petretta at unina.it
2010-Dec-05 18:11 UTC
[R] HOW to use str() after the survivalROC (or another library in R) to get optimal cut-off values
I have the same problem of a previous request HOW to use the survivalROC (or another library in R) to get optimal cut-off values? I want to use the time-dependent survivalROC package.according to the,reference material,it only gives a partial set of ordered cut-off values .eg. -------------------------------------------------------------------------------- data(mayo) str(mayo) attach(mayo) ROC.1=survivalROC(Stime=time,status=censor,marker=mayoscore4,predict.time=365,lambda=0.05) str(ROC.1) plot(ROC.1$FP, ROC.1$TP, type="l", xlim=c(0,1), ylim=c(0,1), xlab=paste( "FP", "\n", "AUC = ",round(ROC.1$AUC,3)), ylab="TP",main="Mayoscore 4, Method = NNE \n Year = 1") abline(0,1) List of 6 $ cut.values : num [1:313] -Inf 4.58 4.9 4.93 4.93 ... *only 5 values * $ TP : num [1:313] 1 0.999 0.999 0.999 0.998 ... $ FP : num [1:313] 1 0.997 0.993 0.99 0.987 ... $ predict.time: num 365 $ Survival : num 0.93 $ AUC : num 0.888 -------------------------------------------------------------------------------- In particular I'm unable to see and print all values after str(ROC.1) and NOT only the 5 values listed above in the example in order to to get optimal cut-off values Thank you very much! Mario Petretta Dipartimento di Medicina Clinica Scienze Cardiovascolari e Immunologiche Facolt? di Medicina e Chirurgia Universit? di Napoli Federico II 081 - 7462233 Mario Petretta Dipartimento di Medicina Clinica Scienze Cardiovascolari e Immunologiche Facolt? di Medicina e Chirurgia Universit? di Napoli Federico II 081 - 7462233
Joshua Wiley
2010-Dec-05 18:34 UTC
[R] HOW to use str() after the survivalROC (or another library in R) to get optimal cut-off values
Hi Mario, On Sun, Dec 5, 2010 at 10:11 AM, <petretta at unina.it> wrote:> > I have the same problem of a previous request > > HOW to use the survivalROC (or another library in R) to get optimal cut-off values? > > I want to use the time-dependent survivalROC package.according to the,reference > material,it only gives a partial set of ordered cut-off values .eg.I'm not exactly sure how to parse that sentence. Do you mean you are trying to follow the reference, but only get a partial set of cut-off values? Or do you mean that according to the reference, it only gives a partial set of ordered cut-off values?> -------------------------------------------------------------------------------- > > data(mayo) > str(mayo) > attach(mayo) > ROC.1=survivalROC(Stime=time,status=censor,marker=mayoscore4,predict.time=365,lambda=0.05) > str(ROC.1)this prints the str()ucture of the ROC.1 object to the console so you can see how the object is stored in R> > plot(ROC.1$FP, ROC.1$TP, type="l", xlim=c(0,1), ylim=c(0,1), ? xlab=paste( "FP", "\n", > "AUC = ",round(ROC.1$AUC,3)), ? ylab="TP",main="Mayoscore 4, Method = NNE \n Year = 1") > abline(0,1) > > List of 6 > $ cut.values : num [1:313] -Inf 4.58 4.9 4.93 4.93 ... *only 5 values > > * $ TP ? ? ? ? ?: num [1:313] 1 0.999 0.999 0.999 0.998 ... > > ?$ FP ? ? ? ? ?: num [1:313] 1 0.997 0.993 0.99 0.987 ... > ?$ predict.time: num 365 > ?$ Survival ? ?: num 0.93 > > ?$ AUC ? ? ? ? : num 0.888This is the output you should have gotten from str(ROC.1)> -------------------------------------------------------------------------------- > In particular I'm unable to see and print all values after str(ROC.1) > and NOT only the 5 values listed above in the example in order to to get optimal cut-off valuesIs this what you are looking for? ROC.1[["cut.values"]] or are you have some other problem?> > Thank you very much! > > > > Mario Petretta > Dipartimento di Medicina Clinica Scienze Cardiovascolari e Immunologiche > Facolt? di Medicina e Chirurgia > Universit? di Napoli Federico II > 081 - 7462233 > > > > Mario Petretta > Dipartimento di Medicina Clinica Scienze Cardiovascolari e Immunologiche > Facolt? di Medicina e Chirurgia > Universit? di Napoli Federico II > 081 - 7462233 > > ______________________________________________ > R-help at 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.-- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/