library(survival)
attach(cancer.df)
survVar <- Surv(fumo,status=="D")
fit <- survfit( survVar ~ chemo,conf.int=FALSE)
plot(fit,xlab="Months", main="Survival following Surgery")
invisible(plotAtRisk(fit,5*(1:12),cex=.8,line1=2.2))
legend("bottomleft",lty=1:2,legend=levels(chemo))
survdiff( survVar ~ chemo)
plot(fit, main="log-log plot",fun="cloglog")
plot( survfit(survVar ~ age.gp) ,lty=1:3,main="Age Group")
legend("bottomleft",lty=1:5,legend=levels(age.gp))
cfit <- coxph(survVar ~ age.gp + sex + chemo + met)
summary(cfit)
cfit2 <- coxph(survVar ~ age + sex + chemo + met)
anova(cfit2,test="Chi")
chemo.met <- factor(paste("chemo",chemo,"met",met))
plot(survfit(survVar ~ chemo.met),lty=1:4 ,main="Chemo*Met")
legend("bottomleft",lty=1:4,legend=levels(chemo.met))
mresid <- residuals(cfit2,type="martingale")
plot(age,mresid ,xlab="age",ylab="residual",main="Martingale Residuals")
lines(supsmu(age,mresid))
cfit <- coxph(survVar ~ age + sex + chemo + met)
zph <- cox.zph(cfit)
print(zph)
plot(zph[1])