search for: gabraham

Hi, I have two example packages, test1 and test2, where the only code in them is: setGeneric("predict", function(object, ...) standardGeneric("predict")) (get them from http://www.cs.mu.oz.au/~gabraham/test1.tar and http://www.cs.mu.oz.au/~gabraham/test2.tar) The difference between them is that first does not have a namespace, and loads fine. The second has a namespace but generates a warning: > library(test2) Attaching package: 'test2' The following object(s) are masked from p...

Hi, I'm trying to use Frank Harrell's Design:::ols function to do regression of y (numeric) on the interaction of two factors (x1 and x2), but Lapack throws an error: > library(Design) ... > load(url("http://www.csse.unimelb.edu.au/~gabraham/x")) > ols(y ~ x1 * x2, data=x) Error in chol2inv(fit$qr$qr) : 'size' cannot exceed nrow(x) = 20 > traceback() 6: .Call("La_chol2inv", x, size, PACKAGE = "base") 5: chol2inv(fit$qr$qr) 4: ols(y ~ x1 * x2, data = x) 3: eval.with.vis(expr, envir, enclos) 2: ev...

...test1::train(foo) and test2::train(bar), which gets cumbersome for non-trivial code, or b) make test2 depend on test1 so it doesn't have to define the generic, but I'd rather keep the packages compatible but not dependent. Any suggestions? You can get the code at http://www.cs.mu.oz.au/~gabraham/test1_0.1.tar.gz and http://www.cs.mu.oz.au/~gabraham/test2_0.1.tar.gz Thanks, Gad > library(test1) > f <- new('foo') > f An object of class ?foo? Slot "x": [,1] [1,] NA Slot "y": logical(0) > x <- matrix(rnorm(9), 3, 3) > y <- rn...

...3 > Is there a way of getting more PCs and eigenvalues than rows? Is the eigen-decomposition of the covariance matrix really that numerically bad? (i.e., eigen(cov(x)) ) Thanks, Gad -- Gad Abraham Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham

Hi, I have an RData file containing a GeneSetCollection object (Bioconductor), http://www.cs.mu.oz.au/~gabraham/c2.RData. I think it uses lazy loading because packages are only loaded when I access the object (see below) in the R console. When I try the same with Rscript, it segfaults. This happens on 2.9.0 both on Linux and Mac: Rscript -e 'load("c2.RData"); c2[1]' *** caught segfa...

...ger(c(100, 100))) Error in validObject(.Object) : invalid class "dsyMatrix" object: length of x slot != prod(Dim) Is there an easier way of doing this? Thanks, Gad -- Gad Abraham PhD Student, Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham

...tion) [1] 20 5 All predict.prcomp really does is x2 %*% p$rotation, which is a perfectly legal operation that should yield a 5x5 matrix: > dim(x2 %*% p$rotation) [1] 5 5 Thanks, Gad -- Gad Abraham Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham

...following packages will be REMOVED: r-base-dev refblas3-dev The following NEW packages will be installed: libblas-dev libfftw3-dev libhdf5-serial-dev liblapack-dev octave3.0-headers -- Gad Abraham Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham

...b/debian-amd64/testing/Packages.bz2 Hash Sum mismatch My /etc/apt/sources contains: deb http://debian.cran.r-project.org/cran2deb/debian-amd64 testing/ Any idea? Thanks, Gad -- Gad Abraham PhD Student, Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham

...age, but on wide matrices (28 observations, 1891 variables) so L2 penalisation is used. I get the following error, although I've tried different penalties and different tolerances. The X matrix is scaled and centred. > library(Design) > load(url("http://www.csse.unimelb.edu.au/~gabraham/data2.Rdata")) > l <- lrm(y ~ X, penalty=100, tol=1e-13) Error in solvet(info.matrix, tol = tol) : apparently singular matrix > traceback() 4: stop("apparently singular matrix") 3: solvet(info.matrix, tol = tol) 2: fitter(X, Y, initial = f$coef, maxit = 1, tol = tol) 1: l...

...ly work out which day was the first day of each month? I'm using zoo 1.0-3 with R 2.2.1. Thanks, Gad -- Gad Abraham Department of Mathematics and Statistics University of Melbourne Parkville 3010, Victoria, Australia email: g.abraham at ms.unimelb.edu.au web: http://www.ms.unimelb.edu.au/~gabraham

Hi R helpers, I'm fitting large number of single factor logistic regression models as a way to immediatly discard factor which are insignificant. Everything works fine expect that for some factors I get error message "Singular information matrix in lrm.fit" which breaks whole execution loop... how to make LRM not to throw this error and simply skip factors with singularity

...quot; "series" "code" "n.cond" "model" Thanks, Gad -- Gad Abraham Department of Mathematics and Statistics The University of Melbourne Parkville 3010, Victoria, Australia email: g.abraham at ms.unimelb.edu.au web: http://www.ms.unimelb.edu.au/~gabraham

...a) lag.plot(b) What's the trick to this? I'm using R 2.2.1 (2005-12-20 r36812) on Ubuntu Linux. Thanks, Gad -- Gad Abraham Department of Mathematics and Statistics University of Melbourne Victoria 3010, Australia email: g.abraham at ms.unimelb.edu.au web: http://www.ms.unimelb.edu.au/~gabraham

...such as queue size and season). Does anyone know which algorithm survreg() uses for this? Thanks, Gad -- Gad Abraham Department of Mathematics and Statistics The University of Melbourne Parkville 3010, Victoria, Australia email: g.abraham at ms.unimelb.edu.au web: http://www.ms.unimelb.edu.au/~gabraham

...t(p, newdata=x.test, center=p$center, scale=p$center) or use the training set's own centers and scales: x.test.pc <- predict(p, newdata=x.test, center=TRUE, scale=TRUE) Thanks, Gad -- Gad Abraham Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham

Hi! Is there any package or function on R to ARMA models (Box & Jenkins, without sazonality and trend) with resources to automatic identification for p and q ? Regards, Raphael Saldanha Brazil [[alternative HTML version deleted]]

Hi, We're using stats4 for a logistic regression. The code is chdreg.logit2 <- glm(chd ~ age + sex, family = binomial) summary(chdreg.logit2) oddsratios <- coef(chdreg.logit2) exp(oddsratios) # Calculate model predicted values pred <- predict(chdreg.logit2,type="response") The glm part runs fine, and up to now so has the predict function. However, now we're

Hi, I want to use R to do user-submitted jobs in a (java-based) webapp. Specifically, I want * users to upload R scripts * run the R job on user data * save the results to database I'm concerned about sandbox issues. * Is it possible to disable file read/write capability? * Can I prevent the user from loading packages (e.g. the database package). * Can I have users work on separate data

I am new to 'R' and also new to the concept of a 'Hessian' with non-linear optimization. I would like to avoid going through all of the reference articles given with ?optim as access to a library is not handy. Would someone be able to elighten me on what is in the Hessian matrix if 'hessian = TRUE' with optim? The documentation indicates that this is a numerically