#  R code to fit the Cox model to data from the 
#  VA lung cancer trial of 137 male patients 
#  with inoperable lung cancer.  This code is 
#  posted as  
#             vacoxph.R   

# Variables
#     Treatment: 1=standard, 2=test (chemotherapy)
#     Celltype: 1=squamous, 2=smallcell, 
#               3=adeno, 4=large
#     Survival in days
#     Status: 1=dead, 0=censored
#     Karnofsky score
#     Months from Diagnosis
#     Age in years
#     Prior therapy: 0=no, 10=yes
      

# Enter the data into a data frame.

va <- read.table("c:/stat565/data/va.dat",
      header=F, col.names=c("rx", "cellt", "time", 
       "status", "karno", "months", "age", "priorrx")) 
va$rx <- va$rx-1
va$priorrx <- va$priorrx/10;    
va$celltf<-as.factor(va$cellt)
va


library(survival)

options(contrasts=c("contr.treatment", "contr.poly"))

vafit <- coxph(Surv(time, status) ~ rx+celltf+karno 
                +months + age + priorrx, data = va,
                x=T, y=T, robust=T,
               method="efron", singular.ok=T)

summary(vafit) 

names(vafit)

vafit$x

vafit$coef

vafit$var


#  Model selection

step(vafit, direction="both", trace=1, steps=1000, k=2)