Nothing
##' Visualizing the result of \code{\link{mctp}}
##'
##' This function takes an object of class "mctp" and creates a plot of the
##' confidence intervals for the estimated effects.
##'
##' It is not possible to change any parameter set in the
##' \code{\link{mctp}}-statement.
##'
##' Since plot.mctp is a S3 method it suffices to use plot(x) as long as x is
##' of class "mctp". It will be interpreted as plot.mctp(x).
##'
##' @param x An object of class "mctp", i.e. the result when applying
##' \code{\link{mctp}} to a dataset. Otherwise an error will occur.
##' @param ... Arguments to be passed to methods.
##' @return plot.mctp returns a graph that contains a confidence interval for
##' the estimated effect of each contrast. It just visualizes the result of the
##' \code{\link{mctp}}-statement.
##' @note It is possible to create a graphical result of the multiple
##' comparison test procedure directly by setting plot.simci=TRUE in the
##' \code{\link{mctp}}-statement.
##'
##' To get a complete result summary of \code{\link{mctp}} the function
##' \code{\link{summary.mctp}} can be used.
##' @author Frank Konietschke, Kimihiro Noguchi
##' @seealso For further information on the usage of mctp, see
##' \code{\link{mctp}}.
##' @references F. Konietschke, L.A. Hothorn, E. Brunner: Rank-Based Multiple
##' Test Procedures and Simultaneous Confidence Intervals. Electronic Journal
##' of Statistics, Vol.0 (2011) 1-8.
##' @keywords aplot
##' @examples
##'
##' data(liver)
##' a<-mctp(weight ~dosage, data=liver, asy.method = "fisher",
##' type = "Dunnett", alternative = "two.sided", plot.simci = FALSE,
##' info = FALSE)
##' plot(a)
##'
plot.mctp <-
function(x,...)
{
nc <- length(x$connames)
text.Ci <- paste(x$input$conf.level*100, "%", "Simultaneous Confidence Intervals")
Lowerp <- "|"
#updated
asy.method <- x$input$asy.method
alternative <- x$input$alternative
if(asy.method!="log.odds") {
plot(x$Analysis.Inf$Estimator,1:nc,xlim=c(-1,1), pch=15,axes=FALSE,xlab="",ylab="")
points(x$Analysis.Inf$Lower,1:nc, pch=Lowerp,font=2,cex=2)
points(x$Analysis.Inf$Upper,1:nc, pch=Lowerp,font=2,cex=2)
abline(v=0, lty=3,lwd=2)
for (ss in 1:nc){
polygon(x=c(x$Analysis.Inf$Lower[ss],x$Analysis.Inf$Upper[ss]),y=c(ss,ss),lwd=2)
}
axis(1, at = seq(-1, 1, 0.1))
}
else {#log.odds
if(alternative=="two.sided") {
LowerPlot <- x$Analysis.Inf$Lower
UpperPlot <- x$Analysis.Inf$Upper
}
else if(alternative=="less") {
LowerPlot <- x$Analysis.Inf$Estimator - (x$Analysis.Inf$Upper - x$Analysis.Inf$Estimator)
UpperPlot <- x$Analysis.Inf$Upper
}
else { #alternative=="greater"
LowerPlot <- x$Analysis.Inf$Lower
UpperPlot <- x$Analysis.Inf$Estimator + (x$Analysis.Inf$Estimator - x$Analysis.Inf$Lower)
}
plot(x$Analysis.Inf$Estimator, 1:nc, xlim = c(floor(min(LowerPlot)), ceiling(max(UpperPlot))),
pch = 15, axes = FALSE, xlab = "", ylab = "")
axis(1, at = seq(floor(min(LowerPlot)), ceiling(max(UpperPlot)),
0.05*(ceiling(max(UpperPlot))-floor(min(LowerPlot)))))
hugenumber<-10000000
if(alternative=="two.sided") {
points(LowerPlot, 1:nc, pch = Lowerp, font = 2, cex = 2)
points(UpperPlot, 1:nc, pch = Lowerp, font = 2, cex = 2)
for (ss in 1:nc) {
polygon(x = c(LowerPlot[ss], UpperPlot[ss]), y = c(ss, ss), lwd = 2)
}
}
else if(alternative=="less") {
points(UpperPlot, 1:nc, pch = Lowerp, font = 2, cex = 2)
for (ss in 1:nc) {
polygon(x = c(-hugenumber, UpperPlot[ss]), y = c(ss, ss), lwd = 2)
}
}
else{ #greater
points(LowerPlot, 1:nc, pch = Lowerp, font = 2, cex = 2)
for (ss in 1:nc) {
polygon(x = c(LowerPlot[ss], hugenumber), y = c(ss, ss), lwd = 2)
}
}
abline(v = 0, lty = 3, lwd = 2)
}
axis(2,at=1:nc,labels=x$connames)
box()
title(main=c(text.Ci, paste("Type of Contrast:",x$input$type), paste("Method:", x$AsyMethod)))
}
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