On Sun, 10 May 2009, John Sorkin wrote:
R 2.8.1
Windows XP
I am trying to plot the results of a coxph using plot(survfit()). The plot
should, I believe, show two lines one for survival in each of two treatment
(Drug) groups, however my plot shows only one line. What am I doing wrong?
Expecting two lines. To get survival curves from a Cox model you need to
specify the covariate values. If you don't, you get the baseline survival (ie,
at the mean covariate values).
Look at the example on ?survfit.coxph
fit <- coxph(Surv(futime, fustat) ~ age, data = ovarian)
plot(survfit(fit, newdata=data.frame(age=60)),
xscale=365.25, xlab = "Years", ylab="Survival")
This plots the fitted curve for age 60. If you wanted multiple ages you can
specify them, eg,
plot(survfit(fit, newdata=data.frame(age=c(40,50,60))),
xscale=365.25, xlab = "Years", ylab="Survival")
gives three curves.
-thomas
My code is reproduced below, my figure is attached to this EMail message.
John
#Create simple survival object
GVHDdata<-list(Time=GVHD$Time,Time30=(GVHD$Time)/30,
+ Age=GVHD$Age,Drug=GVHD$Drug,Died=GVHD$Died,
+ AgeGrp=cut(GVHD$Age,breaks=c(0,15,25,45)))
summary(GVHD$Drug)
MTX MXT+CSP
32 32
fit0<-coxph(Surv(Time30,Died)~Drug,data=GVHDdata)
summary(fit0)
Call:
coxph(formula = Surv(Time30, Died) ~ Drug, data = GVHDdata)
n= 64
coef exp(coef) se(coef) z p
Drug[T.MXT+CSP] -1.15 0.316 0.518 -2.23 0.026
exp(coef) exp(-coef) lower .95 upper .95
Drug[T.MXT+CSP] 0.316 3.16 0.115 0.871
Rsquare= 0.086 (max possible= 0.915 )
Likelihood ratio test= 5.75 on 1 df, p=0.0165
Wald test = 4.96 on 1 df, p=0.026
Score (logrank) test = 5.52 on 1 df, p=0.0188
plot(survfit(fit0))
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
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