Plotting an adjusted survival curve
First a statistical issue: The survfit routine will produce predicted survival curves for
any requested combination of the covariates in the original model. This is not the same
thing as an "adjusted" survival curve. Confusion on this is prevalent, however. True
adjustment requires a population average over the confounding factors and is closely
related to the standardized incidence ratio concept found in epidemiology.
To answer your technical question:
fit <- coxph(Surv(.........
mysurv <- survfit(fit, newdata= mydata)
This will give a set of predicted curves, one for each observation in mydata. If we
assume 2 treatments and 4 ethnicities, this means that there are 8 possible predicted
curves. You can certainly take the curves for "trt=1, white" and "trt=2, white", plot
them together on one graph, and call this your "adjusted" survival curves; the mydata data
set would have two observations. This is not a correct label but is certainly common.
Terry Therneau
On 11/26/2012 05:00 AM, r-help-request at r-project.org wrote:
Dear R-users
I am trying to make an adjusted Kaplan-Meier curve (using the Survival package) but I am having difficulty with
plotting it so that the plot only shows the curves for the adjusted results.
My data come from a randomised controlled trial, and I would like the adjusted Kaplan-Meier
curve to only show two curves for the adjusted survival: one for those on treatment (Treatment==1)
and another curve for those on placebo (Treatment==0).
My problem is that when I plot the survfit of my coxph, I think it displays a curve for
every single individual factor in my coxph, whereas I would like it to only display the
adjusted curves for when Treatment==1 and Treatment==0. How can I do this?
A simplified example of my code with only one effect-modifier is:
simple.cox.ethnicity<- coxph(Surv(whenfailed,failed) ~ factor(Treatment) + factor(ethnicity)) #I've my data are attached already
survfit.simple.cox.ethnicity<- survfit(simple.cox.ethnicity,survmat) #survmat is a data.frame that contains Treatment and ethnicity
plot(survfit.simple.cox.ethnicity, col=c("red","black"), main="survfit.simple.cox", xlab="survival time", ylab="propotion surviving")
Thank you so much for your help.
Yours gratefully,
Brent Caldwell