R help - Jul 2013 - prediction survival curves for coxph-models; how to extract the right strata per individual

Hello everyone, 

 

It somehow seems like a strange question, but I don't find the answer.

I think my question is the same
<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=user_nodes&u
ser=23573> stephenb wanted  to ask in January, but it seems he didn't get
an answer (see
http://r.789695.n4.nabble.com/obtainl-survival-curves-for-single-strata-td
4657177.html).

 

My problem is: 

 

I have a coxph.model with several strata and other covariables. 

Now I want to fit the estimated survival-curves for new data, using
survfit.coxph. 

But this returns a prediction for each stratum per individual. So if I
have 15 new individuals and 10 strata, I have 150 fitted surivival curves
(or if I don't use the subscripts I have 15 predictions with the curves
for all strata pasted together)

 

Is there any possibility to get only the survival curves for the stratum
the new individual belongs to? 

 

I think the newstrata argument at survfit.coxph should do this, but trying
to use the argument I get the message "Warning message:

In survfit.coxph(coxph.3, newdata = activisale_join[1:15, ], na.action na.pass, 
:

  newstrata argument under construction, value ignored"

(below the documentation for survfit.coxph)

 

So did anyone a workaround? Or does anyone know a fast solution to
automatically use the right subscripts? (beside the one supplied by
Stephen, which seems to take a little bit too much time.)

 

All the best 

 

Julian

 

Ps.: I use survival in version 2.37-4

 

"newstrata" if the original coxph model had strata, should the
predictions
be for all strata,

or only for those in newdata? The default for this is TRUE if either the
id or

individual argument is present, as these require strata for the resulting
curves

to make sense. Otherwise the default is FALSE, which means to ignore any

strata variable in the newdata data set, and produce predicted survivals
for the

entire set of strata in the original model. In this case some components
of the

output will be matrices with one column for each row of newdata.


	[[alternative HTML version deleted]]

It would help me to give advice if I knew what you wanted to do with the new
curves.
Plot, print, extract?

A more direct solution to your question will appear in the next release of the
code, btw.

Terry T.


On 07/25/2013 05:00 AM, r-help-request at r-project.org
wrote:
> My problem is:
>
>
>
> I have a coxph.model with several strata and other covariables.
>
> Now I want to fit the estimated survival-curves for new data, using
> survfit.coxph.
>
> But this returns a prediction for each stratum per individual. So if I
> have 15 new individuals and 10 strata, I have 150 fitted surivival curves
> (or if I don't use the subscripts I have 15 predictions with the curves
> for all strata pasted together)
>
>
>
> Is there any possibility to get only the survival curves for the stratum
> the new individual belongs to?
>
>