##### CHANGE TO YOUR WORKING DIRECTORY
setwd("~/DocInvest/MyPapers/sqj2012/datasets/sideeffects")

########################
######   Figures 5 and 6 

# actual values. Add this script to the others scripts  R
ci1score <- c(7.96, 9.71)
ci1Xscore <- c(5.70, 8.96)
#ci2score <- c(3.48, 5.52)
ci2score <- c(5.21, 8.29) #scaled

lowdelta20 <- -2.18
lowdelta25 <- -2.72
lowdelta50 <- -5.44
updelta20 <-  2.18
updelta25 <-  2.72
updelta50 <- 5.44

limxscore <- 11
namethisfile <- paste0(getwd(),"/Fig5",".pdf")
pdf(file=namethisfile, height=3, width=4.5)

#windows.options(width=10, height=5)
par(mar=c(3,0,0,0))
plot(0,0,type="n", xlim=c(lowdelta20,limxscore), ylim=c(0,1.5),axes=FALSE, ann=FALSE)

equivintervals <- c(limxscore,lowdelta20,0,updelta20,updelta50)
equivintervals <- sort(equivintervals)

labels <- c(
 #           expression(-Delta[paste(50,'%',sep="")]),
            expression(-Delta[paste(20,'%',sep="")]),
            0,
            expression(Delta[paste(20,'%',sep="")]),
            expression(Delta[paste(50,'%',sep="")]),
            limxscore)
axis(1, at=equivintervals, labels = labels, pos=0)
mtext(expression(mu[T]-mu[R]),at=0,side=1,line=2)
mtext("More Score in SEF",at=updelta50,side=1,line=2)

#abline(v=equivintervals,lty="dotted")
segments(c(lowdelta50,updelta50),c(0,0),c(lowdelta50,updelta50),c(1.5,1.5), lty=3,lwd=1)
segments(c(lowdelta20,updelta20),c(0,0),c(lowdelta20,updelta20),c(1,1), lty=3,lwd=1)

segments(ci1score[1],0.2,ci1score[2],lty=1,lwd=5, lend=2)
text(ci1score[1],0.2,"|",offset=0.5,cex=1.1,adj=1,font=2)
text(ci1score[2],0.2,"|",offset=0.5,cex=1.1,adj=0,font=2)
segments(ci1Xscore[1],0.7,ci1Xscore[2],lty=1,lwd=5, lend=2)
text(ci1Xscore[1],0.7,"|",offset=0.5,cex=1.1,adj=1,font=2)
text(ci1Xscore[2],0.7,"|",offset=0.5,cex=1.1,adj=0,font=2)
segments(ci2score[1],1.2,ci2score[2],lty=1,lwd=5, lend=2)
text(ci2score[1],1.2,"|",offset=0.5,cex=1.1,adj=1,font=2)
text(ci2score[2],1.2,"|",offset=0.5,cex=1.1,adj=0,font=2)

text(7.1,0.2,
     "Trial 1",
     offset=0.5,cex=0.9,adj=1)
text(8.7,0.2,
     paste("(",
           round(ci1score[1],2),",",
           round(ci1score[2],2),
           ")"),
     pos=3,offset=0.5,cex=0.8,adj=1)
text(5,0.7,
     "Trial 1X",
     offset=0.5,cex=0.9,adj=1)
text(7.2,0.7,
     paste("(",
           round(ci1Xscore[1],2),",",
           round(ci1Xscore[2],2),
           ")"),
     pos=3,offset=0.5,cex=0.8,adj=1)
text(3,1.2,
     "Trial 2",
     offset=0.5,cex=0.9,adj=1)
text(6.5,1.2,
     paste("(",
           round(ci2score[1],2),",",
           round(ci2score[2],2),
           ")"),
     pos=3,offset=0.5,cex=0.8,adj=1)
dev.off()  # for pdf et al


###################################################################3
## now for the TIME variable 
###################################################################3

namethisfile <- paste0(getwd(),"/Fig6",".pdf")
pdf(file=namethisfile, height=3, width=4.5) # ,pagecentre=TRUE) #, pagecentre=TRUE) 
#pdf("~/FigTime.pdf", height=5, width=9) #, pagecentre=TRUE) 

#limxtime <- max(abs(c(ci1time,ci1Xtime,ci2time)))
## should round to the largest and nearest digit plus extra axis space
#charlim <- as.character(ceiling(limxtime))
#limxtime <- (as.numeric(substr(charlim,1,1))+1)*10^(nchar(charlim)-1)

ci1time <- c(-119.22, -70.45)
ci1Xtime <- c(-98.48, -40.57)
#ci2time <- c(-368.22, -121.53)
ci2time <- c(-104.62, -34.53)  # scaled to Trial 1

# actual values
lowdelta20t <- -74.62
lowdelta25t <- -93.28
lowdelta50t <- -186.56
updelta20t <-  74.62
updelta25t <-  93.28
updelta50t <- 186.56

limxtime <- 220


par(mar=c(3,0,0,0))
plot(0,0,type="n", xlim=c(lowdelta50t,updelta20t), ylim=c(0,1.5),axes=FALSE, ann=FALSE)

equivintervals <- c(lowdelta50t,lowdelta20t,0,updelta20t)
equivintervals <- sort(equivintervals)

labels <- c(
  expression(-Delta[paste(50,'%',sep="")]),
  expression(-Delta[paste(20,'%',sep="")]),
  0,
  expression(Delta[paste(20,'%',sep="")]))       
#  expression(Delta[paste(20,'%',sep="")]))

axis(1, at=equivintervals, labels = labels, pos=0)
mtext(expression(mu[T]-mu[R]),at=0,side=1,line=2)
mtext("Less Time in SEF",at=-120,side=1,line=2)

#abline(v=equivintervals,lty="dotted")
segments(c(lowdelta50t,updelta50t),c(0,0),c(lowdelta50t,updelta50t),c(1.5,1.5), lty=3,lwd=1)
segments(c(lowdelta20t,updelta20t),c(0,0),c(lowdelta20t,updelta20t),c(1,1), lty=3,lwd=1)

segments(ci1time[1],0.2,ci1time[2],lty=1,lwd=5, lend=2)
text(ci1time[1],0.2,"|",offset=0.5,cex=1.1,adj=1, font=2)
text(ci1time[2],0.2,"|",offset=0.5,cex=1.1,adj=0,font=2)
segments(ci1Xtime[1],0.7,ci1Xtime[2],lty=1,lwd=5, lend=2)
text(ci1Xtime[1],0.7,"|",offset=0.5,cex=1.1,adj=1,font=2)
text(ci1Xtime[2],0.7,"|",offset=0.5,cex=1.1,adj=0,font=2)
segments(ci2time[1],1.2,ci2time[2],lty=1,lwd=5, lend=2)
text(ci2time[1],1.2,"|",offset=0.5,cex=1.1,adj=1,font=2)
text(ci2time[2],1.2,"|",offset=0.5,cex=1.1,adj=0,font=2)

text(-140,0.2,
     "Trial 1",
     offset=0.5,cex=0.9,adj=1)
text(-90,0.2,
     paste("(",
           round(ci1time[1],2),",",
           round(ci1time[2],2),
           ")"),
     pos=3,offset=0.5,cex=0.8,adj=1)
text(-120,0.7,
     "Trial 1X",
     offset=0.5,cex=0.9,adj=1)
text(-70,0.7,
     paste("(",
           round(ci1Xtime[1],2),",",
           round(ci1Xtime[2],2),
           ")"),
     pos=3,offset=0.5,cex=0.8,adj=1)
text(-140,1.2,
     "Trial 2",
     offset=0.5,cex=0.9,adj=0)
text(-70,1.2,
     paste("(",
           round(ci2time[1],2),",",
           round(ci2time[2],2),
           ")"),
     pos=3,offset=0.5,cex=0.8,adj=1)

dev.off()  # for pdf etc.