From: Kylie-Anne Richards <kar_at_itga.com.au>

Date: Sat 16 Jul 2005 - 18:07:01 EST

> In any case, to specify f.pom You need it to be a factor with the same set

*> of levels. You don't say what the lowest level of pom is, but if it is,
*

*> say, -3.
*

*>
*

*> f.pom=factor(-3, levels=seq(-3,2.5, by=0.5))
*

> I would first note that the survival function at zero covariates is not a

*> very useful thing and is usually numerically unstable, and it's often more
*

*> useful to get the survival function at some reasonable set of covariates.
*

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat Jul 16 18:11:45 2005

Date: Sat 16 Jul 2005 - 18:07:01 EST

> In any case, to specify f.pom You need it to be a factor with the same set

For this particular model, f.pom starts at -5.5 going to 2 in 0.5 increments. I seem to have misunderstood your explanation, as R is still producing an error.

>final<-coxph(Surv(time.sec,done)~f.pom+vo+po,data=DATA)

*>final.surv<-survfit((final),
**>data.frame(po=0,vo=10000,f.pom=factor(-5.5,levels=seq(-5.5,2,by=0.5)),individual=T))
**>summary(final.surv)
*

Error in x2 %*% coef : non-conformable arguments
Execution halted

> I would first note that the survival function at zero covariates is not a

- Original Message ----- From: "Thomas Lumley" <tlumley@u.washington.edu> To: "Kylie-Anne Richards" <kar@itga.com.au> Cc: <r-help@stat.math.ethz.ch> Sent: Saturday, July 16, 2005 12:31 AM Subject: Re: [R] Coxph with factors

> On Fri, 15 Jul 2005, Kylie-Anne Richards wrote:

*>>
**>> FIRST Q: The default uses the mean of 'vo' and mean of 'po', but what is
**>> it
**>> using for the factors?? Is it the sum of the coef of the factors divided
**>> by
**>> the number of factors??
**>
**> It uses the mean of each factor variable. The $means component of the fit
**> gives the values it uses.
**>
**>> SECOND Q: For a model with covariates I would normally specify:
**>> final.surv<-survfit((final), data.frame(po=0,vo=0,pom=0,individual=T)) to
**>> get the baseline survival prob.; what would I specify for a model with a
**>> factor, i.e., 'f.pom' ??
**>
**> I would first note that the survival function at zero covariates is not a
**> very useful thing and is usually numerically unstable, and it's often more
**> useful to get the survival function at some reasonable set of covariates.
**>
**> In any case, to specify f.pom You need it to be a factor with the same set
**> of levels. You don't say what the lowest level of pom is, but if it is,
**> say, -3.
**>
**> f.pom=factor(-3, levels=seq(-3,2.5, by=0.5))
**>
**>
**> =thomas
**>
*

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat Jul 16 18:11:45 2005

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