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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1652] trunk/SASxport/man

From: <wa...@us...> - 2013-05-11 20:06:58

Revision: 1652
          http://sourceforge.net/p/r-gregmisc/code/1652
Author:   warnes
Date:     2013-05-11 20:06:55 +0000 (Sat, 11 May 2013)
Log Message:
-----------
Replace file.path(path.package(...)) with system.file(...)

Modified Paths:
--------------
    trunk/SASxport/man/Alfalfa.Rd
    trunk/SASxport/man/lookup.xport.Rd

Modified: trunk/SASxport/man/Alfalfa.Rd
===================================================================
--- trunk/SASxport/man/Alfalfa.Rd	2013-05-11 20:05:57 UTC (rev 1651)
+++ trunk/SASxport/man/Alfalfa.Rd	2013-05-11 20:06:55 UTC (rev 1652)
@@ -30,7 +30,7 @@
 
 # go were the data is...
 here <- getwd()
-setwd(file.path(path.package("SASxport"),"extdata"))
+setwd(system.file("extdata",package="SASxport"))
 
 # Description of the file contents
 lookup.xport("Alfalfa.xpt")

Modified: trunk/SASxport/man/lookup.xport.Rd
===================================================================
--- trunk/SASxport/man/lookup.xport.Rd	2013-05-11 20:05:57 UTC (rev 1651)
+++ trunk/SASxport/man/lookup.xport.Rd	2013-05-11 20:06:55 UTC (rev 1652)
@@ -45,7 +45,8 @@
 }
 \examples{
 \dontshow{
-setwd(file.path(path.package("SASxport"),"extData"))
+setwd(system.file("extdata", package="SASxport"))
+
 }
 ## Get information on a local file
 lookup.xport("Alfalfa.xpt")

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1651] trunk/SASxport/tests

From: <wa...@us...> - 2013-05-11 20:05:59

Revision: 1651
          http://sourceforge.net/p/r-gregmisc/code/1651
Author:   warnes
Date:     2013-05-11 20:05:57 +0000 (Sat, 11 May 2013)
Log Message:
-----------
Carry bug fix forward to handle loading xport data when a dataset ends on exactly 80 byte block boundry.

Added Paths:
-----------
    trunk/SASxport/tests/events.csv
    trunk/SASxport/tests/exposure.csv
    trunk/SASxport/tests/testBlockBoundary.R

Added: trunk/SASxport/tests/events.csv
===================================================================
--- trunk/SASxport/tests/events.csv	                        (rev 0)
+++ trunk/SASxport/tests/events.csv	2013-05-11 20:05:57 UTC (rev 1651)
@@ -0,0 +1,11 @@
+"NID","TIME","DINTV","EVID","AUC","CMAX","TMAX","RT","CMIN","IPRED","CWRES","DV","PRED","RES","WRES"
+1,0,1,1,0,-1,-1,-1,9999,0,0,0,0,0,0
+1,1,1,0,7.8964,14.918,1,1,14.918,14.918,-3.0776,5.24,24.54,-19.3,-3.3211
+1,2,1,2,22.436,15.298,1.2179,1.2179,12.845,12.845,0,0,14.455,0,0
+1,3,1,2,32.934,15.298,1.2179,1.2179,8.2815,8.2815,0,0,9.0077,0,0
+1,4,1,2,39.464,15.298,1.2179,1.2179,5.0233,5.0233,0,0,5.9024,0,0
+1,5,1,2,43.403,15.298,1.2179,1.2179,3.0246,3.0246,0,0,4.0132,0,0
+1,6,1,2,45.78,15.298,1.2179,1.2179,1.8323,1.8323,0,0,2.7974,0,0
+1,7,1,2,47.224,15.298,1.2179,1.2179,1.1164,1.1164,0,0,1.9773,0,0
+1,8,1,2,48.105,15.298,1.2179,1.2179,0.68056,0.68057,0,0,1.4036,0,0
+1,9,1,2,48.641,15.298,1.2179,1.2179,0.41253,0.41253,0,0,0.99249,0,0

Added: trunk/SASxport/tests/exposure.csv
===================================================================
--- trunk/SASxport/tests/exposure.csv	                        (rev 0)
+++ trunk/SASxport/tests/exposure.csv	2013-05-11 20:05:57 UTC (rev 1651)
@@ -0,0 +1,2 @@
+"NID","DINTV","CMAX","TMAX","CMIN","AUC"
+NA,NA,NA,NA,NA,NA

Added: trunk/SASxport/tests/testBlockBoundary.R
===================================================================
--- trunk/SASxport/tests/testBlockBoundary.R	                        (rev 0)
+++ trunk/SASxport/tests/testBlockBoundary.R	2013-05-11 20:05:57 UTC (rev 1651)
@@ -0,0 +1,33 @@
+##  This script tests an edge case where a dataset ends exactly on a
+##  block boundery.  Previously, this could lead to an error in
+##  loading the created data file.
+
+library(SASxport)
+events <- read.csv('events.csv')
+exposure <- read.csv('exposure.csv')
+events
+exposure
+
+
+write.xport(events,exposure,file='dat.xpt')
+write.xport(exposure,events,file='tad.xpt')
+
+l1.s <- SASxport::lookup.xport('dat.xpt')
+l2.s <- SASxport::lookup.xport('tad.xpt')
+
+stopifnot( identical( l1.s$EXPOSURE, l2.s$EXPOSURE) ) 
+stopifnot( identical( l1.s$EVENTS,   l2.s$EVENTS  ) )
+
+d1.s <- SASxport::read.xport(file='dat.xpt')
+d2.s <- SASxport::read.xport(file='tad.xpt')
+
+stopifnot( identical( d1.s$EXPOSURE, d2.s$EXPOSURE) )
+stopifnot( identical( d1.s$EVENTS,   d2.s$EVENTS)   )
+
+
+
+
+
+
+
+

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1650] trunk/SASxport/R/zzz.R

From: <wa...@us...> - 2013-05-11 17:00:02

Revision: 1650
          http://sourceforge.net/p/r-gregmisc/code/1650
Author:   warnes
Date:     2013-05-11 16:59:58 +0000 (Sat, 11 May 2013)
Log Message:
-----------
Remove obsolete .First.lib()

Modified Paths:
--------------
    trunk/SASxport/R/zzz.R

Modified: trunk/SASxport/R/zzz.R
===================================================================
--- trunk/SASxport/R/zzz.R	2013-03-24 05:42:57 UTC (rev 1649)
+++ trunk/SASxport/R/zzz.R	2013-05-11 16:59:58 UTC (rev 1650)
@@ -10,12 +10,6 @@
 }
 
 
-
-.First.lib <- function(lib, pkg) {
-  library.dynam("SASxport", pkg, lib)
-  loadMessage()
-}
-
 .onLoad <- function(lib, pkg) {
   loadMessage()
 }

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1649] trunk/SASxport

From: <wa...@us...> - 2013-03-24 05:43:00

Revision: 1649
          http://sourceforge.net/p/r-gregmisc/code/1649
Author:   warnes
Date:     2013-03-24 05:42:57 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Update for release 1.3.1

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

Modified: trunk/SASxport/DESCRIPTION
===================================================================
--- trunk/SASxport/DESCRIPTION	2013-03-24 05:41:53 UTC (rev 1648)
+++ trunk/SASxport/DESCRIPTION	2013-03-24 05:42:57 UTC (rev 1649)
@@ -1,34 +1,34 @@
 Package: SASxport
 Type: Package
 Title: Read and Write SAS XPORT Files
-Version: 1.3.0
-Date: 2012-06-29
+Version: 1.3.1
+Date: 2013-03-24
 Description: This package provides functions for reading, listing
-  the contents of, and writing SAS xport format files. 
+  the contents of, and writing SAS xport format files.
   The functions support reading and writing of either
   individual data frames or sets of data frames.  Further,
   a mechanism has been provided for customizing how
-  variables of different data types are stored. 
-Author: 
+  variables of different data types are stored.
+Author:
   Unless otherwise noted, the contents of this package were written by
   Gregory R. Warnes <gr...@wa...> and are provided under the
-  terms of the GNU General Public License, version 2.0 or later. 
+  terms of the GNU General Public License, version 2.0 or later.
   --
-  The files 'ieee2ibm.c' and 'ibm2ieee.c' were extracted from BRL-CAD, 
-  file /brlcad/src/libbu/htond.c written by Michael John Muuss, 
+  The files 'ieee2ibm.c' and 'ibm2ieee.c' were extracted from BRL-CAD,
+  file /brlcad/src/libbu/htond.c written by Michael John Muuss,
   Copyright (c) 2004-2007 United States Government as represented by
   the U.S. Army Research Laboratory, and is utilized and redistributed
   under the terms of the  GNU Lesser General Public License, version 2.1.
   --
   The files 'AFirst.lib.s', 'all.is.numeric.R',
-  'importConvertDateTime.R', 'in.opererator.R', 'makeNames.R', 
+  'importConvertDateTime.R', 'in.opererator.R', 'makeNames.R',
   'read.xport.R', and 'testDateTime.R' are copied or adapted from the
-  'Hmisc' package created by Frank E. Harrell, Jr. 
+  'Hmisc' package created by Frank E. Harrell, Jr.
   <f.h...@va...>, and are utilized and redistributed under
-  the terms of the GNU General Public License, version 2.0 or later. 
-  --     
+  the terms of the GNU General Public License, version 2.0 or later.
+  --
   The creation of this package was partially funded by Metrum Institute
-  <http://metruminstitute.org>.  
+  <http://metruminstitute.org>.
 Maintainer: Gregory R. Warnes <gr...@wa...>
 License: GPL-2
 Depends: R (>= 2.4.0)

Modified: trunk/SASxport/inst/NEWS
===================================================================
--- trunk/SASxport/inst/NEWS	2013-03-24 05:41:53 UTC (rev 1648)
+++ trunk/SASxport/inst/NEWS	2013-03-24 05:42:57 UTC (rev 1649)
@@ -1,3 +1,10 @@
+Version 1.3.1 2013-03-24
+------------------------
+
+Changes:
+
+- Replace use of depreciated .path.package() with path.package() for R 3.0.0.
+
 Version 1.3.0 2012-06-27
 ------------------------
 
@@ -37,7 +44,7 @@
 Bug fixes:
 
 -  Apply patches to fix problems on 64 bit platforms, as sumitted by
-   Brian Ripley.  
+   Brian Ripley.
 
 
 Version 1.2.1 2007-11-05
@@ -63,27 +70,27 @@
 - Copies of the code for foreign::read.xport and foreign::lookup.xport
   is now part of the SASxport package, permitting extension to these
   functions as needed, and removing the dependency on the foreign
-  package. 
+  package.
 
 - Overflow of SASxport numeric format values, which have a smaller
   range than IEEE 754 numeric values now standard,  now generates NAN
-  instead of 0.0.  
+  instead of 0.0.
 
 
 Bug Fixes:
 
 - Fix for problem storing negative numbers.
 
-- SAS format length and digit information is now properly captured 
+- SAS format length and digit information is now properly captured
   by read.xport().  This is supported by an improved version of
-  lookup.xport(). 
+  lookup.xport().
 
-- SAS format information was not being properly utilized when more 
+- SAS format information was not being properly utilized when more
   than one format was present.
 
 - Improved handling of SAS date formats
- 
 
+
 Other:
 
 - Test routines added to test handling of numeric values.
@@ -95,7 +102,7 @@
 -  Display support information at package startup
 
 
-Version 1.1.0 - 
+Version 1.1.0 -
 -------------------------
 
 New Features:
@@ -133,7 +140,7 @@
 New features:
 
 - read.xport's names.tolower argument now defaults to FALSE so that
-  variable (and data set) names are now left as uppercase. 
+  variable (and data set) names are now left as uppercase.
 
 - Improved crediting of BRL-CAD source code
 
@@ -143,7 +150,7 @@
 
 Other:
 
-- Augmented ieee2ibm code with corresponding ibm2ieee code for 
+- Augmented ieee2ibm code with corresponding ibm2ieee code for
   completeness.
 
 
@@ -152,7 +159,7 @@
 
 New Features:
 
-- Replaced IEEE to IBM translation code with GPL'ed version from BPL-CAD. 
+- Replaced IEEE to IBM translation code with GPL'ed version from BPL-CAD.
 
 Bug Fixes:
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1648] trunk/SASxport/man

From: <wa...@us...> - 2013-03-24 05:41:56

Revision: 1648
          http://sourceforge.net/p/r-gregmisc/code/1648
Author:   warnes
Date:     2013-03-24 05:41:53 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Replace obsolete use of .path.package() with path.package()

Modified Paths:
--------------
    trunk/SASxport/man/Alfalfa.Rd
    trunk/SASxport/man/lookup.xport.Rd

Modified: trunk/SASxport/man/Alfalfa.Rd
===================================================================
--- trunk/SASxport/man/Alfalfa.Rd	2013-03-24 05:21:31 UTC (rev 1647)
+++ trunk/SASxport/man/Alfalfa.Rd	2013-03-24 05:41:53 UTC (rev 1648)
@@ -30,7 +30,7 @@
 
 # go were the data is...
 here <- getwd()
-setwd(file.path(.path.package("SASxport"),"extdata"))
+setwd(file.path(path.package("SASxport"),"extdata"))
 
 # Description of the file contents
 lookup.xport("Alfalfa.xpt")

Modified: trunk/SASxport/man/lookup.xport.Rd
===================================================================
--- trunk/SASxport/man/lookup.xport.Rd	2013-03-24 05:21:31 UTC (rev 1647)
+++ trunk/SASxport/man/lookup.xport.Rd	2013-03-24 05:41:53 UTC (rev 1648)
@@ -45,7 +45,7 @@
 }
 \examples{
 \dontshow{
-setwd(file.path(.path.package("SASxport"),"extData"))
+setwd(file.path(path.package("SASxport"),"extData"))
 }
 ## Get information on a local file
 lookup.xport("Alfalfa.xpt")

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1647] trunk/gplots/inst/NEWS

From: <wa...@us...> - 2013-03-24 05:21:33

Revision: 1647
          http://sourceforge.net/p/r-gregmisc/code/1647
Author:   warnes
Date:     2013-03-24 05:21:31 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Update news for release 2.11.2

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

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2013-03-24 05:19:04 UTC (rev 1646)
+++ trunk/gplots/inst/NEWS	2013-03-24 05:21:31 UTC (rev 1647)
@@ -1,3 +1,17 @@
+Release 2.11.2 - 2013-03-24
+---------------------------
+
+Enhancements:
+
+- Add ci.width argument to barplot2() to allow varying the length of
+  the 't' at the end of confidence interval bars.
+
+Updates:
+
+- Update manual page for lowess.default() to
+  match changed argument list for lowess() in R 3.0.0
+
+
 Release 2.11.1 - 2012-12-14
 ---------------------------
 
@@ -41,7 +55,7 @@
 New Features:
 
 - New ci2d() function to create 2-dimensional empirical confidence
-  intervals utilizing KernSmooth:bkde2D and gplots::hist2d().  
+  intervals utilizing KernSmooth:bkde2D and gplots::hist2d().
   See ?ci2d for details.
 
 - Add 'alpha' argument to rich.colors() to control transparency.
@@ -66,7 +80,7 @@
 - venn() now returns an object of class venn() and a plot method for
   this class is provided.
 
-- Manual page for venn has been improved, based on contributions by 
+- Manual page for venn has been improved, based on contributions by
   Steffen Moeller
 
 
@@ -75,7 +89,7 @@
 
 Improvements:
 
-- Performance of 'hist2d' improved thanks to a suggestion from 
+- Performance of 'hist2d' improved thanks to a suggestion from
   Joerg van den Hoff.
 
 Release 2.7.4 - 2009-11-12
@@ -126,14 +140,14 @@
       colDendrogram, breaks, col, vline, hline, and colorTable. Of
       these, the most useful are breaks, col, and colorTable.  The
       latter is a three-column data frame providing the lower and
-      upper bound and color for each bin.  
+      upper bound and color for each bin.
 
   See the manual page for complete details and examples.
 
 
 - New function venn(), contributed by Steffen Moeller (Thanks
   Steffen!) to generate Venn diagrams for up to 5 sets. See ?venn for
-  details. 
+  details.
 
 - Performance of bandplot() has been dramatically improved, in part by
   using runsd() and runmean() from the caTools package.  As a
@@ -151,10 +165,10 @@
 Bug Fixes:
 
 - balloonplot() now properly handles dimension labels provided by
-  'xlab' and 'ylab' 
+  'xlab' and 'ylab'
 
 - plotCI now properly handles 'NULL' and 'NA' values for ui, li, uiw,
-  and liw. 
+  and liw.
 
 - Corrections of minor typos in man pages
 
@@ -164,7 +178,7 @@
 Release 2.6.0 - 2008-04-07
 --------------------------
 
-New Features: 
+New Features:
 
 - heatmap() now allows control of the location of individual plot components
    (e.g. color key)
@@ -179,7 +193,7 @@
 
 - Restore plot layout settings to default state at end of ooplot() example
 
-- Various typo fixes 
+- Various typo fixes
 
 Release 2.5.0 - 2007-11-02
 --------------------------
@@ -187,7 +201,7 @@
 New Features:
 
 - textplot() now converts tab characters to spaces before processing to
-  avoid problems with computing height and width of text that includes 
+  avoid problems with computing height and width of text that includes
   tabs.
 
 - Add col2hex() function to convert color names to rgb hex codes
@@ -195,7 +209,7 @@
 Bug Fixes:
 
 - Correct balloonplot.default to properly show specified x and y axis
-  labels when explicitly provided 
+  labels when explicitly provided
 
 - R/balloonplot.R: Correct error in balloonplot when z contains NA values.
 
@@ -204,7 +218,7 @@
 Other:
 
 - Clarify GPL version
-  
+
 Release 2.4.0 - 2007-02-08
 --------------------------
 
@@ -218,7 +232,7 @@
 Bug Fixes:
 
 
-Other: 
+Other:
 
 
 Release 2.3.2 - 2006-11-14
@@ -254,9 +268,9 @@
 -------------
 
  - plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza's
-	        suggestion (the function didn't account for factors 
+	        suggestion (the function didn't account for factors
 		unused levels, returning an error.)
- 
+
  - exported plot.lm to NAMESPACE, Remove .Alias calls in plot.lm.R
  		since .Alias is defunct.
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1646] trunk/gplots

From: <wa...@us...> - 2013-03-24 05:19:07

Revision: 1646
          http://sourceforge.net/p/r-gregmisc/code/1646
Author:   warnes
Date:     2013-03-24 05:19:04 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Add ci.width argument to barplot2() to allow varying the length of the 't' at the end of confidence interval bars.

Modified Paths:
--------------
    trunk/gplots/R/barplot2.R
    trunk/gplots/man/barplot2.Rd

Modified: trunk/gplots/R/barplot2.R
===================================================================
--- trunk/gplots/R/barplot2.R	2013-03-24 04:50:22 UTC (rev 1645)
+++ trunk/gplots/R/barplot2.R	2013-03-24 05:19:04 UTC (rev 1646)
@@ -12,30 +12,60 @@
 barplot2 <- function(height, ...) UseMethod("barplot2")
 
 barplot2.default <-
-  function(
-           height,
-           width = 1,
-           space = NULL,
-           names.arg = NULL,
-           legend.text = NULL,
-           beside = FALSE,
-           horiz = FALSE,
-           density = NULL,
-           angle = 45,
-           col = NULL,
-           prcol = NULL,
-           border = par("fg"),
-           main = NULL,
-           sub = NULL, xlab = NULL, ylab = NULL,
-       xlim = NULL, ylim = NULL, xpd = TRUE, log = "",
-       axes = TRUE, axisnames = TRUE,
-       cex.axis = par("cex.axis"), cex.names = par("cex.axis"),
-       inside = TRUE, plot = TRUE, axis.lty = 0, offset = 0,
-       plot.ci = FALSE, ci.l = NULL, ci.u = NULL,
-       ci.color = "black", ci.lty = "solid", ci.lwd = 1,
-       plot.grid = FALSE, grid.inc = NULL,
-       grid.lty = "dotted", grid.lwd = 1, grid.col = "black",
-       add = FALSE, panel.first = NULL, panel.last = NULL, ...)
+    function(
+        height,
+        width = 1,
+        space = NULL,
+        names.arg = NULL,
+        legend.text = NULL,
+        beside = FALSE,
+        horiz = FALSE,
+        density = NULL,
+        angle = 45,
+        col = NULL,
+        prcol = NULL,
+        border = par("fg"),
+        main = NULL,
+        sub = NULL,
+         xlab = NULL,
+         ylab = NULL,
+
+        xlim = NULL,
+        ylim = NULL,
+        xpd = TRUE,
+        log = "",
+
+        axes = TRUE,
+        axisnames = TRUE,
+
+        cex.axis = par("cex.axis"),
+        cex.names = par("cex.axis"),
+
+        inside = TRUE,
+        plot = TRUE,
+        axis.lty = 0,
+        offset = 0,
+
+        plot.ci = FALSE,
+        ci.l = NULL,
+        ci.u = NULL,
+
+        ci.color = "black",
+        ci.lty = "solid",
+        ci.lwd = 1,
+        ci.width = 0.5,
+
+        plot.grid = FALSE,
+        grid.inc = NULL,
+
+        grid.lty = "dotted",
+        grid.lwd = 1,
+        grid.col = "black",
+
+        add = FALSE,
+        panel.first = NULL,
+        panel.last = NULL,
+        ...)
 {
     if (!missing(inside)) .NotYetUsed("inside", error = FALSE)# -> help(.)
 
@@ -137,10 +167,10 @@
       # Check for NA values and issue warning if required
       height.na <- sum(is.na(height))
       if (height.na > 0)
-      {  
+      {
          warning(sprintf("%.0f values == NA in 'height' omitted from logarithmic plot",
                           height.na), domain = NA)
-      }   
+      }
 
       # Check for 0 values and issue warning if required
       # _FOR NOW_ change 0's to NA's so that other calculations are not
@@ -148,15 +178,15 @@
       # except for stacked bars, so don't change those.
       height.lte0 <- sum(height <= 0, na.rm = TRUE)
       if (height.lte0 > 0)
-      {  
+      {
         warning(sprintf("%0.f values <=0 in 'height' omitted from logarithmic plot",
                          height.lte0), domain = NA)
-        
+
         # If NOT stacked bars, modify 'height'
         if (beside)
           height[height <= 0] <- NA
-      }  
-      
+      }
+
       if (plot.ci && (min(ci.l) <= 0))
         stop("log scale error: at least one lower c.i. value <= 0")
 
@@ -172,12 +202,12 @@
       {
         rectbase <- c(height[is.finite(height)], ci.l)
         rectbase <- min(0.9 * rectbase[rectbase > 0])
-      }  
+      }
       else
       {
         rectbase <- height[is.finite(height)]
         rectbase <- min(0.9 * rectbase[rectbase > 0])
-      }  
+      }
 
       # if axis limit is set to < above, adjust bar base value
       # to draw a full bar
@@ -253,7 +283,7 @@
       # Execute the panel.first expression. This will work here
       # even if 'add = TRUE'
       panel.first
-      
+
       # Set plot region coordinates
       usr <- par("usr")
 
@@ -335,23 +365,23 @@
 
       # Execute the panel.last expression here
       panel.last
-      
+
       if (plot.ci)
       {
         # CI plot width = barwidth / 2
-        ci.width = width / 4
+        half.ci.width = width * ci.width / 2
 
         if (horiz)
         {
           segments(ci.l, w.m, ci.u, w.m, col = ci.color, lty = ci.lty, lwd = ci.lwd)
-          segments(ci.l, w.m - ci.width, ci.l, w.m + ci.width, col = ci.color, lty = ci.lty, lwd = ci.lwd)
-          segments(ci.u, w.m - ci.width, ci.u, w.m + ci.width, col = ci.color, lty = ci.lty, lwd = ci.lwd)
+          segments(ci.l, w.m - half.ci.width, ci.l, w.m + half.ci.width, col = ci.color, lty = ci.lty, lwd = ci.lwd)
+          segments(ci.u, w.m - half.ci.width, ci.u, w.m + half.ci.width, col = ci.color, lty = ci.lty, lwd = ci.lwd)
         }
         else
         {
           segments(w.m, ci.l, w.m, ci.u, col = ci.color, lty = ci.lty, lwd = ci.lwd)
-          segments(w.m - ci.width, ci.l, w.m + ci.width, ci.l, col = ci.color, lty = ci.lty, lwd = ci.lwd)
-          segments(w.m - ci.width, ci.u, w.m + ci.width, ci.u, col = ci.color, lty = ci.lty, lwd = ci.lwd)
+          segments(w.m - half.ci.width, ci.l, w.m + half.ci.width, ci.l, col = ci.color, lty = ci.lty, lwd = ci.lwd)
+          segments(w.m - half.ci.width, ci.u, w.m + half.ci.width, ci.u, col = ci.color, lty = ci.lty, lwd = ci.lwd)
         }
       }
 

Modified: trunk/gplots/man/barplot2.Rd
===================================================================
--- trunk/gplots/man/barplot2.Rd	2013-03-24 04:50:22 UTC (rev 1645)
+++ trunk/gplots/man/barplot2.Rd	2013-03-24 05:19:04 UTC (rev 1646)
@@ -84,8 +84,8 @@
         axes = TRUE, axisnames = TRUE,
         cex.axis = par("cex.axis"), cex.names = par("cex.axis"),
         inside = TRUE, plot = TRUE, axis.lty = 0, offset = 0,
-        plot.ci = FALSE, ci.l = NULL,
-        ci.u = NULL, ci.color = "black", ci.lty = "solid", ci.lwd = 1,
+        plot.ci = FALSE, ci.l = NULL, ci.u = NULL,
+        ci.color = "black", ci.lty = "solid", ci.lwd = 1, ci.width = 0.5,
         plot.grid = FALSE, grid.inc = NULL,
         grid.lty = "dotted", grid.lwd = 1, grid.col = "black",
         add = FALSE, panel.first = NULL, panel.last = NULL, \dots)
@@ -176,7 +176,10 @@
    the same dim structure as \code{height}.}
   \item{ci.color}{the color for the confidence interval line segments}
   \item{ci.lty}{the line type for the confidence interval line segments}
-  \item{ci.lwd}{the line width for the confidence interval line segments}
+  \item{ci.lwd}{the line width for the confidence interval line
+    segments}
+  \item{ci.width}{length of lines used for the "t" at the end of confidence
+    interval line segments, as a multple of \code{width}.  Defaults to 0.5.}
   \item{plot.grid}{if \code{TRUE} a lined grid will be plotted behind the bars}
   \item{grid.inc}{the number of grid increments to be plotted}
   \item{grid.lty}{the line type for the grid}

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1645] trunk/gdata/tests

From: <wa...@us...> - 2013-03-24 04:50:25

Revision: 1645
          http://sourceforge.net/p/r-gregmisc/code/1645
Author:   warnes
Date:     2013-03-24 04:50:22 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Update test files for code changes

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	2013-03-24 04:36:45 UTC (rev 1644)
+++ trunk/gdata/tests/test.read.xls.Rout.save	2013-03-24 04:50:22 UTC (rev 1645)
@@ -1,8 +1,8 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
+R version 2.15.3 Patched (2013-03-13 r62287) -- "Security Blanket"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
-Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
+Platform: i386-apple-darwin9.8.0/i386 (32-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -38,7 +38,7 @@
 +   }
 > 
 > # iris.xls is included in the gregmisc package for use as an example
-> xlsfile <- file.path(.path.package('gdata'),'xls','iris.xls')
+> xlsfile <- file.path(path.package('gdata'),'xls','iris.xls')
 > 
 > iris.1 <- read.xls(xlsfile) # defaults to csv format
 > iris.1
@@ -505,10 +505,10 @@
 > stopifnot(all.equal(iris.1, iris.2))
 > stopifnot(all.equal(iris.1, iris.3))
 > 
-> exampleFile <- file.path(.path.package('gdata'),'xls',
+> exampleFile <- file.path(path.package('gdata'),'xls',
 +                          'ExampleExcelFile.xls')
 > 
-> exampleFile2007 <- file.path(.path.package('gdata'),'xls',
+> exampleFile2007 <- file.path(path.package('gdata'),'xls',
 +                          'ExampleExcelFile.xlsx')
 > 
 > # see the number and names of sheets:
@@ -669,18 +669,28 @@
 > 
 > ## Check handing of fileEncoding for latin-1 characters
 > 
-> latin1File <- file.path(.path.package('gdata'),'xls', 'latin-1.xls')
-> latin1FileX <- file.path(.path.package('gdata'),'xls', 'latin-1.xlsx')
+> latin1File <- file.path(path.package('gdata'),'xls', 'latin-1.xls')
+> latin1FileX <- file.path(path.package('gdata'),'xls', 'latin-1.xlsx')
 > 
 > example.latin1 <- read.xls(latin1File, fileEncoding='latin1')
+Warning messages:
+1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
+  invalid input found on input connection '/var/folders/dG/dGl84jhkHAe+alfrBBIYKE+++TQ/-Tmp-//RtmpGQaXAS/file4640360d0390.csv'
+2: In read.table(file = file, header = header, sep = sep, quote = quote,  :
+  incomplete final line found by readTableHeader on '/var/folders/dG/dGl84jhkHAe+alfrBBIYKE+++TQ/-Tmp-//RtmpGQaXAS/file4640360d0390.csv'
 > 
 > if( 'XLSX' %in% xlsFormats() )
 +   {
 +     example.latin1.x <- read.xls(latin1FileX, fileEncoding='latin1')
 +   }
+Warning messages:
+1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
+  invalid input found on input connection '/var/folders/dG/dGl84jhkHAe+alfrBBIYKE+++TQ/-Tmp-//RtmpGQaXAS/file46401064fea9.csv'
+2: In read.table(file = file, header = header, sep = sep, quote = quote,  :
+  incomplete final line found by readTableHeader on '/var/folders/dG/dGl84jhkHAe+alfrBBIYKE+++TQ/-Tmp-//RtmpGQaXAS/file46401064fea9.csv'
 > 
 > 
 > 
 > proc.time()
    user  system elapsed 
-  3.564   0.436   4.186 
+  6.693   0.979   7.921 

Modified: trunk/gdata/tests/tests.write.fwf.Rout.save
===================================================================
--- trunk/gdata/tests/tests.write.fwf.Rout.save	2013-03-24 04:36:45 UTC (rev 1644)
+++ trunk/gdata/tests/tests.write.fwf.Rout.save	2013-03-24 04:50:22 UTC (rev 1645)
@@ -1,8 +1,8 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
+R version 2.15.3 Patched (2013-03-13 r62287) -- "Security Blanket"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
-Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
+Platform: i386-apple-darwin9.8.0/i386 (32-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -232,4 +232,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.430   0.041   0.465 
+  0.830   0.090   0.906 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1644] trunk/gdata/inst/NEWS

From: <wa...@us...> - 2013-03-24 04:36:48

Revision: 1644
          http://sourceforge.net/p/r-gregmisc/code/1644
Author:   warnes
Date:     2013-03-24 04:36:45 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Fix formatting in NEWS

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

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2013-03-24 04:34:45 UTC (rev 1643)
+++ trunk/gdata/inst/NEWS	2013-03-24 04:36:45 UTC (rev 1644)
@@ -3,7 +3,8 @@
 
 Enhancements:
 
-- Replaced calls to depreciated function ".path.package" with the new public function "path.package".
+- Replaced calls to depreciated function ".path.package" with the new
+  public function "path.package".
 
 
 Changes in 2.13.0 (2012-09-20)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1643] trunk/gdata

From: <wa...@us...> - 2013-03-24 04:34:48

Revision: 1643
          http://sourceforge.net/p/r-gregmisc/code/1643
Author:   warnes
Date:     2013-03-24 04:34:45 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Replaced calls to depreciated function ".path.package" with the new public function "path.package".

Modified Paths:
--------------
    trunk/gdata/DESCRIPTION
    trunk/gdata/inst/NEWS
    trunk/gdata/man/read.xls.Rd
    trunk/gdata/man/sheetCount.Rd
    trunk/gdata/tests/test.read.xls.R

Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION	2013-03-24 04:20:02 UTC (rev 1642)
+++ trunk/gdata/DESCRIPTION	2013-03-24 04:34:45 UTC (rev 1643)
@@ -4,8 +4,8 @@
 Depends: R (>= 2.13.0)
 SystemRequirements: perl
 Imports: gtools
-Version: 2.13.0
-Date: 2012-09-20
+Version: 2.13.1
+Date: 2013-03-24
 Author: Gregory R. Warnes, with contributions from Liviu Andronic, Ben
         Bolker, Gregor Gorjanc, Gabor Grothendieck, Ales Korosec,
         Thomas Lumley, Don MacQueen, Arni Magnusson, Jim Rogers, and

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2013-03-24 04:20:02 UTC (rev 1642)
+++ trunk/gdata/inst/NEWS	2013-03-24 04:34:45 UTC (rev 1643)
@@ -1,3 +1,11 @@
+Changes in 2.13.1 (2013-03-24)
+------------------------------
+
+Enhancements:
+
+- Replaced calls to depreciated function ".path.package" with the new public function "path.package".
+
+
 Changes in 2.13.0 (2012-09-20)
 -----------------------------
 
@@ -31,9 +39,9 @@
 - 'stats::aggregate' was made into a generic on 27-Jan-2010, so that
    attempting to call 'aggregate' on a 'table' object will now
    incorrectly call 'aggregate.table'.  Since 'aggregate.table' can be
-   replaced by a call to tapply using two index vectors, e.g. 
-       aggregate.table(x, by1=a, by2=b, mean) 
-   can be replaced by 
+   replaced by a call to tapply using two index vectors, e.g.
+       aggregate.table(x, by1=a, by2=b, mean)
+   can be replaced by
        tapply(x, INDEX=list(a, b), FUN=mean),
    the 'aggregate.table' function will now display a warning that it
    is depreciated and recommending the equivalent call to tapply. It
@@ -161,7 +169,7 @@
 
 Enhancements:
 
-- nPairs() gains a summary method that shows how many times each variable 
+- 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:
@@ -222,7 +230,7 @@
   build issues, particularly on Windows.
 
 - All perl code can now operate (but generate warnings) when perl modules Compress::Raw::Zlib and
-  Spreadsheet::XLSX when are not installed. 
+  Spreadsheet::XLSX when are not installed.
 
 - Also update Greg's email address.
 
@@ -231,8 +239,8 @@
 
 Enhancements:
 
-- on Windows attempts to locate ActiveState perl if perl= not specified and 
-  Rtools perl would have otherwise been used in read.xls and other perl 
+- on Windows attempts to locate ActiveState perl if perl= not specified and
+  Rtools perl would have otherwise been used in read.xls and other perl
   dependent functions.
 
 CHANGES IN 2.7.0 (2010-01-25)
@@ -260,7 +268,7 @@
 
 New Functions:
 
-- sheetCount() and sheetNames() to determine the number and names of 
+- sheetCount() and sheetNames() to determine the number and names of
   worksheets in an Excel file, respectively.
 
 Bug Fixes:
@@ -285,7 +293,7 @@
 Bug Fixes
 
 - Correct minor typos & issues in man pages for write.fwf(),
-  resample() (Greg Warnes) 
+  resample() (Greg Warnes)
 
 - Correct calculation of object sizes in env() and ll() (Gregor Gorjanc)
 
@@ -297,20 +305,20 @@
 - Enhanced function object.size that returns the size of multiple
   objects. There is also a handy print method that can print size of
   an object in "human readable" format when
-    options(humanReadable=TRUE) 
-  or 
-    print(object.size(x), humanReadable=TRUE). 
-  (Gregor Gorjanc) 
+    options(humanReadable=TRUE)
+  or
+    print(object.size(x), humanReadable=TRUE).
+  (Gregor Gorjanc)
 
 - New function wideByFactor that reshapes given dataset by a given
-  factor - it creates a "multivariate" data.frame. (Gregor Gorjanc) 
+  factor - it creates a "multivariate" data.frame. (Gregor Gorjanc)
 
 - New function nPairs that gives the number of variable pairs in a
-  data.frame or a matrix. (Gregor Gorjanc) 
+  data.frame or a matrix. (Gregor Gorjanc)
 
 - New functions getYear, getMonth, getDay, getHour, getMin, and getSec
   for extracting the date/time parts from objects of a date/time
-  class. (Gregor Gorjanc) 
+  class. (Gregor Gorjanc)
 
 - New function bindData that binds two data frames into a multivariate
   data frame in a different way than merge. (Gregor Gorjanc)
@@ -332,7 +340,7 @@
 
 - New function bindData that binds two data frames into a multivariate data frame
   in a different way than merge.
-  
+
 - New function wideByFactor that reshapes given dataset by a given factor -
   it creates a "multivariate" data.frame.
 
@@ -346,7 +354,7 @@
 
 - New function cbindX that can bind objects with different number of rows.
 
-- write.fwf gains the width argument. The value for unknown can increase or 
+- write.fwf gains the width argument. The value for unknown can increase or
   decrease the width of the columns. Additional tests and documentation fixes.
 
 CHANGES IN 2.4.2 (2008-05-11)

Modified: trunk/gdata/man/read.xls.Rd
===================================================================
--- trunk/gdata/man/read.xls.Rd	2013-03-24 04:20:02 UTC (rev 1642)
+++ trunk/gdata/man/read.xls.Rd	2013-03-24 04:34:45 UTC (rev 1643)
@@ -67,7 +67,7 @@
 \examples{
 
    # iris.xls is included in the gregmisc package for use as an example
-   xlsfile <- file.path(.path.package('gdata'),'xls','iris.xls')
+   xlsfile <- file.path(path.package('gdata'),'xls','iris.xls')
    xlsfile
 
    iris <- read.xls(xlsfile) # defaults to csv format
@@ -121,9 +121,9 @@
 
    ## Examples demonstrating selection of specific 'sheets'
    ## from the example XLS file 'ExampleExcelFile.xls'
-   exampleFile <- file.path(.path.package('gdata'),'xls',
+   exampleFile <- file.path(path.package('gdata'),'xls',
                             'ExampleExcelFile.xls')
-   exampleFile2007 <- file.path(.path.package('gdata'),'xls',
+   exampleFile2007 <- file.path(path.package('gdata'),'xls',
                             'ExampleExcelFile.xlsx')
 
    ## see the number and names of sheets:
@@ -147,7 +147,7 @@
 
    ## load a file containing data and column names using latin-1
    ## characters
-   latinFile <- file.path(.path.package('gdata'),'xls','latin-1.xls')
+   latinFile <- file.path(path.package('gdata'),'xls','latin-1.xls')
    latin1 <- read.xls(latinFile, fileEncoding="latin1")
    colnames(latin1)
 

Modified: trunk/gdata/man/sheetCount.Rd
===================================================================
--- trunk/gdata/man/sheetCount.Rd	2013-03-24 04:20:02 UTC (rev 1642)
+++ trunk/gdata/man/sheetCount.Rd	2013-03-24 04:34:45 UTC (rev 1643)
@@ -34,9 +34,9 @@
    sheetCount(xlsfile)
 
 
-   exampleFile <- file.path(.path.package('gdata'),'xls',
+   exampleFile <- file.path(path.package('gdata'),'xls',
                             'ExampleExcelFile.xls')
-   exampleFile2007 <- file.path(.path.package('gdata'),'xls',
+   exampleFile2007 <- file.path(path.package('gdata'),'xls',
                             'ExampleExcelFile.xlsx')
 
    sheetCount(exampleFile)

Modified: trunk/gdata/tests/test.read.xls.R
===================================================================
--- trunk/gdata/tests/test.read.xls.R	2013-03-24 04:20:02 UTC (rev 1642)
+++ trunk/gdata/tests/test.read.xls.R	2013-03-24 04:34:45 UTC (rev 1643)
@@ -6,7 +6,7 @@
   }
 
 # iris.xls is included in the gregmisc package for use as an example
-xlsfile <- file.path(.path.package('gdata'),'xls','iris.xls')
+xlsfile <- file.path(path.package('gdata'),'xls','iris.xls')
 
 iris.1 <- read.xls(xlsfile) # defaults to csv format
 iris.1
@@ -20,10 +20,10 @@
 stopifnot(all.equal(iris.1, iris.2))
 stopifnot(all.equal(iris.1, iris.3))
 
-exampleFile <- file.path(.path.package('gdata'),'xls',
+exampleFile <- file.path(path.package('gdata'),'xls',
                          'ExampleExcelFile.xls')
 
-exampleFile2007 <- file.path(.path.package('gdata'),'xls',
+exampleFile2007 <- file.path(path.package('gdata'),'xls',
                          'ExampleExcelFile.xlsx')
 
 # see the number and names of sheets:
@@ -86,8 +86,8 @@
 
 ## Check handing of fileEncoding for latin-1 characters
 
-latin1File <- file.path(.path.package('gdata'),'xls', 'latin-1.xls')
-latin1FileX <- file.path(.path.package('gdata'),'xls', 'latin-1.xlsx')
+latin1File <- file.path(path.package('gdata'),'xls', 'latin-1.xls')
+latin1FileX <- file.path(path.package('gdata'),'xls', 'latin-1.xlsx')
 
 example.latin1 <- read.xls(latin1File, fileEncoding='latin1')
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1642] trunk/gplots/DESCRIPTION

From: <wa...@us...> - 2013-03-24 04:20:04

Revision: 1642
          http://sourceforge.net/p/r-gregmisc/code/1642
Author:   warnes
Date:     2013-03-24 04:20:02 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Update for release 2.11.2

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

Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION	2013-03-24 04:18:22 UTC (rev 1641)
+++ trunk/gplots/DESCRIPTION	2013-03-24 04:20:02 UTC (rev 1642)
@@ -5,10 +5,10 @@
          datasets
 Recommends: grid
 Suggests: gtools
-Version: 2.11.1
-Date: 2012-12-14
+Version: 2.11.2
+Date: 2012-03-24
 Author: Gregory R. Warnes. Includes R source code and/or documentation
-        contributed by (in alphabetical order): 
+        contributed by (in alphabetical order):
  	  Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang
  	  Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni
  	  Magnusson, Steffen Moeller, Marc Schwartz, Bill Venables

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1641] trunk/gplots/man/lowess.Rd

From: <wa...@us...> - 2013-03-24 04:18:26

Revision: 1641
          http://sourceforge.net/p/r-gregmisc/code/1641
Author:   warnes
Date:     2013-03-24 04:18:22 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Update manual page for lowess.default() to match changed argument list for lowess() in R 3.0.0

Modified Paths:
--------------
    trunk/gplots/man/lowess.Rd

Modified: trunk/gplots/man/lowess.Rd
===================================================================
--- trunk/gplots/man/lowess.Rd	2013-03-17 02:21:43 UTC (rev 1640)
+++ trunk/gplots/man/lowess.Rd	2013-03-24 04:18:22 UTC (rev 1641)
@@ -23,7 +23,7 @@
 \usage{
 lowess(x, ...)
 \method{lowess}{default}(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 *
-                  diff(range(xy$x[o])), ...)
+                  diff(range(x)), ...)
 \method{lowess}{formula}(formula,data = parent.frame(), subset, na.action, 
                f=2/3,  iter=3, delta=.01*diff(range(mf[-response])), ... )
 }

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1640] trunk/gtools/R/smartbind.R

From: <wa...@us...> - 2013-03-17 02:21:46

Revision: 1640
          http://sourceforge.net/p/r-gregmisc/code/1640
Author:   warnes
Date:     2013-03-17 02:21:43 +0000 (Sun, 17 Mar 2013)
Log Message:
-----------
Fix error in smartbind: factor levels were not being handled if the factor column was not present in the first data frame.

Modified Paths:
--------------
    trunk/gtools/R/smartbind.R

Modified: trunk/gtools/R/smartbind.R
===================================================================
--- trunk/gtools/R/smartbind.R	2013-01-14 20:47:57 UTC (rev 1639)
+++ trunk/gtools/R/smartbind.R	2013-03-17 02:21:43 UTC (rev 1640)
@@ -19,9 +19,9 @@
     retval <- list()
     rowLens <- unlist(lapply(data, nrow))
     nrows <- sum(rowLens)
-    
+
     rowNameList <- unlist(lapply( names(data),
-                                 function(x) 
+                                 function(x)
                                    if(rowLens[x]<=1) x
                                    else paste(x, seq(1,rowLens[x]),sep=sep))
                           )
@@ -29,8 +29,8 @@
     colClassList     <- vector(mode="list", length=length(data))
     factorColumnList <- vector(mode="list", length=length(data))
     factorLevelList  <- vector(mode="list", length=length(data))
-    
-       
+
+
     start      <- 1
     blockIndex <- 1
     for(block in data)
@@ -38,7 +38,7 @@
         colClassList    [[blockIndex]] <- list()
         factorColumnList[[blockIndex]] <- character(length=0)
         factorLevelList [[blockIndex]] <- list()
-        
+
         if(verbose) print(head(block))
         end <- start+nrow(block)-1
         for(col in colnames(block))
@@ -49,14 +49,14 @@
             colClassList[[blockIndex]][[col]] <- classVec
             if("factor" %in% classVec)
               {
-                
+
                 factorColumnList[[blockIndex]] <-
                   c(factorColumnList[[blockIndex]], col)
-                
+
                 factorLevelList[[blockIndex]][[col]] <-
                   levels(block[,col])
             }
-            
+
             if( !(col %in% names(retval)))
               {
                 if(verbose) cat("Start:", start,
@@ -69,10 +69,10 @@
                   }
                 else
                   newclass <- classVec
-                
+
                 retval[[col]] <- as.vector(rep(fill,nrows), mode=newclass)
               }
-            
+
             retval[[col]][start:end] <- as.vector(block[,col],
                                                   mode=class(retval[[col]]))
           }
@@ -87,48 +87,53 @@
         else
           return(all.equal(x,y,...))
       }
-    
+
     ## Handle factors, merging levels
     for( col in unique(unlist(factorColumnList)) )
       {
         ## Ensure column classes match across blocks
         colClasses <- lapply(colClassList, function(x) x[[col]])
-        allSame <- all(sapply(colClasses[-1],
-                              function(x) isTRUE(all.equal.or.null(colClasses[[1]], x))
+        firstNotNull <- which(!sapply(colClasses, is.null))[1]
+        allSameOrNull <- all(sapply(colClasses[-firstNotNull],
+                              function(x) isTRUE(all.equal.or.null(colClasses[[firstNotNull]], x))
                               )
                        )
 
-        if(allSame)
-          colClass <- colClasses[[1]]
+        if(allSameOrNull)
+          {
+            # grab the first *non-NULL* class information
+            colClass <- colClasses[[firstNotNull]]
+          }
         else
           {
             warning("Column class mismatch for '", col, "'. ",
                     "Converting column to class 'character'.")
             next()
           }
-        
 
+
         ## check if factor levels are all the same
         colLevels <- lapply(factorLevelList, function(x) x[[col]])
-        allSame <- all(sapply(colLevels[-1],
-                              function(x) isTRUE(all.equal.or.null(colLevels[[1]], x))
-                              )
-                       )
+        firstNotNull <- which(!sapply(colLevels, is.null))[1]
+        allSameOrNull <- all(sapply(colLevels[-firstNotNull],
+                                    function(x) isTRUE(all.equal.or.null(colLevels[[firstNotNull]], x))
+                                    )
+                             )
 
-        
-        if(allSame)
+
+        if(allSameOrNull)
           {
             if("ordered" %in% colClass)
-              retval[[col]] <- ordered(retval[[col]], levels=colLevels[[1]] )
+              retval[[col]] <- ordered(retval[[col]], levels=colLevels[[firstNotNull]] )
             else
-              retval[[col]] <- factor(retval[[col]], levels=colLevels[[1]] )
+              retval[[col]] <- factor(retval[[col]], levels=colLevels[[firstNotNull]] )
           }
         else
           {
             ## Check if longest set of levels is a superset of all others,
             ## and use that one
             longestIndex  <- which.max( sapply(colLevels, length) )
-            longestLevels <- colLevels[[longestIndex]] 
+            longestLevels <- colLevels[[longestIndex]]
             allSubset <- sapply(colLevels[-longestIndex],
                                 function(l) all(l %in% longestLevels)
                                 )
@@ -144,7 +149,7 @@
                 # form superset by appending to longest level set
                 levelSuperSet <- unique(c(longestLevels, unlist(colLevels)))
                 retval[[col]] <- factor(retval[[col]], levels=levelSuperSet )
-                
+
                 if(length(colClass)>1) # not just plain factor
                    {
                      browser()
@@ -157,7 +162,7 @@
               }
           }
       }
-    
+
     attr(retval,"row.names") <- rowNameList
     class(retval) <- "data.frame"
     return(retval)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1639] trunk/gdata/R

From: <wa...@us...> - 2013-01-14 20:47:59

Revision: 1639
          http://sourceforge.net/p/r-gregmisc/code/1639
Author:   warnes
Date:     2013-01-14 20:47:57 +0000 (Mon, 14 Jan 2013)
Log Message:
-----------
Replace (obsolete) '.path.package' with 'find.package' function.

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

Modified: trunk/gdata/R/installXLSXsupport.R
===================================================================
--- trunk/gdata/R/installXLSXsupport.R	2012-12-14 22:50:47 UTC (rev 1638)
+++ trunk/gdata/R/installXLSXsupport.R	2013-01-14 20:47:57 UTC (rev 1639)
@@ -10,7 +10,7 @@
   
   ##
   ## directories
-  package.dir <- .path.package('gdata')
+  package.dir <- find.package('gdata')
   perl.dir <- file.path(package.dir,'perl')
   ##
   ##

Modified: trunk/gdata/R/sheetCount.R
===================================================================
--- trunk/gdata/R/sheetCount.R	2012-12-14 22:50:47 UTC (rev 1638)
+++ trunk/gdata/R/sheetCount.R	2013-01-14 20:47:57 UTC (rev 1639)
@@ -15,7 +15,7 @@
 
   ##
   ## directories
-  package.dir <- .path.package('gdata')
+  package.dir <- find.package('gdata')
   perl.dir <- file.path(package.dir,'perl')
   ##
   ##

Modified: trunk/gdata/R/xls2sep.R
===================================================================
--- trunk/gdata/R/xls2sep.R	2012-12-14 22:50:47 UTC (rev 1638)
+++ trunk/gdata/R/xls2sep.R	2013-01-14 20:47:57 UTC (rev 1639)
@@ -36,7 +36,7 @@
 
     ##
     ## directories
-    package.dir <- .path.package('gdata')
+    package.dir <- find.package('gdata')
     perl.dir <- file.path(package.dir,'perl')
     ##
 

Modified: trunk/gdata/R/xlsFormats.R
===================================================================
--- trunk/gdata/R/xlsFormats.R	2012-12-14 22:50:47 UTC (rev 1638)
+++ trunk/gdata/R/xlsFormats.R	2013-01-14 20:47:57 UTC (rev 1639)
@@ -10,7 +10,7 @@
   
   ##
   ## directories
-  package.dir <- .path.package('gdata')
+  package.dir <- find.package('gdata')
   perl.dir <- file.path(package.dir,'perl')
   ##
   ##

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1622] trunk/gdata/man

From: <wa...@us...> - 2012-09-20 17:35:09

Revision: 1622
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1622&view=rev
Author:   warnes
Date:     2012-09-20 17:35:03 +0000 (Thu, 20 Sep 2012)
Log Message:
-----------
Correct .Rd file errors detected by 'R CMD check'.

Modified Paths:
--------------
    trunk/gdata/man/MedUnits.Rd
    trunk/gdata/man/ans.Rd
    trunk/gdata/man/duplicated2.Rd

Modified: trunk/gdata/man/MedUnits.Rd
===================================================================
--- trunk/gdata/man/MedUnits.Rd	2012-09-20 17:15:20 UTC (rev 1621)
+++ trunk/gdata/man/MedUnits.Rd	2012-09-20 17:35:03 UTC (rev 1622)
@@ -17,9 +17,9 @@
   \describe{
     \item{Abbreviation}{Common Abbreviation (mostly missing)}
     \item{Measurement}{Measurement Name}
+    \item{ConventionalUnit}{Conventional Unit}
+    \item{Conversion}{Conversion factor}
     \item{SIUnit}{SI Unit}
-    \item{Conversion}{Conversion factor}
-    \item{ConvetionalUnit}{Conventional Unit}
   }
 }
 \details{

Modified: trunk/gdata/man/ans.Rd
===================================================================
--- trunk/gdata/man/ans.Rd	2012-09-20 17:15:20 UTC (rev 1621)
+++ trunk/gdata/man/ans.Rd	2012-09-20 17:35:03 UTC (rev 1622)
@@ -11,13 +11,13 @@
 }
 \details{
   This function retrieves \code{.Last.value}. For more details see 
-  \code{\link{Last.value}}.  
+  \code{\link[base]{.Last.value}}.  
 }
 \value{
   \code{.Last.value}
 }
 \seealso{
-  \code{\link{Last.value}}, \code{\link{eval}}
+  \code{\link[base]{.Last.value}}, \code{\link[base]{eval}}
 }
 \author{Liviu Andronic}
 \examples{

Modified: trunk/gdata/man/duplicated2.Rd
===================================================================
--- trunk/gdata/man/duplicated2.Rd	2012-09-20 17:15:20 UTC (rev 1621)
+++ trunk/gdata/man/duplicated2.Rd	2012-09-20 17:35:03 UTC (rev 1622)
@@ -38,7 +38,7 @@
     For more details see \code{\link{duplicated}}.
 }
 \seealso{
-  \code{\link{duplicated}}, \code{\link{unique}}
+  \code{\link[base]{duplicated}}, \code{\link[base]{unique}}
 }
 \author{Liviu Andronic}
 \examples{

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1621] trunk/gdata/NAMESPACE

From: <wa...@us...> - 2012-09-20 17:15:30

Revision: 1621
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1621&view=rev
Author:   warnes
Date:     2012-09-20 17:15:20 +0000 (Thu, 20 Sep 2012)
Log Message:
-----------
Add duplicated() and ans() to the NAMESPACE.

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

Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE	2012-09-20 17:12:14 UTC (rev 1620)
+++ trunk/gdata/NAMESPACE	2012-09-20 17:15:20 UTC (rev 1621)
@@ -1,6 +1,7 @@
 
 export(
        .onAttach,
+       ans,
        Args,
        aggregate.table,
        bindData,
@@ -10,6 +11,7 @@
        combine,
        ConvertMedUnits,
        drop.levels,
+       duplicated2,
        elem,
        env,
        frameApply,

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1620] trunk/gdata

From: <wa...@us...> - 2012-09-20 17:12:21

Revision: 1620
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1620&view=rev
Author:   warnes
Date:     2012-09-20 17:12:14 +0000 (Thu, 20 Sep 2012)
Log Message:
-----------
Update for gdata 2.13.0.

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

Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION	2012-09-20 15:42:08 UTC (rev 1619)
+++ trunk/gdata/DESCRIPTION	2012-09-20 17:12:14 UTC (rev 1620)
@@ -4,10 +4,11 @@
 Depends: R (>= 2.13.0)
 SystemRequirements: perl
 Imports: gtools
-Version: 2.12.0
-Date: 2012-10-12
-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
+Version: 2.13.0
+Date: 2012-09-20
+Author: Gregory R. Warnes, with contributions from Liviu Andronic, Ben
+        Bolker, Gregor Gorjanc, Gabor Grothendieck, Ales Korosec,
+        Thomas Lumley, Don MacQueen, Arni Magnusson, Jim Rogers, and
+        others
 Maintainer: Gregory Warnes <gr...@wa...>
 License: GPL-2

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2012-09-20 15:42:08 UTC (rev 1619)
+++ trunk/gdata/inst/NEWS	2012-09-20 17:12:14 UTC (rev 1620)
@@ -1,4 +1,29 @@
-Changes in 2.12.0 (2012-10-12)
+Changes in 2.13.0 (2012-09-20)
+-----------------------------
+
+New features:
+
+- New 'duplicated2' function which returns TRUE for *all* elements
+  that are duplicated, including the first, contributed by Liviu
+  Andronic.  This differs from 'duplicated', which only returns the
+  second and following (second-to last and previous when
+  'fromLast=TRUE') duplicate elements.
+
+- New 'ans' functon to return the value of the last evaluated
+  top-level function (a convenience function for accessing
+  .Last.value), contributed by Liviu Andonic.
+
+Bug Fixes:
+
+- On windows, warning messages printed to stdout by perl were being
+  included in the return value from 'system', resulting in errors in
+  'sheetCount' and 'sheetNames'.  Corrected.
+
+- The 'MedUnits' column names 'SIUnits' and 'ConventionalUnits' were
+  reversed and misspelled.
+
+
+Changes in 2.12.0 (2012-09-12)
 ------------------------------
 
 Other Changes:
@@ -14,7 +39,7 @@
    is depreciated and recommending the equivalent call to tapply. It
    will be removed entirely in a future version of gdata.
 
-Changes in 2.11.1 (2012-09-22)
+Changes in 2.11.1 (2012-08-22)
 ------------------------------
 
 Enhancements:

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1619] trunk/gdata/man/ConvertMedUnits.Rd

From: <wa...@us...> - 2012-09-20 15:42:14

Revision: 1619
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1619&view=rev
Author:   warnes
Date:     2012-09-20 15:42:08 +0000 (Thu, 20 Sep 2012)
Log Message:
-----------
Fix typographic error.

Modified Paths:
--------------
    trunk/gdata/man/ConvertMedUnits.Rd

Modified: trunk/gdata/man/ConvertMedUnits.Rd
===================================================================
--- trunk/gdata/man/ConvertMedUnits.Rd	2012-09-20 15:39:43 UTC (rev 1618)
+++ trunk/gdata/man/ConvertMedUnits.Rd	2012-09-20 15:42:08 UTC (rev 1619)
@@ -30,7 +30,7 @@
   This function converts between SI and US 'Conventional' units.
 
   If \code{exact=FALSE}, \code{grep} will be used to do a
-  case-insensitive sub-string search for matching measurment names.  If
+  case-insensitive sub-string search for matching measurement names.  If
   more than one match is found, an error will be generated, along with a
   list of the matching entries.
   

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1618] trunk/gdata

From: <wa...@us...> - 2012-09-20 15:39:54

Revision: 1618
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1618&view=rev
Author:   warnes
Date:     2012-09-20 15:39:43 +0000 (Thu, 20 Sep 2012)
Log Message:
-----------
Add 'ans()' and 'duplicated()' contributed by Liviu Andronic.

Added Paths:
-----------
    trunk/gdata/R/ans.R
    trunk/gdata/R/duplicated2.R
    trunk/gdata/man/ans.Rd
    trunk/gdata/man/duplicated2.Rd

Added: trunk/gdata/R/ans.R
===================================================================
--- trunk/gdata/R/ans.R	                        (rev 0)
+++ trunk/gdata/R/ans.R	2012-09-20 15:39:43 UTC (rev 1618)
@@ -0,0 +1 @@
+ans <- function() .Last.value

Added: trunk/gdata/R/duplicated2.R
===================================================================
--- trunk/gdata/R/duplicated2.R	                        (rev 0)
+++ trunk/gdata/R/duplicated2.R	2012-09-20 15:39:43 UTC (rev 1618)
@@ -0,0 +1,8 @@
+duplicated2 <- function(x, bothWays=TRUE, ...)
+    {
+        if(!bothWays) {
+            return(duplicated(x, ...))
+        } else if(bothWays) {
+            return((duplicated(x, ...) | duplicated(x, fromLast=TRUE, ...)))
+        }
+    }

Added: trunk/gdata/man/ans.Rd
===================================================================
--- trunk/gdata/man/ans.Rd	                        (rev 0)
+++ trunk/gdata/man/ans.Rd	2012-09-20 15:39:43 UTC (rev 1618)
@@ -0,0 +1,34 @@
+\name{ans}
+\alias{ans}
+\title{Value of Last Evaluated Expression}
+\usage{
+ans()
+}
+\description{
+  The functon returns the value of the last evaluated \emph{top-level}
+  expression, which is always assigned to \code{.Last.value} (in
+  \code{package:base}).
+}
+\details{
+  This function retrieves \code{.Last.value}. For more details see 
+  \code{\link{Last.value}}.  
+}
+\value{
+  \code{.Last.value}
+}
+\seealso{
+  \code{\link{Last.value}}, \code{\link{eval}}
+}
+\author{Liviu Andronic}
+\examples{
+  2+2                  # Trivial calculation...
+  ans()                # See the answer again
+
+  gamma(1:15)          # Some intensive calculation...
+  fac14 <- ans()       # store the results into a variable
+
+  rnorm(20)            # Generate some standard normal values
+  ans()^2              # Convert to Chi-square(1) values...
+  stem(ans())          # Now show a stem-and-leaf table
+}
+\keyword{programming}

Added: trunk/gdata/man/duplicated2.Rd
===================================================================
--- trunk/gdata/man/duplicated2.Rd	                        (rev 0)
+++ trunk/gdata/man/duplicated2.Rd	2012-09-20 15:39:43 UTC (rev 1618)
@@ -0,0 +1,51 @@
+\name{duplicated2}
+\alias{duplicated2}
+\title{Determine Duplicate Elements}
+\description{
+  \code{duplicated2()} determines which elements of a vector or data 
+  frame are duplicates, and returns a logical vector indicating which 
+  elements (rows) are duplicates.
+}
+\usage{
+duplicated2(x, bothWays=TRUE, ...)
+}
+\arguments{
+  \item{x}{a vector or a data frame or an array or \code{NULL}.}
+  \item{bothWays}{if \code{TRUE} (the default), duplication should be 
+    considered from both sides. For more information see the argument \code{fromLast}
+    to the function \code{\link{duplicated}}.}
+  \item{\dots}{further arguments passed down to \code{duplicated()} and
+    its methods.}
+}
+\details{
+  The standard \code{\link{duplicated}} function (in \code{package:base}) 
+  only returns \code{TRUE} for the second and following copies of each
+  duplicated value (second-to-last and earlier when
+  \code{fromLast=TRUE}).  This function returns all duplicated
+  elementes, including the first (last) value.
+  
+  When \code{bothWays} is \code{FALSE}, \code{duplicated2()} defaults to 
+  a \code{\link{duplicated}} call. When \code{bothWays} is \code{TRUE}, 
+  the following call is being executed: 
+  \code{duplicated(x, ...) | duplicated(x, fromLast=TRUE, ...)}
+}
+\value{
+    For a vector input, a logical vector of the same length as
+    \code{x}.  For a data frame, a logical vector with one element for
+    each row.  For a matrix or array, and when \code{MARGIN = 0}, a
+    logical array with the same dimensions and dimnames.
+    
+    For more details see \code{\link{duplicated}}.
+}
+\seealso{
+  \code{\link{duplicated}}, \code{\link{unique}}
+}
+\author{Liviu Andronic}
+\examples{
+  data(iris)
+  iris[duplicated(iris), ]                 # 2nd duplicated value
+  iris[duplicated(iris, fromLast=TRUE), ]  # 1st duplicated value
+  iris[duplicated2(iris), ]                # both duplicated values
+}
+\keyword{logic}
+\keyword{manip}

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1617] trunk/gdata/data/MedUnits.rda

From: <wa...@us...> - 2012-09-19 18:30:40

Revision: 1617
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1617&view=rev
Author:   warnes
Date:     2012-09-19 18:30:31 +0000 (Wed, 19 Sep 2012)
Log Message:
-----------
Correct column names.  Unit columns were reversed and misspelled.

Modified Paths:
--------------
    trunk/gdata/data/MedUnits.rda

Modified: trunk/gdata/data/MedUnits.rda
===================================================================
(Binary files differ)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1616] trunk/gdata/R/sheetCount.R

From: <wa...@us...> - 2012-09-19 18:02:28

Revision: 1616
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1616&view=rev
Author:   warnes
Date:     2012-09-19 18:02:18 +0000 (Wed, 19 Sep 2012)
Log Message:
-----------
Add ignore.stderr to system command in sheetCmd() to prevent stderr
messages from being included in the captured output from the perl
script.

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

Modified: trunk/gdata/R/sheetCount.R
===================================================================
--- trunk/gdata/R/sheetCount.R	2012-09-19 17:17:15 UTC (rev 1615)
+++ trunk/gdata/R/sheetCount.R	2012-09-19 18:02:18 UTC (rev 1616)
@@ -61,7 +61,7 @@
       cat("... \n\n")
     }
   ##
-  output <- system(cmd, intern=TRUE)
+  output <- system(cmd, intern=TRUE, ignore.stderr=TRUE)
   if(verbose) cat("Results: ", output, "\n")
   ##
   tc <- textConnection(output)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1615] trunk/namespace/DESCRIPTION

From: <wa...@us...> - 2012-09-19 17:17:21

Revision: 1615
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1615&view=rev
Author:   warnes
Date:     2012-09-19 17:17:15 +0000 (Wed, 19 Sep 2012)
Log Message:
-----------
Move comment about origin of 'makeNamespace' to DESCRIPTION field.

Modified Paths:
--------------
    trunk/namespace/DESCRIPTION

Modified: trunk/namespace/DESCRIPTION
===================================================================
--- trunk/namespace/DESCRIPTION	2012-09-19 17:15:45 UTC (rev 1614)
+++ trunk/namespace/DESCRIPTION	2012-09-19 17:17:15 UTC (rev 1615)
@@ -4,11 +4,13 @@
 Version: 0.9.1
 Date: 2012-09-19
 Author: Winston Chang, Daniel Adler, Hadley Wickham, Gregory
-	R. Warnes, R Core Team ('makeNamespaces' is extracted from the
-	R 'base' package source code: src/library/base/R/namespace.R)
+	R. Warnes, R Core Team
 Maintainer: Gregory R. Warnes <gr...@wa...>
 Description: This package provides user-level functions to manage
 	     namespaces not (yet) available in base R:
 	     'registerNamespace', 'unregisterNamespace',
 	     'makeNamespace', and 'getRegisteredNamespace'
+	     .
+	     ('makeNamespaces' is extracted from the R 'base' package
+	     source code: src/library/base/R/namespace.R)
 License: GPL-2

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1614] trunk/namespace/.Rinstignore

From: <wa...@us...> - 2012-09-19 17:15:51

Revision: 1614
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1614&view=rev
Author:   warnes
Date:     2012-09-19 17:15:45 +0000 (Wed, 19 Sep 2012)
Log Message:
-----------
Tell R CMD BUILD to ignore Emacs temporary files.

Modified Paths:
--------------
    trunk/namespace/.Rinstignore

Modified: trunk/namespace/.Rinstignore
===================================================================
--- trunk/namespace/.Rinstignore	2012-09-19 17:05:48 UTC (rev 1613)
+++ trunk/namespace/.Rinstignore	2012-09-19 17:15:45 UTC (rev 1614)
@@ -1,4 +1,5 @@
 doc/.*\.tex$
 doc/.*\.sty$
 doc/.*\.dtx$
-\.svn
\ No newline at end of file
+\.svn
+.*~$
\ No newline at end of file

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1613] trunk/namespace

From: <wa...@us...> - 2012-09-19 17:05:58

Revision: 1613
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1613&view=rev
Author:   warnes
Date:     2012-09-19 17:05:48 +0000 (Wed, 19 Sep 2012)
Log Message:
-----------
Update for release 0.9.1

Modified Paths:
--------------
    trunk/namespace/DESCRIPTION
    trunk/namespace/inst/doc/NEWS

Modified: trunk/namespace/DESCRIPTION
===================================================================
--- trunk/namespace/DESCRIPTION	2012-09-19 16:57:08 UTC (rev 1612)
+++ trunk/namespace/DESCRIPTION	2012-09-19 17:05:48 UTC (rev 1613)
@@ -1,9 +1,14 @@
 Package: namespace
 Type: Package
 Title: Provide namespace managment functions not (yet) present in base R
-Version: 0.9.0
-Date: 2012-09-13
-Author: Winston Chang, Daniel Adler, Hadley Wickham, Gregory R. Warnes, some code from the R 'base' package.
+Version: 0.9.1
+Date: 2012-09-19
+Author: Winston Chang, Daniel Adler, Hadley Wickham, Gregory
+	R. Warnes, R Core Team ('makeNamespaces' is extracted from the
+	R 'base' package source code: src/library/base/R/namespace.R)
 Maintainer: Gregory R. Warnes <gr...@wa...>
-Description: More about what it does (maybe more than one line)
+Description: This package provides user-level functions to manage
+	     namespaces not (yet) available in base R:
+	     'registerNamespace', 'unregisterNamespace',
+	     'makeNamespace', and 'getRegisteredNamespace'
 License: GPL-2

Modified: trunk/namespace/inst/doc/NEWS
===================================================================
--- trunk/namespace/inst/doc/NEWS	2012-09-19 16:57:08 UTC (rev 1612)
+++ trunk/namespace/inst/doc/NEWS	2012-09-19 17:05:48 UTC (rev 1613)
@@ -1,4 +1,11 @@
-namespace - 0.9.0 - 2012-10-13
+namespace - 0.9.1 - 2012-09-19
 ------------------------------
 
+- Improve package description in 'DESCRIPTION'
+- Move 'makeNamespace' to a separate file and include the original
+  copyright notice.
+
+namespace - 0.9.0 - 2012-09-13
+------------------------------
+
 Initial version. 
\ No newline at end of file

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1612] trunk/namespace/R

From: <wa...@us...> - 2012-09-19 16:57:18

Revision: 1612
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1612&view=rev
Author:   warnes
Date:     2012-09-19 16:57:08 +0000 (Wed, 19 Sep 2012)
Log Message:
-----------
Move makeNamespace function into a separate file and include the original copyright notice.

Modified Paths:
--------------
    trunk/namespace/R/namespace.R

Added Paths:
-----------
    trunk/namespace/R/makeNamespace.R

Added: trunk/namespace/R/makeNamespace.R
===================================================================
--- trunk/namespace/R/makeNamespace.R	                        (rev 0)
+++ trunk/namespace/R/makeNamespace.R	2012-09-19 16:57:08 UTC (rev 1612)
@@ -0,0 +1,46 @@
+#  Copy of function defined inside of base::loadNamespace() in  
+#  The R package source at src/library/base/R/namespace.R, 
+#  Part of the R package, http://www.R-project.org
+#
+#  Copyright (C) 1995-2012 The R Core Team
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  A copy of the GNU General Public License is available at
+#  http://www.r-project.org/Licenses/
+
+# [NB: Other comments and code omitted]
+
+makeNamespace <- function(name, version = NULL, lib = NULL) {
+    impenv <- new.env(parent = .BaseNamespaceEnv, hash = TRUE)
+    attr(impenv, "name") <- paste("imports", name, sep=":")
+    env <- new.env(parent = impenv, hash = TRUE)
+    name <- as.character(as.name(name))
+    version <- as.character(version)
+    info <- new.env(hash = TRUE, parent = baseenv())
+    assign(".__NAMESPACE__.", info, envir = env)
+    assign("spec", c(name = name,version = version), envir = info)
+    setNamespaceInfo(env, "exports", new.env(hash = TRUE, parent = baseenv()))
+    dimpenv <- new.env(parent = baseenv(), hash = TRUE)
+    attr(dimpenv, "name") <- paste("lazydata", name, sep=":")
+    setNamespaceInfo(env, "lazydata", dimpenv)
+    setNamespaceInfo(env, "imports", list("base" = TRUE))
+    ## this should be an absolute path
+    setNamespaceInfo(env, "path",
+                     normalizePath(file.path(lib, name), "/", TRUE))
+    setNamespaceInfo(env, "dynlibs", NULL)
+    setNamespaceInfo(env, "S3methods", matrix(NA_character_, 0L, 3L))
+    assign(".__S3MethodsTable__.",
+           new.env(hash = TRUE, parent = baseenv()),
+           envir = env)
+    registerNamespace(name, env)
+    env
+}

Modified: trunk/namespace/R/namespace.R
===================================================================
--- trunk/namespace/R/namespace.R	2012-09-13 23:54:38 UTC (rev 1611)
+++ trunk/namespace/R/namespace.R	2012-09-19 16:57:08 UTC (rev 1612)
@@ -56,30 +56,3 @@
       return(getNamespace(name))
   }
 }
-
-## Copy of function defined inside of base::loadNamespace
-makeNamespace <- function(name, version = NULL, lib = NULL) {
-    impenv <- new.env(parent = .BaseNamespaceEnv, hash = TRUE)
-    attr(impenv, "name") <- paste("imports", name, sep=":")
-    env <- new.env(parent = impenv, hash = TRUE)
-    name <- as.character(as.name(name))
-    version <- as.character(version)
-    info <- new.env(hash = TRUE, parent = baseenv())
-    assign(".__NAMESPACE__.", info, envir = env)
-    assign("spec", c(name = name,version = version), envir = info)
-    setNamespaceInfo(env, "exports", new.env(hash = TRUE, parent = baseenv()))
-    dimpenv <- new.env(parent = baseenv(), hash = TRUE)
-    attr(dimpenv, "name") <- paste("lazydata", name, sep=":")
-    setNamespaceInfo(env, "lazydata", dimpenv)
-    setNamespaceInfo(env, "imports", list("base" = TRUE))
-    ## this should be an absolute path
-    setNamespaceInfo(env, "path",
-                     normalizePath(file.path(lib, name), "/", TRUE))
-    setNamespaceInfo(env, "dynlibs", NULL)
-    setNamespaceInfo(env, "S3methods", matrix(NA_character_, 0L, 3L))
-    assign(".__S3MethodsTable__.",
-           new.env(hash = TRUE, parent = baseenv()),
-           envir = env)
-    registerNamespace(name, env)
-    env
-}

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