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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1484] trunk/fork/DESCRIPTION

From: <wa...@us...> - 2011-08-26 23:35:16

Revision: 1484
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1484&view=rev
Author:   warnes
Date:     2011-08-26 23:35:07 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Update Greg's email address.

Modified Paths:
--------------
    trunk/fork/DESCRIPTION

Modified: trunk/fork/DESCRIPTION
===================================================================
--- trunk/fork/DESCRIPTION	2011-08-26 23:28:17 UTC (rev 1483)
+++ trunk/fork/DESCRIPTION	2011-08-26 23:35:07 UTC (rev 1484)
@@ -1,14 +1,13 @@
 Package: fork
 Title: R functions for handling multiple processes.
-Version: 1.2.3
-Date: 2009-07-17
+Version: 1.2.4
+Date: 2011-08-26
 Author: Gregory R. Warnes <gr...@ra...>. Financial 
   support for some aspects of this package provided by Metrum Research Group, 
   LLC <http://www.metrumrg.com>.
 Description: These functions  provides simple wrappers around the Unix process 
     management API calls: fork, signal, wait, waitpid, kill, and _exit.  This
     enables construction of programs that utilize and mange multiple concurrent
-    processes.  Commercial support for this package available from 
-    Random Technologies, LLC <http://www.random-technologies-llc.com>
-Maintainer: Gregory R. Warnes <gr...@ra...>
+    processes.
+Maintainer: Gregory R. Warnes <gr...@wa...>
 License: GPL-2

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1483] trunk/gregmisc/R/First.R

From: <wa...@us...> - 2011-08-26 23:28:23

Revision: 1483
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1483&view=rev
Author:   warnes
Date:     2011-08-26 23:28:17 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Use packageStartupMessage() instead of warning() to display a startup message on package load.

Modified Paths:
--------------
    trunk/gregmisc/R/First.R

Modified: trunk/gregmisc/R/First.R
===================================================================
--- trunk/gregmisc/R/First.R	2011-08-26 20:48:15 UTC (rev 1482)
+++ trunk/gregmisc/R/First.R	2011-08-26 23:28:17 UTC (rev 1483)
@@ -2,13 +2,10 @@
 
 .First.lib <- function(libname, pkgname)
 {
-  library(gdata)
-  library(gplots)
-  library(gmodels)
-  library(gtools)
-  warning(paste("",
-          "The `gregmisc' *package* has converted into a *bundle*",
-          "containing four sub-packages: gdata, gtools, gmodels, and gplots.", 
-          "Please load these packages directly.", sep="\n\t"), 
-          call.=FALSE)
+  packageStartupMessage(
+          "All functionality of the `gregmisc' package has been moved",
+          "into the four 'g' packages: gdata, gtools, gmodels, and gplots. ",
+          "This package is retained to make it easy to install and load",
+          "the set. Please consider loading these packages directly."
+                        )
 }

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1482] trunk/fork/man

From: <wa...@us...> - 2011-08-26 20:48:23

Revision: 1482
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1482&view=rev
Author:   warnes
Date:     2011-08-26 20:48:15 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Update Greg's email address

Modified Paths:
--------------
    trunk/fork/man/exit.Rd
    trunk/fork/man/fork.Rd
    trunk/fork/man/getpid.Rd
    trunk/fork/man/handleSIGCLD.Rd
    trunk/fork/man/kill.Rd
    trunk/fork/man/signal.Rd
    trunk/fork/man/signame.Rd
    trunk/fork/man/wait.Rd

Modified: trunk/fork/man/exit.Rd
===================================================================
--- trunk/fork/man/exit.Rd	2011-08-26 20:45:32 UTC (rev 1481)
+++ trunk/fork/man/exit.Rd	2011-08-26 20:48:15 UTC (rev 1482)
@@ -25,7 +25,7 @@
   argument, so it is usually not necessary to directly call exit().
   }
 \references{"\_exit" man page}
-\author{ Gregory R. Warnes \email{gr...@ra...}}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
 \seealso{\code{\link{fork}}, \code{\link{getpid}}, \code{\link{wait}},
          \code{\link{kill}}, \code{\link{killall}} }
 \examples{

Modified: trunk/fork/man/fork.Rd
===================================================================
--- trunk/fork/man/fork.Rd	2011-08-26 20:45:32 UTC (rev 1481)
+++ trunk/fork/man/fork.Rd	2011-08-26 20:48:15 UTC (rev 1482)
@@ -88,7 +88,7 @@
    function returns 0 to the  child  process.
 }
 \references{'fork' man page}
-\author{ Gregory R. Warnes \email{gr...@ra...}}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
 \seealso{\code{\link{getpid}}, \code{\link{exit}}, \code{\link{wait}},
          \code{\link{kill}}, \code{\link{killall}} }
 \examples{

Modified: trunk/fork/man/getpid.Rd
===================================================================
--- trunk/fork/man/getpid.Rd	2011-08-26 20:45:32 UTC (rev 1481)
+++ trunk/fork/man/getpid.Rd	2011-08-26 20:48:15 UTC (rev 1482)
@@ -15,7 +15,7 @@
   Integer process id.
 }
 \references{Unix "getpid" man page}
-\author{ Gregory R. Warnes \email{gr...@ra...}}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
 \seealso{\code{\link{fork}}, \code{\link{exit}}, \code{\link{wait}},
          \code{\link{kill}}, \code{\link{killall}} }
 \examples{

Modified: trunk/fork/man/handleSIGCLD.Rd
===================================================================
--- trunk/fork/man/handleSIGCLD.Rd	2011-08-26 20:45:32 UTC (rev 1481)
+++ trunk/fork/man/handleSIGCLD.Rd	2011-08-26 20:48:15 UTC (rev 1482)
@@ -30,7 +30,7 @@
   }
 \references{W.R. Stevens and S.A. Rago, Advanced Programming in the UNIX
   environment, 2nd ed. (c) 2005, Pearson Education, pp 308-310.}
-\author{Gregory R. Warnes \email{gr...@ra...},
+\author{Gregory R. Warnes \email{gr...@wa...},
   with financial support from Metrum Research Group, LLC
   \url{http://www.metrumrg.com}.
 }

Modified: trunk/fork/man/kill.Rd
===================================================================
--- trunk/fork/man/kill.Rd	2011-08-26 20:45:32 UTC (rev 1481)
+++ trunk/fork/man/kill.Rd	2011-08-26 20:48:15 UTC (rev 1482)
@@ -28,7 +28,7 @@
   \code{killall} does not return a value.
 }
 \references{"kill" and "waitpid"  man pages}
-\author{ Gregory R. Warnes \email{gr...@ra...}}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
 \seealso{\code{\link{getpid}}, \code{\link{exit}}, \code{\link{wait}},
          \code{\link{kill}}, \code{\link{killall}} }
 \examples{

Modified: trunk/fork/man/signal.Rd
===================================================================
--- trunk/fork/man/signal.Rd	2011-08-26 20:45:32 UTC (rev 1481)
+++ trunk/fork/man/signal.Rd	2011-08-26 20:48:15 UTC (rev 1482)
@@ -22,7 +22,7 @@
   Nothing of interest.
 }
 \references{ See the unix man page for "signal" for more information}
-\author{Gregory R. Warnes \email{gr...@ra...},
+\author{Gregory R. Warnes \email{gr...@wa...},
   with financial support from Metrum Research Group, LLC
   \url{http://www.metrumrg.com}.
 }

Modified: trunk/fork/man/signame.Rd
===================================================================
--- trunk/fork/man/signame.Rd	2011-08-26 20:45:32 UTC (rev 1481)
+++ trunk/fork/man/signame.Rd	2011-08-26 20:48:15 UTC (rev 1482)
@@ -29,7 +29,7 @@
   \item{desc}{Description}
 }
 \references{Unix "signal" man page.}
-\author{ Gregory R. Warnes \email{gr...@ra...}}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
 \seealso{\code{\link{getpid}}, \code{\link{exit}}, \code{\link{wait}},
          \code{\link{kill}}, \code{\link{killall}} }
 \examples{

Modified: trunk/fork/man/wait.Rd
===================================================================
--- trunk/fork/man/wait.Rd	2011-08-26 20:45:32 UTC (rev 1481)
+++ trunk/fork/man/wait.Rd	2011-08-26 20:48:15 UTC (rev 1482)
@@ -34,7 +34,7 @@
   and the meanings of the status indicator.
 }
 \references{"wait" and "waitpid"  man pages}
-\author{ Gregory R. Warnes \email{gr...@ra...}}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
 \seealso{\code{\link{fork}}, \code{\link{exit}}, \code{\link{getpid}},
          \code{\link{kill}}, \code{\link{killall}}}
 \examples{

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1481] trunk/SII/man/SII-package.Rd

From: <wa...@us...> - 2011-08-26 20:45:38

Revision: 1481
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1481&view=rev
Author:   warnes
Date:     2011-08-26 20:45:32 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Update Greg's email address

Modified Paths:
--------------
    trunk/SII/man/SII-package.Rd

Modified: trunk/SII/man/SII-package.Rd
===================================================================
--- trunk/SII/man/SII-package.Rd	2011-08-26 20:44:35 UTC (rev 1480)
+++ trunk/SII/man/SII-package.Rd	2011-08-26 20:45:32 UTC (rev 1481)
@@ -19,7 +19,7 @@
    required frequencies.
 }
 \author{
-  Gregory R. Warnes \email{su...@ra...}
+  Gregory R. Warnes \email{gr...@wa...}
 }
 \references{
 ANSI S3.5-1997, "American National Standard Methods for 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1480] trunk/SII/DESCRIPTION

From: <wa...@us...> - 2011-08-26 20:44:41

Revision: 1480
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1480&view=rev
Author:   warnes
Date:     2011-08-26 20:44:35 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Update Greg's email address

Modified Paths:
--------------
    trunk/SII/DESCRIPTION

Modified: trunk/SII/DESCRIPTION
===================================================================
--- trunk/SII/DESCRIPTION	2011-08-26 20:41:56 UTC (rev 1479)
+++ trunk/SII/DESCRIPTION	2011-08-26 20:44:35 UTC (rev 1480)
@@ -1,10 +1,10 @@
 Package: SII
 Type: Package
 Title: Calculate ANSI S3.5-1997 Speech Intelligibility Index
-Version: 1.0.0
-Date: 2010-07-22
+Version: 1.0.1
+Date: 2011-08-26
 Author: Gregory R. Warnes
-Maintainer: Gregory R. Warnes <su...@ra...>
+Maintainer: Gregory R. Warnes <gr...@wa...>
 Description: 
    This package calculates ANSI S3.5-1997 Speech Intelligibility Index
    (SII), a standard method for computing the intelligibility of

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1479] trunk/gregmisc/DESCRIPTION

From: <wa...@us...> - 2011-08-26 20:42:04

Revision: 1479
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1479&view=rev
Author:   warnes
Date:     2011-08-26 20:41:56 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Update Greg's email address

Modified Paths:
--------------
    trunk/gregmisc/DESCRIPTION

Modified: trunk/gregmisc/DESCRIPTION
===================================================================
--- trunk/gregmisc/DESCRIPTION	2011-08-26 20:38:12 UTC (rev 1478)
+++ trunk/gregmisc/DESCRIPTION	2011-08-26 20:41:56 UTC (rev 1479)
@@ -9,7 +9,7 @@
              way to access the original combined functionality.  To this
              end, it simply depends on all of the new packages so that 
              these will installed/loaded when this package is installed/loaded.
-Version: 2.1.1
+Version: 2.1.2
 Author: Gregory R. Warnes.
-Maintainer: Gregory R. Warnes <wa...@bs...>
+Maintainer: Gregory R. Warnes <gr...@wa...>
 License: GPL-2

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1478] trunk/gplots/inst/NEWS

From: <wa...@us...> - 2011-08-26 20:38:19

Revision: 1478
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1478&view=rev
Author:   warnes
Date:     2011-08-26 20:38:12 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Update NEWS for 2.10.0 release

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

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2011-08-26 20:29:58 UTC (rev 1477)
+++ trunk/gplots/inst/NEWS	2011-08-26 20:38:12 UTC (rev 1478)
@@ -1,3 +1,25 @@
+Release 2.10.0 - 2011-08-26
+---------------------------
+
+New Features:
+
+- New ci2d() function to create 2-dimensional empirical confidence
+  intervals utilizing hist2d().  See ?ci2d for details.
+
+- Add 'alpha' argument to rich.colors() to control transparency.
+
+Improvements:
+
+- Accellerate hist2d by replacing for() loop with tapply(), and allow
+  user to specify summary function applied (per suggestion by Peter
+  Hagedorn).
+
+Bug Fixes:
+
+- Correct error in heatmap.2() that arises when data includes NA values
+  (identified by Melissa Key).
+
+
 Release 2.8.0 - 2010-06-10
 --------------------------
 
@@ -15,7 +37,7 @@
 
 Improvements:
 
-- Performance of 'hist2d' improved thanks to a suggestion from i
+- Performance of 'hist2d' improved thanks to a suggestion from 
   Joerg van den Hoff.
 
 Release 2.7.4 - 2009-11-12

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1477] trunk/gplots/DESCRIPTION

From: <wa...@us...> - 2011-08-26 20:30:04

Revision: 1477
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1477&view=rev
Author:   warnes
Date:     2011-08-26 20:29:58 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Add dependency on R>= 2.10 to handle compressed Rda data file.

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

Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION	2011-08-26 13:45:26 UTC (rev 1476)
+++ trunk/gplots/DESCRIPTION	2011-08-26 20:29:58 UTC (rev 1477)
@@ -3,6 +3,7 @@
 Description: Various R programming tools for plotting data
 Depends: gtools, gdata, stats, caTools, grid
 Recommends: datasets, grid, MASS
+Requires: R (>= 2.10)
 Suggests: gtools
 Version: 2.9.0
 Date: 2011-08-15

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1476] trunk/gplots/data/rtPCR.rda

From: <wa...@us...> - 2011-08-26 13:45:34

Revision: 1476
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1476&view=rev
Author:   warnes
Date:     2011-08-26 13:45:26 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Compress rtPCR example data set to make distributed package smaller.

Modified Paths:
--------------
    trunk/gplots/data/rtPCR.rda

Modified: trunk/gplots/data/rtPCR.rda
===================================================================
(Binary files differ)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1475] trunk/gplots/R/ci2d.R

From: <wa...@us...> - 2011-08-26 13:39:37

Revision: 1475
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1475&view=rev
Author:   warnes
Date:     2011-08-26 13:39:31 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Remove '1.0' confidence line from ci2d(..,show="contour").

Modified Paths:
--------------
    trunk/gplots/R/ci2d.R

Modified: trunk/gplots/R/ci2d.R
===================================================================
--- trunk/gplots/R/ci2d.R	2011-08-25 03:10:05 UTC (rev 1474)
+++ trunk/gplots/R/ci2d.R	2011-08-26 13:39:31 UTC (rev 1475)
@@ -38,27 +38,41 @@
     h2d$density <- h2d$counts / sum(h2d$counts, na.rm=TRUE)
 
     uniqueVals <- rev(unique(sort(h2d$density)))
-    cumProbs <- sapply( uniqueVals, function(val) sum( h2d$density[h2d$density>=val] ) )
+    cumProbs <- sapply(uniqueVals,
+                       function(val) sum( h2d$density[h2d$density>=val] ) )
     names(cumProbs) <- uniqueVals
     h2d$cumDensity <- matrix(nrow=nrow(h2d$density), ncol=ncol(h2d$density))
     h2d$cumDensity[] <- cumProbs[as.character(h2d$density)]
 
     if(show=="image")
       {
-        image( h2d$x, h2d$y, h2d$cumDensity, xlab=xlab, ylab=ylab, breaks=breaks, col=col)
+        image(h2d$x, h2d$y, h2d$cumDensity,
+              xlab=xlab, ylab=ylab,
+              breaks=breaks, col=col)
       }
     else if(show=="filled.contour")
       {
         filled.contour(h2d$x, h2d$y, h2d$cumDensity,
                        levels=breaks,
                        col=col,
-                       key.axes={axis(4, at=breaks); title("\nCI Level")}
+                       key.axes={ axis(4, at=breaks);
+                                  title("\nCI Level") }
                        )
        }
     else if(show=="contour")
-        contour(h2d$x, h2d$y, h2d$cumDensity, levels=breaks, nlevels=length(breaks))
+      {
+        tmpBreaks <- breaks[breaks<1]  # avoid having 1.0 line
+        contour(h2d$x, h2d$y, h2d$cumDensity,
+                levels=tmpBreaks,
+                labels=tmpBreaks,
+                nlevels=length(tmpBreaks),
+                col=col
+                )
+      }
+    
 
-    h2d$contours <- contourLines(h2d$x, h2d$y, h2d$cumDensity, levels=breaks, nlevels=length(breaks))
+    h2d$contours <- contourLines(h2d$x, h2d$y, h2d$cumDensity,
+                                 levels=breaks, nlevels=length(breaks))
     names
     invisible(h2d)
   }

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1474] trunk/gplots

From: <wa...@us...> - 2011-08-25 03:10:11

Revision: 1474
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1474&view=rev
Author:   warnes
Date:     2011-08-25 03:10:05 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
- Add 'ci2d()' to compute 2-dimensional emipirical confidence interval. 
- Fix parse error in help page for 'rich.colors()'.

Modified Paths:
--------------
    trunk/gplots/DESCRIPTION
    trunk/gplots/NAMESPACE
    trunk/gplots/man/rich.colors.Rd

Added Paths:
-----------
    trunk/gplots/R/ci2d.R
    trunk/gplots/man/ci2d.Rd

Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION	2011-08-16 01:17:20 UTC (rev 1473)
+++ trunk/gplots/DESCRIPTION	2011-08-25 03:10:05 UTC (rev 1474)
@@ -4,7 +4,7 @@
 Depends: gtools, gdata, stats, caTools, grid
 Recommends: datasets, grid, MASS
 Suggests: gtools
-Version: 2.8.1
+Version: 2.9.0
 Date: 2011-08-15
 Author: Gregory R. Warnes. Includes R source code and/or documentation
         contributed by (in alphabetical order): 

Modified: trunk/gplots/NAMESPACE
===================================================================
--- trunk/gplots/NAMESPACE	2011-08-16 01:17:20 UTC (rev 1473)
+++ trunk/gplots/NAMESPACE	2011-08-25 03:10:05 UTC (rev 1474)
@@ -4,6 +4,7 @@
        barplot2,
        bluered,
        boxplot.n,
+       ci2d,
        col2hex,
        colorpanel,
        greenred,

Added: trunk/gplots/R/ci2d.R
===================================================================
--- trunk/gplots/R/ci2d.R	                        (rev 0)
+++ trunk/gplots/R/ci2d.R	2011-08-25 03:10:05 UTC (rev 1474)
@@ -0,0 +1,64 @@
+## first(...) selects the first element of which(...)
+first <- function(x,...)
+  {
+  w <- which(x,...)
+  if(length(x)>1)
+    w[1]
+  else
+    w
+}
+
+## first(...) selects the first element of which(...)
+last <- function(x,...)
+  {
+  w <- which(x,...)
+  if(length(x)>1)
+    rev(w)[1]
+  else
+    w
+}
+
+## non-parametric 2 dimensional approximate confidence interval
+## based on 2 dimensional histogram
+ci2d <- function(x,
+                 y = NULL,
+                 nbins=25,
+                 ci.levels=c(0.50,0.75,0.90,0.95,0.975),
+                 show=c("filled.contour","contour","image","none"),
+                 xlab=deparse(substitute(x)),
+                 ylab=deparse(substitute(y)),
+                 col=topo.colors(length(breaks)-1),
+                 ...)
+  {
+
+    show=match.arg(show)
+    breaks <- unique(c(0, ci.levels, 1.0))
+    
+    h2d <- hist2d(x,y, show=FALSE, nbins=nbins, ...)
+    h2d$density <- h2d$counts / sum(h2d$counts, na.rm=TRUE)
+
+    uniqueVals <- rev(unique(sort(h2d$density)))
+    cumProbs <- sapply( uniqueVals, function(val) sum( h2d$density[h2d$density>=val] ) )
+    names(cumProbs) <- uniqueVals
+    h2d$cumDensity <- matrix(nrow=nrow(h2d$density), ncol=ncol(h2d$density))
+    h2d$cumDensity[] <- cumProbs[as.character(h2d$density)]
+
+    if(show=="image")
+      {
+        image( h2d$x, h2d$y, h2d$cumDensity, xlab=xlab, ylab=ylab, breaks=breaks, col=col)
+      }
+    else if(show=="filled.contour")
+      {
+        filled.contour(h2d$x, h2d$y, h2d$cumDensity,
+                       levels=breaks,
+                       col=col,
+                       key.axes={axis(4, at=breaks); title("\nCI Level")}
+                       )
+       }
+    else if(show=="contour")
+        contour(h2d$x, h2d$y, h2d$cumDensity, levels=breaks, nlevels=length(breaks))
+
+    h2d$contours <- contourLines(h2d$x, h2d$y, h2d$cumDensity, levels=breaks, nlevels=length(breaks))
+    names
+    invisible(h2d)
+  }

Added: trunk/gplots/man/ci2d.Rd
===================================================================
--- trunk/gplots/man/ci2d.Rd	                        (rev 0)
+++ trunk/gplots/man/ci2d.Rd	2011-08-25 03:10:05 UTC (rev 1474)
@@ -0,0 +1,76 @@
+\name{ci2d}
+\alias{ci2d}
+\title{
+  Create 2-dimensional empirical confidence regions
+}
+\description{
+  Create 2-dimensional empirical confidence regions based on a
+  2-dimensoinal histogram.
+}
+\usage{
+ci2d(x, y=NULL,
+     nbins=25,
+     ci.levels=c(0.5, 0.75, 0.9, 0.95, 0.975),
+     show=c("filled.contour", "contour", "image", "none"),
+     xlab=deparse(substitute(x)),
+     ylab=deparse(substitute(y)),
+     col=topo.colors(length(breaks) - 1),
+     ...)
+}
+\arguments{
+  \item{x}{either a vector containing the x coordinates
+    or a matrix with 2 columns. }
+  \item{y}{a vector contianing the y coordinates, not required if `x'
+    is matrix}
+  \item{nbins}{number of bins in each dimension. May be a scalar or a
+    2 element vector.  Defaults to 25.}
+  \item{ci.levels}{Confidence level(s) to use for plotting
+    data. Defaults to \code{c(0.5, 0.75, 0.9, 0.95, 0.975)} }
+  \item{show}{Plot type to be displaed.  One of "filled.contour",
+    "contour", "image", or "none".  Defaults to "filled.contour".}
+  \item{xlab, ylab}{Axis labels}
+  \item{col}{Colors to use for plots.}
+  \item{\dots}{Additional arguments passed to \code{hist2d}. }
+}
+\details{
+  This function utilizes \code{hist2d} to create a 2-dimensional
+  histogram of the data passed as an argument.  This data is then
+  converted into densities and used to create and display confidence
+  regions.
+}
+\value{
+  A list containing 3 elements:
+  \item{counts}{Matrix containing the number of points falling into each
+    bin}
+  \item{x}{lower x limit of each bin}
+  \item{y}{lower y limit of each bin}
+  \item{density}{Matrix containing the probability density of each bin (count in bin/total
+    count)}
+  \item{cumDensity}{Matrix where each element contains the cumulative probability density
+    of all elements with the same density (used to create the confidence
+    region plots) }
+  \item{contours}{Contours of each confidence region}
+}
+%\references{
+%}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
+\seealso{
+  \code{\link{hist2d}}
+}
+\examples{
+   # example data, bivariate normal, no correlation
+   x <- rnorm(2000, sd=4)
+   y <- rnorm(2000, sd=1)
+
+   # 2-d confidence intervals based on 2d histogram
+   ci2d(x,y)
+
+   # same scale for each axis, this looks oval
+   ci2d(x,y, same.scale=TRUE)
+
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{dplot}
+\keyword{hplot}
+\keyword{nonparametric}

Modified: trunk/gplots/man/rich.colors.Rd
===================================================================
--- trunk/gplots/man/rich.colors.Rd	2011-08-16 01:17:20 UTC (rev 1473)
+++ trunk/gplots/man/rich.colors.Rd	2011-08-25 03:10:05 UTC (rev 1474)
@@ -15,7 +15,7 @@
     black-blue-white.}
   \item{alpha}{alpha transparency, from 0 (fully transparent)  to 1
     (opaque).} 
-  \item{rgb}{if ‘TRUE’ then a matrix of RGBA values is included as an
+  \item{rgb}{if \code{TRUE} then a matrix of RGBA values is included as an
           attribute.}
   \item{plot}{whether to plot a descriptive color diagram.}
 }

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1473] trunk/gplots/DESCRIPTION

From: <wa...@us...> - 2011-08-16 01:17:26

Revision: 1473
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1473&view=rev
Author:   warnes
Date:     2011-08-16 01:17:20 +0000 (Tue, 16 Aug 2011)

Log Message:
-----------
Update DESCRIPTION file for 2.8.1.

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

Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION	2011-08-16 01:16:00 UTC (rev 1472)
+++ trunk/gplots/DESCRIPTION	2011-08-16 01:17:20 UTC (rev 1473)
@@ -2,10 +2,10 @@
 Title: Various R programming tools for plotting data
 Description: Various R programming tools for plotting data
 Depends: gtools, gdata, stats, caTools, grid
-Recommends: datasets, grid
+Recommends: datasets, grid, MASS
 Suggests: gtools
-Version: 2.8.0
-Date: 2010-06-10
+Version: 2.8.1
+Date: 2011-08-15
 Author: Gregory R. Warnes. Includes R source code and/or documentation
         contributed by (in alphabetical order): 
  	  Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1472] trunk/gplots

From: <wa...@us...> - 2011-08-16 01:16:06

Revision: 1472
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1472&view=rev
Author:   warnes
Date:     2011-08-16 01:16:00 +0000 (Tue, 16 Aug 2011)

Log Message:
-----------
Add 'alpha' argument to rich.colors() to control transparency.

Modified Paths:
--------------
    trunk/gplots/R/rich.colors.R
    trunk/gplots/man/rich.colors.Rd

Modified: trunk/gplots/R/rich.colors.R
===================================================================
--- trunk/gplots/R/rich.colors.R	2011-08-16 01:03:31 UTC (rev 1471)
+++ trunk/gplots/R/rich.colors.R	2011-08-16 01:16:00 UTC (rev 1472)
@@ -1,4 +1,8 @@
-rich.colors <- function(n, palette="temperature", alpha=1, plot=FALSE)
+rich.colors <- function(n,
+                        palette="temperature",
+                        alpha=1,
+                        rgb=FALSE,
+                        plot=FALSE)
 {
   if(n <= 0)
     return(character(0))
@@ -20,9 +24,13 @@
     b[x>0.4] <- 1
   }
 
-  rgb.m <- matrix(c(r,g,b), ncol=3, dimnames=list(NULL,c("red","green","blue")))
+  rgb.m <- matrix(c(r,g,b), ncol=3,
+                  dimnames=list(NULL,c("red","green","blue")))
   col <- mapply(rgb, r, g, b, alpha)
 
+  if(rgb) 
+    attr(col, "rgb") <- cbind(rgb.m, alpha)
+  
   if(plot)
   {
     opar <- par("fig", "plt")

Modified: trunk/gplots/man/rich.colors.Rd
===================================================================
--- trunk/gplots/man/rich.colors.Rd	2011-08-16 01:03:31 UTC (rev 1471)
+++ trunk/gplots/man/rich.colors.Rd	2011-08-16 01:16:00 UTC (rev 1472)
@@ -6,14 +6,17 @@
   and in an order that is easy to interpret.
 }
 \usage{
-rich.colors(n, palette="temperature", rgb=FALSE, plot=FALSE)
+rich.colors(n, palette="temperature", alpha=1.0, rgb=FALSE, plot=FALSE)
 }
 \arguments{
   \item{n}{number of colors to generate.}
   \item{palette}{palette to use: \code{"temperature"} contains
     blue-green-yellow-red, and \code{"blues"} contains
     black-blue-white.}
-  \item{alpha}{alpha transparency, from 0 to 1.}
+  \item{alpha}{alpha transparency, from 0 (fully transparent)  to 1
+    (opaque).} 
+  \item{rgb}{if ‘TRUE’ then a matrix of RGBA values is included as an
+          attribute.}
   \item{plot}{whether to plot a descriptive color diagram.}
 }
 \value{A character vector of color codes.}


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1471] trunk/gplots

From: <wa...@us...> - 2011-08-16 01:03:38

Revision: 1471
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1471&view=rev
Author:   warnes
Date:     2011-08-16 01:03:31 +0000 (Tue, 16 Aug 2011)

Log Message:
-----------
Accellerate hist2d by replacing for() loop with tapply(), and allow user to specify summary function applied, per suggestion by Peter Hagedorn (PHA -at- santaris -dot- com).

Modified Paths:
--------------
    trunk/gplots/R/hist2d.R
    trunk/gplots/man/hist2d.Rd

Modified: trunk/gplots/R/hist2d.R
===================================================================
--- trunk/gplots/R/hist2d.R	2011-05-02 14:02:34 UTC (rev 1470)
+++ trunk/gplots/R/hist2d.R	2011-08-16 01:03:31 UTC (rev 1471)
@@ -1,7 +1,16 @@
 # $Id$
 
 if(is.R())
-hist2d <- function( x,y=NULL, nbins=200, same.scale=FALSE, na.rm=TRUE, show=TRUE, col=c("black", heat.colors(12)), ... )
+
+  hist2d <- function(x,
+                     y=NULL,
+                     nbins=200,
+                     same.scale=FALSE,
+                     na.rm=TRUE,
+                     show=TRUE,
+                     col=c("black", heat.colors(12)),
+                     FUN=base::length,
+                     ... )
   {
     if(is.null(y))
       {
@@ -34,18 +43,17 @@
         y.cuts <- seq( from=min(y), to=max(y), length=nbins[2]+1, labels=FALSE)
       }
 
-
-
     index.x <- cut( x, x.cuts, include.lowest=TRUE)
     index.y <- cut( y, y.cuts, include.lowest=TRUE)
 
-    m <- matrix( 0, nrow=nbins[1], ncol=nbins[2],
-                dimnames=list( levels(index.x),
-                               levels(index.y) ) )
+    ## tapply is faster than old for() loop, and allows
+    ## use of any user-specified summary function 
+    m <- tapply(x,list(index.x,index.y),FUN)
 
-    for( i in 1:length(index.x) )
-      m[ index.x[i], index.y[i] ] <-  m[ index.x[i], index.y[i] ] + 1
-
+    ## If we're using length, set empty cells to 0 instead of NA
+    if(identical(FUN,base::length))
+      m[is.na(m)] <- 0
+        
     xvals <- x.cuts[1:nbins[1]]
     yvals <- y.cuts[1:nbins[2]]
 
@@ -54,9 +62,3 @@
 
     invisible(list(counts=m,x=xvals,y=yvals))
   }
-
-
-
-
-
-

Modified: trunk/gplots/man/hist2d.Rd
===================================================================
--- trunk/gplots/man/hist2d.Rd	2011-05-02 14:02:34 UTC (rev 1470)
+++ trunk/gplots/man/hist2d.Rd	2011-08-16 01:03:31 UTC (rev 1471)
@@ -27,9 +27,8 @@
 }
 \usage{
 hist2d(x,y=NULL, nbins=200, same.scale=FALSE, na.rm=TRUE, show=TRUE,
-       col=c("black", heat.colors(12)), ... )
+       col=c("black", heat.colors(12)), FUN=base::length, ... )
 }
-%- maybe also `usage' for other objects documented here.
 \arguments{
   \item{x}{either a vector containing the x coordinates
     or a matrix with 2 columns. }
@@ -45,6 +44,10 @@
     been computed. Defaults to TRUE.}
   \item{col}{ Colors for the histogram. Defaults to "black" for
     bins containing no elements, a set of 16 heat colors for other bins.}
+  \item{FUN}{Function used to summarize bin contents.  Defaults to
+    \code{base::length}. Use, e.g., \code{mean} to calculate means for each bin
+    instead of counts.
+    }
   \item{\dots}{ Parameters passed to the image function. }
 }
 \details{
@@ -61,10 +64,8 @@
     bin}
   \item{x}{lower x limit of each bin}
   \item{y}{lower y limit of each bin}
-}
-%\references{ ~put references to the literature/web site here ~ }
+  }
 \author{ Gregory R. Warnes \email{gr...@wa...}}
-%\note{ ~~further notes~~ }
 
 \seealso{ \code{\link{image}}, \code{\link{persp}}, \code{\link{hist}} }
 


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1470] trunk/gplots

From: <ar...@us...> - 2011-05-02 14:02:40

Revision: 1470
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1470&view=rev
Author:   arnima
Date:     2011-05-02 14:02:34 +0000 (Mon, 02 May 2011)

Log Message:
-----------
Added argument 'alpha' and removed argument 'rgb' in rich.colors()

Modified Paths:
--------------
    trunk/gplots/R/rich.colors.R
    trunk/gplots/man/rich.colors.Rd

Modified: trunk/gplots/R/rich.colors.R
===================================================================
--- trunk/gplots/R/rich.colors.R	2011-04-16 17:04:06 UTC (rev 1469)
+++ trunk/gplots/R/rich.colors.R	2011-05-02 14:02:34 UTC (rev 1470)
@@ -1,4 +1,4 @@
-rich.colors <- function(n, palette="temperature", rgb=FALSE, plot=FALSE)
+rich.colors <- function(n, palette="temperature", alpha=1, plot=FALSE)
 {
   if(n <= 0)
     return(character(0))
@@ -20,14 +20,9 @@
     b[x>0.4] <- 1
   }
 
-  rgb.m <- matrix(c(r,g,b), ncol=3,
-                  dimnames=list(as.character(seq(length=n)),
-                    c("red","green","blue")))
-  rich.vector <- apply(rgb.m, 1, function(v) rgb(v[1],v[2],v[3]))
+  rgb.m <- matrix(c(r,g,b), ncol=3, dimnames=list(NULL,c("red","green","blue")))
+  col <- mapply(rgb, r, g, b, alpha)
 
-  if(rgb)
-    attr(rich.vector, "rgb") <- rgb.m
-
   if(plot)
   {
     opar <- par("fig", "plt")
@@ -40,10 +35,11 @@
     axis(1, at=0:1)
     axis(2, at=0:1, las=1)
     par(fig=c(0,1,0.75,0.9), plt=c(0.08,0.97,0,1), new=TRUE)
-    midpoints <- barplot(rep(1,n), col=rich.vector, border=FALSE, space=FALSE,
+    midpoints <- barplot(rep(1,n), col=col, border=FALSE, space=FALSE,
                          axes=FALSE)
     axis(1, at=midpoints, labels=1:n, lty=0, cex.axis=0.6)
     par(opar)
   }
-  return(rich.vector)
+
+  return(col)
 }

Modified: trunk/gplots/man/rich.colors.Rd
===================================================================
--- trunk/gplots/man/rich.colors.Rd	2011-04-16 17:04:06 UTC (rev 1469)
+++ trunk/gplots/man/rich.colors.Rd	2011-05-02 14:02:34 UTC (rev 1470)
@@ -13,18 +13,16 @@
   \item{palette}{palette to use: \code{"temperature"} contains
     blue-green-yellow-red, and \code{"blues"} contains
     black-blue-white.}
-  \item{rgb}{if \code{TRUE} then a matrix of RGB values is included as
-    an attribute.}
-  \item{plot}{if \code{TRUE} then a descriptive color diagram is plotted
-    on the current device.}
+  \item{alpha}{alpha transparency, from 0 to 1.}
+  \item{plot}{whether to plot a descriptive color diagram.}
 }
 \value{A character vector of color codes.}
-\author{Arni Magnusson}
+\author{Arni Magnusson.}
 \seealso{
   \code{\link{rgb}}, \code{\link{rainbow}}, \code{\link{heat.colors}}.
 }
 \examples{
-m <- matrix(1:120+rnorm(120), nrow=15, ncol=8)
+m <- abs(matrix(1:120+rnorm(120), nrow=15, ncol=8))
 opar <- par(bg="gray", mfrow=c(1,2))
 matplot(m, type="l", lty=1, lwd=3, col=rich.colors(8))
 matplot(m, type="l", lty=1, lwd=3, col=rich.colors(8,"blues"))
@@ -33,8 +31,11 @@
 barplot(rep(1,100), col=rich.colors(100), space=0, border=0, axes=FALSE)
 barplot(rep(1,20), col=rich.colors(40)[11:30]) # choose subset
 
-rich.colors(100, plot=TRUE, rgb=TRUE)  # describe rgb recipe
+plot(m, rev(m), ylim=c(120,0), pch=16, cex=2,
+     col=rich.colors(200,"blues",alpha=0.6)[1:120]) # semitransparent
 
+rich.colors(100, plot=TRUE)  # describe rgb recipe
+
 par(mfrow=c(2,2))
 barplot(m, col=heat.colors(15), main="\nheat.colors")
 barplot(m, col=1:15, main="\ndefault palette")


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1469] trunk/gdata

From: <wa...@us...> - 2011-04-16 17:04:12

Revision: 1469
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1469&view=rev
Author:   warnes
Date:     2011-04-16 17:04:06 +0000 (Sat, 16 Apr 2011)

Log Message:
-----------
Update for release 2.8.2

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

Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION	2011-04-15 20:25:24 UTC (rev 1468)
+++ trunk/gdata/DESCRIPTION	2011-04-16 17:04:06 UTC (rev 1469)
@@ -3,8 +3,8 @@
 Description: Various R programming tools for data manipulation
 Depends: R (>= 2.6.0)
 Imports: gtools
-Version: 2.8.1
-Date: 2010-11-12
+Version: 2.8.2
+Date: 2011-04-15
 Author: Gregory R. Warnes, with contributions from Ben Bolker, Gregor Gorjanc, 
         Gabor Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, 
         Arni Magnusson, Jim Rogers, and others

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2011-04-15 20:25:24 UTC (rev 1468)
+++ trunk/gdata/inst/NEWS	2011-04-16 17:04:06 UTC (rev 1469)
@@ -1,5 +1,4 @@
-
-CHANGES IN 2.?.? (2011-??-??)
+CHANGES IN 2.8.1 (2011-04-15)
 -----------------------------
 
 Enhancements:
@@ -7,6 +6,11 @@
 - nPairs() gains a summary method that shows how many times each variable 
   is known, while the other variable of a pair is not
 
+Bug fixes:
+
+- Fix errors on windows when R or Perl install path includes spaces by properly quoting the path.
+
+
 CHANGES IN 2.8.1 (2010-11-12)
 -----------------------------
 


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1468] trunk/gdata/R

From: <wa...@us...> - 2011-04-15 20:25:30

Revision: 1468
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1468&view=rev
Author:   warnes
Date:     2011-04-15 20:25:24 +0000 (Fri, 15 Apr 2011)

Log Message:
-----------
Fix errors on windows when R or Perl install path includes spaces by properly quoting the path.

Modified Paths:
--------------
    trunk/gdata/R/installXLSXsupport.R
    trunk/gdata/R/read.xls.R
    trunk/gdata/R/sheetCount.R
    trunk/gdata/R/xls2sep.R

Removed Paths:
-------------
    trunk/gdata/R/dQuote.ascii.R

Deleted: trunk/gdata/R/dQuote.ascii.R
===================================================================
--- trunk/gdata/R/dQuote.ascii.R	2011-04-15 19:43:55 UTC (rev 1467)
+++ trunk/gdata/R/dQuote.ascii.R	2011-04-15 20:25:24 UTC (rev 1468)
@@ -1,9 +0,0 @@
-## s$Id: read.xls.R 1342 2009-07-16 02:49:11Z warnes $
-
-## Double quote string using *ASCII* double quotes.
-##
-## (The base 'dQuote' uses local-specific quotes (e.g UTF-8 quotes)
-## which Unix command line doesn't like.)
-##
-dQuote.ascii <- function(x) paste('"',x,'"',sep='')
-

Modified: trunk/gdata/R/installXLSXsupport.R
===================================================================
--- trunk/gdata/R/installXLSXsupport.R	2011-04-15 19:43:55 UTC (rev 1467)
+++ trunk/gdata/R/installXLSXsupport.R	2011-04-15 20:25:24 UTC (rev 1468)
@@ -24,7 +24,7 @@
   ##
   ## execution command
 
-  cmd <- paste(perl, sc, sep=" ")
+  cmd <- paste(shQuote(perl), shQuote(sc), sep=" ")
 
   ##
 

Modified: trunk/gdata/R/read.xls.R
===================================================================
--- trunk/gdata/R/read.xls.R	2011-04-15 19:43:55 UTC (rev 1467)
+++ trunk/gdata/R/read.xls.R	2011-04-15 20:25:24 UTC (rev 1468)
@@ -33,7 +33,7 @@
   if (missing(pattern))
     {
       if(verbose)
-        cat("Reading", method, "file ", dQuote.ascii(tfn), "...\n")
+        cat("Reading", method, "file ", dQuote(tfn), "...\n")
       
       if(method=="csv")
         retval <- read.csv(con, ...)
@@ -59,7 +59,7 @@
     seek(con, 0)
 
     if(verbose)
-      cat("Reading", method, "file ", dQuote.ascii(tfn), "...\n")
+      cat("Reading", method, "file ", dQuote(tfn), "...\n")
 
     if(method=="csv")
       retval <- read.csv(con, skip = idx[1]-1, ...)

Modified: trunk/gdata/R/sheetCount.R
===================================================================
--- trunk/gdata/R/sheetCount.R	2011-04-15 19:43:55 UTC (rev 1467)
+++ trunk/gdata/R/sheetCount.R	2011-04-15 20:25:24 UTC (rev 1468)
@@ -29,8 +29,8 @@
       tf <- paste(tempfile(), "xls", sep = ".")
       if(verbose)
         cat("Downloading",
-            dQuote.ascii(xls), " to ",
-            dQuote.ascii(tf), "...\n")
+            dQuote(xls), " to ",
+            dQuote(tf), "...\n")
       else
         cat("Downloading...\n")
       download.file(xls, tf, mode = "wb")
@@ -47,7 +47,7 @@
   ##
   ## execution command
 
-  cmd <- paste(perl, sc, dQuote.ascii(xls), sep=" ")
+  cmd <- paste(shQuote(perl), shQuote(sc), shQuote(xls), sep=" ")
   ##
   ##
 
@@ -57,7 +57,7 @@
     {
       cat("\n")
       cat("Extracting sheet information from\n")
-      cat("   ", dQuote.ascii(xls), "\n")
+      cat("   ", dQuote(xls), "\n")
       cat("... \n\n")
     }
   ##

Modified: trunk/gdata/R/xls2sep.R
===================================================================
--- trunk/gdata/R/xls2sep.R	2011-04-15 19:43:55 UTC (rev 1467)
+++ trunk/gdata/R/xls2sep.R	2011-04-15 20:25:24 UTC (rev 1468)
@@ -38,8 +38,8 @@
         tf <- paste(tempfile(), "xls", sep = ".")
         if(verbose)
           cat("Downloading",
-              dQuote.ascii(xls), " to ",
-              dQuote.ascii(tf), "...\n")
+              dQuote(xls), " to ",
+              dQuote(tf), "...\n")
         download.file(xls, tf, mode = "wb")
         if(verbose) cat("Done.\n")
         xls <- tf
@@ -70,11 +70,11 @@
 
     ##
     ## execution command
-    cmd <- paste(dQuote.ascii(perl),
-                 dQuote.ascii(script),
-                 dQuote.ascii(xls),
-                 dQuote.ascii(targetFile),
-                 dQuote.ascii(sheet),
+    cmd <- paste(shQuote(perl),
+                 shQuote(script),
+                 shQuote(xls),
+                 shQuote(targetFile),
+                 shQuote(sheet),
                  sep=" ")
     ##
     ##
@@ -83,9 +83,9 @@
       {
         cat("\n")
         cat("Converting xls file\n")
-        cat("   ", dQuote.ascii(xls), "\n")
+        cat("   ", dQuote(xls), "\n")
         cat("to", method, " file \n")
-        cat("   ", dQuote.ascii(targetFile), "\n")
+        cat("   ", dQuote(targetFile), "\n")
         cat("... \n\n")
       }
     


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1467] trunk/gdata/R/xlsFormats.R

From: <wa...@us...> - 2011-04-15 19:44:01

Revision: 1467
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1467&view=rev
Author:   warnes
Date:     2011-04-15 19:43:55 +0000 (Fri, 15 Apr 2011)

Log Message:
-----------
Fix error in xlsFormat() on windows when R or Perl install path includes spaces by quoting the path.

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

Modified: trunk/gdata/R/xlsFormats.R
===================================================================
--- trunk/gdata/R/xlsFormats.R	2011-01-16 22:17:17 UTC (rev 1466)
+++ trunk/gdata/R/xlsFormats.R	2011-04-15 19:43:55 UTC (rev 1467)
@@ -24,7 +24,7 @@
   ##
   ## execution command
 
-  cmd <- paste(perl, sc, sep=" ")
+  cmd <- paste(shQuote(perl), shQuote(sc), sep=" ")
 
   ##
 


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1466] trunk/gmodels

From: <wa...@us...> - 2011-01-16 22:17:24

Revision: 1466
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1466&view=rev
Author:   warnes
Date:     2011-01-16 22:17:17 +0000 (Sun, 16 Jan 2011)

Log Message:
-----------
Fix warnings reported by R CMD check. Update version number to 2.15.1.

Modified Paths:
--------------
    trunk/gmodels/DESCRIPTION
    trunk/gmodels/inst/NEWS
    trunk/gmodels/man/ci.Rd
    trunk/gmodels/man/estimable.Rd
    trunk/gmodels/man/fast.prcomp.Rd
    trunk/gmodels/man/fit.contrast.Rd
    trunk/gmodels/man/glh.test.Rd
    trunk/gmodels/man/make.contrasts.Rd

Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION	2011-01-15 21:58:56 UTC (rev 1465)
+++ trunk/gmodels/DESCRIPTION	2011-01-16 22:17:17 UTC (rev 1466)
@@ -1,5 +1,5 @@
 Package: gmodels
-Version: 2.15.0
+Version: 2.15.1
 Title: Various R programming tools for model fitting
 Author: Gregory R. Warnes. Includes R source code and/or documentation
         contributed by Ben Bolker, Thomas Lumley, and Randall C
@@ -7,10 +7,10 @@
         (2005) SAIC-Frederick, Inc. Funded by the Intramural Research
         Program, of the NIH, National Cancer Institute, Center for
         Cancer Research under NCI Contract NO1-CO-12400.
-Maintainer: Gregory R. Warnes <gr...@ra...>
+Maintainer: Gregory R. Warnes <gr...@wa...>
 Description: Various R programming tools for model fitting
 Depends: R (>= 1.9.0)
-Suggests: gplots, Matrix, nlme, lme4
+Suggests: gplots, gtools, Matrix, nlme, lme4
 Imports: MASS, gdata
 License: GPL-2
 URL: http://cran.r-project.org/src/contrib/PACKAGES.html 

Modified: trunk/gmodels/inst/NEWS
===================================================================
--- trunk/gmodels/inst/NEWS	2011-01-15 21:58:56 UTC (rev 1465)
+++ trunk/gmodels/inst/NEWS	2011-01-16 22:17:17 UTC (rev 1466)
@@ -1,3 +1,11 @@
+Version 2.15.1
+--------------
+
+Bug fixes:
+
+- Fix warnings reported by new versions of R CMD check.
+
+
 Version 2.15.0
 --------------
 

Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd	2011-01-15 21:58:56 UTC (rev 1465)
+++ trunk/gmodels/man/ci.Rd	2011-01-16 22:17:17 UTC (rev 1466)
@@ -30,9 +30,9 @@
     removed. Defaults to \code{FALSE}.}
   \item{\dots}{Arguments for methods}
   \item{sim.mer}{Logical value. If TRUE confidence
-    intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for mer
+    intervals will be estimated using \code{mcmcsamp}. This option only takes effect for mer
     objects.}
-  \item{n.sim}{Number of samples to take in \code{\Link[Matrix]{mcmcsamp}}.}
+  \item{n.sim}{Number of samples to take in \code{mcmcsamp}.}
 }
 %\details{
 %  ~~ If necessary, more details than the __description__  above ~~
@@ -42,7 +42,7 @@
   \code{Estimate}, \code{CI lower}, \code{CI upper}, \code{Std. Error},
   \code{DF} (for lme objects only), and \code{p-value}.
 }
-\author{ Gregory R. Warnes \email{gr...@ra...}
+\author{ Gregory R. Warnes \email{gr...@wa...}
 }
 \seealso{
   \code{\link[stats]{confint}},

Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd	2011-01-15 21:58:56 UTC (rev 1465)
+++ trunk/gmodels/man/estimable.Rd	2011-01-16 22:17:17 UTC (rev 1466)
@@ -38,10 +38,10 @@
      included in the output table.  Defaults to TRUE when beta0 is
      specified, FALSE otherwise.}
    \item{sim.mer}{Logical value. If TRUE p-values and confidence
-     intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}.
+     intervals will be estimated using \code{mcmcsamp}.
    }
    \item{n.sim}{Number of MCMC samples to take in
-     \code{\Link[Matrix]{mcmcsamp}}.
+     \code{mcmcsamp}.
    }
    \item{...}{ignored}
 }
@@ -71,7 +71,7 @@
   linear functions are meaningful.
 
   For computing contrasts among levels of a single factor,
-  \code{\link{fit.contrast}} may be more convenient.  For computing
+  \code{fit.contrast} may be more convenient.  For computing
   contrasts between two specific combinations of model parameters, the
   \code{contrast} function in Frank Harrell's Design library may be more
   convenient.
@@ -95,13 +95,14 @@
 }
 \author{
   BXC (Bendix Carstensen) \email{bxc\@novonordisk.com}, 
-  Gregory R. Warnes \email{gr...@ra...},
+  Gregory R. Warnes \email{gr...@wa...},
   Soren Hojsgaard \email{so...@ag...}, and
   Randall C Johnson \email{rjo...@nc...}
 }
 \seealso{
   \code{\link{fit.contrast}},
-  \code{\link[stats]{lm}}, \code{\link[nlme]{lme}},
+  \code{\link[stats]{lm}},
+  \code{\link[nlme]{lme}},
   \code{\link[stats]{contrasts}},
   \code{\link[Design]{contrast}},
   }

Modified: trunk/gmodels/man/fast.prcomp.Rd
===================================================================
--- trunk/gmodels/man/fast.prcomp.Rd	2011-01-15 21:58:56 UTC (rev 1465)
+++ trunk/gmodels/man/fast.prcomp.Rd	2011-01-16 22:17:17 UTC (rev 1466)
@@ -69,7 +69,7 @@
   \code{\link{svd}} .
 }
 \author{Modifications by Gregory R. Warnes
-  \email{gr...@ra...} }
+  \email{gr...@wa...} }
 
 \seealso{
     \code{\link[stats]{prcomp}}, \code{\link{svd}}, \code{\link{La.svd}}

Modified: trunk/gmodels/man/fit.contrast.Rd
===================================================================
--- trunk/gmodels/man/fit.contrast.Rd	2011-01-15 21:58:56 UTC (rev 1465)
+++ trunk/gmodels/man/fit.contrast.Rd	2011-01-16 22:17:17 UTC (rev 1466)
@@ -35,9 +35,9 @@
     degrees of freedom.}
   \item{\dots}{optional arguments provided by methods.}
   \item{sim.mer}{Logical value. If TRUE p-values and confidence
-    intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for mer
+    intervals will be estimated using \code{mcmcsamp}. This option only takes effect for mer
     objects.}
-  \item{n.sim}{Number of samples to use in \code{\Link[Matrix]{mcmcsamp}}.}
+  \item{n.sim}{Number of samples to use in \code{mcmcsamp}.}
   }
   
 \details{
@@ -52,7 +52,7 @@
   specified lower and upper confidence limits are also returned.}
 \references{Venables & Ripley, Section 6.2}
   
-\author{ Gregory R. Warnes \email{gr...@ra...}}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
 
 \seealso{ \code{\link{lm}}, \code{\link{contrasts}},
   \code{\link{contr.treatment}},  \code{\link{contr.poly}},

Modified: trunk/gmodels/man/glh.test.Rd
===================================================================
--- trunk/gmodels/man/glh.test.Rd	2011-01-15 21:58:56 UTC (rev 1465)
+++ trunk/gmodels/man/glh.test.Rd	2011-01-16 22:17:17 UTC (rev 1466)
@@ -65,7 +65,7 @@
 }
 \references{ R.H. Myers, Classical and Modern Regression with
   Applications,  2nd Ed, 1990, p. 105}
-\author{Gregory R. Warnes \email{gr...@ra...} }
+\author{Gregory R. Warnes \email{gr...@wa...} }
 \seealso{\code{\link{fit.contrast}}, \code{\link{estimable}},
   \code{\link{contrasts}} }
 \examples{

Modified: trunk/gmodels/man/make.contrasts.Rd
===================================================================
--- trunk/gmodels/man/make.contrasts.Rd	2011-01-15 21:58:56 UTC (rev 1465)
+++ trunk/gmodels/man/make.contrasts.Rd	2011-01-16 22:17:17 UTC (rev 1466)
@@ -31,7 +31,7 @@
   \code{\link{contrasts}} or to the \code{contrasts} argument of model
   functions (eg, \code{\link{lm}}).
 }
-\author{ Gregory R. Warnes \email{gr...@ra...}}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
 \seealso{ \code{\link{lm}}, \code{\link{contrasts}},
   \code{\link{contr.treatment}},  \code{\link{contr.poly}},
   Computation and testing of General Linear Hypothesis:


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1465] trunk/gdata

From: <gg...@us...> - 2011-01-15 21:59:02

Revision: 1465
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1465&view=rev
Author:   ggorjan
Date:     2011-01-15 21:58:56 +0000 (Sat, 15 Jan 2011)

Log Message:
-----------
Adding summary method for nPairs

Modified Paths:
--------------
    trunk/gdata/NAMESPACE
    trunk/gdata/R/nPairs.R
    trunk/gdata/inst/NEWS
    trunk/gdata/inst/unitTests/runit.nPairs.R
    trunk/gdata/man/nPairs.Rd

Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE	2011-01-06 19:33:26 UTC (rev 1464)
+++ trunk/gdata/NAMESPACE	2011-01-15 21:58:56 UTC (rev 1465)
@@ -62,6 +62,8 @@
 
 S3method(reorder, factor)
 
+S3method(summary, nPairs)
+
 ## drop.levels stuff
 S3method(drop.levels, default)
 S3method(drop.levels, factor)

Modified: trunk/gdata/R/nPairs.R
===================================================================
--- trunk/gdata/R/nPairs.R	2011-01-06 19:33:26 UTC (rev 1464)
+++ trunk/gdata/R/nPairs.R	2011-01-15 21:58:56 UTC (rev 1465)
@@ -42,8 +42,22 @@
       colnames(ret) <- tmp
     }
   }
+  class(ret) <- c("nPairs", class(ret))
   ret
 }
 
+summary.nPairs <- function(object, ...)
+{
+  n <- nrow(object)
+  ret <- matrix(data=0, nrow=n, ncol=n)
+  for(i in 1:n) {
+    tmp <- 1:n
+    tmp <- tmp[!(tmp == i)]
+    ret[i, tmp] <- object[i, i] - object[i, tmp]
+  }
+  dimnames(ret) <- dimnames(object)
+  ret
+}
+
 ###------------------------------------------------------------------------
 ### nPairs.R ends here

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2011-01-06 19:33:26 UTC (rev 1464)
+++ trunk/gdata/inst/NEWS	2011-01-15 21:58:56 UTC (rev 1465)
@@ -1,3 +1,12 @@
+
+CHANGES IN 2.?.? (2011-??-??)
+-----------------------------
+
+Enhancements:
+
+- nPairs() gains a summary method that shows how many times each variable 
+  is known, while the other variable of a pair is not
+
 CHANGES IN 2.8.1 (2010-11-12)
 -----------------------------
 

Modified: trunk/gdata/inst/unitTests/runit.nPairs.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.nPairs.R	2011-01-06 19:33:26 UTC (rev 1464)
+++ trunk/gdata/inst/unitTests/runit.nPairs.R	2011-01-15 21:58:56 UTC (rev 1465)
@@ -26,11 +26,12 @@
                      V2=c(NA, 2, 3, 4, 5),
                      V3=c(1, NA, NA, NA, NA),
                      V4=c(1, 2, 3, NA, NA))
-  testCheck <- matrix(as.integer(c(5, 4, 1, 3,
-                                   4, 4, 0, 2,
-                                   1, 0, 1, 1,
-                                   3, 2, 1, 3)),
+  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)
@@ -41,10 +42,21 @@
   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:

Modified: trunk/gdata/man/nPairs.Rd
===================================================================
--- trunk/gdata/man/nPairs.Rd	2011-01-06 19:33:26 UTC (rev 1464)
+++ trunk/gdata/man/nPairs.Rd	2011-01-15 21:58:56 UTC (rev 1465)
@@ -31,6 +31,14 @@
   \item{\dots}{other arguments passed to \code{\link{abbreviate}}}
 }
 
+\details{
+
+The class of returned matrix is nPairs and matrix. There is a summary method,
+which shows the opposite information - counts how many times each variable is 
+known, while the other variable of a pair is not. See examples.
+
+}
+
 \value{
 
 Matrix of order \eqn{k}, where \eqn{k} is the number of columns in \code{x}.
@@ -65,6 +73,8 @@
 ## Margin
 nPairs(x=test, margin=TRUE)
 
+## Summary
+summary(object=nPairs(x=test))
 }
 
 \keyword{misc}


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1463] trunk/gplots/R/heatmap.2.R

From: <wa...@us...> - 2010-12-13 16:44:24

Revision: 1463
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1463&view=rev
Author:   warnes
Date:     2010-12-13 16:44:17 +0000 (Mon, 13 Dec 2010)

Log Message:
-----------
Correct error that arises when data includes NA values, identified by Melissa Key

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

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2010-11-12 19:14:06 UTC (rev 1462)
+++ trunk/gplots/R/heatmap.2.R	2010-12-13 16:44:17 UTC (rev 1463)
@@ -493,8 +493,8 @@
         {
           max.raw <- max(abs(c(x,breaks)),na.rm=TRUE)
           min.raw <- -max.raw
-          tmpbreaks[1] <- -max(abs(x))
-          tmpbreaks[length(tmpbreaks)] <- max(abs(x))
+          tmpbreaks[1] <- -max(abs(x), na.rm=TRUE)
+          tmpbreaks[length(tmpbreaks)] <- max(abs(x), na.rm=TRUE)
         }
       else
         {


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1462] trunk/gdata/inst/NEWS

From: <wa...@us...> - 2010-11-12 19:14:12

Revision: 1462
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1462&view=rev
Author:   warnes
Date:     2010-11-12 19:14:06 +0000 (Fri, 12 Nov 2010)

Log Message:
-----------
Update NEWS for gdata 2.8.1

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

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2010-11-12 19:09:00 UTC (rev 1461)
+++ trunk/gdata/inst/NEWS	2010-11-12 19:14:06 UTC (rev 1462)
@@ -1,3 +1,19 @@
+CHANGES IN 2.8.1 (2010-11-12)
+-----------------------------
+
+Enhancements:
+
+- Minor improvement to Args(), read.xls() man page.
+
+Bug fixes:
+
+- Modify write.fwf() to capture and pass on additional arguments for
+  write.table(). This resolves a bug reported by Jan Wijffels.
+
+- Modify xls2sep.R to avoid use of file.access() which is unreliable
+  on Windows network shares.
+
+
 CHANGES IN 2.8.0 (2010-04-03)
 -----------------------------
 
@@ -15,9 +31,9 @@
   installXLSXsupport() function to attempt to install the necessary
   perl libraries.
 
-- The function function installXLSXsupport() has been provided to
-  install the binary perl modules that read.xls needs to support Excel
-  2007+ 'XLSX' files.
+- The function installXLSXsupport() has been provided to install the
+  binary perl modules that read.xls needs to support Excel 2007+
+  'XLSX' files.
 
 
 CHANGES IN 2.7.3 (2010-04-02)


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1461] trunk/gdata/DESCRIPTION

From: <wa...@us...> - 2010-11-12 19:09:06

Revision: 1461
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1461&view=rev
Author:   warnes
Date:     2010-11-12 19:09:00 +0000 (Fri, 12 Nov 2010)

Log Message:
-----------
Update DEScription file for 2.8.1 release

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

Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION	2010-11-12 19:08:39 UTC (rev 1460)
+++ trunk/gdata/DESCRIPTION	2010-11-12 19:09:00 UTC (rev 1461)
@@ -3,8 +3,8 @@
 Description: Various R programming tools for data manipulation
 Depends: R (>= 2.6.0)
 Imports: gtools
-Version: 2.8.0
-Date: 2010-04-03
+Version: 2.8.1
+Date: 2010-11-12
 Author: Gregory R. Warnes, with contributions from Ben Bolker, Gregor Gorjanc, 
         Gabor Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, 
         Arni Magnusson, Jim Rogers, and others


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1460] trunk/gdata/tests

From: <wa...@us...> - 2010-11-12 19:08:45

Revision: 1460
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1460&view=rev
Author:   warnes
Date:     2010-11-12 19:08:39 +0000 (Fri, 12 Nov 2010)

Log Message:
-----------
Update test output to match latest code

Modified Paths:
--------------
    trunk/gdata/tests/test.read.xls.Rout.save
    trunk/gdata/tests/tests.write.fwf.Rout.save

Modified: trunk/gdata/tests/test.read.xls.Rout.save
===================================================================
--- trunk/gdata/tests/test.read.xls.Rout.save	2010-11-12 19:08:12 UTC (rev 1459)
+++ trunk/gdata/tests/test.read.xls.Rout.save	2010-11-12 19:08:39 UTC (rev 1460)
@@ -1,14 +1,13 @@
 
-R version 2.11.0 (2010-04-22)
+R version 2.12.0 (2010-10-15)
 Copyright (C) 2010 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
+Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
 Type 'license()' or 'licence()' for distribution details.
 
-  Natural language support but running in an English locale
-
 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.
@@ -18,7 +17,10 @@
 Type 'q()' to quit R.
 
 > library(gdata)
+gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
 
+gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
+
 Attaching package: 'gdata'
 
 The following object(s) are masked from 'package:utils':
@@ -26,14 +28,15 @@
     object.size
 
 > 
+> if ( ! 'XLSX' %in% xlsFormats() )
++   {
++     try( installXLSXModules() )
++   }
 > 
 > # iris.xls is included in the gregmisc package for use as an example
 > xlsfile <- file.path(.path.package('gdata'),'xls','iris.xls')
 > 
 > iris.1 <- read.xls(xlsfile) # defaults to csv format
-WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
-WARNING: Perl module Spreadsheet::XLSX cannot be loaded.
-WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
 > iris.1
     Sepal.Length Sepal.Width Petal.Length Petal.Width     Species
 1            5.1         3.5          1.4         0.2     setosa 
@@ -188,9 +191,6 @@
 150          5.9         3.0          5.1         1.8  virginica 
 > 
 > iris.2 <- read.xls(xlsfile,method="csv") # specify csv format
-WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
-WARNING: Perl module Spreadsheet::XLSX cannot be loaded.
-WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
 > iris.2
     Sepal.Length Sepal.Width Petal.Length Petal.Width     Species
 1            5.1         3.5          1.4         0.2     setosa 
@@ -345,9 +345,6 @@
 150          5.9         3.0          5.1         1.8  virginica 
 > 
 > iris.3 <- read.xls(xlsfile,method="tab") # specify tab format
-WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
-WARNING: Perl module Spreadsheet::XLSX cannot be loaded.
-WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
 > iris.3
     Sepal.Length Sepal.Width Petal.Length Petal.Width     Species
 1            5.1         3.5          1.4         0.2     setosa 
@@ -512,28 +509,22 @@
 > 
 > # see the number and names of sheets:
 > sheetCount(exampleFile)
-WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
-WARNING: Perl module Spreadsheet::XLSX cannot be loaded.
-WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
 [1] 4
 > 
 > if( 'XLSX' %in% xlsFormats() )
 +   sheetCount(exampleFile2007)
+[1] 4
 > 
 > sheetNames(exampleFile)
-WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
-WARNING: Perl module Spreadsheet::XLSX cannot be loaded.
-WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
 [1] "Sheet First"                  "Sheet Second"                
 [3] "Sheet with a very long name!" "Sheet with initial text"     
 > 
 > if( 'XLSX' %in% xlsFormats() )
 +   sheetNames(exampleFile2007)
+[1] "Sheet First"                  "Sheet Second"                
+[3] "Sheet with a very long name!" "Sheet with initial text"     
 > 
 > example.1 <- read.xls(exampleFile, sheet=1) # default is first worksheet
-WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
-WARNING: Perl module Spreadsheet::XLSX cannot be loaded.
-WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
 > example.1
   A  B   C
 1 1  1   1
@@ -545,9 +536,6 @@
 7 7 49 343
 > 
 > example.2 <- read.xls(exampleFile, sheet=2) # second worksheet by number
-WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
-WARNING: Perl module Spreadsheet::XLSX cannot be loaded.
-WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
 > example.2
           X D  E  F  G Factor
 1  FirstRow 1 NA NA NA   Red 
@@ -556,9 +544,6 @@
 4 FourthRow 4  3  2  1 Black 
 > 
 > example.3 <- read.xls(exampleFile, sheet=3) # second worksheet by number
-WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
-WARNING: Perl module Spreadsheet::XLSX cannot be loaded.
-WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
 > example.3
   X1 X2001.01.01 X1.01 X0.205818150587141   X.DIV.0.  A
 1  2  2002-02-02  2:02          0.2910708         NA B 
@@ -572,9 +557,6 @@
 9 10  2010-10-10 10:10          0.6508541  0.0000000 A 
 > 
 > example.4 <- read.xls(exampleFile, sheet=3) # second worksheet by number
-WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
-WARNING: Perl module Spreadsheet::XLSX cannot be loaded.
-WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
 > example.4
   X1 X2001.01.01 X1.01 X0.205818150587141   X.DIV.0.  A
 1  2  2002-02-02  2:02          0.2910708         NA B 
@@ -608,7 +590,47 @@
 +   data <- read.xls(exampleFile2007, sheet="Sheet with initial text", skip=2)
 +   print(data)
 + }
+  A  B   C
+1 1  1   1
+2 2  4   8
+3 3  9  27
+4 4 16  64
+5 5 25 125
+6 6 36 216
+7 7 49 343
+          X D  E  F  G Factor
+1  FirstRow 1 NA NA NA   Red 
+2 SecondRow 2  1 NA NA Green 
+3  ThirdRow 3  2  1 NA   Red 
+4 FourthRow 4  3  2  1 Black 
+  X1 X2001.01.01 X1.01 X0.205818150587141   X.DIV.0.  A
+1  2  2002-02-02  2:02          0.2910708         NA B 
+2  3  2003-03-03  3:03          0.3564875 -0.8414710 C 
+3  4  2004-04-04  4:04          0.4116363  0.7080734   
+4  5  2005-05-05  5:05          0.4602234  0.5013680 A 
+5  6  2006-06-06  6:06                 NA  0.2513698 B 
+6  7  2007-07-07  7:07          0.5445436  0.0631868 B 
+7  8  2008-08-08  8:08          0.5821416         NA C 
+8  9  2009-09-09  9:09          0.6174545  0.0000000 A 
+9 10  2010-10-10 10:10          0.6508541  0.0000000 A 
+  X1 X2001.01.01 X1.01 X0.205818150587141   X.DIV.0.  A
+1  2  2002-02-02  2:02          0.2910708         NA B 
+2  3  2003-03-03  3:03          0.3564875 -0.8414710 C 
+3  4  2004-04-04  4:04          0.4116363  0.7080734   
+4  5  2005-05-05  5:05          0.4602234  0.5013680 A 
+5  6  2006-06-06  6:06                 NA  0.2513698 B 
+6  7  2007-07-07  7:07          0.5445436  0.0631868 B 
+7  8  2008-08-08  8:08          0.5821416         NA C 
+8  9  2009-09-09  9:09          0.6174545  0.0000000 A 
+9 10  2010-10-10 10:10          0.6508541  0.0000000 A 
+          X D  E  F  G Factor
+1  FirstRow 1 NA NA NA   Red 
+2 SecondRow 2  1 NA NA Green 
+3  ThirdRow 3  2  1 NA   Red 
+4 FourthRow 4  3  2  1 Black 
+   X       X.1 D  E  F  G Factor
+1 NA  FirstRow 1 NA NA NA   Red 
+2 NA SecondRow 2  1 NA NA Green 
+3 NA  ThirdRow 3  2  1 NA   Red 
+4 NA FourthRow 4  3  2  1 Black 
 > 
-> proc.time()
-   user  system elapsed 
-  1.350   0.285   1.659 

Modified: trunk/gdata/tests/tests.write.fwf.Rout.save
===================================================================
--- trunk/gdata/tests/tests.write.fwf.Rout.save	2010-11-12 19:08:12 UTC (rev 1459)
+++ trunk/gdata/tests/tests.write.fwf.Rout.save	2010-11-12 19:08:39 UTC (rev 1460)
@@ -1,7 +1,8 @@
 
-R version 2.9.0 (2009-04-17)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.12.0 (2010-10-15)
+Copyright (C) 2010 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
+Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -23,14 +24,16 @@
 > ###------------------------------------------------------------------------
 > 
 > library(gdata)
+gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
 
+gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
+
 Attaching package: 'gdata'
 
+The following object(s) are masked from 'package:utils':
 
-The following object(s) are masked from package:utils :
+    object.size
 
-	 object.size 
-
 > 
 > ## --- Test data ---
 > 


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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1459] trunk/gdata

From: <wa...@us...> - 2010-11-12 19:08:23

Revision: 1459
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1459&view=rev
Author:   warnes
Date:     2010-11-12 19:08:12 +0000 (Fri, 12 Nov 2010)

Log Message:
-----------
Modify write.fwf() to capture and pass on additional arguments for
write.table().  This resolves a bug reported by Jan Wijffels.

Modified Paths:
--------------
    trunk/gdata/R/write.fwf.R
    trunk/gdata/man/write.fwf.Rd

Added Paths:
-----------
    trunk/gdata/tests/test.write.fwf.eol.R

Modified: trunk/gdata/R/write.fwf.R
===================================================================
--- trunk/gdata/R/write.fwf.R	2010-11-12 02:59:29 UTC (rev 1458)
+++ trunk/gdata/R/write.fwf.R	2010-11-12 19:08:12 UTC (rev 1459)
@@ -5,10 +5,22 @@
 ### Time-stamp: <2008-08-05 12:11:27 ggorjan>
 ###------------------------------------------------------------------------
 
-write.fwf <- function(x, file="", append=FALSE, quote=FALSE, sep=" ",
-                      na="", rownames=FALSE, colnames=TRUE, rowCol=NULL,
-                      justify="left", formatInfo=FALSE, quoteInfo=TRUE,
-                      width=NULL, ...)
+write.fwf <- function(x,
+                      file="",
+                      append=FALSE,
+                      quote=FALSE,
+                      sep=" ",
+                      na="",
+                      rownames=FALSE,
+                      colnames=TRUE,
+                      rowCol=NULL,
+                      justify="left",
+                      formatInfo=FALSE,
+                      quoteInfo=TRUE,
+                      width=NULL,
+                      eol="\n",
+                      qmethod=c("escape", "double"),
+                      ...)
 {
   ## --- Setup ---
 
@@ -137,12 +149,28 @@
 
   if(colnames) {
     if(rownames && is.null(rowCol)) colnamesMy <- colnamesMy[-1]
-    write.table(t(as.matrix(colnamesMy)), file=file, append=append,
-                quote=quote, sep=sep, row.names=FALSE, col.names=FALSE, ...)
-  }
+    write.table(t(as.matrix(colnamesMy)),
+                file=file,
+                append=append,
+                quote=quote,
+                sep=sep,
+                eol=eol,
+                na=na,
+                row.names=FALSE,
+                col.names=FALSE,
+                qmethod=qmethod) 
+ }
 
-  write.table(x=x, file=file, append=(colnames || append), quote=quote,
-              sep=sep, row.names=FALSE, col.names=FALSE, ...)
+  write.table(x=x,
+              file=file,
+              append=(colnames || append),
+              quote=quote,
+              sep=sep,
+              eol=eol,
+              na=na,
+              row.names=FALSE,
+              col.names=FALSE,
+              qmethod=qmethod)
 
   ## --- Return format and fixed width information ---
 

Modified: trunk/gdata/man/write.fwf.Rd
===================================================================
--- trunk/gdata/man/write.fwf.Rd	2010-11-12 02:59:29 UTC (rev 1458)
+++ trunk/gdata/man/write.fwf.Rd	2010-11-12 19:08:12 UTC (rev 1459)
@@ -22,7 +22,8 @@
 
 write.fwf(x, file="", append=FALSE, quote=FALSE, sep=" ", na="",
   rownames=FALSE, colnames=TRUE, rowCol=NULL, justify="left",
-  formatInfo=FALSE, quoteInfo=TRUE, width=NULL, \dots)
+  formatInfo=FALSE, quoteInfo=TRUE, width=NULL, eol="\n",
+  qmethod=c("escape", "double"),  \dots)
 
 }
 
@@ -44,8 +45,18 @@
     widths and format}
   \item{quoteInfo}{logical, should \code{formatInfo} account for quotes}
   \item{width}{numeric, width of the columns in the output}
-  \item{\dots}{further arguments to \code{\link{format.info}},
-    \code{\link{format}} and \code{\link{write.table}}}
+  \item{eol}{the character(s) to print at the end of each line (row).
+    For example, 'eol="\\r\\n"' will produce Windows' line endings on a
+    Unix-alike OS, and 'eol="\\r"' will produce files as expected by Mac
+    OS Excel 2004.}
+  \item{qmethod}{a character string specifying how to deal with embedded
+    double quote characters when quoting strings.  Must be one of
+    '"escape"' (default), in which case the quote character is
+    escaped in C style by a backslash, or '"double"', in which
+    case it is doubled.  You can specify just the initial letter.}
+  \item{\dots}{further arguments to
+    \code{\link{format.info}} and \code{\link{format}}
+  }
 }
 
 \details{

Added: trunk/gdata/tests/test.write.fwf.eol.R
===================================================================
--- trunk/gdata/tests/test.write.fwf.eol.R	                        (rev 0)
+++ trunk/gdata/tests/test.write.fwf.eol.R	2010-11-12 19:08:12 UTC (rev 1459)
@@ -0,0 +1,5 @@
+library(gdata)
+saveto <- tempfile(pattern = "test.txt", tmpdir = tempdir())
+
+write.fwf(x = data.frame(a=1:length(LETTERS), b=LETTERS),
+          file=saveto, eol="\r\n")


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