# PRACTICAL EXERCISE 6
# ====================

# Read bonemarrow transplantation data:
path="http://www.uio.no/studier/emner/matnat/math/STK4080/h14/bone-marrow.txt"
bonemarrow=read.table(path,header=T)

# We will use the survival package, so this has to be loaded.
library(survival)

# Question a

# We make Nelson-Aalen plots for the cumulative relapse-free survival hazards for the three disease groups:
fit.group=coxph(Surv(T2,DF)~strata(g),data=bonemarrow)
surv.group=survfit(fit.group)
plot(surv.group,fun="cumhaz", mark.time=F,xlim=c(0,1000),xlab="Days post-transplant",ylab="Cumulative hazard",lty=1:3)
legend("topleft",c("ALL","AML low-risk","AML high-risk"),lty=1:3)


# Qustion b

# We use the logrank test to see if the observed differences are significant:
survdiff(Surv(T2,DF)~g,data=bonemarrow)

# We find that the disease groups are significantly different (p-value 0.1%).