[R] survfit & number of variables != number of variable names

[Georges Dupret]

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Hi Terry,

I attached a small data set to this email. This is what I get (I
restricted the formula to avoid NA's):

> surv = with(small, Surv(time=absence, event=(censored==FALSE))) 
> (cox.s = coxph(surv ~  bucket*(today) + strata(activity), data =
> small))
Call:
coxph(formula = surv ~ bucket * (today) + strata(activity), data = small)


                       coef exp(coef) se(coef)      z    p
bucket575            0.4526     1.572    0.740  0.612 0.54
todayTRUE           -0.0886     0.915    0.676 -0.131 0.90
bucket575:todayTRUE -0.1670     0.846    0.794 -0.210 0.83

Likelihood ratio test=2.32  on 3 df, p=0.509  n= 100, number of
events= 100
> fit = survfit(cox.s, newdata=small[1:50,])
Error in model.frame.default(data = small[1:50, ], formula = ~bucket +  :
  number of variables != number of variable names

> 

also:

> R.version
               _
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          15.1
year           2012
month          06
day            22
svn rev        59600
language       R
version.string R version 2.15.1 (2012-06-22)
nickname       Roasted Marshmallows

package ‘survival’ is version 2.36-14

and finally, variable absence is numeric, bucket & activity are
factors and all other variables are logical.

I tested the same formula without 'strata' and I had no problem.

Best and thank you,

ge

On 11/19/2012 09:01 AM, Terry Therneau wrote:
> I can't reproduce the problem.
> 
> Tell us what version of R and what version of the survival
> package. Create a reproducable example.  I don't know if some
> variables are numeric and some are factors, how/where the "surv"
> object was defined, etc.
> 
> Terry Therneau
> 
> 
> 
> On 11/17/2012 05:00 AM, r-help-request at r-project.org wrote:
>> This works ok:
>> 
>>>> cox = coxph(surv ~ bucket*(today + accor + both) + activity,
>>>> data
>>> = data)
>>>> fit = survfit(cox, newdata=data[1:100,])
>> but using strata leads to problems:
>> 
>>>> cox.s = coxph(surv ~  bucket*(today + accor + both) +
>>> strata(activity),
>>>> data = data) fit.s = survfit(cox.s, newdata=data[1:100,])
>> Error in model.frame.default(data = data[1:100, ], formula =
>> ~bucket +  : number of variables != number of variable names
>> 
>> Note that the following give rise to the same error:
>> 
>>>> fit.s = survfit(cox.s, newdata=data)
>> Error in model.frame.default(data = data, formula = ~bucket +
>> today +  : number of variables != number of variable names
>> 
>> but if I use data implicitly, all is working fine:
>>>> fit.s = survfit(cox.s)
>> Any idea on how I could solve this?
>> 
>> Best, and thank you,
>> 
>> ge
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