R help - Aug 2007 - (Censboot, Z-score, Cox) How to use Z-score as the statistic within censboot?

Dear R Help list,

My question is regarding extracting the standard error or Z-score from a
cph or coxph call. My Cox model is: -

modz=cph(Surv(TSURV,STATUS)~RAGE+DAGE+REG_WTIME_M+CLD_ISCH+POLY_VS,
data=kidneyT,method="breslow", x=T, y=T)

I've used names(modz) but can't see anything that will let me extract
the Z scores for each coefficient or the standard errors in the same way
one can use coef (modz).

I need to get either the se or Zscore as I am hoping to be able to use
the Zscore within a statistic function used in censboot. I wish to find
the proportion of times each of the variables in the cox model are
significant out of the R=1000 bootstrap resamples.

My current function for us with the bootstrap only gives me the
coefficients: - 

func=function(kidneyT,indices)
{

kidneyT=kidneyT[indices,]
modz=coxph(Surv(TSURV,STATUS)~RAGE+DAGE+REG_WTIME_M+CLD_ISCH+POLY_VS,dat
a=kidneyT,method="breslow")

coefficients(modz)

}


I would like to be able to modify the following code so modz.cens.boot$t
below gives me an array of the Z-scores for each variable and each
resample - not the coefficients

modz.cens.boot=censboot(kidneyT, func,R=1000,sim="ordinary")
modz.cens.boot


I hope this is clear enough? I'm still getting to terms with the
Bootstrap, having only just started trying to use it a few days ago.

Any help on this would clear a massive headache for me as I've been
going around in circles for hours and hours on this.

Thx 

DaveL





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David Lloyd wrote:
> Dear R Help list,
> 
> My question is regarding extracting the standard error or Z-score from a
> cph or coxph call. My Cox model is: -
> 
> modz=cph(Surv(TSURV,STATUS)~RAGE+DAGE+REG_WTIME_M+CLD_ISCH+POLY_VS,
> data=kidneyT,method="breslow", x=T, y=T)
You are assuming linearity for all predictors, which is unlikely.  When 
you expand predictors into multiple parameters to allow for 
nonlinearity, or when you have factors with >2 levels, individual 
P-values will be meaningless.  You can get all Wald multiple d.f. test 
stats and P-values by saving the result of anova(modz) using 
anova.Design, which creates a matrix.

Frank
> 
> I've used names(modz) but can't see anything that will let me
extract
> the Z scores for each coefficient or the standard errors in the same way
> one can use coef (modz).
> 
> I need to get either the se or Zscore as I am hoping to be able to use
> the Zscore within a statistic function used in censboot. I wish to find
> the proportion of times each of the variables in the cox model are
> significant out of the R=1000 bootstrap resamples.
> 
> My current function for us with the bootstrap only gives me the
> coefficients: - 
> 
> func=function(kidneyT,indices)
> {
> 
> kidneyT=kidneyT[indices,]
> modz=coxph(Surv(TSURV,STATUS)~RAGE+DAGE+REG_WTIME_M+CLD_ISCH+POLY_VS,dat
> a=kidneyT,method="breslow")
> 
> coefficients(modz)
> 
> }
> 
> 
> I would like to be able to modify the following code so modz.cens.boot$t
> below gives me an array of the Z-scores for each variable and each
> resample - not the coefficients
> 
> modz.cens.boot=censboot(kidneyT, func,R=1000,sim="ordinary")
> modz.cens.boot
> 
> 
> I hope this is clear enough? I'm still getting to terms with the
> Bootstrap, having only just started trying to use it a few days ago.
> 
> Any help on this would clear a massive headache for me as I've been
> going around in circles for hours and hours on this.
> 
> Thx 
> 
> DaveL
> 
> 
> 
> 
> 
> Click to find information on your credit score and your credit report.
> <http://tagline.bidsystem.com/fc/Ioyw36XIe1IYw28KqOSu66l6ED7AsGYWlz4EWyK
> N5OTcqKjQM8gfiW/> 
> 
> 
> 
> <span id=m2wTl><p><font face="Arial, Helvetica,
sans-serif" size="2"
style="font-size:13.5px">_______________________________________________________________<BR>Get
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> 	[[alternative HTML version deleted]]
> 
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-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University