On Jul 2, 2012, at 19:27 , agittens wrote: > > 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 >>> dataset. >>> 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 >>> data. >>> >>> 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 >> column?) >> > > 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.
I gather that type="expected" requires a follow-up time which the routine needs to get from somewhere. Presumably those columns _are_ required. > If I put in these columns, then I get the > error > > Error in predict.coxph(coxphfit, newdata = testTimeSeries, type = > "expected", : > object 'x' not found > Do you have an "x" somewhere in your model specification? Otherwise, I'm out of clues. Perhaps try a traceback() or options(error=recover) and see where the error comes from. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd....@cbs.dk Priv: pda...@gmail.com ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
