similar to: HOW to use the survivalROC 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)

I have some question about metafor package. I'm interest to perform a random effect meta-analysis of proportion (single group summary of prevalence of disease in a population as reported by different study) It ask: 1. "PFT": The Freeman-Tukey double arcsine transformed proportion is reported to be equal to 1/2*(asin(sqrt(xi/(ni+1))) + asin(sqrt((xi+1)/(ni+1)))). Hovewer, i

Dear all, I use R 2.14.2 for Windows XP I have no problem with R Commander version 1.7-2, but now I have a problem with R Commander (Rcmdr) version 1.8-3. After I lunch R Commander (sdi as well standard) if I try to import data (i. from Stata datafile) I have this Warning message: Error in structure(.External("dotTclObjv", objv, PACKAGE = "tcltk"), class =

Subject: Re: [R] Problems with R Commander version 1.8-3 Many thanks for your kindly replay. I just use a At this time I use an earlier version of the package. I try to install the Rcmdr from R-Forge. Many tanks again Message: 21 Date: Wed, 28 Mar 2012 08:04:09 -0400 From: "John Fox" <jfox at mcmaster.ca> To: <petretta at unina.it> Cc: r-help at r-project.org

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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

Dear all I generated predicted risk of death for each subject in the study by means of Cox proportional hazards model at 8 year of follow-up, a time point at which follow-up was more than 90% complete. It is possible to extrapolate to 10-year the predicted risk of each subjet by assuming an exponential distribution? Any help would be greatly appreciated. Thanks for your consideration.

Dear R help My problem is very similar to the analysis detailed here. If we use the mayo dataset provided with the survivalROC package the estimate for Somer's Dxy is very negative -0.56. The Nagelkerke R2 is positive though 0.32. I know there is a difference between explained variation and predictive ability but I am surprised there is usch a difference given that even a non predictive model

Hola, Marta, Por lo que he podido ver tus datos ya tienen calculados las tasas de verdaderos y falsos positivos (TPR y FPR). También parece que los tienes ordenados por la variable FishSpeed y supongo que también por las que parecen marcas de tiempo. No necesitas ROCR porque con un simple plot te sale algo parecido a una curva. Eso sí, veo que son medidas repetidas en el tiempo para cada valor de

if nobody knows the answer to my question on time-dependent ROC (see below), does any body know how TP and FP are related to classes and samples (orders) in non-time dependent ROC? Any reference? Thanks --- On Tue, 11/3/09, carol white <wht_crl at yahoo.com> wrote: > From: carol white <wht_crl at yahoo.com> > Subject: ROC > To: r-help at stat.math.ethz.ch > Date:

My question would be related more to time-dependent ROC (survivalROC package): I would like to know how true positives (TP) and false positives (FP) are related to the order of survival times and diagnostic markers. That is, having the a set of TP and FP, each of them is calculated from which diagnostic marker and survival times. Let's take mayo data set. How could I match the TP and FP

Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]]

Dear all, I am using the "caret" Package for predictors selection with a randomForest model. The following is the train function: rfFit<- train(x=trainRatios, y=trainClass, method="rf", importance = TRUE, do.trace = 100, keep.inbag = TRUE, tuneGrid = grid, trControl=bootControl, scale = TRUE, metric = "ROC") I wanted to use ROC as the metric for variable

Hello friends of R list, Im a physician and Im not that good in statistics. I have posted similar email in the epi-sig list but no one aswered so far. Im cunducting a systematic review on two diagnostic test for a particular tropical disease. I found a free software that make most of the analysis called MetaDiSc. However there is a paticular analysis that I wuould like to try that it is not

hello, I am using the ROC package to evaluate predictive models I have successfully plot the ROC curve, however ?is there anyway to obtain the value of operating point=optimal threshold value (i.e. the nearest point of the curve to the top-left corner of the axes)? thank you very much, jose daniel anadon area de ecologia universidad miguel hernandez espa?a

Dear all, I would like to calculate the optimal cut off (threshold) of a test using the Epi package. Here I am presenting some data based on the output of two tests. I am interested in identifying the optimal cut off an its 95% CI. Running the ROC() function with the Epi package I obtain a nice picture that returns what I interpret as the optimal cut off with lr.eta=0.431. would be this the

Hi, I understand that dichotimization of the predicted probabilities after logistic regression is philosophically questionable, throwing out information, etc. But I want to do it anyway. I'd like to include as a measure of fit % of observations correctly classified because it's measured in units that non-statisticians can understand more easily than area under the ROC curve, Dxy, etc.

Hi, I need to build ROC curve in R, can you please provide data steps / code or guide me through it. Thanks and Regards Rithesh M Mohan [[alternative HTML version deleted]]

The name conflicts in Epi and ROC packages (2 'ROC' functions are the problem) cause the following code to work once, but not twice: library(MASS); data(cats); x = cats[,2] y = ifelse(cats[,1]=='F',0,1) library(Epi); ROC(x,y,grid=0)$AUC library(ROC); AUC(rocdemo.sca(y, x, dxrule.sca)) What is the standard way of resolving name conflicts? Ask maintainers to resolve

*Hi, *Does anyone know how can I show an *ROC curve for R-SVM*? I understand in R-SVM we are not optimizing over SVM cost parameter. Any example ROC for R-SVM code or guidance can be really useful. Thanks, Angel. [[alternative HTML version deleted]]