[R] R: net reclassification index after Cox survival analysis

[petretta at unina.it]

Thanks to David Winsemius for the replay. i use the latest update of  
Hmisc package and I try as reported in the example:

set.seed(1)
library(survival)
x1 <- rnorm(400)
x2 <- x1 + rnorm(400)
d.time <- rexp(400) + (x1 - min(x1))
cens <- runif(400,.5,2)
death <- d.time <= cens
d.time <- pmin(d.time, cens)
rcorrp.cens(x1, x2, Surv(d.time, death))

but to me it appears that NRI and IDi are not reported in the results:

Dxy               S.D. x1 more concordant x2 more concordant
      -8.212107e-02       1.370738e-01       4.589395e-01       5.410605e-01
                  n            missing         uncensored     Relevant Pairs
       4.000000e+02       0.000000e+00       1.100000e+01       4.262000e+03
          Uncertain               C X1               C X2             Dxy X1
       1.553380e+05       9.920225e-01       9.258564e-01       9.840450e-01
             Dxy X2
       8.517128e-01

but only after:

#rcorrp.cens(x1, x2, y) ## no censoring
set.seed(1)
x1 <- runif(1000)
x2 <- runif(1000)
y <- sample(0:1, 1000, TRUE)
rcorrp.cens(x1, x2, y)
improveProb(x1, x2, y)

thus censoring not allowed. Or I'm in error?

Many thanks

David Winsemius <dwinsemius at comcast.net> ha scritto:

>
> On Nov 7, 2012, at 6:54 AM, petretta at unina.it wrote:
>
>> Dear all,
>>
>> I am interested to evaluate reclassification using net
>> reclassification improvement and Integrated Discrimination Index IDI after
>> survival analysis (Cox proportional hazards using stcox). I search a R
>> package or a R code that specifically addresses the categorical NRI for
>> time-to-event data in the presence of censored observation and, if
>> possible, at different follow-up time points.
>> I know that the ‘PredictABEL’ Package contains functions for NRI and IDI
>> calculation but it is unclear for me if it allows censored observation.
>> Package ‘survIDINRI’ calculates only continuous NRI and the function of
>> Package ‘Hmisc’[#rcorrp.cens(x1, x2, y) ##] is only for no censored
>> observations.
>
> ???. Doesn't its name , 'rcorrp.cens' suggest otherwise? Not to  
> mention its description int the Hmisc Index: "Rank Correlation for  
> Paired Predictors with a Possibly Censored Response, and Integrated  
> Discrimination Index". rcoop.cens is a fairly recent addition to  
> Hmisc and I am looking at Hmisc version 3.10-1. If you are looking  
> at a version that is a couple of years old, you may be seeing  
> something different. The argument list you list looks like the one  
> for improveProb(), which does not appear to handle censoring. The  
> rcorrp.cens argument list is:
>
> rcorrp.cens(x1, x2, S, outx=FALSE, method=1)
>
> And the "S" object is a Surv-object.
>
>
>> Many thanks.
>>
>> Sincerely,
>>
>> Mario Petretta
>> Dpt. Internal Medicine, Cardiology and Heart Surgery
>> Naples University Federico II - Italy
>>
>> ______________________________________________
>> 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.
>
> David Winsemius, MD
> Alameda, CA, USA
>
>
>



Mario Petretta
Dipartimento di Medicina Clinica Scienze Cardiovascolari e Immunologiche
Facolt� di Medicina e Chirurgia
Universit� di Napoli Federico II
081 - 7462233