r-gregmisc-users Mailing List for R gregmisc package (Page 28)
Brought to you by:
warnes
Menu
▾
▴
r-gregmisc-users — Discussion list for R gregmisc packages (gplot, gmodels, gdata, gtools)
You can subscribe to this list here.
| 2006 |
Jan
|
Feb
|
Mar
(12) |
Apr
(5) |
May
(3) |
Jun
(5) |
Jul
(2) |
Aug
(5) |
Sep
(7) |
Oct
(15) |
Nov
(34) |
Dec
(3) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2007 |
Jan
(3) |
Feb
(16) |
Mar
(28) |
Apr
(5) |
May
|
Jun
(5) |
Jul
(9) |
Aug
(50) |
Sep
(29) |
Oct
(9) |
Nov
(25) |
Dec
(7) |
| 2008 |
Jan
(6) |
Feb
(4) |
Mar
(5) |
Apr
(8) |
May
(26) |
Jun
(11) |
Jul
|
Aug
(2) |
Sep
|
Oct
|
Nov
|
Dec
(9) |
| 2009 |
Jan
|
Feb
(1) |
Mar
|
Apr
(2) |
May
(26) |
Jun
|
Jul
(10) |
Aug
(6) |
Sep
|
Oct
(7) |
Nov
(3) |
Dec
(2) |
| 2010 |
Jan
(45) |
Feb
(11) |
Mar
|
Apr
(1) |
May
(8) |
Jun
(7) |
Jul
(3) |
Aug
(1) |
Sep
|
Oct
(1) |
Nov
(9) |
Dec
(1) |
| 2011 |
Jan
(2) |
Feb
|
Mar
|
Apr
(3) |
May
(1) |
Jun
|
Jul
|
Aug
(14) |
Sep
(29) |
Oct
(3) |
Nov
|
Dec
(3) |
| 2012 |
Jan
|
Feb
|
Mar
|
Apr
(7) |
May
(6) |
Jun
(59) |
Jul
|
Aug
(8) |
Sep
(21) |
Oct
|
Nov
|
Dec
|
| 2013 |
Jan
(1) |
Feb
|
Mar
(10) |
Apr
|
May
(18) |
Jun
(25) |
Jul
(18) |
Aug
(1) |
Sep
(6) |
Oct
(28) |
Nov
(4) |
Dec
(13) |
| 2014 |
Jan
(7) |
Feb
(5) |
Mar
(4) |
Apr
(36) |
May
(3) |
Jun
(7) |
Jul
(46) |
Aug
(14) |
Sep
(12) |
Oct
(2) |
Nov
|
Dec
(12) |
| 2015 |
Jan
(4) |
Feb
|
Mar
|
Apr
(80) |
May
(36) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: <wa...@us...> - 2009-05-09 03:15:18
|
Revision: 1326
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1326&view=rev
Author: warnes
Date: 2009-05-09 03:15:10 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Move actual NEWS file into inst.
Added Paths:
-----------
trunk/gtools/inst/
trunk/gtools/inst/NEWS
Removed Paths:
-------------
trunk/gtools/NEWS
Deleted: trunk/gtools/NEWS
===================================================================
--- trunk/gtools/NEWS 2009-05-09 03:13:19 UTC (rev 1325)
+++ trunk/gtools/NEWS 2009-05-09 03:15:10 UTC (rev 1326)
@@ -1,78 +0,0 @@
-gtools 2.5.0
-------------
-
-New features:
-
-- Add checkRVersion() function to determin if a newer version of R is
- available.
-
-- Deprecated assert() in favor of base::stopifnot
-
-Bug fixes:
-
-- Fix bug in binsearch() identified by 2.6.0 R CMD CHECK
-
-Other changes:
-
-- Improve text explanation of how defmacro() and strmacro() differ from
- function().
-
-- Update definitions of odd() and even() to use modulus operator
- instead of division.
-
-gtools 2.4.0
-------------
-
-- Add binsearch() function, previously in the genetics() package.
-
-
-gtools 2.3.1
-------------
-
-- Add ask() function to prompt the user and collect a single response.
-
-
-gtools 2.3.0
-------------
-
-- Update email address for Greg
-
-- Add new 'smartbind' function, which combines data frames
- efficiently, even if they have different column names.
-
-gtools 2.2.3
-------------
-
- - setTCPNoDelay now compiles & works properly on Windows
-
-
-gtools 2.2.2
-------------
-
- - src/setTCPNoDelay.c: Add C source code for setTCPNoDelay.
-
- - NAMESPACE: Add UseDynLib to NAMESPACE so the shared library gets
- properly loaded.
-
- - Updated Greg's email address.
-
-gtools 2.2.1
-------------
-
- - New function 'addLast' that adds functions to R's .Last() so
- that they will be executed when R is terminating.
-
- - New function setTCPNoDelay() that allows the TCP_NODELAY flag to
- be changed on socket objects.
-
-gtools 2.1.0
-------------
-
- - Added assert.R (and documentation)
-
- - Added the defmacro() function, extracted from Lumley T. "Programmer's Niche:
- Macros in {R}", R News, 2001, Vol 1, No. 3, pp 11--13,
- \url{http://CRAN.R-project.org/doc/Rnews/}
-
- - Added DESCRIPTION and removed DESCRIPTION.in
-
Copied: trunk/gtools/inst/NEWS (from rev 1324, trunk/gtools/NEWS)
===================================================================
--- trunk/gtools/inst/NEWS (rev 0)
+++ trunk/gtools/inst/NEWS 2009-05-09 03:15:10 UTC (rev 1326)
@@ -0,0 +1,78 @@
+gtools 2.5.0
+------------
+
+New features:
+
+- Add checkRVersion() function to determin if a newer version of R is
+ available.
+
+- Deprecated assert() in favor of base::stopifnot
+
+Bug fixes:
+
+- Fix bug in binsearch() identified by 2.6.0 R CMD CHECK
+
+Other changes:
+
+- Improve text explanation of how defmacro() and strmacro() differ from
+ function().
+
+- Update definitions of odd() and even() to use modulus operator
+ instead of division.
+
+gtools 2.4.0
+------------
+
+- Add binsearch() function, previously in the genetics() package.
+
+
+gtools 2.3.1
+------------
+
+- Add ask() function to prompt the user and collect a single response.
+
+
+gtools 2.3.0
+------------
+
+- Update email address for Greg
+
+- Add new 'smartbind' function, which combines data frames
+ efficiently, even if they have different column names.
+
+gtools 2.2.3
+------------
+
+ - setTCPNoDelay now compiles & works properly on Windows
+
+
+gtools 2.2.2
+------------
+
+ - src/setTCPNoDelay.c: Add C source code for setTCPNoDelay.
+
+ - NAMESPACE: Add UseDynLib to NAMESPACE so the shared library gets
+ properly loaded.
+
+ - Updated Greg's email address.
+
+gtools 2.2.1
+------------
+
+ - New function 'addLast' that adds functions to R's .Last() so
+ that they will be executed when R is terminating.
+
+ - New function setTCPNoDelay() that allows the TCP_NODELAY flag to
+ be changed on socket objects.
+
+gtools 2.1.0
+------------
+
+ - Added assert.R (and documentation)
+
+ - Added the defmacro() function, extracted from Lumley T. "Programmer's Niche:
+ Macros in {R}", R News, 2001, Vol 1, No. 3, pp 11--13,
+ \url{http://CRAN.R-project.org/doc/Rnews/}
+
+ - Added DESCRIPTION and removed DESCRIPTION.in
+
Property changes on: trunk/gtools/inst/NEWS
___________________________________________________________________
Added: svn:keywords
+ Author Date Id Revision
Added: svn:mergeinfo
+
Added: svn:eol-style
+ native
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 03:13:26
|
Revision: 1325
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1325&view=rev
Author: warnes
Date: 2009-05-09 03:13:19 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Update Greg's email address and fix Rd syntax errors
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/man/addLast.Rd
trunk/gtools/man/binsearch.Rd
trunk/gtools/man/capture.Rd
trunk/gtools/man/combinations.Rd
trunk/gtools/man/defmacro.Rd
trunk/gtools/man/dirichlet.Rd
trunk/gtools/man/foldchange.Rd
trunk/gtools/man/gtools-deprecated.Rd
trunk/gtools/man/invalid.Rd
trunk/gtools/man/logit.Rd
trunk/gtools/man/mixedsort.Rd
trunk/gtools/man/oddeven.Rd
trunk/gtools/man/permute.Rd
trunk/gtools/man/quantcut.Rd
trunk/gtools/man/running.Rd
trunk/gtools/man/scat.Rd
trunk/gtools/man/setTCPNoDelay.Rd
trunk/gtools/man/smartbind.Rd
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/DESCRIPTION 2009-05-09 03:13:19 UTC (rev 1325)
@@ -1,9 +1,9 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 2.6.0
-Date: 2008-08-15
+Version: 2.6.1
+Date: 2009-05-08
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
-Maintainer: Gregory R. Warnes <wa...@bs...>
+Maintainer: Gregory R. Warnes <gr...@ra...>
License: LGPL-2.1
Modified: trunk/gtools/man/addLast.Rd
===================================================================
--- trunk/gtools/man/addLast.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/addLast.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -20,7 +20,7 @@
\value{
None.
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link[base]{.Last}} }
\examples{
Modified: trunk/gtools/man/binsearch.Rd
===================================================================
--- trunk/gtools/man/binsearch.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/binsearch.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -41,7 +41,7 @@
and the function value at both are returned.
Note that when the specified target value falls between integers, the
- \em{two} closest values are returned. If the specified target falls
+ \emph{two} closest values are returned. If the specified target falls
outside of the specified \code{range}, the closest endpoint of the
range will be returned, and an warning message will be generated. If
the maximum number if iterations was reached, the endpoints of the
@@ -60,7 +60,7 @@
\code{where}.}
}
%\references{ ~put references to the literature/web site here ~ }
-\author{Gregory R. Warnes \email{wa...@bs...} }
+\author{Gregory R. Warnes \email{gr...@ra...} }
\note{This function often returns two values for \code{where} and
\code{value}. Be sure to check the \code{flag} parameter to see what
these values mean.}
Modified: trunk/gtools/man/capture.Rd
===================================================================
--- trunk/gtools/man/capture.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/capture.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -30,8 +30,11 @@
\section{WARNING}{R 1.7.0+ includes \code{capture.output}, which
duplicates the functionality of \code{capture}. Thus, \code{capture}
is depreciated.}
-\author{Gregory R. Warnes \email{wa...@bs...} }
-\seealso{\code{\link[session]{texteval}}, \code{\link[base]{capture.output}}}}
+\author{Gregory R. Warnes \email{gr...@ra...} }
+\seealso{
+ \code{\link[session]{texteval}},
+ \code{\link[base]{capture.output}}
+}
\examples{
# capture the results of a loop
Modified: trunk/gtools/man/combinations.Rd
===================================================================
--- trunk/gtools/man/combinations.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/combinations.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -40,7 +40,7 @@
\author{ Original versions by Bill Venables
\email{Bil...@cm...}. Extended to handle
\code{repeats.allowed} by Gregory R. Warnes
- \email{wa...@bs...}.
+ \email{gr...@ra...}.
}
\seealso{ \code{\link[base]{choose}}, \code{\link[base]{options}} }
\examples{
Modified: trunk/gtools/man/defmacro.Rd
===================================================================
--- trunk/gtools/man/defmacro.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/defmacro.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -60,11 +60,11 @@
\references{
The original \code{defmacro} code was directly taken from:
- Lumley T. "Programmer's Niche: Macros in {R}", R News, 2001, Vol 1,
+ Lumley T. "Programmer's Niche: Macros in R", R News, 2001, Vol 1,
No. 3, pp 11--13, \url{http://CRAN.R-project.org/doc/Rnews/}
}
\author{ Thomas Lumley wrote \code{defmacro}. Gregory R. Warnes
- \email{wa...@bs...} enhanced it and created
+ \email{gr...@ra...} enhanced it and created
\code{strmacro}.
}
\seealso{
Modified: trunk/gtools/man/dirichlet.Rd
===================================================================
--- trunk/gtools/man/dirichlet.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/dirichlet.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -36,7 +36,7 @@
\url{http://www.r-project.org/nocvs/mail/r-help/2000/3865.html}. Ben
attributed the code to Ian Wilson \email{i.w...@ma...}.
Subsequent modifications by Gregory R. Warnes
- \email{wa...@bs...}.
+ \email{gr...@ra...}.
}
\seealso{ \code{\link{dbeta}}, \code{\link{rbeta}} }
\examples{
Modified: trunk/gtools/man/foldchange.Rd
===================================================================
--- trunk/gtools/man/foldchange.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/foldchange.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -37,7 +37,7 @@
A vector or matrix of the same dimensions as the input containing the
converted values.
}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\examples{
a <- 1:21
Modified: trunk/gtools/man/gtools-deprecated.Rd
===================================================================
--- trunk/gtools/man/gtools-deprecated.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/gtools-deprecated.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -19,6 +19,6 @@
\code{assert} is a deprecated synonym for \code{\link[base]{stopifnot}}.
}
\seealso{
- \code{\link{Deprecated}} }
+ \code{\link{Deprecated}}
}
\keyword{misc}
Modified: trunk/gtools/man/invalid.Rd
===================================================================
--- trunk/gtools/man/invalid.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/invalid.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -17,7 +17,7 @@
\value{
Logical value.
}
-\author{Gregory R. Warnes \email{wa...@bs...} }
+\author{Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link[base]{missing}}, \code{\link[base]{is.na}},
\code{\link[base]{is.null}} }
\examples{
Modified: trunk/gtools/man/logit.Rd
===================================================================
--- trunk/gtools/man/logit.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/logit.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -42,7 +42,7 @@
\value{
Transformed value(s).
}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link[car]{logit}}, \code{\link[moc]{inv.glogit}} }
\examples{
Modified: trunk/gtools/man/mixedsort.Rd
===================================================================
--- trunk/gtools/man/mixedsort.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/mixedsort.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -36,7 +36,7 @@
\code{mixedorder} returns a vector giving the sort order of the input
elements. \code{mixedsort} returns the sorted vector.
}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link[base]{sort}}, \code{\link[base]{order}} }
\examples{
# compound & dose labels
Modified: trunk/gtools/man/oddeven.Rd
===================================================================
--- trunk/gtools/man/oddeven.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/oddeven.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -17,7 +17,7 @@
\value{
Vector of TRUE/FALSE values.
}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link[base]{round}} }
\examples{
Modified: trunk/gtools/man/permute.Rd
===================================================================
--- trunk/gtools/man/permute.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/permute.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -18,7 +18,7 @@
\value{
Vector with the original items reordered.
}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link{sample}} }
\examples{
Modified: trunk/gtools/man/quantcut.Rd
===================================================================
--- trunk/gtools/man/quantcut.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/quantcut.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -3,7 +3,7 @@
\name{quantcut}
\alias{quantcut}
-\title{ Create a Factor Variable Using the Quantiles of a Continuous Variable}}
+\title{ Create a Factor Variable Using the Quantiles of a Continuous Variable}
\description{
Create a factor variable using the quantiles of a continous variable.
}
@@ -34,7 +34,7 @@
Factor variable with one level for each quantile interval given by \code{q}.
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link{cut}}, \code{\link{quantile}} }
Modified: trunk/gtools/man/running.Rd
===================================================================
--- trunk/gtools/man/running.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/running.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -55,7 +55,7 @@
Note that this function will create a vector or matrix even for
objects which are not simplified by \code{sapply}.
}
-\author{ Gregory R. Warnes \email{wa...@bs...},
+\author{ Gregory R. Warnes \email{gr...@ra...},
with contributions by Nitin Jain \email{nit...@pf...}.}
\seealso{ \code{\link[gplots]{wapply}} to apply a function over an x-y window
centered at each x point, \code{\link[base]{sapply}},
Modified: trunk/gtools/man/scat.Rd
===================================================================
--- trunk/gtools/man/scat.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/scat.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -18,7 +18,7 @@
\value{
NULL (invisibly)
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link[base]{cat}}}
\examples{
options(DEBUG=NULL) # makee sure DEBUG isn't set
Modified: trunk/gtools/man/setTCPNoDelay.Rd
===================================================================
--- trunk/gtools/man/setTCPNoDelay.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/setTCPNoDelay.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -26,8 +26,6 @@
This function allows this feature to be disabled (de-Nagling,
\code{value=TRUE}) or enabled (Nagling, \code{value=FALSE}) for the
specified socket.
- }
-
}
\value{
The character string "SUCCESS" will be returned invisible if the
@@ -41,7 +39,7 @@
Request for Comments 896, January 1984.
\url{http://www.ietf.org/rfc/rfc0896.txt?number=896}
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{
\code{\link[utils]{make.socket}},
\code{\link[utils]{socketConnection}}
Modified: trunk/gtools/man/smartbind.Rd
===================================================================
--- trunk/gtools/man/smartbind.Rd 2009-05-08 23:07:20 UTC (rev 1324)
+++ trunk/gtools/man/smartbind.Rd 2009-05-09 03:13:19 UTC (rev 1325)
@@ -22,7 +22,7 @@
character strings. The user will need to coerce such character
columns into an appropriate type.
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link{rbind}}, \code{\link{cbind}} }
\examples{
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-08 23:07:28
|
Revision: 1324
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1324&view=rev
Author: warnes
Date: 2009-05-08 23:07:20 +0000 (Fri, 08 May 2009)
Log Message:
-----------
Add test of using a dendrogram created by heatmap() with heatmap.2()
Added Paths:
-----------
trunk/gplots/tests/heatmap_to_heatmap.2_test.R
Added: trunk/gplots/tests/heatmap_to_heatmap.2_test.R
===================================================================
--- trunk/gplots/tests/heatmap_to_heatmap.2_test.R (rev 0)
+++ trunk/gplots/tests/heatmap_to_heatmap.2_test.R 2009-05-08 23:07:20 UTC (rev 1324)
@@ -0,0 +1,16 @@
+library(gplots)
+data(mtcars)
+
+x <- as.matrix(mtcars)
+
+## draws expected image
+testHeatmap <- heatmap(x, Colv=NA, col=bluered(256), scale="column",
+ keep.dendro=TRUE)
+
+# to prove this dendro is OK, redraw with same function:
+heatmap(x, Colv=NA, col=bluered(256), scale="column",
+ keep.dendro=TRUE, Rowv=testHeatmap$Rowv)
+
+# but it doesn't work with heatmap.2()
+heatmap.2(x, Colv=NA, col=bluered(256), scale="column",
+ Rowv=testHeatmap$Rowv, dendrogram="row")
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-08 22:51:25
|
Revision: 1323
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1323&view=rev
Author: warnes
Date: 2009-05-08 22:51:07 +0000 (Fri, 08 May 2009)
Log Message:
-----------
heatmap.2: handle NA for RowV or ColV the same way as NULL
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2009-05-08 22:35:25 UTC (rev 1322)
+++ trunk/gplots/R/heatmap.2.R 2009-05-08 22:51:07 UTC (rev 1323)
@@ -103,9 +103,9 @@
## key=FALSE
## }
- if ( is.null(Rowv) )
+ if ( is.null(Rowv) || is.na(Rowv) )
Rowv <- FALSE
- if ( is.null(Colv) )
+ if ( is.null(Colv) || is.na(Colv) )
Colv <- FALSE
else if( Colv=="Rowv" && !isTRUE(Rowv) )
Colv <- FALSE
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-08 22:35:55
|
Revision: 1322
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1322&view=rev
Author: warnes
Date: 2009-05-08 22:35:25 +0000 (Fri, 08 May 2009)
Log Message:
-----------
Fix typo
Modified Paths:
--------------
trunk/gplots/man/plotCI.Rd
Modified: trunk/gplots/man/plotCI.Rd
===================================================================
--- trunk/gplots/man/plotCI.Rd 2009-05-08 22:32:28 UTC (rev 1321)
+++ trunk/gplots/man/plotCI.Rd 2009-05-08 22:35:25 UTC (rev 1322)
@@ -147,7 +147,7 @@
# better yet, just use plotmeans ... #
plotmeans( state.area ~ state.region )
-/dontshow{
+\dontshow{
## Just for testing
plotCI(x=means, uiw=NA)
plotCI(x=means, uiw=NULL)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-08 22:32:36
|
Revision: 1321
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1321&view=rev
Author: warnes
Date: 2009-05-08 22:32:28 +0000 (Fri, 08 May 2009)
Log Message:
-----------
Update NEWS for release 2.7.0
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2009-05-08 22:30:55 UTC (rev 1320)
+++ trunk/gplots/inst/NEWS 2009-05-08 22:32:28 UTC (rev 1321)
@@ -1,8 +1,31 @@
-Release 2.7.0 - 2008-08-05
+Release 2.7.0 - 2009-05-08
--------------------------
New Features:
+
+- Enhancements to heatmap.2()
+
+ - New arguments 'lmat', 'lhei', and 'lwid' that allow controlling
+ component plot layout. Users can now resize and rearrange plot
+ components.
+
+ - heatmap.2() will now compute color breakpoints that are
+ symmetric about 0 when the new 'symbreak' parameter is TRUE. This
+ parameter, as well as the symkey parameter now default to TRUE
+ whenever negative values of x are present, and to FALSE othewise.
+
+ - the heatmap.2() return value now includes additional useful
+ information, including: call, rowMeans, rowSDs, colMeans,
+ colSDs, carpet (reordered and scaled 'x' values), rowDendrogram,
+ 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.
+
+ 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.
@@ -15,10 +38,6 @@
using the new bandplot() and by using fitted() instead of predict()
to obtain y-hat.
-- New arguments for heatmap.2 ('lmat', 'lhei', and 'lwid') that allow
- controlling component plot layout. This allows the user to both
- resize and rearrange plot components.
-
- Add 'scale.range' argument to balloonplot(), option to scale
balloons so [min,max]->[0,1] ('relative') or [0,max] -> [0,1]
('absolute').
@@ -29,9 +48,14 @@
- balloonplot() now properly handles dimension labels provided by
'xlab' and 'ylab'
+- plotCI now properly handles 'NULL' and 'NA' values for ui, li, uiw,
+ and liw.
+
- Corrections of minor typos in man pages
+- Update Greg's email address to 'gr...@ra...'
+
Release 2.6.0 - 2008-04-07
--------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-08 22:31:03
|
Revision: 1320
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1320&view=rev
Author: warnes
Date: 2009-05-08 22:30:55 +0000 (Fri, 08 May 2009)
Log Message:
-----------
We don't want the Changelog in svn, since it is autogenerated from svn logs!
Removed Paths:
-------------
trunk/gplots/inst/ChangeLog
Deleted: trunk/gplots/inst/ChangeLog
===================================================================
--- trunk/gplots/inst/ChangeLog 2009-05-08 22:01:12 UTC (rev 1319)
+++ trunk/gplots/inst/ChangeLog 2009-05-08 22:30:55 UTC (rev 1320)
@@ -1,1759 +0,0 @@
-2008-06-16 14:18 warnes
-
- * TODO, inst/TODO: Add TODO list to gplots
-
-2008-05-20 01:13 warnes
-
- * DESCRIPTION, man/plot.lm2.Rd: Update man page to match recent
- changes to plot.lm2()
-
-2008-05-20 01:08 warnes
-
- * man/venn.Rd: More work on documentation for venn()
-
-2008-05-20 01:07 warnes
-
- * R/bandplot.R, man/bandplot.Rd: Fix code/doc mismatch due to
- recent changes to bandplot()
-
-2008-05-20 00:14 warnes
-
- * DESCRIPTION, NAMESPACE, R/venn.R, man/venn.Rd: Add Venn Diagram
- plot submitted by Steffen Moeller
-
-2008-05-07 18:59 warnes
-
- * DESCRIPTION, R/bandplot.R: Improve performance of bandplot by
- calculating running standard deviation using caTools::runsd()
- instead of (ver slow) window() call. In addtion, the standard
- deviations are now only calculated once, rather than once for
- each band.
-
-2008-05-07 18:57 warnes
-
- * R/plot.lm.R: Improve performance of plot.lm for large lm objects
- by using fitted() instead of predict() to get y-hat
-
-2008-05-05 20:28 warnes
-
- * DESCRIPTION, R/bandplot.R: Use caTools's runsd in bandplot for a
- dramatic speedup for large data
-
-2008-05-05 20:28 warnes
-
- * NAMESPACE: Add import of gtools::reorder.factor for ballonplot
- man page
-
-2008-05-05 20:27 warnes
-
- * R/balloonplot.R, man/balloonplot.Rd: balloonplot: Add option to
- scale balloons so [min,max]->[0,1] (relative) or so [0,max] <-
- [0,1] (absolute)
-
-2008-04-07 17:09 warnes
-
- * man/barplot2.Rd: Fix typo in barplot2() man page
-
-2008-04-07 16:52 warnes
-
- * DESCRIPTION, inst/ChangeLog, inst/NEWS: Updates for gplots 2.6.0
-
-2008-04-07 16:47 warnes
-
- * R/heatmap.2.R, man/heatmap.2.Rd: Add ability to control location
- of individual heatmap.2 components
-
-2008-03-27 22:36 warnes
-
- * R/heatmap.2.R: Fix bug in handling rowsep, per suggestion by
- Steven Paugh
-
-2008-01-04 18:59 warnes
-
- * man/overplot.Rd: Fix examples for overplot()
-
-2008-01-02 16:58 warnes
-
- * man/barplot2.Rd: Update Marc's email address
-
-2007-12-20 22:48 warnes
-
- * man/heatmap.2.Rd: Two letter clarification of help text for
- heatmap.2()
-
-2007-12-20 22:24 warnes
-
- * man/ooplot.Rd: Restore plot layout at end of ooplot() example
-
-2007-11-06 16:24 warnes
-
- * man/hist2d.Rd: Remove extraneous closing brace in the hist2d
- documentation file
-
-2007-11-05 15:32 warnes
-
- * inst/NEWS: Fix typo in NEWS: col2hex() is the new function, not
- col2rgb() which is part of grDevices
-
-2007-11-02 19:32 warnes
-
- * DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/NEWS: Updates for
- gplots 2.5.0
-
-2007-11-02 19:32 warnes
-
- * tests/heatmap2Test.Rout.save: Update saved test output due to
- changes in how R reports warnings
-
-2007-11-02 18:22 warnes
-
- * ChangeLog, NEWS: Create soft links of gmodels/ChangeLog ->
- gmodels/inst/ChangeLog, and gmodels/NEWS -> gmodels/inst/NEWS for
- my convenience
-
-2007-11-02 18:21 warnes
-
- * ChangeLog, NEWS, inst/ChangeLog, inst/NEWS: Move actual ChangeLog
- and NEWS files to gmodels/inst so they will be copied into the
- installed R package area
-
-2007-11-02 18:18 warnes
-
- * man/bandplot.Rd, man/textplot.Rd: Fix code/doc mismatches
-
-2007-11-02 18:18 warnes
-
- * R/plot.lm.R: Update plot.lm2 to match changes made to bandplot
-
-2007-11-01 20:20 warnes
-
- * ChangeLog, DESCRIPTION, R/replaceTabs.R, R/textplot.R: in
- textplot(), convert tab characters to spaces before processing to
- avoid problems with computing height and width of text including
- tabs when using pdf()
-
-2007-11-01 20:18 warnes
-
- * R/overplot.R, man/overplot.Rd: Minor reformatting of overplot
- code and docs
-
-2007-10-22 02:24 warnes
-
- * branches/GenerateFORMATSfromFactorObjects/SASxport/DESCRIPTION,
- trunk/MSOfficeUtil/DESCRIPTION, trunk/RMCMC/DESCRIPTION,
- trunk/Rlsf/DESCRIPTION, trunk/SASxport/DESCRIPTION,
- trunk/bwRF/DESCRIPTION, trunk/exp.ssize/DESCRIPTION,
- trunk/fork/DESCRIPTION, trunk/gdata/DESCRIPTION,
- trunk/gmodels/DESCRIPTION, DESCRIPTION,
- trunk/gregmisc/DESCRIPTION, trunk/ssize/DESCRIPTION: Clarify GPL
- version
-
-2007-08-14 19:14 warnes
-
- * R/balloonplot.R: Correct error in balloonplot when z contains NA
- values.
-
-2007-08-14 18:48 warnes
-
- * R/balloonplot.R, man/balloonplot.Rd: Augment balloonplot() with
- control of character size and color for text and label items
-
-2007-08-14 18:11 warnes
-
- * R/balloonplot.R: Correct balloonplot.default to properly show
- specified x and y axis labels when explicitly provided
-
-2007-03-09 09:05 ggorjan
-
- * man/ooplot.Rd: use of \method in Rd markup - issues a warning
- with _R_CHECK_RD_STYLE_=TRUE env. variable with R 2.5.0
-
-2007-02-08 23:05 warnes
-
- * DESCRIPTION: Bump version number
-
-2007-02-08 22:03 warnes
-
- * man/textplot.Rd: Update documentation for textplot()
-
-2007-02-08 21:56 warnes
-
- * R/col2hex.R, man/col2hex.Rd: Add col2rgb() function to convert
- color names to rgb hex codes
-
-2007-02-08 21:32 warnes
-
- * R/textplot.R: Add paramaeters 'col.data', 'col.rows', and
- 'col.columns' to
- textplot.matrix to allow specification of the color of the matrix
- data, rows, and columns.
-
-2007-02-08 16:56 warnes
-
- * R/bandplot.R: Add parameters to control line width and line type.
-
-2006-11-14 22:25 ggorjan
-
- * trunk/gdata/man/combine.Rd, trunk/gdata/man/frameApply.Rd,
- trunk/gmodels/R/ci.R, trunk/gmodels/R/fast.prcomp.R,
- trunk/gmodels/man/ci.Rd, R/bandplot.R, R/boxplot.n.R, R/lowess.R,
- R/plot.lm.R, R/plotCI.R, R/plotmeans.R, R/residplot.R,
- R/wapply.R, man/boxplot.n.Rd, man/plotCI.Rd, man/plotmeans.Rd,
- trunk/gtools/R/combinations.R, trunk/gtools/R/running.R,
- trunk/gtools/man/ELISA.Rd, trunk/gtools/man/combinations.Rd:
- Removed executable property
-
-2006-11-14 18:29 warnes
-
- * tests/heatmap2Test.Rout.save: Update output file to match
- (trivial) changes in the test code.
-
-2006-11-14 18:07 warnes
-
- * ChangeLog, NEWS: Update ChangeLog and NEWS files for release
- 2.3.2.
-
-2006-11-14 17:59 warnes
-
- * DESCRIPTION: Update version number
-
-2006-11-14 17:57 warnes
-
- * DESCRIPTION: Update version number and maintainer
-
-2006-11-14 17:56 warnes
-
- * man/heatmap.2.Rd: Correct problem with labeled correlation matrix
- example. Thanks to Jean Vidal for reporting the error..
-
-2006-08-02 22:21 warnes
-
- * trunk/BalloonPlotPaper/BalloonPlot.pdf,
- trunk/BalloonPlotPaper/BalloonPlot.tex,
- trunk/MSOfficeUtil/DESCRIPTION,
- trunk/PathwayModeling/thesispaper/slides.tex,
- trunk/RMCMC/DESCRIPTION, trunk/RMCMC/man/make.density.Rd,
- trunk/Rlsf/DESCRIPTION, trunk/Rlsf/man/lsf.numcpu.Rd,
- trunk/Rlsf/man/lsf.parRapply.Rd, trunk/Rlsf/man/scat.Rd,
- trunk/bwRF/DESCRIPTION, trunk/bwRF/man/RF.Rd,
- trunk/exp.ssize/inst/doc/ssize.pdf,
- trunk/exp.ssize/inst/doc/ssize.tex, trunk/fork/DESCRIPTION,
- trunk/fork/man/exit.Rd, trunk/fork/man/fork.Rd,
- trunk/fork/man/getpid.Rd, trunk/fork/man/kill.Rd,
- trunk/fork/man/signame.Rd, trunk/fork/man/wait.Rd,
- trunk/gdata/inst/doc/gregmisc.tex,
- trunk/gdata/man/ConvertMedUnits.Rd,
- trunk/gdata/man/aggregate.table.Rd, trunk/gdata/man/combine.Rd,
- trunk/gdata/man/interleave.Rd, trunk/gdata/man/matchcols.Rd,
- trunk/gdata/man/nobs.Rd, trunk/gdata/man/read.xls.Rd,
- trunk/gdata/man/rename.vars.Rd, trunk/gdata/man/reorder.Rd,
- trunk/gdata/man/trim.Rd, trunk/gdata/man/unmatrix.Rd,
- trunk/gdata/man/upperTriangle.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, inst/doc/BalloonPlot.pdf,
- man/balloonplot.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
- man/colorpanel.Rd, man/hist2d.Rd, man/ooplot.Rd, man/overplot.Rd,
- man/plot.lm2.Rd, man/plotCI.Rd, man/plotmeans.Rd,
- man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
- man/space.Rd, man/textplot.Rd, man/wapply.Rd,
- trunk/gregmisc/DESCRIPTION,
- trunk/gregmisc/gregmisc/DESCRIPTION.standalone,
- trunk/gregmisc/inst/doc/gregmisc.tex,
- trunk/gtools/man/addLast.Rd, trunk/gtools/man/assert.Rd,
- trunk/gtools/man/capture.Rd, trunk/gtools/man/combinations.Rd,
- trunk/gtools/man/defmacro.Rd, trunk/gtools/man/dirichlet.Rd,
- trunk/gtools/man/foldchange.Rd, trunk/gtools/man/invalid.Rd,
- trunk/gtools/man/logit.Rd, trunk/gtools/man/mixedsort.Rd,
- trunk/gtools/man/oddeven.Rd, trunk/gtools/man/permute.Rd,
- trunk/gtools/man/quantcut.Rd, trunk/gtools/man/running.Rd,
- trunk/gtools/man/scat.Rd, trunk/gtools/man/setTCPNoDelay.Rd,
- trunk/nws/DESCRIPTION, trunk/qvalue/DESCRIPTION,
- trunk/qvalue/man/print.qvalue.Rd, trunk/ssize/DESCRIPTION,
- trunk/ssize/man/pow.Rd: Update my email address
-
-2006-06-26 21:08 nj7w
-
- * R/heatmap.2.R: Fixed a bug which displayed warnings when Rowv and
- Colv were specified as dendrograms
-
-2006-03-10 17:24 warnes
-
- * tests/heatmap2Test.R: Remove code that added a local path
-
-2006-03-09 22:53 nj7w
-
- * tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added the
- correct library path where gplots is installed locally and
- corresponding .save file
-
-2006-03-09 22:40 nj7w
-
- * tests/heatmap2Test.R: Updated the tests file
-
-2006-03-09 22:39 nj7w
-
- * R/heatmap.2.R: Removed the condition Colv != Rowv as it has
- already been taken care of
-
-2006-03-09 22:17 nj7w
-
- * rtPCR.rda: Deleted rtPCR.rda from the main directory
-
-2006-03-09 22:09 nj7w
-
- * ChangeLog: Added ChangeLog
-
-2006-03-07 18:18 nj7w
-
- * DESCRIPTION, NEWS: Updated ChangeLog and NEWS
-
-2006-03-07 18:10 nj7w
-
- * tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added
- the tests and fixed corrupted files
-
-2006-03-07 16:22 nj7w
-
- * data/rtPCR.rda: Replaced the corrupted rtPCR.rda file in data
- directory
-
-2006-03-07 16:14 nj7w
-
- * tests: Removed the corrputed tests directory
-
-2006-03-07 16:12 nj7w
-
- * data/rtPCR.rda, rtPCR.rda: Replaced the corrupted rtPCR.rda file
- in data directory
-
-2006-03-03 21:03 nj7w
-
- * R/heatmap.2.R, man/heatmap.2.Rd: Updated the code and man page to
- make sure the Rowv and Colv values are properly handled
-
-2006-03-02 21:43 warnes
-
- * R/balloonplot.R: Adjust row total placement to adjust for width
- of the totals
-
-2006-03-02 21:26 warnes
-
- * DESCRIPTION, R/balloonplot.R, man/1: Row totals in ballonplot
- were in reverse order. Fixed.
-
-2006-02-23 22:00 nj7w
-
- * R/heatmap.2.R, tests/heatmap2Test.R: Add ability to scale the
- color key using the new 'keysize' argument.
-
-2006-02-23 21:34 nj7w
-
- * tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Add
- tests for heatmap.2
-
-2006-02-23 21:25 nj7w
-
- * inst/doc/Figure1.eps, inst/doc/Table.eps, inst/doc/bka.bst,
- inst/doc/heatmap2.R, inst/doc/heatmap2.tex,
- inst/doc/regression_rank_image.Rda,
- inst/doc/regression_rank_image_II.Rda: Move heatmap and
- ballonplot paper source materials to their respective cvs modules
-
-2006-02-23 21:20 nj7w
-
- * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex,
- inst/doc/Figure1.pdf, inst/doc/Figure2.pdf, inst/doc/Figure3.pdf,
- inst/doc/Figure4.pdf, inst/doc/Rnews.sty,
- inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
- inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Moved
- balloonplot paper materials to BallonPlotPaper cvs module
-
-2006-02-23 21:18 nj7w
-
- * inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
- inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
- inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
- inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
- inst/doc/scaled.pdf: Remove heatmap paper files and move them to
- the HeatmapPaper cvs module.
-
-2006-02-23 19:57 nj7w
-
- * inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
- inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
- inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
- inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
- inst/doc/scaled.pdf: Added figures for heatmap2 paper
-
-2006-02-23 19:54 nj7w
-
- * inst/doc/regression_rank_image.Rda,
- inst/doc/regression_rank_image_II.Rda: Added the .Rda files for
- the heatmap2 paper
-
-2006-02-23 19:52 nj7w
-
- * inst/doc/heatmap2.tex: Added the source - (tex file) of the
- heatmap paper
-
-2006-02-23 19:51 nj7w
-
- * inst/doc/heatmap2.R: Added the code for the figures of heatmap
- paper
-
-2006-02-21 22:19 nj7w
-
- * R/heatmap.2.R, man/heatmap.2.Rd: Minor updates to heatmap.2 -
- fixed Rowv, Colv and dendrogram behaviour. Now Rowv=NULL or FALSE
- both imply no dendrogram computation.
-
-2006-01-12 23:10 warnes
-
- * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
- inst/doc/BalloonPlot.tex, inst/doc/Figure1.pdf,
- inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
- more updates
-
-2006-01-12 23:01 warnes
-
- * inst/doc/bka.bst: Add Biometrica bibliography style file
-
-2006-01-12 22:34 warnes
-
- * inst/doc/BalloonPlot.tex: A little more.
-
-2006-01-12 22:32 warnes
-
- * inst/doc/BalloonPlot.tex: Updates to respond to referee.
-
-2006-01-12 19:59 nj7w
-
- * inst/doc/BalloonPlot.tex: Added references
-
-2005-12-13 17:01 nj7w
-
- * inst/doc/BalloonPlot.tex: Fixed Nitin's company name
-
-2005-12-13 16:18 nj7w
-
- * ChangeLog, NEWS, trunk/gtools/NEWS: Updated NEWS and removed
- ChangeLog
-
-2005-12-12 22:20 nj7w
-
- * R/plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza's
- suggestion
-
-2005-12-07 18:52 nj7w
-
- * DESCRIPTION: Updated version number
-
-2005-12-07 18:50 nj7w
-
- * NAMESPACE, R/plot.lm.R, man/plot.lm2.Rd: Added plot.lm
-
-2005-12-07 18:48 nj7w
-
- * man/barplot2.Rd: Changed the default grey colors to heat colors,
- if height is matrix
-
-2005-12-07 18:48 nj7w
-
- * R/barplot2.R: Changed the default greay colors to heat colors, if
- height is matrix
-
-2005-12-06 22:41 nj7w
-
- * man/barplot2.Rd: Fixed minor error in documentation of barplot2
-
-2005-12-02 21:11 warnes
-
- * R/plot.lm.R: Remove .Alias calls, since .Alias is defunct.
-
-2005-12-01 16:54 nj7w
-
- * trunk/gmodels/man/ci.Rd, trunk/gmodels/man/coefFrame.Rd,
- trunk/gmodels/man/estimable.Rd,
- trunk/gmodels/man/fit.contrast.Rd,
- trunk/gmodels/man/make.contrasts.Rd, man/balloonplot.Rd,
- man/bandplot.Rd, man/boxplot.n.Rd, man/colorpanel.Rd,
- man/overplot.Rd, man/plotmeans.Rd, man/textplot.Rd,
- man/wapply.Rd, trunk/gtools/man/combinations.Rd,
- trunk/gtools/man/foldchange.Rd, trunk/gtools/man/invalid.Rd,
- trunk/gtools/man/logit.Rd, trunk/gtools/man/mixedsort.Rd,
- trunk/gtools/man/oddeven.Rd, trunk/gtools/man/quantcut.Rd,
- trunk/gtools/man/running.Rd: Updated Greg's email address
-
-2005-11-23 22:05 nj7w
-
- * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
- inst/doc/BalloonPlot.tex, inst/doc/Figure2.pdf: Updated Figure 2
- colors
-
-2005-11-18 20:40 warnes
-
- * inst/doc/BalloonPlot.pdf, inst/doc/Figure1.pdf,
- inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
- Latest version of the pdf files
-
-2005-11-18 20:37 warnes
-
- * inst/doc/BalloonPlot.tex: Nitin works for the Cambrige Group, not
- Pfizer.
-
-2005-11-18 20:34 warnes
-
- * inst/doc/BalloonPlot.tex: Minor text rewording.
-
-2005-11-18 20:31 warnes
-
- * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: More edits.
-
-2005-11-18 19:50 warnes
-
- * R/balloonplot.R: Recent changes to align row totals with the
- overall total broke how
- the marginal cumulative fractions were displayed. This patch
- fixes
- the problem.
-
-2005-11-18 01:17 warnes
-
- * DESCRIPTION, R/balloonplot.R, R/plot.lm.R,
- inst/doc/BalloonPlot.pdf, man/balloonplot.Rd: - Update
- documentation for balloonplot to match the latest code.
- - Correct spelling of 'show.zeroes' to 'show.zeros'
-
-2005-11-18 00:16 warnes
-
- * R/colorpanel.R: More changes: colorpanel now allows only 2 colors
- to be specified if
- no 'middle' color is desired.
-
-2005-11-17 22:08 warnes
-
- * R/balloonplot.R: Allow user to control removal of duplicate
- entries in balloonplot.
-
-2005-11-17 22:06 warnes
-
- * R/colorpanel.R, man/colorpanel.Rd: Extend colorpanel to handle
- just two-colors in addition to three.
-
-2005-11-09 22:39 nj7w
-
- * inst/doc/BalloonPlot.pdf: Updated the pdf file
-
-2005-11-09 22:38 nj7w
-
- * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: Updated the
- changes
-
-2005-11-09 22:29 nj7w
-
- * inst/doc/Figure4.pdf: Modified figure 4
-
-2005-11-09 22:29 nj7w
-
- * inst/doc/BalloonPlot.R: Updated code
-
-2005-11-09 22:20 nj7w
-
- * inst/doc/Figure3.pdf: Modified figure 3
-
-2005-11-09 22:20 nj7w
-
- * inst/doc/Figure2.pdf: Modified figure 2
-
-2005-11-09 22:19 nj7w
-
- * inst/doc/Figure1.pdf: Modified figure 1
-
-2005-11-08 16:19 nj7w
-
- * man/plotCI.Rd: Updated Greg's email
-
-2005-11-07 16:58 nj7w
-
- * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Minor
- modifications to fit the code properly on pdf
-
-2005-11-07 14:22 warnes
-
- * inst/doc/BalloonPlot.R: Add R code that generates plots
-
-2005-11-07 14:18 warnes
-
- * inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
- Add figures to CVS
-
-2005-11-07 14:18 warnes
-
- * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
- inst/doc/Figure1.pdf: Text changes
-
-2005-11-04 21:48 warnes
-
- * R/balloonplot.R: Fix some alignment issues.
-
-2005-11-04 19:05 warnes
-
- * inst/doc/BalloonPlot.pdf, inst/doc/Table.pdf: Remove Table.pdf
- since it is no longer needed
-
-2005-11-04 19:04 warnes
-
- * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
- inst/doc/Figure1.pdf: Nitin's Changes
-
-2005-11-04 19:00 warnes
-
- * inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
- inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Add figure
- plots
-
-2005-11-04 18:59 warnes
-
- * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Fix paths
-
-2005-10-20 18:36 nj7w
-
- * inst/doc/Figure1.eps, inst/doc/Table.eps: added the eps version
- of figures
-
-2005-10-20 18:35 nj7w
-
- * inst/doc/BalloonPlot.pdf: Updated BallonPlot.pdf
-
-2005-10-20 18:34 nj7w
-
- * inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
- inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Removed Old
- Figure
-
-2005-10-20 18:31 nj7w
-
- * inst/doc/Figure1.pdf, inst/doc/Table.pdf: Added the new figure -
- for total popluation - Balloonplot
-
-2005-10-20 18:29 nj7w
-
- * inst/doc/BalloonPlot.tex: Modified the BallonPlot article
-
-2005-10-20 14:12 nj7w
-
- * inst/doc/BalloonPlot.tex: Added references
-
-2005-10-19 16:57 arnima
-
- * man/rich.color.Rd: The last example now displays the correct
- heat.colors.
- Default 'palette' argument is now a single string, not a vector.
-
-2005-10-19 16:56 arnima
-
- * R/rich.color.R: Default 'palette' argument is now a single
- string, not a vector.
-
-2005-10-14 19:13 warnes
-
- * DESCRIPTION, R/balloonplot.R, man/balloonplot.Rd: Formatting
- fixes:
- - Handle multiple row or column category variables
- - Separate rows/columns of category labels by lines
- - Fix handling of 'cumsum' plots on row/column labels
- - Improve display of row/column sums
-
-2005-10-13 20:00 warnes
-
- * man/balloonplot.Rd: Add example using Titanic data that exercises
- the multi-factor
- display.
-
-2005-10-11 21:20 warnes
-
- * R/balloonplot.R: Initial changes to allow multiple x and y factor
- variables. Yet to
- be done: 1) remove extra 'boxes'. 2) omit duplicated values
-
-2005-10-04 19:39 warnes
-
- * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: more minor
- fixes
-
-2005-10-04 19:29 warnes
-
- * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: fix spacing
-
-2005-10-04 19:08 warnes
-
- * inst/doc/Rnews.sty: Inlcude Rnews.sty
-
-2005-10-04 19:07 warnes
-
- * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Some textual
- edits.
-
-2005-10-03 16:23 nj7w
-
- * inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
- inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Added figures
- for the R-News Article
-
-2005-09-29 21:02 nj7w
-
- * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Updated the
- documentation - added the name of the person who asked the
- question
-
-2005-09-29 20:29 nj7w
-
- * inst, inst/doc, inst/doc/BalloonPlot.pdf,
- inst/doc/BalloonPlot.tex: Added R-news article
-
-2005-09-12 15:44 nj7w
-
- * trunk/gdata/man/aggregate.table.Rd,
- trunk/gdata/man/interleave.Rd, trunk/gdata/man/matchcols.Rd,
- trunk/gdata/man/nobs.Rd, trunk/gdata/man/read.xls.Rd,
- trunk/gdata/man/rename.vars.Rd, trunk/gdata/man/trim.Rd,
- trunk/gdata/man/unmatrix.Rd, trunk/gmodels/man/fast.prcomp.Rd,
- trunk/gmodels/man/glh.test.Rd, man/hist2d.Rd, man/ooplot.Rd,
- man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
- man/space.Rd, trunk/gtools/man/assert.Rd,
- trunk/gtools/man/dirichlet.Rd, trunk/gtools/man/permute.Rd,
- trunk/gtools/man/scat.Rd: Updated Greg's email
-
-2005-09-12 14:45 nj7w
-
- * R/balloonplot.R: Updated version of balloonplot - by Romain
- Francois <fra...@fr...>
-
-2005-09-09 20:34 nj7w
-
- * ChangeLog, DESCRIPTION: Updated the version and ChangeLog
-
-2005-09-09 20:32 nj7w
-
- * R/balloonplot.R, man/balloonplot.Rd: Changes in ballon plot based
- on Romain Francois (fra...@fr...) suggestions
-
-2005-09-06 21:41 nj7w
-
- * DESCRIPTION: Updated package dependencies
-
-2005-09-06 21:41 nj7w
-
- * NEWS: Added NEWS
-
-2005-09-02 23:10 nj7w
-
- * trunk/gmodels/ChangeLog, ChangeLog: Added ChangeLog
-
-2005-08-31 16:28 nj7w
-
- * trunk/gdata/DESCRIPTION, trunk/gmodels/DESCRIPTION, DESCRIPTION:
- Added DESCRIPTION file
-
-2005-08-31 16:27 nj7w
-
- * trunk/gdata/DESCRIPTION.in, trunk/gmodels/DESCRIPTION.in,
- DESCRIPTION.in: removed DESCRIPTION.in
-
-2005-06-09 14:20 nj7w
-
- * trunk/gdata/R/Args.R, trunk/gdata/R/aggregate.table.R,
- trunk/gdata/R/combine.R, trunk/gdata/R/elem.R,
- trunk/gdata/R/env.R, trunk/gdata/R/frameApply.R,
- trunk/gdata/R/interleave.R, trunk/gdata/R/is.what.R,
- trunk/gdata/R/keep.R, trunk/gdata/R/ll.R,
- trunk/gdata/R/matchcols.R, trunk/gdata/R/nobs.R,
- trunk/gdata/R/read.xls.R, trunk/gdata/R/rename.vars.R,
- trunk/gdata/R/reorder.R, trunk/gdata/R/trim.R,
- trunk/gdata/R/unmatrix.R, trunk/gdata/inst/perl/IO/AtomicFile.pm,
- trunk/gdata/inst/perl/IO/InnerFile.pm,
- trunk/gdata/inst/perl/IO/Lines.pm,
- trunk/gdata/inst/perl/IO/Scalar.pm,
- trunk/gdata/inst/perl/IO/Scalar.pm.html,
- trunk/gdata/inst/perl/IO/ScalarArray.pm,
- trunk/gdata/inst/perl/IO/Stringy.pm,
- trunk/gdata/inst/perl/IO/Wrap.pm,
- trunk/gdata/inst/perl/IO/WrapTie.pm,
- trunk/gdata/man/aggregate.table.Rd, trunk/gdata/man/combine.Rd,
- trunk/gdata/man/drop.levels.Rd, trunk/gdata/man/interleave.Rd,
- trunk/gdata/man/nobs.Rd, trunk/gdata/man/rename.vars.Rd,
- trunk/gdata/man/reorder.Rd, trunk/gmodels/R/ci.R,
- trunk/gmodels/R/coefFrame.R, trunk/gmodels/R/estimable.R,
- trunk/gmodels/R/fast.prcomp.R, trunk/gmodels/R/fit.contrast.R,
- trunk/gmodels/R/glh.test.R, trunk/gmodels/R/make.contrasts.R,
- trunk/gmodels/man/CrossTable.Rd, trunk/gmodels/man/ci.Rd,
- trunk/gmodels/man/coefFrame.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, R/balloonplot.R,
- R/bandplot.R, R/boxplot.n.R, R/colorpanel.R, R/heatmap.2.R,
- R/hist2d.R, R/lowess.R, R/ooplot.R, R/overplot.R, R/plotCI.R,
- R/plotmeans.R, R/qqnorm.aov.R, R/residplot.R, R/rich.color.R,
- R/sinkplot.R, R/smartlegend.R, R/space.R, R/textplot.R,
- R/wapply.R, man/1, man/bandplot.Rd, man/barplot2.Rd,
- man/boxplot.n.Rd, man/hist2d.Rd, man/lowess.Rd, man/plotCI.Rd,
- man/plotmeans.Rd, man/residplot.Rd, man/space.Rd, man/wapply.Rd,
- trunk/gtools/R/RSCompat.S, trunk/gtools/R/combinations.R,
- trunk/gtools/R/dirichlet.R, trunk/gtools/R/foldchange.R,
- trunk/gtools/R/invalid.R, trunk/gtools/R/logit.R,
- trunk/gtools/R/mixedsort.R, trunk/gtools/R/oddeven.R,
- trunk/gtools/R/permute.R, trunk/gtools/R/quantcut.R,
- trunk/gtools/R/running.R, trunk/gtools/R/scat.R,
- trunk/gtools/man/ELISA.Rd, trunk/gtools/man/combinations.Rd,
- trunk/gtools/man/dirichlet.Rd, trunk/gtools/man/foldchange.Rd,
- trunk/gtools/man/invalid.Rd, trunk/gtools/man/logit.Rd,
- trunk/gtools/man/mixedsort.Rd, trunk/gtools/man/oddeven.Rd,
- trunk/gtools/man/permute.Rd, trunk/gtools/man/quantcut.Rd,
- trunk/gtools/man/running.Rd, trunk/gtools/man/scat.Rd: Updating
- the version number, and various help files to synchronize
- splitting of gregmisc bundle in 4 individual components.
-
-2005-06-09 14:15 nj7w
-
- * R/barplot2.R: Changes based on Marc Schwartz's suggestions to
- handel 0's and NA's appropriately.
-
-2005-05-13 18:59 nj7w
-
- * trunk/gdata/R/read.xls.R, trunk/gmodels/man/CrossTable.Rd,
- man/heatmap.2.Rd: 1) Using dQuote.ascii function in read.xls as
- the new version of dQuote doesn't work proprly with UTF-8 locale.
- 2) Modified CrossTable.Rd usage in gmodels
- 3) Modified heatmap.2 usage in gplots.
-
-2005-04-04 14:23 warnes
-
- * R/overplot.R: Explicitly reference package containing
- lowess.formula in
- panel.overplot(). This should fix the error reported by Troels
- Ring
- <tr...@gv...>.
-
-2005-02-26 01:15 nj7w
-
- * trunk/gdata/NAMESPACE, trunk/gdata/man/elem.Rd,
- trunk/gdata/man/env.Rd, trunk/gdata/man/ll.Rd,
- trunk/gdata/man/read.xls.Rd, R/heatmap.2.R, man/heatmap.2.Rd,
- man/rich.color.Rd, man/sinkplot.Rd, man/textplot.Rd: *** empty
- log message ***
-
-2005-02-25 23:22 warnes
-
- * trunk/gdata/R/elem.R, trunk/gdata/R/env.R, trunk/gdata/R/ll.R,
- trunk/gdata/man/Args.Rd, trunk/gdata/man/env.Rd,
- trunk/gdata/man/ll.Rd, man/rich.color.Rd: Integrate changes
- submitted by Arni Magnusson
-
-2005-02-25 22:31 warnes
-
- * NAMESPACE: Add dependency imports from 'stats' package.
-
-2005-02-22 21:01 warnes
-
- * R/bandplot.R: Fix problem in passing graphical parameters
- (xlim,etc).@
-
-2005-02-08 16:41 warnes
-
- * DESCRIPTION.in: Improve package title.
-
-2005-02-08 16:40 warnes
-
- * R/heatmap.2.R: Ignore missing values when computing symmetric
- range.
-
-2005-02-02 19:25 warnes
-
- * man/plotmeans.Rd: Add more extensive example.
-
-2005-01-14 19:05 warnes
-
- * R/textplot.R: Code can be simplified because R now supports
- selecting a fixed width font.
-
-2005-01-12 20:50 warnes
-
- * trunk/gdata/DESCRIPTION.in, trunk/gmodels/DESCRIPTION.in,
- DESCRIPTION.in, trunk/gtools/DESCRIPTION.in: Add dependency on R
- 1.9.0+ to prevent poeple from installing on old
- versions of R which don't support namespaces.
-
-2004-11-30 01:06 warnes
-
- * R/heatmap.2.R, man/heatmap.2.Rd: 1. Add new parameters for
- controlling color key:
- - If `symkey==TRUE', the color key will be made symmetric about
- 0.
- - The `densadj' parameter can be used to modify the smoother
- width
- (see the `adjust' parameter under `help(density)') for the
- density
- plotted in the key.
-
- 2. Fix handling of rowsep/colsep.
-
- 3. Vector of length 2 giving the width (colsep) or height
- (rowsep) the separator box
- drawn by colsep and rowsep as a function of the width (colsep) or
- height (rowsep) of a cell.
-
- 4. Appropriate changes to the corresponding help page, plus some
- minor formatting changes.
-
-2004-11-03 19:43 warnes
-
- * R/heatmap.2.R: Fix bugs in layout of cell notes. They were being
- plotted top down
- rather than bottom up. Further reordering of the x matrix didn't
- also reorder the notes. Both issues should now be resolved.
-
-2004-09-27 21:01 warneg
-
- * trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
- trunk/gdata/NAMESPACE, trunk/gdata/man/.Rhistory,
- trunk/gmodels/DESCRIPTION, trunk/gmodels/DESCRIPTION.in,
- DESCRIPTION, DESCRIPTION.in, man/sinkplot.Rd, man/textplot.Rd,
- trunk/gregmisc/.Rhistory, trunk/gregmisc/DESCRIPTION,
- trunk/gtools/DESCRIPTION, trunk/gtools/DESCRIPTION.in,
- trunk/gtools/man/running.Rd: Updated to pass R CMD check.
-
-2004-09-03 22:50 warneg
-
- * man/textplot.Rd: Provide explicit package for call to nobs.
-
-2004-09-03 22:50 warneg
-
- * man/heatmap.2.Rd: Fix typos.
-
-2004-09-03 17:27 warneg
-
- * trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
- trunk/gdata/NAMESPACE, trunk/gdata/R/Args.R,
- trunk/gdata/R/aggregate.table.R, trunk/gdata/R/combine.R,
- trunk/gdata/R/elem.R, trunk/gdata/R/env.R,
- trunk/gdata/R/interleave.R, trunk/gdata/R/is.what.R,
- trunk/gdata/R/keep.R, trunk/gdata/R/ll.R,
- trunk/gdata/R/matchcols.R, trunk/gdata/R/nobs.R,
- trunk/gdata/R/read.xls.R, trunk/gdata/R/rename.vars.R,
- trunk/gdata/R/reorder.R, trunk/gdata/R/trim.R,
- trunk/gdata/man/reorder.Rd, trunk/gmodels/DESCRIPTION,
- trunk/gmodels/NAMESPACE, trunk/gmodels/R/CrossTable.R,
- trunk/gmodels/R/ci.R, trunk/gmodels/R/estimable.R,
- trunk/gmodels/R/fast.prcomp.R, trunk/gmodels/R/fit.contrast.R,
- trunk/gmodels/R/glh.test.R, trunk/gmodels/R/make.contrasts.R,
- trunk/gmodels/man/estimable.Rd,
- trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
- trunk/gmodels/man/make.contrasts.Rd, DESCRIPTION, NAMESPACE,
- R/balloonplot.R, R/bandplot.R, R/barplot2.R, R/boxplot.n.R,
- R/colorpanel.R, R/heatmap.2.R, R/hist2d.R, R/lowess.R,
- R/ooplot.R, R/overplot.R, R/plotCI.R, R/plotmeans.R,
- R/qqnorm.aov.R, R/residplot.R, R/rich.color.R, R/sinkplot.R,
- R/smartlegend.R, R/space.R, R/textplot.R, R/wapply.R,
- trunk/gtools/DESCRIPTION, trunk/gtools/NAMESPACE,
- trunk/gtools/R/dirichlet.R, trunk/gtools/R/foldchange.R,
- trunk/gtools/R/invalid.R, trunk/gtools/R/mixedsort.R,
- trunk/gtools/R/oddeven.R, trunk/gtools/R/permute.R,
- trunk/gtools/R/quantcut.R, trunk/gtools/R/running.R,
- trunk/gtools/man/running.Rd: initial bundle checkin
-
-2004-09-02 17:14 warneg
-
- * trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
- trunk/gdata/NAMESPACE, trunk/gdata/man/.Rhistory,
- trunk/gmodels/DESCRIPTION, trunk/gmodels/DESCRIPTION.in,
- trunk/gmodels/NAMESPACE, DESCRIPTION, DESCRIPTION.in, NAMESPACE,
- man/1, man/residplot.Rd, trunk/gregmisc/.Rhistory,
- trunk/gtools/DESCRIPTION, trunk/gtools/DESCRIPTION.in,
- trunk/gtools/NAMESPACE: Initial revision
-
-2004-07-29 14:49 warnes
-
- * R/plotCI.R, man/plotCI.Rd: Integrate changes from the version of
- plotCI maintained by Martin Maechler.
-
-2004-06-30 19:32 warnes
-
- * R/textplot.R: Remove commented-out code.
-
-2004-06-30 19:26 warnes
-
- * R/textplot.R: Fixed text size calculations
-
-2004-06-28 20:16 warnes
-
- * R/barplot2.R, man/barplot2.Rd: - Default 2-d color set to grey as
- in (v2.0.0) r-devel
- - The default (v1.9.1) barplot method now handles vectors and 1-d
- arrays
- (e.g., obtained by table()) the same, and uses grey instead of
- heat color palettes in these cases. (Also fixes PR#6776.)
- - Updated to reflect the addition of 'offset' argument in base
- - Fix bug in stacked barplots, which would not be plotted
- properly
-
-2004-06-24 16:57 warnes
-
- * R/heatmap.2.R, man/heatmap.2.Rd: Add ability to specify color of
- NA cells.
-
-2004-05-27 15:11 warnes
-
- * man/plotCI.Rd: Fix spelling error.
-
-2004-05-26 14:56 warnes
-
- * R/overplot.R: One more fix to get it right.
-
-2004-05-26 13:50 warnes
-
- * R/overplot.R: Use triple-colon operator ':::' to access
- plot.formula from the graphics package.
-
-2004-05-26 13:19 warnes
-
- * man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R CMD check.
-
-2004-05-25 18:32 warnes
-
- * R/overplot.R: Work around bug in R 1.9.X due to plot.formula()
- not having the same
- arguments as plot().
-
-2004-05-25 17:33 warnes
-
- * R/rich.color.R, man/rich.color.Rd: Add rich.colors() submitted by
- Arni Magnusson <arnima@u.washington.edu>.
-
-2004-05-25 02:58 warnes
-
- * R/ooplot.R, man/ooplot.Rd: ??
-
-2004-05-24 23:43 warnes
-
- * R/plotCI.R, R/plotmeans.R: Modified to use invalid() to check
- arguments instead of missing().
- This fixes some build errors under R-1.9.0-Patched.
-
-2004-04-22 15:44 warnes
-
- * R/ooplot.R, man/ooplot.Rd: Integrate changes from Lodewijk
- Bonebakker <bon...@co...>
-
-2004-04-13 13:42 warnes
-
- * R/space.R, man/space.Rd: Add ability to space points along 'y'
- direction.
-
-2004-04-02 19:06 warnes
-
- * R/smartlegend.R: Fixed smartlegend() positioning when x and/or y
- axis are log-scale.
-
-2004-03-30 19:04 warnes
-
- * R/textplot.R, trunk/gregmisc/DESCRIPTION: - Fix bug in textplot()
- reported by Wright, Kevin <kev...@pi...>.
-
-2004-03-26 22:27 warnes
-
- * man/textplot.Rd: Update to match changes in textplot() code.
-
-2004-03-26 22:25 warnes
-
- * man/ooplot.Rd: Remove Windows EOL characters.
-
-2004-03-26 22:20 warnes
-
- * man/barplot2.Rd: - Remove some commented-out code.
- - Remove cvs log tag.
-
-2004-03-26 22:16 warnes
-
- * R/textplot.R: Misc changes.
-
-2004-02-17 22:22 warnes
-
- * man/ooplot.Rd: Minor fix to ooplot documentation.
-
-2004-02-17 22:21 warnes
-
- * R/ooplot.R, man/ooplot.Rd: Integrate ooplot updates provided by
- Lodewijk Bonebakker
- <bon...@co...>
-
-2004-02-02 16:26 warnes
-
- * R/colorpanel.R, man/colorpanel.Rd: - Add colorpanel function,
- which generates a smoothly varying band of
- colors over a three color range (lo, mid, high).
-
-2004-01-21 12:07 warnes
-
- * man/textplot.Rd: - Correct arguments to halign to match code.
-
-2004-01-21 05:17 warnes
-
- * R/lowess.R: Track R 1.9.0's move of 'lowess' from the base
- package to the (new)
- stats package.
-
-2004-01-21 04:44 warnes
-
- * man/sinkplot.Rd: - Fix sinkplot() example by replacing 'T' with
- 'TRUE'.
-
-2004-01-21 04:42 warnes
-
- * man/ooplot.Rd: - Add some more details to the ooplot()
- documentation. The
- documentation is *not* complete.
-
-2004-01-21 04:31 warnes
-
- * R/textplot.R, trunk/gtools/R/capture.R: - Mark sprint() as
- depreciated.
- - Replace references to sprint with capture.output()
- - Use match.arg for halign and valign arguments to
- textplot.default.
- - Fix textplot.character so that a vector of characters is
- properly
- displayed. Previouslt, character vectors were plotted on top of
- each
- other.
-
-2004-01-19 23:43 warnes
-
- * R/sinkplot.R, man/sinkplot.Rd: New function sinkplot(), as
- requested on R-devel by Kevin Wright
- <kw...@es...> in
- https://www.stat.math.ethz.ch/pipermail/r-devel/2004-January/028483.html.
-
-2004-01-15 05:14 warnes
-
- * R/ooplot.R, man/ooplot.Rd: Add initial code and docs for ooplot()
- function submitted by Lodewijk
- Bonebakker <bon...@co...>.
-
-2003-12-03 02:46 warnes
-
- * trunk/gdata/man/elem.Rd, trunk/gdata/man/ll.Rd, man/lowess.Rd,
- man/textplot.Rd, man/wapply.Rd, trunk/gtools/man/foldchange.Rd: -
- match function argument defaults with 'usage'
-
-2003-12-03 02:42 warnes
-
- * R/heatmap.2.R, man/heatmap.2.Rd: - Fix buglets in heatmap
- function
- - Make a slight enhancement to the example code.
-
-2003-12-02 22:49 warnes
-
- * R/heatmap.2.R: Integrated some suggestions from Sean Davis
- <sd...@ma...>.
-
-2003-12-02 18:22 warnes
-
- * man/heatmap.2.Rd: - Make final example use 16 colors instead of
- 8. This looks nicer.
-
-2003-12-02 16:58 warnes
-
- * man/barplot2.Rd: - Remove '%' character from example code to
- avoid errors.
-
-2003-12-02 16:54 warnes
-
- * R/plotCI.R: - Add '...' parameter to call to text to allow user
- to control size/color/etc.
-
-2003-12-01 16:00 warnes
-
- * man/barplot2.Rd: - updated to match changes to barplot() in base.
-
-2003-12-01 15:59 warnes
-
- * data, data/rtPCR.rda: - Renamed rtPCR.Rda to rtPCR.rda so that R
- will properly load the file
- when data(rtPCR) is executed.
-
-2003-12-01 15:55 warnes
-
- * R/barplot2.R: - Follow patches applied to barplot() in base.
-
-2003-11-24 21:32 warnes
-
- * man/heatmap.2.Rd: Fix unbalanced braces.
-
-2003-11-24 15:09 warnes
-
- * R/overplot.R, man/overplot.Rd: Fix errors reported by R CMD
- check.
-
-2003-11-21 23:13 warnes
-
- * man/overplot.Rd: Added missing closing brace.
-
-2003-11-21 23:08 warnes
-
- * man/rtPCR.Rd: Initial addition of these files. Used in examples
- of overplot().
-
-2003-11-21 22:59 warnes
-
- * R/heatmap.2.R, man/heatmap.2.Rd: Applied my enhancements to the
- heatmap() code from R 1.8.0, and added
- documentation of these changes.
-
-2003-11-21 22:58 warnes
-
- * R/overplot.R, man/overplot.Rd: - Discovered that axis(N) does the
- right thing without needing to be
- given location for tick marks. This allowed simplification of the
- code.
-
- - Minor other changes for distribution
-
- - Addition of overplot.Rd documentation.
-
-2003-11-21 19:50 warnes
-
- * R/heatmap.2.R, man/heatmap.2.Rd: - Integrated my extensions into
- the R 1.8.0 version of heatmap.
- - Add Rd documentation.
-
-2003-11-19 14:52 warnes
-
- * man/bandplot.Rd: Remove extranious NULL that confused R CMD
- check.
-
-2003-11-18 18:59 warnes
-
- * man/barplot2.Rd: - Tiny fix to remove R CMD check error.
-
-2003-11-18 18:58 warnes
-
- * man/smartlegend.Rd: - Added missing closing brace.
-
-2003-11-18 18:45 warnes
-
- * trunk/gdata/R/elem.R, trunk/gdata/R/env.R,
- trunk/gdata/R/is.what.R, trunk/gdata/R/keep.R,
- trunk/gdata/R/ll.R, R/overplot.R: - Convert from MS-Dos to Unix
- line endings.
- - Reformat to 80 columns.
-
-2003-11-10 22:11 warnes
-
- * trunk/gdata/R/elem.R, trunk/gdata/R/env.R,
- trunk/gdata/R/is.what.R, trunk/gdata/R/keep.R,
- trunk/gdata/R/ll.R, trunk/gdata/man/elem.Rd,
- trunk/gdata/man/env.Rd, trunk/gdata/man/is.what.Rd,
- trunk/gdata/man/keep.Rd, trunk/gdata/man/ll.Rd, R/heatmap.2.R,
- R/overplot.R, R/plotmeans.R, R/space.R, R/wapply.R,
- trunk/gregmisc/DESCRIPTION, trunk/gtools/R/capture.R,
- trunk/gtools/man/capture.Rd: - Add files contributed by Arni
- Magnusson
- <arnima@u.washington.edu>. As well as some of my own.
-
-2003-08-19 14:58 warnes
-
- * R/heatmap.2.R: - Copy of local changes.
-
-2003-08-19 14:57 warnes
-
- * R/heatmap.2.R: - Checkin before re-integrating local changes.
-
-2003-06-19 21:23 warnes
-
- * R/heatmap.2.R: - Added enhanced heatmap function.
-
-2003-06-09 15:10 warnes
-
- * man/smartlegend.Rd: - Add help text for smartlegend.
-
-2003-06-09 14:57 warnes
-
- * R/smartlegend.R: - New function smartlegend().
-
-2003-04-22 17:28 warnes
-
- * R/plotmeans.R: - Fixeed warning messing caused when 'connect' is
- a vector.
-
-2003-04-22 15:34 warnes
-
- * R/barplot2.R: Update from Marc Schwartz, modified by Gregory
- Warnes:
-
- - Modified dim() checks for 'ci.l' and 'ci.u' against 'height'
- to remove R v1.7.0 if() based error msgs for vector conditions.
-
-2003-04-04 13:49 warnes
-
- * R/balloonplot.R, man/qqnorm.aov.Rd, trunk/gtools/R/dirichlet.R: -
- Change occurences of 'T' to 'TRUE'
-
-2003-04-04 13:44 warnes
-
- * man/textplot.Rd: - Updated to match changes in textplot function:
- - Added textplot.character
- - Renamed arguments "col.margin" and "row.margin" to "cmar", and
- "rmar" so that specifying "col='red'" is possible.
- - Fixed R CMD check errors
- - Improve comments in example
- - Add textplot.matrix example
-
-2003-04-04 13:41 warnes
-
- * R/textplot.R: - Added textplot.character to handle character
- strings.
- - Moved test for vector and matrix arguments to textplot.default.
- - Renamed arguments "col.margin" and "row.margin" to "cmar", and
- "rmar" so that specifying "col='red'" is possible.
-
-2003-04-02 22:29 warnes
-
- * R/textplot.R, man/textplot.Rd: - Added textplot function and
- friends, as well as documentation.
-
-2003-03-08 16:30 warnes
-
- * man/balloonplot.Rd: - Forgot to update arglist in \usage section.
-
-2003-03-08 16:22 warnes
-
- * R/balloonplot.R, man/balloonplot.Rd: - Added parameters for
- rotation of and amount of space allocated for
- the row and column labels.
-
-2003-03-07 15:48 warnes
-
- * trunk/gmodels/R/fast.prcomp.R, R/hist2d.R, R/qqnorm.aov.R,
- trunk/gregmisc/DESCRIPTION, trunk/gtools/R/RSCompat.S: - Minor
- changes to code to allow the package to be provided as an
- S-Plus chapter.
-
-2003-03-07 15:43 warnes
-
- * R/lowess.R: - Add 'NULL' as the last element of if statement that
- defines
- lowess.default so that when the file is sourced, S-Plus doesn't
- display the function definition.
-
-2003-03-07 15:41 warnes
-
- * R/lowess.R: - Specify where the defualt lowess function should be
- found.
- - Use getFunction in S-Plus instead of 'get'
-
-2003-01-30 21:43 warnes
-
- * R/barplot2.R, man/barplot2.Rd: - Added argument 'add' to allow
- for the addition of a barplot to an
- existing graphic. Default is FALSE
-
-2003-01-20 18:35 warnes
-
- * R/balloonplot.R, man/balloonplot.Rd: - Updated balloonplot help
- page.
-
-2003-01-20 17:13 warnes
-
- * R/wapply.R, man/wapply.Rd: - Updated wapply.R to allow
- specification of evaluation points when
- method is 'width' or 'range' using the 'pts' argument.
- - Updated wapply.Rd to add 'pts' argument
- - Fixed typos, spelling errors, gramatical errors and lack of
- clarity
- in wapply.Rd help text.
-
-2003-01-03 21:34 warnes
-
- * R/balloonplot.R, man/balloonplot.Rd: - Initial checkin of
- balloonplot functions and documentation.
-
-2003-01-03 19:23 warnes
-
- * man/space.Rd: - Added reference to and comparison example of
- sunflowerplot.
- - Added code to put example plots on same plot window using
- par(mfrow=...).
-
-2003-01-02 16:09 warnes
-
- * R/barplot2.R: - Changed assignment statements that used "=" to
- "<-" to avoid syntax
- errors in older versions of the S language.
-
-2003-01-02 16:07 warnes
-
- * R/lowess.R: - Added wrapper code so that R-specific fiddling
- won't be executed
- under S-Plus.
-
-2003-01-02 15:40 warnes
-
- * R/qqnorm.aov.R, man/qqnorm.aov.Rd: - Renamed first parameter to
- match qqnorm generic.
-
-2003-01-02 15:14 warnes
-
- * man/qqnorm.aov.Rd: Added additional help text from Kjeitl.
-
-2002-12-31 19:50 warnes
-
- * R/qqnorm.aov.R, man/qqnorm.aov.Rd: Initial checkin of qqnorm.aov
- function and documentation submitted by
- Kjetil Halvorsen <kj...@ju...>.
-
-2002-11-04 14:21 warnes
-
- * R/barplot2.R, man/barplot2.Rd: Updates from Marc Schwartz:
-
- - Updated underlying code to be based upon the new barplot() in R
- v1.6.1
- - This now uses the 'axis.lty' and 'border' arguments
- - In R v1.6.0, R Core introduced a new function called axTicks().
- This is an R equivalent of the C code for CreateAtVector in
- plot.c.
- This now enables me to get the axis tick mark positions
- consistently
- when the 'height' related axis is either linear or log. Thus, I
- can
- now have consistent tick marks and can plot grid lines in either
- situation. If 'plot.grid = TRUE' and 'grid.inc' is specified,
- then
- I still use pretty() to determine the tick marks and lines.
- - This code now depends on R 1.6.0 or later.
-
-2002-10-30 02:21 warnes
-
- * R/plot.lm.R: - Commented out plot.lm() code since recent changes
- in R have broken it.
-
-2002-10-11 18:02 warnes
-
- * R/barplot2.R: - Fixed log scale errors in legend() call
-
-2002-10-01 18:16 warnes
-
- * man/hist2d.Rd: - Added examples of using 'contour' and
- 'filled.contour' for display.
-
-2002-09-24 14:53 warnes
-
- * R/plotmeans.R: - Changed digits=options("digits") which produces
- a list of length 1
- to digits=getOption("digits") which returns a vector of length
- one.
- The former was causing an error when passed to round().
-
-2002-09-23 14:27 warnes
-
- * trunk/gmodels/man/CrossTable.Rd, trunk/gmodels/man/glh.test.Rd,
- man/barplot2.Rd: - Fixed syntax errors in barplot2.Rd and
- CrossTable.Rd
- - Fixed incorrect translation of 'F' (distribution) to 'FALSE' in
- glh.test.Rd
-
-2002-09-23 13:59 warnes
-
- * trunk/gdata/R/aggregate.table.R, trunk/gdata/R/combine.R,
- trunk/gdata/R/interleave.R, trunk/gdata/R/nobs.R,
- trunk/gdata/man/aggregate.table.Rd, trunk/gdata/man/combine.Rd,
- trunk/gdata/man/interleave.Rd, trunk/gdata/man/nobs.Rd,
- trunk/gdata/man/rename.vars.Rd, trunk/gdata/man/reorder.Rd,
- trunk/gmodels/R/ci.R, trunk/gmodels/man/estimable.Rd,
- trunk/gmodels/man/glh.test.Rd, R/boxplot.n.R, R/hist2d.R,
- R/lowess.R, R/residplot.R, man/bandplot.Rd, man/hist2d.Rd,
- man/lowess.Rd, man/plotCI.Rd, man/space.Rd,
- trunk/gtools/man/combinations.Rd, trunk/gtools/man/quantcut.Rd: -
- Modified all files to include CVS Id and Log tags.
-
-2002-09-23 13:38 warnes
-
- * trunk/gmodels/R/CrossTable.R, trunk/gmodels/man/CrossTable.Rd,
- R/barplot2.R, man/barplot2.Rd, trunk/gregmisc/DESCRIPTION,
- trunk/gtools/R/combinations.R: - Added CrossTable() and
- barplot2() code and docs contributed by Marc Schwartz.
- - Permit combinations() to be used when r>n provided
- repeat.allowed=TRUE
- - Bumped up version number
-
-2002-08-01 19:37 warnes
-
- * trunk/gmodels/R/ci.R, trunk/gmodels/man/ci.Rd,
- trunk/gmodels/man/estimable.Rd, trunk/gmodels/man/glh.test.Rd,
- R/hist2d.R, R/wapply.R, trunk/gregmisc/DESCRIPTION,
- trunk/gtools/R/running.R: - Corrected documentation mismatch for
- ci, ci.default.
-
- - Replaced all occurences of '_' for assignment with '<-'.
-
- - Replaced all occurences of 'T' or 'F' for 'TRUE' and 'FALSE'
- with
- the spelled out version.
-
- - Updaded version number and date.
-
-2002-04-09 00:51 warneg
-
- * trunk/gdata/R/rename.vars.R, trunk/gdata/man/aggregate.table.Rd,
- trunk/gdata/man/interleave.Rd, trunk/gdata/man/reorder.Rd,
- trunk/gmodels/R/ci.R, trunk/gmodels/R/estimable.R,
- trunk/gmodels/R/glh.test.R, trunk/gmodels/man/glh.test.Rd,
- R/bandplot.R, R/boxplot.n.R, R/hist2d.R, R/plot.lm.R, R/plotCI.R,
- R/plotmeans.R, R/residplot.R, R/space.R, R/wapply.R,
- man/bandplot.Rd, man/boxplot.n.Rd, man/hist2d.Rd,
- man/plotmeans.Rd, man/space.Rd, man/wapply.Rd,
- trunk/gregmisc/DESCRIPTION, trunk/gtools/R/combinations.R,
- trunk/gtools/man/combinations.Rd, trunk/gtools/man/running.Rd:
- Checkin for version 0.5.3
-
-2002-03-27 20:51 warneg
-
- * man/lowess.Rd: Added "..." argument to lowess.default.
-
-2002-03-27 19:48 warneg
-
- * R/lowess.R: - Added code to append "..." to the argument list of
- lowess.default.
-
- - Fixed a wrong default for f in lowess.formula. Was 3, but
- should
- have been 2/3.
-
-2002-03-26 21:22 warneg
-
- * trunk/gdata/man/reorder.Rd, trunk/gmodels/R/ci.R,
- trunk/gmodels/R/glh.test.R, trunk/gmodels/man/ci.Rd,
- trunk/gmodels/man/glh.test.Rd, R/lowess.R, man/lowess.Rd: -
- Changed methods to include '...' to match the generic.
- - Updated for version 0.5.1
-
-2002-03-26 19:24 warneg
-
- * man/hist2d.Rd: Initial checkin.
-
-2002-03-20 04:17 warneg
-
- * R/plotmeans.R: - Changes to add compatibility with S-Plus 2000
-
-2002-03-20 04:16 warneg
-
- * R/plotCI.R: - Changes to add compatibility with S-Plus 2000.
-
-2002-03-20 03:48 warneg
-
- * R/boxplot.n.R: - Updated to work in S-Plus 2000 as well as R.
-
-2002-03-05 16:44 warneg
-
- * R/plotmeans.R: - Replace "T" with "TRUE". Problems arrive when
- there is a variable named "T".
-
-2002-02-20 20:09 warneg
-
- * trunk/gdata/man/rename.vars.Rd, trunk/gmodels/man/ci.Rd,
- trunk/gmodels/man/estimable.Rd, trunk/gmodels/man/glh.test.Rd,
- man/lowess.Rd, man/plotCI.Rd, man/space.Rd: Minor changes, typo
- and formatting fixes.
-
-2002-02-20 20:06 warneg
-
- * R/bandplot.R, man/bandplot.Rd: - Generalized to allow
- specification of the multiples of the standard deviation levels
- to be plotted (0=mean, 1=1 sd, ..).
- - Now (invisibly) returnes computed smooths.
-
-2002-02-16 18:16 warneg
-
- * man/bandplot.Rd: Added bandplot documentation.
-
-2002-02-16 17:58 warneg
-
- * R/wapply.R: - Fixed Bug: When method=="range", the absolute range
- of x was being
- used to compute the relative width instead of the (correct)
- relative
- range.
-
-2002-02-16 17:23 warneg
-
- * R/wapply.R: - Corrected problem removing missing values: The
- missing values of $x
- and $y were being removed indepdendently, leaving an uneven
- number
- of points in the result.
-
-2002-02-04 23:20 warneg
-
- * R/space.R: - Add na.rm parameter and make the default TRUE.
-
-2002-02-04 23:19 warneg
-
- * R/hist2d.R: Initial checkin.
-
-2002-02-04 19:12 warneg
-
- * R/plotCI.R: - When err="x", 'col' was being used to plot bars,
- rather than 'barcol'.
-
-2002-02-04 19:09 warneg
-
- * R/plotCI.R: - fixed typo, when err="x", lty was 'slty' causing an
- error.
-
-2001-12-12 01:41 warneg
-
- * man/space.Rd: - Quoted underscore character in my email address.
- - Added correct keyword.
-
-2001-12-12 01:37 warneg
-
- * man/plotmeans.Rd: Added documentation for xaxt parameter.
-
-2001-12-12 01:34 warneg
-
- * R/lowess.R: Updated to explicitly list control arguments to
- lowess.formula.
-
-2001-12-12 01:34 warneg
-
- * man/lowess.Rd: Initial checkin. Code copied from R source package
- and extended.
-
-2001-12-07 23:34 warneg
-
- * man/wapply.Rd: Fixed an problem where \code was incorrectly
- delimited by parens
- rather than curly brackets.
-
-2001-12-07 22:33 warneg
-
- * R/lowess.R, R/plot.lm.R, R/residplot.R, man/space.Rd: Initial
- checkin.
-
-2001-12-07 22:24 warneg
-
- * R/space.R: - Added cvs tags.
-
-2001-12-07 22:23 warneg
-
- * R/space.R: - Leave first point at center, rather than shifting by
- s/2 to the left. This looks better when there are more than 2
- 'spaced' points.
-
-2001-12-05 19:49 warneg
-
- * R/plotmeans.R: - Added ability to use the t-distribution to
- compute confidence
- intervals. This is controlled using the 'use.t' parameter.
-
-2001-12-05 19:41 warneg
-
- * man/plotmeans.Rd: - Added documentation of use.t parameter.
-
-2001-12-05 19:36 warneg
-
- * man/wapply.Rd: - Clarified how the width of the window is
- computed when method="nobs".
-
-2001-12-05 19:29 warneg
-
- * R/wapply.R: - Added a better default for "width" when
- method="nobs". For this case,
- width=max(5, length(x)/10).
-
- - Allow omission of x values which result in missing y values via
- 'drop.na' parameter.
-
-2001-10-26 02:48 warneg
-
- * R/plotmeans.R: Added correct handling of 'xaxt="n"'.
-
-2001-10-16 23:15 warneg
-
- * trunk/gmodels/man/ci.Rd, man/wapply.Rd: Fixed unbalanced brace.
-
-2001-10-16 23:06 warneg
-
- * man/plotCI.Rd: Added minbar and maxbar parameters.
-
-2001-10-16 23:04 warneg
-
- * man/plotmeans.Rd: Forgot to add minbar and maxbar to usage
- section.
-
-2001-10-16 23:03 warneg
-
- * man/plotmeans.Rd: Added description of minbar and maxbar.
-
-2001-10-16 23:00 warneg
-
- * R/plotCI.R: - Added minbar and maxbar parameters
- - Added cvs id and log tags to header
-
-2001-10-16 22:59 warneg
-
- * R/plotmeans.R: Added cvs id and log tag to file header
-
-2001-10-16 22:57 warneg
-
- * R/plotmeans.R: Added minbar and maxbar parameters.
-
-2001-10-16 22:35 warneg
-
- * man/plotmeans.Rd: Added description of minsd parameter.
-
-2001-10-16 22:35 warneg
-
- * R/plotmeans.R: Added minsd parameter.
-
-2001-09-18 14:15 warneg
-
- * R/plotCI.R, R/plotmeans.R, trunk/gregmisc/DESCRIPTION,
- trunk/gtools/R/RSCompat.S: Release 0.3.2
-
-2001-09-01 00:01 warneg
-
- * man/wapply.Rd, trunk/gregmisc/DESCRIPTION,
- trunk/gtools/R/running.R, trunk/gtools/man/running.Rd: Release
- 0.3.0
-
-2001-08-31 23:45 warneg
-
- * R/wapply.R: Used wrong character in header (% instead of #).
- Fixed.
-
-2001-08-31 23:41 warneg
-
- * R/bandplot.R: Used wrong comment character (% instead of #) in
- header. Fixed.
-
-2001-08-25 05:48 warneg
-
- * R/wapply.R: Initial checkin.
-
-2001-08-25 05:46 warneg
-
- * man/boxplot.n.Rd, man/plotmeans.Rd: Added CVS header.
-
-2001-08-25 05:45 warneg
-
- * man/wapply.Rd: Initial Checkin
-
-2001-05-30 13:23 warneg
-
- * trunk/gmodels, trunk/gmodels/R, trunk/gmodels/R/ci.R,
- trunk/gmodels/man, trunk/gmodels/man/ci.Rd, ., R, R/boxplot.n.R,
- R/plotCI.R, R/plotmeans.R, man, man/boxplot.n.Rd, man/plotCI.Rd,
- man/plotmeans.Rd, trunk/gregmisc, trunk/gregmisc/DESCRIPTION:
- Initial revision
-
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-08 22:01:18
|
Revision: 1319
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1319&view=rev
Author: warnes
Date: 2009-05-08 22:01:12 +0000 (Fri, 08 May 2009)
Log Message:
-----------
Update Greg's email address to 'gr...@ra...'
Modified Paths:
--------------
trunk/gplots/man/balloonplot.Rd
trunk/gplots/man/bandplot.Rd
trunk/gplots/man/boxplot.n.Rd
trunk/gplots/man/colorpanel.Rd
trunk/gplots/man/hist2d.Rd
trunk/gplots/man/ooplot.Rd
trunk/gplots/man/overplot.Rd
trunk/gplots/man/plot.lm2.Rd
trunk/gplots/man/plotCI.Rd
trunk/gplots/man/plotmeans.Rd
trunk/gplots/man/residplot.Rd
trunk/gplots/man/sinkplot.Rd
trunk/gplots/man/smartlegend.Rd
trunk/gplots/man/space.Rd
trunk/gplots/man/textplot.Rd
trunk/gplots/man/wapply.Rd
Modified: trunk/gplots/man/balloonplot.Rd
===================================================================
--- trunk/gplots/man/balloonplot.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/balloonplot.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -118,7 +118,7 @@
\references{Function inspired by question posed on R-help by Ramon
Alonso-Allende \email{al...@cn...}.}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link{plot.table}} }
Modified: trunk/gplots/man/bandplot.Rd
===================================================================
--- trunk/gplots/man/bandplot.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/bandplot.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -60,7 +60,7 @@
\value{
Invisibly returns a list containing the x,y points plotted for each line.
}
-\author{ Gregory R. Warnes \email{wa...@bs...}
+\author{ Gregory R. Warnes \email{gr...@ra...}
}
\seealso{ \code{\link{wapply}}, \code{\link{lowess}}}
\examples{
Modified: trunk/gplots/man/boxplot.n.Rd
===================================================================
--- trunk/gplots/man/boxplot.n.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/boxplot.n.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -38,7 +38,7 @@
\item{shrink}{ value to shrink character size (cex) when annotating.}
\item{textcolor}{ text color. }
}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link{boxplot}}, \code{\link{text}}}
\examples{
Modified: trunk/gplots/man/colorpanel.Rd
===================================================================
--- trunk/gplots/man/colorpanel.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/colorpanel.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -42,7 +42,7 @@
\value{
Vector of HTML-style RGB colors.
}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link[base]{colors} } }
\examples{
Modified: trunk/gplots/man/hist2d.Rd
===================================================================
--- trunk/gplots/man/hist2d.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/hist2d.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -63,7 +63,7 @@
\item{y}{lower y limit of each bin}
}
%\references{ ~put references to the literature/web site here ~ }
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
%\note{ ~~further notes~~ }
\seealso{ \code{\link{image}}, \code{\link{persp}}, \code{\link{hist}} }
Modified: trunk/gplots/man/ooplot.Rd
===================================================================
--- trunk/gplots/man/ooplot.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/ooplot.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -157,7 +157,7 @@
midpoints of each \emph{group} of bars, see example.
}
\author{Lodewijk Bonebakker \email{bon...@co...} with modifications
- by Gregory R. Warnes \email{wa...@bs...}.
+ by Gregory R. Warnes \email{gr...@ra...}.
Based on barplot2().
}
\seealso{ \code{\link[plot]{plot}}, \code{\link[plot]{boxplot}} }
Modified: trunk/gplots/man/overplot.Rd
===================================================================
--- trunk/gplots/man/overplot.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/overplot.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -55,7 +55,7 @@
\value{
A copy of the data split by the conditioning variable.
}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\seealso{
\code{\link[base]{interaction.plot}},
\code{\link[base]{coplot}} for alternative visualizations of 3-way data.}
Modified: trunk/gplots/man/plot.lm2.Rd
===================================================================
--- trunk/gplots/man/plot.lm2.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/plot.lm2.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -53,7 +53,7 @@
\item{width}{Fraction of the data to use for plot smooths}
\item{max.n}{Maximum number of points to display in plots}
}
-\author{Gregory R. Warnes \email{wa...@bs...} and Nitin
+\author{Gregory R. Warnes \email{gr...@ra...} and Nitin
Jain \email{nit...@pf...}}
\examples{
ctl <- rnorm(100, 4)
Modified: trunk/gplots/man/plotCI.Rd
===================================================================
--- trunk/gplots/man/plotCI.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/plotCI.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -115,7 +115,7 @@
Sep. 20, 1997. Enhanced version posted to r-help by Ben Bolker
\email{be...@zo...} on Apr. 16, 2001. This version was modified
and extended by Gregory R. Warnes
- \email{wa...@bs...}. Additional changes
+ \email{gr...@ra...}. Additional changes
suggested by Martin Maechler \email{mae...@st...}
integrated on July 29, 2004.
}
Modified: trunk/gplots/man/plotmeans.Rd
===================================================================
--- trunk/gplots/man/plotmeans.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/plotmeans.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -137,7 +137,7 @@
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{\code{\link{plotCI}}, \code{\link{boxplot}}}
Modified: trunk/gplots/man/residplot.Rd
===================================================================
--- trunk/gplots/man/residplot.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/residplot.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -20,5 +20,5 @@
These functions are undocumented. Some are internal and not intended
for direct use. Others simply haven't been documented yet.
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\keyword{misc}
Modified: trunk/gplots/man/sinkplot.Rd
===================================================================
--- trunk/gplots/man/sinkplot.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/sinkplot.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -32,7 +32,7 @@
\references{Functionality requested by Kevin Wright
\email{kw...@es...} in the R-devel newlist posting
\url{https://www.stat.math.ethz.ch/pipermail/r-devel/2004-January/028483.html}}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link[utils]{capture.output}}, \code{\link{textplot}} }
\examples{
\dontrun{
Modified: trunk/gplots/man/smartlegend.Rd
===================================================================
--- trunk/gplots/man/smartlegend.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/smartlegend.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -23,7 +23,7 @@
\value{
Same as \code{legend}
}
-\author{Gregory R. Warnes \email{wa...@bs...} }
+\author{Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link[base]{legend}} }
\examples{
Modified: trunk/gplots/man/space.Rd
===================================================================
--- trunk/gplots/man/space.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/space.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -63,7 +63,7 @@
\item{x}{(modified) x location for each input point}
\item{y}{y location of each input point}
}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link{jitter}}, \code{\link[base]{sunflowerplot}} }
\examples{
Modified: trunk/gplots/man/textplot.Rd
===================================================================
--- trunk/gplots/man/textplot.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/textplot.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -79,7 +79,7 @@
\value{
The character scaling factor (\code{cex}) used.
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link{plot}}, \code{\link{text}},
\code{\link[utils]{capture.output}}
}
Modified: trunk/gplots/man/wapply.Rd
===================================================================
--- trunk/gplots/man/wapply.Rd 2009-05-08 21:56:38 UTC (rev 1318)
+++ trunk/gplots/man/wapply.Rd 2009-05-08 22:01:12 UTC (rev 1319)
@@ -103,7 +103,7 @@
\item{x }{x location'}
\item{y }{Result of applying \code{fun} to the window about each x location}
}
-\author{ Gregory R. Warnes \email{wa...@bs...}
+\author{ Gregory R. Warnes \email{gr...@ra...}
}
\examples{
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-08 21:57:03
|
Revision: 1318
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1318&view=rev
Author: warnes
Date: 2009-05-08 21:56:38 +0000 (Fri, 08 May 2009)
Log Message:
-----------
plotCI now properly handles 'NULL' and 'NA' values for ui, li, uiw, and liw.
Modified Paths:
--------------
trunk/gplots/R/plotCI.R
trunk/gplots/man/plotCI.Rd
Modified: trunk/gplots/R/plotCI.R
===================================================================
--- trunk/gplots/R/plotCI.R 2009-05-08 21:55:05 UTC (rev 1317)
+++ trunk/gplots/R/plotCI.R 2009-05-08 21:56:38 UTC (rev 1318)
@@ -67,6 +67,12 @@
else
z <- x
+ if(invalid(uiw))
+ uiw <- NA
+ if(invalid(liw))
+ liw <- NA
+
+
if(invalid(ui))
ui <- z + uiw
if(invalid(li))
Modified: trunk/gplots/man/plotCI.Rd
===================================================================
--- trunk/gplots/man/plotCI.Rd 2009-05-08 21:55:05 UTC (rev 1317)
+++ trunk/gplots/man/plotCI.Rd 2009-05-08 21:56:38 UTC (rev 1318)
@@ -41,18 +41,18 @@
defaults to \code{1:n}.}
\item{uiw}{ width of the upper or right error bar. Set to \code{NULL}
- omit upper bars.}
+ or \code{NA} to omit upper bars.}
\item{liw}{ width of the lower or left error bar. Defaults to same value as
- \code{uiw}. Set to \code{NULL} to omit lower bars. }
+ \code{uiw}. Set to \code{NULL} or \code{NA} to omit lower bars. }
\item{ui}{ upper end of error bars. Defaults to \code{y + uiw} or
- \code{x + uiw} depeding on \code{err}. Set to \code{NULL} omit
- upper bars. }
+ \code{x + uiw} depeding on \code{err}. Set to \code{NULL} or
+ \code{NA} to omit upper bars. }
\item{li}{ lower end of error bars. Defaults to \code{y - liw} or
- \code{x - liw} depedning on \code{err}. Set to \code{NULL} to omit
- lower bars.}
+ \code{x - liw} depedning on \code{err}. Set to \code{NULL} or
+ \code{NA} to omit lower bars.}
\item{err}{ direction for error bars. Set to "y" for vertical bars.
Set to "x" for horizontal bars. Defaults to "y".}
@@ -147,6 +147,22 @@
# better yet, just use plotmeans ... #
plotmeans( state.area ~ state.region )
+/dontshow{
+## Just for testing
+ plotCI(x=means, uiw=NA)
+ plotCI(x=means, uiw=NULL)
+ plotCI(x=means, uiw=ciw)
+ plotCI(x=means, uiw=ciw, liw=NULL)
+ plotCI(x=means, uiw=ciw, liw=NA)
+ plotCI(x=means, liw=ciw, ciw=NULL)
+ plotCI(x=means, liw=ciw, ciw=NA)
+ ciw.na <- ciw
+ ciw.na[3] <- NA
+ plotCI(x=means, uiw=ciw.na, liw=ciw)
+ plotCI(x=means, liw=ciw.na, uiw=ciw)
}
+
+}
+
\keyword{ hplot }
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-08 21:55:20
|
Revision: 1317
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1317&view=rev
Author: warnes
Date: 2009-05-08 21:55:05 +0000 (Fri, 08 May 2009)
Log Message:
-----------
heatmap.2: Add option to create breakpoints symmetric around 0, provide additional information in the return value
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
trunk/gplots/man/heatmap.2.Rd
trunk/gplots/tests/heatmap2Test.Rout.save
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2009-05-08 21:27:55 UTC (rev 1316)
+++ trunk/gplots/R/heatmap.2.R 2009-05-08 21:55:05 UTC (rev 1317)
@@ -1,164 +1,177 @@
-# $Id$
+## $Id$
heatmap.2 <- function (x,
- # dendrogram control
- Rowv = TRUE,
- Colv=if(symm)"Rowv" else TRUE,
- distfun = dist,
- hclustfun = hclust,
- dendrogram = c("both","row","column","none"),
- symm = FALSE,
+ ## dendrogram control
+ Rowv = TRUE,
+ Colv=if(symm)"Rowv" else TRUE,
+ distfun = dist,
+ hclustfun = hclust,
+ dendrogram = c("both","row","column","none"),
+ symm = FALSE,
- # data scaling
- scale = c("none","row", "column"),
- na.rm=TRUE,
+ ## data scaling
+ scale = c("none","row", "column"),
+ na.rm=TRUE,
- # image plot
- revC = identical(Colv, "Rowv"),
- add.expr,
- breaks,
- col="heat.colors",
+ ## image plot
+ revC = identical(Colv, "Rowv"),
+ add.expr,
- # block sepration
- colsep,
- rowsep,
- sepcolor="white",
- sepwidth=c(0.05,0.05),
+ ## mapping data to colors
+ breaks,
+ symbreaks=min(x < 0, na.rm=TRUE) || scale!="none",
- # cell labeling
- cellnote,
- notecex=1.0,
- notecol="cyan",
- na.color=par("bg"),
+ ## colors
+ col="heat.colors",
- # level trace
- trace=c("column","row","both","none"),
- tracecol="cyan",
- hline=median(breaks),
- vline=median(breaks),
- linecol=tracecol,
+ ## block sepration
+ colsep,
+ rowsep,
+ sepcolor="white",
+ sepwidth=c(0.05,0.05),
- # Row/Column Labeling
- margins = c(5, 5),
- ColSideColors,
- RowSideColors,
- cexRow = 0.2 + 1/log10(nr),
- cexCol = 0.2 + 1/log10(nc),
- labRow = NULL,
- labCol = NULL,
+ ## cell labeling
+ cellnote,
+ notecex=1.0,
+ notecol="cyan",
+ na.color=par("bg"),
- # color key + density info
- key = TRUE,
- keysize = 1.5,
- density.info=c("histogram","density","none"),
- denscol=tracecol,
- #symkey = TRUE, # should be something like
- symkey = min(x < 0, na.rm=TRUE),
- densadj = 0.25,
+ ## level trace
+ trace=c("column","row","both","none"),
+ tracecol="cyan",
+ hline=median(breaks),
+ vline=median(breaks),
+ linecol=tracecol,
- # plot labels
- main = NULL,
- xlab = NULL,
- ylab = NULL,
+ ## Row/Column Labeling
+ margins = c(5, 5),
+ ColSideColors,
+ RowSideColors,
+ cexRow = 0.2 + 1/log10(nr),
+ cexCol = 0.2 + 1/log10(nc),
+ labRow = NULL,
+ labCol = NULL,
- # plot layout
- lmat = NULL,
- lhei = NULL,
- lwid = NULL,
+ ## color key + density info
+ key = TRUE,
+ keysize = 1.5,
+ density.info=c("histogram","density","none"),
+ denscol=tracecol,
+ symkey = min(x < 0, na.rm=TRUE) || symbreaks,
+ densadj = 0.25,
- # extras
- ...
- )
+ ## plot labels
+ main = NULL,
+ xlab = NULL,
+ ylab = NULL,
+
+ ## plot layout
+ lmat = NULL,
+ lhei = NULL,
+ lwid = NULL,
+
+ ## extras
+ ...
+ )
{
scale01 <- function(x, low=min(x), high=max(x) )
{
x <- (x-low)/(high - low)
x
}
+
+ retval <- list()
+
+ scale <- if(symm && missing(scale)) "none" else match.arg(scale)
+ dendrogram <- match.arg(dendrogram)
+ trace <- match.arg(trace)
+ density.info <- match.arg(density.info)
- scale <- if(symm && missing(scale)) "none" else match.arg(scale)
- dendrogram <- match.arg(dendrogram)
- trace <- match.arg(trace)
- density.info <- match.arg(density.info)
+ if(length(col)==1 && is.character(col) )
+ col <- get(col, mode="function")
- if(!missing(breaks) && (scale!="none"))
- warning("Using scale=\"row\" or scale=\"column\" when breaks are",
- "specified can produce unpredictable results.",
- "Please consider using only one or the other.")
+ if(!missing(breaks) && (scale!="none"))
+ warning("Using scale=\"row\" or scale=\"column\" when breaks are",
+ "specified can produce unpredictable results.",
+ "Please consider using only one or the other.")
- # key & density don't make sense when data is not all on the same scale
-# if(scale!="none" && key==TRUE)
-# {
-# warning("Key cannot be plotted when scale!=\"none\".")
-# key=FALSE
-# }
+ ## key & density don't make sense when data is not all on the same scale
+ ## if(scale!="none" && key==TRUE)
+ ## {
+ ## warning("Key cannot be plotted when scale!=\"none\".")
+ ## key=FALSE
+ ## }
-
-
- if ( (Colv=="Rowv") && (!isTRUE(Rowv) || is.null(Rowv) ) )
+ if ( is.null(Rowv) )
+ Rowv <- FALSE
+ if ( is.null(Colv) )
Colv <- FALSE
+ else if( Colv=="Rowv" && !isTRUE(Rowv) )
+ Colv <- FALSE
- if(length(di <- dim(x)) != 2 || !is.numeric(x))
- stop("`x' must be a numeric matrix")
+
+ if(length(di <- dim(x)) != 2 || !is.numeric(x))
+ stop("`x' must be a numeric matrix")
- nr <- di[1]
- nc <- di[2]
+ nr <- di[1]
+ nc <- di[2]
- if(nr <= 1 || nc <= 1)
- stop("`x' must have at least 2 rows and 2 columns")
+ if(nr <= 1 || nc <= 1)
+ stop("`x' must have at least 2 rows and 2 columns")
- if(!is.numeric(margins) || length(margins) != 2)
- stop("`margins' must be a numeric vector of length 2")
+ if(!is.numeric(margins) || length(margins) != 2)
+ stop("`margins' must be a numeric vector of length 2")
- if(missing(cellnote))
- cellnote <- matrix("", ncol=ncol(x), nrow=nrow(x))
+ if(missing(cellnote))
+ cellnote <- matrix("", ncol=ncol(x), nrow=nrow(x))
- if(!inherits(Rowv, "dendrogram")) {
- ## Check if Rowv and dendrogram arguments are consistent
- if ( ( (!isTRUE(Rowv)) || (is.null(Rowv))) && (dendrogram %in% c("both","row") ) )
- {
- if (is.logical(Colv) && (Colv))
- dendrogram <- "column"
- else
- dedrogram <- "none"
-
- warning("Discrepancy: Rowv is FALSE, while dendrogram is `",
- dendrogram, "'. Omitting row dendogram.")
-
+ if(!inherits(Rowv, "dendrogram")) {
+ ## Check if Rowv and dendrogram arguments are consistent
+ if ( ( (!isTRUE(Rowv)) || (is.null(Rowv))) &&
+ (dendrogram %in% c("both","row") ) )
+ {
+ if (is.logical(Colv) && (Colv))
+ dendrogram <- "column"
+ else
+ dedrogram <- "none"
+
+ warning("Discrepancy: Rowv is FALSE, while dendrogram is `",
+ dendrogram, "'. Omitting row dendogram.")
+
+ }
}
-}
- if(!inherits(Colv, "dendrogram")) {
- ## Check if Colv and dendrogram arguments are consistent
- if ( ( (!isTRUE(Colv)) || (is.null(Colv)))
- && (dendrogram %in% c("both","column")) )
- {
- if (is.logical(Rowv) && (Rowv))
- dendrogram <- "row"
- else
- dendrogram <- "none"
-
- warning("Discrepancy: Colv is FALSE, while dendrogram is `",
- dendrogram, "'. Omitting column dendogram.")
- }
-}
+ if(!inherits(Colv, "dendrogram")) {
+ ## Check if Colv and dendrogram arguments are consistent
+ if ( ( (!isTRUE(Colv)) || (is.null(Colv)))
+ && (dendrogram %in% c("both","column")) )
+ {
+ if (is.logical(Rowv) && (Rowv))
+ dendrogram <- "row"
+ else
+ dendrogram <- "none"
+
+ warning("Discrepancy: Colv is FALSE, while dendrogram is `",
+ dendrogram, "'. Omitting column dendogram.")
+ }
+ }
## by default order by row/col mean
## if(is.null(Rowv)) Rowv <- rowMeans(x, na.rm = na.rm)
## if(is.null(Colv)) Colv <- colMeans(x, na.rm = na.rm)
- ## get the dendrograms and reordering indices
+ ## get the dendrograms and reordering indices
- ## if( dendrogram %in% c("both","row") )
- ## { ## dendrogram option is used *only* for display purposes
+ ## if( dendrogram %in% c("both","row") )
+ ## { ## dendrogram option is used *only* for display purposes
if(inherits(Rowv, "dendrogram"))
{
ddr <- Rowv ## use Rowv 'as-is', when it is dendrogram
rowInd <- order.dendrogram(ddr)
}
-else if (is.integer(Rowv))
+ else if (is.integer(Rowv))
{ ## Compute dendrogram and do reordering based on given vector
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
@@ -208,308 +221,342 @@
if(nc != length(colInd))
stop("column dendrogram ordering gave index of wrong length")
}
-else if (isTRUE(Colv))
- {## If TRUE, compute dendrogram and do reordering based on rowMeans
- Colv <- colMeans(x, na.rm = na.rm)
- hcc <- hclustfun(distfun(if(symm)x else t(x)))
- ddc <- as.dendrogram(hcc)
- ddc <- reorder(ddc, Colv)
+ else if (isTRUE(Colv))
+ {## If TRUE, compute dendrogram and do reordering based on rowMeans
+ Colv <- colMeans(x, na.rm = na.rm)
+ hcc <- hclustfun(distfun(if(symm)x else t(x)))
+ ddc <- as.dendrogram(hcc)
+ ddc <- reorder(ddc, Colv)
- colInd <- order.dendrogram(ddc)
- if(nc != length(colInd))
- stop("column dendrogram ordering gave index of wrong length")
- }
-else
- {
- colInd <- 1:nc
- }
+ colInd <- order.dendrogram(ddc)
+ if(nc != length(colInd))
+ stop("column dendrogram ordering gave index of wrong length")
+ }
+ else
+ {
+ colInd <- 1:nc
+ }
+
+ retval$rowInd <- rowInd
+ retval$colInd <- colInd
+ retval$call <- match.call()
+
- ## reorder x & cellnote
- x <- x[rowInd, colInd]
- x.unscaled <- x
- cellnote <- cellnote[rowInd, colInd]
+ ## reorder x & cellnote
+ x <- x[rowInd, colInd]
+ x.unscaled <- x
+ cellnote <- cellnote[rowInd, colInd]
- if(is.null(labRow))
- labRow <- if(is.null(rownames(x))) (1:nr)[rowInd] else rownames(x)
- else
- labRow <- labRow[rowInd]
+ if(is.null(labRow))
+ labRow <- if(is.null(rownames(x))) (1:nr)[rowInd] else rownames(x)
+ else
+ labRow <- labRow[rowInd]
- if(is.null(labCol))
- labCol <- if(is.null(colnames(x))) (1:nc)[colInd] else colnames(x)
- else
- labCol <- labCol[colInd]
+ if(is.null(labCol))
+ labCol <- if(is.null(colnames(x))) (1:nc)[colInd] else colnames(x)
+ else
+ labCol <- labCol[colInd]
- if(scale == "row") {
- x <- sweep(x, 1, rowMeans(x, na.rm = na.rm))
- sx <- apply(x, 1, sd, na.rm = na.rm)
- x <- sweep(x, 1, sx, "/")
- }
- else if(scale == "column") {
- x <- sweep(x, 2, colMeans(x, na.rm = na.rm))
- sx <- apply(x, 2, sd, na.rm = na.rm)
- x <- sweep(x, 2, sx, "/")
- }
+ if(scale == "row") {
+ retval$rowMeans <- rm <- rowMeans(x, na.rm = na.rm)
+ x <- sweep(x, 1, rm)
+ retval$rowSDs <- sx <- apply(x, 1, sd, na.rm = na.rm)
+ x <- sweep(x, 1, sx, "/")
+ }
+ else if(scale == "column") {
+ retval$colMeans <- rm <- colMeans(x, na.rm = na.rm)
+ x <- sweep(x, 2, rm)
+ retval$colSDs <- sx <- apply(x, 2, sd, na.rm = na.rm)
+ x <- sweep(x, 2, sx, "/")
+ }
- ## Set up breaks and force values outside the range into the endmost bins
- if(missing(breaks) || is.null(breaks) || length(breaks)<1 )
- if(missing(col))
+ ## Set up breaks and force values outside the range into the endmost bins
+ if(missing(breaks) || is.null(breaks) || length(breaks)<1 )
+ {
+ if( missing(col) || is.function(col) )
breaks <- 16
- else
+ else
breaks <- length(col)+1
- if(length(breaks)==1)
- {
+ }
+
+ if(length(breaks)==1)
+ {
+ if(!symbreaks)
breaks <- seq( min(x, na.rm=na.rm), max(x,na.rm=na.rm), length=breaks)
- }
+ else
+ {
+ extreme <- max(abs(x), na.rm=TRUE)
+ breaks <- seq( -extreme, extreme, length=breaks )
+ }
+ }
- nbr <- length(breaks)
- ncol <- length(breaks)-1
+ nbr <- length(breaks)
+ ncol <- length(breaks)-1
- if(class(col)=="function")
- col <- col(ncol)
- else if(is.character(col) && length(col)==1)
- col <- do.call(col,list(ncol))
+ if(class(col)=="function")
+ col <- col(ncol)
- min.breaks <- min(breaks)
- max.breaks <- max(breaks)
+ min.breaks <- min(breaks)
+ max.breaks <- max(breaks)
- x[] <- ifelse(x<min.breaks, min.breaks, x)
- x[] <- ifelse(x>max.breaks, max.breaks, x)
+ x[x<min.breaks] <- min.breaks
+ x[x>max.breaks] <- max.breaks
-
-
+ ## Calculate the plot layout
+ if( missing(lhei) || is.null(lhei) )
+ lhei <- c(keysize, 4)
-
- ## Calculate the plot layout
- if( missing(lhei) || is.null(lhei) )
- lhei <- c(keysize, 4)
+ if( missing(lwid) || is.null(lwid) )
+ lwid <- c(keysize, 4)
- if( missing(lwid) || is.null(lwid) )
- lwid <- c(keysize, 4)
+ if( missing(lmat) || is.null(lmat) )
+ {
+ lmat <- rbind(4:3, 2:1)
+
+ if(!missing(ColSideColors)) { ## add middle row to layout
+ if(!is.character(ColSideColors) || length(ColSideColors) != nc)
+ stop("'ColSideColors' must be a character vector of length ncol(x)")
+ lmat <- rbind(lmat[1,]+1, c(NA,1), lmat[2,]+1)
+ lhei <- c(lhei[1], 0.2, lhei[2])
+ }
- if( missing(lmat) || is.null(lmat) )
- {
- lmat <- rbind(4:3, 2:1)
-
- if(!missing(ColSideColors)) { ## add middle row to layout
- if(!is.character(ColSideColors) || length(ColSideColors) != nc)
- stop("'ColSideColors' must be a character vector of length ncol(x)")
- lmat <- rbind(lmat[1,]+1, c(NA,1), lmat[2,]+1)
- lhei <- c(lhei[1], 0.2, lhei[2])
- }
+ if(!missing(RowSideColors)) { ## add middle column to layout
+ if(!is.character(RowSideColors) || length(RowSideColors) != nr)
+ stop("'RowSideColors' must be a character vector of length nrow(x)")
+ lmat <- cbind(lmat[,1]+1, c(rep(NA, nrow(lmat)-1), 1), lmat[,2]+1)
+ lwid <- c(lwid[1], 0.2, lwid[2])
+ }
- if(!missing(RowSideColors)) { ## add middle column to layout
- if(!is.character(RowSideColors) || length(RowSideColors) != nr)
- stop("'RowSideColors' must be a character vector of length nrow(x)")
- lmat <- cbind(lmat[,1]+1, c(rep(NA, nrow(lmat)-1), 1), lmat[,2]+1)
- lwid <- c(lwid[1], 0.2, lwid[2])
- }
+ lmat[is.na(lmat)] <- 0
+ }
+
+ if(length(lhei) != nrow(lmat))
+ stop("lhei must have length = nrow(lmat) = ", nrow(lmat))
- lmat[is.na(lmat)] <- 0
- }
-
- if(length(lhei) != nrow(lmat))
- stop("lhei must have length = nrow(lmat) = ", nrow(lmat))
+ if(length(lwid) != ncol(lmat))
+ stop("lwid must have length = ncol(lmat) =", ncol(lmat))
- if(length(lwid) != ncol(lmat))
- stop("lwid must have length = ncol(lmat) =", ncol(lmat))
+ ## Graphics `output' -----------------------
- ## Graphics `output' -----------------------
+ op <- par(no.readonly = TRUE)
+ on.exit(par(op))
+ layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
- op <- par(no.readonly = TRUE)
- on.exit(par(op))
- layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
-
- ## draw the side bars
- if(!missing(RowSideColors)) {
- par(mar = c(margins[1],0, 0,0.5))
- image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
+ ## draw the side bars
+ if(!missing(RowSideColors)) {
+ par(mar = c(margins[1],0, 0,0.5))
+ image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
+ }
+ if(!missing(ColSideColors)) {
+ par(mar = c(0.5,0, 0,margins[2]))
+ image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
+ }
+ ## draw the main carpet
+ par(mar = c(margins[1], 0, 0, margins[2]))
+ if(!symm || scale != "none")
+ {
+ x <- t(x)
+ cellnote <- t(cellnote)
}
- if(!missing(ColSideColors)) {
- par(mar = c(0.5,0, 0,margins[2]))
- image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
+ if(revC)
+ { ## x columns reversed
+ iy <- nr:1
+ if(exists("ddr"))
+ ddr <- rev(ddr)
+ x <- x[,iy]
+ cellnote <- cellnote[,iy]
}
- ## draw the main carpet
- par(mar = c(margins[1], 0, 0, margins[2]))
- if(!symm || scale != "none")
- {
- x <- t(x)
- cellnote <- t(cellnote)
- }
- if(revC)
- { # x columns reversed
- iy <- nr:1
- ddr <- rev(ddr)
- x <- x[,iy]
- cellnote <- cellnote[,iy]
- }
- else iy <- 1:nr
+ else iy <- 1:nr
- image(1:nc, 1:nr, x, xlim = 0.5+ c(0, nc), ylim = 0.5+ c(0, nr),
- axes = FALSE, xlab = "", ylab = "", col=col, breaks=breaks,
- ...)
+ ## display the main carpet
+ image(1:nc, 1:nr, x, xlim = 0.5+ c(0, nc), ylim = 0.5+ c(0, nr),
+ axes = FALSE, xlab = "", ylab = "", col=col, breaks=breaks,
+ ...)
+ retval$carpet <- x
+ if(exists("ddr"))
+ retval$rowDendrogram <- ddr
+ if(exists("ddc"))
+ retval$colDendrogram <- ddc
+ retval$breaks <- breaks
+ retval$col <- col
+
+ ## fill 'na' positions with na.color
+ if(!invalid(na.color) & any(is.na(x)))
+ {
+ mmat <- ifelse(is.na(x), 1, NA)
+ image(1:nc, 1:nr, mmat, axes = FALSE, xlab = "", ylab = "",
+ col=na.color, add=TRUE)
+ }
- if(!invalid(na.color) & any(is.na(x)))
- {
- mmat <- ifelse(is.na(x), 1, NA)
- image(1:nc, 1:nr, mmat, axes = FALSE, xlab = "", ylab = "",
- col=na.color, add=TRUE)
- }
+ ## add labels
+ axis(1, 1:nc, labels= labCol, las= 2, line= -0.5, tick= 0, cex.axis= cexCol)
+ if(!is.null(xlab)) mtext(xlab, side = 1, line = margins[1] - 1.25)
+ axis(4, iy, labels= labRow, las= 2, line= -0.5, tick= 0, cex.axis= cexRow)
+ if(!is.null(ylab)) mtext(ylab, side = 4, line = margins[2] - 1.25)
+ ## perform user-specified function
+ if (!missing(add.expr))
+ eval(substitute(add.expr))
- axis(1, 1:nc, labels= labCol, las= 2, line= -0.5, tick= 0, cex.axis= cexCol)
- if(!is.null(xlab)) mtext(xlab, side = 1, line = margins[1] - 1.25)
- axis(4, iy, labels= labRow, las= 2, line= -0.5, tick= 0, cex.axis= cexRow)
- if(!is.null(ylab)) mtext(ylab, side = 4, line = margins[2] - 1.25)
+ ## add 'background' colored spaces to visually separate sections
+ if(!missing(colsep))
+ for(csep in colsep)
+ rect(xleft =csep+0.5, ybottom=rep(0,length(csep)),
+ xright=csep+0.5+sepwidth[1], ytop=rep(ncol(x)+1,csep),
+ lty=1, lwd=1, col=sepcolor, border=sepcolor)
- if (!missing(add.expr))
- eval(substitute(add.expr))
+ if(!missing(rowsep))
+ for(rsep in rowsep)
+ rect(xleft =0, ybottom= (ncol(x)+1-rsep)-0.5,
+ xright=nrow(x)+1, ytop = (ncol(x)+1-rsep)-0.5 - sepwidth[2],
+ lty=1, lwd=1, col=sepcolor, border=sepcolor)
- ## add 'background' colored spaces to visually separate sections
- if(!missing(colsep))
- for(csep in colsep)
- rect(xleft =csep+0.5, ybottom=rep(0,length(csep)),
- xright=csep+0.5+sepwidth[1], ytop=rep(ncol(x)+1,csep),
- lty=1, lwd=1, col=sepcolor, border=sepcolor)
+
+ ## show traces
+ min.scale <- min(breaks)
+ max.scale <- max(breaks)
+ x.scaled <- scale01(t(x), min.scale, max.scale)
- if(!missing(rowsep))
- for(rsep in rowsep)
- rect(xleft =0, ybottom= (ncol(x)+1-rsep)-0.5,
- xright=nrow(x)+1, ytop = (ncol(x)+1-rsep)-0.5 - sepwidth[2],
- lty=1, lwd=1, col=sepcolor, border=sepcolor)
+ if(trace %in% c("both","column") )
+ {
+ retval$vline <- vline
+ vline.vals <- scale01(vline, min.scale, max.scale)
+ for( i in colInd )
+ {
+ if(!is.null(vline))
+ {
+ abline(v=i-0.5 + vline.vals, col=linecol, lty=2)
+ }
+ xv <- rep(i, nrow(x.scaled)) + x.scaled[,i] - 0.5
+ xv <- c(xv[1], xv)
+ yv <- 1:length(xv)-0.5
+ lines(x=xv, y=yv, lwd=1, col=tracecol, type="s")
+ }
+ }
- # show traces
- min.scale <- min(breaks)
- max.scale <- max(breaks)
- x.scaled <- scale01(t(x), min.scale, max.scale)
+ if(trace %in% c("both","row") )
+ {
+ retval$hline <- hline
+ hline.vals <- scale01(hline, min.scale, max.scale)
+ for( i in rowInd )
+ {
+ if(!is.null(hline))
+ {
+ abline(h=i + hline, col=linecol, lty=2)
+ }
+ yv <- rep(i, ncol(x.scaled)) + x.scaled[i,] - 0.5
+ yv <- rev(c(yv[1], yv))
+ xv <- length(yv):1-0.5
+ lines(x=xv, y=yv, lwd=1, col=tracecol, type="s")
+ }
+ }
- if(trace %in% c("both","column") )
- {
- for( i in colInd )
- {
- if(!is.null(vline))
- {
- vline.vals <- scale01(vline, min.scale, max.scale)
- abline(v=i-0.5 + vline.vals, col=linecol, lty=2)
- }
- xv <- rep(i, nrow(x.scaled)) + x.scaled[,i] - 0.5
- xv <- c(xv[1], xv)
- yv <- 1:length(xv)-0.5
- lines(x=xv, y=yv, lwd=1, col=tracecol, type="s")
- }
- }
-
- if(trace %in% c("both","row") )
- {
- for( i in rowInd )
- {
- if(!is.null(hline))
- {
- hline.vals <- scale01(hline, min.scale, max.scale)
- abline(h=i + hline, col=linecol, lty=2)
- }
- yv <- rep(i, ncol(x.scaled)) + x.scaled[i,] - 0.5
- yv <- rev(c(yv[1], yv))
- xv <- length(yv):1-0.5
- lines(x=xv, y=yv, lwd=1, col=tracecol, type="s")
- }
- }
+ if(!missing(cellnote))
+ text(x=c(row(cellnote)),
+ y=c(col(cellnote)),
+ labels=c(cellnote),
+ col=notecol,
+ cex=notecex)
+ ## the two dendrograms :
+ par(mar = c(margins[1], 0, 0, 0))
+ if( dendrogram %in% c("both","row") )
+ {
+ plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab = "none")
+ }
+ else
+ plot.new()
- if(!missing(cellnote))
- text(x=c(row(cellnote)),
- y=c(col(cellnote)),
- labels=c(cellnote),
- col=notecol,
- cex=notecex)
+ par(mar = c(0, 0, if(!is.null(main)) 5 else 0, margins[2]))
- ## the two dendrograms :
- par(mar = c(margins[1], 0, 0, 0))
- if( dendrogram %in% c("both","row") )
- {
- plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab = "none")
- }
- else
- plot.new()
+ if( dendrogram %in% c("both","column") )
+ {
+ plot(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
+ }
+ else
+ plot.new()
- par(mar = c(0, 0, if(!is.null(main)) 5 else 0, margins[2]))
+ ## title
+ if(!is.null(main)) title(main, cex.main = 1.5*op[["cex.main"]])
- if( dendrogram %in% c("both","column") )
- {
- plot(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
- }
- else
- plot.new()
+ ## Add the color-key
+ if(key)
+ {
+ par(mar = c(5, 4, 2, 1), cex=0.75)
+ tmpbreaks <- breaks
- ## title
- if(!is.null(main)) title(main, cex.main = 1.5*op[["cex.main"]])
+ if(symkey)
+ {
+ 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))
+ }
+ else
+ {
+ min.raw <- min(x, na.rm=TRUE) ## Again, modified to use scaled
+ max.raw <- max(x, na.rm=TRUE) ## or unscaled (SD 12/2/03)
+ }
- ## Add the color-key
- if(key)
- {
- par(mar = c(5, 4, 2, 1), cex=0.75)
+ z <- seq(min.raw, max.raw, length=length(col))
+ image(z=matrix(z, ncol=1),
+ col=col, breaks=tmpbreaks,
+ xaxt="n", yaxt="n")
- if(symkey)
- {
- max.raw <- max(abs(x),na.rm=TRUE)
- min.raw <- -max.raw
- }
- else
- {
- min.raw <- min(x, na.rm=TRUE) # Again, modified to use scaled
- max.raw <- max(x, na.rm=TRUE) # or unscaled (SD 12/2/03)
- }
+ par(usr=c(0,1,0,1))
+ lv <- pretty(breaks)
+ xv <- scale01(as.numeric(lv), min.raw, max.raw)
+ axis(1, at=xv, labels=lv)
+ if(scale=="row")
+ mtext(side=1,"Row Z-Score", line=2)
+ else if(scale=="column")
+ mtext(side=1,"Column Z-Score", line=2)
+ else
+ mtext(side=1,"Value", line=2)
- z <- seq(min.raw,max.raw,length=length(col))
- image(z=matrix(z, ncol=1),
- col=col, breaks=breaks,
- xaxt="n", yaxt="n" )
+ if(density.info=="density")
+ {
+ ## Experimental : also plot density of data
+ dens <- density(x, adjust=densadj, na.rm=TRUE)
+ omit <- dens$x < min(breaks) | dens$x > max(breaks)
+ dens$x <- dens$x[-omit]
+ dens$y <- dens$y[-omit]
+ dens$x <- scale01(dens$x,min.raw,max.raw)
+ lines(dens$x, dens$y / max(dens$y) * 0.95, col=denscol, lwd=1)
+ axis(2, at=pretty(dens$y)/max(dens$y) * 0.95, pretty(dens$y) )
+ title("Color Key\nand Density Plot")
+ par(cex=0.5)
+ mtext(side=2,"Density", line=2)
+ }
+ else if(density.info=="histogram")
+ {
+ h <- hist(x, plot=FALSE, breaks=breaks)
+ hx <- scale01(breaks,min.raw,max.raw)
+ hy <- c(h$counts, h$counts[length(h$counts)])
+ lines(hx, hy/max(hy)*0.95, lwd=1, type="s", col=denscol)
+ axis(2, at=pretty(hy)/max(hy) * 0.95, pretty(hy) )
+ title("Color Key\nand Histogram")
+ par(cex=0.5)
+ mtext(side=2,"Count", line=2)
+ }
+ else
+ title("Color Key")
- par(usr=c(0,1,0,1))
- lv <- pretty(breaks)
- xv <- scale01(as.numeric(lv), min.raw, max.raw)
- axis(1, at=xv, labels=lv)
- if(scale=="row")
- mtext(side=1,"Row Z-Score", line=2)
- else if(scale=="column")
- mtext(side=1,"Column Z-Score", line=2)
- else
- mtext(side=1,"Value", line=2)
+ }
+ else
+ plot.new()
- if(density.info=="density")
- {
- # Experimental : also plot density of data
- dens <- density(x, adjust=densadj, na.rm=TRUE)
- omit <- dens$x < min(breaks) | dens$x > max(breaks)
- dens$x <- dens$x[-omit]
- dens$y <- dens$y[-omit]
- dens$x <- scale01(dens$x,min.raw,max.raw)
- lines(dens$x, dens$y / max(dens$y) * 0.95, col=denscol, lwd=1)
- axis(2, at=pretty(dens$y)/max(dens$y) * 0.95, pretty(dens$y) )
- title("Color Key\nand Density Plot")
- par(cex=0.5)
- mtext(side=2,"Density", line=2)
- }
- else if(density.info=="histogram")
- {
- h <- hist(x, plot=FALSE, breaks=breaks)
- hx <- scale01(breaks,min.raw,max.raw)
- hy <- c(h$counts, h$counts[length(h$counts)])
- lines(hx, hy/max(hy)*0.95, lwd=1, type="s", col=denscol)
- axis(2, at=pretty(hy)/max(hy) * 0.95, pretty(hy) )
- title("Color Key\nand Histogram")
- par(cex=0.5)
- mtext(side=2,"Count", line=2)
- }
- else
- title("Color Key")
+ ## Create a table showing how colors match to (transformed) data ranges
+ retval$colorTable <- data.frame(
+ low=retval$breaks[-length(retval$breaks)],
+ high=retval$breaks[-1],
+ color=retval$col
+ )
- }
- else
- plot.new()
-
- invisible(list(rowInd = rowInd, colInd = colInd))
+
+ invisible( retval )
}
Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd 2009-05-08 21:27:55 UTC (rev 1316)
+++ trunk/gplots/man/heatmap.2.Rd 2009-05-08 21:55:05 UTC (rev 1317)
@@ -1,85 +1,92 @@
\name{heatmap.2}
\alias{heatmap.2}
-\title{ Draw a Heat Map }
+\title{ Enhanced Heat Map }
\description{
A heat map is a false color image (basically
\code{\link{image}(t(x))}) with a dendrogram added to the left side
and/or to the top. Typically, reordering of the rows and columns
according to some set of values (row or column means) within the
restrictions imposed by the dendrogram is carried out.
+
+ This heatmap provides a number of extensions to the standard R
+ \code{\link[stats]{heatmap}} function.
}
\usage{
heatmap.2 (x,
- # dendrogram control
- Rowv = TRUE,
- Colv=if(symm)"Rowv" else TRUE,
- distfun = dist,
- hclustfun = hclust,
- dendrogram = c("both","row","column","none"),
- symm = FALSE,
+ # dendrogram control
+ Rowv = TRUE,
+ Colv=if(symm)"Rowv" else TRUE,
+ distfun = dist,
+ hclustfun = hclust,
+ dendrogram = c("both","row","column","none"),
+ symm = FALSE,
- # data scaling
- scale = c("none","row", "column"),
- na.rm=TRUE,
+ # data scaling
+ scale = c("none","row", "column"),
+ na.rm=TRUE,
- # image plot
- revC = identical(Colv, "Rowv"),
- add.expr,
- breaks,
- col="heat.colors",
+ # image plot
+ revC = identical(Colv, "Rowv"),
+ add.expr,
- # block sepration
- colsep,
- rowsep,
- sepcolor="white",
- sepwidth=c(0.05,0.05),
+ # mapping data to colors
+ breaks,
+ symbreaks=min(x < 0, na.rm=TRUE) || scale!="none",
- # cell labeling
- cellnote,
- notecex=1.0,
- notecol="cyan",
- na.color=par("bg"),
+ # colors
+ col="heat.colors",
- # level trace
- trace=c("column","row","both","none"),
- tracecol="cyan",
- hline=median(breaks),
- vline=median(breaks),
- linecol=tracecol,
+ # block sepration
+ colsep,
+ rowsep,
+ sepcolor="white",
+ sepwidth=c(0.05,0.05),
- # Row/Column Labeling
- margins = c(5, 5),
- ColSideColors,
- RowSideColors,
- cexRow = 0.2 + 1/log10(nr),
- cexCol = 0.2 + 1/log10(nc),
- labRow = NULL,
- labCol = NULL,
+ # cell labeling
+ cellnote,
+ notecex=1.0,
+ notecol="cyan",
+ na.color=par("bg"),
- # color key + density info
- key = TRUE,
- keysize = 1.5,
- density.info=c("histogram","density","none"),
- denscol=tracecol,
- #symkey = TRUE, # should be something like
- symkey = min(x < 0, na.rm=TRUE),
- densadj = 0.25,
+ # level trace
+ trace=c("column","row","both","none"),
+ tracecol="cyan",
+ hline=median(breaks),
+ vline=median(breaks),
+ linecol=tracecol,
- # plot labels
- main = NULL,
- xlab = NULL,
- ylab = NULL,
+ # Row/Column Labeling
+ margins = c(5, 5),
+ ColSideColors,
+ RowSideColors,
+ cexRow = 0.2 + 1/log10(nr),
+ cexCol = 0.2 + 1/log10(nc),
+ labRow = NULL,
+ labCol = NULL,
- # plot layout
- lmat = NULL,
- lhei = NULL,
- lwid = NULL,
+ # color key + density info
+ key = TRUE,
+ keysize = 1.5,
+ density.info=c("histogram","density","none"),
+ denscol=tracecol,
+ symkey = min(x < 0, na.rm=TRUE) || symbreaks,
+ densadj = 0.25,
- # extras
- ...
- )
- }
+ # plot labels
+ main = NULL,
+ xlab = NULL,
+ ylab = NULL,
+
+ # plot layout
+ lmat = NULL,
+ lhei = NULL,
+ lwid = NULL,
+
+ # extras
+ ...
+ )
+ }
\arguments{
% Dendogram Control
\item{x}{numeric matrix of the values to be plotted. }
@@ -121,6 +128,9 @@
splitting points for binning \code{x} into colors, or a integer
number of break points to be used, in which case the break points
will be spaced equally between \code{min(x)} and \code{max(x)}.}
+ \item{symbreaks}{Boolean indicating whether breaks should be
+ made symmetric about 0. Defaults to \code{TRUE} if the data includes
+ negative values, and to \code{FALSE} otherwise.}
\item{col}{colors used for the image. Defaults to heat colors
(\code{heat.colors}).}
% block separation
@@ -178,7 +188,8 @@
display specified by \code{density.info}, defaults to the same value
as \code{tracecol}.}
\item{symkey}{Boolean indicating whether the color key should be
- made symmetric about 0. Defaults to \code{TRUE}.}
+ made symmetric about 0. Defaults to \code{TRUE} if the data includes
+ negative values, and to \code{FALSE} otherwise.}
\item{densadj}{Numeric scaling value for tuning the kernel width when
a density plot is drawn on the color key. (See the \code{adjust}
parameter for the \code{density} function for details.) Defaults to
@@ -244,9 +255,26 @@
}
\value{
Invisibly, a list with components
- \item{rowInd}{\bold{r}ow index permutation vector as returned by
+ \item{rowInd}{row index permutation vector as returned by
\code{\link{order.dendrogram}}.}
- \item{colInd}{\bold{c}olumn index permutation vector.}
+ \item{colInd}{column index permutation vector.}
+ \item{call}{the matched call}
+ \item{rowMeans, rowSDs}{mean and standard deviation of each row: only
+ present if \code{scale="row"}}
+ \item{colMeans, colSDs}{mean and standard deviation of each column: only
+ present if \code{scale="column"}}
+ \item{carpet}{reordered and scaled 'x' values used generate the main
+ 'carpet'}
+ \item{rowDendrogram}{row dendrogram, if present}
+ \item{colDendrogram}{column dendrogram, if present}
+ \item{breaks}{values used for color break points}
+ \item{col}{colors used}
+ \item{vline}{center-line value used for column trace, present only if
+ \code{trace="both"} or \code{trace="column"} }
+ \item{hline}{center-line value used for row trace, present only if
+ \code{trace="both"} or \code{trace="row"} }
+ \item{colorTable}{A three-column data frame providing the lower and upper
+ bound and color for each bin}
}
\author{Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber,
G. Warnes, revisions.}
@@ -260,6 +288,9 @@
rc <- rainbow(nrow(x), start=0, end=.3)
cc <- rainbow(ncol(x), start=0, end=.3)
+ ##
+ ## demonstrate the effect of row and column dendogram options
+ ##
heatmap.2(x) ## default - dendrogram plotted and reordering done.
heatmap.2(x, dendrogram="none") ## no dendrogram plotted, but reordering done.
heatmap.2(x, dendrogram="row") ## row dendrogram plotted and row reordering done.
@@ -267,22 +298,45 @@
heatmap.2(x, keysize=2) ## default - dendrogram plotted and reordering done.
-
heatmap.2(x, Rowv=FALSE, dendrogram="both") ## generate warning!
heatmap.2(x, Rowv=NULL, dendrogram="both") ## generate warning!
heatmap.2(x, Colv=FALSE, dendrogram="both") ## generate warning!
+ ##
+ ## Show effect of z-score scaling within columns, blue-red color scale
+ ##
+ hv <- heatmap.2(x, col=bluered, scale="column", tracecol="#303030")
+ ###
+ ## Look at the return values
+ ###
+ names(hv)
+ ## Show the mapping of z-score values to color bins
+ hv$colorTable
- hv <- heatmap.2(x, col=cm.colors(256), scale="column",
+ ## Extract the range associated with white
+ hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",]
+
+ ## Determine the original data values that map to white
+ whiteBin <- unlist(hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",1:2])
+ rbind(whiteBin[1] * hv$colSDs + hv$colMeans,
+ whiteBin[2] * hv$colSDs + hv$colMeans )
+ ##
+ ## A more decorative heatmap, with z-score scaling along columns
+ ##
+ hv <- heatmap.2(x, col=cm.colors(255), scale="column",
RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
xlab="specification variables", ylab= "Car Models",
main="heatmap(<Mtcars data>, ..., scale=\"column\")",
tracecol="green", density="density")
+ ## Note that the breakpoints are now symmetric about 0
- str(hv) # the two re-ordering index vectors
+
+
+
+
%% want example using the `add.exp' argument!
data(attitude)
Modified: trunk/gplots/tests/heatmap2Test.Rout.save
===================================================================
--- trunk/gplots/tests/heatmap2Test.Rout.save 2009-05-08 21:27:55 UTC (rev 1316)
+++ trunk/gplots/tests/heatmap2Test.Rout.save 2009-05-08 21:55:05 UTC (rev 1317)
@@ -1,6 +1,6 @@
-R version 2.6.0 (2007-10-03)
-Copyright (C) 2007 The R Foundation for Statistical Computing
+R version 2.9.0 (2009-04-17)
+Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -18,6 +18,9 @@
> library(gplots)
Loading required package: gtools
Loading required package: gdata
+Loading required package: caTools
+Loading required package: bitops
+Loading required package: grid
Attaching package: 'gplots'
@@ -112,8 +115,108 @@
+ tracecol="green", density="density")
>
> str(hv) # the two re-ordering index vectors
-List of 2
- $ rowInd: int [1:32] 31 17 16 15 5 25 29 24 7 6 ...
- $ colInd: int [1:11] 2 9 8 11 6 5 10 7 1 4 ...
+List of 12
+ $ rowInd : int [1:32] 31 17 16 15 5 25 29 24 7 6 ...
+ $ colInd : int [1:11] 2 9 8 11 6 5 10 7 1 4 ...
+ $ call : language heatmap.2(x = x, scale = "column", col = cm.colors(256), tracecol = "green", margins = c(5, 10), ColSideColors = cc, RowSideColors = rc, ...
+ $ colMeans : Named num [1:11] 6.188 0.406 0.438 2.812 3.217 ...
+ ..- attr(*, "names")= chr [1:11] "cyl" "am" "vs" "carb" ...
+ $ colSDs : Named num [1:11] 1.786 0.499 0.504 1.615 0.978 ...
+ ..- attr(*, "names")= chr [1:11] "cyl" "am" "vs" "carb" ...
+ $ carpet : num [1:11, 1:32] 1.015 1.19 -0.868 3.212 0.361 ...
+ ..- attr(*, "dimnames")=List of 2
+ .. ..$ : chr [1:11] "cyl" "am" "vs" "carb" ...
+ .. ..$ : chr [1:32] "Maserati Bora" "Chrysler Imperial" "Lincoln Continental" "Cadillac Fleetwood" ...
+ $ rowDendrogram: ..--[dendrogram w/ 2 branches and 32 members at h = 425, midpoint = 8.58, value = 1267]
+ .. |--[dendrogram w/ 2 branches and 9 members at h = 215, midpoint = 1.84, value = 552]
+ .. | |--leaf "Maserati Bora" ( value.Maserati Bora = 63.2 )
+ .. | `--[dendrogram w/ 2 branches and 8 members at h = 135, midpoint = 2.69, value = 489]
+ .. | |--[dendrogram w/ 2 branches and 3 members at h = 40.8, midpoint = 0.75, value = 198]
+ .. | | |--leaf "Chrysler Imperial" ( value.Chrysler Imperial = 66 )
+ .. | | `--[dendrogram w/ 2 branches and 2 members at h = 15.6, midpoint = 0.5, value = 132]
+ .. | | |--leaf "Lincoln Continental" ( value.Lincoln Continental = 66 )
+ .. | | `--leaf "Cadillac Fleetwood" ( value.Cadillac Fleetwood = 66.2 )
+ .. | `--[dendrogram w/ 2 branches and 5 members at h = 102, midpoint = 1.62, value = 290]
+ .. | |--[dendrogram w/ 2 branches and 2 members at h = 40, midpoint = 0.5, value = 111]
+ .. | | |--leaf "Hornet Sportabout" ( value.Hornet Sportabout = 53.7 )
+ .. | | `--leaf "Pontiac Firebird" ( value.Pontiac Firebird = 57.4 )
+ .. | `--[dendrogram w/ 2 branches and 3 members at h = 21.3, midpoint = 0.75, value = 179]
+ .. | |--leaf "Ford Pantera L" ( value.Ford Pantera L = 61 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 10.1, midpoint = 0.5, value = 118]
+ .. | |--leaf "Camaro Z28" ( value.Camaro Z28 = 58.8 )
+ .. | `--leaf "Duster 360" ( value.Duster 360 = 59.7 )
+ .. `--[dendrogram w/ 2 branches and 23 members at h = 262, midpoint = 6.33, value = 716]
+ .. |--[dendrogram w/ 2 branches and 7 members at h = 103, midpoint = 2.06, value = 306]
+ .. | |--[dendrogram w/ 2 branches and 2 members at h = 33.6, midpoint = 0.5, value = 73.8]
+ .. | | |--leaf "Valiant" ( value.Valiant = 35.0 )
+ .. | | `--leaf "Hornet 4 Drive" ( value.Hornet 4 Drive = 38.7 )
+ .. | `--[dendrogram w/ 2 branches and 5 members at h = 51.8, midpoint = 1.62, value = 233]
+ .. | |--[dendrogram w/ 2 branches and 2 members at h = 14.0, midpoint = 0.5, value = 93.2]
+ .. | | |--leaf "AMC Javelin" ( value.AMC Javelin = 46 )
+ .. | | `--leaf "Dodge Challenger" ( value.Dodge Challenger = 47.2 )
+ .. | `--[dendrogram w/ 2 branches and 3 members at h = 2.14, midpoint = 0.75, value = 139]
+ .. | |--leaf "Merc 450SLC" ( value.Merc 450SLC = 46.4 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 0.983, midpoint = 0.5, value = 93]
+ .. | |--leaf "Merc 450SE" ( value.Merc 450SE = 46.4 )
+ .. | `--leaf "Merc 450SL" ( value.Merc 450SL = 46.5 )
+ .. `--[dendrogram w/ 2 branches and 16 members at h = 142, midpoint = 3.59, value = 409]
+ .. |--[dendrogram w/ 2 branches and 4 members at h = 14.8, midpoint = 0.875, value = 75]
+ .. | |--leaf "Honda Civic" ( value.Honda Civic = 17.7 )
+ .. | `--[dendrogram w/ 2 branches and 3 members at h = 10.4, midpoint = 0.75, value = 57.2]
+ .. | |--leaf "Toyota Corolla" ( value.Toyota Corolla = 18.8 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 5.15, midpoint = 0.5, value = 38.4]
+ .. | |--leaf "Fiat X1-9" ( value.Fiat X1-9 = 18.9 )
+ .. | `--leaf "Fiat 128" ( value.Fiat 128 = 19.4 )
+ .. `--[dendrogram w/ 2 branches and 12 members at h = 113, midpoint = 2.30, value = 334]
+ .. |--leaf "Ferrari Dino" ( value.Ferrari Dino = 34.5 )
+ .. `--[dendrogram w/ 2 branches and 11 members at h = 74.4, midpoint = 3.61, value = 300]
+ .. |--[dendrogram w/ 2 branches and 5 members at h = 64.9, midpoint = 1.25, value = 148]
+ .. | |--leaf "Merc 240D" ( value.Merc 240D = 24.6 )
+ .. | `--[dendrogram w/ 2 branches and 4 members at h = 15.7, midpoint = 1.5, value = 124]
+ .. | |--[dendrogram w/ 2 branches and 2 members at h = 0.615, midpoint = 0.5, value = 59.9]
+ .. | | |--leaf "Mazda RX4" ( value.Mazda RX4 = 29.9 )
+ .. | | `--leaf "Mazda RX4 Wag" ( value.Mazda RX4 Wag = 30 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 1.52, midpoint = 0.5, value = 63.6]
+ .. | |--leaf "Merc 280C" ( value.Merc 280C = 31.8 )
+ .. | `--leaf "Merc 280" ( value.Merc 280 = 31.9 )
+ .. `--[dendrogram w/ 2 branches and 6 members at h = 50.1, midpoint = 0.969, value = 152]
+ .. |--leaf "Lotus Europa" ( value.Lotus Europa = 24.9 )
+ .. `--[dendrogram w/ 2 branches and 5 members at h = 33.2, midpoint = 0.938, value = 127]
+ .. |--leaf "Merc 230" ( value.Merc 230 = 27.2 )
+ .. `--[dendrogram w/ 2 branches and 4 members at h = 20.7, midpoint = 0.875, value = 99.5]
+ .. |--leaf "Volvo 142E" ( value.Volvo 142E = 26.3 )
+ .. `--[dendrogram w/ 2 branches and 3 members at h = 13.1, midpoint = 0.75, value = 73.3]
+ .. |--leaf "Datsun 710" ( value.Datsun 710 = 23.6 )
+ .. `--[dendrogram w/ 2 branches and 2 members at h = 8.65, midpoint = 0.5, value = 49.7]
+ .. |--leaf "Porsche 914-2" ( value.Porsche 914-2 = 24.8 )
+ .. `--leaf "Toyota Corona" ( value.Toyota Corona = 24.9 )
+ $ colDendrogram: ..--[dendrogram w/ 2 branches and 11 members at h = 1475, midpoint = 7, value = 436]
+ .. |--[dendrogram w/ 2 branches and 9 members at h = 116, midpoint = 4.5, value = 58.3]
+ .. | |--[dendrogram w/ 2 branches and 7 members at h = 34.8, midpoint = 1.5, value = 20.3]
+ .. | | |--leaf "cyl" ( value.cyl = 6.19 )
+ .. | | `--[dendrogram w/ 2 branches and 6 members at h = 18.9, midpoint = 2, value = 14.2]
+ .. | | |--[dendrogram w/ 2 branches and 2 members at h = 3.61, midpoint = 0.5, value = 0.844]
+ .. | | | |--leaf "am" ( value.am = 0.406 )
+ .. | | | `--leaf "vs" ( value.vs = 0.438 )
+ .. | | `--[dendrogram w/ 2 branches and 4 members at h = 10.7, midpoint = 1.5, value = 13.3]
+ .. | | |--[dendrogram w/ 2 branches and 2 members at h = 8.6, midpoint = 0.5, value = 6.03]
+ .. | | | |--leaf "carb" ( value.carb = 2.81 )
+ .. | | | `--leaf "wt" ( value.wt = 3.22 )
+ .. | | `--[dendrogram w/ 2 branches and 2 members at h = 2.98, midpoint = 0.5, value = 7.28]
+ .. | | |--leaf "drat" ( value.drat = 3.6 )
+ .. | | `--leaf "gear" ( value.gear = 3.69 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 33.3, midpoint = 0.5, value = 37.9]
+ .. | |--leaf "qsec" ( value.qsec = 17.8 )
+ .. | `--leaf "mpg" ( value.mpg = 20.1 )
+ .. `--[dendrogram w/ 2 branches and 2 members at h = 657, midpoint = 0.5, value = 377]
+ .. |--leaf "hp" ( value.hp = 147 )
+ .. `--leaf "disp" ( value.disp = 231 )
+ $ breaks : num [1:257] -3.21 -3.19 -3.16 -3.14 -3.11 ...
+ $ col : chr [1:256] "#80FFFFFF" "#80FFFFFF" "#81FFFFFF" "#82FFFFFF" ...
+ $ vline : num 0
+ $ colorTable :'data.frame': 256 obs. of 3 variables:
+ ..$ low : num [1:256] -3.21 -3.19 -3.16 -3.14 -3.11 ...
+ ..$ high : num [1:256] -3.19 -3.16 -3.14 -3.11 -3.09 ...
+ ..$ color: Factor w/ 254 levels "#80FFFFFF","#81FFFFFF",..: 1 1 2 3 4 5 6 7 8 9 ...
>
>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-08 21:28:25
|
Revision: 1316
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1316&view=rev
Author: warnes
Date: 2009-05-08 21:27:55 +0000 (Fri, 08 May 2009)
Log Message:
-----------
Fix Rd syntax error
Modified Paths:
--------------
trunk/gplots/man/space.Rd
Modified: trunk/gplots/man/space.Rd
===================================================================
--- trunk/gplots/man/space.Rd 2009-04-22 17:15:11 UTC (rev 1315)
+++ trunk/gplots/man/space.Rd 2009-05-08 21:27:55 UTC (rev 1316)
@@ -64,7 +64,7 @@
\item{y}{y location of each input point}
}
\author{ Gregory R. Warnes \email{wa...@bs...} }
-\seealso{ \code{\link{jitter}}, \code{link}[base]{sunflowerplot} }
+\seealso{ \code{\link{jitter}}, \code{\link[base]{sunflowerplot}} }
\examples{
x <- rep(1:5, 10)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-04-22 17:15:31
|
Revision: 1315
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1315&view=rev
Author: warnes
Date: 2009-04-22 17:15:11 +0000 (Wed, 22 Apr 2009)
Log Message:
-----------
VADeaths data set has move to dataset package
Modified Paths:
--------------
trunk/gplots/man/barplot2.Rd
trunk/gplots/man/ooplot.Rd
Modified: trunk/gplots/man/barplot2.Rd
===================================================================
--- trunk/gplots/man/barplot2.Rd 2009-04-19 23:25:04 UTC (rev 1314)
+++ trunk/gplots/man/barplot2.Rd 2009-04-22 17:15:11 UTC (rev 1315)
@@ -237,7 +237,7 @@
barplot2(tN, space = 1.5, axisnames = FALSE,
sub = "barplot2(..., space = 1.5, axisnames = FALSE)")
-data(VADeaths, package = "base")
+data(VADeaths, package = "datasets")
barplot2(VADeaths, plot = FALSE)
barplot2(VADeaths, plot = FALSE, beside = TRUE)
Modified: trunk/gplots/man/ooplot.Rd
===================================================================
--- trunk/gplots/man/ooplot.Rd 2009-04-19 23:25:04 UTC (rev 1314)
+++ trunk/gplots/man/ooplot.Rd 2009-04-22 17:15:11 UTC (rev 1315)
@@ -162,7 +162,7 @@
}
\seealso{ \code{\link[plot]{plot}}, \code{\link[plot]{boxplot}} }
\examples{
- data(VADeaths, package = "base")
+ data(VADeaths, package = "datasets")
VADeaths <- cbind( Age=c(50,55,60,65,70), VADeaths)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ar...@us...> - 2009-04-19 23:25:17
|
Revision: 1314
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1314&view=rev
Author: arnima
Date: 2009-04-19 23:25:04 +0000 (Sun, 19 Apr 2009)
Log Message:
-----------
Changed object.size(object) to unclass(object.size(object)).
Modified Paths:
--------------
trunk/gdata/R/env.R
trunk/gdata/R/ll.R
Modified: trunk/gdata/R/env.R
===================================================================
--- trunk/gdata/R/env.R 2009-02-16 15:34:40 UTC (rev 1313)
+++ trunk/gdata/R/env.R 2009-04-19 23:25:04 UTC (rev 1314)
@@ -3,7 +3,7 @@
get.object.size <- function(object.name, pos)
{
object <- get(object.name, pos=pos)
- size <- try(object.size(object), silent=TRUE)
+ size <- try(unclass(object.size(object)), silent=TRUE)
if(class(size) == "try-error")
size <- 0
return(size)
Modified: trunk/gdata/R/ll.R
===================================================================
--- trunk/gdata/R/ll.R 2009-02-16 15:34:40 UTC (rev 1313)
+++ trunk/gdata/R/ll.R 2009-04-19 23:25:04 UTC (rev 1314)
@@ -23,7 +23,7 @@
get.object.size <- function(object.name, pos)
{
object <- get(object.name, pos=pos)
- size <- try(object.size(object), silent=TRUE)
+ size <- try(unclass(object.size(object)), silent=TRUE)
if(class(size) == "try-error")
size <- 0
return(size)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-02-16 15:34:44
|
Revision: 1313
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1313&view=rev
Author: warnes
Date: 2009-02-16 15:34:40 +0000 (Mon, 16 Feb 2009)
Log Message:
-----------
Correct windows make flags as suggested by Brian Ripley.
Modified Paths:
--------------
trunk/gtools/src/Makevars.win
Modified: trunk/gtools/src/Makevars.win
===================================================================
--- trunk/gtools/src/Makevars.win 2008-12-31 13:30:45 UTC (rev 1312)
+++ trunk/gtools/src/Makevars.win 2009-02-16 15:34:40 UTC (rev 1313)
@@ -1 +1 @@
-DLLLIBS:=$(DLLLIBS) -lwsock32
+PKG_LIBS = -lws2_32
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2008-12-31 13:30:54
|
Revision: 1312
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1312&view=rev
Author: ggorjan
Date: 2008-12-31 13:30:45 +0000 (Wed, 31 Dec 2008)
Log Message:
-----------
Documenting changes and exporting the functions.
Modified Paths:
--------------
trunk/gdata/NAMESPACE
trunk/gdata/inst/NEWS
Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE 2008-12-31 13:30:07 UTC (rev 1311)
+++ trunk/gdata/NAMESPACE 2008-12-31 13:30:45 UTC (rev 1312)
@@ -2,6 +2,7 @@
export(
Args,
aggregate.table,
+ bindData,
cbindX,
combine,
ConvertMedUnits,
@@ -17,31 +18,35 @@
"lowerTriangle<-",
matchcols,
nobs,
+ nPairs,
read.xls,
rename.vars,
remove.vars,
reorder.factor,
resample,
trim,
- trimSum,
+ trimSum,
unmatrix,
upperTriangle,
"upperTriangle<-",
+ wideByFactor,
write.fwf,
xls2csv,
+ ## Object size stuff
+ object.size, as.object_size, is.object_size, humanReadable,
+
+ ## getDateTime stuff
+ getYear, getMonth, getDay, getHour, getMin, getSec,
+
## mapLevels stuff
- mapLevels,
- as.levelsMap,
- as.listLevelsMap,
- is.levelsMap,
- is.listLevelsMap,
- "mapLevels<-",
+ mapLevels, as.levelsMap, as.listLevelsMap, is.levelsMap, is.listLevelsMap, "mapLevels<-",
## unknown stuff
- isUnknown,
- unknownToNA,
- NAToUnknown
+ isUnknown, unknownToNA, NAToUnknown,
+
+ ## Unit testing
+ .runRUnitTestsGdata
)
importFrom(stats, reorder)
@@ -55,6 +60,28 @@
S3method(drop.levels, list)
S3method(drop.levels, data.frame)
+## getDateTime stuff
+S3method(getYear, default)
+S3method(getYear, Date)
+S3method(getYear, POSIXct)
+S3method(getYear, POSIXlt)
+
+S3method(getMonth, default)
+S3method(getMonth, Date)
+S3method(getMonth, POSIXct)
+S3method(getMonth, POSIXlt)
+
+S3method(getDay, default)
+S3method(getDay, Date)
+S3method(getDay, POSIXct)
+S3method(getDay, POSIXlt)
+
+S3method(getHour, default)
+
+S3method(getMin, default)
+
+S3method(getSec, default)
+
## mapLevels stuff
S3method(mapLevels, default)
S3method(mapLevels, character)
@@ -83,6 +110,10 @@
S3method(nobs, default)
S3method(nobs, lm)
+## Object size stuff
+S3method(print, object_size)
+S3method(c, object_size)
+
## unknown stuff
S3method(isUnknown, default)
S3method(isUnknown, POSIXlt)
Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS 2008-12-31 13:30:07 UTC (rev 1311)
+++ trunk/gdata/inst/NEWS 2008-12-31 13:30:45 UTC (rev 1312)
@@ -1,12 +1,31 @@
-CHANGES IN 2.5.0 (2008-??-??)
+CHANGES IN 2.5.0 (2009-??-??)
-----------------------------
-- New function trimSum that sums trimmed values
+- New function .runRUnitTestsGdata that enables run of all RUnit tests during
+ the R CMD check as well as directly from within R.
+- 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(x, humanReadable=TRUE).
+
+- 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.
+
+- New functions getYear, getMonth, getDay, getHour, getMin, and getSec for
+ extracting the date/time parts from objects of a date/time class.
+
+- New function nPairs that gives the number of variable pairs in a data.frame
+ or a matrix.
+
+- New function trimSum that sums trimmed values.
+
- New function cbindX that can bind objects with different number of rows.
-- write.fwf gains width argument. Unknown values can increase or decrease
- the width of the columns. Additional tests and documentation fixes.
+- 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)
-----------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2008-12-31 13:30:10
|
Revision: 1311
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1311&view=rev
Author: ggorjan
Date: 2008-12-31 13:30:07 +0000 (Wed, 31 Dec 2008)
Log Message:
-----------
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).
Added Paths:
-----------
trunk/gdata/R/object.size.R
trunk/gdata/man/humanReadable.Rd
trunk/gdata/man/object.size.Rd
Added: trunk/gdata/R/object.size.R
===================================================================
--- trunk/gdata/R/object.size.R (rev 0)
+++ trunk/gdata/R/object.size.R 2008-12-31 13:30:07 UTC (rev 1311)
@@ -0,0 +1,92 @@
+### object.size.R
+###------------------------------------------------------------------------
+### What: Print object size in human readable format - code
+### $Id$
+### Time-stamp: <2008-12-30 08:05:43 ggorjan>
+###------------------------------------------------------------------------
+
+object.size <- function(...)
+{
+ structure(sapply(list(...), function(x) .Internal(object.size(x))),
+ class=c("object_size", "numeric"))
+}
+
+print.object_size <- function(x, quote=FALSE, humanReadable, ...)
+{
+ xOrig <- x
+ if(missing(humanReadable)) {
+ opt <- getOption("humanReadable")
+ humanReadable <- ifelse(!is.null(opt), opt, FALSE)
+ }
+ if(humanReadable) {
+ print(humanReadable(x), quote=quote, ...)
+ } else {
+ class(x) <- "numeric"
+ NextMethod()
+ }
+ invisible(xOrig)
+}
+
+is.object_size <- function(x) inherits(x, what="object_size")
+
+as.object_size <- function(x)
+{
+ if(!is.numeric(x)) stop("'x' must be numeric/integer")
+ class(x) <- c("object_size", "numeric")
+ x
+}
+
+c.object_size <- function(..., recursive=FALSE)
+{
+ x <- NextMethod()
+ if(is.numeric(x)) class(x) <- c("object_size", "numeric")
+ x
+}
+
+humanReadable <- function(x, standard="SI", digits=1, width=3, sep=" ")
+{
+ ## --- Setup ---
+
+ if(any(x < 0)) stop("'x' must be positive")
+ if(standard == "SI") {
+ suffix <- c("B", "kB", "MB", "GB", "TB", "PB", "EB", "ZB", "YB")
+ base <- 1000
+ } else {
+ suffix <- c("B", "KiB", "MiB", "GiB", "TiB", "PiB", "EiB", "ZiB", "YiB")
+ base <- 1024
+ }
+
+ ## --- Apply ---
+
+ .applyHuman <- function(x, base, suffix, digits, width, sep)
+ {
+ ## Which suffix should we use?
+ n <- length(suffix)
+ for(i in 1:n) {
+ if(x >= base) {
+ if(i < n) x <- x / base
+ } else {
+ break
+ }
+ }
+ ## Formatting
+ if(is.null(width)) { ## the same formatting for all
+ x <- format(round(x=x, digits=digits), nsmall=digits)
+ } else { ## similar to ls, du, and df
+ lenX <- nchar(x)
+ if(lenX > width) {
+ digitsMy <- width - (lenX - (lenX - (nchar(round(x)) + 1)))
+ digits <- ifelse(digitsMy > digits, digits, digitsMy)
+ }
+ if(i == 1) digits <- 0
+ x <- round(x, digits=digits)
+ }
+ paste(x, suffix[i], sep=sep)
+ }
+
+ sapply(X=x, FUN=".applyHuman", base=base, suffix=suffix, digits=digits,
+ width=width, sep=sep)
+}
+
+###------------------------------------------------------------------------
+### object.size.R ends here
Property changes on: trunk/gdata/R/object.size.R
___________________________________________________________________
Added: svn:keywords
+
Added: trunk/gdata/man/humanReadable.Rd
===================================================================
--- trunk/gdata/man/humanReadable.Rd (rev 0)
+++ trunk/gdata/man/humanReadable.Rd 2008-12-31 13:30:07 UTC (rev 1311)
@@ -0,0 +1,131 @@
+% humanReadable.Rd
+%--------------------------------------------------------------------------
+% What: Print byte size in human readable format man page
+% $Id$
+% Time-stamp: <2008-12-30 13:26:35 ggorjan>
+%--------------------------------------------------------------------------
+
+\name{humanReadable}
+
+\alias{humanReadable}
+
+\title{Print byte size in human readable format}
+
+\description{
+
+\code{humanReadable} converts byte size in human readable format such as
+kB, MB, GB, etc.
+
+}
+
+\usage{
+
+humanReadable(x, standard="SI", digits=1, width=3, sep=" ")
+
+}
+
+\arguments{
+ \item{x}{integer, byte size}
+ \item{standard}{character, "SI" for powers of 1000 or anything else for
+ powers of 1024, see details}
+ \item{digits}{integer, number of digits after decimal point}
+ \item{width}{integer, width of number string}
+ \item{sep}{character, separator between number and unit}
+}
+
+\details{
+
+Basic unit used to store information in computers is a bit. Bits are
+represented as zeroes and ones - binary number system. Although, the binary
+number system is not the same as the decimal number system, decimal prefixes
+for binary multiples such as kilo and mega are often used. In the decimal system
+kilo represent 1000, which is close to \eqn{1024 = 2^{10}} in the binary system.
+This sometimes causes problems as it is not clear which powers (2 or 10) are used
+in a notation like 1 kB. To overcome this problem International Electrotechnical
+Commission (IEC) has provided the following solution to this problem:
+
+\tabular{lrcll}{
+Name \tab System \tab Symbol \tab Size \tab Conversion \cr
+byte \tab binary \tab B \tab \eqn{2^3} \tab 8 bits \cr
+kilobyte \tab decimal \tab kB \tab \eqn{10^3} \tab 1000 bytes \cr
+kibibyte \tab binary \tab KiB \tab \eqn{2^{10}} \tab 1024 bytes \cr
+megabyte \tab decimal \tab MB \tab \eqn{(10^3)^2} \tab 1000 kilobytes\cr
+mebibyte \tab binary \tab MiB \tab \eqn{(2^{10})^2} \tab 1024 kibibytes\cr
+gigabyte \tab decimal \tab GB \tab \eqn{(10^3)^3} \tab 1000 megabytes\cr
+gibibyte \tab binary \tab GiB \tab \eqn{(2^{10})^3} \tab 1024 mebibytes\cr
+terabyte \tab decimal \tab TB \tab \eqn{(10^3)^4} \tab 1000 gigabytes\cr
+tebibyte \tab binary \tab TiB \tab \eqn{(2^{10})^4} \tab 1024 gibibytes\cr
+petabyte \tab decimal \tab PB \tab \eqn{(10^3)^5} \tab 1000 terabytes\cr
+pebibyte \tab binary \tab PiB \tab \eqn{(2^{10})^5} \tab 1024 tebibytes\cr
+exabyte \tab decimal \tab EB \tab \eqn{(10^3)^6} \tab 1000 petabytes\cr
+exbibyte \tab binary \tab EiB \tab \eqn{(2^{10})^6} \tab 1024 pebibytes\cr
+zettabyte \tab decimal \tab ZB \tab \eqn{(10^3)^7} \tab 1000 exabytes\cr
+zebibyte \tab binary \tab ZiB \tab \eqn{(2^{10})^7} \tab 1024 exbibytes\cr
+yottabyte \tab decimal \tab YB \tab \eqn{(10^3)^8} \tab 1000 zettabytes\cr
+yebibyte \tab binary \tab YiB \tab \eqn{(2^{10})^8} \tab 1024 zebibytes\cr
+}
+
+where Zi and Yi are GNU extensions to IEC. To get the output in the decimal
+system (powers of 1000) use \code{standard="SI"}. Otherwise IEC standard
+(powers of 1024) is used.
+
+For printout both \code{digits} and \code{width} can be specified. If
+\code{width} is \code{NULL}, all values have given number of digits. If
+\code{width} is not \code{NULL}, output is rounded to a given width and
+formated similar to human readable format of \code{ls}, \code{df} or
+\code{du} shell commands.
+
+}
+
+\references{
+
+Wikipedia:
+\url{http://en.wikipedia.org/wiki/Byte}
+\url{http://en.wikipedia.org/wiki/SI_prefix}
+\url{http://en.wikipedia.org/wiki/Binary_prefix}
+
+GNU manual for coreutils:
+\url{http://www.gnu.org/software/coreutils/manual/html_node/Block-size.html#Block-size}
+
+}
+
+\value{
+
+Byte size in human readable format as character with proper unit symbols
+added at the end of the string.
+
+}
+
+\author{Ales Korosec and Gregor Gorjanc}
+
+\seealso{
+ \code{\link{object.size}}, \code{\link[gdata]{ll}}
+}
+
+\examples{
+
+baseSI <- 10
+powerSI <- seq(from=3, to=27, by=3)
+SI0 <- (baseSI)^powerSI
+k <- length(SI0) - 1
+SI1 <- SI0 - SI0 / c(2, runif(n=k, min=1.01, max=5.99))
+SI2 <- SI0 + SI0 / c(2, runif(n=k, min=1.01, max=5.99))
+
+baseIEC <- 2
+powerIEC <- seq(from=10, to=90, by=10)
+IEC0 <- (baseIEC)^powerIEC
+IEC1 <- IEC0 - IEC0 / c(2, runif(n=k, min=1.01, max=5.99))
+IEC2 <- IEC0 + IEC0 / c(2, runif(n=k, min=1.01, max=5.99))
+
+cbind(humanReadable(x=SI1, width=NULL, digits=3),
+ humanReadable(x=SI0, width=NULL, digits=2),
+ humanReadable(x=SI2, width=NULL, digits=1),
+ humanReadable(x=IEC1, standard="IEC", width=7, digits=3),
+ humanReadable(x=IEC0, standard="IEC", width=7, digits=2),
+ humanReadable(x=IEC2, standard="IEC", width=7, digits=1))
+}
+
+\keyword{misc}
+
+%--------------------------------------------------------------------------
+% humanReadable.Rd ends here
Added: trunk/gdata/man/object.size.Rd
===================================================================
--- trunk/gdata/man/object.size.Rd (rev 0)
+++ trunk/gdata/man/object.size.Rd 2008-12-31 13:30:07 UTC (rev 1311)
@@ -0,0 +1,85 @@
+% File src/library/utils/man/object.size.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2007 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{object.size}
+\alias{object.size}
+\alias{print.object_size}
+\alias{c.object_size}
+\alias{as.object_size}
+\alias{is.object_size}
+
+\title{Report the Space Allocated for an Object}
+\description{
+ Provides an estimate of the memory that is being used to store an \R object.
+}
+\usage{
+object.size(\dots)
+
+\method{print}{object_size}(x, quote=FALSE, humanReadable, \dots)
+}
+\arguments{
+ \item{\dots}{\code{object.size}: \R objects; \code{print}; arguments
+ to be passed to or from other methods.}
+ \item{x}{output from \code{object.size}}
+ \item{quote}{logical, indicating whether or not the result should be
+ printed with surrounding quotes.}
+ \item{humanReadable}{logical, use the \dQuote{human readable} format.}
+}
+\details{
+
+ This is a modified copy from the utils package in R as fo 2008-12-15.
+
+ Exactly which parts of the memory allocation should be attributed to
+ which object is not clear-cut. This function merely provides a rough
+ indication: it should be reasonably accurate for atomic vectors, but
+ does not detect if elements of a list are shared, for example.
+ (Sharing amongst elements of a character vector is taken into account,
+ but not that between character vectors in a single object.)
+
+ The calculation is of the size of the object, and excludes the space
+ needed to store its name in the symbol table.
+
+ Associated space (e.g. the environment of a function and what the
+ pointer in a \code{EXTPTRSXP} points to) is not included in the
+ calculation.
+
+ Object sizes are larger on 64-bit platforms than 32-bit ones, but will
+ very likely be the same on different platforms with the same word
+ length and pointer size.
+
+ % Modificitaion start
+ Class of returned object is \code{c("byte", "numeric")} with
+ appropriate \code{print} and \code{c} methods.
+
+ By default \code{object.size} outputs size in bytes, but human
+ readable format similar to \code{ls}, \code{df} or \code{du} shell
+ commands can be invoked with \code{options(humanReadable=TRUE)}.
+ % Modificitaion end
+
+}
+\value{
+ An object of class \code{"object.size"} with a length-one double value,
+ an estimate of the memory allocation attributable to the object in bytes.
+}
+\seealso{
+ \code{\link{Memory-limits}} for the design limitations on object size.
+ \code{\link{humanReadable}} for human readable format.
+}
+
+\examples{
+object.size(letters)
+object.size(ls)
+## find the 10 largest objects in the base package
+z <- sapply(ls("package:base"), function(x)
+ object.size(get(x, envir = baseenv())))
+(tmp <- as.matrix(rev(sort(z))[1:10]))
+
+as.object_size(14567567)
+options(humanReadable=TRUE)
+(z <- object.size(letters, c(letters, letters), rep(letters, 100), rep(letters, 10000)))
+is.object_size(z)
+as.object_size(14567567)
+}
+\keyword{utilities}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2008-12-31 13:29:09
|
Revision: 1310
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1310&view=rev
Author: ggorjan
Date: 2008-12-31 13:29:03 +0000 (Wed, 31 Dec 2008)
Log Message:
-----------
New function wideByFactor that reshapes given dataset by a given factor - it creates a "multivariate" data.frame.
Added Paths:
-----------
trunk/gdata/R/wideByFactor.R
trunk/gdata/inst/unitTests/runit.wideByFactor.R
trunk/gdata/man/wideByFactor.Rd
Added: trunk/gdata/R/wideByFactor.R
===================================================================
--- trunk/gdata/R/wideByFactor.R (rev 0)
+++ trunk/gdata/R/wideByFactor.R 2008-12-31 13:29:03 UTC (rev 1310)
@@ -0,0 +1,40 @@
+### wideByFactor.R
+###------------------------------------------------------------------------
+### What: Reshape by factor levels - code
+### $Id$
+### Time-stamp: <2008-12-30 22:17:32 ggorjan>
+###------------------------------------------------------------------------
+
+wideByFactor <- function(x, factor, common, sort=TRUE, keepFactor=TRUE)
+{
+ ## --- Setup ---
+ if(!is.data.frame(x)) stop("'x' must be a data frame")
+ if(length(factor) != 1) stop("'factor' can be only of length one")
+ if(!is.factor(x[[factor]])) stop("column defined in 'factor' must be a factor")
+ if(sort) x <- x[order(x[[factor]]), ]
+
+ ## --- Extend by factors levels ---
+ y <- x[common]
+ if(keepFactor) y[factor] <- x[factor]
+ levs <- levels(x[[factor]])
+
+ ## Remove common and factor from the list of column names
+ other <- names(x)
+ other <- other[!(other %in% common) & !(other %in% factor)]
+
+ ## Add all other columns but as a set for each level of a factor
+ for(level in levs) {
+ for(col in other) {
+ ## add a column col
+ y[paste(col, level, sep=".")] <- x[col]
+ ## fill with NA for other levels than level
+ y[x[factor] != level, paste(col, level, sep=".")] <- NA
+ ## This filling migth be inefficient if there is large number
+ ## of levels, since there will be quite a lot of filling.
+ }
+ }
+ y
+}
+
+###------------------------------------------------------------------------
+### wideByFactor.R ends here
\ No newline at end of file
Property changes on: trunk/gdata/R/wideByFactor.R
___________________________________________________________________
Added: svn:keywords
+
Added: trunk/gdata/inst/unitTests/runit.wideByFactor.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.wideByFactor.R (rev 0)
+++ trunk/gdata/inst/unitTests/runit.wideByFactor.R 2008-12-31 13:29:03 UTC (rev 1310)
@@ -0,0 +1,55 @@
+### runit.wideByFactor.R
+###------------------------------------------------------------------------
+### What: Reshape by factor levels - unit tests
+### $Id$
+### Time-stamp: <2008-12-30 11:58:50 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+ library("RUnit")
+ library("gdata")
+}
+
+### }}}
+### {{{ --- wideByFactor ---
+
+test.wideByFactor <- function()
+{
+ n <- 10
+ f <- 2
+ tmp <- data.frame(y1=(1:n)/2,
+ y2=(n:1)*2,
+ f1=factor(rep(letters[1:f], n/2)),
+ f2=factor(c(rep(c("M"), n/2), rep(c("F"), n/2))),
+ c1=1:n,
+ c2=2*(1:n))
+
+ ## 'x' must be a data.frame
+ checkException(wideByFactor(x=1:10))
+ checkException(wideByFactor(x=matrix(1:10)))
+ ## 'factor' can be only of length one
+ checkException(wideByFactor(x=tmp, factor=c("f1", "f2")))
+ ## column defined in 'factor' must be a factor
+ checkException(wideByFactor(x=tmp, factor="c1"))
+
+ tmp2 <- wideByFactor(x=tmp, factor="f1", common=c("c1", "c2"), sort=FALSE)
+ checkEquals(tmp2[c("c1", "c2")], tmp[c("c1", "c2")])
+ checkEquals(names(tmp2), c("c1", "c2", "f1", "y1.a", "y2.a", "f2.a", "y1.b", "y2.b", "f2.b"))
+ checkEquals(tmp2$y1.a, c(0.5, NA, 1.5, NA, 2.5, NA, 3.5, NA, 4.5, NA))
+ checkEquals(tmp2$f2.a, factor(c("M", NA, "M", NA, "M", NA, "F", NA, "F", NA)))
+ tmp2 <- wideByFactor(x=tmp, factor="f1", common=c("c1", "c2"), sort=TRUE, keepFactor=FALSE)
+ checkEquals(tmp2$f2.a, factor(c("M", "M", "M", "F", "F", NA, NA, NA, NA, NA)))
+ checkEquals(names(tmp2), c("c1", "c2", "y1.a", "y2.a", "f2.a", "y1.b", "y2.b", "f2.b"))
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.wideByFactor.R ends here
Property changes on: trunk/gdata/inst/unitTests/runit.wideByFactor.R
___________________________________________________________________
Added: svn:keywords
+
Added: trunk/gdata/man/wideByFactor.Rd
===================================================================
--- trunk/gdata/man/wideByFactor.Rd (rev 0)
+++ trunk/gdata/man/wideByFactor.Rd 2008-12-31 13:29:03 UTC (rev 1310)
@@ -0,0 +1,73 @@
+% wideByFactor.Rd
+%--------------------------------------------------------------------------
+% What: Reshape by factor levels - help
+% $Id$
+% Time-stamp: <2008-12-30 13:49:50 ggorjan>
+%--------------------------------------------------------------------------
+
+\name{wideByFactor}
+\alias{wideByFactor}
+
+\title{Create multivariate data by a given factor}
+
+\description{
+
+\code{wideByFactor} modifies data.frame in such a way that variables are
+\dQuote{separated} into several columns by factor levels.
+
+}
+
+\usage{
+ wideByFactor(x, factor, common, sort=TRUE, keepFactor=TRUE)
+}
+
+\arguments{
+ \item{x}{data frame}
+ \item{factor}{character, column name of a factor by which variables will
+ be divided}
+ \item{common}{character, column names of (common) columns that should not
+ be divided}
+ \item{sort}{logical, sort resulting data frame by factor levels}
+ \item{keepFactor}{logical, keep the \sQuote{factor} column}
+}
+
+\details{
+
+Given data frame is modified in such a way, that output represents a data frame
+with \eqn{c + f + n * v} columns, where \eqn{c} is a number of common columns
+for all levels of a factor, \eqn{f} is a factor column, \eqn{n} is a number of
+levels in factor \eqn{f} and \eqn{v} is a number of variables that should be
+divided for each level of a factor. Number of rows stays the same!
+}
+
+\value{
+ A data frame where divided variables have sort of \dQuote{diagonalized} structure
+}
+
+\author{Gregor Gorjanc}
+
+\seealso{
+ \code{\link[stats]{reshape}} in the \pkg{stats} package,
+ \code{\link[reshape]{melt}} and \code{\link[reshape]{cast}} in
+ the \pkg{reshape} package
+}
+
+\examples{
+n <- 10
+f <- 2
+tmp <- data.frame(y1=rnorm(n=n),
+ y2=rnorm(n=n),
+ f1=factor(rep(letters[1:f], n/2)),
+ f2=factor(c(rep(c("M"), n/2), rep(c("F"), n/2))),
+ c1=1:n,
+ c2=2*(1:n))
+
+wideByFactor(x=tmp, factor="f1", common=c("c1", "c2", "f2"))
+wideByFactor(x=tmp, factor="f1", common=c("c1", "c2"))
+}
+
+\keyword{manip}
+\keyword{misc}
+
+%--------------------------------------------------------------------------
+% wideByFactor.Rd ends here
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2008-12-31 13:28:05
|
Revision: 1309
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1309&view=rev
Author: ggorjan
Date: 2008-12-31 13:28:02 +0000 (Wed, 31 Dec 2008)
Log Message:
-----------
New function nPairs that gives the number of variable pairs in a data.frame or a matrix.
Added Paths:
-----------
trunk/gdata/R/nPairs.R
trunk/gdata/inst/unitTests/runit.nPairs.R
trunk/gdata/man/nPairs.Rd
Added: trunk/gdata/R/nPairs.R
===================================================================
--- trunk/gdata/R/nPairs.R (rev 0)
+++ trunk/gdata/R/nPairs.R 2008-12-31 13:28:02 UTC (rev 1309)
@@ -0,0 +1,49 @@
+### nPairs.R
+###------------------------------------------------------------------------
+### What: Number of variable pairs - code
+### $Id$
+### Time-stamp: <2008-12-30 18:29:58 ggorjan>
+###------------------------------------------------------------------------
+
+nPairs <- function(x, margin=FALSE, names=TRUE, abbrev=TRUE, ...)
+{
+ ## --- Setup ---
+ if(!is.data.frame(x) & !is.matrix(x)) stop("'x' must be a data.frame or a matrix")
+ k <- ncol(x)
+ if(!margin) {
+ ret <- matrix(nrow=k, ncol=k)
+ } else {
+ ret <- matrix(nrow=k, ncol=k + 1)
+ }
+
+ ## --- Count ---
+ diag(ret)[1:k] <- apply(X=x, MARGIN=2, FUN=function(x) sum(!is.na(x)))
+ for(i in 1:k) {
+ for(j in i:k) {
+ ret[i, j] <- ret[j, i] <- sum(!is.na(x[, i]) & !is.na(x[, j]))
+ if(margin) {
+ if(i == 1) {
+ ret[i, (k + 1)] <- ret[1, 1]
+ } else {
+ ret[i, (k + 1)] <- sum(rowSums(!is.na(x[, c(1:i)])) == i)
+ }
+ }
+ }
+ }
+
+ ## --- Names ---
+ if(names) {
+ tmp <- colnames(x)
+ if(abbrev) tmp <- as.character(abbreviate(tmp, ...))
+ rownames(ret) <- tmp
+ if(margin) {
+ colnames(ret) <- c(tmp, "all")
+ } else {
+ colnames(ret) <- tmp
+ }
+ }
+ ret
+}
+
+###------------------------------------------------------------------------
+### nPairs.R ends here
Property changes on: trunk/gdata/R/nPairs.R
___________________________________________________________________
Added: svn:keywords
+
Added: trunk/gdata/inst/unitTests/runit.nPairs.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.nPairs.R (rev 0)
+++ trunk/gdata/inst/unitTests/runit.nPairs.R 2008-12-31 13:28:02 UTC (rev 1309)
@@ -0,0 +1,56 @@
+### runit.nPairs.R
+###------------------------------------------------------------------------
+### What: Number of variable pairs - unit tests
+### $Id$
+### Time-stamp: <2008-12-30 18:24:59 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+ library("RUnit")
+ library("gdata")
+}
+
+### }}}
+### {{{ --- nPairs ---
+
+test.nPairs <- function()
+{
+ ## 'x' must be a data.frame or a matrix
+ x <- rpois(100, lambda=10)
+ checkException(nPairs(x=x))
+ checkException(nPairs(x=table(x)))
+
+ test <- data.frame(V1=c(1, 2, 3, 4, 5),
+ V2=c(NA, 2, 3, 4, 5),
+ V3=c(1, NA, NA, NA, NA),
+ V4=c(1, 2, 3, NA, NA))
+ testCheck <- matrix(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)
+
+ testCheckNames <- testCheck
+ colnames(testCheckNames) <- rownames(testCheckNames) <- colnames(test)
+
+ checkIdentical(nPairs(x=test), testCheckNames)
+ checkIdentical(nPairs(x=test, names=FALSE), testCheck)
+ checkIdentical(nPairs(x=as.matrix(test)), testCheckNames)
+ checkIdentical(nPairs(x=as.matrix(test), names=FALSE), testCheck)
+
+ testCheck <- cbind(testCheckNames, as.integer(c(5, 4, 0, 0)))
+ colnames(testCheck) <- c(colnames(test), "all")
+ checkIdentical(nPairs(x=test, margin=TRUE), testCheck)
+}
+
+### }}}
+### {{{ Dear Emacs
+### Local variables:
+### folded-file: t
+### end:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.nPairs.R ends here
Property changes on: trunk/gdata/inst/unitTests/runit.nPairs.R
___________________________________________________________________
Added: svn:keywords
+
Added: trunk/gdata/man/nPairs.Rd
===================================================================
--- trunk/gdata/man/nPairs.Rd (rev 0)
+++ trunk/gdata/man/nPairs.Rd 2008-12-31 13:28:02 UTC (rev 1309)
@@ -0,0 +1,73 @@
+% nPairs.Rd
+%--------------------------------------------------------------------------
+% What: Number of variable pairs - help
+% $Id$
+% Time-stamp: <2008-12-30 18:30:11 ggorjan>
+%--------------------------------------------------------------------------
+
+\name{nPairs}
+
+\alias{nPairs}
+
+\concept{pairs}
+
+\title{Number of variable pairs}
+
+\description{
+
+\code{nPairs} counts the number of pairs between variables.
+
+}
+
+\usage{
+nPairs(x, margin=FALSE, names=TRUE, abbrev=TRUE, ...)
+}
+
+\arguments{
+ \item{x}{data.frame or a matrix}
+ \item{margin}{logical, calculate the cumulative number of \dQuote{pairs}}
+ \item{names}{logical, add row/col-names to the output}
+ \item{abbrev}{logical, abbreviate names}
+ \item{\ldots}{other arguments passed to \code{\link{abbreviate}}}
+}
+
+\value{
+
+Matrix of order \eqn{k}, where \eqn{k} is the number of columns in \code{x}.
+Values in a matrix represent the number of pairs between columns/variables in
+\code{x}. If \code{margin=TRUE}, the number of columns is \eqn{k+1} and the
+last column represents the cumulative number of pairing all variables.
+
+}
+
+\author{Gregor Gorjanc}
+
+\seealso{\code{\link{abbreviate}}}
+
+\examples{
+
+## Test data
+test <- data.frame(V1=c(1, 2, 3, 4, 5),
+ V2=c(NA, 2, 3, 4, 5),
+ V3=c(1, NA, NA, NA, NA),
+ V4=c(1, 2, 3, NA, NA))
+
+## Number of variable pairs
+nPairs(x=test)
+
+## Without names
+nPairs(x=test, names=FALSE)
+
+## Longer names
+colnames(test) <- c("Variable1", "Variable2", "Variable3", "Variable4")
+nPairs(x=test)
+
+## Margin
+nPairs(x=test, margin=TRUE)
+
+}
+
+\keyword{misc}
+
+%--------------------------------------------------------------------------
+% nPairs.Rd ends here
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2008-12-31 13:27:01
|
Revision: 1308
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1308&view=rev
Author: ggorjan
Date: 2008-12-31 13:26:51 +0000 (Wed, 31 Dec 2008)
Log Message:
-----------
New functions getYear, getMonth, getDay, getHour, getMin, and getSec for extracting the date/time parts from objects of a date/time class.
Added Paths:
-----------
trunk/gdata/R/getDateTimeParts.R
trunk/gdata/inst/unitTests/runit.getDateTimeParts.R
trunk/gdata/man/getDateTimePart.Rd
Added: trunk/gdata/R/getDateTimeParts.R
===================================================================
--- trunk/gdata/R/getDateTimeParts.R (rev 0)
+++ trunk/gdata/R/getDateTimeParts.R 2008-12-31 13:26:51 UTC (rev 1308)
@@ -0,0 +1,90 @@
+### getDateTimePart.R
+###------------------------------------------------------------------------
+### What: Extract date and time parts from various date and time classes
+### $Id$
+### Time-stamp: <2008-12-30 22:42:58 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ getYear
+###------------------------------------------------------------------------
+
+getYear <- function(x, format, ...)
+ UseMethod("getYear")
+
+getYear.default <- function(x, format, ...)
+ stop("'getYear' can only be used on objects of a date/time class")
+
+getYear.Date <-
+getYear.POSIXct <-
+getYear.POSIXlt <- function(x, format="%Y", ...)
+ format(x=x, format=format, ...)
+
+### }}}
+### {{{ getMonth
+###------------------------------------------------------------------------
+
+getMonth <- function(x, format, ...)
+ UseMethod("getMonth")
+
+getMonth.default <- function(x, format, ...)
+ stop("'getMonth' can only be used on objects of a date/time class")
+
+getMonth.Date <-
+getMonth.POSIXct <-
+getMonth.POSIXlt <- function(x, format="%m", ...)
+ format(x=x, format=format)
+
+### }}}
+### {{{ getDay
+###------------------------------------------------------------------------
+
+getDay <- function(x, format, ...)
+ UseMethod("getDay")
+
+getDay.default <- function(x, format, ...)
+ stop("'getDay' can only be used on objects of a date/time class")
+
+getDay.Date <-
+getDay.POSIXct <-
+getDay.POSIXlt <- function(x, format="%d", ...)
+ format(x=x, format=format)
+
+### }}}
+### {{{ getHour
+###------------------------------------------------------------------------
+
+getHour <- function(x, format, ...)
+ UseMethod("getHour")
+
+getHour.default <- function(x, format, ...)
+ stop("'getHour' can only be used on objects of a date/time class")
+
+### }}}
+### {{{ getMin
+###------------------------------------------------------------------------
+
+getMin <- function(x, format, ...)
+ UseMethod("getMin")
+
+getMin.default <- function(x, format, ...)
+ stop("'getMin' can only be used on objects of a date/time class")
+
+### }}}
+### {{{ getSec
+###------------------------------------------------------------------------
+
+getSec <- function(x, format, ...)
+ UseMethod("getSec")
+
+getSec.default <- function(x, format, ...)
+ stop("'getSec' can only be used on objects of a date/time class")
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### getDateTimePart.R ends here
\ No newline at end of file
Property changes on: trunk/gdata/R/getDateTimeParts.R
___________________________________________________________________
Added: svn:keywords
+
Added: trunk/gdata/inst/unitTests/runit.getDateTimeParts.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.getDateTimeParts.R (rev 0)
+++ trunk/gdata/inst/unitTests/runit.getDateTimeParts.R 2008-12-31 13:26:51 UTC (rev 1308)
@@ -0,0 +1,121 @@
+### runit.getDateTimeParts.R
+###------------------------------------------------------------------------
+### What: Extract date and time parts from ... - unit tests
+### $Id$
+### Time-stamp: <2008-12-30 22:41:18 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+ library("RUnit")
+ library("gdata")
+}
+
+num <- 1
+cha <- "a"
+fac <- factor(c("A"))
+
+tYear <- as.character(c(2006, 1995, 1005, 3067))
+tMonth <- c("01", "04", "06", "12")
+tDay <- c("01", "12", "22", "04")
+tDate <- paste(tYear, tMonth, tDay, sep="-")
+
+tHour <- c("05", "16", "20", "03")
+tMin <- c("16", "40", "06", "52")
+tSec <- c("56", "34", "05", "15")
+tTime <- paste(tHour, tMin, tSec, sep=":")
+
+# tDateTime <- paste()
+
+cDate <- as.Date(tDate)
+cDatePOSIXct <- as.POSIXct(cDate)
+cDatePOSIXlt <- as.POSIXlt(cDate)
+
+### }}}
+### {{{ --- getYear ---
+
+test.getYear <- function()
+{
+ checkException(getYear(x=num))
+ checkException(getYear(x=cha))
+ checkException(getYear(x=fac))
+
+ checkIdentical(getYear(x=cDate), tYear)
+ checkIdentical(getYear(x=cDatePOSIXct), tYear)
+ checkIdentical(getYear(x=cDatePOSIXlt), tYear)
+}
+
+### }}}
+### {{{ --- getMonth ---
+
+test.getMonth <- function()
+{
+ checkException(getMonth(x=num))
+ checkException(getMonth(x=cha))
+ checkException(getMonth(x=fac))
+
+ checkIdentical(getMonth(x=cDate), tMonth)
+ checkIdentical(getMonth(x=cDatePOSIXct), tMonth)
+ checkIdentical(getMonth(x=cDatePOSIXlt), tMonth)
+}
+
+### }}}
+### {{{ --- getDay ---
+
+test.getDay <- function()
+{
+ checkException(getDay(x=num))
+ checkException(getDay(x=cha))
+ checkException(getDay(x=fac))
+
+ checkIdentical(getDay(x=cDate), tDay)
+ checkIdentical(getDay(x=cDatePOSIXct), tDay)
+ checkIdentical(getDay(x=cDatePOSIXlt), tDay)
+}
+
+### }}}
+### {{{ --- getHour ---
+
+test.getHour <- function()
+{
+ checkException(getHour(x=num))
+ checkException(getHour(x=cha))
+ checkException(getHour(x=fac))
+
+## checkIdentical(getHour(x=cDate), tHour)
+}
+
+### }}}
+### {{{ --- getMin ---
+
+test.getMin <- function()
+{
+ checkException(getMin(x=num))
+ checkException(getMin(x=cha))
+ checkException(getMin(x=fac))
+
+## checkIdentical(getMin(x=cDate), tMin)
+}
+
+### }}}
+### {{{ --- getSec ---
+
+test.getSec <- function()
+{
+ checkException(getSec(x=num))
+ checkException(getSec(x=cha))
+ checkException(getSec(x=fac))
+
+## checkIdentical(getSec(x=cDate), tSec)
+}
+
+### }}}
+### {{{ Dear Emacs
+### Local variables:
+### folded-file: t
+### end:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.getDateTimeParts.R ends here
Property changes on: trunk/gdata/inst/unitTests/runit.getDateTimeParts.R
___________________________________________________________________
Added: svn:keywords
+
Added: trunk/gdata/man/getDateTimePart.Rd
===================================================================
--- trunk/gdata/man/getDateTimePart.Rd (rev 0)
+++ trunk/gdata/man/getDateTimePart.Rd 2008-12-31 13:26:51 UTC (rev 1308)
@@ -0,0 +1,106 @@
+% getDateTimeParts.Rd
+%--------------------------------------------------------------------------
+% What: Extract date and time parts from ... - help
+% $Id$
+% Time-stamp: <2008-12-30 22:44:20 ggorjan>
+%--------------------------------------------------------------------------
+
+\name{getYear}
+
+\alias{getDateTimeParts}
+\alias{getYear}
+\alias{getYear.default}
+\alias{getYear.Date}
+\alias{getYear.POSIXct}
+\alias{getYear.POSIXlt}
+
+\alias{getMonth}
+\alias{getMonth.default}
+\alias{getMonth.Date}
+\alias{getMonth.POSIXct}
+\alias{getMonth.POSIXlt}
+
+\alias{getDay}
+\alias{getDay.default}
+\alias{getDay.Date}
+\alias{getDay.POSIXct}
+\alias{getDay.POSIXlt}
+
+\alias{getHour}
+\alias{getHour.default}
+
+\alias{getMin}
+\alias{getMin.default}
+
+\alias{getSec}
+\alias{getSec.default}
+
+\title{Get date/time parts from date and time objects}
+
+\description{get* functions provide an *experimental* approach for
+ extracting the date/time parts from objects of a date/time class.
+ They are designed to be intiutive and thus lowering the learning
+ curve for work with date and time classes in \R{}.}
+
+\usage{
+
+getYear(x, format, \ldots)
+getMonth(x, format, \ldots)
+getDay(x, format, \ldots)
+getHour(x, format, \ldots)
+getMin(x, format, \ldots)
+getSec(x, format, \ldots)
+
+}
+
+
+\arguments{
+ \item{x}{generic, date/time object}
+ \item{format}{character, format}
+ \item{\ldots}{arguments pased to other methods}
+}
+
+\value{Character}
+
+\author{Gregor Gorjanc}
+
+\seealso{
+ \code{\link{Date}},
+ \code{\link{DateTimeClasses}},
+ \code{\link{strptime}}
+}
+
+\examples{
+
+## --- Date class ---
+
+tmp <- Sys.Date()
+tmp
+
+getYear(tmp)
+getMonth(tmp)
+getDay(tmp)
+
+## --- POSIXct class ---
+
+tmp <- as.POSIXct(tmp)
+
+getYear(tmp)
+getMonth(tmp)
+getDay(tmp)
+
+## --- POSIXlt class ---
+
+tmp <- as.POSIXlt(tmp)
+
+getYear(tmp)
+getMonth(tmp)
+getDay(tmp)
+
+}
+
+\keyword{manip}
+\keyword{misc}
+
+%--------------------------------------------------------------------------
+% getDateTimeParts.Rd ends here
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2008-12-31 13:26:03
|
Revision: 1307
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1307&view=rev
Author: ggorjan
Date: 2008-12-31 13:25:52 +0000 (Wed, 31 Dec 2008)
Log Message:
-----------
New function bindData that binds two data frames into a multivariate data frame in a different way than merge.
Added Paths:
-----------
trunk/gdata/R/bindData.R
trunk/gdata/inst/unitTests/runit.bindData.R
trunk/gdata/man/bindData.Rd
Added: trunk/gdata/R/bindData.R
===================================================================
--- trunk/gdata/R/bindData.R (rev 0)
+++ trunk/gdata/R/bindData.R 2008-12-31 13:25:52 UTC (rev 1307)
@@ -0,0 +1,38 @@
+### bindData.R
+###------------------------------------------------------------------------
+### What: Bind two data frames - code
+### $Id$
+### Time-stamp: <2008-12-30 22:01:00 ggorjan>
+###------------------------------------------------------------------------
+
+bindData <- function(x, y, common)
+{
+ ## --- Setup ---
+ if(!is.data.frame(x)) stop("'x' must be a data frame")
+ if(!is.data.frame(y)) stop("'y' must be a data frame")
+
+ ## --- New data frame ---
+
+ ## First add common column and a dataset indicator column
+ z <- rbind(x[common], y[common])
+
+ ## Other columns
+ ## - remove common columns in x and y
+ namesz <- names(z)
+ otherx <- names(x)
+ otherx <- otherx[!(otherx %in% namesz)]
+ othery <- names(y)
+ othery <- othery[!(othery %in% namesz)]
+
+ ## - add all other columns but as a set for each input data frame
+ rx <- nrow(x); cx <- length(otherx)
+ ry <- nrow(y); cy <- length(othery)
+
+ z <- cbind(z, rbind(x[otherx], matrix(rep(NA, times=(ry * cx)), nrow=ry, ncol=cx, dimnames=list(NULL, otherx))))
+ z <- cbind(z, rbind(matrix(rep(NA, times=(rx * cy)), nrow=rx, ncol=cy, dimnames=list(NULL, othery)), y[othery]))
+
+ z
+}
+
+###------------------------------------------------------------------------
+### bindData.R ends here
Property changes on: trunk/gdata/R/bindData.R
___________________________________________________________________
Added: svn:keywords
+
Added: trunk/gdata/inst/unitTests/runit.bindData.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.bindData.R (rev 0)
+++ trunk/gdata/inst/unitTests/runit.bindData.R 2008-12-31 13:25:52 UTC (rev 1307)
@@ -0,0 +1,75 @@
+### runit.bindData.R
+###------------------------------------------------------------------------
+### What: Bind two data frames - unit tests
+### $Id$
+### Time-stamp: <2008-12-30 11:58:50 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+ library("RUnit")
+ library("gdata")
+}
+
+### }}}
+### {{{ --- bindData ---
+
+test.bindData <- function()
+{
+ ## 'x'/'y' must be a data.frame
+ checkException(bindData(x=1:10, y=1:10))
+ checkException(bindData(x=matrix(1:10), y=matrix(1:10)))
+
+ n1 <- 6; n2 <- 12; n3 <- 4
+ ## Single trait 1
+ num <- c(5:n1, 10:13)
+ tmp1 <- data.frame(y1=rnorm(n=n1),
+ f1=factor(rep(c("A", "B"), n1/2)),
+ ch=letters[num],
+ fa=factor(letters[num]),
+ nu=(num) + 0.5,
+ id=factor(num), stringsAsFactors=FALSE)
+
+ ## Single trait 2 with repeated records, some subjects also in tmp1
+ num <- 4:9
+ tmp2 <- data.frame(y2=rnorm(n=n2),
+ f2=factor(rep(c("C", "D"), n2/2)),
+ ch=letters[rep(num, times=2)],
+ fa=factor(letters[rep(c(num), times=2)]),
+ nu=c((num) + 0.5, (num) + 0.25),
+ id=factor(rep(num, times=2)), stringsAsFactors=FALSE)
+
+ ## Single trait 3 with completely distinct set of subjects
+ num <- 1:4
+ tmp3 <- data.frame(y3=rnorm(n=n3),
+ f3=factor(rep(c("E", "F"), n3/2)),
+ ch=letters[num],
+ fa=factor(letters[num]),
+ nu=(num) + 0.5,
+ id=factor(num), stringsAsFactors=FALSE)
+
+ ## Combine all datasets
+ tmp12 <- bindData(x=tmp1, y=tmp2, common=c("id", "nu", "ch", "fa"))
+ tmp123 <- bindData(x=tmp12, y=tmp3, common=c("id", "nu", "ch", "fa"))
+
+ checkEquals(names(tmp123), c("id", "nu", "ch", "fa", "y1", "f1", "y2", "f2", "y3", "f3"))
+ checkEquals(rbind(tmp1["id"], tmp2["id"], tmp3["id"]), tmp123["id"])
+ checkEquals(rbind(tmp1["fa"], tmp2["fa"], tmp3["fa"]), tmp123["fa"])
+ checkEquals(is.na(tmp123$y1), c(rep(FALSE, times=n1), rep(TRUE, times=n2+n3)))
+ checkEquals(is.na(tmp123$f1), c(rep(FALSE, times=n1), rep(TRUE, times=n2+n3)))
+ checkEquals(is.na(tmp123$y2), c(rep(TRUE, times=n1), rep(FALSE, times=n2), rep(TRUE, times=n3)))
+ checkEquals(is.na(tmp123$f2), c(rep(TRUE, times=n1), rep(FALSE, times=n2), rep(TRUE, times=n3)))
+ checkEquals(is.na(tmp123$y3), c(rep(TRUE, times=n1+n2), rep(FALSE, times=n3)))
+ checkEquals(is.na(tmp123$f3), c(rep(TRUE, times=n1+n2), rep(FALSE, times=n3)))
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.bindData.R ends here
Property changes on: trunk/gdata/inst/unitTests/runit.bindData.R
___________________________________________________________________
Added: svn:keywords
+
Added: trunk/gdata/man/bindData.Rd
===================================================================
--- trunk/gdata/man/bindData.Rd (rev 0)
+++ trunk/gdata/man/bindData.Rd 2008-12-31 13:25:52 UTC (rev 1307)
@@ -0,0 +1,93 @@
+% bindData.Rd
+%--------------------------------------------------------------------------
+% What: Bind two data frames - help
+% $Id$
+% Time-stamp: <2008-12-30 13:49:50 ggorjan>
+%--------------------------------------------------------------------------
+
+\name{bindData}
+\alias{bindData}
+
+\title{Bind two data frames into a multivariate data frame}
+
+\description{
+ Usually data frames represent one set of variables and one needs to
+ bind/join them for multivariate analysis. When \code{\link{merge}} is not
+ the approriate solution, \code{bindData} might perform an appropriate binding
+ for two data frames. This is especially usefull when some variables are
+ measured once, while others are repeated.
+}
+
+\usage{
+ bindData(x, y, common)
+}
+
+\arguments{
+ \item{x}{data.frame}
+ \item{y}{data.frame}
+ \item{common}{character, list of column names that are common to both
+ input data frames}
+}
+
+\details{
+ Data frames are joined in a such a way, that the new data frame has
+ \eqn{c + (n_1 - c) + (n_2 - c)} columns, where \eqn{c} is the number of
+ common columns, and \eqn{n_1} and \eqn{n_2} are the number of columns
+ in the first and in the second data frame, respectively.
+}
+
+\value{
+ A data frame.
+}
+
+\author{Gregor Grojanc}
+
+\seealso{
+ \code{\link[base]{merge}},
+ \code{\link{wideByFactor}}
+}
+
+\examples{
+n1 <- 6
+n2 <- 12
+n3 <- 4
+## Single trait 1
+num <- c(5:n1, 10:13)
+(tmp1 <- data.frame(y1=rnorm(n=n1),
+ f1=factor(rep(c("A", "B"), n1/2)),
+ ch=letters[num],
+ fa=factor(letters[num]),
+ nu=(num) + 0.5,
+ id=factor(num), stringsAsFactors=FALSE))
+
+## Single trait 2 with repeated records, some subjects also in tmp1
+num <- 4:9
+(tmp2 <- data.frame(y2=rnorm(n=n2),
+ f2=factor(rep(c("C", "D"), n2/2)),
+ ch=letters[rep(num, times=2)],
+ fa=factor(letters[rep(c(num), times=2)]),
+ nu=c((num) + 0.5, (num) + 0.25),
+ id=factor(rep(num, times=2)), stringsAsFactors=FALSE))
+
+## Single trait 3 with completely distinct set of subjects
+num <- 1:4
+(tmp3 <- data.frame(y3=rnorm(n=n3),
+ f3=factor(rep(c("E", "F"), n3/2)),
+ ch=letters[num],
+ fa=factor(letters[num]),
+ nu=(num) + 0.5,
+ id=factor(num), stringsAsFactors=FALSE))
+
+## Combine all datasets
+(tmp12 <- bindData(x=tmp1, y=tmp2, common=c("id", "nu", "ch", "fa")))
+(tmp123 <- bindData(x=tmp12, y=tmp3, common=c("id", "nu", "ch", "fa")))
+
+## Sort by subject
+tmp123[order(tmp123$ch), ]
+}
+
+\keyword{manip}
+\keyword{misc}
+
+%--------------------------------------------------------------------------
+% bindData.Rd ends here
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2008-12-31 13:24:53
|
Revision: 1306
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1306&view=rev
Author: ggorjan
Date: 2008-12-31 13:24:42 +0000 (Wed, 31 Dec 2008)
Log Message:
-----------
New function .runRUnitTestsGdata that enables run of all RUnit tests during the R CMD check as well as directly from within R.
Modified Paths:
--------------
trunk/gdata/inst/unitTests/Makefile
trunk/gdata/man/gdata-package.Rd
Added Paths:
-----------
trunk/gdata/R/runRUnitTests.R
trunk/gdata/inst/unitTests/runRUnitTests.R
trunk/gdata/man/runRUnitTests.Rd
Removed Paths:
-------------
trunk/gdata/tests/doRUnit.R
Added: trunk/gdata/R/runRUnitTests.R
===================================================================
--- trunk/gdata/R/runRUnitTests.R (rev 0)
+++ trunk/gdata/R/runRUnitTests.R 2008-12-31 13:24:42 UTC (rev 1306)
@@ -0,0 +1,27 @@
+### runRUnitTests.R
+###------------------------------------------------------------------------
+### What: Run RUnit tests (wrapper function) - R code
+### $Id$
+### Time-stamp: <2008-12-30 20:59:11 ggorjan>
+###------------------------------------------------------------------------
+
+.runRUnitTestsGdata <- function(testFileRegexp="^runit.+\\.[rR]$")
+{
+ ## Setup
+ .pkg <- environmentName(environment(.runRUnitTestsGdata))
+ .path <- system.file("unitTests", package=.pkg)
+ .suite <- file.path(.path, "runRUnitTests.R")
+
+ ## Some checks
+ stopifnot(file.exists(.path),
+ file.info(path.expand(.path))$isdir,
+ file.exists(.suite))
+
+ ## Run the suite
+ .way <- "function"
+ source(.suite, local=TRUE)
+ ## local=TRUE since .pkg and other vars do not exists in .suite environment
+}
+
+###------------------------------------------------------------------------
+### runRUnitTests.R ends here
Property changes on: trunk/gdata/R/runRUnitTests.R
___________________________________________________________________
Added: svn:keywords
+
Modified: trunk/gdata/inst/unitTests/Makefile
===================================================================
--- trunk/gdata/inst/unitTests/Makefile 2008-12-20 22:34:57 UTC (rev 1305)
+++ trunk/gdata/inst/unitTests/Makefile 2008-12-31 13:24:42 UTC (rev 1306)
@@ -1,18 +1,16 @@
TOP=../..
PKG=${shell cd ${TOP};pwd}
-SUITE=doRUnit.R
-R=${R_HOME}/bin/R
+SUITE=runRUnitTests.R
+R=R
-all: inst test
+test: # Run unit tests
+ ${R} --vanilla --slave < ${SUITE}
inst: # Install package
cd ${TOP}/..;\
${R} CMD INSTALL ${PKG}
-test: # Run unit tests
- export RCMDCHECK=FALSE;\
- cd ${TOP}/tests;\
- ${R} --vanilla --slave < ${SUITE}
+all: inst test
echo: # Echo env. variables
@echo "Package folder: ${PKG}"
Added: trunk/gdata/inst/unitTests/runRUnitTests.R
===================================================================
--- trunk/gdata/inst/unitTests/runRUnitTests.R (rev 0)
+++ trunk/gdata/inst/unitTests/runRUnitTests.R 2008-12-31 13:24:42 UTC (rev 1306)
@@ -0,0 +1,104 @@
+### runRUnitTests.R
+###------------------------------------------------------------------------
+### What: Run RUnit tests (the core)- R code
+### $Id$
+### Time-stamp: <2008-12-30 12:52:51 ggorjan>
+###------------------------------------------------------------------------
+
+## The setup seems to be quite messy, but it is so to enable use of this in
+## several ways as shown bellow.
+
+## "R CMD check" way should be the most authoritative way to run the RUnit
+## tests for a developer. RUnit tests are issued during R CMD check of the
+## package due to example section of .runRUnitTests() function. If any test
+## fails (failure) or if there are any R errors during RUnit testing, R CMD
+## check fails. These are variable values specific for this way:
+## - .path DEVEL/PATH/PKG.Rcheck/PKG/unitTests
+## - .way function
+
+## ".runRUnitTests()" way from within R after library(PKG) is handy for
+## package useRs, since it enables useRs to be sure that all tests pass for
+## their installation. This is just a convenient wrapper function to run
+## the RUnit testing suite. These are variable values specific for this
+## way:
+## - .path INSTALL/PATH/PKG/unitTests
+## - .way function
+
+## "Shell" way is another possibility mainly for a developer in order to
+## skip possibly lengthy R CMD check and perform just RUnit testing with an
+## installed version of a pcakage. These are variable values specific for
+## this way:
+## - .path DEVEL/PATH/PKG/inst/unitTests
+## - .way shell
+##
+## Rscript runRUnitTests.R
+## R CMD BATCH runRUnitTests.R
+## make
+## make all
+
+## Sourced via shell (Makefile, Rscript, R CMD BATCH)
+if(!exists(".pkg")) {
+ .path <- getwd()
+ .way <- "shell"
+ .pkg <- c(read.dcf(file="../../DESCRIPTION", fields="Package"))
+ print(.pkg)
+ testFileRegexp <- "^base.+\\.[rR]$"
+}
+
+if(require("RUnit", quietly=TRUE)) {
+
+ ## Debugging echo
+ cat("\nRunning RUnit tests\n")
+ print(list(pkg=.pkg, getwd=getwd(), pathToRUnitTests=.path))
+
+ ## Load the package - not needed for .runRUnitTests()
+ if(.way %in% c("shell"))
+ library(package=.pkg, character.only=TRUE)
+
+ ## Define tests
+ testSuite <- defineTestSuite(name=paste(.pkg, "RUnit testing"),
+ dirs=.path, testFileRegexp=testFileRegexp)
+
+ ## Run
+ tests <- runTestSuite(testSuite)
+
+ if(file.access(.path, 02) != 0) {
+ ## cannot write to .path -> use writable one
+ tdir <- tempfile(paste(.pkg, "RUnitTests", sep="_"))
+ dir.create(tdir)
+ pathReport <- file.path(tdir, "report")
+ } else {
+ pathReport <- file.path(.path, "report")
+ }
+
+ ## Print results:
+ printTextProtocol(tests)
+ printTextProtocol(tests,
+ fileName=paste(pathReport, ".txt", sep=""))
+
+ ## Print HTML Version of results:
+ printHTMLProtocol(tests,
+ fileName=paste(pathReport, ".html", sep=""))
+
+ cat("\nRUnit reports also written to\n",
+ pathReport, ".(txt|html)\n\n", sep="")
+
+ ## Return stop() to cause R CMD check stop in case of
+ ## - failures i.e. FALSE to RUnit tests or
+ ## - errors i.e. R errors
+ tmp <- getErrors(tests)
+ if(tmp$nFail > 0 || tmp$nErr > 0) {
+ stop(paste("\n\nRUnit testing failed:\n",
+ " - #test failures: ", tmp$nFail, "\n",
+ " - #R errors: ", tmp$nErr, "\n\n", sep=""))
+ }
+
+} else {
+
+ cat("R package 'RUnit' cannot be loaded - no unit tests run\n",
+ "for package", .pkg,"\n")
+
+}
+
+###------------------------------------------------------------------------
+### runRUnitTests.R ends here
Property changes on: trunk/gdata/inst/unitTests/runRUnitTests.R
___________________________________________________________________
Added: svn:keywords
+
Modified: trunk/gdata/man/gdata-package.Rd
===================================================================
--- trunk/gdata/man/gdata-package.Rd 2008-12-20 22:34:57 UTC (rev 1305)
+++ trunk/gdata/man/gdata-package.Rd 2008-12-31 13:24:42 UTC (rev 1306)
@@ -32,4 +32,13 @@
}
+\section{Testing}{
+
+If you want to perform the validity/unit testing of the installed
+\pkg{ggmisc} package on your own computer, take a look at
+\code{\link{.runRUnitTestsGdata}} function - please note that
+you need the \pkg{RUnit} package for this to work.
+
+}
+
\keyword{package}
\ No newline at end of file
Added: trunk/gdata/man/runRUnitTests.Rd
===================================================================
--- trunk/gdata/man/runRUnitTests.Rd (rev 0)
+++ trunk/gdata/man/runRUnitTests.Rd 2008-12-31 13:24:42 UTC (rev 1306)
@@ -0,0 +1,54 @@
+% runRUnitTests.Rd
+%--------------------------------------------------------------------------
+% What: Run RUnit tests - help
+% $Id$
+% Time-stamp: <2008-12-30 20:58:26 ggorjan>
+%--------------------------------------------------------------------------
+
+\name{.runRUnitTestsGdata}
+\alias{.runRUnitTestsGdata}
+
+\title{Run RUnit tests for the gdata package}
+
+\description{
+
+Run \pkg{RUnit} tests to perform the validity/unit testing of installed
+\pkg{gdata} package on your own computer.
+
+}
+
+\usage{.runRUnitTestsGdata(testFileRegexp="^runit.+\\\\.[rR]$")}
+
+\arguments{
+ \item{testFileRegexp}{regular expression; see details}
+}
+
+\details{
+
+Argument \code{testFileRegexp} can be used to specify different sets of
+tests provided by the package. The following values are sensible:
+\itemize{
+ \item \code{"^runit.+\\\\.[rR]$"} for basic tests
+}
+
+}
+
+\value{
+
+None, just the print out of \pkg{RUnit} testing.
+
+}
+
+\seealso{
+ \code{\link[RUnit]{defineTestSuite}} in \pkg{RUnit} package
+}
+
+\examples{
+ ## Basic testing
+ .runRUnitTestsGdata()
+}
+
+\keyword{misc}
+
+%--------------------------------------------------------------------------
+% runRUnitTests.Rd ends here
Deleted: trunk/gdata/tests/doRUnit.R
===================================================================
--- trunk/gdata/tests/doRUnit.R 2008-12-20 22:34:57 UTC (rev 1305)
+++ trunk/gdata/tests/doRUnit.R 2008-12-31 13:24:42 UTC (rev 1306)
@@ -1,63 +0,0 @@
-### doRUnit.R
-###------------------------------------------------------------------------
-### What: Run unit tests with RUnit
-### $Id$
-### Time-stamp: <2007-06-06 14:02:41 ggorjan>
-###------------------------------------------------------------------------
-
-## unit tests will not be done if RUnit is not available
-if(require("RUnit", quietly=TRUE)) {
-
- ## --- Setup ---
-
- pkg <- "gdata"
- if(Sys.getenv("RCMDCHECK") == "FALSE") {
- ## Path to unit tests for standalone running under Makefile (not R CMD check)
- ## PKG/tests/../inst/unitTests
- path <- file.path(getwd(), "..", "inst", "unitTests")
- } else {
- ## Path to unit tests for R CMD check
- ## PKG.Rcheck/tests/../PKG/unitTests
- path <- system.file(package=pkg, "unitTests")
- }
- cat("\nRunning unit tests\n")
- print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
-
- library(package=pkg, character.only=TRUE)
-
- ## --- Testing ---
-
- ## Define tests
- testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
- dirs=path)
- ## Run
- tests <- runTestSuite(testSuite)
-
- ## Default report name
- pathReport <- file.path(path, "report")
-
- ## Report to stdout and text files
- cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
- printTextProtocol(tests, showDetails=FALSE)
- printTextProtocol(tests, showDetails=FALSE,
- fileName=paste(pathReport, "Summary.txt", sep=""))
- printTextProtocol(tests, showDetails=TRUE,
- fileName=paste(pathReport, ".txt", sep=""))
-
- ## Report to HTML file
- printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
-
- ## Return stop() to cause R CMD check stop in case of
- ## - failures i.e. FALSE to unit tests or
- ## - errors i.e. R errors
- tmp <- getErrors(tests)
- if(tmp$nFail > 0 | tmp$nErr > 0) {
- stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
- ", #R errors: ", tmp$nErr, ")\n\n", sep=""))
- }
-} else {
- warning("cannot run unit tests -- package RUnit is not available")
-}
-
-###------------------------------------------------------------------------
-### doRUnit.R ends here
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2008-12-20 22:35:01
|
Revision: 1305
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1305&view=rev
Author: ggorjan
Date: 2008-12-20 22:34:57 +0000 (Sat, 20 Dec 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/gdata/NAMESPACE
trunk/gdata/inst/NEWS
Added Paths:
-----------
trunk/gdata/R/trimSum.R
trunk/gdata/inst/unitTests/runit.trimSum.R
trunk/gdata/man/trimSum.Rd
Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE 2008-12-20 22:28:35 UTC (rev 1304)
+++ trunk/gdata/NAMESPACE 2008-12-20 22:34:57 UTC (rev 1305)
@@ -23,6 +23,7 @@
reorder.factor,
resample,
trim,
+ trimSum,
unmatrix,
upperTriangle,
"upperTriangle<-",
Added: trunk/gdata/R/trimSum.R
===================================================================
--- trunk/gdata/R/trimSum.R (rev 0)
+++ trunk/gdata/R/trimSum.R 2008-12-20 22:34:57 UTC (rev 1305)
@@ -0,0 +1,37 @@
+### trimSum.R
+###------------------------------------------------------------------------
+### What: Sum trimmed values - code
+### $Id$
+### Time-stamp: <2008-12-20 12:11:27 ggorjan>
+###------------------------------------------------------------------------
+
+trimSum <- function(x, n, right=TRUE, na.rm=FALSE, ...)
+{
+ ## --- Setup ---
+
+ if(!is.vector(x) | is.list(x))
+ stop("'x' must be a vector - for now")
+ if(!is.numeric(x))
+ stop("'x' must be numeric")
+ if(length(x) <= n)
+ stop("'n' must be smaller than the length of x")
+
+ ## --- Trim ---
+
+ N <- length(x)
+ if(right) {
+ x2 <- x[1:n]
+ x2[n] <- sum(x[n:N], na.rm=na.rm)
+ } else {
+ k <- (N - n + 1)
+ x2 <- x[k:N]
+ x2[1] <- sum(x[1:k], na.rm=na.rm)
+ }
+
+ ## --- Return ---
+
+ x2
+}
+
+###------------------------------------------------------------------------
+### trimSum.R ends here
Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS 2008-12-20 22:28:35 UTC (rev 1304)
+++ trunk/gdata/inst/NEWS 2008-12-20 22:34:57 UTC (rev 1305)
@@ -1,6 +1,8 @@
CHANGES IN 2.5.0 (2008-??-??)
-----------------------------
+- New function trimSum that sums trimmed values
+
- New function cbindX that can bind objects with different number of rows.
- write.fwf gains width argument. Unknown values can increase or decrease
Added: trunk/gdata/inst/unitTests/runit.trimSum.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.trimSum.R (rev 0)
+++ trunk/gdata/inst/unitTests/runit.trimSum.R 2008-12-20 22:34:57 UTC (rev 1305)
@@ -0,0 +1,61 @@
+### runit.trimSum.R
+###------------------------------------------------------------------------
+### What: Unit tests for trimSum
+### $Id$
+### Time-stamp: <2008-12-20 11:58:50 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+ library("RUnit")
+ library("gdata")
+}
+
+### }}}
+### {{{ --- trimSum ---
+
+test.trimSum <- function()
+{
+
+ ## 'x' must be a vector - for now
+ checkException(trimSum(matrix(1:10)))
+ checkException(trimSum(data.frame(1:10)))
+ checkException(trimSum(list(1:10)))
+
+ ## 'x' must be numeric
+ checkException(trimSum(letters))
+
+ ## 'n' must be smaller than the length of x
+ checkException(trimSum(x=1:10, n=11))
+ checkException(trimSum(x=1, n=1))
+
+ ## Default
+ x <- trimSum(x=1:10, n=5)
+ x2 <- c(1:4, 45)
+ checkEquals(x, x2)
+
+ ## Left
+ x <- trimSum(x=1:10, n=5, right=FALSE)
+ x2 <- c(21, 7:10)
+ checkEquals(x, x2)
+
+ ## NA
+ x <- trimSum(x=c(1:9, NA), n=5)
+ x2 <- c(1:4, NA)
+ checkEquals(x, x2)
+
+ x <- trimSum(x=c(1:9, NA), n=5, na.rm=TRUE)
+ x2 <- c(1:4, 35)
+ checkEquals(x, x2)
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.trimSum.R ends here
Added: trunk/gdata/man/trimSum.Rd
===================================================================
--- trunk/gdata/man/trimSum.Rd (rev 0)
+++ trunk/gdata/man/trimSum.Rd 2008-12-20 22:34:57 UTC (rev 1305)
@@ -0,0 +1,52 @@
+% trimSum.Rd
+%--------------------------------------------------------------------------
+% What: Sum trimmed values - help
+% $Id$
+% Time-stamp: <2008-12-20 00:15:57 ggorjan>
+%--------------------------------------------------------------------------
+
+\name{trimSum}
+
+\alias{trimSum}
+
+\title{Trim a vector such that the last/first value represents the sum of
+ trimmed values}
+
+\description{\code{trimSum} trims (shortens) a vector in such a way that
+ the last or first value represents the sum of trimmed values. User needs
+ to specify the desired length of a trimmed vector.
+}
+
+\usage{trimSum(x, n, right=TRUE, na.rm=FALSE, \ldots)}
+
+\arguments{
+ \item{x}{numeric, a vector of numeric values}
+ \item{n}{numeric, desired length of the output}
+ \item{right}{logical, trim on the right/bottom or the left/top side}
+ \item{na.rm}{logical, remove \code{NA} values when applying a function}
+ \item{\ldots}{arguments passed to other methods - currently not used}
+}
+
+\value{Trimmed vector with a last/first value representing the sum of
+ trimmed values}
+
+\author{Gregor Gorjanc}
+
+\seealso{\code{\link[gdata]{trim}}}
+
+\examples{
+
+x <- 1:10
+trimSum(x, n=5)
+trimSum(x, n=5, right=FALSE)
+
+x[9] <- NA
+trimSum(x, n=5)
+trimSum(x, n=5, na.rm=TRUE)
+
+}
+
+\keyword{manip}
+
+%--------------------------------------------------------------------------
+% trimSum.Rd ends here
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2008-12-20 22:28:58
|
Revision: 1304
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1304&view=rev
Author: ggorjan
Date: 2008-12-20 22:28:35 +0000 (Sat, 20 Dec 2008)
Log Message:
-----------
To remove some output in the R CMD check
Modified Paths:
--------------
trunk/gdata/tests/tests.write.fwf.Rout.save
Modified: trunk/gdata/tests/tests.write.fwf.Rout.save
===================================================================
--- trunk/gdata/tests/tests.write.fwf.Rout.save 2008-08-15 13:15:26 UTC (rev 1303)
+++ trunk/gdata/tests/tests.write.fwf.Rout.save 2008-12-20 22:28:35 UTC (rev 1304)
@@ -21,7 +21,7 @@
> ### tests.write.fwf.R
> ###------------------------------------------------------------------------
> ### What: Tests for write.fwf
-> ### $Id: tests.write.fwf.R 997 2006-10-30 19:04:53Z ggorjan $
+> ### $Id: tests.write.fwf.R 1300 2008-08-05 11:47:18Z ggorjan $
> ### Time-stamp: <2008-08-05 12:25:05 ggorjan>
> ###------------------------------------------------------------------------
>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-08-15 13:15:28
|
Revision: 1303
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1303&view=rev
Author: warnes
Date: 2008-08-15 13:15:26 +0000 (Fri, 15 Aug 2008)
Log Message:
-----------
Add keywords() function to show /doc/KEYWORDS file
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/NAMESPACE
Added Paths:
-----------
trunk/gtools/R/keywords.R
trunk/gtools/man/keywords.Rd
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2008-08-14 20:06:22 UTC (rev 1302)
+++ trunk/gtools/DESCRIPTION 2008-08-15 13:15:26 UTC (rev 1303)
@@ -1,8 +1,8 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 2.5.0
-Date: 2008-05-22
+Version: 2.6.0
+Date: 2008-08-15
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
Maintainer: Gregory R. Warnes <wa...@bs...>
Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE 2008-08-14 20:06:22 UTC (rev 1302)
+++ trunk/gtools/NAMESPACE 2008-08-15 13:15:26 UTC (rev 1303)
@@ -15,6 +15,7 @@
foldchange2logratio,
inv.logit,
invalid,
+ keywords,
logit,
logratio2foldchange,
mixedorder,
Added: trunk/gtools/R/keywords.R
===================================================================
--- trunk/gtools/R/keywords.R (rev 0)
+++ trunk/gtools/R/keywords.R 2008-08-15 13:15:26 UTC (rev 1303)
@@ -0,0 +1,5 @@
+keywords <- function( ... )
+{
+ file <- file.path(R.home("doc"),"KEYWORDS")
+ file.show(file, ...)
+}
Added: trunk/gtools/man/keywords.Rd
===================================================================
--- trunk/gtools/man/keywords.Rd (rev 0)
+++ trunk/gtools/man/keywords.Rd 2008-08-15 13:15:26 UTC (rev 1303)
@@ -0,0 +1,25 @@
+\name{keywords}
+\alias{keywords}
+\title{List valid keywords for R man pages}
+\description{
+ List valid keywords for R man pages
+}
+\usage{
+keywords(...)
+}
+\arguments{
+ \item{\dots}{Optional argumenst to pass to show.file()}
+}
+\details{
+ This function simply determines the path $RHOME/doc/KEYWORDS and calls
+ show.file() to display it.
+}
+\value{
+ Nothing of interest.
+}
+\author{Gregory R. Warnes \email{gr...@ra...}}
+\seealso{ \code{\link[utils]{help}} }
+\examples{
+keywords()
+}
+\keyword{documentation}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-08-14 20:06:27
|
Revision: 1302
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1302&view=rev
Author: warnes
Date: 2008-08-14 20:06:22 +0000 (Thu, 14 Aug 2008)
Log Message:
-----------
balloonpot() was incorrectly displaying warning about z values below 0 when scale.method="relative". Fixed.
Modified Paths:
--------------
trunk/gplots/R/balloonplot.R
Modified: trunk/gplots/R/balloonplot.R
===================================================================
--- trunk/gplots/R/balloonplot.R 2008-08-07 13:40:43 UTC (rev 1301)
+++ trunk/gplots/R/balloonplot.R 2008-08-14 20:06:22 UTC (rev 1302)
@@ -77,7 +77,7 @@
scale.method <- match.arg(scale.method)
scale.range <- match.arg(scale.range)
- if( any(z < 0, na.rm=TRUE ) )
+ if( scale.method=="absolute" && any(z < 0, na.rm=TRUE ) )
warning("z value(s) below zero detected.",
" No balloons will be displayed for these cells.")
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
3 messages has been excluded from this view by a project administrator.
