[R] HOW to use str() after the survivalROC (or another library in R) to get optimal cut-off values

[Joshua Wiley]

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 0.888

This 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 values

Is 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
> Facoltà di Medicina e Chirurgia
> Università di Napoli Federico II
> 081 - 7462233
>
>
>
> Mario Petretta
> Dipartimento di Medicina Clinica Scienze Cardiovascolari e Immunologiche
> Facoltà di Medicina e Chirurgia
> Università di Napoli Federico II
> 081 - 7462233
>
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--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/