On 2012-07-02 14:14, peter dalgaard wrote:
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.
As I read the OP's previous response, s/he has not necessarily
added sampledLifetime and sampledCensoredQ to *testTimeSeries*
but perhaps only to *sampledTimeSeries*. (But I don't know why
the error refers to "x".)
It is also not clear from the original post just where
sampledLifetime and sampledCensoredQ resided in the original
call to coxph.
Perhaps we could have a look at
str(sampledTimeSeries)
str(testTimeSeries)
?
Peter Ehlers
______________________________________________
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.
