# PRACTICAL EXERCISE 3
# ====================

# 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

# We compute Kaplan-Meier estimates for females and males 
# with standard confidence intervals:
fit.sex=survfit(Surv(lifetime,status==1)~sex,data=melanoma,conf.type="plain")

# We then make a plot of the estimestes:
plot(fit.sex, mark.time=F, xlab="Years after operation",lty=1:2)
legend("bottomleft",c("females","males"),lty=1:2)

# Finally we use the summary command to obtain the estimated survival 
# with confidence interval
summary(fit.sex)

# From the summary we may read of an estimate for the lower quartile 
# with confidence limits, cf. section 3.2.3 and exercise 3.8 in the ABG-book. 

# For females the lower quartile becomes 8.33 years with 
# 95% confidence limit from 5.30 years and upwards 
# (no upper limit can be obtained)

# For males the lower quartile becomes 3.36 years with 
# 95% confidence limits from 2.17 to 5.76 years.

# We may also find the lower quartile with confidence limits by the commands (given here for males)
fit.female=survfit(Surv(lifetime,status==1)~1,data=melanoma,subset=(sex==2),conf.type="plain")
q1=min(fit.female$time[fit.female$surv <= 0.75])
q1.L=min(fit.female$time[fit.female$lower <= 0.75])
q1.U=min(fit.female$time[fit.female$upper <= 0.75])
c(q1,q1.L,q1.U)

# Questions b and c

# The commands are as for question a, but using "ulcer" and "grthick" 
# instead of "sex" when computing the Kaplan-Meier estimates