# This R code is posted as  benignbreast.R
 
# The data file is posted as benignbreast.txt
# It does not have variable names on 
# the first line.  First enter the data 
# into a data frame.


set1 <- read.table("c:/stat565/bbreast.txt",
      header=F, col.names=c("stratum", "obs", "agmt", "fndx", "higd", 
      "deg", "chk", "agp1", "agmn", "nlv", "liv",  "wt", "aglp", "mst"))
set1$time <- rep(2,length(set1$fndx))-set1$fndx
set1$nvmr <-set1$mst
set1$nvmr[set1$nvmr<5] <- 0
set1$nvmr <- set1$nvmr/5

# Attach the library with survival analysis functions

library(survival)


 coxout <- coxph(Surv(time,fndx) ~ chk +  wt + agmn + nvmr
            +strata(stratum), data=set1, method="exact")

summary(coxout)