[R] error fitting coxph model
David Winsemius
dwinsemius at comcast.net
Thu May 3 16:00:50 CEST 2012
On May 2, 2012, at 3:02 PM, Jessica Myers wrote:
> Hi,
>
> I am using coxph from the survival package to fit a large model
> (100,000 observations, ~35 covariates) using both ridge regression
> (on binary covariates) and penalized splines (for continuous
> covariates).
>
> In fitting, I get a strange error:
>
> Error in if (abs((y[nx] - target)/(y[nx - 1] - target)) > 0.6)
> doing.well <- FALSE else doing.well <- TRUE :
> missing value where TRUE/FALSE needed
You appear to have missing values in 'y', 'nx', or `target`. This
could be a case of the newbie error of using if(){}else{} when
ifelse() should have been used. Without at least the code we probably
cannot resolve those two possibilities.
>
> Unfortunately, I can't reproduce this error without handing over my
> entire dataset,
Why not? If the removal of missing values is unsuccessful and you were
not committing the error I mentioned, then run it on two halves. Pick
the one with the error. Rinse, lather, repeat.
> but I thought it would be worth checking if anyone had any insight.
> I should note that the outcome that I'm using has almost everyone
> having an event (~98,000 events out of 100,000). I have fit other
> models like this with no problem, but on one particular dataset it
> fails.
>
> Thanks!
>
> Jessica Myers
> Instructor in Medicine
David Winsemius, MD
West Hartford, CT
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