Lu, Jiang wrote:
Thank you very much, Frank. I installed Design package and tried
survplot().
#R code
survplot(testfit,time.inc=365.25,xaxt='n',xlim=c(0,1826.25),ylim=c(0,1),conf='none',
fun=function(y)1-y,label.curves=list(keys=c('Med','Rev')),
abbrev.label=TRUE,n.risk=TRUE)
# End of R code
I have achieved my goal with the 'fun' argument you advised. But I have
a difficult time to do the following fine tune.
1. The X axis scale was labeled as 'Days'. I would like something like
'xscale=365.25' in plot.survfit to put time into Years and label the
ticks from 0 to 5, instead of from 0 to 1826.25 by each 365.25
increment. I tried xaxt='n' as you can see in the code above. Then I
noticed that xaxt='n' only work for plot(survfit), not in survplot().
Any advice how to change the tick label using survplot()?
There are options to do all that, described in the documentation.
2. The n.risk was beautifully printed for each specified time point
along the x axis. However, since I am plotting the failure rate, the
n.risk looks busy with the failure rate curves. Is there a way to move
the n.risk to the top of the plot where there are lots of space?
May be best to move it to the bottom margin. See the help file.
3. I also tried label.curves=list(). It is very convenient. The curves
are labeled and the legend is created as well. Could I only keep the
curve label and get rid of the legend since the legend is not so
necessary once the curve is labeled. How do you think?
Should be options for that too.
Frank
I really appreciate any help you give.
Best regards,
Jiang Lu
Statistician
Department of Epidemiology
University of Pittsburgh
On Thu, Nov 6, 2008 at 1:21 PM, Frank E Harrell Jr
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
Lu, Jiang wrote:
Dear R helper,
I encountered a problem when I tried to plot the cumulative
failure rate
(i.e. 1 - survival probability). I have used the following code
to plot. The
scenario is that patients are randomized to different treatment
arm (rev in
the code), the PCI revascularization was monitored over 5 years.
#R code
testfit <- survfit(Surv(pcifu,pci)~rev,data=subproc)
testfit$surv <- 1 - testfit$surv
testfail <- plot(testfit, mark.time=FALSE,col=1:2,
main='Failure Rate')
#End of R code
I arbitarily replaced testfit$surv by computing 1 minus the original
survival rate. So far so good. However, when I plot the manipulated
"testfit", there is a vertical line plotted at x=0, y=0:1. I checked
testfit$time and testfit$surv, nothing weird there. I am very
confused where
the vertical line at starting point of time 0 came from. How can
I get rid
of it?
Would you pleae help me with this? Thanks a lot!
Jiang
Also see the survplot.* functions in the Design package and their
fun argument, e.g., fun=function(y)1-y
Frank
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--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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