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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2029] pkg/gtools/tests/test_ddirichlet.R

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

Revision: 2029
          http://sourceforge.net/p/r-gregmisc/code/2029
Author:   warnes
Date:     2015-05-25 14:30:24 +0000 (Mon, 25 May 2015)
Log Message:
-----------
Add library call.

Modified Paths:
--------------
    pkg/gtools/tests/test_ddirichlet.R

Modified: pkg/gtools/tests/test_ddirichlet.R
===================================================================
--- pkg/gtools/tests/test_ddirichlet.R	2015-05-25 14:29:59 UTC (rev 2028)
+++ pkg/gtools/tests/test_ddirichlet.R	2015-05-25 14:30:24 UTC (rev 2029)
@@ -1,5 +1,4 @@
-## Bug reported by John Nolan:
-
+## Regression test for bug reported by John Nolan:
 ##
 ## Whenever the pair (x[i], a[i]) == (0,1), NA would be returned, due
 ## to an internal computation of ( 0 * -Inf ) => NaN
@@ -7,6 +6,8 @@
 ## The code now checks for this particular issue and sets the value of
 ## ( 0 * -Inf ) to 0, which is correct for this calculation.
 ##
+library(gtools)
+
 x = c(0,0,1)
 alpha = c(1,2,3)
 

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2028] pkg/gtools/man/unByteCode.Rd

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

Revision: 2028
          http://sourceforge.net/p/r-gregmisc/code/2028
Author:   warnes
Date:     2015-05-25 14:29:59 +0000 (Mon, 25 May 2015)
Log Message:
-----------
Fix typo and add documentation for argument 'name'.

Modified Paths:
--------------
    pkg/gtools/man/unByteCode.Rd

Modified: pkg/gtools/man/unByteCode.Rd
===================================================================
--- pkg/gtools/man/unByteCode.Rd	2015-05-25 14:29:37 UTC (rev 2027)
+++ pkg/gtools/man/unByteCode.Rd	2015-05-25 14:29:59 UTC (rev 2028)
@@ -1,7 +1,7 @@
 \name{unByteCode}
 \alias{unByteCode}
 \alias{unByteCodeAssign}
-\alias{assignEdgeWise}
+\alias{assignEdgewise}
 \title{
   Convert a Byte-Code Function to an Interpreted-Code Function
 }
@@ -15,6 +15,7 @@
 }
 \arguments{
   \item{fun}{function to be modified}
+  \item{name}{object name}
   \item{env}{namespace}
   \item{value}{new function body}
 }

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2027] pkg/gtools/man/mixedsort.Rd

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

Revision: 2027
          http://sourceforge.net/p/r-gregmisc/code/2027
Author:   warnes
Date:     2015-05-25 14:29:37 +0000 (Mon, 25 May 2015)
Log Message:
-----------
Fix typo.

Modified Paths:
--------------
    pkg/gtools/man/mixedsort.Rd

Modified: pkg/gtools/man/mixedsort.Rd
===================================================================
--- pkg/gtools/man/mixedsort.Rd	2015-05-25 14:16:17 UTC (rev 2026)
+++ pkg/gtools/man/mixedsort.Rd	2015-05-25 14:29:37 UTC (rev 2027)
@@ -22,7 +22,7 @@
   \item{na.last}{for controlling the treatment of \code{NA} values.  If \code{TRUE}, missing
     values in the data are put last; if \code{FALSE}, they are put
     first; if \code{NA}, they are removed.}
-  \item{blanklast}{for controlling the treatment of blank values.  If \code{TRUE}, blank
+  \item{blank.last}{for controlling the treatment of blank values.  If \code{TRUE}, blank
     values in the data are put last; if \code{FALSE}, they are put
     first; if \code{NA}, they are removed.}
 }

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2026] pkg/gtools/man/mixedsort.Rd

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

Revision: 2026
          http://sourceforge.net/p/r-gregmisc/code/2026
Author:   warnes
Date:     2015-05-25 14:16:17 +0000 (Mon, 25 May 2015)
Log Message:
-----------
Add description of blanklast argument, fix typo.

Modified Paths:
--------------
    pkg/gtools/man/mixedsort.Rd

Modified: pkg/gtools/man/mixedsort.Rd
===================================================================
--- pkg/gtools/man/mixedsort.Rd	2015-05-25 14:13:12 UTC (rev 2025)
+++ pkg/gtools/man/mixedsort.Rd	2015-05-25 14:16:17 UTC (rev 2026)
@@ -18,10 +18,13 @@
   \item{x}{Vector to be sorted.}
   \item{decreasing}{logical.  Should the sort be increasing or
     decreasing? Note that \code{descending=TRUE} reverses the meanings of
-    \code{na.lst} and \code{blanks.last}.}
-  \item{na.last}{for controlling the treatment of \code{NA}s.  If \code{TRUE}, missing
+    \code{na.last} and \code{blanks.last}.}
+  \item{na.last}{for controlling the treatment of \code{NA} values.  If \code{TRUE}, missing
     values in the data are put last; if \code{FALSE}, they are put
     first; if \code{NA}, they are removed.}
+  \item{blanklast}{for controlling the treatment of blank values.  If \code{TRUE}, blank
+    values in the data are put last; if \code{FALSE}, they are put
+    first; if \code{NA}, they are removed.}
 }
 \details{
   I often have character vectors (e.g. factor labels), such as compound

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2025] pkg/gtools/man/quantcut.Rd

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

Revision: 2025
          http://sourceforge.net/p/r-gregmisc/code/2025
Author:   warnes
Date:     2015-05-25 14:13:12 +0000 (Mon, 25 May 2015)
Log Message:
-----------
Change usage to match actual definition.

Modified Paths:
--------------
    pkg/gtools/man/quantcut.Rd

Modified: pkg/gtools/man/quantcut.Rd
===================================================================
--- pkg/gtools/man/quantcut.Rd	2015-05-25 14:10:01 UTC (rev 2024)
+++ pkg/gtools/man/quantcut.Rd	2015-05-25 14:13:12 UTC (rev 2025)
@@ -8,7 +8,7 @@
   Create a factor variable using the quantiles of a continous variable.
 }
 \usage{
-quantcut(x, q=seq(0,1,by=0.25), na.rm=TRUE, ...)
+quantcut(x, q=4, na.rm=TRUE, ...)
 }
 %- maybe also `usage' for other objects documented here.
 \arguments{
@@ -55,8 +55,8 @@
   ## cut into deciles
   deciles.1 <- quantcut( x, 10 )
   table(deciles.1)
-  # or equivalently 
-  deciles.2 <- quantcut( x, seq(0,1,by=0.1) ) 
+  # or equivalently
+  deciles.2 <- quantcut( x, seq(0,1,by=0.1) )
 
   \testonly{
     stopifnot(identical(deciles.1, deciles.2))
@@ -67,7 +67,7 @@
   stem(x)        # display the ties
   deciles <- quantcut( x, 10 )
 
-  table(deciles) # note that there are only 5 groups (not 10) 
+  table(deciles) # note that there are only 5 groups (not 10)
                  # due to duplicates
 
 }

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2024] pkg/gtools/man/mixedsort.Rd

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

Revision: 2024
          http://sourceforge.net/p/r-gregmisc/code/2024
Author:   warnes
Date:     2015-05-25 14:10:01 +0000 (Mon, 25 May 2015)
Log Message:
-----------
Note characters sorting ignores case.

Modified Paths:
--------------
    pkg/gtools/man/mixedsort.Rd

Modified: pkg/gtools/man/mixedsort.Rd
===================================================================
--- pkg/gtools/man/mixedsort.Rd	2015-05-25 14:08:33 UTC (rev 2023)
+++ pkg/gtools/man/mixedsort.Rd	2015-05-25 14:10:01 UTC (rev 2024)
@@ -32,7 +32,8 @@
   character and numeric sections, and then sorting along these sections,
   with numbers being sorted by numeric value (e.g. "50" comes before
   "100"), followed by characters strings sorted by character
-  value (e.g. "A" comes before "B").
+  value (e.g. "A" comes before "B") \emph{ignoring case} (e.g. 'A' has
+  the same sort order as 'a').
 
   By default, sort order is ascending, empty strings are sorted to the front,
   and \code{NA} values to the end.   Setting \code{descending=TRUE}

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2023] pkg/gtools/man/mixedsort.Rd

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

Revision: 2023
          http://sourceforge.net/p/r-gregmisc/code/2023
Author:   warnes
Date:     2015-05-25 14:08:33 +0000 (Mon, 25 May 2015)
Log Message:
-----------
Remove '...' from arglist to match source code.

Modified Paths:
--------------
    pkg/gtools/man/mixedsort.Rd

Modified: pkg/gtools/man/mixedsort.Rd
===================================================================
--- pkg/gtools/man/mixedsort.Rd	2015-05-25 14:05:38 UTC (rev 2022)
+++ pkg/gtools/man/mixedsort.Rd	2015-05-25 14:08:33 UTC (rev 2023)
@@ -11,8 +11,8 @@
   that "a", will come before "B" and "C".
 }
 \usage{
-mixedsort(x,  decreasing=FALSE, na.last=TRUE, blank.last=FALSE, ...)
-mixedorder(x, decreasing=FALSE, na.last=TRUE, blank.last=FALSE, ...)
+mixedsort(x,  decreasing=FALSE, na.last=TRUE, blank.last=FALSE)
+mixedorder(x, decreasing=FALSE, na.last=TRUE, blank.last=FALSE)
 }
 \arguments{
   \item{x}{Vector to be sorted.}
@@ -20,8 +20,8 @@
     decreasing? Note that \code{descending=TRUE} reverses the meanings of
     \code{na.lst} and \code{blanks.last}.}
   \item{na.last}{for controlling the treatment of \code{NA}s.  If \code{TRUE}, missing
-          values in the data are put last; if \code{FALSE}, they are put
-          first; if \code{NA}, they are removed.}
+    values in the data are put last; if \code{FALSE}, they are put
+    first; if \code{NA}, they are removed.}
 }
 \details{
   I often have character vectors (e.g. factor labels), such as compound

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2022] pkg/gtools/man/mixedsort.Rd

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

Revision: 2022
          http://sourceforge.net/p/r-gregmisc/code/2022
Author:   warnes
Date:     2015-05-25 14:05:38 +0000 (Mon, 25 May 2015)
Log Message:
-----------
Replace unicode quotes with \code{..}.

Modified Paths:
--------------
    pkg/gtools/man/mixedsort.Rd

Modified: pkg/gtools/man/mixedsort.Rd
===================================================================
--- pkg/gtools/man/mixedsort.Rd	2015-05-23 22:21:39 UTC (rev 2021)
+++ pkg/gtools/man/mixedsort.Rd	2015-05-25 14:05:38 UTC (rev 2022)
@@ -19,9 +19,9 @@
   \item{decreasing}{logical.  Should the sort be increasing or
     decreasing? Note that \code{descending=TRUE} reverses the meanings of
     \code{na.lst} and \code{blanks.last}.}
-  \item{na.last}{for controlling the treatment of ‘NA’s.  If ‘TRUE’, missing
-          values in the data are put last; if ‘FALSE’, they are put
-          first; if ‘NA’, they are removed.}
+  \item{na.last}{for controlling the treatment of \code{NA}s.  If \code{TRUE}, missing
+          values in the data are put last; if \code{FALSE}, they are put
+          first; if \code{NA}, they are removed.}
 }
 \details{
   I often have character vectors (e.g. factor labels), such as compound

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2021] pkg/gtools/tests/test_ddirichlet.R

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

Revision: 2021
          http://sourceforge.net/p/r-gregmisc/code/2021
Author:   warnes
Date:     2015-05-23 22:21:39 +0000 (Sat, 23 May 2015)
Log Message:
-----------
Add regression test ddirichlet() bug for x[i]=0, alpha[i]=1:
ddirichlet(x, alpha) was returning NA rather than 0.

Added Paths:
-----------
    pkg/gtools/tests/test_ddirichlet.R

Added: pkg/gtools/tests/test_ddirichlet.R
===================================================================
--- pkg/gtools/tests/test_ddirichlet.R	                        (rev 0)
+++ pkg/gtools/tests/test_ddirichlet.R	2015-05-23 22:21:39 UTC (rev 2021)
@@ -0,0 +1,14 @@
+## Bug reported by John Nolan:
+
+##
+## Whenever the pair (x[i], a[i]) == (0,1), NA would be returned, due
+## to an internal computation of ( 0 * -Inf ) => NaN
+##
+## The code now checks for this particular issue and sets the value of
+## ( 0 * -Inf ) to 0, which is correct for this calculation.
+##
+x = c(0,0,1)
+alpha = c(1,2,3)
+
+stopifnot( ddirichlet(x=x, alpha=alpha) == 0 )
+

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2020] pkg/gtools/R/dirichlet.R

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

Revision: 2020
          http://sourceforge.net/p/r-gregmisc/code/2020
Author:   warnes
Date:     2015-05-23 22:12:57 +0000 (Sat, 23 May 2015)
Log Message:
-----------
ddirichlet() was incorrectly returning NA when x[i]=0 and
alpha[i]=1.  In this case, the one calculation became (-Inf * 0),
which R evaluates to NaN.   The correction is to detect this case and
substitute -Inf instead of NaN.

Modified Paths:
--------------
    pkg/gtools/R/dirichlet.R

Modified: pkg/gtools/R/dirichlet.R
===================================================================
--- pkg/gtools/R/dirichlet.R	2015-05-08 22:49:28 UTC (rev 2019)
+++ pkg/gtools/R/dirichlet.R	2015-05-23 22:12:57 UTC (rev 2020)
@@ -29,9 +29,9 @@
   dirichlet1 <- function(x, alpha)
     {
       logD <- sum(lgamma(alpha)) - lgamma(sum(alpha))
-      s<-sum((alpha-1)*log(x))
+      s <-(alpha-1)*log(x)
+      s <- ifelse(alpha==1 & x==0, -Inf, s)
       exp(sum(s)-logD)
-
     }
 
   # make sure x is a matrix

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2019] pkg/gtools/R/mixedsort.R

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

Revision: 2019
          http://sourceforge.net/p/r-gregmisc/code/2019
Author:   warnes
Date:     2015-05-08 22:49:28 +0000 (Fri, 08 May 2015)
Log Message:
-----------
Summary: Speed up mixedorder by moving suppressWarnings outside of
lapply loops.  (Suggestion by Henrik Bengtsson.)

Modified Paths:
--------------
    pkg/gtools/R/mixedsort.R

Modified: pkg/gtools/R/mixedsort.R
===================================================================
--- pkg/gtools/R/mixedsort.R	2015-05-02 17:38:35 UTC (rev 2018)
+++ pkg/gtools/R/mixedsort.R	2015-05-08 22:49:28 UTC (rev 2019)
@@ -24,12 +24,12 @@
 
     numeric <- function(x)
       {
-        suppressWarnings( as.numeric(x) )
+        as.numeric(x)
       }
 
     nonnumeric <- function(x)
       {
-        suppressWarnings( ifelse(is.na(as.numeric(x)), toupper(x), NA) )
+        ifelse(is.na(as.numeric(x)), toupper(x), NA)
       }
 
     x <- as.character(x)
@@ -53,10 +53,10 @@
     step1 <- lapply( step1, function(x) x[x>""] )
 
     # create numeric version of data
-    step1.numeric <- lapply( step1, numeric )
+    suppressWarnings( step1.numeric <-  lapply( step1, numeric ) )
 
     # create non-numeric version of data
-    step1.character <- lapply( step1, nonnumeric )
+    suppressWarnings( step1.character <- lapply( step1, nonnumeric ) )
 
     # now transpose so that 1st vector contains 1st element from each
     # original string

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2018]

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

Revision: 2018
          http://sourceforge.net/p/r-gregmisc/code/2018
Author:   warnes
Date:     2015-05-02 17:38:35 +0000 (Sat, 02 May 2015)
Log Message:
-----------
Rename 'trunk' to 'pkg' for compatibility with R-forge

Added Paths:
-----------
    pkg/

Removed Paths:
-------------
    trunk/

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2017] trunk/gtools/man/ASCIIfy.Rd

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

Revision: 2017
          http://sourceforge.net/p/r-gregmisc/code/2017
Author:   warnes
Date:     2015-05-02 13:50:13 +0000 (Sat, 02 May 2015)
Log Message:
-----------
Minor layout change.

Modified Paths:
--------------
    trunk/gtools/man/ASCIIfy.Rd

Modified: trunk/gtools/man/ASCIIfy.Rd
===================================================================
--- trunk/gtools/man/ASCIIfy.Rd	2015-05-02 13:48:35 UTC (rev 2016)
+++ trunk/gtools/man/ASCIIfy.Rd	2015-05-02 13:50:13 UTC (rev 2017)
@@ -22,8 +22,7 @@
 }
 \author{Arni Magnusson \email{ar...@ha...}}
 \note{
-  To render single backslashes, use these or similar techniques:
-  \preformatted{
+  To render single backslashes, use these or similar techniques:\preformatted{
     write(ASCIIfy(x), "file.txt")
     cat(paste(ASCIIfy(x), collapse="\n"), "\n", sep="")}
 

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2016] trunk/gtools/R/mixedsort.R

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

Revision: 2016
          http://sourceforge.net/p/r-gregmisc/code/2016
Author:   warnes
Date:     2015-05-02 13:48:35 +0000 (Sat, 02 May 2015)
Log Message:
-----------
Remove stray 'svn' that was inserted into the code.

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

Modified: trunk/gtools/R/mixedsort.R
===================================================================
--- trunk/gtools/R/mixedsort.R	2015-05-02 13:47:47 UTC (rev 2015)
+++ trunk/gtools/R/mixedsort.R	2015-05-02 13:48:35 UTC (rev 2016)
@@ -1,6 +1,6 @@
 mixedsort <- function(x, decreasing=FALSE, na.last=TRUE, blank.last=FALSE)
     {
-        svn ord <- mixedorder(x, decreasing=decreasing, na.last=na.last,
+        ord <- mixedorder(x, decreasing=decreasing, na.last=na.last,
                              blank.last=blank.last)
         x[ord]
     }

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2015] trunk/gtools/man/unByteCode.Rd

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

Revision: 2015
          http://sourceforge.net/p/r-gregmisc/code/2015
Author:   warnes
Date:     2015-05-02 13:47:47 +0000 (Sat, 02 May 2015)
Log Message:
-----------
Add man page for unByteCode(), assignEdgeWise(), and unByteCodeAssign()

Added Paths:
-----------
    trunk/gtools/man/unByteCode.Rd

Added: trunk/gtools/man/unByteCode.Rd
===================================================================
--- trunk/gtools/man/unByteCode.Rd	                        (rev 0)
+++ trunk/gtools/man/unByteCode.Rd	2015-05-02 13:47:47 UTC (rev 2015)
@@ -0,0 +1,82 @@
+\name{unByteCode}
+\alias{unByteCode}
+\alias{unByteCodeAssign}
+\alias{assignEdgeWise}
+\title{
+  Convert a Byte-Code Function to an Interpreted-Code Function
+}
+\description{
+  Convert a byte-code function to an interpreted-code function
+}
+\usage{
+unByteCode(fun)
+assignEdgewise(name, env, value)
+unByteCodeAssign(fun)
+}
+\arguments{
+  \item{fun}{function to be modified}
+  \item{env}{namespace}
+  \item{value}{new function body}
+}
+\details{
+  The purpose of these functions is to allow a byte coded function to be
+  converted back into a fully interpreted function as a \emph{temporary}
+  work around for issues in byte-code interpretation.
+
+  \code{unByteCode} returns a copy of the function that is directly interpreted
+  from text rather than from byte-code.
+
+  \code{assignEdgewise} makes an assignment into a locked environemnt.
+
+  \code{unByteCodeAssign} changes the specified function \emph{in its source
+  environment} to be directly interpreted from text rather than from byte-code.
+}
+\value{
+  All three functions return a copy of the modified function or assigned value.
+}
+\references{
+  These functions were inspired as a work-around to R bug
+  \url{https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15215}.
+}
+\author{
+  Gregory R. Warnes \email{gr...@wa...}
+}
+\note{
+  These functions are not intended as a permanent solution to issues
+  with byte-code compilation or interpretation.  Any such issues should
+  be promtply reported to the R maintainers via the R Bug Tracking
+  System at \url{https://bugs.r-project.org} and via the R-devel
+  mailing list \url{https://stat.ethz.ch/mailman/listinfo/r-devel}.
+}
+\seealso{
+  \code{\link[compiler]{disassemble}},
+  \code{\link{assign}}
+}
+\examples{
+datURL <- "https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659"
+dat <- as.matrix(read.csv(file=datURL, row.names=1))
+dist2 <- function(x) as.dist(1-cor(t(x), method="pearson"))
+hclust1 <- function(x) hclust(x, method = "single")
+
+distance <- dist2(dat)
+cluster  <- hclust1(distance)
+
+dend <- as.dendrogram(cluster)
+
+\dontrun{
+    ## In R 2.3.0 and earlier crashes R: with a node stack overflow error
+    plot(dend)
+    ## Error in xy.coords(x, y, recycle = TRUE) : node stack overflow
+}
+
+## convert stats:::plotNode from byte-code to interpreted-code
+unByteCodeAssign(stats:::plotNode)
+
+# increase recursion limit
+options("expressions"=5e4)
+
+# now the function does not crash
+plot(dend)
+}
+\keyword{programming}
+\keyword{utilites}

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2014] trunk/gplots/inst

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

Revision: 2014
          http://sourceforge.net/p/r-gregmisc/code/2014
Author:   warnes
Date:     2015-05-01 18:10:13 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Again...

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

Modified: trunk/gplots/inst/ChangeLog
===================================================================
--- trunk/gplots/inst/ChangeLog	2015-05-01 17:54:46 UTC (rev 2013)
+++ trunk/gplots/inst/ChangeLog	2015-05-01 18:10:13 UTC (rev 2014)
@@ -1,5 +1,6 @@
 2015-05-01  warnes
 
+	* [r2013] inst/ChangeLog: Update ChangeLog (again)
 	* [r2012] man/gplots-defunct.Rd: Summary: Correct man page name
 	* [r2011] man/gplots-deprecated.Rd: Summary: Forgot to add \alias
 	  for smartlegend.

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2015-05-01 17:54:46 UTC (rev 2013)
+++ trunk/gplots/inst/NEWS	2015-05-01 18:10:13 UTC (rev 2014)
@@ -1,4 +1,4 @@
-Release 2.17.0 - 2015-04-28
+Release 2.17.0 - 2015-05-01
 ---------------------------
 
 New Features:

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2013] trunk/gplots/inst/ChangeLog

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

Revision: 2013
          http://sourceforge.net/p/r-gregmisc/code/2013
Author:   warnes
Date:     2015-05-01 17:54:46 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Update ChangeLog (again)

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

Modified: trunk/gplots/inst/ChangeLog
===================================================================
--- trunk/gplots/inst/ChangeLog	2015-05-01 17:54:07 UTC (rev 2012)
+++ trunk/gplots/inst/ChangeLog	2015-05-01 17:54:46 UTC (rev 2013)
@@ -1,5 +1,10 @@
 2015-05-01  warnes
 
+	* [r2012] man/gplots-defunct.Rd: Summary: Correct man page name
+	* [r2011] man/gplots-deprecated.Rd: Summary: Forgot to add \alias
+	  for smartlegend.
+	* [r2010] man/lmplot2.Rd: Remove leftover alias
+	* [r2009] inst/ChangeLog: Commit ChangeLog
 	* [r2008] NAMESPACE, inst/NEWS: Update NEWS again.
 	* [r2007] man/gplots-defunct.Rd, man/gplots-deprecated.Rd,
 	  man/lmplot2.Rd, man/smartlegend.Rd: Mark boxplot.n and()

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2012] trunk/gplots/man/gplots-defunct.Rd

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

Revision: 2012
          http://sourceforge.net/p/r-gregmisc/code/2012
Author:   warnes
Date:     2015-05-01 17:54:07 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Summary: Correct man page name

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

Modified: trunk/gplots/man/gplots-defunct.Rd
===================================================================
--- trunk/gplots/man/gplots-defunct.Rd	2015-05-01 17:51:37 UTC (rev 2011)
+++ trunk/gplots/man/gplots-defunct.Rd	2015-05-01 17:54:07 UTC (rev 2012)
@@ -1,4 +1,4 @@
-\name{gplots-deprecated}
+\name{gplots-defunct}
 \alias{boxplot.n}
 \alias{plot.lm2}
 \title{Defunct functions}

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2011] trunk/gplots/man/gplots-deprecated.Rd

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

Revision: 2011
          http://sourceforge.net/p/r-gregmisc/code/2011
Author:   warnes
Date:     2015-05-01 17:51:37 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Summary: Forgot to add \alias for smartlegend.

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

Modified: trunk/gplots/man/gplots-deprecated.Rd
===================================================================
--- trunk/gplots/man/gplots-deprecated.Rd	2015-05-01 17:50:10 UTC (rev 2010)
+++ trunk/gplots/man/gplots-deprecated.Rd	2015-05-01 17:51:37 UTC (rev 2011)
@@ -1,5 +1,6 @@
 \name{gplots-deprecated}
 \alias{deprecated}
+\alias{smartlegend}
 \title{Deprecated functions}
 \description{
   These funcntion have been deprecated and will be removed in future

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2010] trunk/gplots/man/lmplot2.Rd

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

Revision: 2010
          http://sourceforge.net/p/r-gregmisc/code/2010
Author:   warnes
Date:     2015-05-01 17:50:10 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Remove leftover alias

Modified Paths:
--------------
    trunk/gplots/man/lmplot2.Rd

Modified: trunk/gplots/man/lmplot2.Rd
===================================================================
--- trunk/gplots/man/lmplot2.Rd	2015-05-01 17:49:06 UTC (rev 2009)
+++ trunk/gplots/man/lmplot2.Rd	2015-05-01 17:50:10 UTC (rev 2010)
@@ -1,6 +1,5 @@
 \name{lmplot2}
 \alias{lmplot2}
-\alais{plot.lm2}
 \title{
   Plots to assess the goodness of fit for the linear model objects
 }

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2009] trunk/gplots/inst/ChangeLog

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

Revision: 2009
          http://sourceforge.net/p/r-gregmisc/code/2009
Author:   warnes
Date:     2015-05-01 17:49:06 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Commit ChangeLog

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

Modified: trunk/gplots/inst/ChangeLog
===================================================================
--- trunk/gplots/inst/ChangeLog	2015-05-01 17:48:26 UTC (rev 2008)
+++ trunk/gplots/inst/ChangeLog	2015-05-01 17:49:06 UTC (rev 2009)
@@ -1,5 +1,14 @@
 2015-05-01  warnes
 
+	* [r2008] NAMESPACE, inst/NEWS: Update NEWS again.
+	* [r2007] man/gplots-defunct.Rd, man/gplots-deprecated.Rd,
+	  man/lmplot2.Rd, man/smartlegend.Rd: Mark boxplot.n and()
+	  plot.lm2() as defunct.
+	* [r2006] R/boxplot2.R, R/lmplot2.R: Make ballonplot.n() and
+	  plot.lm2() 'defunct'.
+	* [r2005] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog
+	  again.
+	* [r2004] man/sinkplot.Rd: Summary: Punctuation.
 	* [r2003] NAMESPACE: Correct URLs in man pages.
 	* [r2002] man/heatmap.2.Rd, man/sinkplot.Rd: Correct URLs in man
 	  pages.

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2008] trunk/gplots

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

Revision: 2008
          http://sourceforge.net/p/r-gregmisc/code/2008
Author:   warnes
Date:     2015-05-01 17:48:26 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Update NEWS again.

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

Modified: trunk/gplots/NAMESPACE
===================================================================
--- trunk/gplots/NAMESPACE	2015-05-01 17:47:42 UTC (rev 2007)
+++ trunk/gplots/NAMESPACE	2015-05-01 17:48:26 UTC (rev 2008)
@@ -3,8 +3,8 @@
        bandplot,
        barplot2,
        bluered,
+       boxplot.n,
        boxplot2,
-       boxplot.n,
        ci2d,
        col2hex,
        colorpanel,

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2015-05-01 17:47:42 UTC (rev 2007)
+++ trunk/gplots/inst/NEWS	2015-05-01 17:48:26 UTC (rev 2008)
@@ -35,10 +35,13 @@
 
 Other Changes:
 
-- smartlegend() is now marked as deprecated, since the relative
-  positioning feature ('top', 'right') has been added to
-  graphics::legend()
+- smartlegend() is now deprecated because the relative positioning
+  feature ('top', 'right') has been added to graphics::legend().
+  Calling smartlegend() will generate a warning.
 
+- boxplot.n() and plot.lm2() are defunct have been removed.  Use of
+  these functions will now generate an error.
+
 - Update out-of-date URLs in man pages.
 
 Release 2.16.0 - 2015-01-02

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2007] trunk/gplots/man

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

Revision: 2007
          http://sourceforge.net/p/r-gregmisc/code/2007
Author:   warnes
Date:     2015-05-01 17:47:42 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Mark boxplot.n and() plot.lm2() as defunct.

Modified Paths:
--------------
    trunk/gplots/man/gplots-deprecated.Rd
    trunk/gplots/man/lmplot2.Rd

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

Removed Paths:
-------------
    trunk/gplots/man/smartlegend.Rd

Added: trunk/gplots/man/gplots-defunct.Rd
===================================================================
--- trunk/gplots/man/gplots-defunct.Rd	                        (rev 0)
+++ trunk/gplots/man/gplots-defunct.Rd	2015-05-01 17:47:42 UTC (rev 2007)
@@ -0,0 +1,51 @@
+\name{gplots-deprecated}
+\alias{boxplot.n}
+\alias{plot.lm2}
+\title{Defunct functions}
+\description{
+  These funcntion are defunct and have been removed from the gplots package.
+}
+\usage{
+   boxplot.n(..., top=FALSE, shrink=1, textcolor=NULL)
+   plot.lm2(
+            x,
+            which = 1:5,
+            caption = c("Residuals vs Fitted", "Normal Q-Q plot",
+              "Scale-Location plot", "Cook's distance plot"),
+            panel = panel.smooth,
+            sub.caption = deparse(x$call),
+            main = "",
+            ask,
+            ...,
+            id.n = 3,
+            labels.id = names(residuals(x)),
+            cex.id = 0.75,
+            band=TRUE,
+            rug=TRUE,
+            width=1/10,
+            max.n=5000
+            )
+}
+\arguments{
+  \item{\dots}{see man page for the corresponding replacement function}
+  \item{top, shrink, textcolor}{See man page for
+    \code{\link{boxplot2}}.}
+  \item{x, which, caption, panel, sub.caption, main, ask, id.n,
+    labels.id, cex.id, band, rug, width, max.n}{See man page for
+    \code{\link{lmplot2}}.}
+}
+\details{
+These functions are no longer available.  Please refer to the manual page
+for the replacement function:
+  \itemize{
+    \item \code{boxplot.n} has been replaced by \code{\link{boxplot2}}
+    \item \code{plot.lm2} has been replaced by \code{\link{lmplot2}}
+  }
+}
+\author{Gregory R. Warnes \email{gr...@wa...}}
+\seealso{
+  \code{\link{boxplot2}},
+  \code{\link{lmplot2}},
+  \code{\link[base]{Defunct}}
+}
+\keyword{misc}

Modified: trunk/gplots/man/gplots-deprecated.Rd
===================================================================
--- trunk/gplots/man/gplots-deprecated.Rd	2015-05-01 17:44:30 UTC (rev 2006)
+++ trunk/gplots/man/gplots-deprecated.Rd	2015-05-01 17:47:42 UTC (rev 2007)
@@ -1,52 +1,30 @@
 \name{gplots-deprecated}
-\alias{boxplot.n}
-\alias{plot.lm2}
+\alias{deprecated}
 \title{Deprecated functions}
 \description{
   These funcntion have been deprecated and will be removed in future
   releases of gplots.
 }
 \usage{
-   boxplot.n(..., top=FALSE, shrink=1, textcolor=NULL)
-   plot.lm2(
-            x,
-            which = 1:5,
-            caption = c("Residuals vs Fitted", "Normal Q-Q plot",
-              "Scale-Location plot", "Cook's distance plot"),
-            panel = panel.smooth,
-            sub.caption = deparse(x$call),
-            main = "",
-            ask,
+smartlegend(x = c("left", "center", "right"),
+            y = c("top", "center", "bottom"),
             ...,
-            id.n = 3,
-            labels.id = names(residuals(x)),
-            cex.id = 0.75,
-            band=TRUE,
-            rug=TRUE,
-            width=1/10,
-            max.n=5000
-            )
+            inset = 0.05)
 }
 \arguments{
-  \item{\dots}{see man page for the corresponding replacement function}
-  \item{top, shrink, textcolor}{See man page for
-    \code{\link{boxplot2}}.}
-  \item{x, which, caption, panel, sub.caption, main, ask, id.n,
-    labels.id, cex.id, band, rug, width, max.n}{See man page for
-    \code{\link{lmplot2}}.}
+  \item{x, y, inset, \dots}{see man page for the corresponding replacement function}
 }
 \details{
 These functions have been deprecated.  Please refer to the manual page
 for the replacement function:
   \itemize{
-    \item \code{boxplot.n} has been replaced by \code{\link{boxplot2}} 
-    \item \code{plot.lm2} has been replaced by \code{\link{lmplot2}}
+    \item \code{smartlegend} is no longer needed because relative
+    positioning has been implemented in graphics::legend().
   }
 }
 \author{Gregory R. Warnes \email{gr...@wa...}}
 \seealso{
-  \code{\link{boxplot2}},
-  \code{\link{lmplot2}},
+  \code{\link{legend}},
   \code{\link[base]{Deprecated}}
 }
 \keyword{misc}

Modified: trunk/gplots/man/lmplot2.Rd
===================================================================
--- trunk/gplots/man/lmplot2.Rd	2015-05-01 17:44:30 UTC (rev 2006)
+++ trunk/gplots/man/lmplot2.Rd	2015-05-01 17:47:42 UTC (rev 2007)
@@ -1,5 +1,6 @@
 \name{lmplot2}
 \alias{lmplot2}
+\alais{plot.lm2}
 \title{
   Plots to assess the goodness of fit for the linear model objects
 }
@@ -29,7 +30,7 @@
 }
 \arguments{
   \item{x}{lm object}
-  \item{which}{Numerical values between 1 and 5, indicating which plots 
+  \item{which}{Numerical values between 1 and 5, indicating which plots
     to be shown. The codes are:
     \describe{
       \item{1}{Fitted vs residuals}
@@ -43,7 +44,7 @@
   \item{panel}{ function to draw on the existing plot}
   \item{sub.caption}{ SubCaption for the plots }
   \item{main}{Main title of the plot}
-  \item{ask}{whether interactive graphics or postscript }
+  \item{ask}{whether interactive graphics}
   \item{\dots}{ parameters passed to \code{lmplot2}. }
   \item{id.n}{ integer value, less than or equal to residuals of lm object }
   \item{labels.id}{Names of the residuals of the lm object}
@@ -55,8 +56,8 @@
   \item{max.n}{Maximum number of points to display in plots}
 }
 \note{
-  This function replaces \code{boxplot.n}, which has been deprecated
-  avoid potential problems with S3 method dispatching.
+  This function replaces \code{plot.lm2}, which has been deprecated
+  to avoid potential problems with S3 method dispatching.
 }
 \author{Gregory R. Warnes \email{gr...@wa...} and Nitin
   Jain \email{nit...@pf...}}

Deleted: trunk/gplots/man/smartlegend.Rd
===================================================================
--- trunk/gplots/man/smartlegend.Rd	2015-05-01 17:44:30 UTC (rev 2006)
+++ trunk/gplots/man/smartlegend.Rd	2015-05-01 17:47:42 UTC (rev 2007)
@@ -1,45 +0,0 @@
-\name{smartlegend}
-\alias{smartlegend}
-\title{Place a legend in a specified logical ("top","bottom", "left",
-  "right", etc) location on a plot.}
-\description{
-  This function places a legend in a specified logical ("top","bottom", "left",
-  "right", etc) location on a plot.
-}
-\usage{
-smartlegend(x = c("left", "center", "right"),
-            y = c("top", "center", "bottom"),
-            ..., inset = 0.05)
-}
-\arguments{
-  \item{x}{horizontal location on the plot.  One of "left", "center" or
-    "right".}
-  \item{y}{vertical location on the plot.  One of "top", "center", or
-    "bottom".}
-  \item{\dots}{arguments for \code{legend}}
-  \item{inset}{inset distance from the margin as a fraction of the plot
-    region.}
-}
-\value{
-  Same as \code{legend}
-}
-\note{
-  This function is deprecated because \code{\link{legend}} has
-  implemented relative positioning (e.g. \code{x="topright"}).
-}
-\author{Gregory R. Warnes \email{gr...@wa...} }
-\seealso{ \code{\link{legend}} }
-\examples{
-
-x <- rnorm(100)
-y <- rnorm(100, x^2 )
-plot(x,y)
-abline( lm(y~x), col="red", lty=1, type="b") # regression fit
-lines( lowess(y~x), col="blue", lty=2, type="b") # lowess fit
-
-smartlegend(x="center", y="top",
-            c("Regression","Locally Linear Smooth"),
-            col=c("red","blue"), lty=1:2)
-
-}
-\keyword{hplot}

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2006] trunk/gplots/R

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

Revision: 2006
          http://sourceforge.net/p/r-gregmisc/code/2006
Author:   warnes
Date:     2015-05-01 17:44:30 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Make ballonplot.n() and plot.lm2() 'defunct'.

Modified Paths:
--------------
    trunk/gplots/R/boxplot2.R
    trunk/gplots/R/lmplot2.R

Modified: trunk/gplots/R/boxplot2.R
===================================================================
--- trunk/gplots/R/boxplot2.R	2015-05-01 17:24:09 UTC (rev 2005)
+++ trunk/gplots/R/boxplot2.R	2015-05-01 17:44:30 UTC (rev 2006)
@@ -1,11 +1,7 @@
 # $Id$
 boxplot.n <- function( ..., top=FALSE, shrink=1.0, textcolor=NULL )
     {
-        .Deprecated("gboxplot", package="gplots")
-        cl <- match.call()
-        mf <- match.call(expand.dots = FALSE)
-        mf[[1L]] <- quote(boxplot2)
-        eval(mf, parent.frame())
+        .Defunct("gboxplot", package="gplots")
     }
 
 boxplot2  <- function( ..., top=FALSE, shrink=1.0, textcolor=NULL )

Modified: trunk/gplots/R/lmplot2.R
===================================================================
--- trunk/gplots/R/lmplot2.R	2015-05-01 17:24:09 UTC (rev 2005)
+++ trunk/gplots/R/lmplot2.R	2015-05-01 17:44:30 UTC (rev 2006)
@@ -17,10 +17,7 @@
                      max.n=5000
                      )
 {
-    cl <- match.call()
-    mf <- match.call(expand.dots = FALSE)
-    mf[[1L]] <- quote(lmplot2)
-    eval(mf, parent.frame())
+    .Defunct("lmplot", "gplots")
 }
 
 

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

[R-gregmisc-users] SF.net SVN: r-gregmisc:[2005] trunk/gplots/inst

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

Revision: 2005
          http://sourceforge.net/p/r-gregmisc/code/2005
Author:   warnes
Date:     2015-05-01 17:24:09 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Update NEWS and ChangeLog again.

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

Modified: trunk/gplots/inst/ChangeLog
===================================================================
--- trunk/gplots/inst/ChangeLog	2015-05-01 17:22:14 UTC (rev 2004)
+++ trunk/gplots/inst/ChangeLog	2015-05-01 17:24:09 UTC (rev 2005)
@@ -1,5 +1,17 @@
 2015-05-01  warnes
 
+	* [r2003] NAMESPACE: Correct URLs in man pages.
+	* [r2002] man/heatmap.2.Rd, man/sinkplot.Rd: Correct URLs in man
+	  pages.
+	* [r2001] inst/NEWS: Update NEWS again.
+	* [r2000] DESCRIPTION: Improve package description.
+	* [r1999] man/smartlegend.Rd: Mark 'smartlegend' as deprecated
+	* [r1998] R/smartlegend.R: Summary: Mark smartlegend() as
+	  deprecated.
+	* [r1997] man/venn.Rd: Summary: venn example used 'F' instead of
+	  'FALSE'.
+	* [r1996] DESCRIPTION, inst/ChangeLog, inst/NEWS: Update
+	  DESCRIPTION, NEWS, and ChangeLog again for gplots 2.17.0.
 	* [r1995] R/heatmap.2.R: - heatmap.2: row traces could be plotted
 	  in the wrong order.
 	* [r1994] R/heatmap.2.R, man/heatmap.2.Rd: - heatmap.2: column

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2015-05-01 17:22:14 UTC (rev 2004)
+++ trunk/gplots/inst/NEWS	2015-05-01 17:24:09 UTC (rev 2005)
@@ -39,6 +39,7 @@
   positioning feature ('top', 'right') has been added to
   graphics::legend()
 
+- Update out-of-date URLs in man pages.
 
 Release 2.16.0 - 2015-01-02
 ---------------------------

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