Many thanks for Your time. M.P.
> > On Nov 7, 2012, at 9:59 AM, petre...@unina.it wrote: > >> 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 > > The NRI is not reported but an equivalent measure is. As far as getting > output that is labeled the way you expect it, I also looked at the > PredictABEL::reclassification function help page: > > "The function also computes continuous NRI, which does not require any > discrete risk categories and relies on the proportions of individuals with > outcome correctly assigned a higher probability and individuals without > outcome correctly assigned a lower probability by an updated model > compared with the initial model." > > I think that is essentiality what rcorrp.cens is providing, just not with > the labels you expected. > > " The function requires predicted risks estimated by using two separate > risk models. Predicted risks can be obtained using the > functionsfitLogRegModel and predRisk or be imported from other methods or > packages." > > So it would seem that you could use results from any censored survival > models that had a predict method. > > -- > David. > > >> >> 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 <dwinsem...@comcast.net> ha scritto: >> >>> >>> On Nov 7, 2012, at 6:54 AM, petre...@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 âPredictABELâ Package contains functions for NRI >>>> and IDI >>>> calculation but it is unclear for me if it allows censored >>>> observation. >>>> Package âsurvIDINRIâ calculates only continuous NRI and the >>>> function of >>>> Package âHmiscâ[#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@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 >> >> ______________________________________________ >> 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. > > David Winsemius, MD > Alameda, CA, USA > > > ______________________________________________ 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.
