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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("http://www.ats.ucla.edu/stat/R/examples/asa/hmohiv.csv", sep=",", header = TRUE)
attach(hmohiv)
age.coxph <- coxph( Surv(time,censor)~age, method="breslow")
summary(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 <- coxph( Surv(time,censor)~age+drug+age*drug, method="breslow")
summary(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 <- coxph( Surv(time,censor)~age+drug, method="breslow")
summary(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
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