library(Hmisc)
load('~/Analyses/SUPPORT/combined.sav')
combined <- subset(combined, dzclass=='ARF/MOSF', select=c(id,hospdead))
load('~/Analyses/SUPPORT/combphys.sav')
combphys <- subset(combphys, !is.na(crea1+crea14), select=c(id,crea1,crea14))

w <- merge(combined, combphys, by='id')
w <- upData(w, labels=c(crea1='Serum Creatinine, Day 1',
		                crea14='Serum Creatinine Day 14'),
		    units=c(crea1='mg/dl', crea14='mg/dl'))
#ecdf(w$crea1)
library(lattice)
trellis.device(png, file='creatinine1.png', color=FALSE, bg='white')
xYplot(crea14 ~ crea1, method='quantile', data=w, nx=100, 
	   xlim=c(0,12), ylim=c(0,12),
	   main='Quartiles of Serum Creatinine in 2476 Patients with ARF/MOSF')
dev.off()

set.seed(1)
a <- areg.boot(crea14 ~ crea1, data=w)
png('creatinineOptimum.png')
par(mfrow=c(2,2), oma=c(0,0,2,0))
plot(a, boot=FALSE)
mtitle('Optimum Transformations of Serum Creatinine', cex.m=1.5)
g <- Function(a)$crea14
s <- seq(.3,13,length=150)
plot(log(s), g(s), xlab='log(creatinine)', ylab='Optimum Transformation',
	 type='l')
scat1d(log(w$crea14))
dev.off()


f <- g		
s <- c(.3,.5,.8,1,1.5,2,3,4,5,6,8,12)
trellis.device(png, file='creatinine2.png', color=FALSE, bg='white')
xYplot(f(crea14) ~ f(crea1), method='quantile', data=w, nx=100, 
	   xlim=f(c(.3,12)), ylim=f(c(.3,12)),
	   main='Quartiles of Serum Creatinine in 2476 Patients with ARF/MOSF',
	   xlab='Serum Creatinine, Day 1', ylab='Serum Creatinine, Day 14',
	   scales=list(x=list(at=f(s), labels=format(s)),
		           y=list(at=f(s), labels=format(s))))
dev.off()

png('creatinine3.png')
with(w, {
 par(mfrow=c(1,2))
 plot(.5*(crea1+crea14), crea14-crea1)
 plot(.5*(log(crea1)+log(crea14)), log(crea14)-log(crea1))
   })
dev.off()


# Not used:
load('~/data/teaching/support2.sav')
with(subset(support,dzclass='ARF/MOSF'), plsmo(crea, hospdead, fun=qlogis))