r-gregmisc-users Mailing List for R gregmisc package (Page 12)
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From: <wa...@us...> - 2013-12-06 21:40:14
|
Revision: 1751
http://sourceforge.net/p/r-gregmisc/code/1751
Author: warnes
Date: 2013-12-06 21:40:11 +0000 (Fri, 06 Dec 2013)
Log Message:
-----------
Update NEWS for SII 1.0.3
Modified Paths:
--------------
trunk/SII/inst/NEWS
Modified: trunk/SII/inst/NEWS
===================================================================
--- trunk/SII/inst/NEWS 2013-12-06 21:37:41 UTC (rev 1750)
+++ trunk/SII/inst/NEWS 2013-12-06 21:40:11 UTC (rev 1751)
@@ -1,7 +1,14 @@
+VERSION 1.0.3 (2013-12-06)
+--------------------------
+
+- Remove obsolete .First.lib() function to comply with current CRAN
+ package requirments.
+
+
VERSION 1.0.2 (2011-09-01)
--------------------------
-- Update Greg's emamill address.
+- Update Greg's email address.
- Minor changes to comply with new package standards
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|
|
From: <wa...@us...> - 2013-12-06 21:37:43
|
Revision: 1750
http://sourceforge.net/p/r-gregmisc/code/1750
Author: warnes
Date: 2013-12-06 21:37:41 +0000 (Fri, 06 Dec 2013)
Log Message:
-----------
Update affiliation to "Gregory R. Warnes Consulting"
Modified Paths:
--------------
trunk/SII/inst/doc/SII.Rnw
Modified: trunk/SII/inst/doc/SII.Rnw
===================================================================
--- trunk/SII/inst/doc/SII.Rnw 2013-12-06 21:36:09 UTC (rev 1749)
+++ trunk/SII/inst/doc/SII.Rnw 2013-12-06 21:37:41 UTC (rev 1750)
@@ -36,7 +36,7 @@
}
\author{
Gregory R. Warnes, Ph.D. \\
- Random Technologies LLC.
+ Gregory R. Warnes Consulting
}
\begin{document}
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|
|
From: <wa...@us...> - 2013-12-06 21:36:12
|
Revision: 1749
http://sourceforge.net/p/r-gregmisc/code/1749
Author: warnes
Date: 2013-12-06 21:36:09 +0000 (Fri, 06 Dec 2013)
Log Message:
-----------
Remove obsolete .First.lib() function and instead call data() within sii.excel().
Modified Paths:
--------------
trunk/SII/DESCRIPTION
trunk/SII/R/sii.excel.R
Removed Paths:
-------------
trunk/SII/R/First.lib.R
Modified: trunk/SII/DESCRIPTION
===================================================================
--- trunk/SII/DESCRIPTION 2013-11-26 14:38:58 UTC (rev 1748)
+++ trunk/SII/DESCRIPTION 2013-12-06 21:36:09 UTC (rev 1749)
@@ -1,8 +1,8 @@
Package: SII
Type: Package
Title: Calculate ANSI S3.5-1997 Speech Intelligibility Index
-Version: 1.0.2
-Date: 2011-09-01
+Version: 1.0.3
+Date: 2013-12-06
Author: Gregory R. Warnes
Maintainer: Gregory R. Warnes <gr...@wa...>
Description:
Deleted: trunk/SII/R/First.lib.R
===================================================================
--- trunk/SII/R/First.lib.R 2013-11-26 14:38:58 UTC (rev 1748)
+++ trunk/SII/R/First.lib.R 2013-12-06 21:36:09 UTC (rev 1749)
@@ -1,4 +0,0 @@
-.First.lib <- function(libname, pkgname)
- {
- data(sii.constants, package=pkgname)
- }
Modified: trunk/SII/R/sii.excel.R
===================================================================
--- trunk/SII/R/sii.excel.R 2013-11-26 14:38:58 UTC (rev 1748)
+++ trunk/SII/R/sii.excel.R 2013-12-06 21:36:09 UTC (rev 1749)
@@ -10,6 +10,8 @@
if(length(THDI) != length(freq))
stop("THDI must have the same length as freq")
+ data(sii.constants, package="SII", envir=parent.frame())
+
# Interpolate unobserved frequencies
sii.freqs <- sii.constants[,1]
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From: <wa...@us...> - 2013-11-26 14:39:04
|
Revision: 1748
http://sourceforge.net/p/r-gregmisc/code/1748
Author: warnes
Date: 2013-11-26 14:38:58 +0000 (Tue, 26 Nov 2013)
Log Message:
-----------
mixedorder() was failing to correctly handle numbers including
decimals due to a faulty regular expression. Prior to the fix:
> drr
[1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg"
> gtools::mixedsort(drr)
[1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg"
After the fix:
> drr
[1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg"
> mixedsort(drr)
[1] "Dose 0.04 mg" "Dose 0.3 mg" "Dose 0.5 mg"
In addition, an optimization was added that checked if the input vector
was numeric. If so, simply use the existing base::order function.
Modified Paths:
--------------
trunk/gtools/R/mixedsort.R
Modified: trunk/gtools/R/mixedsort.R
===================================================================
--- trunk/gtools/R/mixedsort.R 2013-11-18 16:06:26 UTC (rev 1747)
+++ trunk/gtools/R/mixedsort.R 2013-11-26 14:38:58 UTC (rev 1748)
@@ -13,7 +13,11 @@
return(NULL)
else if(length(x)==1)
return(1)
-
+
+ if( is.numeric(x) )
+ return( order(x) )
+
+
delim="\\$\\@\\$"
numeric <- function(x)
@@ -26,16 +30,16 @@
suppressWarnings( ifelse(is.na(as.numeric(x)), toupper(x), NA) )
}
-
x <- as.character(x)
which.nas <- which(is.na(x))
which.blanks <- which(x=="")
if(length(which.blanks) >0)
- x[ which.blanks ] <- -Inf
+ x[ which.blanks ] <- -Inf
+
if(length(which.nas) >0)
- x[ which.nas ] <- Inf
+ x[ which.nas ] <- Inf
####
# - Convert each character string into an vector containing single
@@ -43,7 +47,7 @@
####
# find and mark numbers in the form of +1.23e+45.67
- delimited <- gsub("([+-]{0,1}[0-9]+([eE][\\+\\-]{0,1}[0-9]+){0,1})",
+ delimited <- gsub("([+-]{0,1}[0-9]+.{0,1}[0-9]*([eE][\\+\\-]{0,1}[0-9]+.{0,1}[0-9]*){0,1})",
paste(delim,"\\1",delim,sep=""), x)
# separate out numbers
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|
|
From: <wa...@us...> - 2013-11-18 16:06:28
|
Revision: 1747
http://sourceforge.net/p/r-gregmisc/code/1747
Author: warnes
Date: 2013-11-18 16:06:26 +0000 (Mon, 18 Nov 2013)
Log Message:
-----------
Use ".Deprecated" instead of warning.
Modified Paths:
--------------
trunk/gtools/R/capture.R
Modified: trunk/gtools/R/capture.R
===================================================================
--- trunk/gtools/R/capture.R 2013-11-06 14:53:52 UTC (rev 1746)
+++ trunk/gtools/R/capture.R 2013-11-18 16:06:26 UTC (rev 1747)
@@ -26,7 +26,7 @@
capture <- function( expression, collapse="\n")
{
- warning("Depreciated. Use capture.output(...) from base instead.")
+ .Deprecated("capture.output", "base", )
resultText <- capture.output( expression )
@@ -39,6 +39,6 @@
sprint <- function(x,...)
{
- warning("Depreciated. Use capture.output(print(...)) from base instead.")
+ .Deprecated("capture.output", "base")
capture(print(x,...))
}
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|
From: <wa...@us...> - 2013-11-06 14:53:56
|
Revision: 1746
http://sourceforge.net/p/r-gregmisc/code/1746
Author: warnes
Date: 2013-11-06 14:53:52 +0000 (Wed, 06 Nov 2013)
Log Message:
-----------
Update files for gtools 3.1.1
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/inst/NEWS
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2013-11-06 14:51:16 UTC (rev 1745)
+++ trunk/gtools/DESCRIPTION 2013-11-06 14:53:52 UTC (rev 1746)
@@ -1,8 +1,8 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 3.1.0
-Date: 2013-09-22
+Version: 3.1.1
+Date: 2013-11-06
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <gr...@wa...>
License: LGPL-2.1
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2013-11-06 14:51:16 UTC (rev 1745)
+++ trunk/gtools/inst/NEWS 2013-11-06 14:53:52 UTC (rev 1746)
@@ -1,3 +1,12 @@
+gtools 3.1.1 - 2013-11-06
+-------------------------
+
+Bug fixes:
+
+- Fix problem with mixedorder/mixedsort when there is zero or one
+ elements in the argument vector.
+
+
gtools 3.1.0 - 2013-09-22
-------------------------
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|
|
From: <wa...@us...> - 2013-11-06 14:51:18
|
Revision: 1745
http://sourceforge.net/p/r-gregmisc/code/1745
Author: warnes
Date: 2013-11-06 14:51:16 +0000 (Wed, 06 Nov 2013)
Log Message:
-----------
Fix problem with mixedorder/mixedsort when there is only zero or one elements in the vector.
Modified Paths:
--------------
trunk/gtools/R/mixedsort.R
Modified: trunk/gtools/R/mixedsort.R
===================================================================
--- trunk/gtools/R/mixedsort.R 2013-10-21 23:33:29 UTC (rev 1744)
+++ trunk/gtools/R/mixedsort.R 2013-11-06 14:51:16 UTC (rev 1745)
@@ -9,6 +9,11 @@
# - Separately rank numbers and strings
# - Combine orders so that strings follow numbers
+ if(length(x)<1)
+ return(NULL)
+ else if(length(x)==1)
+ return(1)
+
delim="\\$\\@\\$"
numeric <- function(x)
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|
From: <wa...@us...> - 2013-10-21 23:33:32
|
Revision: 1744
http://sourceforge.net/p/r-gregmisc/code/1744
Author: warnes
Date: 2013-10-21 23:33:29 +0000 (Mon, 21 Oct 2013)
Log Message:
-----------
Handle 'ask' argument in lmplot2 function proper, rather than in (depreciated) plot.lm2 wrapper.
Modified Paths:
--------------
trunk/gplots/man/gplots-deprecated.Rd
Modified: trunk/gplots/man/gplots-deprecated.Rd
===================================================================
--- trunk/gplots/man/gplots-deprecated.Rd 2013-10-21 23:32:57 UTC (rev 1743)
+++ trunk/gplots/man/gplots-deprecated.Rd 2013-10-21 23:33:29 UTC (rev 1744)
@@ -16,8 +16,7 @@
panel = panel.smooth,
sub.caption = deparse(x$call),
main = "",
- ask = interactive() && nb.fig < length(which)
- && .Device != "postscript",
+ ask,
...,
id.n = 3,
labels.id = names(residuals(x)),
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|
From: <wa...@us...> - 2013-10-21 23:32:59
|
Revision: 1743
http://sourceforge.net/p/r-gregmisc/code/1743
Author: warnes
Date: 2013-10-21 23:32:57 +0000 (Mon, 21 Oct 2013)
Log Message:
-----------
Correct release number
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2013-10-21 23:32:26 UTC (rev 1742)
+++ trunk/gplots/inst/NEWS 2013-10-21 23:32:57 UTC (rev 1743)
@@ -1,4 +1,4 @@
-Release 2.12.0 - 2013-10-14
+Release 2.12.1 - 2013-10-14
---------------------------
API Changes:
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From: <wa...@us...> - 2013-10-21 23:32:32
|
Revision: 1742
http://sourceforge.net/p/r-gregmisc/code/1742
Author: warnes
Date: 2013-10-21 23:32:26 +0000 (Mon, 21 Oct 2013)
Log Message:
-----------
Handle 'ask' argument in lmplot2 function proper, rather than in (depreciated) plot.lm2 wrapper.
Modified Paths:
--------------
trunk/gplots/R/lmplot2.R
Modified: trunk/gplots/R/lmplot2.R
===================================================================
--- trunk/gplots/R/lmplot2.R 2013-10-21 23:31:16 UTC (rev 1741)
+++ trunk/gplots/R/lmplot2.R 2013-10-21 23:32:26 UTC (rev 1742)
@@ -6,8 +6,7 @@
panel = panel.smooth,
sub.caption = deparse(x$call),
main = "",
- ask = interactive() && nb.fig < length(which)
- && .Device != "postscript",
+ ask,
...,
id.n = 3,
labels.id = names(residuals(x)),
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From: <wa...@us...> - 2013-10-21 23:31:18
|
Revision: 1741
http://sourceforge.net/p/r-gregmisc/code/1741
Author: warnes
Date: 2013-10-21 23:31:16 +0000 (Mon, 21 Oct 2013)
Log Message:
-----------
Fix typo
Modified Paths:
--------------
trunk/gplots/man/lmplot2.Rd
Modified: trunk/gplots/man/lmplot2.Rd
===================================================================
--- trunk/gplots/man/lmplot2.Rd 2013-10-15 02:22:29 UTC (rev 1740)
+++ trunk/gplots/man/lmplot2.Rd 2013-10-21 23:31:16 UTC (rev 1741)
@@ -74,6 +74,6 @@
lmplot2(x)
lmplot2(x, which=1, width=1/3)
-lmplot2(x, which=1:3, widht=1/3)
+lmplot2(x, which=1:3, width=1/3)
}
\keyword{hplot}
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|
From: <wa...@us...> - 2013-10-15 02:22:32
|
Revision: 1740
http://sourceforge.net/p/r-gregmisc/code/1740
Author: warnes
Date: 2013-10-15 02:22:29 +0000 (Tue, 15 Oct 2013)
Log Message:
-----------
Add boxplot2 and lmplot2 to NAMESPACE
Modified Paths:
--------------
trunk/gplots/NAMESPACE
Modified: trunk/gplots/NAMESPACE
===================================================================
--- trunk/gplots/NAMESPACE 2013-10-15 02:13:13 UTC (rev 1739)
+++ trunk/gplots/NAMESPACE 2013-10-15 02:22:29 UTC (rev 1740)
@@ -3,6 +3,7 @@
bandplot,
barplot2,
bluered,
+ boxplot2,
boxplot.n,
ci2d,
col2hex,
@@ -10,6 +11,7 @@
greenred,
heatmap.2,
hist2d,
+ lmplot2,
lowess,
ooplot,
overplot,
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From: <wa...@us...> - 2013-10-15 02:13:16
|
Revision: 1739
http://sourceforge.net/p/r-gregmisc/code/1739
Author: warnes
Date: 2013-10-15 02:13:13 +0000 (Tue, 15 Oct 2013)
Log Message:
-----------
Update for gplots release 2.12.1
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/inst/NEWS
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2013-10-15 02:09:31 UTC (rev 1738)
+++ trunk/gplots/DESCRIPTION 2013-10-15 02:13:13 UTC (rev 1739)
@@ -4,8 +4,8 @@
Depends: R (>= 3.0)
Imports: gtools, gdata, stats, caTools, KernSmooth
Suggests: grid, MASS
-Version: 2.12.0
-Date: 2013-10-11
+Version: 2.12.1
+Date: 2013-10-14
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2013-10-15 02:09:31 UTC (rev 1738)
+++ trunk/gplots/inst/NEWS 2013-10-15 02:13:13 UTC (rev 1739)
@@ -1,6 +1,14 @@
-Release 2.12.0 - 2013-10-11
+Release 2.12.0 - 2013-10-14
---------------------------
+API Changes:
+
+- boxplot.n() has been renamed to boxplot2() to avoid potential S3
+ method calling issues.
+
+- plot.lm2() has been rename to lmplot2() to avoid potential S3 method
+ calling issues.
+
Enhancements:
- Add heatmap.2() parameters to control row and column label rotation
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From: <wa...@us...> - 2013-10-15 02:09:33
|
Revision: 1738
http://sourceforge.net/p/r-gregmisc/code/1738
Author: warnes
Date: 2013-10-15 02:09:31 +0000 (Tue, 15 Oct 2013)
Log Message:
-----------
Rename boxplot.n to boxplt2 and plot.lm2 to lmplot2
Modified Paths:
--------------
trunk/gplots/man/gplots-deprecated.Rd
Added Paths:
-----------
trunk/gplots/R/boxplot2.R
trunk/gplots/R/lmplot2.R
trunk/gplots/man/boxplot2.Rd
trunk/gplots/man/lmplot2.Rd
Removed Paths:
-------------
trunk/gplots/R/boxplot.n.R
trunk/gplots/R/plot.lm.R
trunk/gplots/man/boxplot.n.Rd
trunk/gplots/man/boxplot2.Rd
trunk/gplots/man/lmplot2.Rd
trunk/gplots/man/plot.lm2.Rd
Deleted: trunk/gplots/R/boxplot.n.R
===================================================================
--- trunk/gplots/R/boxplot.n.R 2013-10-15 01:47:31 UTC (rev 1737)
+++ trunk/gplots/R/boxplot.n.R 2013-10-15 02:09:31 UTC (rev 1738)
@@ -1,52 +0,0 @@
-# $Id$
-
-boxplot.n <- function( ..., top=FALSE, shrink=1.0, textcolor=NULL )
- {
- boxcall <- match.call() # get call
- boxcall$top <- boxcall$shrink <- boxcall$textcolor <- NULL
- boxcall[[1]] <- as.name("boxplot")
-
- if(is.R())
- {
- box <- eval(boxcall, parent.frame())
- mids <- 1:length(box$n)
- }
- else
- {
- mids <- eval(boxcall, parent.frame())
- boxcall$plot <- FALSE
- box <- eval(boxcall, parent.frame())
- }
-
- if(top)
- {
- where <- par("usr")[4]
- adj <- c(0.5,1)
- }
- else
- {
- where <- par("usr")[3]
- adj <- c(0.5,0)
- }
- tcex <- par("cex")
- par(cex=shrink*tcex)
-
- if(is.R())
- text( x=mids, y=where, labels=paste("n=",box$n,sep=""), adj=adj,
- col=textcolor)
- else
- {
- if( is.null(textcolor) )
- textcolor <- 1
- space <- ifelse(top, -1, 1) * par("1em")[2] / 2
-
- text( x=mids, y=where + space, labels=paste("n=",box$n,sep=""), adj=adj[1],
- col=textcolor)
-
- }
-
- par(cex=tcex)
-
- invisible(box)
- }
-
Copied: trunk/gplots/R/boxplot2.R (from rev 1672, trunk/gplots/R/boxplot.n.R)
===================================================================
--- trunk/gplots/R/boxplot2.R (rev 0)
+++ trunk/gplots/R/boxplot2.R 2013-10-15 02:09:31 UTC (rev 1738)
@@ -0,0 +1,60 @@
+# $Id$
+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())
+ }
+
+boxplot2 <- function( ..., top=FALSE, shrink=1.0, textcolor=NULL )
+ {
+ boxcall <- match.call() # get call
+ boxcall$top <- boxcall$shrink <- boxcall$textcolor <- NULL
+ boxcall[[1]] <- as.name("boxplot")
+
+ if(is.R())
+ {
+ box <- eval(boxcall, parent.frame())
+ mids <- 1:length(box$n)
+ }
+ else
+ {
+ mids <- eval(boxcall, parent.frame())
+ boxcall$plot <- FALSE
+ box <- eval(boxcall, parent.frame())
+ }
+
+ if(top)
+ {
+ where <- par("usr")[4]
+ adj <- c(0.5,1)
+ }
+ else
+ {
+ where <- par("usr")[3]
+ adj <- c(0.5,0)
+ }
+ tcex <- par("cex")
+ par(cex=shrink*tcex)
+
+ if(is.R())
+ text( x=mids, y=where, labels=paste("n=",box$n,sep=""), adj=adj,
+ col=textcolor)
+ else
+ {
+ if( is.null(textcolor) )
+ textcolor <- 1
+ space <- ifelse(top, -1, 1) * par("1em")[2] / 2
+
+ text( x=mids, y=where + space, labels=paste("n=",box$n,sep=""), adj=adj[1],
+ col=textcolor)
+
+ }
+
+ par(cex=tcex)
+
+ invisible(box)
+ }
+
Copied: trunk/gplots/R/lmplot2.R (from rev 1672, trunk/gplots/R/plot.lm.R)
===================================================================
--- trunk/gplots/R/lmplot2.R (rev 0)
+++ trunk/gplots/R/lmplot2.R 2013-10-15 02:09:31 UTC (rev 1738)
@@ -0,0 +1,183 @@
+plot.lm2 <- function(
+ x,
+ which = 1:5,
+ caption = c("Residuals vs Fitted", "Normal Q-Q plot",
+ "Scale-Location plot", "Cook's distance plot"),
+ panel = panel.smooth,
+ sub.caption = deparse(x$call),
+ main = "",
+ ask = interactive() && nb.fig < length(which)
+ && .Device != "postscript",
+ ...,
+ id.n = 3,
+ labels.id = names(residuals(x)),
+ cex.id = 0.75,
+ band=TRUE,
+ rug=TRUE,
+ width=1/10,
+ max.n=5000
+ )
+{
+ cl <- match.call()
+ mf <- match.call(expand.dots = FALSE)
+ mf[[1L]] <- quote(lmplot2)
+ eval(mf, parent.frame())
+}
+
+
+lmplot2 <- function(
+ 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$call),
+ main = "",
+ ask = interactive() && nb.fig < length(which)
+ && .Device != "postscript",
+ ...,
+ id.n = 3,
+ labels.id = names(residuals(x)),
+ cex.id = 0.75,
+ band=TRUE,
+ rug=TRUE,
+ width=1/10,
+ max.n=5000
+ )
+{
+ if (!inherits(x, "lm"))
+ stop("Use only with 'lm' objects")
+ show <- rep(FALSE, 5)
+ if(!is.numeric(which) || any(which < 1) || any(which > 5))
+ stop("`which' must be in 1:5")
+ show[which] <- TRUE
+ r <- residuals(x)
+ n <- length(r)
+ if(inherits(x,"glm"))
+ yh <- predict(x) # != fitted() for glm
+ else
+ yh <- fitted(x)
+ if (any(show[2:4]))
+ s <- if(inherits(x, "rlm")) x$s else sqrt(deviance(x)/df.residual(x))
+ if (any(show[2:3])) {
+ ylab23 <- if(inherits(x, "glm"))
+ "Std. deviance resid." else "Standardized residuals"
+ hii <- lm.influence(x)$hat
+ w <- weights(x)
+ # r.w := weighted.residuals(x):
+ r.w <- if(is.null(w)) r else (sqrt(w)*r)[w!=0]
+ rs <- r.w/(s * sqrt(1 - hii))
+ }
+ if (any(show[c(1,3)]))
+ l.fit <- if(inherits(x,"glm"))
+ "Predicted values" else "Fitted values"
+ if (is.null(id.n))
+ id.n <- 0
+ else {
+ id.n <- as.integer(id.n)
+ if(id.n < 0 || id.n > n)
+ stop(paste("`id.n' must be in { 1,..,",n,"}"))
+ }
+ if(id.n > 0) {
+ if(is.null(labels.id))
+ labels.id <- paste(1:n)
+ iid <- 1:id.n
+ show.r <- order(-abs(r))[iid]
+ if(any(show[2:3]))
+ show.rs <- order(-abs(rs))[iid]
+ text.id <- function(x,y, ind, adj.x = FALSE)
+ text(x - if(adj.x) strwidth(" ")*cex.id else 0, y, labels.id[ind],
+ cex = cex.id, xpd = TRUE, adj = if(adj.x) 1)
+ }
+ nb.fig <- prod(par("mfcol"))
+ one.fig <- prod(par("mfcol")) == 1
+ if (ask) {
+ op <- par(ask = TRUE)
+ on.exit(par(op))
+ }
+ ##---------- Do the individual plots : ----------
+ if (show[1]) {
+ ylim <- range(r)
+ if(id.n > 0)
+ ylim <- ylim + c(-1,1)* 0.08 * diff(ylim)
+ plot(yh, r, xlab = l.fit, ylab = "Residuals", main = main,
+ ylim = ylim, type = "n", ...)
+ panel(yh, r, ...)
+ if(rug) rug(yh) ## GRW 2001-06-08
+ if(band) bandplot(yh,r,add=TRUE,width=width) ## GRW 2001-06-08
+ if (one.fig)
+ title(sub = sub.caption, ...)
+ mtext(caption[1], 3, 0.25)
+ if(id.n > 0) {
+ y.id <- r[show.r]
+ y.id[y.id < 0] <- y.id[y.id < 0] - strheight(" ")/3
+ text.id(yh[show.r], y.id, show.r, adj.x = TRUE)
+ }
+ abline(h = 0, lty = 3, col = "gray")
+ }
+ if (show[2]) {
+ ylim <- range(rs)
+ ylim[2] <- ylim[2] + diff(ylim) * 0.075
+ qq <- qqnorm(rs, main = main, ylab = ylab23, ylim = ylim, ...)
+ qqline(rs)
+ if (one.fig)
+ title(sub = sub.caption, ...)
+ mtext(caption[2], 3, 0.25)
+ if(id.n > 0)
+ text.id(qq$x[show.rs], qq$y[show.rs], show.rs, adj.x = TRUE)
+ }
+ if (show[3]) {
+ sqrtabsr <- sqrt(abs(rs))
+ ylim <- c(0, max(sqrtabsr))
+ yl <- as.expression(substitute(sqrt(abs(YL)), list(YL=as.name(ylab23))))
+ yhn0 <- if(is.null(w)) yh else yh[w!=0]
+ plot(yhn0, sqrtabsr, xlab = l.fit, ylab = yl, main = main,
+ ylim = ylim, type = "n", ...)
+ panel(yhn0, sqrtabsr, ...)
+
+ abline(h=mean(sqrtabsr),lty = 3, col = "gray")
+ if(rug) rug(yh) ## GRW 2001-06-08
+ if(band) bandplot(yhn0,sqrtabsr,add=TRUE) ## GRW 2001-06-08
+
+ if (one.fig)
+ title(sub = sub.caption, ...)
+ mtext(caption[3], 3, 0.25)
+ if(id.n > 0)
+ text.id(yhn0[show.rs], sqrtabsr[show.rs], show.rs, adj.x = TRUE)
+ }
+ if (show[4]) {
+ cook <- cooks.distance(x, sd=s)
+ if(id.n > 0) {
+ show.r <- order(-cook)[iid]# index of largest `id.n' ones
+ ymx <- cook[show.r[1]] * 1.075
+ } else ymx <- max(cook)
+ plot(cook, type = "h", ylim = c(0, ymx), main = main,
+ xlab = "Obs. number", ylab = "Cook's distance", ...)
+ if (one.fig)
+ title(sub = sub.caption, ...)
+ mtext(caption[4], 3, 0.25)
+ if(id.n > 0)
+ text.id(show.r, cook[show.r] + 0.4*cex.id * strheight(" "), show.r)
+ }
+ if (show[5])
+ {
+ ## plot residuals against each predictor ##
+ data <- model.frame(x)
+ for( i in 2:ncol(data) )
+ {
+ test <- try(
+ {
+ plot.default( x=data[,i], y=r,
+ xlab=names(data)[i], ylab="Residuals", type="n")
+ panel( data[,i], r, ... )
+ if(rug) rug(data[,i])
+ if(band) bandplot(data[,i],r,add=TRUE)
+ abline(h=0,lty = 3, col = "gray")
+ }
+ )
+ }
+ }
+ if (!one.fig && par("oma")[3] >= 1)
+ mtext(sub.caption, outer = TRUE, cex = 1.25)
+ invisible()
+}
Deleted: trunk/gplots/R/plot.lm.R
===================================================================
--- trunk/gplots/R/plot.lm.R 2013-10-15 01:47:31 UTC (rev 1737)
+++ trunk/gplots/R/plot.lm.R 2013-10-15 02:09:31 UTC (rev 1738)
@@ -1,156 +0,0 @@
-plot.lm2 <- function(
- 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 = interactive() && nb.fig < length(which)
- && .Device != "postscript",
- ...,
- id.n = 3,
- labels.id = names(residuals(x)),
- cex.id = 0.75,
- band=TRUE,
- rug=TRUE,
- width=1/10,
- max.n=5000
- )
-{
- if (!inherits(x, "lm"))
- stop("Use only with 'lm' objects")
- show <- rep(FALSE, 5)
- if(!is.numeric(which) || any(which < 1) || any(which > 5))
- stop("`which' must be in 1:5")
- show[which] <- TRUE
- r <- residuals(x)
- n <- length(r)
- if(inherits(x,"glm"))
- yh <- predict(x) # != fitted() for glm
- else
- yh <- fitted(x)
- if (any(show[2:4]))
- s <- if(inherits(x, "rlm")) x$s else sqrt(deviance(x)/df.residual(x))
- if (any(show[2:3])) {
- ylab23 <- if(inherits(x, "glm"))
- "Std. deviance resid." else "Standardized residuals"
- hii <- lm.influence(x)$hat
- w <- weights(x)
- # r.w := weighted.residuals(x):
- r.w <- if(is.null(w)) r else (sqrt(w)*r)[w!=0]
- rs <- r.w/(s * sqrt(1 - hii))
- }
- if (any(show[c(1,3)]))
- l.fit <- if(inherits(x,"glm"))
- "Predicted values" else "Fitted values"
- if (is.null(id.n))
- id.n <- 0
- else {
- id.n <- as.integer(id.n)
- if(id.n < 0 || id.n > n)
- stop(paste("`id.n' must be in { 1,..,",n,"}"))
- }
- if(id.n > 0) {
- if(is.null(labels.id))
- labels.id <- paste(1:n)
- iid <- 1:id.n
- show.r <- order(-abs(r))[iid]
- if(any(show[2:3]))
- show.rs <- order(-abs(rs))[iid]
- text.id <- function(x,y, ind, adj.x = FALSE)
- text(x - if(adj.x) strwidth(" ")*cex.id else 0, y, labels.id[ind],
- cex = cex.id, xpd = TRUE, adj = if(adj.x) 1)
- }
- nb.fig <- prod(par("mfcol"))
- one.fig <- prod(par("mfcol")) == 1
- if (ask) {
- op <- par(ask = TRUE)
- on.exit(par(op))
- }
- ##---------- Do the individual plots : ----------
- if (show[1]) {
- ylim <- range(r)
- if(id.n > 0)
- ylim <- ylim + c(-1,1)* 0.08 * diff(ylim)
- plot(yh, r, xlab = l.fit, ylab = "Residuals", main = main,
- ylim = ylim, type = "n", ...)
- panel(yh, r, ...)
- if(rug) rug(yh) ## GRW 2001-06-08
- if(band) bandplot(yh,r,add=TRUE,width=width) ## GRW 2001-06-08
- if (one.fig)
- title(sub = sub.caption, ...)
- mtext(caption[1], 3, 0.25)
- if(id.n > 0) {
- y.id <- r[show.r]
- y.id[y.id < 0] <- y.id[y.id < 0] - strheight(" ")/3
- text.id(yh[show.r], y.id, show.r, adj.x = TRUE)
- }
- abline(h = 0, lty = 3, col = "gray")
- }
- if (show[2]) {
- ylim <- range(rs)
- ylim[2] <- ylim[2] + diff(ylim) * 0.075
- qq <- qqnorm(rs, main = main, ylab = ylab23, ylim = ylim, ...)
- qqline(rs)
- if (one.fig)
- title(sub = sub.caption, ...)
- mtext(caption[2], 3, 0.25)
- if(id.n > 0)
- text.id(qq$x[show.rs], qq$y[show.rs], show.rs, adj.x = TRUE)
- }
- if (show[3]) {
- sqrtabsr <- sqrt(abs(rs))
- ylim <- c(0, max(sqrtabsr))
- yl <- as.expression(substitute(sqrt(abs(YL)), list(YL=as.name(ylab23))))
- yhn0 <- if(is.null(w)) yh else yh[w!=0]
- plot(yhn0, sqrtabsr, xlab = l.fit, ylab = yl, main = main,
- ylim = ylim, type = "n", ...)
- panel(yhn0, sqrtabsr, ...)
-
- abline(h=mean(sqrtabsr),lty = 3, col = "gray")
- if(rug) rug(yh) ## GRW 2001-06-08
- if(band) bandplot(yhn0,sqrtabsr,add=TRUE) ## GRW 2001-06-08
-
- if (one.fig)
- title(sub = sub.caption, ...)
- mtext(caption[3], 3, 0.25)
- if(id.n > 0)
- text.id(yhn0[show.rs], sqrtabsr[show.rs], show.rs, adj.x = TRUE)
- }
- if (show[4]) {
- cook <- cooks.distance(x, sd=s)
- if(id.n > 0) {
- show.r <- order(-cook)[iid]# index of largest `id.n' ones
- ymx <- cook[show.r[1]] * 1.075
- } else ymx <- max(cook)
- plot(cook, type = "h", ylim = c(0, ymx), main = main,
- xlab = "Obs. number", ylab = "Cook's distance", ...)
- if (one.fig)
- title(sub = sub.caption, ...)
- mtext(caption[4], 3, 0.25)
- if(id.n > 0)
- text.id(show.r, cook[show.r] + 0.4*cex.id * strheight(" "), show.r)
- }
- if (show[5])
- {
- ## plot residuals against each predictor ##
- data <- model.frame(x)
- for( i in 2:ncol(data) )
- {
- test <- try(
- {
- plot.default( x=data[,i], y=r,
- xlab=names(data)[i], ylab="Residuals", type="n")
- panel( data[,i], r, ... )
- if(rug) rug(data[,i])
- if(band) bandplot(data[,i],r,add=TRUE)
- abline(h=0,lty = 3, col = "gray")
- }
- )
- }
- }
- if (!one.fig && par("oma")[3] >= 1)
- mtext(sub.caption, outer = TRUE, cex = 1.25)
- invisible()
-}
Deleted: trunk/gplots/man/boxplot.n.Rd
===================================================================
--- trunk/gplots/man/boxplot.n.Rd 2013-10-15 01:47:31 UTC (rev 1737)
+++ trunk/gplots/man/boxplot.n.Rd 2013-10-15 02:09:31 UTC (rev 1738)
@@ -1,57 +0,0 @@
-% $Id$
-%
-% $Log$
-% Revision 1.5 2005/12/01 16:46:52 nj7w
-% Updated Greg's email address
-%
-% Revision 1.4 2005/06/09 14:20:28 nj7w
-% Updating the version number, and various help files to synchronize splitting of gregmisc bundle in 4 individual components.
-%
-% Revision 1.1.1.1 2005/05/25 22:15:30 nj7w
-% Initial submission as an individual package
-%
-% Revision 1.3 2002/04/09 00:51:31 warneg
-%
-% Checkin for version 0.5.3
-%
-% Revision 1.2 2001/08/25 05:46:21 warneg
-% Added CVS header.
-%
-% Revision 1.1 2001/08/25 05:45:10 warneg
-% Initial Checkin
-%
-\name{boxplot.n}
-\alias{boxplot.n}
-\title{Produce a Boxplot Annotated with the Number of Observations}
-\description{
- This funcntion uses \code{boxplot} to produce a boxplot which is then
- annotated with the number of observations in each group.
-}
-\usage{
-boxplot.n(..., top=FALSE, shrink=1, textcolor=NULL)
-}
-\arguments{
- \item{\dots}{ parameters passed to \code{boxplot}. }
- \item{top}{ logical indicating whether the number of observations
- should be added to the top or the bottom of the plotting
- region. Defaults to \code{FALSE}. }
- \item{shrink}{ value to shrink character size (cex) when annotating.}
- \item{textcolor}{ text color. }
-}
-\author{ Gregory R. Warnes \email{gr...@wa...}}
-\seealso{ \code{\link{boxplot}}, \code{\link{text}}}
-
-\examples{
-data(state)
-
-# n's at bottom
-boxplot.n( state.area ~ state.region)
-
-# n's at top
-boxplot.n( state.area ~ state.region, top=TRUE)
-
-# small red text
-boxplot.n( state.area ~ state.region, shrink=0.8, textcolor="red")
-}
-
-\keyword{ hplot }
Deleted: trunk/gplots/man/boxplot2.Rd
===================================================================
--- trunk/gplots/man/boxplot2.Rd 2013-10-15 01:47:31 UTC (rev 1737)
+++ trunk/gplots/man/boxplot2.Rd 2013-10-15 02:09:31 UTC (rev 1738)
@@ -1,57 +0,0 @@
-% $Id$
-%
-% $Log$
-% Revision 1.5 2005/12/01 16:46:52 nj7w
-% Updated Greg's email address
-%
-% Revision 1.4 2005/06/09 14:20:28 nj7w
-% Updating the version number, and various help files to synchronize splitting of gregmisc bundle in 4 individual components.
-%
-% Revision 1.1.1.1 2005/05/25 22:15:30 nj7w
-% Initial submission as an individual package
-%
-% Revision 1.3 2002/04/09 00:51:31 warneg
-%
-% Checkin for version 0.5.3
-%
-% Revision 1.2 2001/08/25 05:46:21 warneg
-% Added CVS header.
-%
-% Revision 1.1 2001/08/25 05:45:10 warneg
-% Initial Checkin
-%
-\name{boxplot.n}
-\alias{boxplot.n}
-\title{Produce a Boxplot Annotated with the Number of Observations}
-\description{
- This funcntion uses \code{boxplot} to produce a boxplot which is then
- annotated with the number of observations in each group.
-}
-\usage{
-boxplot.n(..., top=FALSE, shrink=1, textcolor=NULL)
-}
-\arguments{
- \item{\dots}{ parameters passed to \code{boxplot}. }
- \item{top}{ logical indicating whether the number of observations
- should be added to the top or the bottom of the plotting
- region. Defaults to \code{FALSE}. }
- \item{shrink}{ value to shrink character size (cex) when annotating.}
- \item{textcolor}{ text color. }
-}
-\author{ Gregory R. Warnes \email{gr...@wa...}}
-\seealso{ \code{\link{boxplot}}, \code{\link{text}}}
-
-\examples{
-data(state)
-
-# n's at bottom
-boxplot.n( state.area ~ state.region)
-
-# n's at top
-boxplot.n( state.area ~ state.region, top=TRUE)
-
-# small red text
-boxplot.n( state.area ~ state.region, shrink=0.8, textcolor="red")
-}
-
-\keyword{ hplot }
Copied: trunk/gplots/man/boxplot2.Rd (from rev 1672, trunk/gplots/man/boxplot.n.Rd)
===================================================================
--- trunk/gplots/man/boxplot2.Rd (rev 0)
+++ trunk/gplots/man/boxplot2.Rd 2013-10-15 02:09:31 UTC (rev 1738)
@@ -0,0 +1,42 @@
+\name{boxplot2}
+\alias{boxplot2}
+\title{Produce a Boxplot Annotated with the Number of Observations}
+\description{
+ This funcntion uses \code{boxplot} to produce a boxplot which is then
+ annotated with the number of observations in each group.
+}
+\usage{
+boxplot2(..., top=FALSE, shrink=1, textcolor=NULL)
+}
+\arguments{
+ \item{\dots}{ parameters passed to \code{boxplot}. }
+ \item{top}{ logical indicating whether the number of observations
+ should be added to the top or the bottom of the plotting
+ region. Defaults to \code{FALSE}. }
+ \item{shrink}{ value to shrink character size (cex) when annotating.}
+ \item{textcolor}{ text color. }
+}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
+\note{
+ This function replaces \code{boxplot.n}, which has been deprecated
+ avoid potential problems with S3 method dispatching.
+}
+\seealso{
+ \code{\link{boxplot}},
+ \code{\link{text}}
+}
+
+\examples{
+data(state)
+
+# n's at bottom
+boxplot2( state.area ~ state.region)
+
+# n's at top
+boxplot2( state.area ~ state.region, top=TRUE)
+
+# small red text
+boxplot2( state.area ~ state.region, shrink=0.8, textcolor="red")
+}
+
+\keyword{ hplot }
Modified: trunk/gplots/man/gplots-deprecated.Rd
===================================================================
--- trunk/gplots/man/gplots-deprecated.Rd 2013-10-15 01:47:31 UTC (rev 1737)
+++ trunk/gplots/man/gplots-deprecated.Rd 2013-10-15 02:09:31 UTC (rev 1738)
@@ -1,57 +1,53 @@
-% $Id$
-%
-% $Log$
-% Revision 1.5 2005/12/01 16:46:52 nj7w
-% Updated Greg's email address
-%
-% Revision 1.4 2005/06/09 14:20:28 nj7w
-% Updating the version number, and various help files to synchronize splitting of gregmisc bundle in 4 individual components.
-%
-% Revision 1.1.1.1 2005/05/25 22:15:30 nj7w
-% Initial submission as an individual package
-%
-% Revision 1.3 2002/04/09 00:51:31 warneg
-%
-% Checkin for version 0.5.3
-%
-% Revision 1.2 2001/08/25 05:46:21 warneg
-% Added CVS header.
-%
-% Revision 1.1 2001/08/25 05:45:10 warneg
-% Initial Checkin
-%
-\name{boxplot.n}
+\name{gplots-deprecated}
\alias{boxplot.n}
-\title{Produce a Boxplot Annotated with the Number of Observations}
+\alias{plot.lm2}
+\title{Deprecated functions}
\description{
- This funcntion uses \code{boxplot} to produce a boxplot which is then
- annotated with the number of observations in each group.
+ These funcntion have been deprecated and will be removed in future
+ releases of gplots.
}
\usage{
-boxplot.n(..., top=FALSE, shrink=1, textcolor=NULL)
+ 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 = interactive() && nb.fig < length(which)
+ && .Device != "postscript",
+ ...,
+ 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}{ parameters passed to \code{boxplot}. }
- \item{top}{ logical indicating whether the number of observations
- should be added to the top or the bottom of the plotting
- region. Defaults to \code{FALSE}. }
- \item{shrink}{ value to shrink character size (cex) when annotating.}
- \item{textcolor}{ text color. }
+ \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}}.}
}
-\author{ Gregory R. Warnes \email{gr...@wa...}}
-\seealso{ \code{\link{boxplot}}, \code{\link{text}}}
-
-\examples{
-data(state)
-
-# n's at bottom
-boxplot.n( state.area ~ state.region)
-
-# n's at top
-boxplot.n( state.area ~ state.region, top=TRUE)
-
-# small red text
-boxplot.n( state.area ~ state.region, shrink=0.8, textcolor="red")
+\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}}
+ }
}
-
-\keyword{ hplot }
+\author{Gregory R. Warnes \email{gr...@wa...}}
+\seealso{
+ \code{\link{boxplot2}},
+ \code{\link{lmplot2}},
+ \code{\link[base]{Deprecated}}
+}
+\keyword{misc}
Deleted: trunk/gplots/man/lmplot2.Rd
===================================================================
--- trunk/gplots/man/lmplot2.Rd 2013-10-15 01:47:31 UTC (rev 1737)
+++ trunk/gplots/man/lmplot2.Rd 2013-10-15 02:09:31 UTC (rev 1738)
@@ -1,71 +0,0 @@
-\name{plot.lm2}
-\alias{plot.lm2}
-\title{
- Plots to assess the goodness of fit for the linear model objects
-}
-\description{
- Plots to assess the goodness of fit for the linear model objects
- }
- \usage{
- 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 = interactive() && nb.fig < length(which)
- && .Device != "postscript",
- ...,
- id.n = 3,
- labels.id = names(residuals(x)),
- cex.id = 0.75,
- band=TRUE,
- rug=TRUE,
- width=1/10,
- max.n=5000
- )
-}
-\arguments{
- \item{x}{lm object}
- \item{which}{Numerical values between 1 and 5, indicating which plots
- to be shown. The codes are:
-
- 1- fitted vs residuals plot
- 2- Normal Q-Q plot
- 3- Scale-Location plot
- 4- Cook's distance plot
- 5- residuals vs each predictor plot
- }
- \item{caption}{ Caption for each type of plot}
- \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{\dots}{ parameters passed to \code{plot.lm2}. }
- \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}
- \item{cex.id}{Parameter to control the height of text stringsx}
- \item{band}{logical vector indicating whether bandplot should also be plotted }
- \item{rug}{logical vector indicating whether rug should be added to
- the existing plot }
- \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{gr...@wa...} and Nitin
- Jain \email{nit...@pf...}}
-\examples{
-ctl <- rnorm(100, 4)
-trt <- rnorm(100, 4.5)
-group <- gl(2,100,200, labels=c("Ctl","Trt"))
-weight <- c(ctl, trt)
-wt.err <- rnorm(length(weight), mean=weight, sd=1/2)
-x <- lm(weight ~ group + wt.err)
-
-plot.lm2(x)
-
-plot.lm2(x, which=1, width=1/3)
-plot.lm2(x, which=1:3, widht=1/3)
-}
-\keyword{hplot}
Copied: trunk/gplots/man/lmplot2.Rd (from rev 1735, trunk/gplots/man/plot.lm2.Rd)
===================================================================
--- trunk/gplots/man/lmplot2.Rd (rev 0)
+++ trunk/gplots/man/lmplot2.Rd 2013-10-15 02:09:31 UTC (rev 1738)
@@ -0,0 +1,79 @@
+\name{lmplot2}
+\alias{lmplot2}
+\title{
+ Plots to assess the goodness of fit for the linear model objects
+}
+\description{
+ Plots to assess the goodness of fit for the linear model objects
+ }
+ \usage{
+ lmplot2(
+ 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 = interactive() && nb.fig < length(which)
+ && .Device != "postscript",
+ ...,
+ id.n = 3,
+ labels.id = names(residuals(x)),
+ cex.id = 0.75,
+ band=TRUE,
+ rug=TRUE,
+ width=1/10,
+ max.n=5000
+ )
+}
+\arguments{
+ \item{x}{lm object}
+ \item{which}{Numerical values between 1 and 5, indicating which plots
+ to be shown. The codes are:
+ \describe{
+ \item{1}{Fitted vs residuals}
+ \item{2}{Normal Q-Q}
+ \item{3}{Scale-Location}
+ \item{4}{Cook's distance}
+ \item{5}{Residuals vs. predictor}
+ }
+ }
+ \item{caption}{ Caption for each type of plot}
+ \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{\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}
+ \item{cex.id}{Parameter to control the height of text stringsx}
+ \item{band}{logical vector indicating whether bandplot should also be plotted }
+ \item{rug}{logical vector indicating whether rug should be added to
+ the existing plot }
+ \item{width}{Fraction of the data to use for plot smooths}
+ \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.
+}
+\author{Gregory R. Warnes \email{gr...@wa...} and Nitin
+ Jain \email{nit...@pf...}}
+\seealso{
+ \code{\link[stats]{plot.lm}}
+ }
+\examples{
+ctl <- rnorm(100, 4)
+trt <- rnorm(100, 4.5)
+group <- gl(2,100,200, labels=c("Ctl","Trt"))
+weight <- c(ctl, trt)
+wt.err <- rnorm(length(weight), mean=weight, sd=1/2)
+x <- lm(weight ~ group + wt.err)
+
+lmplot2(x)
+
+lmplot2(x, which=1, width=1/3)
+lmplot2(x, which=1:3, widht=1/3)
+}
+\keyword{hplot}
Deleted: trunk/gplots/man/plot.lm2.Rd
===================================================================
--- trunk/gplots/man/plot.lm2.Rd 2013-10-15 01:47:31 UTC (rev 1737)
+++ trunk/gplots/man/plot.lm2.Rd 2013-10-15 02:09:31 UTC (rev 1738)
@@ -1,71 +0,0 @@
-\name{plot.lm2}
-\alias{plot.lm2}
-\title{
- Plots to assess the goodness of fit for the linear model objects
-}
-\description{
- Plots to assess the goodness of fit for the linear model objects
- }
- \usage{
- 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 = interactive() && nb.fig < length(which)
- && .Device != "postscript",
- ...,
- id.n = 3,
- labels.id = names(residuals(x)),
- cex.id = 0.75,
- band=TRUE,
- rug=TRUE,
- width=1/10,
- max.n=5000
- )
-}
-\arguments{
- \item{x}{lm object}
- \item{which}{Numerical values between 1 and 5, indicating which plots
- to be shown. The codes are:
-
- 1- fitted vs residuals plot
- 2- Normal Q-Q plot
- 3- Scale-Location plot
- 4- Cook's distance plot
- 5- residuals vs each predictor plot
- }
- \item{caption}{ Caption for each type of plot}
- \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{\dots}{ parameters passed to \code{plot.lm2}. }
- \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}
- \item{cex.id}{Parameter to control the height of text stringsx}
- \item{band}{logical vector indicating whether bandplot should also be plotted }
- \item{rug}{logical vector indicating whether rug should be added to
- the existing plot }
- \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{gr...@wa...} and Nitin
- Jain \email{nit...@pf...}}
-\examples{
-ctl <- rnorm(100, 4)
-trt <- rnorm(100, 4.5)
-group <- gl(2,100,200, labels=c("Ctl","Trt"))
-weight <- c(ctl, trt)
-wt.err <- rnorm(length(weight), mean=weight, sd=1/2)
-x <- lm(weight ~ group + wt.err)
-
-plot.lm2(x)
-
-plot.lm2(x, which=1, width=1/3)
-plot.lm2(x, which=1:3, widht=1/3)
-}
-\keyword{hplot}
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|
|
From: <wa...@us...> - 2013-10-15 01:47:34
|
Revision: 1737
http://sourceforge.net/p/r-gregmisc/code/1737
Author: warnes
Date: 2013-10-15 01:47:31 +0000 (Tue, 15 Oct 2013)
Log Message:
-----------
Make lmplot2 manual page from plot.lm.2 manual page.
Added Paths:
-----------
trunk/gplots/man/lmplot2.Rd
Copied: trunk/gplots/man/lmplot2.Rd (from rev 1736, trunk/gplots/man/plot.lm2.Rd)
===================================================================
--- trunk/gplots/man/lmplot2.Rd (rev 0)
+++ trunk/gplots/man/lmplot2.Rd 2013-10-15 01:47:31 UTC (rev 1737)
@@ -0,0 +1,71 @@
+\name{plot.lm2}
+\alias{plot.lm2}
+\title{
+ Plots to assess the goodness of fit for the linear model objects
+}
+\description{
+ Plots to assess the goodness of fit for the linear model objects
+ }
+ \usage{
+ 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 = interactive() && nb.fig < length(which)
+ && .Device != "postscript",
+ ...,
+ id.n = 3,
+ labels.id = names(residuals(x)),
+ cex.id = 0.75,
+ band=TRUE,
+ rug=TRUE,
+ width=1/10,
+ max.n=5000
+ )
+}
+\arguments{
+ \item{x}{lm object}
+ \item{which}{Numerical values between 1 and 5, indicating which plots
+ to be shown. The codes are:
+
+ 1- fitted vs residuals plot
+ 2- Normal Q-Q plot
+ 3- Scale-Location plot
+ 4- Cook's distance plot
+ 5- residuals vs each predictor plot
+ }
+ \item{caption}{ Caption for each type of plot}
+ \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{\dots}{ parameters passed to \code{plot.lm2}. }
+ \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}
+ \item{cex.id}{Parameter to control the height of text stringsx}
+ \item{band}{logical vector indicating whether bandplot should also be plotted }
+ \item{rug}{logical vector indicating whether rug should be added to
+ the existing plot }
+ \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{gr...@wa...} and Nitin
+ Jain \email{nit...@pf...}}
+\examples{
+ctl <- rnorm(100, 4)
+trt <- rnorm(100, 4.5)
+group <- gl(2,100,200, labels=c("Ctl","Trt"))
+weight <- c(ctl, trt)
+wt.err <- rnorm(length(weight), mean=weight, sd=1/2)
+x <- lm(weight ~ group + wt.err)
+
+plot.lm2(x)
+
+plot.lm2(x, which=1, width=1/3)
+plot.lm2(x, which=1:3, widht=1/3)
+}
+\keyword{hplot}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2013-10-15 01:47:00
|
Revision: 1736
http://sourceforge.net/p/r-gregmisc/code/1736
Author: warnes
Date: 2013-10-15 01:46:57 +0000 (Tue, 15 Oct 2013)
Log Message:
-----------
Make boxplot2 manual page from boxplot.n manual page.
Added Paths:
-----------
trunk/gplots/man/boxplot2.Rd
Copied: trunk/gplots/man/boxplot2.Rd (from rev 1735, trunk/gplots/man/boxplot.n.Rd)
===================================================================
--- trunk/gplots/man/boxplot2.Rd (rev 0)
+++ trunk/gplots/man/boxplot2.Rd 2013-10-15 01:46:57 UTC (rev 1736)
@@ -0,0 +1,57 @@
+% $Id$
+%
+% $Log$
+% Revision 1.5 2005/12/01 16:46:52 nj7w
+% Updated Greg's email address
+%
+% Revision 1.4 2005/06/09 14:20:28 nj7w
+% Updating the version number, and various help files to synchronize splitting of gregmisc bundle in 4 individual components.
+%
+% Revision 1.1.1.1 2005/05/25 22:15:30 nj7w
+% Initial submission as an individual package
+%
+% Revision 1.3 2002/04/09 00:51:31 warneg
+%
+% Checkin for version 0.5.3
+%
+% Revision 1.2 2001/08/25 05:46:21 warneg
+% Added CVS header.
+%
+% Revision 1.1 2001/08/25 05:45:10 warneg
+% Initial Checkin
+%
+\name{boxplot.n}
+\alias{boxplot.n}
+\title{Produce a Boxplot Annotated with the Number of Observations}
+\description{
+ This funcntion uses \code{boxplot} to produce a boxplot which is then
+ annotated with the number of observations in each group.
+}
+\usage{
+boxplot.n(..., top=FALSE, shrink=1, textcolor=NULL)
+}
+\arguments{
+ \item{\dots}{ parameters passed to \code{boxplot}. }
+ \item{top}{ logical indicating whether the number of observations
+ should be added to the top or the bottom of the plotting
+ region. Defaults to \code{FALSE}. }
+ \item{shrink}{ value to shrink character size (cex) when annotating.}
+ \item{textcolor}{ text color. }
+}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
+\seealso{ \code{\link{boxplot}}, \code{\link{text}}}
+
+\examples{
+data(state)
+
+# n's at bottom
+boxplot.n( state.area ~ state.region)
+
+# n's at top
+boxplot.n( state.area ~ state.region, top=TRUE)
+
+# small red text
+boxplot.n( state.area ~ state.region, shrink=0.8, textcolor="red")
+}
+
+\keyword{ hplot }
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|
|
From: <wa...@us...> - 2013-10-15 01:33:41
|
Revision: 1735
http://sourceforge.net/p/r-gregmisc/code/1735
Author: warnes
Date: 2013-10-15 01:33:39 +0000 (Tue, 15 Oct 2013)
Log Message:
-----------
Create deprecated man page from boxplot.n man page
Added Paths:
-----------
trunk/gplots/man/gplots-deprecated.Rd
Copied: trunk/gplots/man/gplots-deprecated.Rd (from rev 1734, trunk/gplots/man/boxplot.n.Rd)
===================================================================
--- trunk/gplots/man/gplots-deprecated.Rd (rev 0)
+++ trunk/gplots/man/gplots-deprecated.Rd 2013-10-15 01:33:39 UTC (rev 1735)
@@ -0,0 +1,57 @@
+% $Id$
+%
+% $Log$
+% Revision 1.5 2005/12/01 16:46:52 nj7w
+% Updated Greg's email address
+%
+% Revision 1.4 2005/06/09 14:20:28 nj7w
+% Updating the version number, and various help files to synchronize splitting of gregmisc bundle in 4 individual components.
+%
+% Revision 1.1.1.1 2005/05/25 22:15:30 nj7w
+% Initial submission as an individual package
+%
+% Revision 1.3 2002/04/09 00:51:31 warneg
+%
+% Checkin for version 0.5.3
+%
+% Revision 1.2 2001/08/25 05:46:21 warneg
+% Added CVS header.
+%
+% Revision 1.1 2001/08/25 05:45:10 warneg
+% Initial Checkin
+%
+\name{boxplot.n}
+\alias{boxplot.n}
+\title{Produce a Boxplot Annotated with the Number of Observations}
+\description{
+ This funcntion uses \code{boxplot} to produce a boxplot which is then
+ annotated with the number of observations in each group.
+}
+\usage{
+boxplot.n(..., top=FALSE, shrink=1, textcolor=NULL)
+}
+\arguments{
+ \item{\dots}{ parameters passed to \code{boxplot}. }
+ \item{top}{ logical indicating whether the number of observations
+ should be added to the top or the bottom of the plotting
+ region. Defaults to \code{FALSE}. }
+ \item{shrink}{ value to shrink character size (cex) when annotating.}
+ \item{textcolor}{ text color. }
+}
+\author{ Gregory R. Warnes \email{gr...@wa...}}
+\seealso{ \code{\link{boxplot}}, \code{\link{text}}}
+
+\examples{
+data(state)
+
+# n's at bottom
+boxplot.n( state.area ~ state.region)
+
+# n's at top
+boxplot.n( state.area ~ state.region, top=TRUE)
+
+# small red text
+boxplot.n( state.area ~ state.region, shrink=0.8, textcolor="red")
+}
+
+\keyword{ hplot }
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|
|
From: <wa...@us...> - 2013-10-12 00:14:42
|
Revision: 1734
http://sourceforge.net/p/r-gregmisc/code/1734
Author: warnes
Date: 2013-10-12 00:14:37 +0000 (Sat, 12 Oct 2013)
Log Message:
-----------
Update NEWS with latest changes
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2013-10-12 00:09:52 UTC (rev 1733)
+++ trunk/gplots/inst/NEWS 2013-10-12 00:14:37 UTC (rev 1734)
@@ -9,10 +9,24 @@
Bug Fixes:
-- Fix bug in venn diagram code when number of TRUE cases in each
- variable are equal.
+- Fix error in in venn() when all groups contained the same number of TRUE cases.
+- Correct error in overplot() when that occured when a group-category contained no
+ finite values.
+Other Changes:
+
+- Changes to overplot() to avoid warnings from upcoming enhancements to R CMD check.
+
+- Move several packages from Depends to Imports or Suggests.
+
+- Packages caTools and KernSmooth now have namespaces, so import
+ needed functions in NAMESPACE.
+
+- Mark one example in manual page for ci2d 'dontrun' to avoid timing
+ warning in R CMD check.
+
+
Release 2.11.3 - 2013-06-27
---------------------------
@@ -25,9 +39,7 @@
- Fixed typo/spelling error in plotmeans() man page.
-Other changes
-
Release 2.11.2 - 2013-03-24
---------------------------
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|
|
From: <wa...@us...> - 2013-10-12 00:09:55
|
Revision: 1733
http://sourceforge.net/p/r-gregmisc/code/1733
Author: warnes
Date: 2013-10-12 00:09:52 +0000 (Sat, 12 Oct 2013)
Log Message:
-----------
Mark one example dontrun to avoid --as-cran warning.
Modified Paths:
--------------
trunk/gplots/man/ci2d.Rd
Modified: trunk/gplots/man/ci2d.Rd
===================================================================
--- trunk/gplots/man/ci2d.Rd 2013-10-11 22:09:09 UTC (rev 1732)
+++ trunk/gplots/man/ci2d.Rd 2013-10-12 00:09:52 UTC (rev 1733)
@@ -256,6 +256,7 @@
####
## Test with a large number of points
####
+ \dontrun{
x <- rnorm(60000, sd=1)
y <- c( rnorm(40000, mean=x, sd=1),
rnorm(20000, mean=x+4, sd=1) )
@@ -263,7 +264,7 @@
hist2d(x,y)
ci <- ci2d(x,y)
ci
-
+ }
}
\keyword{dplot}
\keyword{hplot}
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|
From: <wa...@us...> - 2013-10-11 22:09:13
|
Revision: 1732
http://sourceforge.net/p/r-gregmisc/code/1732
Author: warnes
Date: 2013-10-11 22:09:09 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Allow standard S3 method handling to locate the correct function.
Modified Paths:
--------------
trunk/gplots/R/overplot.R
Modified: trunk/gplots/R/overplot.R
===================================================================
--- trunk/gplots/R/overplot.R 2013-10-11 22:06:20 UTC (rev 1731)
+++ trunk/gplots/R/overplot.R 2013-10-11 22:09:09 UTC (rev 1732)
@@ -4,10 +4,10 @@
{
m <- match.call()
- m[[1]] <- graphics:::plot.formula
+ m[[1]] <- as.name("plot")
eval(m, parent.frame() )
- m[[1]] <- gplots:::lowess.formula
+ m[[1]] <- as.name("lowess")
tmp <- eval(m, parent.frame() )
lines( tmp, col=col, lwd=2, lty=lty )
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|
|
From: <wa...@us...> - 2013-10-11 22:06:22
|
Revision: 1731
http://sourceforge.net/p/r-gregmisc/code/1731
Author: warnes
Date: 2013-10-11 22:06:20 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Fix error when a subgroup contains no finite values
Modified Paths:
--------------
trunk/gplots/R/overplot.R
Modified: trunk/gplots/R/overplot.R
===================================================================
--- trunk/gplots/R/overplot.R 2013-10-11 21:20:55 UTC (rev 1730)
+++ trunk/gplots/R/overplot.R 2013-10-11 22:06:20 UTC (rev 1731)
@@ -151,6 +151,10 @@
mycall$lty = i
tmp.y <- y[mycall$subset & cond==level]
+
+ ## If nothing to plot, skip to next level
+ if(!any(is.finite(tmp.y))) next
+
min.tmp.y <- min(tmp.y, na.rm=TRUE)
max.tmp.y <- max(tmp.y, na.rm=TRUE)
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|
|
From: <wa...@us...> - 2013-10-11 21:20:58
|
Revision: 1730
http://sourceforge.net/p/r-gregmisc/code/1730
Author: warnes
Date: 2013-10-11 21:20:55 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Update test output
Modified Paths:
--------------
trunk/gplots/tests/heatmap2Test.Rout.save
Modified: trunk/gplots/tests/heatmap2Test.Rout.save
===================================================================
--- trunk/gplots/tests/heatmap2Test.Rout.save 2013-10-11 21:08:34 UTC (rev 1729)
+++ trunk/gplots/tests/heatmap2Test.Rout.save 2013-10-11 21:20:55 UTC (rev 1730)
@@ -1,5 +1,5 @@
-R version 3.0.1 (2013-05-16) -- "Good Sport"
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)
@@ -16,28 +16,8 @@
Type 'q()' to quit R.
> library(gplots)
-Loading required package: gtools
-Loading required package: gdata
-gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
-
-gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
-
-Attaching package: 'gdata'
-
-The following object is masked from 'package:stats':
-
- nobs
-
-The following object is masked from 'package:utils':
-
- object.size
-
-Loading required package: caTools
-Loading required package: grid
-Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
-Loading required package: MASS
Attaching package: 'gplots'
@@ -244,4 +224,4 @@
>
> proc.time()
user system elapsed
- 5.104 0.356 5.478
+ 4.852 0.372 5.389
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From: <wa...@us...> - 2013-10-11 21:08:37
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Revision: 1729
http://sourceforge.net/p/r-gregmisc/code/1729
Author: warnes
Date: 2013-10-11 21:08:34 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Move several packages from Depends to Imports, Suggests
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2013-10-11 21:07:30 UTC (rev 1728)
+++ trunk/gplots/DESCRIPTION 2013-10-11 21:08:34 UTC (rev 1729)
@@ -1,9 +1,9 @@
Package: gplots
Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
-Depends: R (>= 3.0), gtools, gdata, stats, caTools, grid, KernSmooth,
- MASS, datasets
-Suggests: gtools, grid
+Depends: R (>= 3.0)
+Imports: gtools, gdata, stats, caTools, KernSmooth
+Suggests: grid, MASS
Version: 2.12.0
Date: 2013-10-11
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
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From: <wa...@us...> - 2013-10-11 21:07:32
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Revision: 1728
http://sourceforge.net/p/r-gregmisc/code/1728
Author: warnes
Date: 2013-10-11 21:07:30 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Use gdata::nobs in example
Modified Paths:
--------------
trunk/gplots/man/ci2d.Rd
Modified: trunk/gplots/man/ci2d.Rd
===================================================================
--- trunk/gplots/man/ci2d.Rd 2013-10-11 21:03:34 UTC (rev 1727)
+++ trunk/gplots/man/ci2d.Rd 2013-10-11 21:07:30 UTC (rev 1728)
@@ -208,7 +208,7 @@
sd.x <- sd(geyser$duration)
sd.y <- sd(geyser$waiting)
- t.value <- qt(c(0.05,0.95), df=nobs(geyser$duration), lower=TRUE)
+ t.value <- qt(c(0.05,0.95), df=gdata::nobs(geyser$duration), lower=TRUE)
ci.x <- mean.x + t.value* sd.x
ci.y <- mean.y + t.value* sd.y
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From: <wa...@us...> - 2013-10-11 21:03:36
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Revision: 1727
http://sourceforge.net/p/r-gregmisc/code/1727
Author: warnes
Date: 2013-10-11 21:03:34 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
caTools and KernSmooth now have namespaces, so import from them.
Modified Paths:
--------------
trunk/gplots/NAMESPACE
Modified: trunk/gplots/NAMESPACE
===================================================================
--- trunk/gplots/NAMESPACE 2013-10-11 20:24:57 UTC (rev 1726)
+++ trunk/gplots/NAMESPACE 2013-10-11 21:03:34 UTC (rev 1727)
@@ -40,12 +40,12 @@
importFrom(stats, na.omit)
# No Namespace
-#importFrom(caTools, runsd)
-#importFrom(caTools, runmean)
+importFrom(caTools, runsd)
+importFrom(caTools, runmean)
# No Namespace
-#importFrom(KernSmooth, bkdeD2)
-#importFrom(KernSmooth, dpik)
+importFrom(KernSmooth, bkde2D)
+importFrom(KernSmooth, dpik)
S3method(balloonplot,default)
S3method(balloonplot,table)
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