# This file from www.richardsconsulting.co.uk/lectures

# First load in the survival library
library(survival)

# Now create a list of (i) survival times, (ii) censoring/event status,
# and (iii) genders
#
# Note that '1' = death and '0' = censored in the status variable, and that
#           '0' = male and '1' = female in the gender variable.
example2<-list(time  =c(2, 5, 9, 11, 14, 4, 7, 10, 12, 15),
               status=c(1, 0, 1,  0,  1, 1, 0,  0,  0,  1),
               gender=c(0, 0, 0,  0,  0, 1, 1,  1,  1,  1))

# Fit a Cox proportional-hazards model
coxfit<-coxph(Surv(time, status) ~ gender, example2)

# Take a look at the value for the z test
beta<- coxfit$coef
stderr<-sqrt(coxfit$var)
z<-beta / stderr
z*z

# Now the score test:
coxfit$score

# And finally the LRT:
-2*(coxfit$loglik[1] - coxfit$loglik[2])

# Compare these values with the output given in the summary() command:
summary(coxfit)