Applied Survival Analysis, Chapter 3

The R packages needed for this chapter are the survival package. We currently use R 2.0.1 patched version. You may want to make sure that packages on your local machine are up to date. You can perform update in R using update.packages() function.

Table 1.1 on page 98 using data set hmohiv.

library(survival)
rm(list=ls())
hmohiv<-read.table("https://stats.idre.ucla.edu/stat/r/examples/asa/hmohiv.csv", sep=",", header = TRUE) 
attach(hmohiv)
age.coxph 

  n= 100 
      coef exp(coef) se(coef)    z     p
age 0.0814      1.08   0.0174 4.67 3e-06

    exp(coef) exp(-coef) lower .95 upper .95
age      1.08      0.922      1.05      1.12

Rsquare= 0.192   (max possible= 0.997 )
Likelihood ratio test= 21.4  on 1 df,   p=3.82e-06
Wald test            = 21.8  on 1 df,   p=3.03e-06
Score (logrank) test = 22    on 1 df,   p=2.72e-06

Table 3.2 on page 103 using data set hmohiv created in the previous example.

inter.coxph 

 n= 100 

            coef exp(coef) se(coef)      z       p 
     age  0.0942     1.099   0.0229  4.110 0.00004
    drug  1.1859     3.274   1.2565  0.944 0.35000
age:drug -0.0067     0.993   0.0337 -0.199 0.84000

         exp(coef) exp(-coef) lower .95 upper .95 
     age     1.099      0.910     1.051      1.15
    drug     3.274      0.305     0.279     38.42
age:drug     0.993      1.007     0.930      1.06

Rsquare= 0.295   (max possible= 0.997 )
Likelihood ratio test= 35    on 3 df,   p=1.21e-007
Wald test            = 32.2  on 3 df,   p=4.83e-007
Score (logrank) test = 35.2  on 3 df,   p=1.13e-007

Table 3.3 on page 105 using hmohiv.

main.coxph 

  n= 100 

       coef exp(coef) se(coef)    z        p 
 age 0.0915      1.10   0.0185 4.95 7.4e-007
drug 0.9414      2.56   0.2555 3.68 2.3e-004

     exp(coef) exp(-coef) lower .95 upper .95 
 age      1.10      0.913      1.06      1.14
drug      2.56      0.390      1.55      4.23

Rsquare= 0.295   (max possible= 0.997 )
Likelihood ratio test= 35    on 2 df,   p=2.53e-008
Wald test            = 32.5  on 2 df,   p=8.76e-008
Score (logrank) test = 34.3  on 2 df,   p=3.56e-008

Table 3.4 on page 108 using different methods on data set hmohiv. Notice that although that coxph allows the “exact” option. But this example has a problem with convergence. We therefore do not have the output here.

breslow.coxph <- coxph( Surv(time,censor)~age+drug, hmohiv, method=”breslow”) summary(breslow.coxph)

  n= 100 

       coef exp(coef) se(coef)    z        p 
 age 0.0915      1.10   0.0185 4.95 7.4e-007
drug 0.9414      2.56   0.2555 3.68 2.3e-004

<output omitted>

efron.coxph <- coxph( Surv(time,censor)~age+drug, method=”efron”) summary(efron.coxph)

  n= 100 

       coef exp(coef) se(coef)    z        p 
 age 0.0971      1.10   0.0186 5.21 1.9e-007
drug 1.0167      2.76   0.2562 3.97 7.2e-005