[Gsdesign-commits] r259 - in pkg: gsDesign gsDesign/R gsDesignGUIReview/osx
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jan 18 21:04:30 CET 2010
Author: keaven
Date: 2010-01-18 21:04:29 +0100 (Mon, 18 Jan 2010)
New Revision: 259
Added:
pkg/gsDesignGUIReview/osx/gsDesign_2.2-9.tar.gz
pkg/gsDesignGUIReview/osx/gsDesign_2.2-9.zip
Modified:
pkg/gsDesign/DESCRIPTION
pkg/gsDesign/R/gsCP.R
pkg/gsDesign/R/gsqplot.R
Log:
2.2-9 Conditional power and ggplot2 legend fixes
Modified: pkg/gsDesign/DESCRIPTION
===================================================================
--- pkg/gsDesign/DESCRIPTION 2010-01-18 02:48:05 UTC (rev 258)
+++ pkg/gsDesign/DESCRIPTION 2010-01-18 20:04:29 UTC (rev 259)
@@ -1,5 +1,5 @@
Package: gsDesign
-Version: 2.2-8
+Version: 2.2-9
Title: Group Sequential Design
Author: Keaven Anderson
Maintainer: Keaven Anderson <keaven_anderson at merck.com>
Modified: pkg/gsDesign/R/gsCP.R
===================================================================
--- pkg/gsDesign/R/gsCP.R 2010-01-18 02:48:05 UTC (rev 258)
+++ pkg/gsDesign/R/gsCP.R 2010-01-18 20:04:29 UTC (rev 259)
@@ -96,10 +96,9 @@
len <- x$k-1
test.type <- ifelse(is(x, "gsProbability"), 3, x$test.type)
-
- if (is(x, "gsDesign") || theta != "thetahat")
+ if (theta != "thetahat")
{
- thetahi <- array(x$delta, len)
+ thetahi <- array(theta, len)
if (test.type > 1) thetalow <- thetahi
}else
{
Modified: pkg/gsDesign/R/gsqplot.R
===================================================================
--- pkg/gsDesign/R/gsqplot.R 2010-01-18 02:48:05 UTC (rev 258)
+++ pkg/gsDesign/R/gsqplot.R 2010-01-18 20:04:29 UTC (rev 259)
@@ -93,10 +93,10 @@
cp
}
# qplots for z-values and transforms of z-values
-"qplotit" <- function(x, xlim=NULL, ylim=NULL, main=main, geom=c("line", "text"),
+"qplotit" <- function(x, xlim=NULL, ylim=NULL, main=NULL, geom=c("line", "text"),
dgt=2, lty=c(2,1), col=c(1,1),
lwd=c(1,1), nlabel="TRUE", xlab=NULL, ylab=NULL, fn=function(z,i,x,...){z},
- ratio=1, delta0=0, delta=.05, cex=1, base=FALSE,...)
+ ratio=1, delta0=0, delta=1, cex=1, base=FALSE,...)
{ if (length(lty)==1) lty <- array(lty, 2)
if (length(col)==1) col <- array(col, 2)
if (length(lwd)==1) lwd <- array(lwd, 2)
@@ -136,12 +136,13 @@
main=main, lty=lty[1], col=col[1], lwd=lwd[1], xlab=xlab, ylab=ylab,...)
lines(x=y$N[y$Bound=="Lower"], y=y$Z[y$Bound=="Lower"], lty=lty[2], col=col[2], lwd=lwd[2])
}else
- { p <- qplot(x=as.numeric(N), y=as.numeric(Z), data=y,
- group=factor(Bound), colour=factor(Bound), geom=geom, label=Ztxt,
- xlab=xlab, ylab=ylab, main=main,
- ylim=ylim, xlim=xlim,...) + aes(lty=factor(Bound)) +
- scale_colour_manual(name= "Bound", values=col, labels=c("Lower","Upper")) +
- scale_linetype_manual(name= "Bound", values=lty, labels=c("Lower","Upper"))
+ { GeomText$guide_geom <- function(.) "blank"
+ p <- qplot(x=as.numeric(N), y=as.numeric(Z), data=y,
+ group=factor(Bound), colour=factor(Bound), geom=geom, label=Ztxt,
+ xlab=xlab, ylab=ylab, main=main,
+ ylim=ylim, xlim=xlim,...) + aes(lty=factor(Bound)) +
+ scale_colour_manual(name= "Bound", values=col, labels=c("Lower","Upper")) +
+ scale_linetype_manual(name= "Bound", values=lty, labels=c("Lower","Upper"))
}
if (nlabel==TRUE)
{ y2 <- data.frame(
@@ -157,13 +158,13 @@
{ if (base)
{ text(x=y2$N, y=y2$Z, paste(array("r=",x$k), y2$Ztxt, sep=""), cex=cex)
}else
- { p <- p + geom_text(data=y2, label=paste(array("r=",x$k), y2$Ztxt, sep=""))
+ { p <- p + geom_text(data=y2, colour=1, label=paste(array("r=",x$k), y2$Ztxt, sep=""))
}
}else
{ if(base)
{ text(x=y2$N, y=y2$Z, paste(array("N=",x$k), y2$Ztxt, sep=""), cex=cex)
}else
- { p <- p + geom_text(data=y2, aes(N,Z, group=factor(Bound)), label=paste(array("N=",x$k), y2$Ztxt, sep=""))
+ { p <- p + geom_text(data=y2, aes(N,Z, group=factor(Bound)), colour=1, label=paste(array("N=",x$k), y2$Ztxt, sep=""))
}
} }
if (base)
@@ -174,16 +175,19 @@
}
"plotgsCP" <- function(x, theta="thetahat", main="Conditional power at interim stopping boundaries",
- ylab=NULL, geom="line",
+ ylab=NULL, geom=c("line","text"),
xlab=ifelse(x$n.fix == 1, "Sample size relative to fixed design", "N"), xlim=NULL,
- lty=1, col=1, pch=22, textcex=1, legtext=NULL, dgt=3, nlabel=TRUE,
+ lty=1, col=1, lwd=1, pch=22, textcex=1, legtext=NULL, dgt=3, nlabel=TRUE,
base=FALSE, ...)
-{
+{ if (length(lty)==1) lty <- array(lty, 2)
+ if (length(col)==1) col <- array(col, 2)
+ if (length(lwd)==1) lwd <- array(lwd, 2)
+ if (length(dgt)==1) dgt <- array(dgt, 2)
if (is.null(ylab))
{ ylab <- ifelse(theta == "thetahat",
expression(paste("Conditional power at",
- theta, "=", hat(theta),sep=" ")),
- expression(paste("Conditional power at", theta, "=", delta)))
+ theta, " = ", hat(theta),sep=" ")),
+ "Conditional power")
}
if (!is.numeric(xlim))
{ xlim <- range(x$n.I[1:(x$k-1)])
@@ -233,7 +237,7 @@
else
{
matplot(x$n.I[1:(x$k-1)], y, xlab=xlab, ylab=ylab, main = main,
- lty=lty, col=col, ylim=c(ymin, ymax), xlim=xlim, type="l", ...)
+ lty=lty, col=col, lwd=lwd, ylim=c(ymin, ymax), xlim=xlim, type="l", ...)
matpoints(x$n.I[1:(x$k-1)], y, pch=pch, col=col, ...)
text(xtext, ymin, legtext[3], cex=textcex)
}
@@ -251,15 +255,18 @@
Ztxt <- as.character(c(Ztxt ,round(y[,1],dgt)))
}
y <- data.frame(N=N, CP=CP, Bound=Bound, Ztxt=Ztxt)
+ GeomText$guide_geom <- function(.) "blank"
p <- qplot(x=as.numeric(N), y=as.numeric(CP), data=y, main=main,
- group=Bound, geom=c("line","text"), label=Ztxt,
- xlab=xlab, ylab=ylab, ylim=c(ymin, ymax), xlim=xlim,...)
+ group=factor(Bound), colour=factor(Bound), geom=geom, label=Ztxt,
+ xlab=xlab, ylab=ylab, ylim=c(ymin, ymax), xlim=xlim) + aes(lty=factor(Bound)) +
+ scale_colour_manual(name= "Bound", values=col, labels=c("Lower","Upper")) +
+ scale_linetype_manual(name= "Bound", values=lty, labels=c("Lower","Upper"))
}
if (nlabel==TRUE)
{ y2 <- data.frame(
N=x$n.I[1:(x$k-1)],
CP=array(ymin/2, x$k-1),
- Bound=array("Ntxt", x$k-1),
+ Bound=array("Lower", x$k-1),
Ztxt=as.character(round(x$n.I[1:(x$k-1)],nround)))
if (base)
{ #text(x=x$n.I[1:(x$k-1)], y=array(ymin/2, x$k-1), as.character(round(x$n.I[1:(x$k-1)],nround)), cex=textcex)
@@ -268,13 +275,15 @@
{ if (base)
{ text(x=y2$N, y=y2$CP, paste(array("r=",x$k), y2$Ztxt, sep=""), cex=textcex)
}else
- { p <- p + geom_text(data=y2,label=paste(array("r=",x$k), y2$Ztxt, sep=""))
+ { p <- p + geom_text(data=y2, aes(N,CP, group=factor(Bound)), colour=1,
+ label=paste(array("r=",x$k), y2$Ztxt, sep=""))
}
}else
{ if(base)
{ text(x=y2$N, y=y2$CP, paste(array("N=",x$k), y2$Ztxt, sep=""), cex=textcex)
}else
- { p <- p + geom_text(data=y2,label=paste(array("N=",x$k-1), y2$Ztxt, sep=""))
+ { p <- p + geom_text(data=y2, aes(N,CP, group=factor(Bound)), colour=1,
+ label=paste(array("N=",x$k), y2$Ztxt, sep=""))
}
} }
if (base)
Added: pkg/gsDesignGUIReview/osx/gsDesign_2.2-9.tar.gz
===================================================================
(Binary files differ)
Property changes on: pkg/gsDesignGUIReview/osx/gsDesign_2.2-9.tar.gz
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: pkg/gsDesignGUIReview/osx/gsDesign_2.2-9.zip
===================================================================
(Binary files differ)
Property changes on: pkg/gsDesignGUIReview/osx/gsDesign_2.2-9.zip
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
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