Note that the original C-index is implemented in various validation options in the rms package related to the cph function (which calls coxph in survival). Frank = Eleni Rapsomaniki-2 wrote: > > Hello, > > I am having some trouble with the 'censoring-adjusted C-index' by Uno et > al, in the package survAUC. The relevant function is UnoC. > The question has to do with what happens when I specify a time point t for > the upper limit of the time range under consideration (we want to avoid > using the right-end tail of the KM curve). > > Copying from the example in the help file: > > TR <- ovarian[1:16,] > TE <- ovarian[17:26,] > train.fit <- coxph(Surv(futime, fustat) ~ age,x=TRUE, y=TRUE, > method="breslow", data=TR) > lpnew <- predict(train.fit, newdata=TE) > Surv.rsp <- Surv(TR$futime, TR$fustat) > Surv.rsp.new <- Surv(TE$futime, TE$fustat) > > If time is left NULL, the maximum futime in the TE data is assumed: > UnoC(Surv.rsp, Surv.rsp.new, lpnew, time=NULL) > #same as > UnoC(Surv.rsp, Surv.rsp.new, lpnew, time=max(Surv.rsp.new[,1])) > > #which incidentally is the same as what one gets with the usual C-index > function that also extends to the max event time. > survConcordance(Surv.rsp.new ~ lpnew)$conc > > Now, if I specify a range times 'tau' (as in Table III of the relevant > publication) I still get the same C for each timepoint: > > tau <- Surv.rsp.new[, 1] >> tau > [1] 1040 1106 1129 1206 1227 268 329 353 365 377 > > UnoC(Surv.rsp, Surv.rsp.new, lpnew, time=tau) > > [1] 0.7333333 0.7333333 0.7333333 0.7333333 0.7333333 0.7333333 0.7333333 > 0.7333333 0.7333333 0.7333333 > > #even worse, if I sort tau in ascending times I get 0's > UnoC(Surv.rsp, Surv.rsp.new, lpnew, time=sort(tau)) > [1] 0 0 0 0 0 0 0 0 0 0 > > This is a potentially very useful function so it would be great if someone > could explain the behaviour here. > > Many thanks > > Eleni Rapsomaniki > > Research Associate/Statistician > Strangeways Research Laboratory > Department of Public Health and Primary Care > > University of Cambridge > > > ______________________________________________ > 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. >
----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/UnoC-function-in-survAUC-for-censoring-adjusted-C-index-tp3622181p3622289.html Sent from the R help mailing list archive at Nabble.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.