#
# This file contains R commands that reproduce the analyses 
# presented in Chapter 6
#
# Read data on peak expiratory flow (PEF) from clinical trial to compare
# two drug-treatments for chronic asthma
#
asthma<-read.table("../data/asthma.data",header=T)
#
# Scatterplot of paired values of PEF
#
F<-asthma$F
S<-asthma$S
pdf(file="asthmascatterplot.pdf",paper="special",height=6,width=6)
par(pty="s")
plot(F,S,xlim=c(0,420),ylim=c(0,420),cex.lab=1.5,cex.axis=1.5,pch=19)
lines(c(0,420),c(0,420),lty=2)
dev.off()
#
# Dotplot of unpaired values of PEF
#
F<-asthma$F
S<-asthma$S
pdf(file="asthmadotplot.pdf",paper="special",height=3,width=6)
plot(F,rep(0.25,length(F)),xlim=c(0,420),ylim=c(0,1),cex.lab=1.5,cex.axis=1.5,pch="F",xlab="PEF",ylab=" ",
   bty="n",yaxt="n")
points(S,rep(0.75,length(S)),pch="S")
dev.off()
#
# Analysis of the data according to the (correct) paired design (Section 6.3.1)
#
F<-asthma$F
S<-asthma$S
D<-F-S
Dbar<-mean(D)
n<-length(D)
s2<-var(D)
SE<-sqrt(s2/n)
CI<-Dbar+c(-2,2)*SE
#
# Analysis of the data according to the (incorrect) parallel group design (Section 6.3.2)
#
Fbar<-mean(F)
sF<-sqrt(var(F))
Sbar<-mean(S)
sS<-sqrt(var(S))
s2pooled<-(sF*sF+sS*sS)/2
CI<-(Fbar-Sbar) + c(-2,2)*sqrt(2*s2pooled/n)
#
# Analysis of the data according to the (correct) crossover design - a refinement of the
# paired design (Section 6.4)
#
Dbar1<-mean(D[1:7])
Dbar2<-mean(D[8:13])
#
# Scatterplot of the data, showing clear difference between treatments, in favour of Formoterol
#
pdf(file="sol2.pdf",height=6,width=8)
par(pty="s")
plot(F,S,pch=19,cex=1,xlim=c(0,420),ylim=c(0,420),cex.lab=1.5,cex.axis=1.5)
lines(c(0,420),c(0,420),lty=2)
dev.off()