Kaplan-Meier including survival and transplant data

r, survival-analysis

Solution

With `par(new=TRUE)` you can draw a second plot in the same figure as the first.

Normally I would recommend using `lines()` for adding curves to a plot, since `par(new=TRUE)` performs the filosophically different task of overlaying plots. When using functions in a way they are not intended to be used you risk commiting misstakes, e.g. I nearly forgot the vital `xlim` argument. However, it is not trivial to extract the curves from the `survfit` objects, so I figured it was the lesser of two evils.

# Fake data for the plots
pump <- data.frame(TIME=rweibull(40, 2, 20),
                   CENSUS=runif(40) < .3,
                   DEVICE=rep(0:1, c(20,20)))
# load package
library("survival")

# Fit models
mfit.overall <-survfit(Surv(TIME, CENSUS==0) ~ 1, data=pump)
mfit.htx <- survfit(Surv(TIME, CENSUS==0) ~ 1, data=pump, subset=DEVICE==1)

# Plot
plot(mfit.overall, col=1, xlim=range(pump$TIME), fun=function(x) 1-x)
# `xlim` makes sure the x-axis is the same in both plots
# `fun` flips the curve to start at 0 and increase
par(new=TRUE)
plot(mfit.htx, col=2, xlim=range(pump$TIME), fun=function(x) 1-x,
    ann=FALSE, axes=FALSE, bty="n") # This hides the annotations of the 2nd plot
legend("topright", c("All", "HTX"), col=1:2, lwd=1)

Problem

What I have is a Kaplan-Meier Analysis of patients with mechanical heart support using R. What I need is adding the following data into the plot (like in the example): - patients who survived due to a heart transplantation (HTX) - patients who died In other words, there are two groups where one is a subset (transplanted patients) of the other (all patients). These two curves must start at 0/0 and will increase. My own plot is done by: ``` pump <- read.table(file=datafile, header=FALSE, col.names=c('TIME', 'CENSUS', 'DEVICE')) # convert days to months pump$TIME <- pump$TIME/(730/24) mfit.overall <- survfit(Surv(TIME, CENSUS==0) ~ 1, data=pump) plot(mfit.overall, xlab="months on device", ylab="cum. survival", xaxt="n") axis(1, at=seq(from=0, to=24, by=6), las=0) ``` How may I add the two additional curves? Kind Regards Johann Sample Kaplan Meier Curve: https://i.stack.imgur.com/158e8.jpg Demo Data: Survival Data, which goes into pump: ``` TIME CENSUS DEVICE 426 1 1 349 1 1 558 1 1 402 1 1 12 0 1 84 0 1 308 1 1 174 1 1 315 1 1 734 1 1 544 1 2 1433 1 2 1422 1 2 262 1 2 318 1 2 288 1 2 1000 1 2 ``` TX data: ``` TIME CENSUS DEVICE 426 1 1 288 1 2 308 1 1 ``` deaths: ``` TIME CENSUS DEVICE 12 0 1 84 0 1 ```

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