# PRACTICAL EXERCISE 1
# ====================

# Read data:
melanoma=read.table("http://www.uio.no/studier/emner/matnat/math/STK4080/h12/melanoma.txt",header=T)

# Load survival library:
library(survival)


# Question a:
# -----------
# Nelson-Aalen plots for patients with and without ulcetation: 
fit.a=coxph(Surv(lifetime,status==1)~strata(ulcer),data=melanoma)
surv.a=survfit(fit.a)
plot(surv.a,fun="cumhaz", mark.time=F,xlim=c(0,10),ylim=c(0,1.0),
    xlab="Years since operation",ylab="Cumulative hazard",lty=1:2)
legend("topleft",c("with ulceration","without ulceration"),lty=1:2)

# If we include the option "conf.int=T" in the plot command, 
# we obtain plots with confidence limits


# Question b:
# ----------
# Nelson-Aelen plots for patients according to thickness group: 
fit.b=coxph(Surv(lifetime,status==1)~strata(grthick),data=melanoma)
surv.b=survfit(fit.b)
plot(surv.b,fun="cumhaz", mark.time=F,xlim=c(0,10),ylim=c(0,1.0),
     xlab="Years since operation",ylab="Cumulative hazard",lty=1:3)
legend("topleft",c("0-1 mm","2-5 mm","5+ mm"),lty=1:3)