[Gsdesign-commits] r275 - in pkg: gsDesign gsDesign/R gsDesign/man gsDesignGUI/inst/doc

[noreply at r-forge.r-project.org]

Author: keaven
Date: 2011-02-17 12:02:57 +0100 (Thu, 17 Feb 2011)
New Revision: 275

Modified:
   pkg/gsDesign/NAMESPACE
   pkg/gsDesign/R/gsqplot.R
   pkg/gsDesign/man/gsBoundSummary.Rd
   pkg/gsDesignGUI/inst/doc/gsDesignGUI.pdf
Log:
Added relative risk approximation and bound plot

Modified: pkg/gsDesign/NAMESPACE
===================================================================
--- pkg/gsDesign/NAMESPACE	2011-02-06 22:12:32 UTC (rev 274)
+++ pkg/gsDesign/NAMESPACE	2011-02-17 11:02:57 UTC (rev 275)
@@ -1,6 +1,6 @@
 useDynLib(gsDesign)
 export(gsBoundCP, gsCP, gsPP, gsPOS, gsCPOS, gsDensity)
-export(gsCPz, gsHR, gsDelta, gsBValue)
+export(gsCPz, gsHR, gsDelta, gsBValue, gsRR)
 export(gsBound, gsBound1, gsDesign, gsProbability)
 export(ciBinomial, nBinomial, simBinomial, testBinomial, gsBinomialExact)
 export(nSurvival, nEvents)

Modified: pkg/gsDesign/R/gsqplot.R
===================================================================
--- pkg/gsDesign/R/gsqplot.R	2011-02-06 22:12:32 UTC (rev 274)
+++ pkg/gsDesign/R/gsqplot.R	2011-02-17 11:02:57 UTC (rev 275)
@@ -7,8 +7,10 @@
 #    plot.gsProbability
 #    gsCPz
 #    gsHR
+#    gsRR
 #    gsDelta
 #    gsBValue
+#    qplotit
 #
 #  Hidden Functions:
 #
@@ -21,7 +23,6 @@
 #    sfplot
 #    plotASN
 #    plotgsPower
-#    qplotit
 #
 #  Author(s): Keaven Anderson, PhD.
 # 
@@ -67,7 +68,8 @@
             plotsf=c("5","sf"), 
             plotASN=c("6","asn", "e{n}","n"), 
             plotBval=c("7","b","b-val","b-value"),
-            plotHR=c("8","hr","hazard"))
+            plotHR=c("8","hr","hazard"),
+            plotRR=c("9","rr"))
     
     # perform partial matching on plot type and return name
     plottype <- match.arg(tolower(as.character(plottype)), as.vector(unlist(plots)))
@@ -81,8 +83,9 @@
             plotgsCP=c("4", "cp", "copp"),
             plotASN=c("6","asn", "e{n}","n"), 
             plotBval=c("7","b","b-val","b-value"),
-            plotHR=c("8","hr","hazard"))
-    
+            plotHR=c("8","hr","hazard"),
+            plotRR=c("9","rr"))
+
     # perform partial matching on plot type and return name
     plottype <- match.arg(tolower(as.character(plottype)), as.vector(unlist(plots)))
     names(plots)[which(unlist(lapply(plots, function(x, type) is.element(type, x), type=plottype)))]    
@@ -96,6 +99,7 @@
                    expression(hat(theta)/theta[1]))),...)
 }
 "plotHR" <- function(x=x, ylab="Estimated hazard ratio",main="Hazard ratio at bounds",...){qplotit(x, fn=gsHR,  ylab=ylab, main=main, ratio=1, ...)}
+"plotRR" <- function(x=x, ylab="Estimated risk ratio",main="Risk ratio at bounds",...){qplotit(x, fn=gsRR,  ylab=ylab, main=main, ratio=1, ...)}
 gsBValue <- function(z,i,x,ylab="B-value",...)
 {   Bval <- z * sqrt(x$timing[i])
     Bval
@@ -104,6 +108,10 @@
 {   deltaHat <- z / sqrt(x$n.I[i]) * (x$delta1-x$delta0) / x$delta + x$delta0
     deltaHat
 }
+gsRR <- function(z, i, x, ratio=1, ylab="Estimated risk ratio",...)
+{   deltaHat <- z / sqrt(x$n.I[i]) * (x$delta1-x$delta0) / x$delta + x$delta0
+    exp(deltaHat)
+}
 gsHR <- function(z, i, x, ratio=1, ylab="Estimated hazard ratio", ...)
 {    c <- 1 / (1 + ratio)
      psi <- c * (1 - c)

Modified: pkg/gsDesign/man/gsBoundSummary.Rd
===================================================================
--- pkg/gsDesign/man/gsBoundSummary.Rd	2011-02-06 22:12:32 UTC (rev 274)
+++ pkg/gsDesign/man/gsBoundSummary.Rd	2011-02-17 11:02:57 UTC (rev 275)
@@ -4,6 +4,7 @@
 \alias{gsBValue}
 \alias{gsDelta}
 \alias{gsHR}
+\alias{gsRR}
 \alias{gsCPz}
 
 \title{2.8: Bound Summary and Z-transformations}
@@ -19,6 +20,7 @@
     gsBValue <- function(z, i, x, ylab="B-value", ...)
     gsDelta(z, i, x, ylab=NULL, ...)
     gsHR(z, i, x, ratio=1, ylab="Estimated hazard ratio", ...)
+    gsRR(z, i, x, ratio=1, ylab="Estimated risk ratio",...)
     gsCPz(z, i, x, theta=NULL, ylab=NULL, ...)
     gsBoundSummary(x, upper=TRUE, ratio=1)
     xtable.gsDesign(x, caption=NULL, label=NULL, align=NULL, digits=c(0,0,3,4,4,4,3,3,3,3),
@@ -111,4 +113,8 @@
 # treatment effect at bounds is scaled to these differences
 # in this case, this is the difference in event rates
 gsDelta(z=xp$lower$bound, i=1:3, xp)
+# binomial endpoint with risk ratio estimates
+xrr <- gsDesign(n.fix=np, endpoint="Binomial", delta1=log(2/3))
+gsRR(z=xp$lower$bound, i=1:3, xrr)
+plot(xrr,plottype="RR")
 }

Modified: pkg/gsDesignGUI/inst/doc/gsDesignGUI.pdf
===================================================================
(Binary files differ)