error fitting coxph model
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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