similar to: need help in understanding R code, and maybe some math

Fellipe, CXXR development has moved to github, and we haven't fixed up the build for using git yet. Could you send a pull request with your change to the repo at https://github.com/cxxr-devel/cxxr/? Also, this patch may be useful for pqR too. https://github.com/radfordneal/pqR Thanks On Mon, Jan 19, 2015 at 2:35 PM, Dirk Eddelbuettel <edd at debian.org> wrote: > > On 19

1. Martin Maechler's comments should be taken as replacements for anything I wrote where appropriate. Any apparent conflict is a result of his superior knowledge. 2. 'eigen' returns the eigenvalue decomposition assuming the matrix is symmetric, ignoring anything in m[upper.tri(m)]. 3. The basic idea behind both posdefify and nearPD is to compute the

Hi, If a matrix is not positive definite, make.positive.definite() function in corpcor library finds the nearest positive definite matrix by the method proposed by Higham (1988). However, when I deal with correlation matrices whose diagonals have to be 1 by definition, how do I do it? The above-mentioned function seem to mess up the diagonal entries. [I haven't seen this complication, but

Thank you for your reply. Do you have any idea of how to get rid of the errors? I tried Null function to calculate eigenvectors and nearPD to get approximate positive definite matrix first but they also had errors. -- View this message in context: http://r.789695.n4.nabble.com/error-code-1-from-Lapack-routine-dsyevr-tp4702571p4702639.html Sent from the R devel mailing list archive at

I received the following note this AM. The problem is, I'm not quite sure how to fix it. Can one use PROTECT(coxlist(eval(PROTECT.... , do I create an intermediate variable, or otherwise? I'm willing to update the code if someone will give me a pointer to the right documentation. This particular chunk was written when there was a lot of change going on in the callback mechanism and

The function of crossprod in R puzzled me. I would like to calculate the cross product of two vectors. According to my text book, it defines like this: a = (ax, ay, az) b = (bx, by, bz) then, the cross product of a and b is: a X b = (ay*bz-az*by, az*bx-ax*bz, ax*by-ay*bz) It can also write in a determinant format. But the crossprod or tcrossprod function in R appeared not calculate the cross

Today I built R from source on a 32-bit Ubuntu 10.04.3 LTS box, and saw that the "make check" tests/reg-tests-1b.R failed. From the output at the end of my "tests/reg-tests-1b.Rout.fail" file, the problem is appearing in the "identical(z, x %*% t(y))" test code below. I then tried the stock R provided by the Ubuntu r-base-core binary package, and to my surprise, it

Dear list members; The code given below corresponds to the PCA-NIPALS (principal component analysis) algorithm adapted from the nipals function in the package chemometrics. The reason for using NIPALS instead of SVD is the ability of this algorithm to handle missing values, but that's a different story. I've been trying to find a way to improve (if possible) the efficiency of the code,

What is the correct way to globally configure R to default to single (or at least, << NUM_CPUS) threaded operation? Using R 3.3.1 (both in debian unstable or using the CRAN repository for xenial) with OpenBLAS (0.2.18) defaults to using one thread per available CPU, which isn't ideal for machines more than a couple of CPUs. Setting the environment (OMP_NUM_THREADS or

R Version 2.12.1 (2010-10-15) vs 2.12.0 has slowed down 8 fold for dual core and 17 fold for dual-core-dual-processor Macs. I have checked this result on 3 different macs using the following R-script: Using Version 2.12.0 on a dual core dual processor Mac: > source("http://www.bio.umass.edu/biology/kunkel/pub/R/CuriousResult.R") matrix multiplication 43.543 1.308 14.788

Hi Stefan, Thank you very much for pointing me to the wordspace package. It does the job a bit faster than my C code but is 100 times more convenient. By the way, since the tcrossprod function in the Matrix package is so fast, the Euclidean distance can be computed very fast: euc_dist <- function(m) {mtm <- Matrix::tcrossprod(m); sq <- rowSums(m*m);? sqrt(outer(sq,sq,"+") -

Hi all, I have been searching all sorts of documentation, reference cards, cheat sheets but can't find why R's crossprod(A, B) which is identical to A%*%B does not produce the same as Matlabs cross(A, B) Supposedly both calculate the cross product, and say so, or where do I go wrong? R is only doing sums in the crossprod however, as indicated by (z <- crossprod(1:4)) # = sum(1 +

Hello, I am writing an R interface for one of my C++ programs. The computations in C++ are very time consuming (several hours), so the user needs to be able to interrupt them. Currently, the only way I found to do so is calling R_CheckUserInterrupt() frequently. Unfortunately, there are several problems with that: 1. Calling R_CheckUserInterrupt() interrupts immediately, so I have no

I mistakenly left a write in "/tmp" in the rockchalk package (version 1.8.109) that I uploaded last Friday. Kurt H wrote and asked me to fix today. While uploading a new one, I became aware of a problem I had not seen. The version I uploaded last Friday, 1.8.109, has OK status on all platforms except r-release-windows-ix86+x86_64. I get OK on oldrel-windows and also on devel-windows.

On 2 February 2015 at 10:07, William Dunlap <wdunlap at tibco.com> wrote: <snip> > > If all goes well then > eigen(lastEigenX) > will cause the same error and you or someone on this list can see what > is odd about that matrix (e.g., by looking at its singular values). Preferably *not* this list as this doesn't really seem to be about developing R or with/for

In a newly downloaded version (today) of R-2-4-0alpha, with all packages from CRAN also installed today, I get: > library(Matrix) Erro en loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : in 'Matrix' methods specified for export, but none defined: BIC, anova, coef, confint, deviance, fitted, fixef, formula, head, lmer, logLik, mcmcsamp, plot,

This is a Request For Comment, also BCCed to 390 package maintainers of reverse dependencies of the Matrix package. Most users and package authors working with our 'Matrix' package will be using it for numerical computations, and so will be using "dMatrix" (d : double precision) matrix objects M, and indirectly, e.g., for M >= c will also use "lMatrix" (l:

Hi everyone, I would like to compute the sum of cross products of rows of a matrix. Does anyone know how to do this without an explicit loop for computational efficiency? Below is a code example. Thanks! Stephan # I.e., if I have a matrix like this x <- matrix(rep(c(1,2,3),3),ncol=3) ## > x ## [,1] [,2] [,3] ## [1,] 1 1 1 ## [2,] 2 2 2 ## [3,] 3 3

Hi All, This occurs when I try to install certain r packages via the Spack package manager (the example is for DelayedArray): 70 ** R 71 ** inst 72 ** byte-compile and prepare package for lazy loading >> 73 Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix' 74 Execution halted 75 ERROR: lazy

Dear All, After upgrading to R-2.4.0-dapper2 (my system is ubuntu 6.06 LTS), I often met problems when loading some packages like Matrix. Here is the details: > library(Matrix) Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : in 'Matrix' methods specified for export, but none defined: Arith, Math, Math2, +, %*%, Schur, as.matrix, chol,