I am wondering how to estimate the survival curve for a particular case(s)
given a coxph model
using this example code:
#fit a cox proportional hazards model and plot the
#predicted survival curve
fit <- coxph(
Surv(futime,fustat)~resid.ds+strata(rx)+ecog.ps+age,data=ovarian[1:23,])
z <- survfit(fit,newdata=ovarian[24:26,],individual=F)
zs <- z$surv
zt <- z$time
I get the following output:
24 25 26
[1,] 0.9740399 0.91737529 0.9873785
[2,] 0.9431988 0.82552974 0.9721557
[3,] 0.9023088 0.71387936 0.9515702
[4,] 0.8518865 0.59121499 0.9255099
[5,] 0.7269607 0.35151309 0.8572808
[6,] 0.6130966 0.20108501 0.7895814
[7,] 0.2807720 0.01553603 0.5415119
[8,] 0.9159643 0.74991615 0.9584975
[9,] 0.8225510 0.52704511 0.9099799
[10,] 0.7058027 0.31906859 0.8451399
[1] 59 115 156 268 329 431 638 464 475 563
I am not sure what I am getting here, I was expecting to get three survival
curves for each scenario in the "newdata" however the survival curves don't
seem to be monotonically decreasing with time. I get the feeling that this
has something to do with the use of strata(rx) in the model, but I am no
sure how to sort it out.
any help is appreciated,
best regards,
Spencer
On 12/21/06, Blanchard, Suzette <[EMAIL PROTECTED]> wrote:
>
> Thank you for your help. With your fix I was able to get the correct
> result once but then I would have to close R.
> If I go back to R-2.3.1 Everything seem to work fine. Best to everyone
> that helped.
> Suzette
>
> ________________________________
>
> From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
> Sent: Thu 12/21/2006 5:31 AM
> To: Duncan Murdoch
> Cc: Blanchard, Suzette; [email protected]
> Subject: Re: [R] \Sexpr in MikTex
>
>
>
> Wow, that's a lot of errors in my post. Sorry about that. You should
> probably just ignore it completely.
>
> Duncan Murdoch
>
> On 12/20/2006 10:05 PM, Duncan Murdoch wrote:
> > On 12/20/2006 6:26 PM, Blanchard, Suzette wrote:
> >> Greetings, \Sexpr{} has worked on MikTex with earlier versions of R,
> I can not seem to get it to work with
> >> R-2.4.0. I run Sweave with MikTex using the following statement in Run
> under Accessories.
> >> latex -include-directory="C:\Program Files\R\R-2.4.0\share\texmf"
> "C:\Documents and Settings\Suzette\Desktop\MyFile\MyProgram.tex"
> >
> > There should be two hyphens in the option, i.e. --include-directory,
> > shouldn't there?
> >
> > This should be automatically put in place if you used
> >
> > R CMD Sweave MyProgram.tex
> >
> > from a command line.
> >
> > Duncan Murdoch
> >
> >>
> >> Any advice would be much appreciated,
> >> Suzette
> >>
> >>
> >> Suzette Blanchard, Ph.D.
> >> Assistant Professor, Dept. of Biostatistics
> >> City of Hope National Medical Center
> >> and Beckman Research Institute
> >> 1500 East Duarte Road, Duarte, CA 91010-3000
> >> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> >> ph: (626) 256-4673 ext: 64446
> >>
> >>
> >> "EMF <COH.org>" made the following annotations.
> >>
> ------------------------------------------------------------------------------
> >> SECURITY/CONFIDENTIALITY WARNING: This message and any
> atta...{{dropped}}
> >>
> >> ______________________________________________
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> >> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > ______________________________________________
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> > PLEASE do read the posting guide
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> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
>
>
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>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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