包生存中由survfit函数产生的生存曲线

Question

I am using the survfit function in the R package survival to create survival curves from a survfit.coxph object output by coxph . I have two methods for creating the curve which give different results. I believe the first is the correct answer, but I can't tell why method 2 does not work.

library(survival)
set.seed(1234)

## generate small data set
n <- 10
z <- rnorm(n,mean=0.4)
x <- rexp(n,exp(z))
y <- pmin(1,x)
del <- 1*(x < 1)
dat <- data.frame(y,del,z)

## fit cox model
fit <- coxph(Surv(y,del)~z,ties="breslow",data=dat)

## method 1
newdata <- dat[1,]
newdata[1,3] <- 0
out <- survfit(fit,newdata=newdata)
out$surv
##[1] 0.9557533 0.9048870 0.8545721 0.7599743 0.6397022 0.4218647 0.4218647


## method 2, why not same as method 1?
dat[1,3] <- 0
out <- survfit(fit,newdata=dat[1,])
out$surv
##[1] 0.9570757 0.9079589 0.8593546 0.7710287 0.6610956 0.4787354 0.4787354

Answer 1

In both methods survfit function receives two parameters: fit and newdata .

In the method 1 line newdata[1,3] <- 0 changes only the object newdata and the object dat and consequently object fit are not changed.

In the method 2, instead, dat[1,3] <- 0 changes both, the object newdata and the object fit .

So the newdata objects received by survfit function are identical in both methods, as 42 correctly pointed out, but the fit objects are not.
If you make 3 identical dataframes in the beginning, you can see this.

dat1 <- data.frame(y,del,z)
dat2 <- data.frame(y,del,z)
dat3 <- data.frame(y,del,z)

## fit cox model
fit <- coxph(Surv(y,del)~z,ties="breslow",data=dat1)

## method 1
newdata <- dat2[1,]
newdata[1,3] <- 0

out <- survfit(fit,newdata=newdata)
out$surv
##[1] 0.9557533 0.9048870 0.8545721 0.7599743 0.6397022 0.4218647 0.4218647


## method 2, same as method 1
dat3[1,3] <- 0
out <- survfit(fit,newdata=dat3[1,])
out$surv
##[1] 0.9557533 0.9048870 0.8545721 0.7599743 0.6397022 0.4218647 0.4218647