search for: nry

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 cardiovascular events in patients

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 packages that can calculate NRI and IDI

...swer. 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 matrixprod (SEXP x , SEXP y ) { int nrx , ncx , nry , ncy , mode; SEXP xdims , ydims , ans ; char *transa = "N" , *transb = "N" ; double one = 1.0 , zero = 0.0 ; xdims = getAttrib (x , R_DimSymbol ) ; ydims = getAttrib (y , R_DimSymbol ) ; mode = REALSXP; nrx = INTEGER( xdims ) [ 0 ] ; ncx = INTEGER( xdims ) [ 1 ] ; nry = INTEGER...

...ng 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 responses"), ", ", ngettext(ncx, : invalid format '%d'; use format %s for character objects > traceback() 3: sprintf(ngettext(nry, "%d response", "%d responses"), ", ", ngettext(ncx, "but only...

...-) diff --git a/src/main/array.c b/src/main/array.c index 4b95e33..cedf627 100644 --- a/src/main/array.c +++ b/src/main/array.c @@ -1350,15 +1350,18 @@ SEXP attribute_hidden do_matprod(SEXP call, SEXP op, SEXP args, SEXP rho) if (PRIMVAL(op) == 0) { /* primitive, so use call */ if (ncx != nry) - errorcall(call, _("non-conformable arguments")); + errorcall(call, _("non-conformable arguments of dimension (%d, %d) and (%d, %d)"), + nrx, ncx, nry, ncy); } else if (PRIMVAL(op) == 1) { if (nrx != nry) - error(_("non-conformable arguments&quo...

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

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

...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) { char *transa = "N", *transb = "N"; int i, j, k; double one = 1.0, zero = 0.0, sum; Rboolean have_na = FALSE; if (nrx > 0 && ncx > 0 && nry > 0 && ncy > 0) { /* Don't trust the BLAS to handle NA...

...ray.c b/src/main/array.c >index 4b95e33..cedf627 100644 >--- a/src/main/array.c >+++ b/src/main/array.c >@@ -1350,15 +1350,18 @@ SEXP attribute_hidden do_matprod(SEXP call, SEXP op, SEXP args, SEXP rho) > if (PRIMVAL(op) == 0) { > /* primitive, so use call */ > if (ncx != nry) >- errorcall(call, _("non-conformable arguments")); >+ errorcall(call, _("non-conformable arguments of dimension (%d, %d) and (%d, %d)"), >+ nrx, ncx, nry, ncy); > } > else if (PRIMVAL(op) == 1) { > if (nrx != nry) >- error(_("n...

...39;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 nry, int ncy, double *z) { char *transa = "N", *transb = "N"; double one = 1.0, zero = 0.0; F77_CALL(dgemm)(transa, transb, &nrx, &ncy, &ncx, &one, x, &nrx, y, &nry, &zero, z, &nrx); } SEXP trProd2(SEXP x, SEXP y) { int nrx, ncx,...

...s (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 nry, int ncy, double *z) { > char *transa = "N", *transb = "N"; > double one = 1.0, zero = 0.0; > F77_CALL(dgemm)(transa, transb, &nrx, &ncy, &ncx, &one, > x, &nrx, y, &nry, &zero, z, &nrx); } > > SEXP trProd2(SEXP...

...pilation. > > Below is my modified version of the matprod function in src/main/array.c. > > ? Radford Neal > > ------------------------------------------------------------------------ > > static void matprod(double *x, int nrx, int ncx, > ? ? ? ? ? ? ? ? ? ?double *y, int nry, int ncy, double *z) > { > ? ?char *transa = "N", *transb = "N"; > ? ?int i, ?j, k; > ? ?double one = 1.0, zero = 0.0; > ? ?LDOUBLE sum; > ? ?Rboolean do_it_here; > > ? ?/* NOTE: ncx must be equal to nry. */ > > ? ?if (nrx==1 && ncy==1) { &g...

...39;t change any R configuration options regarding compilation. Below is my modified version of the matprod function in src/main/array.c. Radford Neal ------------------------------------------------------------------------ static void matprod(double *x, int nrx, int ncx, double *y, int nry, int ncy, double *z) { char *transa = "N", *transb = "N"; int i, j, k; double one = 1.0, zero = 0.0; LDOUBLE sum; Rboolean do_it_here; /* NOTE: ncx must be equal to nry. */ if (nrx==1 && ncy==1) { /* Do dot product quickly. */...

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

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_DPX_R2/ BWAG_R2_00135909.dpx

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 =

...ectorized because of the early exit when NaN is detected: /* Don't trust the BLAS to handle NA/NaNs correctly: PR#4582 * The test is only O(n) here. */ for (R_xlen_t i = 0; i < NRX*ncx; i++) if (ISNAN(x[i])) {have_na = TRUE; break;} if (!have_na) for (R_xlen_t i = 0; i < NRY*ncy; i++) if (ISNAN(y[i])) {have_na = TRUE; break;} I tried deleting the 'break'. By inspecting the asm code, I verified that the loop was not being vectorized before, but now is vectorized. Total time goes down: system.time (C <- B %*% A) nancheck: wall time 1.898667s ? dgemm: wall...

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.