options( pl.type="pdf" )
load( file="../data/cervix.Rdata" )

# par( mfrow=c(2,3), mar=c(3,1,1,1), mgp=c(3,1,0)/1.6 )

# Only stage 1 patients, in random order
st1 <- cx[cx$stage==1,]
ns <- nrow( st1 )

plt( "time-ex-en", width=8 )
par( mar=c(3,0,0,0), mgp=c(3,1,0)/1.6 )
plot( NA, NA, xlim=c(1993,2004), ylim=c(0.5,ns), axes=F, type="n",
      xlab="Calendar time", ylab="" )
abline( v=0:11+1993, col=gray(0.8) )
segments( st1$doe, 1:ns, pmin(st1$dox,2004), 1:ns )
points( pmin(st1$dox,2004), 1:110, pch=c(NA,16)[st1$status+1] )
axis( side=1, labels=1993+0:5*2, at=0.5+1993+0:5*2, tick=F )
axis( side=1, at=0:11+1993, labels=NA )

st1 <- st1[order(st1$doe),]

plt( "time-ex-to", width=8 )
par( mar=c(3,0,0,0), mgp=c(3,1,0)/1.6 )
plot( NA, NA, xlim=c(1993,2004), ylim=c(0.5,ns), axes=F, type="n",
      xlab="Calendar time", ylab="" )
abline( v=0:11+1993, col=gray(0.8) )
segments( st1$doe, 1:ns, pmin(st1$dox,2004), 1:ns )
points( pmin(st1$dox,2004), 1:ns, pch=c(NA,16)[st1$status+1] )
axis( side=1, labels=1993+0:5*2, at=0.5+1993+0:5*2, tick=F )
axis( side=1, at=0:11+1993, labels=NA )

plt( "time-ex-to-cut", width=8 )
par( mar=c(3,0,0,0), mgp=c(3,1,0)/1.6 )
plot( NA, NA, xlim=c(1993,2004), ylim=c(0.5,ns), axes=F, type="n",
      xlab="Calendar time", ylab="" )
segments( st1$doe, 1:ns, pmin(st1$dox,2004), 1:ns )
abline( v=0:11+1993, col="white", lwd=2 )
points( pmin(st1$dox,2004), 1:ns, pch=c(NA,16)[st1$status+1] )
axis( side=1, labels=1993+0:5*2, at=0.5+1993+0:5*2, tick=F )
axis( side=1, at=0:11+1993, labels=NA )

plt( "time-ex-tre", width=8 )
par( mar=c(3,0,0,0), mgp=c(3,1,0)/1.6 )
plot( NA, NA, xlim=c(0,11), ylim=c(0.5,ns), axes=F, type="n",
      xlab="Time since diagnosis", ylab="" )
abline( v=0:11, col=gray(0.8) )
segments( 0, 1:ns, pmin(st1$time,11), 1:ns )
points( pmin(st1$time,11), 1:ns, pch=c(NA,16)[st1$status+1] )
axis( side=1 )
axis( side=1, at=c(0:11), labels=NA )

plt( "time-ex-tre-cut", width=8 )
par( mar=c(3,0,0,0), mgp=c(3,1,0)/1.6 )
plot( NA, NA, xlim=c(0,11), ylim=c(0.5,ns), axes=F, type="n",
      xlab="Time since diagnosis", ylab="" )
segments( 0, 1:ns, pmin(st1$time,11), 1:ns )
abline( v=0:11, col="white", lwd=2 )
points( pmin(st1$time,11), 1:ns, pch=c(NA,16)[st1$status+1] )
axis( side=1 )
axis( side=1, at=c(0:11), labels=NA )

st1 <- st1[order(20-st1$time,st1$status),]
plt( "time-ex-fire", width=8 )
par( mar=c(3,0,0,0), mgp=c(3,1,0)/1.6 )
plot( NA, NA, xlim=c(0,11), ylim=c(0,111), axes=F, type="n",
      xlab="Time since diagnosis", ylab="" )
abline( v=0:11, col=gray(0.8) )
segments( rep(0,ns), 1:ns, pmin(st1$time,11), 1:ns )
points( pmin(st1$time,11), 1:ns, pch=c(NA,16)[st1$status+1] )
axis( side=1 )
axis( side=1, at=c(0:11), labels=NA )

plt( "time-ex-fem", width=8 )
par( mar=c(3,0,0,0), mgp=c(3,1,0)/1.6 )
plot( NA, NA, xlim=c(0,11), ylim=c(0,111), axes=F, type="n",
      xlab="Year of follow-up", ylab="" )
abline( v=0:11, col=gray(0.8) )
segments( rep(0,ns), 1:ns, pmin(floor(st1$time)+0.5,10), 1:ns )
points( pmin(floor(st1$time)+0.5,10), 1:ns, pch=c(NA,16)[st1$status+1] )
axis( side=1, at=0:9+0.5, labels=1:10, tick=F, lty=0 )
axis( side=1, at=0:10, labels=NA )

st1 <- st1[order(floor(-st1$time),st1$status),]
plt( "time-ex-seks", width=8  )
par( mar=c(3,0,0,0), mgp=c(3,1,0)/1.6 )
plot( NA, NA, xlim=c(0,11), ylim=c(0.5,ns), axes=F, type="n",
      xlab="Year of follow-up", ylab="" )
abline( v=0:11, col=gray(0.8) )
segments( rep(0,110), 1:110, pmin(floor(st1$time)+0.5,10), 1:110 )
points( pmin(floor(st1$time)+0.5,10), 1:110, pch=c(NA,16)[st1$status+1] )
axis( side=1, at=0:9+0.5, labels=1:10, tick=F, lty=0 )
axis( side=1, at=0:10, labels=NA )