[R] predicting expected number of events using a coxph model
swiftset at gmail.com
Mon Jul 2 19:27:53 CEST 2012
Peter Dalgaard-2 wrote
>> I fit a coxph model:
>> coxphfit <- coxph(Surv(sampledLifetime, !sampledCensoredQ) ~ curpbc6 +
>> prevpbc6, sampledTimeSeries)
>> Now I'm trying to predict the expected number of events using a new
>> The documentation suggests that
>> coxPred <- predict(coxphfit, newdata = testTimeSeries, type="expected")
>> will do what I want, but I get the error
>> Error in model.frame.default(data = testTimeSeries, formula =
>> Surv(sampledLifetime, :
>> variable lengths differ (found for 'curpbc6')
>> when I do this. The dataframes sampledTimeSeries and testTimeSeries were
>> constructed by taking rows from a larger dataframe, so they have the same
>> What am I doing incorrectly?
> Most likely referring to a variable not in testTimeSeries. (I kind of
> suspect that unlike predict.lm, predict.coxph does not ignore the left
> hand side of formulas. Does testTimeSeries contain a sampledLifetime
No, I did not have the lifetime and censored data in the dataframe.
Per your idea, I put the sampledLifetime and and sampledCensoredQ variables
in the dataframe sampledTimeSeries and left the rest of the code the same.
Now when I try with the new data set,
coxPred <- predict(coxphfit, newdata = testTimeSeries, type="expected")
I get different errors. If I use testTimeSeries without the lifetime and
censor indicator columns (which shouldn't be required for prediction), then
i get the same error as before. If I put in these columns, then I get the
Error in predict.coxph(coxphfit, newdata = testTimeSeries, type =
object 'x' not found
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