# [R] Coxph with factors

Thomas Lumley tlumley at u.washington.edu
Fri Jul 15 16:31:17 CEST 2005

```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

```