comparison
-  tmp_xPOSIXlt$isdst   <- NULL
-
-  checkIdentical(tmp_unknownToNA, tmp_xPOSIXlt)
-  ####
-
   ## --- lists and data.frames ---
 
   ## with vector of single unknown values

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1792] trunk/gdata/tests/unitTests/runit.unknown.R

[<wa...@us...>]

Revision: 1792
          http://sourceforge.net/p/r-gregmisc/code/1792
Author:   warnes
Date:     2014-04-05 15:55:48 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Apply changes Brian recommned to NAtoUnknown as well as unknownToNA.

Modified Paths:
--------------
    trunk/gdata/tests/unitTests/runit.unknown.R

Modified: trunk/gdata/tests/unitTests/runit.unknown.R
===================================================================
--- trunk/gdata/tests/unitTests/runit.unknown.R	2014-04-05 14:40:08 UTC (rev 1791)
+++ trunk/gdata/tests/unitTests/runit.unknown.R	2014-04-05 15:55:48 UTC (rev 1792)
@@ -249,7 +249,42 @@
   ## Date-time classes
   checkIdentical(isUnknown(xDateUnk, unknown=dateUnk), xDateTest)
   checkIdentical(isUnknown(xDate1Unk, unknown=dateUnk), xDate1Test)
-  checkIdentical(isUnknown(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXltTest)
+
+  ####
+  ## Per Brian Ripley on 2014-01-15:
+  ##
+  ## On platforms where POSIXlt has a gmtoff component, it does not
+  ## need to be set.  So
+  ##
+  ## > z$gmtoff
+  ## [1] 3600   NA
+  ## > xPOSIXltUnk$gmtoff
+  ## [1] 3600 3600
+  ##
+  ## (or sometimes 0, not NA).
+  ##
+  ## So although identical() correctly reports that they differ, this
+  ## is allowed for optional components.
+  ##
+  ## It would also be wrong to use identical() to compare isdst
+  ## components: isdst = -1 means unknown.
+  ##
+  ## Replaced:
+  ##    checkIdentical(isUnknown(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXltTest)
+  ## With:
+  tmp_isUnknown <- isUnknown(xPOSIXltUnk, unknown=POSIXltUnk)
+  tmp_xPOSIXltTest   <- xPOSIXlt
+
+  tmp_isUnknown$gmtoff    <- NULL  # Remove $gmtoff to avoid comparison
+  tmp_xPOSIXltTest$gmtoff <- NULL
+
+  tmp_isUnknownisdst     <- NULL   # Remove $isdst to avoid comparison
+  tmp_xPOSIXltTest$isdst <- NULL
+
+  checkIdentical(tmp_isUnknown, tmp_xPOSIXltTest)
+  ##
+  ####
+
   checkIdentical(isUnknown(xPOSIXlt1Unk, unknown=POSIXltUnk), xPOSIXlt1Test)
   checkIdentical(isUnknown(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXctTest)
   checkIdentical(isUnknown(xPOSIXct1Unk, unknown=POSIXctUnk), xPOSIXct1Test)
@@ -333,6 +368,7 @@
   checkIdentical(unknownToNA(xDateUnk, unknown=dateUnk), xDate)
   checkIdentical(unknownToNA(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXct)
 
+  ####
   ## Per Brian Ripley on 2014-01-15:
   ##
   ## On platforms where POSIXlt has a gmtoff component, it does not need to be set.  So
@@ -350,6 +386,9 @@
   ## It would also be wrong to use identical() to compare isdst
   ## components: isdst = -1 means unknown.
   ##
+  ## Replaced:
+  ##   checkIdentical(unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXlt)
+  ## With:
   tmp_unknownToNA <- unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk)
   tmp_xPOSIXlt   <- xPOSIXlt
 
@@ -360,8 +399,8 @@
   tmp_xPOSIXlt$isdst   <- NULL
 
   checkIdentical(tmp_unknownToNA, tmp_xPOSIXlt)
+  ####
 
-
   ## --- lists and data.frames ---
 
   ## with vector of single unknown values

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1791] trunk/gdata/inst/NEWS

[<wa...@us...>]

Revision: 1791
          http://sourceforge.net/p/r-gregmisc/code/1791
Author:   warnes
Date:     2014-04-05 14:40:08 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Update NEWS file

Modified Paths:
--------------
    trunk/gdata/inst/NEWS

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2014-04-05 14:38:45 UTC (rev 1790)
+++ trunk/gdata/inst/NEWS	2014-04-05 14:40:08 UTC (rev 1791)
@@ -8,8 +8,9 @@
 
 Other Changes
 
-- Unit tests now follow R standard practice
+- 'aggregate.table' is now defunct.  See '?gdata-defunct' for details.
 
+- Unit tests and vignettes now follow R standard practice.
 
 Changes in 2.13.2 (2013-06-28)
 ------------------------------

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1790] trunk/gdata/inst/doc/Rnews.dtx

[<wa...@us...>]

Revision: 1790
          http://sourceforge.net/p/r-gregmisc/code/1790
Author:   warnes
Date:     2014-04-05 14:38:45 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Don't need latex .dtx source file

Removed Paths:
-------------
    trunk/gdata/inst/doc/Rnews.dtx

Deleted: trunk/gdata/inst/doc/Rnews.dtx
===================================================================
--- trunk/gdata/inst/doc/Rnews.dtx	2014-04-05 14:26:49 UTC (rev 1789)
+++ trunk/gdata/inst/doc/Rnews.dtx	2014-04-05 14:38:45 UTC (rev 1790)
@@ -1,574 +0,0 @@
-\def\fileversion{v0.3.1}
-\def\filename{Rnews}
-\def\filedate{2001/09/04}
-\def\docdate {2001/09/04}
-%
-% \iffalse
-%
-%%
-%% Package `Rnews' to use with LaTeX2e
-%% Copyright (C) 2001 by the R Core Development Team
-%% Please report errors to KH or FL
-%%
-%% -*- LaTeX -*-
-%
-% \fi
-%
-% \iffalse
-% \changes{v0.1}{2001/01/05}{First draft.}
-% \changes{v0.2}{2001/07/01}
-%   {Added macros \cmd\P, \cmd\E, \cmd\VAR, \cmd\COV, \cmd\COR, and
-%    \cmd\operatorname.  Require \pkg{amsfonts} to produce symbols for
-%    sets of positive integers etc.}
-% \changes{v0.3}{2001/08/02}
-%   {Add package option `driver' for typesetting the driver.
-%    Change article environment to use chapters.
-%    Ensure unique figure labels.}
-% \changes{v0.3.1}{2001/09/04}
-%   {Remove redefinition of |\caption|, which had figures hard-wired.
-%    Instead, have our |figure| environment set |\@captype|.}
-% \fi
-%
-% \MakeShortVerb{\|}
-%
-% \newcommand{\AmS}{$${\protect\the\textfont2 A}\kern-.1667em\lower
-%   .5ex\hbox{\protect\the\textfont2 M}\kern
-%   -.125em{\protect\the\textfont2 S}}
-% \newcommand{\AmSLaTeX}{\mbox{\AmS-\LaTeX}}
-%
-% \title{The package \pkg{\filename}}
-% \author{Kurt Hornik \and Friedrich Leisch}
-%
-% \maketitle
-%
-% \section{Introduction}
-%
-% The \LaTeXe{} package \pkg{\filename} provides commands for formatting
-% the R Newsletter.
-%
-% \section{Documentation}
-%
-% \subsection{Marking Words and Phrases}
-%
-% The \pkg{Rnews} package provides roughly the same commands for marking
-% words and phrases as does Texinfo (but note that the \LaTeX special
-% characters still need special treatment).  These commands are
-% \begin{description}
-%  \item[\code{\cmd{\code}\{\var{sample-code}\}}]
-%   Indicate text that is a literal example of a piece of a program.
-%  \item[\code{\cmd{\kbd}\{\var{keyboard-characters}\}}]
-%   Indicate keyboard input.
-%  \item[\code{\cmd{\key}\{\var{key-name}\}}]
-%   Indicate the conventional name for a key on a keyboard.
-%  \item[\code{\cmd{\samp}\{\var{text}\}}]
-%   Indicate text that is a literal example of a sequence of
-%   characters.
-%  \item[\code{\cmd{\var}\{\var{metasyntactic-variable}\}}]
-%   Indicate a metasyntactic variable.
-%  \item[\code{\cmd{\env}\{\var{environment-variable}\}}]
-%   Indicate an environment variable.
-%  \item[\code{\cmd{\file}\{\var{file-name}\}}]
-%   Indicate the name of a file.
-%  \item[\code{\cmd{\command}\{\var{command-name}\}}]
-%   Indicate a command name (such as \samp{ls}).
-%  \item[\code{\cmd{\option}\{\var{option-name}\}}]
-%   Indicate a command line option.
-%  \item[\code{\cmd{\dfn}\{\var{term}\}}]
-%   Indicate the introductory or defining use of a term.
-%  \item[\code{\cmd{\acronym}\{\var{acronym}\}}]
-%   Use for abbreviattions written in all capital letters, such as
-%   \samp{NASA}.
-% \end{description}
-% If this sounds rather confusing, please see the Texinfo documentation
-% for more details.
-%
-% \DescribeMacro{\strong}
-% There is also a |\strong| command for emphasizing text more strongly
-% than with |\emph|.  For example, |\strong{Note:}| gives \strong{Note:}.
-%
-% \DescribeMacro{\pkg}
-% Finally, use |\pkg| for indicating R packages.
-%
-% \subsection{Quotations and Examples}
-%
-% In addition to the standard \LaTeX{} for quotations and examples (such
-% as |quote|, |quotation|, |flushleft|, |center| and |flushright|), the
-% \pkg{\filename} package provides the following environments.
-% \begin{description}
-%  \item[\code{example}]
-%    Illustrate code, commands, and the like.  The text is printed in a
-%    fixed-width font, and indented but not filled.
-%  \item[\code{smallexample}]
-%    Similar to \code{example}, except that text is typeset in a smaller
-%    font.
-% \end{description}
-%
-% \subsection{Mathematics}
-%
-% \DescribeMacro{\P}
-% \DescribeMacro{\E}
-% \DescribeMacro{\VAR}
-% \DescribeMacro{\COV}
-% \DescribeMacro{\COR}
-% The commands |\P|, |\E|, |\VAR|, |\COV|, and |\COR| produce symbols
-% for probability, expectation, variance, covariance and correlation.
-% For example, Chebyshev's inequality
-% \DeleteShortVerb{\|}
-% \begin{displaymath}
-%   \P(|\xi-\E\xi|>\lambda) \le \frac{\VAR(\xi)}{\lambda^2}.
-% \end{displaymath}
-% can be coded as
-% \MakeShortVerb{\|}
-% \begin{quote}
-%   \verb+\P(|\xi-\E\xi|>\lambda) \le \frac{\VAR(\xi)}{\lambda^2}+.
-% \end{quote}
-%
-% \DescribeMacro{\mathbb}
-% The symbols
-% \begin{displaymath}
-%   \mathbb{N}\quad\mathbb{Z}\quad\mathbb{Q}\quad\mathbb{R}\quad\mathbb{C}
-% \end{displaymath}
-% for the positive integers, the integers, and the rational, real and
-% complex numbers, respectively, can be obtained using |\mathbb| from
-% package \pkg{amsfonts} as
-% \begin{quote}
-%   |\mathbb{N}| |\mathbb{Z}| |\mathbb{Q}| |\mathbb{R}| |\mathbb{C}|
-% \end{quote}
-%
-% \section{The Code}
-%
-% \subsection{The Batch File}
-%
-% First comes the code for creating the batch file \file{\filename.ins}
-% which in turn can be used for producing the package and driver files.
-%
-%    \begin{macrocode}
-%<*install>
-\begin{filecontents}{\filename.ins}
-% Simply TeX or LaTeX this file to extract various files from the source
-% file `Rnews.dtx'.
-  \def\filedate{2001/01/05} \def\batchfile{Rnews.ins} \input
-  docstrip.tex \preamble
-\endpreamble
-\generateFile{Rnews.drv}{t}{\from{Rnews.dtx}{driver}}
-\generateFile{Rnews.sty}{t}{\from{Rnews.dtx}{package}}
-\Msg{***********************************************************}
-\Msg{* For documentation, run LaTeX on Rnews.dtx or Rnews.drv. *}
-\Msg{***********************************************************}
-\end{filecontents}
-%</install>
-%    \end{macrocode}
-%
-% \subsection{The Driver}
-%
-% Next comes the documentation driver file for \TeX{}, i.e., the file
-% that will produce the documentation you are currently reading.  It
-% will be extracted from this file by the \texttt{docstrip} program.
-% Since it is the first code in the file one can alternatively process
-% this file directly with \LaTeXe{} to obtain the documentation.
-%
-%    \begin{macrocode}
-%<*driver>
-\documentclass[fleqn]{ltxdoc}
-\usepackage[driver]{\filename}
-\renewcommand{\pkg}[1]{\textsf{#1}}
-\begin{document}
-  \DocInput{\filename.dtx}
-\end{document}
-%</driver>
-%    \end{macrocode}
-%
-% \subsection{The Code}
-%
-% Now comes the code for the package.
-%
-% It the current format is not \LaTeXe{}, we abort immediately.
-% Otherwise, we provide ourselves and show the current version of the
-% package on the screen and in the transscript file.
-%    \begin{macrocode}
-%<*package>
-\NeedsTeXFormat{LaTeX2e}[1995/12/01]
-\ProvidesPackage{\filename}[\filedate\space\fileversion\space
-                        Rnews package]
-\typeout{Package: `\filename\space\fileversion \@spaces <\filedate>'}
-\typeout{English documentation as of <\docdate>}
-%    \end{macrocode}
-%
-% Next, we set up a more or less trivial option handler.  We use option
-% `driver' for conditionalizing package code we do not want executed
-% when typesetting the driver file.
-%    \begin{macrocode}
-\RequirePackage{ifthen}
-\newboolean{Rnews@driver}
-\DeclareOption{driver}{\setboolean{Rnews@driver}{true}}
-\DeclareOption*{\PackageWarning{\filename}{Unknown option
-    `\CurrentOption'}}
-\ProcessOptions\relax
-%    \end{macrocode}
-%
-% Now comes the real code.
-%
-%    \begin{macrocode}
-\ifthenelse{\boolean{Rnews@driver}}{}{
-%    \end{macrocode}
-%
-% First we load some utility packages.
-%    \begin{macrocode}
-\RequirePackage{multicol,graphicx,color,fancyhdr,hyperref}
-%    \end{macrocode}
-%
-% \subsubsection{Basic Structure}
-%
-% Issues of of \emph{R News} are created from the standard \LaTeX{}
-% document class \pkg{report}.  Individual articles correspond to
-% chapters, and are contained in |article| environments.  This makes it
-% easy to have figures counted within articles and hence hyperlinked
-% correctly.
-%
-% Basic front matter information about the issue: volume, number, and
-% date.
-%    \begin{macrocode}
-\newcommand{\volume}[1]{\def\Rnews@volume{#1}}
-\newcommand{\volnumber}[1]{\def\Rnews@number{#1}}
-\renewcommand{\date}[1]{\def\Rnews@date{#1}}
-%    \end{macrocode}
-%
-% We do not want numbered sections.
-%    \begin{macrocode}
-\setcounter{secnumdepth}{-1}
-%    \end{macrocode}
-%
-% \begin{macro}{\author}
-% \begin{macro}{\title}
-% \begin{macro}{\subtitle}
-% An article has an author, a title, and optionally a subtitle.  We use
-% the obvious commands for specifying these.
-%    \begin{macrocode}
-\renewcommand{\author}[1]{\def\Rnews@author{#1}}
-\renewcommand{\title}[1]{\def\Rnews@title{#1}}
-\newcommand{\subtitle}[1]{\def\Rnews@subtitle{#1}}
-%    \end{macrocode}
-% \end{macro}
-% \end{macro}
-% \end{macro}
-%
-% \begin{environment}{article}
-% Environment |article| clears the article header information its begin
-% and restores single column mode at its end.
-%    \begin{macrocode}
-\newenvironment{article}{%
-  \author{}\title{}\subtitle{}}{\end{multicols}}
-%    \end{macrocode}
-% \end{environment}
-%
-% \begin{macro}{\maketitle}
-% The real work is done by a redefined version of |\maketitle|, which
-% also switches to double column mode.  Note that even though we do not
-% want chapters (articles) numbered, we need to increment the chapter
-% counter, so that figures get correct labelling.
-%    \begin{macrocode}
-\renewcommand{\maketitle}{
-  \chapter{\Rnews@title}
-  \refstepcounter{chapter}
-  \begin{multicols}{2}
-    \ifx\empty\Rnews@subtitle\else\par\addvspace{\baselineskip}
-    \noindent\textbf{\Rnews@subtitle}\fi
-    \ifx\empty\Rnews@author\else\par\addvspace{\baselineskip}
-    \noindent\textit{\Rnews@author}\fi}
-%    \end{macrocode}
-% \end{macro}
-%
-% Now for some ugly redefinitions.  We do not want articles to start a
-% new page.
-%    \begin{macrocode}
-\renewcommand\chapter{\secdef\@chapter\@schapter}
-%    \end{macrocode}
-% TOC entries for articles (chapters) should really look like sections.
-%    \begin{macrocode}
-\renewcommand*\l@chapter{\@dottedtocline{0}{0pt}{1em}}
-%    \end{macrocode}
-% We need to adjust vertical spacing in |\@makechapterhead|: extra space
-% before the title only if not at the beginning, no extra space after
-% it.
-%    \begin{macrocode}
-\def\@makechapterhead#1{%
-  \addvspace{2\baselineskip}%
-  {\parindent \z@ \raggedright \normalfont
-    \ifnum \c@secnumdepth >\m@ne
-        \huge\bfseries \@chapapp\space \thechapter
-        \par\nobreak
-        \vskip 20\p@
-    \fi
-    \interlinepenalty\@M
-    \Huge \bfseries #1\par\nobreak}}
-%    \end{macrocode}
-% We want bibliographies as starred sections within articles.  As the
-% standard |thebibliography| environment uses |chapter*|, we simply
-% redefine the latter according to our needs.
-%    \begin{macrocode}
-\def\@schapter#1{\section*#1}
-%    \end{macrocode}
-%
-% Package \pkg{multicol}, which is used for producing two-column output,
-% only allows for starred (single-column) floats (figures and tables).
-% Therefore, we provide a simple non-floating |figure| environment
-% ourselves.
-%    \begin{macrocode}
-\renewenvironment{figure}[1][]{%
-  \def\@captype{figure}
-  \begin{minipage}{0.9\columnwidth}}{
-  \end{minipage}\par\addvspace{\baselineskip}}
-%    \end{macrocode}
-% Equations, figures and tables are counted within articles, but we do
-% not show the article number.
-%    \begin{macrocode}
-\renewcommand{\theequation}{\@arabic\c@equation}
-\renewcommand{\thefigure}{\@arabic\c@figure}
-\renewcommand{\thetable}{\@arabic\c@table}
-%    \end{macrocode}
-%
-% \begin{macro}{\tableofcontents}
-% Need to provide our own version of |\tableofcontents| (no fiddling
-% with the number of columns).  Note that |\section*| is really the same
-% as |\chapter*|).
-%    \begin{macrocode}
-\renewcommand{\contentsname}{Contents of this issue:}
-\renewcommand\tableofcontents{%
-  \section*{\contentsname
-    \@mkboth{%
-      \MakeUppercase\contentsname}{\MakeUppercase\contentsname}}%
-  \@starttoc{toc}}
-%    \end{macrocode}
-% \end{macro}
-% \begin{macro}{\titlepage}
-% The title page of each issue features logo et al at the top and the
-% TOC.  We start with the top.
-%    \begin{macrocode}
-\renewcommand{\titlepage}{%
-  \noindent
-  \rule{\textwidth}{1pt}\\[-.8\baselineskip]
-  \rule{\textwidth}{.5pt}
-  \begin{center}
-    \includegraphics[height=2cm]{Rlogo}\hspace{7mm}
-    \fontsize{2cm}{2cm}\selectfont
-    News
-  \end{center}
-  The Newsletter of the R Project\hfill
-  Volume \Rnews@volume/\Rnews@number, \Rnews@date\\[-.5\baselineskip]
-  \rule{\textwidth}{.5pt}\\[-.8\baselineskip]
-  \rule{\textwidth}{1pt}
-  \vspace{1cm}
-%    \end{macrocode}
-% Now set up the header and footer information for the rest of the
-% document.
-%    \begin{macrocode}  
-  \fancyhf{}
-  \fancyhead[L]{Vol.~\Rnews@volume/\Rnews@number, \Rnews@date}
-  \fancyhead[R]{\thepage}
-  \fancyfoot[L]{R News}
-  \fancyfoot[R]{ISSN 1609-3631}
-  \thispagestyle{empty}
-%    \end{macrocode}
-% And finally, put the TOC at the bottom in a framed box.  Note the way
-% |tocdepth| is adjusted before and after producing the TOC: thus, we
-% can ensure that only articles show up in the printed TOC, but that in
-% the PDF version, bookmarks are created for sections and subsections as
-% well (provided that the non-starred forms are used).
-%    \begin{macrocode}  
-  \begin{bottombox}
-    \begin{multicols}{2}
-      \setcounter{tocdepth}{0}
-      \tableofcontents
-      \setcounter{tocdepth}{2}
-    \end{multicols}
-  \end{bottombox}}
-%    \end{macrocode}
-% \end{macro}
-%
-% \subsubsection{Layout, Fonts and Color}
-%
-% \paragraph{Layout.}
-% We set the basic layout parameters in a way that printouts should be
-% fine for both A4 and Letter paper.
-%    \begin{macrocode}
-\setlength{\textheight}{250mm}
-\setlength{\topmargin}{-10mm}
-\setlength{\textwidth}{17cm}
-\setlength{\oddsidemargin}{-6mm}
-\setlength{\columnseprule}{.1pt}
-\setlength{\columnsep}{20pt}
-%    \end{macrocode}
-%
-% \paragraph{Fonts.}
-% We use the following fonts (all with T1 encoding):
-% \begin{center}
-% \begin{tabular}{lp{0.8\textwidth}}
-%   rm &  palatino \\
-%   tt &  almost european (computer modern working with T1) \\
-%      &  Reason for aett: uses less horizontal space than courier,
-%      which is better for example code \\
-%   sf &  almost european \\
-%   math & palatino
-% \end{tabular}
-% \end{center}
-%
-%    \begin{macrocode}
-\RequirePackage{ae,mathpple}
-\RequirePackage[T1]{fontenc}
-\renewcommand{\rmdefault}{ppl}
-\renewcommand{\sfdefault}{aess}
-\renewcommand{\ttdefault}{aett}
-%    \end{macrocode}
-%
-% \paragraph{Colors.}  These are actually used for |\hypersetup| but we
-% do not call this here, although we should.
-% \marginpar{FIXME}
-%    \begin{macrocode}
-\definecolor{Red}{rgb}{0.7,0,0}
-\definecolor{Blue}{rgb}{0,0,0.8}
-\definecolor{hellgrau}{rgb}{0.55,0.55,0.55}
-%    \end{macrocode}
-%
-% \subsubsection{Miscellania}
-%
-%    \begin{macrocode}
-\newcommand{\R}{R}
-\newcommand{\address}[1]{\addvspace{\baselineskip}\noindent\emph{#1}}
-\newcommand{\email}[1]{\href{mailto:#1}{\normalfont\texttt{#1}}}
-%    \end{macrocode}
-%
-% \begin{environment}{bottombox}
-% Used for creating the TOC and the back matter editorial information.
-%    \begin{macrocode}
-\newsavebox{\Rnews@box}
-\newlength{\Rnews@len}
-\newenvironment{bottombox}{%
-  \begin{figure*}[b]
-    \begin{center}
-      \noindent
-      \begin{lrbox}{\Rnews@box}
-        \begin{minipage}{0.99\textwidth}}{%
-        \end{minipage}
-      \end{lrbox}
-      \addtolength{\Rnews@len}{\fboxsep}
-      \addtolength{\Rnews@len}{\fboxrule}
-      \hspace*{-\Rnews@len}\fbox{\usebox{\Rnews@box}}
-    \end{center}
-  \end{figure*}}
-%    \end{macrocode}
-% \end{environment}
-%
-% \begin{environment}{boxedverbatim}
-% This does not seem to be used any more.
-% \marginpar{FIXME}
-%    \begin{macrocode}
-\newenvironment{boxedverbatim}{%
-  \begin{lrbox}{\Rnews@box}
-    \begin{smallverbatim}}{%
-    \end{smallverbatim}
-  \end{lrbox}
-  \hspace*{-\fboxsep}\fbox{\usebox{\Rnews@box}}}
-%    \end{macrocode}
-% \end{environment}
-%
-% Finally, we turn on fancy page style.
-%    \begin{macrocode}
-\pagestyle{fancy}
-} % \ifthenelse{\boolean{Rnews@driver}}
-%    \end{macrocode}
-%
-% \subsubsection{Marking Words and Phrases}
-%
-% Simple font selection is not good enough.  For example, |\texttt{--}|
-% gives `\texttt{--}', i.e., an endash in typewriter font.  Hence, we
-% need to turn off ligatures, which currently only happens for commands
-% |\code| and |\samp| and the ones derived from them.  Hyphenation is
-% another issue; it should really be turned off inside |\samp|.  And
-% most importantly, \LaTeX{} special characters are a nightmare.  E.g.,
-% one needs |\~{}| to produce a tilde in a file name marked by |\file|.
-% Perhaps a few years ago, most users would have agreed that this may be
-% unfortunate but should not be changed to ensure consistency.  But with
-% the advent of the WWW and the need for getting `|~|' and `|#|' into
-% URLs, commands which only treat the escape and grouping characters
-% specially have gained acceptance (in fact, this is also what
-% \pkg{alltt} does, and hence environments based on it such as our
-% |smallexample|).  Hence, in the long run we should implement the same
-% for |\code|, |\kbd|, |\samp|, |\var|, and |\file|.  (The other
-% Texinfo-style commands do not need this.)
-%
-%    \begin{macrocode}
-%\newcommand\code{\bgroup\@noligs\@codex}
-\newcommand\code{\bgroup\@codex}
-\def\@codex#1{{\normalfont\ttfamily\hyphenchar\font=-1 #1}\egroup}
-\newcommand{\kbd}[1]{{\normalfont\texttt{#1}}}
-\newcommand{\key}[1]{{\normalfont\texttt{\uppercase{#1}}}}
-\newcommand\samp{`\bgroup\@noligs\@sampx}
-\def\@sampx#1{{\normalfont\texttt{#1}}\egroup'}
-\newcommand{\var}[1]{{\normalfont\textsl{#1}}}
-\let\env=\code
-\newcommand{\file}[1]{{`\normalfont\textsf{#1}'}}
-\let\command=\code
-\let\option=\samp
-\newcommand{\dfn}[1]{{\normalfont\textsl{#1}}}
-\newcommand{\acronym}[1]{{\normalfont\textsc{\lowercase{#1}}}}
-\newcommand{\strong}[1]{{\normalfont\fontseries{b}\selectfont #1}}
-\let\pkg=\strong
-%    \end{macrocode}
-%
-% \subsubsection{Quotations and Examples}
-%
-%    \begin{macrocode}
-\RequirePackage{alltt}
-\newenvironment{example}{\begin{alltt}}{\end{alltt}}
-\newenvironment{smallexample}{\begin{alltt}\small}{\end{alltt}}
-\newenvironment{display}{\list{}{}\item\relax}{\endlist}
-%    \end{macrocode}
-%
-% \subsubsection{Mathematics}
-%
-% \begin{macro}{\operatorname}
-% The implementation of |\operatorname| is similar to the mechanism
-% \LaTeXe{} uses for functions like sin and cos, and simpler than the
-% one of \AmSLaTeX{}.  We use |\providecommand| for the definition in
-% order to keep the one of the \pkg{amstex} if this package has
-% already been loaded.
-%    \begin{macrocode}
-\providecommand{\operatorname}[1]{%
-  \mathop{\operator@font#1}\nolimits}
-%    \end{macrocode}
-% \end{macro}
-%
-% \begin{macro}{\P}
-% \begin{macro}{\E}
-% \begin{macro}{\VAR}
-% \begin{macro}{\COV}
-% \begin{macro}{\COR}
-% Next, we provide commands for probability, expectation, variance,
-% covariance and correlation which are obviously useful in probability
-% theory and statistics.
-% (Of course, originally |\P| gives \mathhexbox27B.)
-%    \begin{macrocode}
-\renewcommand{\P}{%
-  \mathop{\operator@font I\hspace{-1.5pt}P\hspace{.13pt}}}
-\newcommand{\E}{%
-  \mathop{\operator@font I\hspace{-1.5pt}E\hspace{.13pt}}}
-\newcommand{\VAR}{\operatorname{var}}
-\newcommand{\COV}{\operatorname{cov}}
-\newcommand{\COR}{\operatorname{cor}}
-%    \end{macrocode}
-% \end{macro}
-% \end{macro}
-% \end{macro}
-% \end{macro}
-% \end{macro}
-%
-% Finally, we load package \pkg{amsfonts} so that |\mathbb| is available
-% for producing the symbols for positive integers etc.
-%    \begin{macrocode}
-\RequirePackage{amsfonts}
-%    \end{macrocode}
-%
-% This ends the implementation of the \pkg{\filename} package.
-%    \begin{macrocode}
-%</package>
-%    \end{macrocode}

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1789] trunk/gdata

[<wa...@us...>]

Revision: 1789
          http://sourceforge.net/p/r-gregmisc/code/1789
Author:   warnes
Date:     2014-04-05 14:26:49 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Move vignettes from inst/doc/ to vignettes/

Added Paths:
-----------
    trunk/gdata/vignettes/
    trunk/gdata/vignettes/mapLevels.Rnw
    trunk/gdata/vignettes/unknown.Rnw

Removed Paths:
-------------
    trunk/gdata/inst/doc/mapLevels.Rnw
    trunk/gdata/inst/doc/unknown.Rnw

Deleted: trunk/gdata/inst/doc/mapLevels.Rnw
===================================================================
--- trunk/gdata/inst/doc/mapLevels.Rnw	2014-04-05 13:57:10 UTC (rev 1788)
+++ trunk/gdata/inst/doc/mapLevels.Rnw	2014-04-05 14:26:49 UTC (rev 1789)
@@ -1,229 +0,0 @@
-
-%\VignetteIndexEntry{Mapping levels of a factor}
-%\VignettePackage{gdata}
-%\VignetteKeywords{levels, factor, manip}
-
-\documentclass[a4paper]{report}
-\usepackage{Rnews}
-\usepackage[round]{natbib}
-\bibliographystyle{abbrvnat}
-
-\usepackage{Sweave}
-\SweaveOpts{strip.white=all, keep.source=TRUE}
-
-\begin{document}
-
-\begin{article}
-
-\title{Mapping levels of a factor}
-\subtitle{The \pkg{gdata} package}
-\author{by Gregor Gorjanc}
-
-\maketitle
-
-\section{Introduction}
-
-Factors use levels attribute to store information on mapping between
-internal integer codes and character values i.e. levels. First level is
-mapped to internal integer code 1 and so on. Although some users do not
-like factors, their use is more efficient in terms of storage than for
-character vectors. Additionally, there are many functions in base \R{} that
-provide additional value for factors. Sometimes users need to work with
-internal integer codes and mapping them back to factor, especially when
-interfacing external programs. Mapping information is also of interest if
-there are many factors that should have the same set of levels. This note
-describes \code{mapLevels} function, which is an utility function for
-mapping the levels of a factor in \pkg{gdata} \footnote{from version 2.3.1}
-package \citep{WarnesGdata}.
-
-\section{Description with examples}
-
-Function \code{mapLevels()} is an (S3) generic function and works on
-\code{factor} and \code{character} atomic classes. It also works on
-\code{list} and \code{data.frame} objects with previously mentioned atomic
-classes. Function \code{mapLevels} produces a so called ``map'' with names
-and values. Names are levels, while values can be internal integer codes or
-(possibly other) levels. This will be clarified later on.  Class of this
-``map'' is \code{levelsMap}, if \code{x} in \code{mapLevels()} was atomic
-or \code{listLevelsMap} otherwise - for \code{list} and \code{data.frame}
-classes. The following example shows the creation and printout of such a
-``map''.
-
-<<ex01>>=
-library(gdata)
-(fac <- factor(c("B", "A", "Z", "D")))
-(map <- mapLevels(x=fac))
-@
-
-If we have to work with internal integer codes, we can transform factor to
-integer and still get ``back the original factor'' with ``map'' used as
-argument in \code{mapLevels<-} function as shown bellow. \code{mapLevels<-}
-is also an (S3) generic function and works on same classes as
-\code{mapLevels} plus \code{integer} atomic class.
-
-<<ex02>>=
-(int <- as.integer(fac))
-mapLevels(x=int) <- map
-int
-identical(fac, int)
-@
-
-Internally ``map'' (\code{levelsMap} class) is a \code{list} (see bellow),
-but its print method unlists it for ease of inspection. ``Map'' from
-example has all components of length 1. This is not mandatory as
-\code{mapLevels<-} function is only a wrapper around workhorse function
-\code{levels<-} and the later can accept \code{list} with components of
-various lengths.
-
-<<ex03>>=
-str(map)
-@
-
-Although not of primary importance, this ``map'' can also be used to remap
-factor levels as shown bellow.  Components ``later'' in the map take over
-the ``previous'' ones. Since this is not optimal I would rather recommend
-other approaches for ``remapping'' the levels of a \code{factor}, say
-\code{recode} in \pkg{car} package \citep{FoxCar}.
-
-<<ex04>>=
-map[[2]] <- as.integer(c(1, 2))
-map
-int <- as.integer(fac)
-mapLevels(x=int) <- map
-int
-@
-
-Up to now examples showed ``map'' with internal integer codes for values
-and levels for names. I call this integer ``map''. On the other hand
-character ``map'' uses levels for values and (possibly other) levels for
-names. This feature is a bit odd at first sight, but can be used to easily
-unify levels and internal integer codes across several factors.  Imagine
-you have a factor that is for some reason split into two factors \code{f1}
-and \code{f2} and that each factor does not have all levels. This is not
-uncommon situation.
-
-<<ex05>>=
-(f1 <- factor(c("A", "D", "C")))
-(f2 <- factor(c("B", "D", "C")))
-@
-
-If we work with this factors, we need to be careful as they do not have the
-same set of levels. This can be solved with appropriately specifying
-\code{levels} argument in creation of factors i.e. \code{levels=c("A", "B",
-  "C", "D")} or with proper use of \code{levels<-} function. I say proper
-as it is very tempting to use:
-
-<<ex06>>=
-fTest <- f1
-levels(fTest) <- c("A", "B", "C", "D")
-fTest
-@
-
-Above example extends set of levels, but also changes level of 2nd and 3rd
-element in \code{fTest}! Proper use of \code{levels<-} (as shown in
-\code{levels} help page) would be:
-
-<<ex07>>=
-fTest <- f1
-levels(fTest) <- list(A="A", B="B",
-                      C="C", D="D")
-fTest
-@
-
-Function \code{mapLevels} with character ``map'' can help us in such
-scenarios to unify levels and internal integer codes across several
-factors. Again the workhorse under this process is \code{levels<-} function
-from base \R{}! Function \code{mapLevels<-} just controls the assignment of
-(integer or character) ``map'' to \code{x}. Levels in \code{x} that match
-``map'' values (internal integer codes or levels) are changed to ``map''
-names (possibly other levels) as shown in \code{levels} help page. Levels
-that do not match are converted to \code{NA}. Integer ``map'' can be
-applied to \code{integer} or \code{factor}, while character ``map'' can be
-applied to \code{character} or \code{factor}. Result of \code{mapLevels<-}
-is always a \code{factor} with possibly ``remapped'' levels.
-
-To get one joint character ``map'' for several factors, we need to put
-factors in a \code{list} or \code{data.frame} and use arguments
-\code{codes=FALSE} and \code{combine=TRUE}. Such map can then be used to
-unify levels and internal integer codes.
-
-<<ex08>>=
-(bigMap <- mapLevels(x=list(f1, f2),
-                     codes=FALSE,
-                     combine=TRUE))
-mapLevels(f1) <- bigMap
-mapLevels(f2) <- bigMap
-f1
-f2
-cbind(as.character(f1), as.integer(f1),
-      as.character(f2), as.integer(f2))
-@
-
-If we do not specify \code{combine=TRUE} (which is the default behaviour)
-and \code{x} is a \code{list} or \code{data.frame}, \code{mapLevels}
-returns ``map'' of class \code{listLevelsMap}. This is internally a
-\code{list} of ``maps'' (\code{levelsMap} objects). Both
-\code{listLevelsMap} and \code{levelsMap} objects can be passed to
-\code{mapLevels<-} for \code{list}/\code{data.frame}. Recycling occurs when
-length of \code{listLevelsMap} is not the same as number of
-components/columns of a \code{list}/\code{data.frame}.
-
-Additional convenience methods are also implemented to ease the work with
-``maps'':
-
-\begin{itemize}
-
-\item \code{is.levelsMap}, \code{is.listLevelsMap}, \code{as.levelsMap} and
-  \code{as.listLevelsMap} for testing and coercion of user defined
-  ``maps'',
-
-\item \code{"["} for subsetting,
-
-\item \code{c} for combining \code{levelsMap} or \code{listLevelsMap}
-  objects; argument \code{recursive=TRUE} can be used to coerce
-  \code{listLevelsMap} to \code{levelsMap}, for example \code{c(llm1, llm2,
-    recursive=TRUE)} and
-
-\item \code{unique} and \code{sort} for \code{levelsMap}.
-
-\end{itemize}
-
-\section{Summary}
-
-Functions \code{mapLevels} and \code{mapLevels<-} can help users to map
-internal integer codes to factor levels and unify levels as well as
-internal integer codes among several factors. I welcome any comments or
-suggestions.
-
-% \bibliography{refs}
-\begin{thebibliography}{1}
-\providecommand{\natexlab}[1]{#1}
-\providecommand{\url}[1]{\texttt{#1}}
-\expandafter\ifx\csname urlstyle\endcsname\relax
-  \providecommand{\doi}[1]{doi: #1}\else
-  \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi
-
-\bibitem[Fox(2006)]{FoxCar}
-J.~Fox.
-\newblock \emph{car: Companion to Applied Regression}, 2006.
-\newblock URL \url{http://socserv.socsci.mcmaster.ca/jfox/}.
-\newblock R package version 1.1-1.
-
-\bibitem[Warnes(2006)]{WarnesGdata}
-G.~R. Warnes.
-\newblock \emph{gdata: Various R programming tools for data manipulation},
-  2006.
-\newblock URL
-  \url{http://cran.r-project.org/src/contrib/Descriptions/gdata.html}.
-\newblock R package version 2.3.1. Includes R source code and/or documentation
-  contributed by Ben Bolker, Gregor Gorjanc and Thomas Lumley.
-
-\end{thebibliography}
-
-\address{Gregor Gorjanc\\
-  University of Ljubljana, Slovenia\\
-\email{gre...@bf...}}
-
-\end{article}
-
-\end{document}

Deleted: trunk/gdata/inst/doc/unknown.Rnw
===================================================================
--- trunk/gdata/inst/doc/unknown.Rnw	2014-04-05 13:57:10 UTC (rev 1788)
+++ trunk/gdata/inst/doc/unknown.Rnw	2014-04-05 14:26:49 UTC (rev 1789)
@@ -1,272 +0,0 @@
-
-%\VignetteIndexEntry{Working with Unknown Values}
-%\VignettePackage{gdata}
-%\VignetteKeywords{unknown, missing, manip}
-
-\documentclass[a4paper]{report}
-\usepackage{Rnews}
-\usepackage[round]{natbib}
-\bibliographystyle{abbrvnat}
-
-\usepackage{Sweave}
-\SweaveOpts{strip.white=all, keep.source=TRUE}
-
-\begin{document}
-
-\begin{article}
-
-\title{Working with Unknown Values}
-\subtitle{The \pkg{gdata} package}
-\author{by Gregor Gorjanc}
-
-\maketitle
-
-This vignette has been published as \cite{Gorjanc}.
-
-\section{Introduction}
-
-Unknown or missing values can be represented in various ways. For example
-SAS uses \code{.}~(dot), while \R{} uses \code{NA}, which we can read as
-Not Available. When we import data into \R{}, say via \code{read.table} or
-its derivatives, conversion of blank fields to \code{NA} (according to
-\code{read.table} help) is done for \code{logical}, \code{integer},
-\code{numeric} and \code{complex} classes. Additionally, the
-\code{na.strings} argument can be used to specify values that should also
-be converted to \code{NA}. Inversely, there is an argument \code{na} in
-\code{write.table} and its derivatives to define value that will replace
-\code{NA} in exported data. There are also other ways to import/export data
-into \R{} as described in the {\emph R Data Import/Export} manual
-\citep{RImportExportManual}.  However, all approaches lack the possibility
-to define unknown value(s) for some particular column. It is possible that
-an unknown value in one column is a valid value in another column. For
-example, I have seen many datasets where values such as 0, -9, 999 and
-specific dates are used as column specific unknown values.
-
-This note describes a set of functions in package \pkg{gdata}\footnote{
-  package version 2.3.1} \citep{WarnesGdata}: \code{isUnknown},
-\code{unknownToNA} and \code{NAToUnknown}, which can help with testing for
-unknown values and conversions between unknown values and \code{NA}. All
-three functions are generic (S3) and were tested (at the time of writing)
-to work with: \code{integer}, \code{numeric}, \code{character},
-\code{factor}, \code{Date}, \code{POSIXct}, \code{POSIXlt}, \code{list},
-\code{data.frame} and \code{matrix} classes.
-
-\section{Description with examples}
-
-The following examples show simple usage of these functions on
-\code{numeric} and \code{factor} classes, where value \code{0} (beside
-\code{NA}) should be treated as an unknown value:
-
-<<ex01>>=
-library("gdata")
-xNum <- c(0, 6, 0, 7, 8, 9, NA)
-isUnknown(x=xNum)
-@
-
-The default unknown value in \code{isUnknown} is \code{NA}, which means
-that output is the same as \code{is.na} --- at least for atomic
-classes. However, we can pass the argument \code{unknown} to define which
-values should be treated as unknown:
-
-<<ex02>>=
-isUnknown(x=xNum, unknown=0)
-@
-
-This skipped \code{NA}, but we can get the expected answer after
-appropriately adding \code{NA} into the argument \code{unknown}:
-
-<<ex03>>=
-isUnknown(x=xNum, unknown=c(0, NA))
-@
-
-Now, we can change all unknown values to \code{NA} with \code{unknownToNA}.
-There is clearly no need to add \code{NA} here. This step is very handy
-after importing data from an external source, where many different unknown
-values might be used. Argument \code{warning=TRUE} can be used, if there is
-a need to be warned about ``original'' \code{NA}s:
-
-<<ex04>>=
-(xNum2 <- unknownToNA(x=xNum, unknown=0))
-@
-
-Prior to export from \R{}, we might want to change unknown values
-(\code{NA} in \R{}) to some other value. Function \code{NAToUnknown} can be
-used for this:
-
-<<ex05>>=
-NAToUnknown(x=xNum2, unknown=999)
-@
-
-Converting \code{NA} to a value that already exists in \code{x} issues an
-error, but \code{force=TRUE} can be used to overcome this if needed. But be
-warned that there is no way back from this step:
-
-<<ex06>>=
-NAToUnknown(x=xNum2, unknown=7, force=TRUE)
-@
-
-Examples below show all peculiarities with class \code{factor}.
-\code{unknownToNA} removes \code{unknown} value from levels and inversely
-\code{NAToUnknown} adds it with a warning. Additionally, \code{"NA"} is
-properly distinguished from \code{NA}. It can also be seen that the
-argument \code{unknown} in functions \code{isUnknown} and
-\code{unknownToNA} need not match the class of \code{x} (otherwise factor
-should be used) as the test is internally done with \code{\%in\%}, which
-nicely resolves coercing issues.
-
-<<ex07>>=
-(xFac <- factor(c(0, "BA", "RA", "BA", NA, "NA")))
-isUnknown(x=xFac)
-isUnknown(x=xFac, unknown=0)
-isUnknown(x=xFac, unknown=c(0, NA))
-isUnknown(x=xFac, unknown=c(0, "NA"))
-isUnknown(x=xFac, unknown=c(0, "NA", NA))
-
-(xFac <- unknownToNA(x=xFac, unknown=0))
-(xFac <- NAToUnknown(x=xFac, unknown=0))
-@
-
-These two examples with classes \code{numeric} and \code{factor} are fairly
-simple and we could get the same results with one or two lines of \R{}
-code. The real benefit of the set of functions presented here is in
-\code{list} and \code{data.frame} methods, where \code{data.frame} methods
-are merely wrappers for \code{list} methods.
-
-We need additional flexibility for \code{list}/\code{data.frame} methods,
-due to possibly having multiple unknown values that can be different among
-\code{list} components or \code{data.frame} columns. For these two methods,
-the argument \code{unknown} can be either a \code{vector} or \code{list},
-both possibly named. Of course, greater flexibility (defining multiple
-unknown values per component/column) can be achieved with a \code{list}.
-
-When a \code{vector}/\code{list} object passed to the argument
-\code{unknown} is not named, the first value/component of a
-\code{vector}/\code{list} matches the first component/column of a
-\code{list}/\code{data.frame}. This can be quite error prone, especially
-with \code{vectors}. Therefore, I encourage the use of a \code{list}. In
-case \code{vector}/\code{list} passed to argument \code{unknown} is named,
-names are matched to names of \code{list} or \code{data.frame}. If lengths
-of \code{unknown} and \code{list} or \code{data.frame} do not match,
-recycling occurs.
-
-The example below illustrates the application of the described functions to
-a list which is composed of previously defined and modified numeric
-(\code{xNum}) and factor (\code{xFac}) classes. First, function
-\code{isUnknown} is used with \code{0} as an unknown value. Note that we
-get \code{FALSE} for \code{NA}s as has been the case in the first example.
-
-<<ex08>>=
-(xList <- list(a=xNum, b=xFac))
-isUnknown(x=xList, unknown=0)
-@
-
-We need to add \code{NA} as an unknown value. However, we do not get the
-expected result this way!
-
-<<ex09>>=
-isUnknown(x=xList, unknown=c(0, NA))
-@
-
-This is due to matching of values in the argument \code{unknown} and
-components in a \code{list}; i.e., \code{0} is used for component \code{a}
-and \code{NA} for component \code{b}.  Therefore, it is less error prone
-and more flexible to pass a \code{list} (preferably a named list) to the
-argument \code{unknown}, as shown below.
-
-<<ex10>>=
-(xList1 <- unknownToNA(x=xList,
-                       unknown=list(b=c(0, "NA"),
-                                    a=0)))
-@
-
-Changing \code{NA}s to some other value (only one per component/column) can
-be accomplished as follows:
-
-<<ex11>>=
-NAToUnknown(x=xList1,
-            unknown=list(b="no", a=0))
-@
-
-A named component \code{.default} of a \code{list} passed to argument
-\code{unknown} has a special meaning as it will match a component/column
-with that name and any other not defined in \code{unknown}. As such it is
-very useful if the number of components/columns with the same unknown
-value(s) is large. Consider a wide \code{data.frame} named \code{df}. Now
-\code{.default} can be used to define unknown value for several columns:
-
-<<ex12, echo=FALSE>>=
-df <- data.frame(col1=c(0, 1, 999, 2),
-                 col2=c("a", "b", "c", "unknown"),
-                 col3=c(0, 1, 2, 3),
-                 col4=c(0, 1, 2, 2))
-@
-
-<<ex13>>=
-tmp <- list(.default=0,
-            col1=999,
-            col2="unknown")
-(df2 <- unknownToNA(x=df,
-                    unknown=tmp))
-@
-
-If there is a need to work only on some components/columns you can of
-course ``skip'' columns with standard \R{} mechanisms, i.e.,
-by subsetting \code{list} or \code{data.frame} objects:
-
-<<ex14>>=
-df2 <- df
-cols <- c("col1", "col2")
-tmp <- list(col1=999,
-            col2="unknown")
-df2[, cols] <- unknownToNA(x=df[, cols],
-                           unknown=tmp)
-df2
-@
-
-\section{Summary}
-
-Functions \code{isUnknown}, \code{unknownToNA} and \code{NAToUnknown}
-provide a useful interface to work with various representations of
-unknown/missing values. Their use is meant primarily for shaping the data
-after importing to or before exporting from \R{}. I welcome any comments or
-suggestions.
-
-% \bibliography{refs}
-
-\begin{thebibliography}{1}
-\providecommand{\natexlab}[1]{#1}
-\providecommand{\url}[1]{\texttt{#1}}
-\expandafter\ifx\csname urlstyle\endcsname\relax
-  \providecommand{\doi}[1]{doi: #1}\else
-  \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi
-
-\bibitem[Gorjanc(2007)]{Gorjanc}
-G.~Gorjanc.
-\newblock Working with unknown values: the gdata package.
-\newblock \emph{R News}, 7\penalty0 (1):\penalty0 24--26, 2007.
-\newblock URL \url{http://CRAN.R-project.org/doc/Rnews/Rnews_2007-1.pdf}.
-
-\bibitem[{R Development Core Team}(2006)]{RImportExportManual}
-{R Development Core Team}.
-\newblock \emph{R Data Import/Export}, 2006.
-\newblock URL \url{http://cran.r-project.org/manuals.html}.
-\newblock ISBN 3-900051-10-0.
-
-\bibitem[Warnes (2006)]{WarnesGdata}
-G.~R. Warnes.
-\newblock \emph{gdata: Various R programming tools for data manipulation},
-  2006.
-\newblock URL
-  \url{http://cran.r-project.org/src/contrib/Descriptions/gdata.html}.
-\newblock R package version 2.3.1. Includes R source code and/or documentation
-  contributed by Ben Bolker, Gregor Gorjanc and Thomas Lumley.
-
-\end{thebibliography}
-
-\address{Gregor Gorjanc\\
-  University of Ljubljana, Slovenia\\
-\email{gre...@bf...}}
-
-\end{article}
-
-\end{document}

Copied: trunk/gdata/vignettes/mapLevels.Rnw (from rev 1786, trunk/gdata/inst/doc/mapLevels.Rnw)
===================================================================
--- trunk/gdata/vignettes/mapLevels.Rnw	                        (rev 0)
+++ trunk/gdata/vignettes/mapLevels.Rnw	2014-04-05 14:26:49 UTC (rev 1789)
@@ -0,0 +1,229 @@
+
+%\VignetteIndexEntry{Mapping levels of a factor}
+%\VignettePackage{gdata}
+%\VignetteKeywords{levels, factor, manip}
+
+\documentclass[a4paper]{report}
+\usepackage{Rnews}
+\usepackage[round]{natbib}
+\bibliographystyle{abbrvnat}
+
+\usepackage{Sweave}
+\SweaveOpts{strip.white=all, keep.source=TRUE}
+
+\begin{document}
+
+\begin{article}
+
+\title{Mapping levels of a factor}
+\subtitle{The \pkg{gdata} package}
+\author{by Gregor Gorjanc}
+
+\maketitle
+
+\section{Introduction}
+
+Factors use levels attribute to store information on mapping between
+internal integer codes and character values i.e. levels. First level is
+mapped to internal integer code 1 and so on. Although some users do not
+like factors, their use is more efficient in terms of storage than for
+character vectors. Additionally, there are many functions in base \R{} that
+provide additional value for factors. Sometimes users need to work with
+internal integer codes and mapping them back to factor, especially when
+interfacing external programs. Mapping information is also of interest if
+there are many factors that should have the same set of levels. This note
+describes \code{mapLevels} function, which is an utility function for
+mapping the levels of a factor in \pkg{gdata} \footnote{from version 2.3.1}
+package \citep{WarnesGdata}.
+
+\section{Description with examples}
+
+Function \code{mapLevels()} is an (S3) generic function and works on
+\code{factor} and \code{character} atomic classes. It also works on
+\code{list} and \code{data.frame} objects with previously mentioned atomic
+classes. Function \code{mapLevels} produces a so called ``map'' with names
+and values. Names are levels, while values can be internal integer codes or
+(possibly other) levels. This will be clarified later on.  Class of this
+``map'' is \code{levelsMap}, if \code{x} in \code{mapLevels()} was atomic
+or \code{listLevelsMap} otherwise - for \code{list} and \code{data.frame}
+classes. The following example shows the creation and printout of such a
+``map''.
+
+<<ex01>>=
+library(gdata)
+(fac <- factor(c("B", "A", "Z", "D")))
+(map <- mapLevels(x=fac))
+@
+
+If we have to work with internal integer codes, we can transform factor to
+integer and still get ``back the original factor'' with ``map'' used as
+argument in \code{mapLevels<-} function as shown bellow. \code{mapLevels<-}
+is also an (S3) generic function and works on same classes as
+\code{mapLevels} plus \code{integer} atomic class.
+
+<<ex02>>=
+(int <- as.integer(fac))
+mapLevels(x=int) <- map
+int
+identical(fac, int)
+@
+
+Internally ``map'' (\code{levelsMap} class) is a \code{list} (see bellow),
+but its print method unlists it for ease of inspection. ``Map'' from
+example has all components of length 1. This is not mandatory as
+\code{mapLevels<-} function is only a wrapper around workhorse function
+\code{levels<-} and the later can accept \code{list} with components of
+various lengths.
+
+<<ex03>>=
+str(map)
+@
+
+Although not of primary importance, this ``map'' can also be used to remap
+factor levels as shown bellow.  Components ``later'' in the map take over
+the ``previous'' ones. Since this is not optimal I would rather recommend
+other approaches for ``remapping'' the levels of a \code{factor}, say
+\code{recode} in \pkg{car} package \citep{FoxCar}.
+
+<<ex04>>=
+map[[2]] <- as.integer(c(1, 2))
+map
+int <- as.integer(fac)
+mapLevels(x=int) <- map
+int
+@
+
+Up to now examples showed ``map'' with internal integer codes for values
+and levels for names. I call this integer ``map''. On the other hand
+character ``map'' uses levels for values and (possibly other) levels for
+names. This feature is a bit odd at first sight, but can be used to easily
+unify levels and internal integer codes across several factors.  Imagine
+you have a factor that is for some reason split into two factors \code{f1}
+and \code{f2} and that each factor does not have all levels. This is not
+uncommon situation.
+
+<<ex05>>=
+(f1 <- factor(c("A", "D", "C")))
+(f2 <- factor(c("B", "D", "C")))
+@
+
+If we work with this factors, we need to be careful as they do not have the
+same set of levels. This can be solved with appropriately specifying
+\code{levels} argument in creation of factors i.e. \code{levels=c("A", "B",
+  "C", "D")} or with proper use of \code{levels<-} function. I say proper
+as it is very tempting to use:
+
+<<ex06>>=
+fTest <- f1
+levels(fTest) <- c("A", "B", "C", "D")
+fTest
+@
+
+Above example extends set of levels, but also changes level of 2nd and 3rd
+element in \code{fTest}! Proper use of \code{levels<-} (as shown in
+\code{levels} help page) would be:
+
+<<ex07>>=
+fTest <- f1
+levels(fTest) <- list(A="A", B="B",
+                      C="C", D="D")
+fTest
+@
+
+Function \code{mapLevels} with character ``map'' can help us in such
+scenarios to unify levels and internal integer codes across several
+factors. Again the workhorse under this process is \code{levels<-} function
+from base \R{}! Function \code{mapLevels<-} just controls the assignment of
+(integer or character) ``map'' to \code{x}. Levels in \code{x} that match
+``map'' values (internal integer codes or levels) are changed to ``map''
+names (possibly other levels) as shown in \code{levels} help page. Levels
+that do not match are converted to \code{NA}. Integer ``map'' can be
+applied to \code{integer} or \code{factor}, while character ``map'' can be
+applied to \code{character} or \code{factor}. Result of \code{mapLevels<-}
+is always a \code{factor} with possibly ``remapped'' levels.
+
+To get one joint character ``map'' for several factors, we need to put
+factors in a \code{list} or \code{data.frame} and use arguments
+\code{codes=FALSE} and \code{combine=TRUE}. Such map can then be used to
+unify levels and internal integer codes.
+
+<<ex08>>=
+(bigMap <- mapLevels(x=list(f1, f2),
+                     codes=FALSE,
+                     combine=TRUE))
+mapLevels(f1) <- bigMap
+mapLevels(f2) <- bigMap
+f1
+f2
+cbind(as.character(f1), as.integer(f1),
+      as.character(f2), as.integer(f2))
+@
+
+If we do not specify \code{combine=TRUE} (which is the default behaviour)
+and \code{x} is a \code{list} or \code{data.frame}, \code{mapLevels}
+returns ``map'' of class \code{listLevelsMap}. This is internally a
+\code{list} of ``maps'' (\code{levelsMap} objects). Both
+\code{listLevelsMap} and \code{levelsMap} objects can be passed to
+\code{mapLevels<-} for \code{list}/\code{data.frame}. Recycling occurs when
+length of \code{listLevelsMap} is not the same as number of
+components/columns of a \code{list}/\code{data.frame}.
+
+Additional convenience methods are also implemented to ease the work with
+``maps'':
+
+\begin{itemize}
+
+\item \code{is.levelsMap}, \code{is.listLevelsMap}, \code{as.levelsMap} and
+  \code{as.listLevelsMap} for testing and coercion of user defined
+  ``maps'',
+
+\item \code{"["} for subsetting,
+
+\item \code{c} for combining \code{levelsMap} or \code{listLevelsMap}
+  objects; argument \code{recursive=TRUE} can be used to coerce
+  \code{listLevelsMap} to \code{levelsMap}, for example \code{c(llm1, llm2,
+    recursive=TRUE)} and
+
+\item \code{unique} and \code{sort} for \code{levelsMap}.
+
+\end{itemize}
+
+\section{Summary}
+
+Functions \code{mapLevels} and \code{mapLevels<-} can help users to map
+internal integer codes to factor levels and unify levels as well as
+internal integer codes among several factors. I welcome any comments or
+suggestions.
+
+% \bibliography{refs}
+\begin{thebibliography}{1}
+\providecommand{\natexlab}[1]{#1}
+\providecommand{\url}[1]{\texttt{#1}}
+\expandafter\ifx\csname urlstyle\endcsname\relax
+  \providecommand{\doi}[1]{doi: #1}\else
+  \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi
+
+\bibitem[Fox(2006)]{FoxCar}
+J.~Fox.
+\newblock \emph{car: Companion to Applied Regression}, 2006.
+\newblock URL \url{http://socserv.socsci.mcmaster.ca/jfox/}.
+\newblock R package version 1.1-1.
+
+\bibitem[Warnes(2006)]{WarnesGdata}
+G.~R. Warnes.
+\newblock \emph{gdata: Various R programming tools for data manipulation},
+  2006.
+\newblock URL
+  \url{http://cran.r-project.org/src/contrib/Descriptions/gdata.html}.
+\newblock R package version 2.3.1. Includes R source code and/or documentation
+  contributed by Ben Bolker, Gregor Gorjanc and Thomas Lumley.
+
+\end{thebibliography}
+
+\address{Gregor Gorjanc\\
+  University of Ljubljana, Slovenia\\
+\email{gre...@bf...}}
+
+\end{article}
+
+\end{document}

Copied: trunk/gdata/vignettes/unknown.Rnw (from rev 1786, trunk/gdata/inst/doc/unknown.Rnw)
===================================================================
--- trunk/gdata/vignettes/unknown.Rnw	                        (rev 0)
+++ trunk/gdata/vignettes/unknown.Rnw	2014-04-05 14:26:49 UTC (rev 1789)
@@ -0,0 +1,272 @@
+
+%\VignetteIndexEntry{Working with Unknown Values}
+%\VignettePackage{gdata}
+%\VignetteKeywords{unknown, missing, manip}
+
+\documentclass[a4paper]{report}
+\usepackage{Rnews}
+\usepackage[round]{natbib}
+\bibliographystyle{abbrvnat}
+
+\usepackage{Sweave}
+\SweaveOpts{strip.white=all, keep.source=TRUE}
+
+\begin{document}
+
+\begin{article}
+
+\title{Working with Unknown Values}
+\subtitle{The \pkg{gdata} package}
+\author{by Gregor Gorjanc}
+
+\maketitle
+
+This vignette has been published as \cite{Gorjanc}.
+
+\section{Introduction}
+
+Unknown or missing values can be represented in various ways. For example
+SAS uses \code{.}~(dot), while \R{} uses \code{NA}, which we can read as
+Not Available. When we import data into \R{}, say via \code{read.table} or
+its derivatives, conversion of blank fields to \code{NA} (according to
+\code{read.table} help) is done for \code{logical}, \code{integer},
+\code{numeric} and \code{complex} classes. Additionally, the
+\code{na.strings} argument can be used to specify values that should also
+be converted to \code{NA}. Inversely, there is an argument \code{na} in
+\code{write.table} and its derivatives to define value that will replace
+\code{NA} in exported data. There are also other ways to import/export data
+into \R{} as described in the {\emph R Data Import/Export} manual
+\citep{RImportExportManual}.  However, all approaches lack the possibility
+to define unknown value(s) for some particular column. It is possible that
+an unknown value in one column is a valid value in another column. For
+example, I have seen many datasets where values such as 0, -9, 999 and
+specific dates are used as column specific unknown values.
+
+This note describes a set of functions in package \pkg{gdata}\footnote{
+  package version 2.3.1} \citep{WarnesGdata}: \code{isUnknown},
+\code{unknownToNA} and \code{NAToUnknown}, which can help with testing for
+unknown values and conversions between unknown values and \code{NA}. All
+three functions are generic (S3) and were tested (at the time of writing)
+to work with: \code{integer}, \code{numeric}, \code{character},
+\code{factor}, \code{Date}, \code{POSIXct}, \code{POSIXlt}, \code{list},
+\code{data.frame} and \code{matrix} classes.
+
+\section{Description with examples}
+
+The following examples show simple usage of these functions on
+\code{numeric} and \code{factor} classes, where value \code{0} (beside
+\code{NA}) should be treated as an unknown value:
+
+<<ex01>>=
+library("gdata")
+xNum <- c(0, 6, 0, 7, 8, 9, NA)
+isUnknown(x=xNum)
+@
+
+The default unknown value in \code{isUnknown} is \code{NA}, which means
+that output is the same as \code{is.na} --- at least for atomic
+classes. However, we can pass the argument \code{unknown} to define which
+values should be treated as unknown:
+
+<<ex02>>=
+isUnknown(x=xNum, unknown=0)
+@
+
+This skipped \code{NA}, but we can get the expected answer after
+appropriately adding \code{NA} into the argument \code{unknown}:
+
+<<ex03>>=
+isUnknown(x=xNum, unknown=c(0, NA))
+@
+
+Now, we can change all unknown values to \code{NA} with \code{unknownToNA}.
+There is clearly no need to add \code{NA} here. This step is very handy
+after importing data from an external source, where many different unknown
+values might be used. Argument \code{warning=TRUE} can be used, if there is
+a need to be warned about ``original'' \code{NA}s:
+
+<<ex04>>=
+(xNum2 <- unknownToNA(x=xNum, unknown=0))
+@
+
+Prior to export from \R{}, we might want to change unknown values
+(\code{NA} in \R{}) to some other value. Function \code{NAToUnknown} can be
+used for this:
+
+<<ex05>>=
+NAToUnknown(x=xNum2, unknown=999)
+@
+
+Converting \code{NA} to a value that already exists in \code{x} issues an
+error, but \code{force=TRUE} can be used to overcome this if needed. But be
+warned that there is no way back from this step:
+
+<<ex06>>=
+NAToUnknown(x=xNum2, unknown=7, force=TRUE)
+@
+
+Examples below show all peculiarities with class \code{factor}.
+\code{unknownToNA} removes \code{unknown} value from levels and inversely
+\code{NAToUnknown} adds it with a warning. Additionally, \code{"NA"} is
+properly distinguished from \code{NA}. It can also be seen that the
+argument \code{unknown} in functions \code{isUnknown} and
+\code{unknownToNA} need not match the class of \code{x} (otherwise factor
+should be used) as the test is internally done with \code{\%in\%}, which
+nicely resolves coercing issues.
+
+<<ex07>>=
+(xFac <- factor(c(0, "BA", "RA", "BA", NA, "NA")))
+isUnknown(x=xFac)
+isUnknown(x=xFac, unknown=0)
+isUnknown(x=xFac, unknown=c(0, NA))
+isUnknown(x=xFac, unknown=c(0, "NA"))
+isUnknown(x=xFac, unknown=c(0, "NA", NA))
+
+(xFac <- unknownToNA(x=xFac, unknown=0))
+(xFac <- NAToUnknown(x=xFac, unknown=0))
+@
+
+These two examples with classes \code{numeric} and \code{factor} are fairly
+simple and we could get the same results with one or two lines of \R{}
+code. The real benefit of the set of functions presented here is in
+\code{list} and \code{data.frame} methods, where \code{data.frame} methods
+are merely wrappers for \code{list} methods.
+
+We need additional flexibility for \code{list}/\code{data.frame} methods,
+due to possibly having multiple unknown values that can be different among
+\code{list} components or \code{data.frame} columns. For these two methods,
+the argument \code{unknown} can be either a \code{vector} or \code{list},
+both possibly named. Of course, greater flexibility (defining multiple
+unknown values per component/column) can be achieved with a \code{list}.
+
+When a \code{vector}/\code{list} object passed to the argument
+\code{unknown} is not named, the first value/component of a
+\code{vector}/\code{list} matches the first component/column of a
+\code{list}/\code{data.frame}. This can be quite error prone, especially
+with \code{vectors}. Therefore, I encourage the use of a \code{list}. In
+case \code{vector}/\code{list} passed to argument \code{unknown} is named,
+names are matched to names of \code{list} or \code{data.frame}. If lengths
+of \code{unknown} and \code{list} or \code{data.frame} do not match,
+recycling occurs.
+
+The example below illustrates the application of the described functions to
+a list which is composed of previously defined and modified numeric
+(\code{xNum}) and factor (\code{xFac}) classes. First, function
+\code{isUnknown} is used with \code{0} as an unknown value. Note that we
+get \code{FALSE} for \code{NA}s as has been the case in the first example.
+
+<<ex08>>=
+(xList <- list(a=xNum, b=xFac))
+isUnknown(x=xList, unknown=0)
+@
+
+We need to add \code{NA} as an unknown value. However, we do not get the
+expected result this way!
+
+<<ex09>>=
+isUnknown(x=xList, unknown=c(0, NA))
+@
+
+This is due to matching of values in the argument \code{unknown} and
+components in a \code{list}; i.e., \code{0} is used for component \code{a}
+and \code{NA} for component \code{b}.  Therefore, it is less error prone
+and more flexible to pass a \code{list} (preferably a named list) to the
+argument \code{unknown}, as shown below.
+
+<<ex10>>=
+(xList1 <- unknownToNA(x=xList,
+                       unknown=list(b=c(0, "NA"),
+                                    a=0)))
+@
+
+Changing \code{NA}s to some other value (only one per component/column) can
+be accomplished as follows:
+
+<<ex11>>=
+NAToUnknown(x=xList1,
+            unknown=list(b="no", a=0))
+@
+
+A named component \code{.default} of a \code{list} passed to argument
+\code{unknown} has a special meaning as it will match a component/column
+with that name and any other not defined in \code{unknown}. As such it is
+very useful if the number of components/columns with the same unknown
+value(s) is large. Consider a wide \code{data.frame} named \code{df}. Now
+\code{.default} can be used to define unknown value for several columns:
+
+<<ex12, echo=FALSE>>=
+df <- data.frame(col1=c(0, 1, 999, 2),
+                 col2=c("a", "b", "c", "unknown"),
+                 col3=c(0, 1, 2, 3),
+                 col4=c(0, 1, 2, 2))
+@
+
+<<ex13>>=
+tmp <- list(.default=0,
+            col1=999,
+            col2="unknown")
+(df2 <- unknownToNA(x=df,
+                    unknown=tmp))
+@
+
+If there is a need to work only on some components/columns you can of
+course ``skip'' columns with standard \R{} mechanisms, i.e.,
+by subsetting \code{list} or \code{data.frame} objects:
+
+<<ex14>>=
+df2 <- df
+cols <- c("col1", "col2")
+tmp <- list(col1=999,
+            col2="unknown")
+df2[, cols] <- unknownToNA(x=df[, cols],
+                           unknown=tmp)
+df2
+@
+
+\section{Summary}
+
+Functions \code{isUnknown}, \code{unknownToNA} and \code{NAToUnknown}
+provide a useful interface to work with various representations of
+unknown/missing values. Their use is meant primarily for shaping the data
+after importing to or before exporting from \R{}. I welcome any comments or
+suggestions.
+
+% \bibliography{refs}
+
+\begin{thebibliography}{1}
+\providecommand{\natexlab}[1]{#1}
+\providecommand{\url}[1]{\texttt{#1}}
+\expandafter\ifx\csname urlstyle\endcsname\relax
+  \providecommand{\doi}[1]{doi: #1}\else
+  \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi
+
+\bibitem[Gorjanc(2007)]{Gorjanc}
+G.~Gorjanc.
+\newblock Working with unknown values: the gdata package.
+\newblock \emph{R News}, 7\penalty0 (1):\penalty0 24--26, 2007.
+\newblock URL \url{http://CRAN.R-project.org/doc/Rnews/Rnews_2007-1.pdf}.
+
+\bibitem[{R Development Core Team}(2006)]{RImportExportManual}
+{R Development Core Team}.
+\newblock \emph{R Data Import/Export}, 2006.
+\newblock URL \url{http://cran.r-project.org/manuals.html}.
+\newblock ISBN 3-900051-10-0.
+
+\bibitem[Warnes (2006)]{WarnesGdata}
+G.~R. Warnes.
+\newblock \emph{gdata: Various R programming tools for data manipulation},
+  2006.
+\newblock URL
+  \url{http://cran.r-project.org/src/contrib/Descriptions/gdata.html}.
+\newblock R package version 2.3.1. Includes R source code and/or documentation
+  contributed by Ben Bolker, Gregor Gorjanc and Thomas Lumley.
+
+\end{thebibliography}
+
+\address{Gregor Gorjanc\\
+  University of Ljubljana, Slovenia\\
+\email{gre...@bf...}}
+
+\end{article}
+
+\end{document}

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1788] trunk/gdata

[<wa...@us...>]

Revision: 1788
          http://sourceforge.net/p/r-gregmisc/code/1788
Author:   warnes
Date:     2014-04-05 13:57:10 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Change 'aggregate.table' from deprecated to defunct.

Modified Paths:
--------------
    trunk/gdata/R/aggregate.table.R

Added Paths:
-----------
    trunk/gdata/man/gdata-defunct.Rd

Removed Paths:
-------------
    trunk/gdata/man/aggregate.table.Rd

Modified: trunk/gdata/R/aggregate.table.R
===================================================================
--- trunk/gdata/R/aggregate.table.R	2014-04-05 12:53:38 UTC (rev 1787)
+++ trunk/gdata/R/aggregate.table.R	2014-04-05 13:57:10 UTC (rev 1788)
@@ -2,32 +2,34 @@
 
 aggregate.table <- function(x, by1, by2, FUN=mean, ...)
   {
-    warning("'aggregate.table' is deprecated and will be removed in a future version of the gdata package. ",
-            "Please use 'tapply(X=",
-            deparse(substitute(x)),
-            ", INDEX=list(",
-            deparse(substitute(by1)),
-            ", ",
-            deparse(substitute(by2)),
-            "), FUN=",
-            deparse(substitute(FUN)),
-            if(length(list(...))>0)
-            {
-              l <- list(...)
-              paste(", ",
-                    paste(names(l),"=",
-                          deparse(substitute(...)),
-                          sep="",
-                          collapse=", ")
-                    )
-            },
-            ")' instead.")
-    tapply(X=x, INDEX=list(by1, by2), FUN=FUN, ...)
+      .Defunct(
+          new=paste(
+              "tapply(X=",
+              deparse(substitute(x)),
+              ", INDEX=list(",
+              deparse(substitute(by1)),
+              ", ",
+              deparse(substitute(by2)),
+              "), FUN=",
+              deparse(substitute(FUN)),
+              if(length(list(...))>0)
+              {
+                  l <- list(...)
+                  paste(", ",
+                        paste(names(l),"=",
+                              deparse(substitute(...)),
+                              sep="",
+                              collapse=", ")
+                        )
+              },
+              ")", sep=""),
+          package="gdata"
+          )
   }
 
 ## aggregate.table <- function(x, by1, by2, FUN=mean, ... )
 ## {
-##    
+##
 ##     tab <- matrix( nrow=nlevels(by1), ncol=nlevels(by2) )
 ##     dimnames(tab) <- list(levels(by1),levels(by2))
 ##

Deleted: trunk/gdata/man/aggregate.table.Rd
===================================================================
--- trunk/gdata/man/aggregate.table.Rd	2014-04-05 12:53:38 UTC (rev 1787)
+++ trunk/gdata/man/aggregate.table.Rd	2014-04-05 13:57:10 UTC (rev 1788)
@@ -1,94 +0,0 @@
-% $Id$
-%
-% $Log$
-% Revision 1.7  2005/09/12 15:42:45  nj7w
-% Updated Greg's email
-%
-% Revision 1.6  2005/06/09 14:20:25  nj7w
-% Updating the version number, and various help files to synchronize splitting of gregmisc bundle in 4 individual components.
-%
-% Revision 1.1.1.1  2005/05/25 22:07:33  nj7w
-% Initial entry for individual package gdata
-%
-% Revision 1.5  2003/11/17 22:09:00  warnes
-% Fix syntax error.
-%
-% Revision 1.4  2003/06/07 17:58:37  warnes
-%
-% - Fixed error in examples.  Had sqrt(var(x)/(n-1)) for the standard
-%   error of the mean instead of sqrt(var(x)/n).
-%
-% Revision 1.3  2002/09/23 13:59:30  warnes
-% - Modified all files to include CVS Id and Log tags.
-%
-%
-
-\name{aggregate.table}
-\alias{aggregate.table}
-\title{Create 2-Way Table of Summary Statistics}
-\description{
-  Splits the data into subsets based on two factors, computes a summary
-  statistic on each subset, and arranges the results in a 2-way table.
-}
-\usage{
-aggregate.table(x, by1, by2, FUN=mean, ...)
-}
-%- maybe also `usage' for other objects documented here.
-\arguments{
-  \item{x}{ data to be summarized }
-  \item{by1}{ first grouping factor.  }
-  \item{by2}{ second grouping factor. }
-  \item{FUN}{ a scalar function to compute the summary statistics which can
-          be applied to all data subsets. Defaults to \code{mean}.}
-  \item{\dots}{ Optional arguments for \code{FUN}. }
-}
-%\details{
-%  ~~ If necessary, more details than the __description__  above ~~
-%}
-\value{
-  Returns a matrix with one element for each combination of \code{by1}
-  and \code{by2}.
-}
-\author{ Gregory R. Warnes \email{gr...@wa...}}
-
-\seealso{ \code{\link{aggregate}}, \code{\link{tapply}},
-          \code{\link{interleave}} }
-\note{This function is DEPRECIATED.  Please use \code{tapply} 
-  instead. See example for illustration.}
-\examples{
-# Useful example:
-#
-# Create a 2-way table of means, standard errors, and # obs
-set.seed(314159)
-g1 <- sample(letters[1:5], 1000, replace=TRUE)
-g2 <- sample(LETTERS[1:3], 1000, replace=TRUE )
-dat <- rnorm(1000)
-
-stderr <- function(x) sqrt( var(x,na.rm=TRUE) / nobs(x) )
-
-## Depreciated:
-means   <- aggregate.table( dat, g1, g2, mean )
-## Instead use:
-means   <- tapply( dat, list(g1, g2), mean )
-
-## Depreciated
-stderrs <- aggregate.table( dat, g1, g2, stderr )
-## Instead use:
-stderrs <- tapply( dat, list(g1, g2), stderr )
-
-## Depreciated
-ns      <- aggregate.table( dat, g1, g2, nobs )
-## Instead use:
-ns      <- tapply( dat, list(g1, g2), nobs )
-
-blanks <- matrix( " ", nrow=5, ncol=3)
-
-tab <- interleave( "Mean"=round(means,2),
-                   "Std Err"=round(stderrs,2),
-                   "N"=ns, " " = blanks, sep=" " )
-
-print(tab, quote=FALSE)
-}
-\keyword{iteration}
-\keyword{category}
-

Copied: trunk/gdata/man/gdata-defunct.Rd (from rev 1786, trunk/gdata/man/aggregate.table.Rd)
===================================================================
--- trunk/gdata/man/gdata-defunct.Rd	                        (rev 0)
+++ trunk/gdata/man/gdata-defunct.Rd	2014-04-05 13:57:10 UTC (rev 1788)
@@ -0,0 +1,24 @@
+\name{gdata-defunct}
+\alias{aggregate.table}
+\title{Defunct Functions in Package 'gdata'}
+\description{
+  The functions or variables listed here are no longer part of 'gdata'.
+}
+\usage{
+aggregate.table(x, by1, by2, FUN=mean, ...)
+}
+%- maybe also `usage' for other objects documented here.
+\arguments{
+  \item{x}{ data to be summarized }
+  \item{by1}{ first grouping factor.  }
+  \item{by2}{ second grouping factor. }
+  \item{FUN}{ a scalar function to compute the summary statistics which can
+          be applied to all data subsets. Defaults to \code{mean}.}
+  \item{\dots}{ Optional arguments for \code{FUN}. }
+}
+\details{
+  \code{aggregate.table(x, by1, by2, FUN=mean, ...)} should be replacede
+  by \code{tapply(X=x, INDEX=list(by1, by2), FUN=FUN, ...)}.
+}
+
+

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1787] trunk/gdata

[<wa...@us...>]

Revision: 1787
          http://sourceforge.net/p/r-gregmisc/code/1787
Author:   warnes
Date:     2014-04-05 12:53:38 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Complete changes so that the unit tests are run as part of R CMD check

Modified Paths:
--------------
    trunk/gdata/DESCRIPTION
    trunk/gdata/man/gdata-package.Rd
    trunk/gdata/tests/runRUnitTests.R

Added Paths:
-----------
    trunk/gdata/tests/unitTests/

Removed Paths:
-------------
    trunk/gdata/inst/unitTests/

Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION	2014-04-05 02:25:54 UTC (rev 1786)
+++ trunk/gdata/DESCRIPTION	2014-04-05 12:53:38 UTC (rev 1787)
@@ -12,4 +12,4 @@
 Maintainer: Gregory R. Warnes <gr...@wa...>
 License: GPL-2
 NeedsCompilation: no
-Depends: RUnit
+Recommends: RUnit

Modified: trunk/gdata/man/gdata-package.Rd
===================================================================
--- trunk/gdata/man/gdata-package.Rd	2014-04-05 02:25:54 UTC (rev 1786)
+++ trunk/gdata/man/gdata-package.Rd	2014-04-05 12:53:38 UTC (rev 1787)
@@ -32,13 +32,4 @@
 
 }
 
-\section{Testing}{
-
-If you want to perform the validity/unit testing of the installed
-\pkg{ggmisc} package on your own computer, take a look at
-\code{\link{.runRUnitTestsGdata}} function - please note that
-you need the \pkg{RUnit} package for this to work.
-
-}
-
 \keyword{package}
\ No newline at end of file

Modified: trunk/gdata/tests/runRUnitTests.R
===================================================================
--- trunk/gdata/tests/runRUnitTests.R	2014-04-05 02:25:54 UTC (rev 1786)
+++ trunk/gdata/tests/runRUnitTests.R	2014-04-05 12:53:38 UTC (rev 1787)
@@ -39,9 +39,10 @@
 if(require("RUnit", quietly=TRUE))
 {
 
-    pkg  <- c(read.dcf(file="../DESCRIPTION", fields="Package"))
-    path <- normalizePath( file.path(getwd(), "..", "inst", "unitTests") )
+    pkg  <- 'gdata'
 
+    path <- normalizePath("unitTests")
+
     cat("\nRunning unit tests\n")
     print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1786] trunk/gdata

[<wa...@us...>]

Revision: 1786
          http://sourceforge.net/p/r-gregmisc/code/1786
Author:   warnes
Date:     2014-04-05 02:25:54 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Update NEWS for gdata 2.13.4

Modified Paths:
--------------
    trunk/gdata/DESCRIPTION
    trunk/gdata/inst/NEWS

Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION	2014-04-05 02:25:02 UTC (rev 1785)
+++ trunk/gdata/DESCRIPTION	2014-04-05 02:25:54 UTC (rev 1786)
@@ -4,11 +4,12 @@
 Depends: R (>= 2.13.0)
 SystemRequirements: perl
 Imports: gtools
-Version: 2.13.2
-Date: 2013-06-28
+Version: 2.13.3
+Date: 2014-04-04
 Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor
         Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni
         Magnusson, Jim Rogers, and others
 Maintainer: Gregory R. Warnes <gr...@wa...>
 License: GPL-2
 NeedsCompilation: no
+Depends: RUnit

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2014-04-05 02:25:02 UTC (rev 1785)
+++ trunk/gdata/inst/NEWS	2014-04-05 02:25:54 UTC (rev 1786)
@@ -1,3 +1,16 @@
+Changes in 2.13.3 (2014-04-04)
+------------------------------
+
+Bug Fixes
+
+- Unit tests were incorrectly checking for equality of optional POSIXlt
+  components.  (Bug reported by Brian Ripley).
+
+Other Changes
+
+- Unit tests now follow R standard practice
+
+
 Changes in 2.13.2 (2013-06-28)
 ------------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1785] trunk/gdata/NAMESPACE

[<wa...@us...>]

Revision: 1785
          http://sourceforge.net/p/r-gregmisc/code/1785
Author:   warnes
Date:     2014-04-05 02:25:02 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Update NAMESPACE file to remove deleted function

Modified Paths:
--------------
    trunk/gdata/NAMESPACE

Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE	2014-04-05 02:23:45 UTC (rev 1784)
+++ trunk/gdata/NAMESPACE	2014-04-05 02:25:02 UTC (rev 1785)
@@ -43,7 +43,7 @@
        write.fwf,
        xls2csv,
        xls2tab,
-       xls2tsv,       
+       xls2tsv,
        xls2sep,
        xlsFormats,
 
@@ -57,10 +57,7 @@
        mapLevels, as.levelsMap, as.listLevelsMap, is.levelsMap, is.listLevelsMap, "mapLevels<-",
 
        ## unknown stuff
-       isUnknown, unknownToNA, NAToUnknown,
-
-       ## Unit testing
-       .runRUnitTestsGdata
+       isUnknown, unknownToNA, NAToUnknown
 )
 
 importFrom(stats, reorder)
@@ -124,7 +121,7 @@
 
 ## nobs stuff
 S3method(nobs, data.frame)
-S3method(nobs, default) 
+S3method(nobs, default)
 S3method(nobs, lm)      # now provided by stats package
 
 ## Object size stuff

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1784] trunk/gdata

[<wa...@us...>]

Revision: 1784
          http://sourceforge.net/p/r-gregmisc/code/1784
Author:   warnes
Date:     2014-04-05 02:23:45 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Move unit test files back to inst/unitTests.  Fix up runRUnitTests.R to work properly in the new location

Modified Paths:
--------------
    trunk/gdata/tests/runRUnitTests.R

Added Paths:
-----------
    trunk/gdata/inst/unitTests/Makefile
    trunk/gdata/inst/unitTests/runit.bindData.R
    trunk/gdata/inst/unitTests/runit.cbindX.R
    trunk/gdata/inst/unitTests/runit.drop.levels.R
    trunk/gdata/inst/unitTests/runit.getDateTimeParts.R
    trunk/gdata/inst/unitTests/runit.mapLevels.R
    trunk/gdata/inst/unitTests/runit.nPairs.R
    trunk/gdata/inst/unitTests/runit.reorder.factor.R
    trunk/gdata/inst/unitTests/runit.trim.R
    trunk/gdata/inst/unitTests/runit.trimSum.R
    trunk/gdata/inst/unitTests/runit.unknown.R
    trunk/gdata/inst/unitTests/runit.wideByFactor.R
    trunk/gdata/inst/unitTests/runit.write.fwf.R

Removed Paths:
-------------
    trunk/gdata/tests/Makefile
    trunk/gdata/tests/runit.bindData.R
    trunk/gdata/tests/runit.cbindX.R
    trunk/gdata/tests/runit.drop.levels.R
    trunk/gdata/tests/runit.getDateTimeParts.R
    trunk/gdata/tests/runit.mapLevels.R
    trunk/gdata/tests/runit.nPairs.R
    trunk/gdata/tests/runit.reorder.factor.R
    trunk/gdata/tests/runit.trim.R
    trunk/gdata/tests/runit.trimSum.R
    trunk/gdata/tests/runit.unknown.R
    trunk/gdata/tests/runit.wideByFactor.R
    trunk/gdata/tests/runit.write.fwf.R

Copied: trunk/gdata/inst/unitTests/Makefile (from rev 1782, trunk/gdata/tests/Makefile)
===================================================================
--- trunk/gdata/inst/unitTests/Makefile	                        (rev 0)
+++ trunk/gdata/inst/unitTests/Makefile	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,18 @@
+TOP=../..
+PKG=${shell cd ${TOP};pwd}
+SUITE=runRUnitTests.R
+R=R
+
+test: # Run unit tests
+	${R} --vanilla --slave < ${SUITE}
+
+all: inst test
+
+echo: # Echo env. variables
+	@echo "Package folder: ${PKG}"
+	@echo "R binary: ${R}"
+
+help: # Help
+	@echo -e '\nTarget: Dependency # Description'; \
+	echo '=================================================='; \
+	egrep '^[[:alnum:].+_()%]*:' ./Makefile

Copied: trunk/gdata/inst/unitTests/runit.bindData.R (from rev 1782, trunk/gdata/tests/runit.bindData.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.bindData.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.bindData.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,75 @@
+### runit.bindData.R
+###------------------------------------------------------------------------
+### What: Bind two data frames - unit tests
+### $Id$
+### Time-stamp: <2008-12-30 11:58:50 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ --- bindData ---
+
+test.bindData <- function()
+{
+  ## 'x'/'y' must be a data.frame
+  checkException(bindData(x=1:10, y=1:10))
+  checkException(bindData(x=matrix(1:10), y=matrix(1:10)))
+  
+  n1 <- 6; n2 <- 12; n3 <- 4
+  ## Single trait 1
+  num <- c(5:n1, 10:13)
+  tmp1 <- data.frame(y1=rnorm(n=n1),
+                     f1=factor(rep(c("A", "B"), n1/2)),
+                     ch=letters[num],
+                     fa=factor(letters[num]),
+                     nu=(num) + 0.5,
+                     id=factor(num), stringsAsFactors=FALSE)
+
+  ## Single trait 2 with repeated records, some subjects also in tmp1 
+  num <- 4:9
+  tmp2 <- data.frame(y2=rnorm(n=n2),
+                     f2=factor(rep(c("C", "D"), n2/2)),
+                     ch=letters[rep(num, times=2)],
+                     fa=factor(letters[rep(c(num), times=2)]),
+                     nu=c((num) + 0.5, (num) + 0.25),
+                     id=factor(rep(num, times=2)), stringsAsFactors=FALSE)
+
+  ## Single trait 3 with completely distinct set of subjects
+  num <- 1:4
+  tmp3 <- data.frame(y3=rnorm(n=n3),
+                     f3=factor(rep(c("E", "F"), n3/2)),
+                     ch=letters[num],
+                     fa=factor(letters[num]),
+                     nu=(num) + 0.5,
+                     id=factor(num), stringsAsFactors=FALSE)
+
+  ## Combine all datasets
+  tmp12 <- bindData(x=tmp1, y=tmp2, common=c("id", "nu", "ch", "fa"))
+  tmp123 <- bindData(x=tmp12, y=tmp3, common=c("id", "nu", "ch", "fa"))
+
+  checkEquals(names(tmp123), c("id", "nu", "ch", "fa", "y1", "f1", "y2", "f2", "y3", "f3"))
+  checkEquals(rbind(tmp1["id"], tmp2["id"], tmp3["id"]), tmp123["id"])
+  checkEquals(rbind(tmp1["fa"], tmp2["fa"], tmp3["fa"]), tmp123["fa"])
+  checkEquals(is.na(tmp123$y1), c(rep(FALSE, times=n1), rep(TRUE, times=n2+n3)))
+  checkEquals(is.na(tmp123$f1), c(rep(FALSE, times=n1), rep(TRUE, times=n2+n3)))
+  checkEquals(is.na(tmp123$y2), c(rep(TRUE, times=n1), rep(FALSE, times=n2), rep(TRUE, times=n3)))
+  checkEquals(is.na(tmp123$f2), c(rep(TRUE, times=n1), rep(FALSE, times=n2), rep(TRUE, times=n3)))
+  checkEquals(is.na(tmp123$y3), c(rep(TRUE, times=n1+n2), rep(FALSE, times=n3)))
+  checkEquals(is.na(tmp123$f3), c(rep(TRUE, times=n1+n2), rep(FALSE, times=n3)))
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.bindData.R ends here

Copied: trunk/gdata/inst/unitTests/runit.cbindX.R (from rev 1782, trunk/gdata/tests/runit.cbindX.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.cbindX.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.cbindX.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,81 @@
+### runit.cbindX.R
+###------------------------------------------------------------------------
+### What: Unit tests for cbindX
+### $Id:$
+### Time-stamp: <2008-08-05 13:40:49 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ --- cbindX ---
+
+test.cbindX <- function()
+{
+  df1 <- data.frame(a=1:3, b=c("A", "B", "C"))
+  df2 <- data.frame(c=as.character(1:5), a=5:1)
+
+  ma1 <- matrix(as.character(1:4), nrow=2, ncol=2)
+  ma2 <- matrix(1:6, nrow=3, ncol=2)
+
+  df12test <- cbindX(df1, df2)
+  df12stand <- data.frame(a=c(1:3, NA, NA),
+                          b=c("A", "B", "C", NA, NA),
+                          c=as.character(1:5),
+                          a=5:1)
+  names(df12stand)[4] <- "a"
+  checkEquals(df12test, df12stand)
+
+  ma12test <- cbindX(ma1, ma2)
+  ma12stand <- matrix(as.character(c(1,   3, 1, 4,
+                                     2,   4, 2, 5,
+                                     NA, NA, 3, 6)), nrow=3, ncol=4, byrow=TRUE)
+  checkEquals(ma12test, ma12stand)
+
+  da11test <- cbindX(df1, ma1)
+  da11stand <- data.frame(a=1:3,
+                          b=c("A", "B", "C"),
+                          as.character(c(1:2, NA)),
+                          as.character(c(3:4, NA)))
+  names(da11stand)[3:4] <- c("1", "2")
+  checkEquals(da11test, da11stand)
+
+  tmpTest <- cbindX(df1, df2, ma1, ma2)
+  tmpStand <- data.frame(a=c(1:3, NA, NA),
+                         b=c("A", "B", "C", NA, NA),
+                         c=as.character(1:5),
+                         a=5:1,
+                         as.character(c(1:2, NA, NA, NA)),
+                         as.character(c(3:4, NA, NA, NA)),
+                         c(1:3, NA, NA),
+                         c(4:6, NA, NA))
+  names(tmpStand)[4:8] <- c("a", "1", "2", "1", "2")
+  checkEquals(tmpTest, tmpStand)
+
+  tmpTest <- cbindX(ma1, ma2, df1, df2)
+  tmpStand <- data.frame(as.character(c(1:2, NA, NA, NA)),
+                         as.character(c(3:4, NA, NA, NA)),
+                         as.character(c(1:3, NA, NA)),
+                         as.character(c(4:6, NA, NA)),
+                         a=c(1:3, NA, NA),
+                         b=c("A", "B", "C", NA, NA),
+                         c=as.character(1:5),
+                         a=5:1)
+  names(tmpStand)[c(1:4, 8)] <- c("1", "2", "3", "4", "a")
+  checkEquals(tmpTest, tmpStand)
+}
+
+### }}}
+### {{{ Dear Emacs
+### Local variables:
+### folded-file: t
+### end:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.cbindX.R ends here

Copied: trunk/gdata/inst/unitTests/runit.drop.levels.R (from rev 1782, trunk/gdata/tests/runit.drop.levels.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.drop.levels.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.drop.levels.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,42 @@
+### runit.drop.levels.R
+###------------------------------------------------------------------------
+### What: Tests for drop.levels
+### $Id$
+### Time-stamp: <2006-08-29 14:21:12 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ --- drop.levels ---
+
+test.drop.levels <- function()
+{
+  f <- factor(c("A", "B", "C", "D"))[1:3]
+  fDrop <- factor(c("A", "B", "C"))
+
+  l <- list(f=f, i=1:3, c=c("A", "B", "D"))
+  lDrop <- list(f=fDrop, i=1:3, c=c("A", "B", "D"))
+
+  df <- as.data.frame(l)
+  dfDrop <- as.data.frame(lDrop)
+
+  checkIdentical(drop.levels(f), fDrop)
+  checkIdentical(drop.levels(l), lDrop)
+  checkIdentical(drop.levels(df), dfDrop)
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.drop.levels.R ends here

Copied: trunk/gdata/inst/unitTests/runit.getDateTimeParts.R (from rev 1782, trunk/gdata/tests/runit.getDateTimeParts.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.getDateTimeParts.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.getDateTimeParts.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,119 @@
+### runit.getDateTimeParts.R
+###------------------------------------------------------------------------
+### What: Extract date and time parts from ... - unit tests
+### $Id$
+### Time-stamp: <2008-12-30 22:41:18 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+num <- 1
+cha <- "a"
+fac <- factor(c("A"))
+
+tYear <- as.character(c(2006, 1995, 1005, 3067))
+tMonth <- c("01", "04", "06", "12")
+tDay <- c("01", "12", "22", "04")
+tDate <- paste( paste(tYear, tMonth, tDay, sep="-"), "GMT" )
+
+tHour <- c("05", "16", "20", "03")
+tMin <- c("16", "40", "06", "52")
+tSec <- c("56", "34", "05", "15")
+tTime <- paste(tHour, tMin, tSec, sep=":")
+
+cDate <- as.Date(tDate)
+cDatePOSIXct <- as.POSIXct(tDate)
+cDatePOSIXlt <- as.POSIXlt(tDate)
+
+### }}}
+### {{{ --- getYear ---
+
+test.getYear <- function()
+{
+  checkException(getYear(x=num))
+  checkException(getYear(x=cha))
+  checkException(getYear(x=fac))
+
+  checkIdentical(getYear(x=cDate), tYear)
+  checkIdentical(getYear(x=cDatePOSIXct), tYear)
+  checkIdentical(getYear(x=cDatePOSIXlt), tYear)
+}
+
+### }}}
+### {{{ --- getMonth ---
+
+test.getMonth <- function()
+{
+  checkException(getMonth(x=num))
+  checkException(getMonth(x=cha))
+  checkException(getMonth(x=fac))
+
+  checkIdentical(getMonth(x=cDate), tMonth)
+  checkIdentical(getMonth(x=cDatePOSIXct), tMonth)
+  checkIdentical(getMonth(x=cDatePOSIXlt), tMonth)
+}
+
+### }}}
+### {{{ --- getDay ---
+
+test.getDay <- function()
+{
+  checkException(getDay(x=num))
+  checkException(getDay(x=cha))
+  checkException(getDay(x=fac))
+
+  checkIdentical(getDay(x=cDate), tDay)
+  checkIdentical(getDay(x=cDatePOSIXct), tDay)
+  checkIdentical(getDay(x=cDatePOSIXlt), tDay)
+}
+
+### }}}
+### {{{ --- getHour ---
+
+test.getHour <- function()
+{
+  checkException(getHour(x=num))
+  checkException(getHour(x=cha))
+  checkException(getHour(x=fac))
+
+##  checkIdentical(getHour(x=cDate), tHour)
+}
+
+### }}}
+### {{{ --- getMin ---
+
+test.getMin <- function()
+{
+  checkException(getMin(x=num))
+  checkException(getMin(x=cha))
+  checkException(getMin(x=fac))
+
+##  checkIdentical(getMin(x=cDate), tMin)
+}
+
+### }}}
+### {{{ --- getSec ---
+
+test.getSec <- function()
+{
+  checkException(getSec(x=num))
+  checkException(getSec(x=cha))
+  checkException(getSec(x=fac))
+
+##  checkIdentical(getSec(x=cDate), tSec)
+}
+
+### }}}
+### {{{ Dear Emacs
+### Local variables:
+### folded-file: t
+### end:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.getDateTimeParts.R ends here

Copied: trunk/gdata/inst/unitTests/runit.mapLevels.R (from rev 1782, trunk/gdata/tests/runit.mapLevels.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.mapLevels.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.mapLevels.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,281 @@
+### runit.mapLevels.R
+###------------------------------------------------------------------------
+### What: Unit tests for mapLevels et al.
+### $Id$
+### Time-stamp: <2006-10-29 16:41:41 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ mapLevels, is.*, as.*, [.*
+
+test.mapLevels <- function()
+{
+  ## Integer and numeric
+  checkException(mapLevels(1:3)) # wrong class(x)
+  checkException(mapLevels(1.5)) # wrong class(x)
+
+  ## Factor
+  f <- factor(c("B", "C", "A"))
+  fMapInt <- list(A=as.integer(1), B=as.integer(2), C=as.integer(3))
+  fMapInt1 <- list(B=as.integer(1), C=as.integer(2))
+  fMapCha <- list(A="A", B="B", C="C")
+  fMapInt <- as.levelsMap(fMapInt)
+  fMapInt1 <- as.levelsMap(fMapInt1)
+  fMapCha <- as.levelsMap(fMapCha)
+  fMapCha1 <- fMapCha[c(1, 3)] # this will test also [.levelsMap
+  checkIdentical(mapLevels(f), fMapInt)
+  checkTrue(is.levelsMap(mapLevels(f))) # test for is.levelsMap
+  checkTrue(is.levelsMap(fMapInt))      # test for as.levelsMap
+  checkTrue(!gdata:::.isCharacterMap(fMapInt))
+  checkIdentical(mapLevels(f, sort=FALSE), fMapInt) # sort is not used for factors
+  checkIdentical(mapLevels(f[1:2], drop=TRUE), fMapInt1)
+  checkIdentical(mapLevels(f, codes=FALSE), fMapCha)
+  checkIdentical(mapLevels(f[c(2, 3)], drop=TRUE, codes=FALSE), fMapCha1)
+
+  ## Character
+  cha <- c("Z", "M", "A")
+  chaMapInt <- list(A=as.integer(1), M=as.integer(2), Z=as.integer(3))
+  chaMapIntO <- list(Z=as.integer(1), M=as.integer(2), A=as.integer(3))
+  chaMapInt1 <- list(M=as.integer(1), Z=as.integer(2))
+  chaMapCha <- list(A="A", M="M", Z="Z")
+  chaMapInt <- as.levelsMap(chaMapInt)
+  chaMapIntO <- as.levelsMap(chaMapIntO)
+  chaMapInt1 <- as.levelsMap(chaMapInt1)
+  chaMapCha <- as.levelsMap(chaMapCha)
+  checkIdentical(mapLevels(cha), chaMapInt)
+  checkIdentical(mapLevels(cha, sort=FALSE), chaMapIntO) # sort works for characters
+  checkIdentical(mapLevels(cha[1:2], drop=TRUE), chaMapInt1)
+  checkIdentical(mapLevels(cha, codes=FALSE), chaMapCha)
+
+  ## List
+  l <- list(f=f, cha=cha)
+  l1 <- list(cha=cha, f=f)
+  l2 <- list(cha=cha, f=f, i=1:10)
+  lMapInt <- list(f=fMapInt, cha=chaMapInt)
+  lMapCha <- list(f=fMapCha, cha=chaMapCha)
+  lMapInt <- as.listLevelsMap(lMapInt)
+  lMapCha <- as.listLevelsMap(lMapCha)
+  lMapChaC <- as.list(sort(unique(c(cha, as.character(f)))))
+  lMapChaCO <- as.list(unique(c(cha, as.character(f))))
+  names(lMapChaC) <- unlist(lMapChaC)
+  names(lMapChaCO) <- unlist(lMapChaCO)
+  lMapChaC <- as.levelsMap(lMapChaC)
+  lMapChaCO <- as.levelsMap(lMapChaCO)
+  checkIdentical(mapLevels(l), lMapInt)
+  checkTrue(is.listLevelsMap(mapLevels(l))) # test for is.listLevelsMap
+  checkTrue(is.listLevelsMap(lMapInt))      # test for as.listLevelsMap
+  checkIdentical(mapLevels(l, codes=FALSE), lMapCha)
+  checkException(mapLevels(l, combine=TRUE)) # can not combine integer maps
+  checkIdentical(mapLevels(l, codes=FALSE, combine=TRUE), lMapChaC)
+  checkIdentical(mapLevels(l1, codes=FALSE, combine=TRUE), lMapChaC)
+  checkIdentical(mapLevels(l1, codes=FALSE, combine=TRUE, sort=FALSE), lMapChaCO)
+  checkException(mapLevels(l2)) # only char and factor
+
+  ## Data.frame
+  df <- data.frame(f1=factor(c("G", "Abc", "Abc", "D", "F")),
+                   f2=factor(c("Abc", "Abc", "B", "D", "K")),
+                         cha=c("jkl", "A", "D", "K", "L"),
+                   int=1:5)
+  dfMapInt <- list(f1=mapLevels(df$f1), f2=mapLevels(df$f2), cha=mapLevels(df$cha))
+  dfMapInt <- as.listLevelsMap(dfMapInt)
+  dfMapInt1 <- dfMapInt[c(1, 3)] # this will test also [.listLevelsMap
+  checkException(mapLevels(df)) # wrong class of int
+  checkIdentical(mapLevels(df[, 1:3]), dfMapInt)
+  checkIdentical(mapLevels(df[, c(1, 3)]), dfMapInt1)
+}
+
+### }}}
+### {{{ .check*
+
+test.checkLevelsMap <- function(x)
+{
+  ## --- levelsMap ---
+
+  ## not a list
+  checkException(gdata:::.checkLevelsMap(x="A", method="raw"))
+  ## list without names
+  checkException(gdata:::.checkLevelsMap(x=list("A"), method="raw"))
+  fMapInt <- list(A=as.integer(1), B=as.integer(2), C=as.integer(3))
+  ## x should be levelsMap
+  checkException(gdata:::.checkLevelsMap(x=fMapInt, method="class"))
+
+  ## --- listLevelsMap ---
+
+  map <- list(as.levelsMap(fMapInt), as.levelsMap(fMapInt))
+  map1 <- list(fMapInt, fMapInt)
+  class(map1) <- "listLevelsMap"
+  ## x should be a listLevelsMap
+  checkException(gdata:::.checkListLevelsMap(x=map, method="class"))
+  ## x should be also a list of levelsMaps
+  checkException(gdata:::.checkListLevelsMap(x=map1, method="class"))
+  ## the rest is done with levelsMap tests
+}
+
+### }}}
+### {{{ c.*
+
+test.cLevelsMap <- function()
+{
+  f1 <- factor(letters[c(2, 1)])
+  f2 <- factor(letters[c(3, 1, 2)])
+  mapCha1 <- mapLevels(f1, codes=FALSE) # get maps
+  mapCha2 <- mapLevels(f2, codes=FALSE)
+  mapCha1S <- mapLevels(as.character(f1), codes=FALSE, sort=FALSE)
+  mapCha2S <- mapLevels(as.character(f2), codes=FALSE, sort=FALSE)
+  mapChaTest <- list(a="a", b="b")
+  mapChaTest1 <- list(a="a", b="b", c="c")
+  mapChaTest2 <- list(c="c", a="a", b="b")
+  class(mapChaTest) <- class(mapChaTest1) <- class(mapChaTest2) <- "levelsMap"
+  mapChaTest3 <- list(mapChaTest, mapChaTest1, mapChaTest, mapChaTest1)
+  class(mapChaTest3)  <- "listLevelsMap"
+  checkIdentical(c(mapCha1), mapChaTest)
+  checkIdentical(c(mapCha2, mapCha1), mapChaTest1)
+  checkIdentical(c(mapCha2S, mapCha1S, sort=FALSE), mapChaTest2)
+
+  l <- list(f1, f2)
+  mapCha <- mapLevels(l, codes=FALSE)
+  checkIdentical(c(mapCha, mapCha), mapChaTest3)
+  checkIdentical(c(mapCha, recursive=TRUE), mapChaTest1)
+
+  checkException(c(mapLevels(f1))) # can not combine integer “levelsMaps”
+
+  ## Example with maps of different length of components
+  map1 <- list(A=c("a", "e", "i", "o", "u"), B="b", C="c", C="m",
+               D=c("d", "e"), F="f")
+  map2 <- list(A=c("a", "z", "w", "y", "x"), F="f", G=c("g", "h", "j"),
+               i="i", k=c("k", "l"), B="B")
+  map0Test <- list(A=c("a", "e", "i", "o", "u"), B="b", C="c", C="m",
+                   D=c("d", "e"), F="f",
+                   A=c("z", "w", "y", "x"), G=c("g", "h", "j"),
+                   i="i", k=c("k", "l"), B="B")
+  map0Test <- as.levelsMap(map0Test)
+  mapTest <- sort(map0Test)
+  map1 <- as.levelsMap(map1)
+  map2 <- as.levelsMap(map2)
+  map <- c(map1, map2)
+  map0 <- c(map1, map2, sort=FALSE)
+  checkIdentical(map, mapTest)
+  checkIdentical(map0, map0Test)
+}
+
+### }}}
+### {{{ unique
+
+test.uniqueLevelsMap <- function()
+{
+  map <- list(A=c(1, 2, 1, 3), B=4, C=1, C=5, D=c(6, 8), E=7, B=4,
+              D=c(6, 8))
+  map1 <- map
+  map1[[1]] <- map[[1]][c(1, 2, 4)]
+  map1[[7]] <- NULL # remove B=4
+  map1[[7]] <- NULL # remove D=c(6, 8)
+  ## unique (used in as.levelsMap), will remove duplicates (A=1)
+  checkIdentical(as.levelsMap(map1), as.levelsMap(map))
+}
+
+### }}}
+### {{{ mapLevels<-
+
+"test.mapLevels<-" <- function()
+{
+  ## Some errors
+  checkException("mapLevels<-"(1.1, value=2))  # wrong class(x)
+  checkException("mapLevels<-"(complex(1.1), value=2)) # wrong class(x)
+
+  f <- factor(c("A", "B", "C"))
+  fMapInt <- mapLevels(f)
+  ## can not apply integer "levelsMap" to "character"
+  checkException("mapLevels<-"(as.character(f), value=fMapInt))
+
+  fMapCha <- mapLevels(f, codes=FALSE)
+  ## can not apply character levelsMap to "integer"
+  checkException("mapLevels<-"(as.integer(f), value=chaMapCha))
+
+  fMapFuzz <- fMapInt
+  fMapFuzz[[1]] <- "A"
+  ## all components of 'value' must be of the same class
+  checkException("mapLevels<-"(as.character(f), value=fMapFuzz))
+  checkException("mapLevels<-"(as.integer(f), value=fMapFuzz))
+
+  ## x integer, value integer levelsMap
+  f <- factor(letters[c(10, 15, 1, 2)])
+  fMapInt <- mapLevels(f)
+  fInt <- as.integer(f)
+  mapLevels(fInt) <- fMapInt
+  checkIdentical(fInt, f)
+
+  ## x factor, value integer levelsMap
+  fInt <- factor(as.integer(f))
+  mapLevels(fInt) <- fMapInt
+  checkIdentical(fInt, f)
+
+  ## above is essentially the same as levels<-.factor
+  fInt1 <- factor(as.integer(f))
+  levels(fInt1) <- fMapInt
+  checkIdentical(fInt1, f)
+
+  ## x character, value character levelsMap
+  cha <- c("B", "A", "C")
+  chaMapCha <- as.levelsMap(list(A1="A", B2="B", C3="C"))
+  mapLevels(cha) <- chaMapCha
+  chaTest <- factor(c("B2", "A1", "C3"))
+  checkIdentical(cha, chaTest)
+  ## and a bit more for components of length > 1
+  cha <- c("G", "I", "B", "A", "C", "D", "Z")
+  chaMapCha <- as.levelsMap(list(A1=c("A", "G", "I"), B2="B", C3=c("C", "D")))
+  mapLevels(cha) <- chaMapCha
+  chaTest <- factor(c("A1", "A1", "B2", "A1", "C3", "C3", NA))
+  checkIdentical(cha, chaTest)
+
+  ## x factor, value character levelsMap
+  f <- factor(c("G", "I", "B", "A", "C", "D", "Z"))
+  fMapCha <- as.levelsMap(list(A1=c("A", "G", "I"), B2="B", C3=c("C", "D")))
+  mapLevels(f) <- fMapCha
+  fTest <- factor(c("A1", "A1", "B2", "A1", "C3", "C3", NA))
+  checkIdentical(f, fTest)
+
+  ## Two factors and character map
+  f1 <- factor(letters[1:10])
+  f2 <- factor(letters[5:14])
+  checkIdentical(as.integer(f1), as.integer(f2)) # the same integer codes
+  mapCha1 <- mapLevels(f1, codes=FALSE) # get maps
+  mapCha2 <- mapLevels(f2, codes=FALSE)
+  mapCha <- c(mapCha1, mapCha2)         # combine maps
+  ## apply map
+  mapLevels(f1) <- mapCha # the same as levels(f1) <- mapCha
+  mapLevels(f2) <- mapCha # the same as levels(f2) <- mapCha
+  checkIdentical(as.integer(f1), 1:10) # \ internal codes are now
+  checkIdentical(as.integer(f2), 5:14) # / "consistent" among factors
+
+  ## The same with list
+  l <- list(f1=f1, f2=f2)
+  mapCha <- mapLevels(l, codes=FALSE, combine=TRUE)
+  mapLevels(l) <- mapCha
+  checkIdentical(as.integer(l$f1), 1:10) # \ internal codes are now
+  checkIdentical(as.integer(l$f2), 5:14) # / "consistent" among factors
+
+  ## and data.frame
+  df <- data.frame(f1=f1, f2=f2)
+  mapCha <- mapLevels(df, codes=FALSE, combine=TRUE)
+  mapLevels(df) <- mapCha
+  checkIdentical(as.integer(df$f1), 1:10) # \ internal codes are now
+  checkIdentical(as.integer(df$f2), 5:14) # / "consistent" among factors
+
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.mapLevels.R ends here

Copied: trunk/gdata/inst/unitTests/runit.nPairs.R (from rev 1782, trunk/gdata/tests/runit.nPairs.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.nPairs.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.nPairs.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,68 @@
+### runit.nPairs.R
+###------------------------------------------------------------------------
+### What: Number of variable pairs - unit tests
+### $Id$
+### Time-stamp: <2008-12-30 18:24:59 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ --- nPairs ---
+
+test.nPairs <- function()
+{
+  ## 'x' must be a data.frame or a matrix
+  x <- rpois(100, lambda=10)
+  checkException(nPairs(x=x))
+  checkException(nPairs(x=table(x)))
+
+  test <- data.frame(V1=c(1, 2, 3, 4, 5),
+                     V2=c(NA, 2, 3, 4, 5),
+                     V3=c(1, NA, NA, NA, NA),
+                     V4=c(1, 2, 3, NA, NA))
+  testCheck <- matrix(data=as.integer(c(5, 4, 1, 3,
+                                        4, 4, 0, 2,
+                                        1, 0, 1, 1,
+                                        3, 2, 1, 3)),
+                      nrow=4, ncol=4, byrow=TRUE)
+  class(testCheck) <- c("nPairs", class(testCheck))
+
+  testCheckNames <- testCheck
+  colnames(testCheckNames) <- rownames(testCheckNames) <- colnames(test)
+
+  checkIdentical(nPairs(x=test), testCheckNames)
+  checkIdentical(nPairs(x=test, names=FALSE), testCheck)
+  checkIdentical(nPairs(x=as.matrix(test)), testCheckNames)
+  checkIdentical(nPairs(x=as.matrix(test), names=FALSE), testCheck)
+
+  testCheck <- cbind(testCheckNames, as.integer(c(5, 4, 0, 0)))
+  class(testCheck) <- class(testCheckNames)
+  colnames(testCheck) <- c(colnames(test), "all")
+  checkIdentical(nPairs(x=test, margin=TRUE), testCheck)
+
+  testCheckSumm <- matrix(data=as.integer(c(0, 1, 4, 2,
+                                            0, 0, 4, 2,
+                                            0, 1, 0, 0,
+                                            0, 1, 2, 0)),
+                          nrow=4, ncol=4, byrow=TRUE)
+  dimnames(testCheckSumm) <- dimnames(testCheckNames)
+  tmp <- summary(nPairs(x=test))
+  checkEquals(tmp, testCheckSumm)
+}
+
+
+### }}}
+### {{{ Dear Emacs
+### Local variables:
+### folded-file: t
+### end:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.nPairs.R ends here

Copied: trunk/gdata/inst/unitTests/runit.reorder.factor.R (from rev 1782, trunk/gdata/tests/runit.reorder.factor.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.reorder.factor.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.reorder.factor.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,64 @@
+### runit.reorder.factor.R
+###------------------------------------------------------------------------
+### What: Tests for reorder.factor
+### $Id$
+### Time-stamp: <2006-10-30 18:25:05 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ --- reorder.factor ---
+
+test.reorder.factor <- function()
+{
+  tmp <- Sys.getlocale(category="LC_COLLATE")
+  Sys.setlocale(category="LC_COLLATE", locale="C")
+
+  ## Create a 4 level example factor
+  levs <- c("PLACEBO", "300 MG", "600 MG", "1200 MG")
+  trt <- factor(rep(x=levs, times=c(22, 24, 28, 26)))
+
+  ## Change the order to something useful
+  ## default "mixedsort" ordering
+  trt2 <- reorder(trt)
+  levsTest <- c("300 MG", "600 MG", "1200 MG", "PLACEBO")
+  checkIdentical(levels(trt2), levsTest)
+
+  ## using indexes:
+  trt3 <- reorder(trt, new.order=c(4, 2, 3, 1))
+  levsTest <- c("PLACEBO", "300 MG", "600 MG", "1200 MG")
+  checkIdentical(levels(trt3), levsTest)
+
+  ## using label names:
+  trt4 <- reorder(trt, new.order=c("PLACEBO", "300 MG", "600 MG", "1200 MG"))
+  levsTest <- c("PLACEBO", "300 MG", "600 MG", "1200 MG")
+  checkIdentical(levels(trt4), levsTest)
+
+  ## using frequency
+  trt5 <- reorder(trt, X=as.numeric(trt), FUN=length)
+  levsTest <- c("PLACEBO", "300 MG", "1200 MG", "600 MG")
+  checkIdentical(levels(trt5), levsTest)
+
+  ## drop out the '300 MG' level
+  trt6 <- reorder(trt, new.order=c("PLACEBO", "600 MG", "1200 MG"))
+  levsTest <- c("PLACEBO", "600 MG", "1200 MG")
+  checkIdentical(levels(trt6), levsTest)
+
+  Sys.setlocale(category="LC_COLLATE", locale=tmp)
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.reorder.factor.R ends here

Copied: trunk/gdata/inst/unitTests/runit.trim.R (from rev 1782, trunk/gdata/tests/runit.trim.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.trim.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.trim.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,55 @@
+### runit.trim.R
+###------------------------------------------------------------------------
+### What: Tests for trim
+### $Id$
+### Time-stamp: <2006-08-29 14:21:02 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ --- trim ---
+
+test.trim <- function()
+{
+  tmp <- Sys.getlocale(category="LC_COLLATE")
+  Sys.setlocale(category="LC_COLLATE", locale="C")
+
+  sTrim <- "    this is an example string    "
+  sTrimR <- "this is an example string"
+
+  fTrim <- factor(c(sTrim, sTrim, " A", " B ", "  C ", "D "))
+  fTrimR <- factor(c(sTrimR, sTrimR, "A", "B", "C", "D"))
+
+  lTrim <- list(s=rep(sTrim, times=6), f=fTrim, i=1:6)
+  lTrimR <- list(s=rep(sTrimR, times=6), f=fTrimR, i=1:6)
+
+  dfTrim <- as.data.frame(lTrim)
+  dfTrimR <- as.data.frame(lTrimR)
+
+  checkIdentical(trim(sTrim), sTrimR)
+  checkIdentical(trim(fTrim), fTrimR)
+  checkIdentical(
+                 levels(trim(fTrim, recode.factor=FALSE)),
+                 c("this is an example string", "C", "A", "B", "D")
+                 )
+  checkIdentical(trim(lTrim), lTrimR)
+  checkIdentical(trim(dfTrim), dfTrimR)
+
+  Sys.setlocale(category="LC_COLLATE", locale=tmp)  
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.trim.R ends here

Copied: trunk/gdata/inst/unitTests/runit.trimSum.R (from rev 1782, trunk/gdata/tests/runit.trimSum.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.trimSum.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.trimSum.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,61 @@
+### runit.trimSum.R
+###------------------------------------------------------------------------
+### What: Unit tests for trimSum
+### $Id$
+### Time-stamp: <2008-12-20 11:58:50 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ --- trimSum ---
+
+test.trimSum <- function()
+{
+
+  ## 'x' must be a vector - for now
+  checkException(trimSum(matrix(1:10)))
+  checkException(trimSum(data.frame(1:10)))
+  checkException(trimSum(list(1:10)))
+
+  ## 'x' must be numeric
+  checkException(trimSum(letters))
+
+  ## 'n' must be smaller than the length of x
+  checkException(trimSum(x=1:10, n=11))
+  checkException(trimSum(x=1, n=1))
+
+  ## Default
+  x <- trimSum(x=1:10, n=5)
+  x2 <- c(1:4, 45)
+  checkEquals(x, x2)  
+
+  ## Left
+  x <- trimSum(x=1:10, n=5, right=FALSE)
+  x2 <- c(21, 7:10)
+  checkEquals(x, x2)
+
+  ## NA
+  x <- trimSum(x=c(1:9, NA), n=5)
+  x2 <- c(1:4, NA)
+  checkEquals(x, x2)
+  
+  x <- trimSum(x=c(1:9, NA), n=5, na.rm=TRUE)
+  x2 <- c(1:4, 35)
+  checkEquals(x, x2)
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.trimSum.R ends here

Copied: trunk/gdata/inst/unitTests/runit.unknown.R (from rev 1783, trunk/gdata/tests/runit.unknown.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.unknown.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.unknown.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,531 @@
+### runit.unknown.R
+###------------------------------------------------------------------------
+### What: Tests for Change given unknown value to NA and vice versa methods
+### $Id$
+### Time-stamp: <2006-10-30 17:46:21 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+library("RUnit")
+library("gdata")
+
+
+### {{{ --- Vectors ---
+
+intUnk <- 9999
+xInt        <- as.integer(c(NA,     1:2, NA,     5, 6, 7, 8, 9))
+xIntUnk     <- as.integer(c(intUnk, 1:2, intUnk, 5, 6, 7, 8, 9))
+xIntUnkTest <- xIntUnk %in% intUnk
+
+numUnk <- 0
+xNum        <- c(9999, NA, 1.5, NA, 5, 6, 7, 8, 9)
+xNumUnk     <- c(9999, 0,  1.5, 0,  5, 6, 7, 8, 9)
+xNumUnkTest <- xNumUnk %in% numUnk
+
+chaUnk <- "notAvail"
+chaUnk1 <- "-"
+xCha        <- c("A", "B", NA,      "C", NA,      "-", "7", "8", "9")
+xChaUnk     <- c("A", "B", chaUnk,  "C", chaUnk,  "-", "7", "8", "9")
+xChaUnk1    <- c("A", "B", chaUnk1, "C", chaUnk1, "-", "7", "8", "9")
+xChaUnkTest  <- xChaUnk %in% chaUnk
+xChaUnk1Test <- xChaUnk %in% chaUnk1
+
+facUnk <- "notAvail"
+facUnk1 <- "NA"
+xFac     <- factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", NA))
+xFacUnk  <- factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", facUnk))
+xFacUnk1 <- factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", facUnk1))
+xFacUnkTest <-     c(0,   0,   0, 0,    0,    0,      0,      0,   1)
+xFacUnkTest <- as.logical(xFacUnkTest)
+xFacUnk1Test <-    c(0,   0,   0, 1,    1,    0,      0,      0,   1)
+xFacUnk1Test <- as.logical(xFacUnk1Test)
+xFac1    <- factor(c("A", "0", 0, NA, NA, intUnk, numUnk, "-", NA))
+
+facLev <- "A"
+xFacUnkLev <- factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", "A"))
+xFacUnkLevTest <-    c(1,    0,  0, 0,    0,    0,      0,      0,   1)
+xFacUnkLevTest <- as.logical(xFacUnkLevTest)
+
+dateUnk <- as.Date("2006-08-14")
+tmp <- as.Date("2006-08-15")
+xDate     <- c(tmp, NA)
+xDateUnk  <- c(tmp,   dateUnk)
+xDateTest <- c(FALSE, TRUE)
+
+xDate1Unk  <- c(tmp,   dateUnk, NA)
+xDate1Test <- c(FALSE, TRUE,    FALSE)
+
+POSIXltUnk <- strptime("2006-08-14", format="%Y-%m-%d")
+tmp <- strptime("2006-08-15", format="%Y-%m-%d")
+xPOSIXlt     <- c(tmp, NA)
+xPOSIXltUnk  <- c(tmp,   POSIXltUnk)
+xPOSIXltTest <- c(FALSE, TRUE)
+
+xPOSIXlt1Unk  <- c(tmp,   POSIXltUnk, NA)
+xPOSIXlt1Test <- c(FALSE, TRUE,       FALSE)
+
+POSIXctUnk <- as.POSIXct(strptime("2006-08-14 01:01:01", format="%Y-%m-%d %H:%M:%S"))
+tmp <- as.POSIXct(strptime("2006-08-15 01:01:01", format="%Y-%m-%d %H:%M:%S"))
+xPOSIXct     <- c(tmp, NA)
+xPOSIXctUnk  <- c(tmp, POSIXctUnk)
+xPOSIXctTest <- xPOSIXltTest
+
+xPOSIXct1Unk  <- c(tmp, POSIXctUnk, NA)
+xPOSIXct1Test <- xPOSIXlt1Test
+
+### }}}
+### {{{ --- Lists and data.frames ---
+
+xList <- list(xInt, xCha, xNum, xFac)
+xListN <- list(int=xInt, cha=xCha, num=xNum, fac=xFac)
+xListUnk <- list(xIntUnk, xChaUnk, xNumUnk, xFacUnk)
+xListUnkTest <- list(xIntUnkTest, xChaUnkTest, xNumUnkTest, xFacUnkTest)
+xListNUnk <- list(int=xIntUnk, cha=xChaUnk, num=xNumUnk, fac=xFacUnk)
+xListNUnkTest <- list(int=xIntUnkTest, cha=xChaUnkTest, num=xNumUnkTest, fac=xFacUnkTest)
+
+xDF <- as.data.frame(xListN)
+xDF$cha <- as.character(xDF$cha)
+xDFUnk <- as.data.frame(xListNUnk)
+xDFUnk$cha <- as.character(xDFUnk$cha)
+xDFUnkTest <- as.data.frame(xListNUnkTest)
+
+unkC <- c(intUnk, chaUnk, numUnk, facUnk)
+unkL <- list(intUnk, chaUnk, numUnk, facUnk)
+unkLN <- list(num=numUnk, cha=chaUnk, fac=facUnk, int=intUnk) ## mixed as it is named
+unkLMN <- list(cha=chaUnk, int=intUnk, num=c(intUnk, numUnk),
+               fac=c(chaUnk1, facUnk))
+
+xListMNUnkF <- list(int=as.integer(c(9999, 1, 2, 9999, 5, 6, 7, 8, 9)),
+                   cha=c("A", "B", "notAvail", "C", "notAvail", "-", "7", "8", "9"),
+                   num=c(9999, 0, 1.5, 0, 5, 6, 7, 8, 9),
+                   fac=factor(c("A", "0", "0", "NA", "NA", 9999, "0", "-", "notAvail")))
+xListMNUnkFTest <- list(int=c(1, 0, 0, 1, 0, 0, 0, 0, 0),
+                        cha=c(0, 0, 1, 0, 1, 0, 0, 0, 0),
+                        num=c(1, 1, 0, 1, 0, 0, 0, 0, 0),
+                        fac=c(0, 0, 0, 0, 0, 0, 0, 1, 1))
+xListMNUnkFTest <- lapply(xListMNUnkFTest, as.logical)
+xListMNF <- list(int=as.integer(c(NA, 1, 2, NA, 5, 6, 7, 8, 9)),
+                 cha=c("A", "B", NA, "C", NA, "-", "7", "8", "9"),
+                 num=c(NA, NA, 1.5, NA, 5, 6, 7, 8, 9),
+                 fac=factor(c("A", "0", "0", "NA", "NA", "9999", "0", NA, NA)))
+
+xDFMUnkF <- as.data.frame(xListMNUnkF)
+xDFMUnkF$cha <- as.character(xDFMUnkF$cha)
+xDFMUnkFTest <- as.data.frame(xListMNUnkFTest)
+xDFMF <- as.data.frame(xListMNF)
+xDFMF$cha <- as.character(xDFMF$cha)
+
+unk1 <- 555555
+xListUnk1 <- list(as.integer(c(unk1, 1, 2, unk1, 5, 6, 7, 8, 9)),
+                  c("A", "B", unk1, "C", unk1, "-", "7", "8", "9"),
+                  c(9999, unk1, 1.5, unk1, 5, 6, 7, 8, 9),
+                  factor(c("A", "0", "0", "NA", "NA", "9999", "0", "-", unk1)))
+xListUnk1Test <- lapply(xListUnk1, function(x) x %in% unk1)
+xListNUnk1 <- xListUnk1
+names(xListNUnk1) <- c("int", "cha", "num", "fac")
+xDFUnk1 <- as.data.frame(xListNUnk1)
+xDFUnk1$cha <- as.character(xDFUnk1$cha)
+xDFUnk1Test <- as.data.frame(xListUnk1Test)
+names(xDFUnk1Test) <- names(xListNUnk1)
+
+unkC2 <- c(0, "notAvail")
+xListUnk2 <- list(as.integer(c(unkC2[1], 1, 2, unkC2[1], 5, 6, 7, 8, 9)),
+                  c("A", "B", unkC2[2], "C", unkC2[2], "-", "7", "8", "9"),
+                  c(9999, as.numeric(unkC2[1]), 1.5, as.numeric(unkC2[1]), 5, 6, 7, 8, 9),
+                  factor(c("A", "0", "0", "NA", "NA", "9999", "0", "-", unkC2[2])))
+xListNUnk2 <- xListUnk2
+names(xListNUnk2) <- c("int", "cha", "num", "fac")
+xDFUnk2 <- as.data.frame(xListNUnk2)
+xDFUnk2$cha <- as.character(xDFUnk2$cha)
+
+xListUnk2Test <- xListUnk2
+xListUnk2Test[[1]] <- xListUnk2Test[[1]] %in% unkC2[1]
+xListUnk2Test[[2]] <- xListUnk2Test[[2]] %in% unkC2[2]
+xListUnk2Test[[3]] <- xListUnk2Test[[3]] %in% unkC2[1]
+xListUnk2Test[[4]] <- xListUnk2Test[[4]] %in% unkC2[2]
+xListNUnk2Test <- xListUnk2Test
+names(xListNUnk2Test) <- names(xListNUnk2)
+xDFUnk2Test <- as.data.frame(xListNUnk2Test)
+
+unkL2 <- as.list(unkC2)
+unkLN2 <- unkL2[c(2, 1)]
+names(unkLN2) <- c("cha", "int")
+xListUnk2a <- list(as.integer(c(NA, 1, 2, NA, 5, 6, 7, 8, 9)),
+                  c("A", "B", unkLN2[[2]], "C", unkLN2[[2]], "-", "7", "8", "9"),
+                  c(9999, NA, 1.5, NA, 5, 6, 7, 8, 9),
+                  factor(c("A", "0", "0", "NA", "NA", "9999", "0", "-", unkLN2[[2]])))
+xListUnk2aTest <- xListUnk2a
+xListUnk2aTest[[1]] <- xListUnk2aTest[[1]] %in% unkLN2[1]
+xListUnk2aTest[[2]] <- xListUnk2aTest[[2]] %in% unkLN2[2]
+xListUnk2aTest[[3]] <- xListUnk2aTest[[3]] %in% unkLN2[1]
+xListUnk2aTest[[4]] <- xListUnk2aTest[[4]] %in% unkLN2[2]
+
+xList2a <- list(xListUnk2a[[1]],
+                c("A", "B", NA, "C", NA, "-", "7", "8", "9"),
+                xListUnk2a[[3]],
+                factor(c("A", NA, NA, "NA", "NA", 9999, NA, "-", NA)))
+
+### }}}
+### {{{ --- Matrix ---
+
+matUnk <- 9999
+mat        <- matrix(1:25, nrow=5, ncol=5)
+mat[1, 2] <- NA; mat[1, 4] <- NA; mat[2, 2] <- NA;
+mat[3, 2] <- NA; mat[3, 5] <- NA; mat[5, 4] <- NA;
+matUnk1       <- mat
+matUnk1[1, 2] <- matUnk; matUnk1[1, 4] <- matUnk; matUnk1[2, 2] <- matUnk;
+matUnk1[3, 2] <- matUnk; matUnk1[3, 5] <- matUnk; matUnk1[5, 4] <- matUnk;
+matUnkTest <- matUnk1Test <- is.na(mat)
+
+matUnk2Test <- matUnkTest | mat == 1
+
+### }}}
+### {{{ --- Use of unknown=list(.default=, ...) or similarly named vector ---
+
+D1 <- "notAvail"
+unkLND1 <- list(.default=D1)
+xListUnkD1 <- list(as.integer(c(NA, 1:2, NA, 5, 6, 7, 8, 9)),
+                   c("A", "B", D1, "C", D1, "-", "7", "8", "9"),
+                   c(9999, NA, 1.5, NA, 5, 6, 7, 8, 9),
+                   factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", D1)))
+xListUnkD1Test <- lapply(xListUnkD1, function(x) x %in% D1)
+xListD1 <- xList
+
+xListNUnkD1     <- xListUnkD1
+xListNUnkD1Test <- xListUnkD1Test
+names(xListNUnkD1) <- names(xListNUnkD1Test) <- names(xListNUnk1)
+xListND1 <- xListN
+
+DSO2 <- c("notAvail", 5678)
+unkLNDSO2 <- as.list(DSO2)
+names(unkLNDSO2) <- c(".default", "someOther")
+xListUnkDSO2 <- list(as.integer(c(NA, 1:2, NA, 5, 6, 7, 8, 9)),
+                      c("A", "B", DSO2[1], "C", DSO2[1], "-", "7", "8", "9"),
+                      c(9999, NA, 1.5, NA, 5, 6, 7, 8, 9),
+                      factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", DSO2[2])))
+xListUnkDSO2Test <- lapply(xListUnkDSO2, function(x) x %in% DSO2)
+
+unkLND3 <- list(.default="notAvail", num=0, int=9999)
+xListNUnkD3 <- list(int=as.integer(c(unkLND3[[3]], 1:2, unkLND3[[3]], 5, 6, 7, 8, 9)),
+                    cha=c("A", "B", unkLND3[[1]], "C", unkLND3[[1]], "-", "7", "8", "9"),
+                    num=c(9999, unkLND3[[2]], 1.5, unkLND3[[2]], 5, 6, 7, 8, 9),
+                    fac=factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", unkLND3[[1]])))
+xListNUnkD3Test <- xListNUnkD3
+xListNUnkD3Test$int <- xListNUnkD3Test$int %in% unkLND3[[3]]
+xListNUnkD3Test$cha <- xListNUnkD3Test$cha %in% unkLND3[[1]]
+xListNUnkD3Test$num <- xListNUnkD3Test$num %in% unkLND3[[2]]
+xListNUnkD3Test$fac <- xListNUnkD3Test$fac %in% unkLND3[[1]]
+
+unkLND2E <- list(.default="notAvail", 9999)
+
+### }}}
+
+### }}}
+### {{{ --- isUnknown ---
+
+test.isUnknown <- function()
+{
+  ## --- base methods for vectors ---
+
+  ## base ...
+  checkIdentical(isUnknown(xIntUnk, unknown=as.integer(intUnk)), xIntUnkTest)
+  checkIdentical(isUnknown(xIntUnk, unknown=intUnk),             xIntUnkTest)
+  checkIdentical(isUnknown(xNumUnk, unknown=numUnk),             xNumUnkTest)
+  checkIdentical(isUnknown(xNumUnk, unknown=as.integer(numUnk)), xNumUnkTest)
+  checkIdentical(isUnknown(xChaUnk, unknown=chaUnk),             xChaUnkTest)
+  checkIdentical(isUnknown(xFacUnk, unknown=facUnk),             xFacUnkTest)
+
+  ## multiple values are allowed for vector methods in vector or list form
+  checkIdentical(isUnknown(xIntUnk, unknown=unkC), xIntUnkTest)
+  checkIdentical(isUnknown(xIntUnk, unknown=unkL), xIntUnkTest)
+
+  ## NA's in factors
+  checkIdentical(isUnknown(xFacUnk1, unknown=facUnk1), xFacUnk1Test)
+  facNA <- factor(c("0", 1, 2, 3, NA, "NA"))
+  facNATest <- c(FALSE, FALSE, FALSE, FALSE, TRUE, FALSE)
+  checkIdentical(isUnknown(facNA), facNATest)
+
+  ## Date-time classes
+  checkIdentical(isUnknown(xDateUnk, unknown=dateUnk), xDateTest)
+  checkIdentical(isUnknown(xDate1Unk, unknown=dateUnk), xDate1Test)
+  checkIdentical(isUnknown(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXltTest)
+  checkIdentical(isUnknown(xPOSIXlt1Unk, unknown=POSIXltUnk), xPOSIXlt1Test)
+  checkIdentical(isUnknown(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXctTest)
+  checkIdentical(isUnknown(xPOSIXct1Unk, unknown=POSIXctUnk), xPOSIXct1Test)
+
+  ## --- lists and data.frames ---
+
+  ## with vector of single unknown values
+  checkIdentical(isUnknown(xListUnk, unknown=unkC), xListUnkTest)
+  checkIdentical(isUnknown(xDFUnk, unknown=unkC),   xDFUnkTest)
+
+  ## with list of single unknown values
+  checkIdentical(isUnknown(xListUnk, unknown=unkL), xListUnkTest)
+  checkIdentical(isUnknown(xDFUnk, unknown=unkL),   xDFUnkTest)
+
+  ## with named list of single unknown values
+  checkIdentical(isUnknown(xListNUnk, unknown=unkLN), xListNUnkTest)
+  checkIdentical(isUnknown(xDFUnk, unknown=unkLN),    xDFUnkTest)
+
+  ## with named list of multiple unknown values - valid here
+  checkIdentical(isUnknown(xListMNUnkF, unknown=unkLMN), xListMNUnkFTest)
+  checkIdentical(isUnknown(xDFMUnkF, unknown=unkLMN), xDFMUnkFTest)
+
+  ## with single unknown value - recycling
+  checkIdentical(isUnknown(xListUnk1, unknown=unk1), xListUnk1Test)
+  checkIdentical(isUnknown(xDFUnk1,   unknown=unk1), xDFUnk1Test)
+
+  ## with vector of two unknown values - recycling
+  checkIdentical(isUnknown(xListUnk2, unknown=unkC2), xListUnk2Test)
+  checkIdentical(isUnknown(xDFUnk2,   unknown=unkC2), xDFUnk2Test)
+
+  ## with list of two unknown values - recycling
+  checkIdentical(isUnknown(xListUnk2, unknown=unkL2), xListUnk2Test)
+  checkIdentical(isUnknown(xDFUnk2,   unknown=unkL2), xDFUnk2Test)
+
+  ## list(.default=)
+  checkIdentical(isUnknown(x=xListUnkD1, unknown=unkLND1), xListUnkD1Test)
+  ## list(.default=, someOther=) we do not know someOther, but should work
+  ## as x is not named
+  checkIdentical(isUnknown(x=xListUnkDSO2, unknown=unkLNDSO2), xListUnkDSO2Test)
+  ## list(.default=) in named list
+  checkIdentical(isUnknown(x=xListNUnkD1, unknown=unkLND1), xListNUnkD1Test)
+  ## list(.default=, someOther=) OK if someOther is in the named list
+  checkIdentical(isUnknown(x=xListNUnkD3, unknown=unkLND3), xListNUnkD3Test)
+  ## list(.default=, 99) ERROR as we do not know where to apply 99
+  checkException(isUnknown(x=xListNUnk, unknown=unkLND2E))
+
+  ## --- matrix ---
+
+  checkIdentical(isUnknown(x=mat, unknown=NA), matUnkTest)
+  checkIdentical(isUnknown(x=matUnk1, unknown=matUnk), matUnkTest)
+  checkIdentical(isUnknown(x=matUnk1, unknown=c(1, matUnk)), matUnk2Test)
+}
+
+### }}}
+### {{{ --- unknownToNA ---
+
+test.unknownToNA <- function()
+{
+  ## --- base methods for vectors ---
+
+  ## base ...
+  checkIdentical(unknownToNA(xIntUnk, as.integer(intUnk)), xInt)
+  checkIdentical(unknownToNA(xIntUnk, intUnk),             xInt) ## with numeric
+  checkIdentical(unknownToNA(xNumUnk, numUnk),             xNum)
+  checkIdentical(unknownToNA(xNumUnk, as.integer(numUnk)), xNum)
+  checkIdentical(unknownToNA(xChaUnk, chaUnk),             xCha)
+  checkIdentical(unknownToNA(xChaUnk, chaUnk),             xCha)
+  checkIdentical(unknownToNA(xFacUnk, facUnk),             xFac)
+
+  ## multiple values are allowed for vector methods in vector or list form
+  checkIdentical(unknownToNA(xIntUnk, unknown=unkC), xInt)
+  checkIdentical(unknownToNA(xIntUnk, unknown=unkL), xInt)
+
+  ## NA's in factors
+  checkIdentical(unknownToNA(xFacUnk1, unknown=facUnk1), xFac1)
+  facNA <- factor(c("0", 1, 2, 3, NA, "NA"))
+  facNATest <- factor(c("0", 1, 2, 3, NA, NA))
+  checkIdentical(unknownToNA(x=facNA, unknown="NA"), facNATest)
+
+  ## Date-time classes
+  checkIdentical(unknownToNA(xDateUnk, unknown=dateUnk), xDate)
+  checkIdentical(unknownToNA(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXct)
+
+  ## Per Brian Ripley on 2014-01-15:
+  ##
+  ## On platforms where POSIXlt has a gmtoff component, it does not need to be set.  So
+  ##
+  ## > z$gmtoff
+  ## [1] 3600   NA
+  ## > xPOSIXltUnk$gmtoff
+  ## [1] 3600 3600
+  ##
+  ## (or sometimes 0, not NA).
+  ##
+  ## So although identical() correctly reports that they differ, this
+  ## is allowed for optional components.
+  ##
+  ## It would also be wrong to use identical() to compare isdst
+  ## components: isdst = -1 means unknown.
+  ##
+  tmp_unknownToNA <- unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk)
+  tmp_xPOSIXlt   <- xPOSIXlt
+
+  tmp_unknownToNA$gmtoff <- NULL  # Remove $gmtoff to avoid comparison
+  tmp_xPOSIXlt$gmtoff   <- NULL
+
+  tmp_unknownToNA$isdst <- NULL   # Remove $isdst to avoid comparison
+  tmp_xPOSIXlt$isdst   <- NULL
+
+  checkIdentical(tmp_unknownToNA, tmp_xPOSIXlt)
+
+
+  ## --- lists and data.frames ---
+
+  ## with vector of single unknown values
+  checkIdentical(unknownToNA(xListUnk, unknown=unkC), xList)
+  checkIdentical(unknownToNA(xDFUnk, unknown=unkC), xDF)
+
+  ## with list of single unknown values
+  checkIdentical(unknownToNA(xListUnk, unknown=unkL), xList)
+  checkIdentical(unknownToNA(xDFUnk, unknown=unkL), xDF)
+
+  ## with named list of single unknown values
+  checkIdentical(unknownToNA(xListNUnk, unknown=unkLN), xListN)
+  checkIdentical(unknownToNA(xDFUnk, unknown=unkLN), xDF)
+
+  ## with names list of multiple unknown values - must be an error
+  checkIdentical(unknownToNA(xListMNUnkF, unknown=unkLMN), xListMNF)
+  checkIdentical(unknownToNA(xDFMUnkF, unknown=unkLMN), xDFMF)
+
+  ## with single unknown value - recycling
+  checkIdentical(unknownToNA(xListUnk1, unknown=unk1), xList)
+  checkIdentical(unknownToNA(xDFUnk1,   unknown=unk1), xDF)
+
+  ## with vector of two unknown values - recycling
+  checkIdentical(unknownToNA(xListUnk2, unknown=unkC2), xList)
+  checkIdentical(unknownToNA(xDFUnk2,   unknown=unkC2), xDF)
+
+  ## with list of two unknown values - recycling
+  checkIdentical(unknownToNA(xListUnk2, unknown=unkL2), xList)
+  checkIdentical(unknownToNA(xDFUnk2,   unknown=unkL2), xDF)
+
+  ## with named list of two unknown values but x is not named so named list
+  ## does not have any effect --> error as we do not know how to recycle
+  checkException(unknownToNA(xListUnk2a, unknown=unkLN2))
+
+  ## but we should get some results with named x
+  checkIdentical(unknownToNA(xListNUnk2, unknown=unkL2), xListN)
+  ## not also necesarilly with recycling of names lists, as it is
+  ## not clear how to properly recycle named lists (only names that match
+  ## can be really properly recycled)
+  checkException(unknownToNA(xListNUnk2, unknown=unkLN2))
+  checkIdentical(unknownToNA(xDFUnk2, unknown=unkL2), xDF)
+  checkException(unknownToNA(xDFUnk2, unknown=unkLN2))
+
+  ## list(.default=)
+  checkIdentical(unknownToNA(x=xListUnkD1, unknown=unkLND1), xListD1)
+  ## list(.default=, someOther=) we do not know someOther, but should work
+  ## as x is not named
+  checkIdentical(unknownToNA(x=xListUnkDSO2, unknown=unkLNDSO2), xList)
+  ## list(.default=) in named list
+  checkIdentical(unknownToNA(x=xListNUnkD1, unknown=unkLND1), xListND1)
+  ## list(.default=, someOther=) OK if someOther is in the named list
+  checkIdentical(unknownToNA(x=xListNUnkD3, unknown=unkLND3), xListN)
+  ## list(.default=, 99) ERROR as we do not know where to apply 99
+  checkException(unknownToNA(x=xListNUnk, unknown=unkLND2E))
+
+  ## --- matrix ---
+
+  checkEquals(unknownToNA(x=matUnk1, unknown=matUnk), mat)
+}
+
+### }}}
+### {{{ --- NAToUnknown ---
+
+test.NAToUnknown <- function()
+{
+  ## --- base methods for vectors ---
+
+  ## base ...
+  checkIdentical(NAToUnknown(xInt, as.integer(intUnk)), xIntUnk)
+  checkIdentical(NAToUnknown(xInt, intUnk),             xIntUnk) ## with numeric
+  checkIdentical(NAToUnknown(xNum, numUnk),             xNumUnk)
+  checkIdentical(NAToUnknown(xNum, as.integer(numUnk)), xNumUnk)
+  checkIdentical(NAToUnknown(xCha, chaUnk),             xChaUnk)
+  checkIdentical(NAToUnknown(xCha, chaUnk),             xChaUnk)
+  checkIdentical(NAToUnknown(xFac, facUnk),             xFacUnk)
+
+  ## only single values are allowed for vector methods
+  checkException(NAToUnknown(xInt, unknown=unkC))
+  checkException(NAToUnknown(xInt, unknown=unkL))
+
+  ## and they should not already be in x unless force=TRUE
+  checkException(NAToUnknown(xCha, unknown=chaUnk1))
+  checkIdentical(NAToUnknown(xCha, unknown=chaUnk1, force=TRUE), xChaUnk1)
+
+  checkException(NAToUnknown(xFac, unknown=facLev))
+  checkIdentical(NAToUnknown(xFac, unknown=facLev, force=TRUE), xFacUnkLev)
+
+  ## NA's in factors
+  checkIdentical(NAToUnknown(xFac, unknown=facUnk1, force=TRUE), xFacUnk1)
+  facNA <- factor(c("0", 1, 2, 3, NA, NA))
+  facNATest <- factor(c("0", 1, 2, 3, "NA", "NA"))
+  checkIdentical(NAToUnknown(x=facNA, unknown="NA"), facNATest)
+
+  ## Date-time classes
+  checkIdentical(NAToUnknown(xDate, unknown=dateUnk), xDateUnk)
+  checkIdentical(NAToUnknown(xPOSIXlt, unknown=POSIXltUnk), xPOSIXltUnk)
+  checkIdentical(NAToUnknown(xPOSIXct, unknown=POSIXctUnk), xPOSIXctUnk)
+
+  ## --- lists and data.frames ---
+
+  ## with vector of single unknown values
+  checkIdentical(NAToUnknown(xList, unknown=unkC), xListUnk)
+  checkIdentical(NAToUnknown(xDF, unknown=unkC), xDFUnk)
+
+  ## with list of single unknown values
+  checkIdentical(NAToUnknown(xList, unknown=unkL), xListUnk)
+  checkIdentical(NAToUnknown(xDF, unknown=unkL), xDFUnk)
+
+  ## with named list of single unknown values
+  checkIdentical(NAToUnknown(xListN, unknown=unkLN), xListNUnk)
+  checkIdentical(NAToUnknown(xDF, unknown=unkLN), xDFUnk)
+
+  ## with names list of multiple unknown values - must be an error
+  checkException(NAToUnknown(xListN, unknown=unkLMN))
+  checkException(NAToUnknown(xDF, unknown=unkLMN))
+
+  ## with single unknown value - recycling
+  checkIdentical(NAToUnknown(xList, unknown=unk1), xListUnk1)
+  checkIdentical(NAToUnknown(xDF,   unknown=unk1), xDFUnk1)
+
+  ## with vector of two unknown values - recycling
+  checkIdentical(NAToUnknown(xList, unknown=unkC2), xListUnk2)
+  checkIdentical(NAToUnknown(xDF,   unknown=unkC2), xDFUnk2)
+
+  ## with list of two unknown values - recycling
+  checkIdentical(NAToUnknown(xList, unknown=unkL2), xListUnk2)
+  checkIdentical(NAToUnknown(xDF,   unknown=unkL2), xDFUnk2)
+
+  ## with named list of two unknown values but x is not named so named list
+  ## does not have any effect --> error as we do not know how to recycle
+  checkException(NAToUnknown(xList, unknown=unkLN2))
+
+  ## but we should get some results with named x
+  checkIdentical(NAToUnknown(xListN, unknown=unkL2), xListNUnk2)
+  ## not also necesarilly with recycling of names lists, as it is
+  ## not clear how to properly recycle named lists (only names that match
+  ## can be really properly recycled)
+  checkException(NAToUnknown(xListN, unknown=unkLN2))
+  checkIdentical(NAToUnknown(xDF, unknown=unkL2), xDFUnk2)
+  checkException(NAToUnknown(xDF, unknown=unkLN2))
+
+  ## list(.default=)
+  checkIdentical(NAToUnknown(x=xList, unknown=unkLND1), xListUnkD1)
+  ## list(.default=, someOther=) we do not know someOther, but should work
+  ## as x is not named
+  checkIdentical(NAToUnknown(x=xList, unknown=unkLNDSO2), xListUnkDSO2)
+  ## list(.default=) in named list
+  checkIdentical(NAToUnknown(x=xListN, unknown=unkLND1), xListNUnkD1)
+  ## list(.default=, someOther=) OK if someOther is in the named list
+  checkIdentical(NAToUnknown(x=xListN, unknown=unkLND3), xListNUnkD3)
+  ## list(.default=, 99) ERROR as we do not know where to apply 99
+  checkException(NAToUnknown(x=xListN, unknown=unkLND2E))
+
+  ## --- matrix ---
+
+  checkEquals(NAToUnknown(x=mat, unknown=matUnk), matUnk1)
+}
+
+### }}}
+### {{{ Dear Emacs
+### Local variables:
+### folded-file: t
+### End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.unknown.R ends here

Copied: trunk/gdata/inst/unitTests/runit.wideByFactor.R (from rev 1782, trunk/gdata/tests/runit.wideByFactor.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.wideByFactor.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.wideByFactor.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,55 @@
+### runit.wideByFactor.R
+###------------------------------------------------------------------------
+### What: Reshape by factor levels - unit tests
+### $Id$
+### Time-stamp: <2008-12-30 11:58:50 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ --- wideByFactor ---
+
+test.wideByFactor <- function()
+{
+  n <- 10
+  f <- 2
+  tmp <- data.frame(y1=(1:n)/2,
+                    y2=(n:1)*2,
+                    f1=factor(rep(letters[1:f], n/2)),
+                    f2=factor(c(rep(c("M"), n/2), rep(c("F"), n/2))),
+                    c1=1:n,
+                    c2=2*(1:n))
+  
+  ## 'x' must be a data.frame
+  checkException(wideByFactor(x=1:10))
+  checkException(wideByFactor(x=matrix(1:10)))
+  ## 'factor' can be only of length one
+  checkException(wideByFactor(x=tmp, factor=c("f1", "f2")))
+  ## column defined in 'factor' must be a factor
+  checkException(wideByFactor(x=tmp, factor="c1"))
+
+  tmp2 <- wideByFactor(x=tmp, factor="f1", common=c("c1", "c2"), sort=FALSE)
+  checkEquals(tmp2[c("c1", "c2")], tmp[c("c1", "c2")])
+  checkEquals(names(tmp2), c("c1", "c2", "f1", "y1.a", "y2.a", "f2.a", "y1.b", "y2.b", "f2.b"))
+  checkEquals(tmp2$y1.a, c(0.5, NA, 1.5, NA, 2.5, NA, 3.5, NA, 4.5, NA))
+  checkEquals(tmp2$f2.a, factor(c("M", NA, "M", NA, "M", NA, "F", NA, "F", NA)))
+  tmp2 <- wideByFactor(x=tmp, factor="f1", common=c("c1", "c2"), sort=TRUE, keepFactor=FALSE)
+  checkEquals(tmp2$f2.a, factor(c("M", "M", "M", "F", "F", NA, NA, NA, NA, NA)))
+  checkEquals(names(tmp2), c("c1", "c2", "y1.a", "y2.a", "f2.a", "y1.b", "y2.b", "f2.b"))
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.wideByFactor.R ends here

Copied: trunk/gdata/inst/unitTests/runit.write.fwf.R (from rev 1782, trunk/gdata/tests/runit.write.fwf.R)
===================================================================
--- trunk/gdata/inst/unitTests/runit.write.fwf.R	                        (rev 0)
+++ trunk/gdata/inst/unitTests/runit.write.fwf.R	2014-04-05 02:23:45 UTC (rev 1784)
@@ -0,0 +1,137 @@
+### runit.write.fwf.R
+###------------------------------------------------------------------------
+### What: Unit tests for write.fwf
+### $Id$
+### Time-stamp: <2008-08-05 11:58:50 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+  library("RUnit")
+  library("gdata")
+}
+
+### }}}
+### {{{ --- write.fwf ---
+
+test.write.fwf <- function()
+{
+
+  ## 'x' must be a data.frame or matrix
+  checkException(write.fwf(1:10))
+  checkException(write.fwf(list(1:10)))
+
+  ## only single value is allowed in 'na'
+  checkException(write.fwf(data.frame(1:10, letters[1:10]), na=c("", " ")))
+
+  ## Example dataset
+  num <- round(c(733070.345678, 1214213.78765456, 553823.798765678,
+                 1085022.8876545678,  571063.88765456, 606718.3876545678,
+                 1053686.6, 971024.187656, 631193.398765456, 879431.1),
+               digits=3)
+
+  testData <- data.frame(num1=c(1:10, NA),
+                         num2=c(NA, seq(from=1, to=5.5, by=0.5)),
+                         num3=c(NA, num),
+                         int1=c(as.integer(1:4), NA, as.integer(4:9)),
+                         fac1=factor(c(NA, letters[1:9], "hjh")),
+                         fac2=factor(c(letters[6:15], NA)),
+                         cha1=c(letters[17:26], NA),
+                         cha2=c(NA, "longer", letters[25:17]),
+                         stringsAsFactors=FALSE)
+  levels(testData$fac1) <- c(levels(testData$fac1), "unusedLevel")
+  testData$Date <- as.Date("1900-1-1")
+  testData$Date[2] <- NA
+  testData$POSIXt <- as.POSIXct(strptime("1900-1-1 01:01:01", format="%Y-%m-%d %H:%M:%S"))
+  testData$POSIXt[5] <- NA
+
+  ## --- output ---
+  ## is tested with regular tests
+
+  ## --- formatInfo ---
+
+  ## default output
+  formatInfoT <- data.frame(colname=c("num1", "num2"),
+                            nlevels=c(0, 0),
+                            position=c(1, 4),
+                            width=c(2, 3),
+                            digits=c(0, 1),
+                            exp=c(0, 0),
+                            stringsAsFactors=FALSE)
+  formatInfo  <- write.fwf(testData[, c("num1", "num2")], formatInfo=TRUE)
+  checkEquals(formatInfo, formatInfoT)
+
+  ## scientific notation
+  dd <- options("digits"); options(digits = 7)
+  testData2 <- data.frame(a=123, b=pi, c=1e8, d=1e222)
+  formatInfo <- write.fwf(x=testData2, formatInfo=TRUE)
+  checkEquals(formatInfo$width, c(3, 8, 5, 6))
+  checkEquals(formatInfo$digits, c(0, 6, 0, 0))
+  checkEquals(formatInfo$exp, c(0, 0, 2, 3))
+  options(dd) ## reset old options
+
+  ## 'na' can either decrease or increase the width
+  ## --> values of int1 have width 1 and using na="" should not increase
+  ##     the width
+  formatInfo  <- write.fwf(testData[, "int1", drop=FALSE], formatInfo=TRUE,
+                           na="")
+  checkEquals(formatInfo$width, 1)
+  ## --> values of int1 have width 1 and using na="1234" should increase
+  ##     the width to 4
+  formatInfo  <- write.fwf(testData...
 
[truncated message content]

[R-gregmisc-users] SF.net SVN: r-gregmisc:[1783] trunk/gdata/tests/runit.unknown.R

[<wa...@us...>]

Revision: 1783
          http://sourceforge.net/p/r-gregmisc/code/1783
Author:   warnes
Date:     2014-04-05 01:27:30 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
- For unit tests, don't check for equality of optional POSIXlt
  components.  (Bug reported by Brian Ripley).

Modified Paths:
--------------
    trunk/gdata/tests/runit.unknown.R

Modified: trunk/gdata/tests/runit.unknown.R
===================================================================
--- trunk/gdata/tests/runit.unknown.R	2014-04-05 01:08:30 UTC (rev 1782)
+++ trunk/gdata/tests/runit.unknown.R	2014-04-05 01:27:30 UTC (rev 1783)
@@ -7,11 +7,10 @@
 
 ### {{{ --- Test setup ---
 
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
+library("RUnit")
+library("gdata")
 
+
 ### {{{ --- Vectors ---
 
 intUnk <- 9999
@@ -332,9 +331,37 @@
 
   ## Date-time classes
   checkIdentical(unknownToNA(xDateUnk, unknown=dateUnk), xDate)
-  checkIdentical(unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXlt)
   checkIdentical(unknownToNA(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXct)
 
+  ## Per Brian Ripley on 2014-01-15:
+  ##
+  ## On platforms where POSIXlt has a gmtoff component, it does not need to be set.  So
+  ##
+  ## > z$gmtoff
+  ## [1] 3600   NA
+  ## > xPOSIXltUnk$gmtoff
+  ## [1] 3600 3600
+  ##
+  ## (or sometimes 0, not NA).
+  ##
+  ## So although identical() correctly reports that they differ, this
+  ## is allowed for optional components.
+  ##
+  ## It would also be wrong to use identical() to compare isdst
+  ## components: isdst = -1 means unknown.
+  ##
+  tmp_unknownToNA <- unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk)
+  tmp_xPOSIXlt   <- xPOSIXlt
+
+  tmp_unknownToNA$gmtoff <- NULL  # Remove $gmtoff to avoid comparison
+  tmp_xPOSIXlt$gmtoff   <- NULL
+
+  tmp_unknownToNA$isdst <- NULL   # Remove $isdst to avoid comparison
+  tmp_xPOSIXlt$isdst   <- NULL
+
+  checkIdentical(tmp_unknownToNA, tmp_xPOSIXlt)
+
+
   ## --- lists and data.frames ---
 
   ## with vector of single unknown values

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[R-gregmisc-users] SF.net SVN: r-gregmisc:[1782] trunk/gdata

[<wa...@us...>]

Revision: 1782
          http://sourceforge.net/p/r-gregmisc/code/1782
Author:   warnes
Date:     2014-04-05 01:08:30 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Move unit test code into the (now) standard location

Added Paths:
-----------
    trunk/gdata/tests/Makefile
    trunk/gdata/tests/runRUnitTests.R
    trunk/gdata/tests/runit.bindData.R
    trunk/gdata/tests/runit.cbindX.R
    trunk/gdata/tests/runit.drop.levels.R
    trunk/gdata/tests/runit.getDateTimeParts.R
    trunk/gdata/tests/runit.mapLevels.R
    trunk/gdata/tests/runit.nPairs.R
    trunk/gdata/tests/runit.reorder.factor.R
    trunk/gdata/tests/runit.trim.R
    trunk/gdata/tests/runit.trimSum.R
    trunk/gdata/tests/runit.unknown.R
    trunk/gdata/tests/runit.wideByFactor.R
    trunk/gdata/tests/runit.write.fwf.R

Removed Paths:
-------------
    trunk/gdata/R/runRUnitTests.R
    trunk/gdata/inst/unitTests/Makefile
    trunk/gdata/inst/unitTests/runRUnitTests.R
    trunk/gdata/inst/unitTests/runit.bindData.R
    trunk/gdata/inst/unitTests/runit.cbindX.R
    trunk/gdata/inst/unitTests/runit.drop.levels.R
    trunk/gdata/inst/unitTests/runit.getDateTimeParts.R
    trunk/gdata/inst/unitTests/runit.mapLevels.R
    trunk/gdata/inst/unitTests/runit.nPairs.R
    trunk/gdata/inst/unitTests/runit.reorder.factor.R
    trunk/gdata/inst/unitTests/runit.trim.R
    trunk/gdata/inst/unitTests/runit.trimSum.R
    trunk/gdata/inst/unitTests/runit.unknown.R
    trunk/gdata/inst/unitTests/runit.wideByFactor.R
    trunk/gdata/inst/unitTests/runit.write.fwf.R
    trunk/gdata/man/runRUnitTests.Rd

Deleted: trunk/gdata/R/runRUnitTests.R
===================================================================
--- trunk/gdata/R/runRUnitTests.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/R/runRUnitTests.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,27 +0,0 @@
-### runRUnitTests.R
-###------------------------------------------------------------------------
-### What: Run RUnit tests (wrapper function) - R code
-### $Id$
-### Time-stamp: <2008-12-30 20:59:11 ggorjan>
-###------------------------------------------------------------------------
-
-.runRUnitTestsGdata <- function(testFileRegexp="^runit.+\\.[rR]$")
-{
-  ## Setup
-  .pkg <- environmentName(environment(.runRUnitTestsGdata))
-  .path <- system.file("unitTests", package=.pkg)
-  .suite <- file.path(.path, "runRUnitTests.R")
-
-  ## Some checks
-  stopifnot(file.exists(.path),
-            file.info(path.expand(.path))$isdir,
-            file.exists(.suite))
-
-  ## Run the suite
-  .way <- "function"
-  source(.suite, local=TRUE)
-  ## local=TRUE since .pkg and other vars do not exists in .suite environment
-}
-
-###------------------------------------------------------------------------
-### runRUnitTests.R ends here

Deleted: trunk/gdata/inst/unitTests/Makefile
===================================================================
--- trunk/gdata/inst/unitTests/Makefile	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/Makefile	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,22 +0,0 @@
-TOP=../..
-PKG=${shell cd ${TOP};pwd}
-SUITE=runRUnitTests.R
-R=R
-
-test: # Run unit tests
-	${R} --vanilla --slave < ${SUITE}
-
-inst: # Install package
-	cd ${TOP}/..;\
-	${R} CMD INSTALL ${PKG}
-
-all: inst test
-
-echo: # Echo env. variables
-	@echo "Package folder: ${PKG}"
-	@echo "R binary: ${R}"
-
-help: # Help
-	@echo -e '\nTarget: Dependency # Description'; \
-	echo '=================================================='; \
-	egrep '^[[:alnum:].+_()%]*:' ./Makefile

Deleted: trunk/gdata/inst/unitTests/runRUnitTests.R
===================================================================
--- trunk/gdata/inst/unitTests/runRUnitTests.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runRUnitTests.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,104 +0,0 @@
-### runRUnitTests.R
-###------------------------------------------------------------------------
-### What: Run RUnit tests (the core)- R code
-### $Id$
-### Time-stamp: <2008-12-30 12:52:51 ggorjan>
-###------------------------------------------------------------------------
-
-## The setup seems to be quite messy, but it is so to enable use of this in
-## several ways as shown bellow.
-
-## "R CMD check" way should be the most authoritative way to run the RUnit
-## tests for a developer. RUnit tests are issued during R CMD check of the
-## package due to example section of .runRUnitTests() function. If any test
-## fails (failure) or if there are any R errors during RUnit testing, R CMD
-## check fails. These are variable values specific for this way:
-##  - .path DEVEL/PATH/PKG.Rcheck/PKG/unitTests
-##  - .way  function
-
-## ".runRUnitTests()" way from within R after library(PKG) is handy for
-## package useRs, since it enables useRs to be sure that all tests pass for
-## their installation. This is just a convenient wrapper function to run
-## the RUnit testing suite. These are variable values specific for this
-## way:
-##  - .path INSTALL/PATH/PKG/unitTests
-##  - .way  function
-
-## "Shell" way is another possibility mainly for a developer in order to
-## skip possibly lengthy R CMD check and perform just RUnit testing with an
-## installed version of a pcakage. These are variable values specific for
-## this way:
-##  - .path DEVEL/PATH/PKG/inst/unitTests
-##  - .way  shell
-##
-## Rscript runRUnitTests.R
-## R CMD BATCH runRUnitTests.R
-## make
-## make all
-
-## Sourced via shell (Makefile, Rscript, R CMD BATCH)
-if(!exists(".pkg")) {
-  .path <- getwd()
-  .way <- "shell"
-  .pkg <- c(read.dcf(file="../../DESCRIPTION", fields="Package"))
-  print(.pkg)
-  testFileRegexp <- "^base.+\\.[rR]$"
-}
-
-if(require("RUnit", quietly=TRUE)) {
-
-  ## Debugging echo
-  cat("\nRunning RUnit tests\n")
-  print(list(pkg=.pkg, getwd=getwd(), pathToRUnitTests=.path))
-
-  ## Load the package - not needed for .runRUnitTests()
-  if(.way %in% c("shell"))
-    library(package=.pkg, character.only=TRUE)
-
-  ## Define tests
-  testSuite <- defineTestSuite(name=paste(.pkg, "RUnit testing"),
-                               dirs=.path, testFileRegexp=testFileRegexp)
-
-  ## Run
-  tests <- runTestSuite(testSuite)
-
-  if(file.access(.path, 02) != 0) {
-    ## cannot write to .path -> use writable one
-    tdir <- tempfile(paste(.pkg, "RUnitTests", sep="_"))
-    dir.create(tdir)
-    pathReport <- file.path(tdir, "report")
-  } else {
-    pathReport <- file.path(.path, "report")
-  }
-
-  ## Print results:
-  printTextProtocol(tests)
-  printTextProtocol(tests,
-                    fileName=paste(pathReport, ".txt", sep=""))
-
-  ## Print HTML Version of results:
-  printHTMLProtocol(tests,
-                    fileName=paste(pathReport, ".html", sep=""))
-
-  cat("\nRUnit reports also written to\n",
-      pathReport, ".(txt|html)\n\n", sep="")
-
-  ## Return stop() to cause R CMD check stop in case of
-  ##  - failures i.e. FALSE to RUnit tests or
-  ##  - errors i.e. R errors
-  tmp <- getErrors(tests)
-  if(tmp$nFail > 0 || tmp$nErr > 0) {
-    stop(paste("\n\nRUnit testing failed:\n",
-               " - #test failures: ", tmp$nFail, "\n",
-               " - #R errors: ",  tmp$nErr, "\n\n", sep=""))
-  }
-
-} else {
-
-  cat("R package 'RUnit' cannot be loaded - no unit tests run\n",
-      "for package", .pkg,"\n")
-
-}
-
-###------------------------------------------------------------------------
-### runRUnitTests.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.bindData.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.bindData.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.bindData.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,75 +0,0 @@
-### runit.bindData.R
-###------------------------------------------------------------------------
-### What: Bind two data frames - unit tests
-### $Id$
-### Time-stamp: <2008-12-30 11:58:50 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### }}}
-### {{{ --- bindData ---
-
-test.bindData <- function()
-{
-  ## 'x'/'y' must be a data.frame
-  checkException(bindData(x=1:10, y=1:10))
-  checkException(bindData(x=matrix(1:10), y=matrix(1:10)))
-  
-  n1 <- 6; n2 <- 12; n3 <- 4
-  ## Single trait 1
-  num <- c(5:n1, 10:13)
-  tmp1 <- data.frame(y1=rnorm(n=n1),
-                     f1=factor(rep(c("A", "B"), n1/2)),
-                     ch=letters[num],
-                     fa=factor(letters[num]),
-                     nu=(num) + 0.5,
-                     id=factor(num), stringsAsFactors=FALSE)
-
-  ## Single trait 2 with repeated records, some subjects also in tmp1 
-  num <- 4:9
-  tmp2 <- data.frame(y2=rnorm(n=n2),
-                     f2=factor(rep(c("C", "D"), n2/2)),
-                     ch=letters[rep(num, times=2)],
-                     fa=factor(letters[rep(c(num), times=2)]),
-                     nu=c((num) + 0.5, (num) + 0.25),
-                     id=factor(rep(num, times=2)), stringsAsFactors=FALSE)
-
-  ## Single trait 3 with completely distinct set of subjects
-  num <- 1:4
-  tmp3 <- data.frame(y3=rnorm(n=n3),
-                     f3=factor(rep(c("E", "F"), n3/2)),
-                     ch=letters[num],
-                     fa=factor(letters[num]),
-                     nu=(num) + 0.5,
-                     id=factor(num), stringsAsFactors=FALSE)
-
-  ## Combine all datasets
-  tmp12 <- bindData(x=tmp1, y=tmp2, common=c("id", "nu", "ch", "fa"))
-  tmp123 <- bindData(x=tmp12, y=tmp3, common=c("id", "nu", "ch", "fa"))
-
-  checkEquals(names(tmp123), c("id", "nu", "ch", "fa", "y1", "f1", "y2", "f2", "y3", "f3"))
-  checkEquals(rbind(tmp1["id"], tmp2["id"], tmp3["id"]), tmp123["id"])
-  checkEquals(rbind(tmp1["fa"], tmp2["fa"], tmp3["fa"]), tmp123["fa"])
-  checkEquals(is.na(tmp123$y1), c(rep(FALSE, times=n1), rep(TRUE, times=n2+n3)))
-  checkEquals(is.na(tmp123$f1), c(rep(FALSE, times=n1), rep(TRUE, times=n2+n3)))
-  checkEquals(is.na(tmp123$y2), c(rep(TRUE, times=n1), rep(FALSE, times=n2), rep(TRUE, times=n3)))
-  checkEquals(is.na(tmp123$f2), c(rep(TRUE, times=n1), rep(FALSE, times=n2), rep(TRUE, times=n3)))
-  checkEquals(is.na(tmp123$y3), c(rep(TRUE, times=n1+n2), rep(FALSE, times=n3)))
-  checkEquals(is.na(tmp123$f3), c(rep(TRUE, times=n1+n2), rep(FALSE, times=n3)))
-}
-
-### }}}
-### {{{ Dear Emacs
-## Local variables:
-## folded-file: t
-## End:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.bindData.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.cbindX.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.cbindX.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.cbindX.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,81 +0,0 @@
-### runit.cbindX.R
-###------------------------------------------------------------------------
-### What: Unit tests for cbindX
-### $Id:$
-### Time-stamp: <2008-08-05 13:40:49 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### }}}
-### {{{ --- cbindX ---
-
-test.cbindX <- function()
-{
-  df1 <- data.frame(a=1:3, b=c("A", "B", "C"))
-  df2 <- data.frame(c=as.character(1:5), a=5:1)
-
-  ma1 <- matrix(as.character(1:4), nrow=2, ncol=2)
-  ma2 <- matrix(1:6, nrow=3, ncol=2)
-
-  df12test <- cbindX(df1, df2)
-  df12stand <- data.frame(a=c(1:3, NA, NA),
-                          b=c("A", "B", "C", NA, NA),
-                          c=as.character(1:5),
-                          a=5:1)
-  names(df12stand)[4] <- "a"
-  checkEquals(df12test, df12stand)
-
-  ma12test <- cbindX(ma1, ma2)
-  ma12stand <- matrix(as.character(c(1,   3, 1, 4,
-                                     2,   4, 2, 5,
-                                     NA, NA, 3, 6)), nrow=3, ncol=4, byrow=TRUE)
-  checkEquals(ma12test, ma12stand)
-
-  da11test <- cbindX(df1, ma1)
-  da11stand <- data.frame(a=1:3,
-                          b=c("A", "B", "C"),
-                          as.character(c(1:2, NA)),
-                          as.character(c(3:4, NA)))
-  names(da11stand)[3:4] <- c("1", "2")
-  checkEquals(da11test, da11stand)
-
-  tmpTest <- cbindX(df1, df2, ma1, ma2)
-  tmpStand <- data.frame(a=c(1:3, NA, NA),
-                         b=c("A", "B", "C", NA, NA),
-                         c=as.character(1:5),
-                         a=5:1,
-                         as.character(c(1:2, NA, NA, NA)),
-                         as.character(c(3:4, NA, NA, NA)),
-                         c(1:3, NA, NA),
-                         c(4:6, NA, NA))
-  names(tmpStand)[4:8] <- c("a", "1", "2", "1", "2")
-  checkEquals(tmpTest, tmpStand)
-
-  tmpTest <- cbindX(ma1, ma2, df1, df2)
-  tmpStand <- data.frame(as.character(c(1:2, NA, NA, NA)),
-                         as.character(c(3:4, NA, NA, NA)),
-                         as.character(c(1:3, NA, NA)),
-                         as.character(c(4:6, NA, NA)),
-                         a=c(1:3, NA, NA),
-                         b=c("A", "B", "C", NA, NA),
-                         c=as.character(1:5),
-                         a=5:1)
-  names(tmpStand)[c(1:4, 8)] <- c("1", "2", "3", "4", "a")
-  checkEquals(tmpTest, tmpStand)
-}
-
-### }}}
-### {{{ Dear Emacs
-### Local variables:
-### folded-file: t
-### end:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.cbindX.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.drop.levels.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.drop.levels.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.drop.levels.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,42 +0,0 @@
-### runit.drop.levels.R
-###------------------------------------------------------------------------
-### What: Tests for drop.levels
-### $Id$
-### Time-stamp: <2006-08-29 14:21:12 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### }}}
-### {{{ --- drop.levels ---
-
-test.drop.levels <- function()
-{
-  f <- factor(c("A", "B", "C", "D"))[1:3]
-  fDrop <- factor(c("A", "B", "C"))
-
-  l <- list(f=f, i=1:3, c=c("A", "B", "D"))
-  lDrop <- list(f=fDrop, i=1:3, c=c("A", "B", "D"))
-
-  df <- as.data.frame(l)
-  dfDrop <- as.data.frame(lDrop)
-
-  checkIdentical(drop.levels(f), fDrop)
-  checkIdentical(drop.levels(l), lDrop)
-  checkIdentical(drop.levels(df), dfDrop)
-}
-
-### }}}
-### {{{ Dear Emacs
-## Local variables:
-## folded-file: t
-## End:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.drop.levels.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.getDateTimeParts.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.getDateTimeParts.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.getDateTimeParts.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,119 +0,0 @@
-### runit.getDateTimeParts.R
-###------------------------------------------------------------------------
-### What: Extract date and time parts from ... - unit tests
-### $Id$
-### Time-stamp: <2008-12-30 22:41:18 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-num <- 1
-cha <- "a"
-fac <- factor(c("A"))
-
-tYear <- as.character(c(2006, 1995, 1005, 3067))
-tMonth <- c("01", "04", "06", "12")
-tDay <- c("01", "12", "22", "04")
-tDate <- paste( paste(tYear, tMonth, tDay, sep="-"), "GMT" )
-
-tHour <- c("05", "16", "20", "03")
-tMin <- c("16", "40", "06", "52")
-tSec <- c("56", "34", "05", "15")
-tTime <- paste(tHour, tMin, tSec, sep=":")
-
-cDate <- as.Date(tDate)
-cDatePOSIXct <- as.POSIXct(tDate)
-cDatePOSIXlt <- as.POSIXlt(tDate)
-
-### }}}
-### {{{ --- getYear ---
-
-test.getYear <- function()
-{
-  checkException(getYear(x=num))
-  checkException(getYear(x=cha))
-  checkException(getYear(x=fac))
-
-  checkIdentical(getYear(x=cDate), tYear)
-  checkIdentical(getYear(x=cDatePOSIXct), tYear)
-  checkIdentical(getYear(x=cDatePOSIXlt), tYear)
-}
-
-### }}}
-### {{{ --- getMonth ---
-
-test.getMonth <- function()
-{
-  checkException(getMonth(x=num))
-  checkException(getMonth(x=cha))
-  checkException(getMonth(x=fac))
-
-  checkIdentical(getMonth(x=cDate), tMonth)
-  checkIdentical(getMonth(x=cDatePOSIXct), tMonth)
-  checkIdentical(getMonth(x=cDatePOSIXlt), tMonth)
-}
-
-### }}}
-### {{{ --- getDay ---
-
-test.getDay <- function()
-{
-  checkException(getDay(x=num))
-  checkException(getDay(x=cha))
-  checkException(getDay(x=fac))
-
-  checkIdentical(getDay(x=cDate), tDay)
-  checkIdentical(getDay(x=cDatePOSIXct), tDay)
-  checkIdentical(getDay(x=cDatePOSIXlt), tDay)
-}
-
-### }}}
-### {{{ --- getHour ---
-
-test.getHour <- function()
-{
-  checkException(getHour(x=num))
-  checkException(getHour(x=cha))
-  checkException(getHour(x=fac))
-
-##  checkIdentical(getHour(x=cDate), tHour)
-}
-
-### }}}
-### {{{ --- getMin ---
-
-test.getMin <- function()
-{
-  checkException(getMin(x=num))
-  checkException(getMin(x=cha))
-  checkException(getMin(x=fac))
-
-##  checkIdentical(getMin(x=cDate), tMin)
-}
-
-### }}}
-### {{{ --- getSec ---
-
-test.getSec <- function()
-{
-  checkException(getSec(x=num))
-  checkException(getSec(x=cha))
-  checkException(getSec(x=fac))
-
-##  checkIdentical(getSec(x=cDate), tSec)
-}
-
-### }}}
-### {{{ Dear Emacs
-### Local variables:
-### folded-file: t
-### end:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.getDateTimeParts.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.mapLevels.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.mapLevels.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.mapLevels.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,281 +0,0 @@
-### runit.mapLevels.R
-###------------------------------------------------------------------------
-### What: Unit tests for mapLevels et al.
-### $Id$
-### Time-stamp: <2006-10-29 16:41:41 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### }}}
-### {{{ mapLevels, is.*, as.*, [.*
-
-test.mapLevels <- function()
-{
-  ## Integer and numeric
-  checkException(mapLevels(1:3)) # wrong class(x)
-  checkException(mapLevels(1.5)) # wrong class(x)
-
-  ## Factor
-  f <- factor(c("B", "C", "A"))
-  fMapInt <- list(A=as.integer(1), B=as.integer(2), C=as.integer(3))
-  fMapInt1 <- list(B=as.integer(1), C=as.integer(2))
-  fMapCha <- list(A="A", B="B", C="C")
-  fMapInt <- as.levelsMap(fMapInt)
-  fMapInt1 <- as.levelsMap(fMapInt1)
-  fMapCha <- as.levelsMap(fMapCha)
-  fMapCha1 <- fMapCha[c(1, 3)] # this will test also [.levelsMap
-  checkIdentical(mapLevels(f), fMapInt)
-  checkTrue(is.levelsMap(mapLevels(f))) # test for is.levelsMap
-  checkTrue(is.levelsMap(fMapInt))      # test for as.levelsMap
-  checkTrue(!gdata:::.isCharacterMap(fMapInt))
-  checkIdentical(mapLevels(f, sort=FALSE), fMapInt) # sort is not used for factors
-  checkIdentical(mapLevels(f[1:2], drop=TRUE), fMapInt1)
-  checkIdentical(mapLevels(f, codes=FALSE), fMapCha)
-  checkIdentical(mapLevels(f[c(2, 3)], drop=TRUE, codes=FALSE), fMapCha1)
-
-  ## Character
-  cha <- c("Z", "M", "A")
-  chaMapInt <- list(A=as.integer(1), M=as.integer(2), Z=as.integer(3))
-  chaMapIntO <- list(Z=as.integer(1), M=as.integer(2), A=as.integer(3))
-  chaMapInt1 <- list(M=as.integer(1), Z=as.integer(2))
-  chaMapCha <- list(A="A", M="M", Z="Z")
-  chaMapInt <- as.levelsMap(chaMapInt)
-  chaMapIntO <- as.levelsMap(chaMapIntO)
-  chaMapInt1 <- as.levelsMap(chaMapInt1)
-  chaMapCha <- as.levelsMap(chaMapCha)
-  checkIdentical(mapLevels(cha), chaMapInt)
-  checkIdentical(mapLevels(cha, sort=FALSE), chaMapIntO) # sort works for characters
-  checkIdentical(mapLevels(cha[1:2], drop=TRUE), chaMapInt1)
-  checkIdentical(mapLevels(cha, codes=FALSE), chaMapCha)
-
-  ## List
-  l <- list(f=f, cha=cha)
-  l1 <- list(cha=cha, f=f)
-  l2 <- list(cha=cha, f=f, i=1:10)
-  lMapInt <- list(f=fMapInt, cha=chaMapInt)
-  lMapCha <- list(f=fMapCha, cha=chaMapCha)
-  lMapInt <- as.listLevelsMap(lMapInt)
-  lMapCha <- as.listLevelsMap(lMapCha)
-  lMapChaC <- as.list(sort(unique(c(cha, as.character(f)))))
-  lMapChaCO <- as.list(unique(c(cha, as.character(f))))
-  names(lMapChaC) <- unlist(lMapChaC)
-  names(lMapChaCO) <- unlist(lMapChaCO)
-  lMapChaC <- as.levelsMap(lMapChaC)
-  lMapChaCO <- as.levelsMap(lMapChaCO)
-  checkIdentical(mapLevels(l), lMapInt)
-  checkTrue(is.listLevelsMap(mapLevels(l))) # test for is.listLevelsMap
-  checkTrue(is.listLevelsMap(lMapInt))      # test for as.listLevelsMap
-  checkIdentical(mapLevels(l, codes=FALSE), lMapCha)
-  checkException(mapLevels(l, combine=TRUE)) # can not combine integer maps
-  checkIdentical(mapLevels(l, codes=FALSE, combine=TRUE), lMapChaC)
-  checkIdentical(mapLevels(l1, codes=FALSE, combine=TRUE), lMapChaC)
-  checkIdentical(mapLevels(l1, codes=FALSE, combine=TRUE, sort=FALSE), lMapChaCO)
-  checkException(mapLevels(l2)) # only char and factor
-
-  ## Data.frame
-  df <- data.frame(f1=factor(c("G", "Abc", "Abc", "D", "F")),
-                   f2=factor(c("Abc", "Abc", "B", "D", "K")),
-                         cha=c("jkl", "A", "D", "K", "L"),
-                   int=1:5)
-  dfMapInt <- list(f1=mapLevels(df$f1), f2=mapLevels(df$f2), cha=mapLevels(df$cha))
-  dfMapInt <- as.listLevelsMap(dfMapInt)
-  dfMapInt1 <- dfMapInt[c(1, 3)] # this will test also [.listLevelsMap
-  checkException(mapLevels(df)) # wrong class of int
-  checkIdentical(mapLevels(df[, 1:3]), dfMapInt)
-  checkIdentical(mapLevels(df[, c(1, 3)]), dfMapInt1)
-}
-
-### }}}
-### {{{ .check*
-
-test.checkLevelsMap <- function(x)
-{
-  ## --- levelsMap ---
-
-  ## not a list
-  checkException(gdata:::.checkLevelsMap(x="A", method="raw"))
-  ## list without names
-  checkException(gdata:::.checkLevelsMap(x=list("A"), method="raw"))
-  fMapInt <- list(A=as.integer(1), B=as.integer(2), C=as.integer(3))
-  ## x should be levelsMap
-  checkException(gdata:::.checkLevelsMap(x=fMapInt, method="class"))
-
-  ## --- listLevelsMap ---
-
-  map <- list(as.levelsMap(fMapInt), as.levelsMap(fMapInt))
-  map1 <- list(fMapInt, fMapInt)
-  class(map1) <- "listLevelsMap"
-  ## x should be a listLevelsMap
-  checkException(gdata:::.checkListLevelsMap(x=map, method="class"))
-  ## x should be also a list of levelsMaps
-  checkException(gdata:::.checkListLevelsMap(x=map1, method="class"))
-  ## the rest is done with levelsMap tests
-}
-
-### }}}
-### {{{ c.*
-
-test.cLevelsMap <- function()
-{
-  f1 <- factor(letters[c(2, 1)])
-  f2 <- factor(letters[c(3, 1, 2)])
-  mapCha1 <- mapLevels(f1, codes=FALSE) # get maps
-  mapCha2 <- mapLevels(f2, codes=FALSE)
-  mapCha1S <- mapLevels(as.character(f1), codes=FALSE, sort=FALSE)
-  mapCha2S <- mapLevels(as.character(f2), codes=FALSE, sort=FALSE)
-  mapChaTest <- list(a="a", b="b")
-  mapChaTest1 <- list(a="a", b="b", c="c")
-  mapChaTest2 <- list(c="c", a="a", b="b")
-  class(mapChaTest) <- class(mapChaTest1) <- class(mapChaTest2) <- "levelsMap"
-  mapChaTest3 <- list(mapChaTest, mapChaTest1, mapChaTest, mapChaTest1)
-  class(mapChaTest3)  <- "listLevelsMap"
-  checkIdentical(c(mapCha1), mapChaTest)
-  checkIdentical(c(mapCha2, mapCha1), mapChaTest1)
-  checkIdentical(c(mapCha2S, mapCha1S, sort=FALSE), mapChaTest2)
-
-  l <- list(f1, f2)
-  mapCha <- mapLevels(l, codes=FALSE)
-  checkIdentical(c(mapCha, mapCha), mapChaTest3)
-  checkIdentical(c(mapCha, recursive=TRUE), mapChaTest1)
-
-  checkException(c(mapLevels(f1))) # can not combine integer “levelsMaps”
-
-  ## Example with maps of different length of components
-  map1 <- list(A=c("a", "e", "i", "o", "u"), B="b", C="c", C="m",
-               D=c("d", "e"), F="f")
-  map2 <- list(A=c("a", "z", "w", "y", "x"), F="f", G=c("g", "h", "j"),
-               i="i", k=c("k", "l"), B="B")
-  map0Test <- list(A=c("a", "e", "i", "o", "u"), B="b", C="c", C="m",
-                   D=c("d", "e"), F="f",
-                   A=c("z", "w", "y", "x"), G=c("g", "h", "j"),
-                   i="i", k=c("k", "l"), B="B")
-  map0Test <- as.levelsMap(map0Test)
-  mapTest <- sort(map0Test)
-  map1 <- as.levelsMap(map1)
-  map2 <- as.levelsMap(map2)
-  map <- c(map1, map2)
-  map0 <- c(map1, map2, sort=FALSE)
-  checkIdentical(map, mapTest)
-  checkIdentical(map0, map0Test)
-}
-
-### }}}
-### {{{ unique
-
-test.uniqueLevelsMap <- function()
-{
-  map <- list(A=c(1, 2, 1, 3), B=4, C=1, C=5, D=c(6, 8), E=7, B=4,
-              D=c(6, 8))
-  map1 <- map
-  map1[[1]] <- map[[1]][c(1, 2, 4)]
-  map1[[7]] <- NULL # remove B=4
-  map1[[7]] <- NULL # remove D=c(6, 8)
-  ## unique (used in as.levelsMap), will remove duplicates (A=1)
-  checkIdentical(as.levelsMap(map1), as.levelsMap(map))
-}
-
-### }}}
-### {{{ mapLevels<-
-
-"test.mapLevels<-" <- function()
-{
-  ## Some errors
-  checkException("mapLevels<-"(1.1, value=2))  # wrong class(x)
-  checkException("mapLevels<-"(complex(1.1), value=2)) # wrong class(x)
-
-  f <- factor(c("A", "B", "C"))
-  fMapInt <- mapLevels(f)
-  ## can not apply integer "levelsMap" to "character"
-  checkException("mapLevels<-"(as.character(f), value=fMapInt))
-
-  fMapCha <- mapLevels(f, codes=FALSE)
-  ## can not apply character levelsMap to "integer"
-  checkException("mapLevels<-"(as.integer(f), value=chaMapCha))
-
-  fMapFuzz <- fMapInt
-  fMapFuzz[[1]] <- "A"
-  ## all components of 'value' must be of the same class
-  checkException("mapLevels<-"(as.character(f), value=fMapFuzz))
-  checkException("mapLevels<-"(as.integer(f), value=fMapFuzz))
-
-  ## x integer, value integer levelsMap
-  f <- factor(letters[c(10, 15, 1, 2)])
-  fMapInt <- mapLevels(f)
-  fInt <- as.integer(f)
-  mapLevels(fInt) <- fMapInt
-  checkIdentical(fInt, f)
-
-  ## x factor, value integer levelsMap
-  fInt <- factor(as.integer(f))
-  mapLevels(fInt) <- fMapInt
-  checkIdentical(fInt, f)
-
-  ## above is essentially the same as levels<-.factor
-  fInt1 <- factor(as.integer(f))
-  levels(fInt1) <- fMapInt
-  checkIdentical(fInt1, f)
-
-  ## x character, value character levelsMap
-  cha <- c("B", "A", "C")
-  chaMapCha <- as.levelsMap(list(A1="A", B2="B", C3="C"))
-  mapLevels(cha) <- chaMapCha
-  chaTest <- factor(c("B2", "A1", "C3"))
-  checkIdentical(cha, chaTest)
-  ## and a bit more for components of length > 1
-  cha <- c("G", "I", "B", "A", "C", "D", "Z")
-  chaMapCha <- as.levelsMap(list(A1=c("A", "G", "I"), B2="B", C3=c("C", "D")))
-  mapLevels(cha) <- chaMapCha
-  chaTest <- factor(c("A1", "A1", "B2", "A1", "C3", "C3", NA))
-  checkIdentical(cha, chaTest)
-
-  ## x factor, value character levelsMap
-  f <- factor(c("G", "I", "B", "A", "C", "D", "Z"))
-  fMapCha <- as.levelsMap(list(A1=c("A", "G", "I"), B2="B", C3=c("C", "D")))
-  mapLevels(f) <- fMapCha
-  fTest <- factor(c("A1", "A1", "B2", "A1", "C3", "C3", NA))
-  checkIdentical(f, fTest)
-
-  ## Two factors and character map
-  f1 <- factor(letters[1:10])
-  f2 <- factor(letters[5:14])
-  checkIdentical(as.integer(f1), as.integer(f2)) # the same integer codes
-  mapCha1 <- mapLevels(f1, codes=FALSE) # get maps
-  mapCha2 <- mapLevels(f2, codes=FALSE)
-  mapCha <- c(mapCha1, mapCha2)         # combine maps
-  ## apply map
-  mapLevels(f1) <- mapCha # the same as levels(f1) <- mapCha
-  mapLevels(f2) <- mapCha # the same as levels(f2) <- mapCha
-  checkIdentical(as.integer(f1), 1:10) # \ internal codes are now
-  checkIdentical(as.integer(f2), 5:14) # / "consistent" among factors
-
-  ## The same with list
-  l <- list(f1=f1, f2=f2)
-  mapCha <- mapLevels(l, codes=FALSE, combine=TRUE)
-  mapLevels(l) <- mapCha
-  checkIdentical(as.integer(l$f1), 1:10) # \ internal codes are now
-  checkIdentical(as.integer(l$f2), 5:14) # / "consistent" among factors
-
-  ## and data.frame
-  df <- data.frame(f1=f1, f2=f2)
-  mapCha <- mapLevels(df, codes=FALSE, combine=TRUE)
-  mapLevels(df) <- mapCha
-  checkIdentical(as.integer(df$f1), 1:10) # \ internal codes are now
-  checkIdentical(as.integer(df$f2), 5:14) # / "consistent" among factors
-
-}
-
-### }}}
-### {{{ Dear Emacs
-## Local variables:
-## folded-file: t
-## End:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.mapLevels.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.nPairs.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.nPairs.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.nPairs.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,68 +0,0 @@
-### runit.nPairs.R
-###------------------------------------------------------------------------
-### What: Number of variable pairs - unit tests
-### $Id$
-### Time-stamp: <2008-12-30 18:24:59 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### }}}
-### {{{ --- nPairs ---
-
-test.nPairs <- function()
-{
-  ## 'x' must be a data.frame or a matrix
-  x <- rpois(100, lambda=10)
-  checkException(nPairs(x=x))
-  checkException(nPairs(x=table(x)))
-
-  test <- data.frame(V1=c(1, 2, 3, 4, 5),
-                     V2=c(NA, 2, 3, 4, 5),
-                     V3=c(1, NA, NA, NA, NA),
-                     V4=c(1, 2, 3, NA, NA))
-  testCheck <- matrix(data=as.integer(c(5, 4, 1, 3,
-                                        4, 4, 0, 2,
-                                        1, 0, 1, 1,
-                                        3, 2, 1, 3)),
-                      nrow=4, ncol=4, byrow=TRUE)
-  class(testCheck) <- c("nPairs", class(testCheck))
-
-  testCheckNames <- testCheck
-  colnames(testCheckNames) <- rownames(testCheckNames) <- colnames(test)
-
-  checkIdentical(nPairs(x=test), testCheckNames)
-  checkIdentical(nPairs(x=test, names=FALSE), testCheck)
-  checkIdentical(nPairs(x=as.matrix(test)), testCheckNames)
-  checkIdentical(nPairs(x=as.matrix(test), names=FALSE), testCheck)
-
-  testCheck <- cbind(testCheckNames, as.integer(c(5, 4, 0, 0)))
-  class(testCheck) <- class(testCheckNames)
-  colnames(testCheck) <- c(colnames(test), "all")
-  checkIdentical(nPairs(x=test, margin=TRUE), testCheck)
-
-  testCheckSumm <- matrix(data=as.integer(c(0, 1, 4, 2,
-                                            0, 0, 4, 2,
-                                            0, 1, 0, 0,
-                                            0, 1, 2, 0)),
-                          nrow=4, ncol=4, byrow=TRUE)
-  dimnames(testCheckSumm) <- dimnames(testCheckNames)
-  tmp <- summary(nPairs(x=test))
-  checkEquals(tmp, testCheckSumm)
-}
-
-
-### }}}
-### {{{ Dear Emacs
-### Local variables:
-### folded-file: t
-### end:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.nPairs.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.reorder.factor.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.reorder.factor.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.reorder.factor.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,64 +0,0 @@
-### runit.reorder.factor.R
-###------------------------------------------------------------------------
-### What: Tests for reorder.factor
-### $Id$
-### Time-stamp: <2006-10-30 18:25:05 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### }}}
-### {{{ --- reorder.factor ---
-
-test.reorder.factor <- function()
-{
-  tmp <- Sys.getlocale(category="LC_COLLATE")
-  Sys.setlocale(category="LC_COLLATE", locale="C")
-
-  ## Create a 4 level example factor
-  levs <- c("PLACEBO", "300 MG", "600 MG", "1200 MG")
-  trt <- factor(rep(x=levs, times=c(22, 24, 28, 26)))
-
-  ## Change the order to something useful
-  ## default "mixedsort" ordering
-  trt2 <- reorder(trt)
-  levsTest <- c("300 MG", "600 MG", "1200 MG", "PLACEBO")
-  checkIdentical(levels(trt2), levsTest)
-
-  ## using indexes:
-  trt3 <- reorder(trt, new.order=c(4, 2, 3, 1))
-  levsTest <- c("PLACEBO", "300 MG", "600 MG", "1200 MG")
-  checkIdentical(levels(trt3), levsTest)
-
-  ## using label names:
-  trt4 <- reorder(trt, new.order=c("PLACEBO", "300 MG", "600 MG", "1200 MG"))
-  levsTest <- c("PLACEBO", "300 MG", "600 MG", "1200 MG")
-  checkIdentical(levels(trt4), levsTest)
-
-  ## using frequency
-  trt5 <- reorder(trt, X=as.numeric(trt), FUN=length)
-  levsTest <- c("PLACEBO", "300 MG", "1200 MG", "600 MG")
-  checkIdentical(levels(trt5), levsTest)
-
-  ## drop out the '300 MG' level
-  trt6 <- reorder(trt, new.order=c("PLACEBO", "600 MG", "1200 MG"))
-  levsTest <- c("PLACEBO", "600 MG", "1200 MG")
-  checkIdentical(levels(trt6), levsTest)
-
-  Sys.setlocale(category="LC_COLLATE", locale=tmp)
-}
-
-### }}}
-### {{{ Dear Emacs
-## Local variables:
-## folded-file: t
-## End:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.reorder.factor.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.trim.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.trim.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.trim.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,55 +0,0 @@
-### runit.trim.R
-###------------------------------------------------------------------------
-### What: Tests for trim
-### $Id$
-### Time-stamp: <2006-08-29 14:21:02 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### }}}
-### {{{ --- trim ---
-
-test.trim <- function()
-{
-  tmp <- Sys.getlocale(category="LC_COLLATE")
-  Sys.setlocale(category="LC_COLLATE", locale="C")
-
-  sTrim <- "    this is an example string    "
-  sTrimR <- "this is an example string"
-
-  fTrim <- factor(c(sTrim, sTrim, " A", " B ", "  C ", "D "))
-  fTrimR <- factor(c(sTrimR, sTrimR, "A", "B", "C", "D"))
-
-  lTrim <- list(s=rep(sTrim, times=6), f=fTrim, i=1:6)
-  lTrimR <- list(s=rep(sTrimR, times=6), f=fTrimR, i=1:6)
-
-  dfTrim <- as.data.frame(lTrim)
-  dfTrimR <- as.data.frame(lTrimR)
-
-  checkIdentical(trim(sTrim), sTrimR)
-  checkIdentical(trim(fTrim), fTrimR)
-  checkIdentical(
-                 levels(trim(fTrim, recode.factor=FALSE)),
-                 c("this is an example string", "C", "A", "B", "D")
-                 )
-  checkIdentical(trim(lTrim), lTrimR)
-  checkIdentical(trim(dfTrim), dfTrimR)
-
-  Sys.setlocale(category="LC_COLLATE", locale=tmp)  
-}
-
-### }}}
-### {{{ Dear Emacs
-## Local variables:
-## folded-file: t
-## End:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.trim.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.trimSum.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.trimSum.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.trimSum.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,61 +0,0 @@
-### runit.trimSum.R
-###------------------------------------------------------------------------
-### What: Unit tests for trimSum
-### $Id$
-### Time-stamp: <2008-12-20 11:58:50 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### }}}
-### {{{ --- trimSum ---
-
-test.trimSum <- function()
-{
-
-  ## 'x' must be a vector - for now
-  checkException(trimSum(matrix(1:10)))
-  checkException(trimSum(data.frame(1:10)))
-  checkException(trimSum(list(1:10)))
-
-  ## 'x' must be numeric
-  checkException(trimSum(letters))
-
-  ## 'n' must be smaller than the length of x
-  checkException(trimSum(x=1:10, n=11))
-  checkException(trimSum(x=1, n=1))
-
-  ## Default
-  x <- trimSum(x=1:10, n=5)
-  x2 <- c(1:4, 45)
-  checkEquals(x, x2)  
-
-  ## Left
-  x <- trimSum(x=1:10, n=5, right=FALSE)
-  x2 <- c(21, 7:10)
-  checkEquals(x, x2)
-
-  ## NA
-  x <- trimSum(x=c(1:9, NA), n=5)
-  x2 <- c(1:4, NA)
-  checkEquals(x, x2)
-  
-  x <- trimSum(x=c(1:9, NA), n=5, na.rm=TRUE)
-  x2 <- c(1:4, 35)
-  checkEquals(x, x2)
-}
-
-### }}}
-### {{{ Dear Emacs
-## Local variables:
-## folded-file: t
-## End:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.trimSum.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.unknown.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.unknown.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.unknown.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,504 +0,0 @@
-### runit.unknown.R
-###------------------------------------------------------------------------
-### What: Tests for Change given unknown value to NA and vice versa methods
-### $Id$
-### Time-stamp: <2006-10-30 17:46:21 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### {{{ --- Vectors ---
-
-intUnk <- 9999
-xInt        <- as.integer(c(NA,     1:2, NA,     5, 6, 7, 8, 9))
-xIntUnk     <- as.integer(c(intUnk, 1:2, intUnk, 5, 6, 7, 8, 9))
-xIntUnkTest <- xIntUnk %in% intUnk
-
-numUnk <- 0
-xNum        <- c(9999, NA, 1.5, NA, 5, 6, 7, 8, 9)
-xNumUnk     <- c(9999, 0,  1.5, 0,  5, 6, 7, 8, 9)
-xNumUnkTest <- xNumUnk %in% numUnk
-
-chaUnk <- "notAvail"
-chaUnk1 <- "-"
-xCha        <- c("A", "B", NA,      "C", NA,      "-", "7", "8", "9")
-xChaUnk     <- c("A", "B", chaUnk,  "C", chaUnk,  "-", "7", "8", "9")
-xChaUnk1    <- c("A", "B", chaUnk1, "C", chaUnk1, "-", "7", "8", "9")
-xChaUnkTest  <- xChaUnk %in% chaUnk
-xChaUnk1Test <- xChaUnk %in% chaUnk1
-
-facUnk <- "notAvail"
-facUnk1 <- "NA"
-xFac     <- factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", NA))
-xFacUnk  <- factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", facUnk))
-xFacUnk1 <- factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", facUnk1))
-xFacUnkTest <-     c(0,   0,   0, 0,    0,    0,      0,      0,   1)
-xFacUnkTest <- as.logical(xFacUnkTest)
-xFacUnk1Test <-    c(0,   0,   0, 1,    1,    0,      0,      0,   1)
-xFacUnk1Test <- as.logical(xFacUnk1Test)
-xFac1    <- factor(c("A", "0", 0, NA, NA, intUnk, numUnk, "-", NA))
-
-facLev <- "A"
-xFacUnkLev <- factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", "A"))
-xFacUnkLevTest <-    c(1,    0,  0, 0,    0,    0,      0,      0,   1)
-xFacUnkLevTest <- as.logical(xFacUnkLevTest)
-
-dateUnk <- as.Date("2006-08-14")
-tmp <- as.Date("2006-08-15")
-xDate     <- c(tmp, NA)
-xDateUnk  <- c(tmp,   dateUnk)
-xDateTest <- c(FALSE, TRUE)
-
-xDate1Unk  <- c(tmp,   dateUnk, NA)
-xDate1Test <- c(FALSE, TRUE,    FALSE)
-
-POSIXltUnk <- strptime("2006-08-14", format="%Y-%m-%d")
-tmp <- strptime("2006-08-15", format="%Y-%m-%d")
-xPOSIXlt     <- c(tmp, NA)
-xPOSIXltUnk  <- c(tmp,   POSIXltUnk)
-xPOSIXltTest <- c(FALSE, TRUE)
-
-xPOSIXlt1Unk  <- c(tmp,   POSIXltUnk, NA)
-xPOSIXlt1Test <- c(FALSE, TRUE,       FALSE)
-
-POSIXctUnk <- as.POSIXct(strptime("2006-08-14 01:01:01", format="%Y-%m-%d %H:%M:%S"))
-tmp <- as.POSIXct(strptime("2006-08-15 01:01:01", format="%Y-%m-%d %H:%M:%S"))
-xPOSIXct     <- c(tmp, NA)
-xPOSIXctUnk  <- c(tmp, POSIXctUnk)
-xPOSIXctTest <- xPOSIXltTest
-
-xPOSIXct1Unk  <- c(tmp, POSIXctUnk, NA)
-xPOSIXct1Test <- xPOSIXlt1Test
-
-### }}}
-### {{{ --- Lists and data.frames ---
-
-xList <- list(xInt, xCha, xNum, xFac)
-xListN <- list(int=xInt, cha=xCha, num=xNum, fac=xFac)
-xListUnk <- list(xIntUnk, xChaUnk, xNumUnk, xFacUnk)
-xListUnkTest <- list(xIntUnkTest, xChaUnkTest, xNumUnkTest, xFacUnkTest)
-xListNUnk <- list(int=xIntUnk, cha=xChaUnk, num=xNumUnk, fac=xFacUnk)
-xListNUnkTest <- list(int=xIntUnkTest, cha=xChaUnkTest, num=xNumUnkTest, fac=xFacUnkTest)
-
-xDF <- as.data.frame(xListN)
-xDF$cha <- as.character(xDF$cha)
-xDFUnk <- as.data.frame(xListNUnk)
-xDFUnk$cha <- as.character(xDFUnk$cha)
-xDFUnkTest <- as.data.frame(xListNUnkTest)
-
-unkC <- c(intUnk, chaUnk, numUnk, facUnk)
-unkL <- list(intUnk, chaUnk, numUnk, facUnk)
-unkLN <- list(num=numUnk, cha=chaUnk, fac=facUnk, int=intUnk) ## mixed as it is named
-unkLMN <- list(cha=chaUnk, int=intUnk, num=c(intUnk, numUnk),
-               fac=c(chaUnk1, facUnk))
-
-xListMNUnkF <- list(int=as.integer(c(9999, 1, 2, 9999, 5, 6, 7, 8, 9)),
-                   cha=c("A", "B", "notAvail", "C", "notAvail", "-", "7", "8", "9"),
-                   num=c(9999, 0, 1.5, 0, 5, 6, 7, 8, 9),
-                   fac=factor(c("A", "0", "0", "NA", "NA", 9999, "0", "-", "notAvail")))
-xListMNUnkFTest <- list(int=c(1, 0, 0, 1, 0, 0, 0, 0, 0),
-                        cha=c(0, 0, 1, 0, 1, 0, 0, 0, 0),
-                        num=c(1, 1, 0, 1, 0, 0, 0, 0, 0),
-                        fac=c(0, 0, 0, 0, 0, 0, 0, 1, 1))
-xListMNUnkFTest <- lapply(xListMNUnkFTest, as.logical)
-xListMNF <- list(int=as.integer(c(NA, 1, 2, NA, 5, 6, 7, 8, 9)),
-                 cha=c("A", "B", NA, "C", NA, "-", "7", "8", "9"),
-                 num=c(NA, NA, 1.5, NA, 5, 6, 7, 8, 9),
-                 fac=factor(c("A", "0", "0", "NA", "NA", "9999", "0", NA, NA)))
-
-xDFMUnkF <- as.data.frame(xListMNUnkF)
-xDFMUnkF$cha <- as.character(xDFMUnkF$cha)
-xDFMUnkFTest <- as.data.frame(xListMNUnkFTest)
-xDFMF <- as.data.frame(xListMNF)
-xDFMF$cha <- as.character(xDFMF$cha)
-
-unk1 <- 555555
-xListUnk1 <- list(as.integer(c(unk1, 1, 2, unk1, 5, 6, 7, 8, 9)),
-                  c("A", "B", unk1, "C", unk1, "-", "7", "8", "9"),
-                  c(9999, unk1, 1.5, unk1, 5, 6, 7, 8, 9),
-                  factor(c("A", "0", "0", "NA", "NA", "9999", "0", "-", unk1)))
-xListUnk1Test <- lapply(xListUnk1, function(x) x %in% unk1)
-xListNUnk1 <- xListUnk1
-names(xListNUnk1) <- c("int", "cha", "num", "fac")
-xDFUnk1 <- as.data.frame(xListNUnk1)
-xDFUnk1$cha <- as.character(xDFUnk1$cha)
-xDFUnk1Test <- as.data.frame(xListUnk1Test)
-names(xDFUnk1Test) <- names(xListNUnk1)
-
-unkC2 <- c(0, "notAvail")
-xListUnk2 <- list(as.integer(c(unkC2[1], 1, 2, unkC2[1], 5, 6, 7, 8, 9)),
-                  c("A", "B", unkC2[2], "C", unkC2[2], "-", "7", "8", "9"),
-                  c(9999, as.numeric(unkC2[1]), 1.5, as.numeric(unkC2[1]), 5, 6, 7, 8, 9),
-                  factor(c("A", "0", "0", "NA", "NA", "9999", "0", "-", unkC2[2])))
-xListNUnk2 <- xListUnk2
-names(xListNUnk2) <- c("int", "cha", "num", "fac")
-xDFUnk2 <- as.data.frame(xListNUnk2)
-xDFUnk2$cha <- as.character(xDFUnk2$cha)
-
-xListUnk2Test <- xListUnk2
-xListUnk2Test[[1]] <- xListUnk2Test[[1]] %in% unkC2[1]
-xListUnk2Test[[2]] <- xListUnk2Test[[2]] %in% unkC2[2]
-xListUnk2Test[[3]] <- xListUnk2Test[[3]] %in% unkC2[1]
-xListUnk2Test[[4]] <- xListUnk2Test[[4]] %in% unkC2[2]
-xListNUnk2Test <- xListUnk2Test
-names(xListNUnk2Test) <- names(xListNUnk2)
-xDFUnk2Test <- as.data.frame(xListNUnk2Test)
-
-unkL2 <- as.list(unkC2)
-unkLN2 <- unkL2[c(2, 1)]
-names(unkLN2) <- c("cha", "int")
-xListUnk2a <- list(as.integer(c(NA, 1, 2, NA, 5, 6, 7, 8, 9)),
-                  c("A", "B", unkLN2[[2]], "C", unkLN2[[2]], "-", "7", "8", "9"),
-                  c(9999, NA, 1.5, NA, 5, 6, 7, 8, 9),
-                  factor(c("A", "0", "0", "NA", "NA", "9999", "0", "-", unkLN2[[2]])))
-xListUnk2aTest <- xListUnk2a
-xListUnk2aTest[[1]] <- xListUnk2aTest[[1]] %in% unkLN2[1]
-xListUnk2aTest[[2]] <- xListUnk2aTest[[2]] %in% unkLN2[2]
-xListUnk2aTest[[3]] <- xListUnk2aTest[[3]] %in% unkLN2[1]
-xListUnk2aTest[[4]] <- xListUnk2aTest[[4]] %in% unkLN2[2]
-
-xList2a <- list(xListUnk2a[[1]],
-                c("A", "B", NA, "C", NA, "-", "7", "8", "9"),
-                xListUnk2a[[3]],
-                factor(c("A", NA, NA, "NA", "NA", 9999, NA, "-", NA)))
-
-### }}}
-### {{{ --- Matrix ---
-
-matUnk <- 9999
-mat        <- matrix(1:25, nrow=5, ncol=5)
-mat[1, 2] <- NA; mat[1, 4] <- NA; mat[2, 2] <- NA;
-mat[3, 2] <- NA; mat[3, 5] <- NA; mat[5, 4] <- NA;
-matUnk1       <- mat
-matUnk1[1, 2] <- matUnk; matUnk1[1, 4] <- matUnk; matUnk1[2, 2] <- matUnk;
-matUnk1[3, 2] <- matUnk; matUnk1[3, 5] <- matUnk; matUnk1[5, 4] <- matUnk;
-matUnkTest <- matUnk1Test <- is.na(mat)
-
-matUnk2Test <- matUnkTest | mat == 1
-
-### }}}
-### {{{ --- Use of unknown=list(.default=, ...) or similarly named vector ---
-
-D1 <- "notAvail"
-unkLND1 <- list(.default=D1)
-xListUnkD1 <- list(as.integer(c(NA, 1:2, NA, 5, 6, 7, 8, 9)),
-                   c("A", "B", D1, "C", D1, "-", "7", "8", "9"),
-                   c(9999, NA, 1.5, NA, 5, 6, 7, 8, 9),
-                   factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", D1)))
-xListUnkD1Test <- lapply(xListUnkD1, function(x) x %in% D1)
-xListD1 <- xList
-
-xListNUnkD1     <- xListUnkD1
-xListNUnkD1Test <- xListUnkD1Test
-names(xListNUnkD1) <- names(xListNUnkD1Test) <- names(xListNUnk1)
-xListND1 <- xListN
-
-DSO2 <- c("notAvail", 5678)
-unkLNDSO2 <- as.list(DSO2)
-names(unkLNDSO2) <- c(".default", "someOther")
-xListUnkDSO2 <- list(as.integer(c(NA, 1:2, NA, 5, 6, 7, 8, 9)),
-                      c("A", "B", DSO2[1], "C", DSO2[1], "-", "7", "8", "9"),
-                      c(9999, NA, 1.5, NA, 5, 6, 7, 8, 9),
-                      factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", DSO2[2])))
-xListUnkDSO2Test <- lapply(xListUnkDSO2, function(x) x %in% DSO2)
-
-unkLND3 <- list(.default="notAvail", num=0, int=9999)
-xListNUnkD3 <- list(int=as.integer(c(unkLND3[[3]], 1:2, unkLND3[[3]], 5, 6, 7, 8, 9)),
-                    cha=c("A", "B", unkLND3[[1]], "C", unkLND3[[1]], "-", "7", "8", "9"),
-                    num=c(9999, unkLND3[[2]], 1.5, unkLND3[[2]], 5, 6, 7, 8, 9),
-                    fac=factor(c("A", "0", 0, "NA", "NA", intUnk, numUnk, "-", unkLND3[[1]])))
-xListNUnkD3Test <- xListNUnkD3
-xListNUnkD3Test$int <- xListNUnkD3Test$int %in% unkLND3[[3]]
-xListNUnkD3Test$cha <- xListNUnkD3Test$cha %in% unkLND3[[1]]
-xListNUnkD3Test$num <- xListNUnkD3Test$num %in% unkLND3[[2]]
-xListNUnkD3Test$fac <- xListNUnkD3Test$fac %in% unkLND3[[1]]
-
-unkLND2E <- list(.default="notAvail", 9999)
-
-### }}}
-
-### }}}
-### {{{ --- isUnknown ---
-
-test.isUnknown <- function()
-{
-  ## --- base methods for vectors ---
-
-  ## base ...
-  checkIdentical(isUnknown(xIntUnk, unknown=as.integer(intUnk)), xIntUnkTest)
-  checkIdentical(isUnknown(xIntUnk, unknown=intUnk),             xIntUnkTest)
-  checkIdentical(isUnknown(xNumUnk, unknown=numUnk),             xNumUnkTest)
-  checkIdentical(isUnknown(xNumUnk, unknown=as.integer(numUnk)), xNumUnkTest)
-  checkIdentical(isUnknown(xChaUnk, unknown=chaUnk),             xChaUnkTest)
-  checkIdentical(isUnknown(xFacUnk, unknown=facUnk),             xFacUnkTest)
-
-  ## multiple values are allowed for vector methods in vector or list form
-  checkIdentical(isUnknown(xIntUnk, unknown=unkC), xIntUnkTest)
-  checkIdentical(isUnknown(xIntUnk, unknown=unkL), xIntUnkTest)
-
-  ## NA's in factors
-  checkIdentical(isUnknown(xFacUnk1, unknown=facUnk1), xFacUnk1Test)
-  facNA <- factor(c("0", 1, 2, 3, NA, "NA"))
-  facNATest <- c(FALSE, FALSE, FALSE, FALSE, TRUE, FALSE)
-  checkIdentical(isUnknown(facNA), facNATest)
-
-  ## Date-time classes
-  checkIdentical(isUnknown(xDateUnk, unknown=dateUnk), xDateTest)
-  checkIdentical(isUnknown(xDate1Unk, unknown=dateUnk), xDate1Test)
-  checkIdentical(isUnknown(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXltTest)
-  checkIdentical(isUnknown(xPOSIXlt1Unk, unknown=POSIXltUnk), xPOSIXlt1Test)
-  checkIdentical(isUnknown(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXctTest)
-  checkIdentical(isUnknown(xPOSIXct1Unk, unknown=POSIXctUnk), xPOSIXct1Test)
-
-  ## --- lists and data.frames ---
-
-  ## with vector of single unknown values
-  checkIdentical(isUnknown(xListUnk, unknown=unkC), xListUnkTest)
-  checkIdentical(isUnknown(xDFUnk, unknown=unkC),   xDFUnkTest)
-
-  ## with list of single unknown values
-  checkIdentical(isUnknown(xListUnk, unknown=unkL), xListUnkTest)
-  checkIdentical(isUnknown(xDFUnk, unknown=unkL),   xDFUnkTest)
-
-  ## with named list of single unknown values
-  checkIdentical(isUnknown(xListNUnk, unknown=unkLN), xListNUnkTest)
-  checkIdentical(isUnknown(xDFUnk, unknown=unkLN),    xDFUnkTest)
-
-  ## with named list of multiple unknown values - valid here
-  checkIdentical(isUnknown(xListMNUnkF, unknown=unkLMN), xListMNUnkFTest)
-  checkIdentical(isUnknown(xDFMUnkF, unknown=unkLMN), xDFMUnkFTest)
-
-  ## with single unknown value - recycling
-  checkIdentical(isUnknown(xListUnk1, unknown=unk1), xListUnk1Test)
-  checkIdentical(isUnknown(xDFUnk1,   unknown=unk1), xDFUnk1Test)
-
-  ## with vector of two unknown values - recycling
-  checkIdentical(isUnknown(xListUnk2, unknown=unkC2), xListUnk2Test)
-  checkIdentical(isUnknown(xDFUnk2,   unknown=unkC2), xDFUnk2Test)
-
-  ## with list of two unknown values - recycling
-  checkIdentical(isUnknown(xListUnk2, unknown=unkL2), xListUnk2Test)
-  checkIdentical(isUnknown(xDFUnk2,   unknown=unkL2), xDFUnk2Test)
-
-  ## list(.default=)
-  checkIdentical(isUnknown(x=xListUnkD1, unknown=unkLND1), xListUnkD1Test)
-  ## list(.default=, someOther=) we do not know someOther, but should work
-  ## as x is not named
-  checkIdentical(isUnknown(x=xListUnkDSO2, unknown=unkLNDSO2), xListUnkDSO2Test)
-  ## list(.default=) in named list
-  checkIdentical(isUnknown(x=xListNUnkD1, unknown=unkLND1), xListNUnkD1Test)
-  ## list(.default=, someOther=) OK if someOther is in the named list
-  checkIdentical(isUnknown(x=xListNUnkD3, unknown=unkLND3), xListNUnkD3Test)
-  ## list(.default=, 99) ERROR as we do not know where to apply 99
-  checkException(isUnknown(x=xListNUnk, unknown=unkLND2E))
-
-  ## --- matrix ---
-
-  checkIdentical(isUnknown(x=mat, unknown=NA), matUnkTest)
-  checkIdentical(isUnknown(x=matUnk1, unknown=matUnk), matUnkTest)
-  checkIdentical(isUnknown(x=matUnk1, unknown=c(1, matUnk)), matUnk2Test)
-}
-
-### }}}
-### {{{ --- unknownToNA ---
-
-test.unknownToNA <- function()
-{
-  ## --- base methods for vectors ---
-
-  ## base ...
-  checkIdentical(unknownToNA(xIntUnk, as.integer(intUnk)), xInt)
-  checkIdentical(unknownToNA(xIntUnk, intUnk),             xInt) ## with numeric
-  checkIdentical(unknownToNA(xNumUnk, numUnk),             xNum)
-  checkIdentical(unknownToNA(xNumUnk, as.integer(numUnk)), xNum)
-  checkIdentical(unknownToNA(xChaUnk, chaUnk),             xCha)
-  checkIdentical(unknownToNA(xChaUnk, chaUnk),             xCha)
-  checkIdentical(unknownToNA(xFacUnk, facUnk),             xFac)
-
-  ## multiple values are allowed for vector methods in vector or list form
-  checkIdentical(unknownToNA(xIntUnk, unknown=unkC), xInt)
-  checkIdentical(unknownToNA(xIntUnk, unknown=unkL), xInt)
-
-  ## NA's in factors
-  checkIdentical(unknownToNA(xFacUnk1, unknown=facUnk1), xFac1)
-  facNA <- factor(c("0", 1, 2, 3, NA, "NA"))
-  facNATest <- factor(c("0", 1, 2, 3, NA, NA))
-  checkIdentical(unknownToNA(x=facNA, unknown="NA"), facNATest)
-
-  ## Date-time classes
-  checkIdentical(unknownToNA(xDateUnk, unknown=dateUnk), xDate)
-  checkIdentical(unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXlt)
-  checkIdentical(unknownToNA(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXct)
-
-  ## --- lists and data.frames ---
-
-  ## with vector of single unknown values
-  checkIdentical(unknownToNA(xListUnk, unknown=unkC), xList)
-  checkIdentical(unknownToNA(xDFUnk, unknown=unkC), xDF)
-
-  ## with list of single unknown values
-  checkIdentical(unknownToNA(xListUnk, unknown=unkL), xList)
-  checkIdentical(unknownToNA(xDFUnk, unknown=unkL), xDF)
-
-  ## with named list of single unknown values
-  checkIdentical(unknownToNA(xListNUnk, unknown=unkLN), xListN)
-  checkIdentical(unknownToNA(xDFUnk, unknown=unkLN), xDF)
-
-  ## with names list of multiple unknown values - must be an error
-  checkIdentical(unknownToNA(xListMNUnkF, unknown=unkLMN), xListMNF)
-  checkIdentical(unknownToNA(xDFMUnkF, unknown=unkLMN), xDFMF)
-
-  ## with single unknown value - recycling
-  checkIdentical(unknownToNA(xListUnk1, unknown=unk1), xList)
-  checkIdentical(unknownToNA(xDFUnk1,   unknown=unk1), xDF)
-
-  ## with vector of two unknown values - recycling
-  checkIdentical(unknownToNA(xListUnk2, unknown=unkC2), xList)
-  checkIdentical(unknownToNA(xDFUnk2,   unknown=unkC2), xDF)
-
-  ## with list of two unknown values - recycling
-  checkIdentical(unknownToNA(xListUnk2, unknown=unkL2), xList)
-  checkIdentical(unknownToNA(xDFUnk2,   unknown=unkL2), xDF)
-
-  ## with named list of two unknown values but x is not named so named list
-  ## does not have any effect --> error as we do not know how to recycle
-  checkException(unknownToNA(xListUnk2a, unknown=unkLN2))
-
-  ## but we should get some results with named x
-  checkIdentical(unknownToNA(xListNUnk2, unknown=unkL2), xListN)
-  ## not also necesarilly with recycling of names lists, as it is
-  ## not clear how to properly recycle named lists (only names that match
-  ## can be really properly recycled)
-  checkException(unknownToNA(xListNUnk2, unknown=unkLN2))
-  checkIdentical(unknownToNA(xDFUnk2, unknown=unkL2), xDF)
-  checkException(unknownToNA(xDFUnk2, unknown=unkLN2))
-
-  ## list(.default=)
-  checkIdentical(unknownToNA(x=xListUnkD1, unknown=unkLND1), xListD1)
-  ## list(.default=, someOther=) we do not know someOther, but should work
-  ## as x is not named
-  checkIdentical(unknownToNA(x=xListUnkDSO2, unknown=unkLNDSO2), xList)
-  ## list(.default=) in named list
-  checkIdentical(unknownToNA(x=xListNUnkD1, unknown=unkLND1), xListND1)
-  ## list(.default=, someOther=) OK if someOther is in the named list
-  checkIdentical(unknownToNA(x=xListNUnkD3, unknown=unkLND3), xListN)
-  ## list(.default=, 99) ERROR as we do not know where to apply 99
-  checkException(unknownToNA(x=xListNUnk, unknown=unkLND2E))
-
-  ## --- matrix ---
-
-  checkEquals(unknownToNA(x=matUnk1, unknown=matUnk), mat)
-}
-
-### }}}
-### {{{ --- NAToUnknown ---
-
-test.NAToUnknown <- function()
-{
-  ## --- base methods for vectors ---
-
-  ## base ...
-  checkIdentical(NAToUnknown(xInt, as.integer(intUnk)), xIntUnk)
-  checkIdentical(NAToUnknown(xInt, intUnk),             xIntUnk) ## with numeric
-  checkIdentical(NAToUnknown(xNum, numUnk),             xNumUnk)
-  checkIdentical(NAToUnknown(xNum, as.integer(numUnk)), xNumUnk)
-  checkIdentical(NAToUnknown(xCha, chaUnk),             xChaUnk)
-  checkIdentical(NAToUnknown(xCha, chaUnk),             xChaUnk)
-  checkIdentical(NAToUnknown(xFac, facUnk),             xFacUnk)
-
-  ## only single values are allowed for vector methods
-  checkException(NAToUnknown(xInt, unknown=unkC))
-  checkException(NAToUnknown(xInt, unknown=unkL))
-
-  ## and they should not already be in x unless force=TRUE
-  checkException(NAToUnknown(xCha, unknown=chaUnk1))
-  checkIdentical(NAToUnknown(xCha, unknown=chaUnk1, force=TRUE), xChaUnk1)
-
-  checkException(NAToUnknown(xFac, unknown=facLev))
-  checkIdentical(NAToUnknown(xFac, unknown=facLev, force=TRUE), xFacUnkLev)
-
-  ## NA's in factors
-  checkIdentical(NAToUnknown(xFac, unknown=facUnk1, force=TRUE), xFacUnk1)
-  facNA <- factor(c("0", 1, 2, 3, NA, NA))
-  facNATest <- factor(c("0", 1, 2, 3, "NA", "NA"))
-  checkIdentical(NAToUnknown(x=facNA, unknown="NA"), facNATest)
-
-  ## Date-time classes
-  checkIdentical(NAToUnknown(xDate, unknown=dateUnk), xDateUnk)
-  checkIdentical(NAToUnknown(xPOSIXlt, unknown=POSIXltUnk), xPOSIXltUnk)
-  checkIdentical(NAToUnknown(xPOSIXct, unknown=POSIXctUnk), xPOSIXctUnk)
-
-  ## --- lists and data.frames ---
-
-  ## with vector of single unknown values
-  checkIdentical(NAToUnknown(xList, unknown=unkC), xListUnk)
-  checkIdentical(NAToUnknown(xDF, unknown=unkC), xDFUnk)
-
-  ## with list of single unknown values
-  checkIdentical(NAToUnknown(xList, unknown=unkL), xListUnk)
-  checkIdentical(NAToUnknown(xDF, unknown=unkL), xDFUnk)
-
-  ## with named list of single unknown values
-  checkIdentical(NAToUnknown(xListN, unknown=unkLN), xListNUnk)
-  checkIdentical(NAToUnknown(xDF, unknown=unkLN), xDFUnk)
-
-  ## with names list of multiple unknown values - must be an error
-  checkException(NAToUnknown(xListN, unknown=unkLMN))
-  checkException(NAToUnknown(xDF, unknown=unkLMN))
-
-  ## with single unknown value - recycling
-  checkIdentical(NAToUnknown(xList, unknown=unk1), xListUnk1)
-  checkIdentical(NAToUnknown(xDF,   unknown=unk1), xDFUnk1)
-
-  ## with vector of two unknown values - recycling
-  checkIdentical(NAToUnknown(xList, unknown=unkC2), xListUnk2)
-  checkIdentical(NAToUnknown(xDF,   unknown=unkC2), xDFUnk2)
-
-  ## with list of two unknown values - recycling
-  checkIdentical(NAToUnknown(xList, unknown=unkL2), xListUnk2)
-  checkIdentical(NAToUnknown(xDF,   unknown=unkL2), xDFUnk2)
-
-  ## with named list of two unknown values but x is not named so named list
-  ## does not have any effect --> error as we do not know how to recycle
-  checkException(NAToUnknown(xList, unknown=unkLN2))
-
-  ## but we should get some results with named x
-  checkIdentical(NAToUnknown(xListN, unknown=unkL2), xListNUnk2)
-  ## not also necesarilly with recycling of names lists, as it is
-  ## not clear how to properly recycle named lists (only names that match
-  ## can be really properly recycled)
-  checkException(NAToUnknown(xListN, unknown=unkLN2))
-  checkIdentical(NAToUnknown(xDF, unknown=unkL2), xDFUnk2)
-  checkException(NAToUnknown(xDF, unknown=unkLN2))
-
-  ## list(.default=)
-  checkIdentical(NAToUnknown(x=xList, unknown=unkLND1), xListUnkD1)
-  ## list(.default=, someOther=) we do not know someOther, but should work
-  ## as x is not named
-  checkIdentical(NAToUnknown(x=xList, unknown=unkLNDSO2), xListUnkDSO2)
-  ## list(.default=) in named list
-  checkIdentical(NAToUnknown(x=xListN, unknown=unkLND1), xListNUnkD1)
-  ## list(.default=, someOther=) OK if someOther is in the named list
-  checkIdentical(NAToUnknown(x=xListN, unknown=unkLND3), xListNUnkD3)
-  ## list(.default=, 99) ERROR as we do not know where to apply 99
-  checkException(NAToUnknown(x=xListN, unknown=unkLND2E))
-
-  ## --- matrix ---
-
-  checkEquals(NAToUnknown(x=mat, unknown=matUnk), matUnk1)
-}
-
-### }}}
-### {{{ Dear Emacs
-### Local variables:
-### folded-file: t
-### End:
-### }}}
-
-###------------------------------------------------------------------------
-### runit.unknown.R ends here

Deleted: trunk/gdata/inst/unitTests/runit.wideByFactor.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.wideByFactor.R	2014-04-05 00:14:24 UTC (rev 1781)
+++ trunk/gdata/inst/unitTests/runit.wideByFactor.R	2014-04-05 01:08:30 UTC (rev 1782)
@@ -1,55 +0,0 @@
-### runit.wideByFactor.R
-###------------------------------------------------------------------------
-### What: Reshape by factor levels - unit tests
-### $Id$
-### Time-stamp: <2008-12-30 11:58:50 ggorjan>
-###------------------------------------------------------------------------
-
-### {{{ --- Test setup ---
-
-if(FALSE) {
-  library("RUnit")
-  library("gdata")
-}
-
-### }}}
-### {{{ --- wideByFactor ---
-
-test.wideByFactor <- function()
-{
-  n <- 10
-  f <- 2
-  tmp <- data.frame(y1=(1:n)/2,
-                    y2=(n:1)*2,
-                    f1=factor(rep(letters[1:f], n/2)),
-                    f2=factor(c(rep(c("M"), n/2), rep(c("F"), n/2))),
-                    c1=1:n,
-                    c2=2*(1:n))
-  
-  ## 'x' must be a data.frame
-  checkException(wideByFactor(x=1:10))
-  checkException(wideByFactor(x=matrix(1:10)))
-  ## 'factor' can be only of length one
-  checkException(wideByFactor(x=tmp, factor=c("f1", "f2")))
-  ## column defined in 'factor' must be a factor
-  checkException(wideByFactor(x=tmp, factor="c1"))
-
-  tmp2 <- wideByFactor(x=tmp, factor="f1", common=c("c1", "c2"), sort=FALSE)
-  checkEquals(tmp2[c("c1", "c2")], tmp[c("c1", "c2")])
-  checkEquals(names(tmp2), c("c1", "c2", "f1", "y1.a", "y2.a", "f2.a", "y1.b", "y2.b", "f2.b"))
-  checkEquals(tmp2$y1.a, c(0.5, NA, 1.5, NA, 2.5, NA, 3.5, NA, 4.5, NA))
-  checkEquals(tmp2$f2.a, factor(c("M", NA, "M", NA, "M", NA, "F", NA, "F", NA)))
-  tmp2 <- wideByFactor(x=tmp, factor="f1", common=c("c1", "c2...
 
[truncated message content]

[R-gregmisc-users] SF.net SVN: r-gregmisc:[1781] trunk/gplots/inst/NEWS

[<wa...@us...>]

Revision: 1781
          http://sourceforge.net/p/r-gregmisc/code/1781
Author:   warnes
Date:     2014-04-05 00:14:24 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Update NEWS

Modified Paths:
--------------
    trunk/gplots/inst/NEWS

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2014-04-05 00:10:13 UTC (rev 1780)
+++ trunk/gplots/inst/NEWS	2014-04-05 00:14:24 UTC (rev 1781)
@@ -8,9 +8,12 @@
 
 Enhancements:
 
-- When the row or column trace is enabled, show the corresponding
-  reference line in the color key.
+- In heatmap.2, when the row or column trace is enabled, show the
+  corresponding reference line in the color key.
 
+- In heatmap.2, a new 'extrafun' argument is provided that allows the
+  user to specify a function to be called before the function returns.
+  This allows the user to add additional plots to the page.
 
 
 Release 2.12.1 - 2013-10-14

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1780] trunk/gplots

[<wa...@us...>]

Revision: 1780
          http://sourceforge.net/p/r-gregmisc/code/1780
Author:   warnes
Date:     2014-04-05 00:10:13 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Add 'extrafun' argument to heatmap.2 to allow the user to perform
additional customization by providing a function to be called before
heatmap.2 exits.

Modified Paths:
--------------
    trunk/gplots/R/heatmap.2.R
    trunk/gplots/man/heatmap.2.Rd

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2014-04-04 22:37:12 UTC (rev 1779)
+++ trunk/gplots/R/heatmap.2.R	2014-04-05 00:10:13 UTC (rev 1780)
@@ -78,6 +78,7 @@
                        lwid = NULL,
 
                        ## extras
+                       extrafun=NULL,
                        ...
                        )
 {
@@ -641,9 +642,6 @@
                   }
           }
 
-
-
-
     }
   else
     plot.new()
@@ -655,6 +653,9 @@
                              color=retval$col
                              )
 
+  ## If user has provided an extra function, call it.
+  if(!is.null(extrafun))
+      extrafun()
 
   invisible( retval )
 }

Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd	2014-04-04 22:37:12 UTC (rev 1779)
+++ trunk/gplots/man/heatmap.2.Rd	2014-04-05 00:10:13 UTC (rev 1780)
@@ -3,7 +3,7 @@
 \title{ Enhanced Heat Map }
 \description{
   A heat map is a false color image (basically
-  \code{\link{image}(t(x))}) with a dendrogram added to the left side 
+  \code{\link{image}(t(x))}) with a dendrogram added to the left side
   and/or to the top.  Typically, reordering of the rows and columns
   according to some set of values (row or column means) within the
   restrictions imposed by the dendrogram is carried out.
@@ -90,6 +90,7 @@
            lwid = NULL,
 
            # extras
+           extrafun=NULL,
            ...
            )
            }
@@ -112,7 +113,7 @@
   \item{hclustfun}{function used to compute the hierarchical clustering
     when \code{Rowv} or \code{Colv} are not dendrograms.  Defaults to
     \code{\link{hclust}}.}
-  \item{dendrogram}{character string indicating whether to draw 'none', 
+  \item{dendrogram}{character string indicating whether to draw 'none',
     'row', 'column' or 'both' dendrograms.  Defaults to 'both'. However,
   if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a
   warning is issued and Rowv (or Colv) arguments are honoured.}
@@ -182,12 +183,12 @@
     for the row or column axis labeling.  The defaults currently only
     use number of rows or columns, respectively.}
   \item{labRow, labCol}{character vectors with row and column labels to
-    use; these default to \code{rownames(x)} or \code{colnames(x)}, 
+    use; these default to \code{rownames(x)} or \code{colnames(x)},
     respectively.}
   \item{srtRow, srtCol}{angle of row/column labels, in degrees from horizontal}
   \item{adjRow, adjCol}{2-element vector giving the (left-right,
     top-bottom) justification of row/column labels (relative to the text
-           orientation).} 
+           orientation).}
   \item{offsetRow, offsetCol}{Number of character-width spaces to place
            between row/column labels and the edge of the plotting region.}
   % Color key and density info
@@ -211,7 +212,9 @@
   % figure layout
   \item{lmat, lhei, lwid}{visual layout: position matrix, column height,
     column width.  See below for details}
-  \item{...}{additional arguments passed on to \code{\link{image}} } %
+  \item{extrafun}{A function to be called after all other work. See
+    examples.}
+  \item{...}{additional arguments passed on to \code{\link{image}} }
 }
 \details{
   If either \code{Rowv} or \code{Colv} are dendrograms they are honored
@@ -221,11 +224,11 @@
 
   If either is a vector (of \dQuote{weights}) then the appropriate
   dendrogram is reordered according to the supplied values subject to
-  the constraints imposed by the dendrogram, by \code{\link{reorder}(dd, 
+  the constraints imposed by the dendrogram, by \code{\link{reorder}(dd,
     Rowv)}, in the row case.
   %%
   If either is missing, as by default, then the ordering of the
-  corresponding dendrogram is by the mean value of the rows/columns, 
+  corresponding dendrogram is by the mean value of the rows/columns,
   i.e., in the case of rows, \code{Rowv <- rowMeans(x, na.rm=na.rm)}.
   %%
   If either is \code{\link{NULL}}, \emph{no reordering} will be done for
@@ -237,7 +240,7 @@
 
   The default colors range from red to white (\code{heat.colors}) and
   are not pretty.  Consider using enhancements such
-  as the \pkg{RColorBrewer} package, 
+  as the \pkg{RColorBrewer} package,
   \url{http://cran.r-project.org/src/contrib/PACKAGES.html#RColorBrewer}
   to select better colors.
 
@@ -286,9 +289,9 @@
   \item{hline}{center-line value used for row trace, present only if
     \code{trace="both"} or \code{trace="row"} }
   \item{colorTable}{A three-column data frame providing the lower and upper
-    bound and color for each bin} 
+    bound and color for each bin}
 }
-\author{Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber, 
+\author{Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber,
   G. Warnes, revisions.}
 
 \seealso{\code{\link{image}}, \code{\link{hclust}}}
@@ -303,7 +306,7 @@
  ##
  ## demonstrate the effect of row and column dendogram options
  ##
- heatmap.2(x)  ## default - dendrogram plotted and reordering done. 
+ heatmap.2(x)  ## default - dendrogram plotted and reordering done.
  heatmap.2(x, dendrogram="none") ##  no dendrogram plotted, but reordering done.
  heatmap.2(x, dendrogram="row") ## row dendrogram plotted and row reordering done.
  heatmap.2(x, dendrogram="col") ## col dendrogram plotted and col reordering done.
@@ -341,7 +344,21 @@
  heatmap.2(x, srtRow=0, srtCol=90, offsetRow=2, offsetCol=2)
  heatmap.2(x, srtRow=0, srtCol=90, offsetRow=-1, offsetCol=-1)
 
- ## 
+ ## Show how to use 'extrafun' to replace the 'key' with a scatterplot
+ lmat <- rbind( c(5,3,4), c(2,1,4) )
+ lhei <- c(1.5, 4)
+ lwid <- c(1.5, 4, 0.75)
+
+ myplot <- function() {
+             oldpar <- par("mar")
+             par(mar=c(5.1, 4.1, 0.5, 0.5))
+             plot(mpg ~ hp, data=x)
+           }
+
+ heatmap.2(x, lmat=lmat, lhei=lhei, lwid=lwid, key=FALSE, extrafun=myplot)
+
+
+ ##
  ## Show effect of z-score scaling within columns, blue-red color scale
  ##
  hv <- heatmap.2(x, col=bluered, scale="column", tracecol="#303030")
@@ -364,18 +381,18 @@
  ##
  ## A more decorative heatmap, with z-score scaling along columns
  ##
- hv <- heatmap.2(x, col=cm.colors(255), scale="column", 
-	       RowSideColors=rc, ColSideColors=cc, margin=c(5, 10), 
-	       xlab="specification variables", ylab= "Car Models", 
-	       main="heatmap(<Mtcars data>, ..., scale=\"column\")", 
+ hv <- heatmap.2(x, col=cm.colors(255), scale="column",
+	       RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
+	       xlab="specification variables", ylab= "Car Models",
+	       main="heatmap(<Mtcars data>, ..., scale=\"column\")",
                tracecol="green", density="density")
  ## Note that the breakpoints are now symmetric about 0
 
 
- 
 
 
 
+
 %% want example using the `add.exp' argument!
 
  data(attitude)
@@ -398,7 +415,7 @@
  data(USJudgeRatings)
  symnum( cU <- cor(USJudgeRatings) )
 
- hU <- heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=topo.colors(16), 
+ hU <- heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=topo.colors(16),
               distfun=function(c) as.dist(1 - c), trace="none")
 
  ## The Correlation matrix with same reordering:
@@ -407,8 +424,8 @@
 
  # now with the correlation matrix on the plot itself
 
- heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=rev(heat.colors(16)), 
-             distfun=function(c) as.dist(1 - c), trace="none", 
+ heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=rev(heat.colors(16)),
+             distfun=function(c) as.dist(1 - c), trace="none",
              cellnote=hM)
 
  ## genechip data examples
@@ -418,15 +435,15 @@
  pms <- SpikeIn@pm
 
  # just the data, scaled across rows
- heatmap.2(pms, col=rev(heat.colors(16)), main="SpikeIn@pm", 
-              xlab="Relative Concentration", ylab="Probeset", 
+ heatmap.2(pms, col=rev(heat.colors(16)), main="SpikeIn@pm",
+              xlab="Relative Concentration", ylab="Probeset",
               scale="row")
 
  # fold change vs "12.50" sample
  data <- pms / pms[, "12.50"]
  data <- ifelse(data>1, data, -1/data)
- heatmap.2(data, breaks=16, col=redgreen, tracecol="blue", 
-               main="SpikeIn@pm Fold Changes\nrelative to 12.50 sample", 
+ heatmap.2(data, breaks=16, col=redgreen, tracecol="blue",
+               main="SpikeIn@pm Fold Changes\nrelative to 12.50 sample",
                xlab="Relative Concentration", ylab="Probeset")
  }
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1779] trunk/gplots

[<wa...@us...>]

Revision: 1779
          http://sourceforge.net/p/r-gregmisc/code/1779
Author:   warnes
Date:     2014-04-04 22:37:12 +0000 (Fri, 04 Apr 2014)
Log Message:
-----------
Update for gplots 2.13.0

Modified Paths:
--------------
    trunk/gplots/DESCRIPTION
    trunk/gplots/inst/NEWS

Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION	2014-04-04 21:32:51 UTC (rev 1778)
+++ trunk/gplots/DESCRIPTION	2014-04-04 22:37:12 UTC (rev 1779)
@@ -4,12 +4,12 @@
 Depends: R (>= 3.0)
 Imports: gtools, gdata, stats, caTools, KernSmooth
 Suggests: grid, MASS
-Version: 2.12.1
-Date: 2013-10-14
+Version: 2.13.0
+Date: 2014-04-04
 Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
 	Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
 	Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
-	Venables 
+	Venables
 Maintainer: Gregory R. Warnes <gr...@wa...>
 License: GPL-2
 NeedsCompilation: No

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2014-04-04 21:32:51 UTC (rev 1778)
+++ trunk/gplots/inst/NEWS	2014-04-04 22:37:12 UTC (rev 1779)
@@ -1,3 +1,18 @@
+Release 2.13.0 - 2014-04-04
+---------------------------
+
+Bug Fixes:
+
+- heatmap.2 was not properly handling row trace reference line ('hline').
+  Patch submitted by Ilia Kats.
+
+Enhancements:
+
+- When the row or column trace is enabled, show the corresponding
+  reference line in the color key.
+
+
+
 Release 2.12.1 - 2013-10-14
 ---------------------------
 
@@ -23,7 +38,7 @@
   finite values.
 
 Other Changes:
- 
+
 - Changes to overplot() to avoid warnings from upcoming enhancements to R CMD check.
 
 - Move several packages from Depends to Imports or Suggests.

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1778] trunk/gplots/R/heatmap.2.R

[<wa...@us...>]

Revision: 1778
          http://sourceforge.net/p/r-gregmisc/code/1778
Author:   warnes
Date:     2014-04-04 21:32:51 +0000 (Fri, 04 Apr 2014)
Log Message:
-----------
Fix handling of row trace (hline).  Bug report and patch provided by Ilia Kats.

Modified Paths:
--------------
    trunk/gplots/R/heatmap.2.R

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2014-03-19 10:04:49 UTC (rev 1777)
+++ trunk/gplots/R/heatmap.2.R	2014-04-04 21:32:51 UTC (rev 1778)
@@ -86,9 +86,9 @@
       x <- (x-low)/(high - low)
       x
     }
-  
+
   retval <- list()
-  
+
   scale <- if(symm && missing(scale)) "none" else match.arg(scale)
   dendrogram <- match.arg(dendrogram)
   trace <- match.arg(trace)
@@ -115,8 +115,8 @@
     Colv <- FALSE
   else if( Colv=="Rowv" && !isTRUE(Rowv) )
     Colv <- FALSE
-  
-  
+
+
   if(length(di <- dim(x)) != 2 || !is.numeric(x))
     stop("`x' must be a numeric matrix")
 
@@ -141,10 +141,10 @@
           dendrogram <- "column"
         else
           dedrogram <- "none"
-        
+
         warning("Discrepancy: Rowv is FALSE, while dendrogram is `",
                 dendrogram, "'. Omitting row dendogram.")
-        
+
       }
   }
 
@@ -157,13 +157,13 @@
           dendrogram <- "row"
         else
           dendrogram <- "none"
-        
+
         warning("Discrepancy: Colv is FALSE, while dendrogram is `",
                 dendrogram, "'. Omitting column dendogram.")
       }
   }
-  
-  
+
+
   ## by default order by row/col mean
   ## if(is.null(Rowv)) Rowv <- rowMeans(x, na.rm = na.rm)
   ## if(is.null(Colv)) Colv <- colMeans(x, na.rm = na.rm)
@@ -175,32 +175,32 @@
   if(inherits(Rowv, "dendrogram"))
     {
       ddr <- Rowv ## use Rowv 'as-is', when it is dendrogram
-      rowInd <- order.dendrogram(ddr)      
+      rowInd <- order.dendrogram(ddr)
     }
   else if (is.integer(Rowv))
     { ## Compute dendrogram and do reordering based on given vector
       hcr <- hclustfun(distfun(x))
       ddr <- as.dendrogram(hcr)
       ddr <-  reorder(ddr, Rowv)
-      
+
       rowInd <- order.dendrogram(ddr)
       if(nr != length(rowInd))
         stop("row dendrogram ordering gave index of wrong length")
     }
-  else if (isTRUE(Rowv)) 
+  else if (isTRUE(Rowv))
     { ## If TRUE, compute dendrogram and do reordering based on rowMeans
       Rowv <- rowMeans(x, na.rm = na.rm)
       hcr <- hclustfun(distfun(x))
       ddr <- as.dendrogram(hcr)
       ddr <- reorder(ddr, Rowv)
-      
+
       rowInd <- order.dendrogram(ddr)
       if(nr != length(rowInd))
         stop("row dendrogram ordering gave index of wrong length")
     } else {
       rowInd <- nr:1
     }
-  
+
   ## if( dendrogram %in% c("both","column") )
   ##   {
   if(inherits(Colv, "dendrogram"))
@@ -247,7 +247,7 @@
   retval$colInd <- colInd
   retval$call <- match.call()
 
-  
+
   ## reorder x & cellnote
   x <- x[rowInd, colInd]
   x.unscaled <- x
@@ -281,10 +281,10 @@
     {
       if( missing(col) ||  is.function(col) )
         breaks <- 16
-      else 
+      else
         breaks <- length(col)+1
     }
-  
+
   if(length(breaks)==1)
     {
       if(!symbreaks)
@@ -308,7 +308,7 @@
   x[x<min.breaks] <- min.breaks
   x[x>max.breaks] <- max.breaks
 
-  
+
   ## Calculate the plot layout
   if( missing(lhei) || is.null(lhei) )
     lhei <- c(keysize, 4)
@@ -319,7 +319,7 @@
   if( missing(lmat) || is.null(lmat) )
     {
       lmat <- rbind(4:3, 2:1)
-      
+
       if(!missing(ColSideColors)) { ## add middle row to layout
         if(!is.character(ColSideColors) || length(ColSideColors) != nc)
           stop("'ColSideColors' must be a character vector of length ncol(x)")
@@ -336,7 +336,7 @@
 
       lmat[is.na(lmat)] <- 0
     }
-  
+
   if(length(lhei) != nrow(lmat))
     stop("lhei must have length = nrow(lmat) = ", nrow(lmat))
 
@@ -386,7 +386,7 @@
     retval$colDendrogram <- ddc
   retval$breaks <- breaks
   retval$col <- col
-  
+
   ## fill 'na' positions with na.color
   if(!invalid(na.color) & any(is.na(x)))
     {
@@ -421,7 +421,7 @@
                y=par("usr")[3] - (1.0 + offsetCol) * strheight("M"),
                labels=labCol,
                ##pos=1,
-               adj=adjCol, 
+               adj=adjCol,
                cex=cexCol,
                srt=srtCol)
           par(xpd=xpd.orig)
@@ -487,7 +487,7 @@
            xright=nrow(x)+1,  ytop   = (ncol(x)+1-rsep)-0.5 - sepwidth[2],
            lty=1, lwd=1, col=sepcolor, border=sepcolor)
 
-  
+
   ## show traces
   min.scale <- min(breaks)
   max.scale <- max(breaks)
@@ -510,7 +510,7 @@
         }
     }
 
-  
+
   if(trace %in% c("both","row") )
     {
       retval$hline <- hline
@@ -519,7 +519,7 @@
         {
           if(!is.null(hline))
             {
-              abline(h=i + hline, col=linecol, lty=2)
+              abline(h=i - 0.5 + hline.vals, col=linecol, lty=2)
             }
           yv <- rep(i, ncol(x.scaled)) + x.scaled[i,] - 0.5
           yv <- rev(c(yv[1], yv))
@@ -573,7 +573,7 @@
         }
       else
         {
-          min.raw <- min(x, na.rm=TRUE) ## Again, modified to use scaled 
+          min.raw <- min(x, na.rm=TRUE) ## Again, modified to use scaled
           max.raw <- max(x, na.rm=TRUE) ## or unscaled (SD 12/2/03)
         }
 
@@ -595,12 +595,11 @@
 
       if(density.info=="density")
         {
-          ## Experimental : also plot density of data
           dens <- density(x, adjust=densadj, na.rm=TRUE)
           omit <- dens$x < min(breaks) | dens$x > max(breaks)
           dens$x <- dens$x[-omit]
           dens$y <- dens$y[-omit]
-          dens$x <- scale01(dens$x,min.raw,max.raw)
+          dens$x <- scale01(dens$x, min.raw, max.raw)
           lines(dens$x, dens$y / max(dens$y) * 0.95, col=denscol, lwd=1)
           axis(2, at=pretty(dens$y)/max(dens$y) * 0.95, pretty(dens$y) )
           title("Color Key\nand Density Plot")
@@ -610,7 +609,7 @@
       else if(density.info=="histogram")
         {
           h <- hist(x, plot=FALSE, breaks=breaks)
-          hx <- scale01(breaks,min.raw,max.raw)
+          hx <- scale01(breaks, min.raw, max.raw)
           hy <- c(h$counts, h$counts[length(h$counts)])
           lines(hx, hy/max(hy)*0.95, lwd=1, type="s", col=denscol)
           axis(2, at=pretty(hy)/max(hy) * 0.95, pretty(hy) )
@@ -621,6 +620,30 @@
       else
         title("Color Key")
 
+
+      if(trace %in% c("both","column") )
+          {
+              vline.vals <- scale01(vline, min.raw, max.raw)
+              if(!is.null(vline))
+                  {
+                      abline(v=vline.vals, col=linecol, lty=2)
+                  }
+          }
+
+
+      if(trace %in% c("both","row") )
+          {
+              hline.vals <- scale01(hline, min.raw, max.raw)
+              if(!is.null(hline))
+                  {
+                      abline(v=hline.vals, col=linecol, lty=2)
+
+                  }
+          }
+
+
+
+
     }
   else
     plot.new()
@@ -630,8 +653,8 @@
                              low=retval$breaks[-length(retval$breaks)],
                              high=retval$breaks[-1],
                              color=retval$col
-                             ) 
+                             )
 
-  
+
   invisible( retval )
 }

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1777] trunk/gdata/R/keep.R

[<ar...@us...>]

Revision: 1777
          http://sourceforge.net/p/r-gregmisc/code/1777
Author:   arnima
Date:     2014-03-19 10:04:49 +0000 (Wed, 19 Mar 2014)
Log Message:
-----------
change warning message to R standards

Modified Paths:
--------------
    trunk/gdata/R/keep.R

Modified: trunk/gdata/R/keep.R
===================================================================
--- trunk/gdata/R/keep.R	2014-03-01 20:15:05 UTC (rev 1776)
+++ trunk/gdata/R/keep.R	2014-03-19 10:04:49 UTC (rev 1777)
@@ -2,8 +2,8 @@
 {
   if(missing(...) && missing(list))
   {
-    warning("Keep something, or use rm(list=ls()) to clear workspace. ",
-            "Nothing was removed.")
+    warning("keep something, or use rm(list=ls()) to clear workspace - ",
+            "nothing was removed")
     return(invisible(NULL))
   }
   names <- as.character(substitute(list(...)))[-1]
@@ -11,8 +11,8 @@
   keep.elements <- match(list, ls(1,all.names=all))
   if(any(is.na(keep.elements)))
   {
-    warning("You tried to keep \"", list[which(is.na(keep.elements))[1]],
-            "\" which doesn't exist in workspace. Nothing was removed.", sep="")
+    warning("you tried to keep \"", list[which(is.na(keep.elements))[1]],
+            "\" which doesn't exist in workspace - nothing was removed", sep="")
     return(invisible(NULL))
   }
 

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