[R] Plotting an adjusted kaplan-meier curve

[David Winsemius]

On Nov 25, 2012, at 5:17 PM, Brent Caldwell 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).

Only give it newdata values that have the desired levels. Failing that  
advice being on point, then please provide str(survmat) and  
str(simple.cox.ethnicity$terms) .

(Could it be the case that your use of factor() around the terms means  
that getting hte names of your terms are not what you think they are?  
If the newdata argument is malformed then it gets discarded and the  
original values get used. Maybe you should do the "factorization"  
before you do the fit.)

>
> 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")
>
>
-- 

David Winsemius, MD
Alameda, CA, USA