Hi David,
Thanks for your input. My first thought was to look for missing
values, but I can tell you there are no missing values in the input.
The error is occurring somewhere deep inside coxpenal.fit, so I can't
identify how any NAs might be created. Also, the if/else syntax is
from coxpenal.fit, so I'm assuming they've done it right.
But I like your idea about searching for the error in data halves.
It's also worth mentioning that when I changed the df parameter on my
pspline terms to df = 3, it worked fine, but the error below occurred
with both df = 2 and df = 4.
Thanks,
Jessica
On May 3, 2012, at 10:00 AM, David Winsemius wrote:
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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