search for: nri

Dear Sirs. I am working with the R packages Hmisc and PredictABEL to make NRI estimates from my Cox models with and without a specific biomarker. According to Pencina et al (Statistics in Medicine 2010, DOI: 0.1002/sim.4085 ), a continuous/non-categorical NRI (NRI>0) is to be used when there are no obvious reason to categorize risk, such as the risk of future cardiovascul...

Hi, I am trying to calculate net reclassification improvement (NRI) and Inegrated Discrimination Improvement (IDI) for a survival dataset to compare 2 risk models. It seems that the improveProb() in Hmisc package does this only for binary outcome, while rcorrp.cens() does take survival object, but doesn't output NRI or IDI. Can anyone suggest any other package...

I have ported some R code to C to make it faster. I can perform .Call("foobar",....) once and it works fine. Absolutely correct answer. If I put a loop inside foobar and run the main code routine more than 100 times, it crashes R. Or if I call .Call("foobar"....) seperately more than two tims it crashes R. For the most part I am doing matirx multiplies using EXP

Hi, in R-3.0 I get the following error when calling lsfit with more observations than variables, which seems to come from an error in the formatting of the error message (note that this was not happening in 2.15.3): > nobs <- 5; nvar <- 6; lsfit(matrix(runif(nobs*nvar), ncol=nvar), runif(nobs), intercept=FALSE) Error in sprintf(ngettext(nry, "%d response", "%d

With this patch, > A <- matrix(1, 2, 2) > B <- matrix(2, 3, 2) > A %*% B Error in A %*% B : non-conformable arguments of dimension (2, 2) and (3, 2) >From 205b591d4d14b5ff667325fb233a6deb08314726 Mon Sep 17 00:00:00 2001 From: Joshua Nathaniel Pritikin <jpritikin at pobox.com> Date: Fri, 5 Apr 2019 12:03:58 -0400 Subject: [PATCH] Improve non-conformable arguments error

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...

As describe in the Hmisc package's improveProb function, that function is for binary Y. And it's best to use category-free methods. Frank Petergodsk wrote > Hi > > I'm new to R. > > Is it possible to use the improveProb function to generate categorybased > NRI using a Cox model? > I believe I saw someone mentioning the possibility, but I can't find the > syntax in the R help. > > Thanks, > Peter Godsk ----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble...

Hi, I was wondering if I could use the matprod function from array.c in my own C routine. I tried the following as a test /* my_matprod.c */ # include <Rinternals.h> /* for REAL, SEXP etc */ # include <R_ext/Applic.h> /* array.c says need for dgemm */ /* following copied from array.c */ static void matprod(double *x, int nrx, int ncx, double *y, int nry, int ncy, double *z)

I think this is a good idea. Is there a reason why it got no interest? Slippery slope? Or maybe others were also just occupied trying to figure out how Joshua's second message had timestamp earlier than his first message? On Fri, Apr 05, 2019 at 12:05:36PM -0400, Joshua N Pritikin wrote: >With this patch, > >> A <- matrix(1, 2, 2) >> B <- matrix(2, 3, 2) >> A

Dear all, I need to calculate tr(xyxy) fast for matrices x and y. Inspired by the R-source code, I've created the following functions (I am *new* to writing external C-functions, so feel free to laugh at my code - or, perhaps, suggest changes): #include <Rinternals.h> #include <R_ext/Applic.h> /* for dgemm */ static void matprod(double *x, int nrx, int ncx, double *y, int

Not an expert in programming either, but to me it seems like you've forgotten to initialize the variable "tr". It just picks up garbage from allocated memory previously initialized by other processes. Med venlig hilsen Frede Aakmann T?gersen > -----Oprindelig meddelelse----- > Fra: r-help-bounces at stat.math.ethz.ch > [mailto:r-help-bounces at stat.math.ethz.ch] P?

.... For instance, matrixStats::anyMissing(x) would flag the "x" object (i) if returning TRUE and (ii) if returning FALSE. Next time it is called, the response could be instant/O(1). Similarly, y <- rowSums(x, na.rm=TRUE/FALSE) can set the state on y, and so on. Just some thoughts /Henrik On Mon, Aug 23, 2010 at 1:50 PM, Radford Neal <radford at cs.toronto.edu> wrote: > I've looked at the code for matrix multiplies in R, and found that it > can speeded up quite a bit, for multiplies that are really vector dot > products, and for other multiplies in which the re...

I've looked at the code for matrix multiplies in R, and found that it can speeded up quite a bit, for multiplies that are really vector dot products, and for other multiplies in which the result matrix is small. Here's my test program: u <- seq(0,1,length=1000) v <- seq(0,2,length=1000) A2 <- matrix(2.1,2,1000) A5 <- matrix(2.1,5,1000) B3 <- matrix(3.2,1000,3) A4 <-

Greetings, I have generated several ROC curves and would like to compare the AUCs. The data are cross sectional and the outcomes are binary. I am testing which of several models provide the best discrimination. Would it be most appropriate to report AUC with 95% CI's? I have been looking in to the "net reclassification improvement" (see below for reference) but thus far I can only

Hi Colton, You could divide your write task into chunks that do not violate the 2^31-1 limit. write.table has an append argument (default FALSE). Figure out a row chunk size nri < nr such that nri * nc is under 2^31-1 and use write.table() to write that out. Then use write.table( append = TRUE, ) for the next chunk of rows, looping over chunks until done. Two chunks will get your 2.8 billion entries done. Best Steve Steven McKinney, Ph.D. Statistician Molecul...

I would like to see how the matrix multiplication operator %*% is implemented (because I want to see which external Fortran/C routines are used). How can I do so? Best S??ren

Hi Steven, Yes, both file systems are the same. rsync -nri --modify-window=1 <src> <dest> Gives me the following for most files >f..T....... 2015_167_1_1__Boy_What_A_Girl_R2/2015_167_1_1__Boy_What_A_Girl__UHD_DPX_R2/ BWAG_R2_00138428.dpx Although a few have >f..T......n 2015_167_1_1__Boy_What_A_Girl_R2/2015_167_1_1__Boy_What_A_Girl__UHD...

Dear useRs, I am trying to import a raster with the line: nlcd <- raster("/home/jpolo/NRI/nlcd_nri5000.tif") And I keep getting an error like this: "Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,? : ? there is no package called 'rgdal' Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLay...

I am using R to multiply some large (30k x 30k double) matrices on a 64 core machine (xeon phi). I added some timers to src/main/array.c to see where the time is going. All of the time is being spent in the matprod function, most of that time is spent in dgemm. 15 seconds is in matprod in some code that is checking if there are NaNs. > system.time (C <- B %*% A) nancheck: wall time

Hi all, I've installed rsync-2.5.6 on a sun box (solaris 8). When I run rsync using the command rsync -a ssh /opt/local/pkgs/httpd/htdocs/ root@remotemachine:/mnt/ I get the error rsync: connection unexpectedly closed (0 bytes read so far) rsync error: error in rsync protocol data stream (code 12) at io.c(165) What could be the reason? Any help would be appreciated. Thanks, Rajesh.