###### Figures SCORE   data at alpha=0.1
# actual values. Add this script to the bioeq....R
setwd("~/DocInvest/MyPapers/sqj2012/datasets/umloml")

ci1score <- c(0.69, 1.51)
ci2score <- c(0.957 , 1.487)

## from other R scripts. uncomment
lowdelta20 <- -0.48
lowdelta25 <- -0.6
lowdelta50 <- -1.2
updelta20 <-  0.48
updelta25 <-  0.6
updelta50 <-  1.2


limxscore <- 3

namethisfile <- paste(getwd(),"/Fig8",".pdf",sep="")
pdf(file=namethisfile, height=2, width=4.5)#, paper="a4",pagecentre=TRUE) #, pagecentre=TRUE) 

#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 OML",at=updelta50,side=1,line=2)

#abline(v=equivintervals,lty="dotted")
segments(c(lowdelta50,updelta50),c(0,0),c(lowdelta50,updelta50),c(1,1), 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)
text(2.5,0.2,
     "Experiment 1",
     offset=0.5,cex=0.9,adj=1)
text(updelta50-0.15,0.2,
     paste("(",
           round(ci1score[1],2),",",
           round(ci1score[2],2),
           ")"),
     pos=3,offset=0.5,cex=0.8,adj=1)

segments(ci2score[1],0.7,ci2score[2],lty=1,lwd=5, lend=2)
text(ci2score[1],0.7,"|",offset=0.5,cex=1.1,adj=1,font=2)
text(ci2score[2],0.7,"|",offset=0.5,cex=1.1,adj=0,font=2)
text(2.95,0.7,
     "Repetition Experiment 1",
     offset=0.5,cex=0.9,adj=1)
text(updelta50,0.7,
     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 <- paste(getwd(),"/Fig9",".pdf",sep="")
pdf(file=namethisfile, height=2, width=4.5)# ,pagecentre=TRUE) #, 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(-815.1 , -569.47) 
ci2time <- c(-804.243,-497.591)


## x-axis. compute the extreme values and add some extra scpace


## from other R scripts. uncomment
lowdelta20t <- -383.8151
lowdelta25t <- -479.768916
lowdelta50t <- -959.537833
updelta20t <-  383.8151
updelta25t <-  479.768916
updelta50t <-  959.537833


limxtime <- 220
#pdf("test.pdf", height=5, width=10) #, paper="letter", pagecentre=TRUE) 
#windows.options(width=10, height=5)
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 OML",at=-500,side=1,line=2)

#abline(v=equivintervals,lty="dotted")
segments(c(lowdelta50t,updelta50t),c(0,0),c(lowdelta50t,updelta50t),c(1,1), 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)

text(-140,0.2,
     "Experiment 1",
     offset=0.5,cex=0.9,adj=1)
text(lowdelta20t-300,0.2,
     paste("(",
           round(ci1time[1],2),",",
           round(ci1time[2],2),
           ")"),
     pos=3,offset=0.5,cex=0.8,adj=1)

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

text(80,0.7,
     "Repetition Experiment 1",
     offset=0.5,cex=0.9,adj=1)
text(lowdelta20t-300,0.7,
     paste("(",
           round(ci2time[1],2),",",
           round(ci2time[2],2),
           ")"),
     pos=3,offset=0.5,cex=0.8,adj=1)

dev.off()  # for pdf etc.