R help - May 2009 - System crash when using surv=T in cph

Can someone help me. I am very new to R. I am fitting a Cox model using Frank
Harrell's cph as I want to produce a Nomogram. This is what I have done:

Srv<- Surv(time,cens)
f.cox<- cph(Srv~ v1+v2+v3+v4, x=T, y=T, surv=T)

As soon as I press enter, Windows XP crashes. If I remove surv=T, then it
works. I have R version 2.9.0.

Is there a way of displaying the parameter estimates (ie beta coefficients)
and HR when I type 
anova(f.cox) as this only displays the Chi squared and p-values.
Any help or advise drawing a Nomogram will be appreciated.

Thanks in advance

Max  
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maxb wrote:
> Can someone help me. I am very new to R. I am fitting a Cox model using
Frank
> Harrell's cph as I want to produce a Nomogram. This is what I have
done:
> 
> Srv<- Surv(time,cens)
> f.cox<- cph(Srv~ v1+v2+v3+v4, x=T, y=T, surv=T)
This is not reproducible for us. Where are the data?
What is cph? I presume the one from package Design?
> As soon as I press enter, Windows XP crashes. If I remove surv=T, then it
> works. I have R version 2.9.0.
Have you updates all your packages? Which versions of survival and 
Design are you using?
Is it really Windows that crashes, or just R?


See
http://cran.r-project.org/web/checks/check_results_Design.html
to learn that even the newest version of Design produces WARNINGs.
If you can send reproducible code to let R crash, please send it to the 
package maintainer of the involved packages.

Best,
Uwe Ligges


> Is there a way of displaying the parameter estimates (ie beta coefficients)
> and HR when I type 
> anova(f.cox) as this only displays the Chi squared and p-values.
> Any help or advise drawing a Nomogram will be appreciated.
> 
> Thanks in advance
> 
> Max

maxb wrote:
> Can someone help me. I am very new to R. I am fitting a Cox model using
Frank
> Harrell's cph as I want to produce a Nomogram. This is what I have
done:
> 
> Srv<- Surv(time,cens)
> f.cox<- cph(Srv~ v1+v2+v3+v4, x=T, y=T, surv=T)
> 
> As soon as I press enter, Windows XP crashes. If I remove surv=T, then it
> works. I have R version 2.9.0.
> 
> Is there a way of displaying the parameter estimates (ie beta coefficients)
> and HR when I type 
> anova(f.cox) as this only displays the Chi squared and p-values.
> Any help or advise drawing a Nomogram will be appreciated.
> 
> Thanks in advance
> 
> Max  
Until Design is updated (which will be very soon)
source('http://biostat.mc.vanderbilt.edu/tmp/cphnew.s') after 
library(Design).

anova is not supposed to display parameter estimates.  For one thing, 
there is often more than one parameter associated with a term in the 
model.  Use summary(fit) to get hazard ratios for sensible covariate ranges.

Frank
-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University