search for: tcrossprod

...while (!ende) { nr <- nr + 1 ph <- t(crossprod(th, Xh) * as.vector(1 / crossprod(th))) ph <- ph * as.vector(1/sqrt(crossprod(ph))) thnew <- t(tcrossprod(t(ph), Xh) * as.vector(1/(crossprod(ph)))) prec <- crossprod(th-thnew) th <- thnew if (prec <= (tol^2)) ende <- TRUE if (it <= nr) ende <- TRUE # didn't converge...

...ay still seem surprising that matrix multiplication does > not behave numerically for a pair of such matrices, and by the > principle of "least surprise" we should provide the boolean arithmetic > matrix products in another way than by the standard %*%, > crossprod() and tcrossprod() functions. > So one possibility could be to change the standard functions to behave > numerically, > and e.g., use %&% (replace the numeric "*" by a logical "&") and > crossprod(A,B, boolean=TRUE), tcrossprod(A,B, boolean=TRUE) > for the three bool...

...ay still seem surprising that matrix multiplication does > not behave numerically for a pair of such matrices, and by the > principle of "least surprise" we should provide the boolean arithmetic > matrix products in another way than by the standard %*%, > crossprod() and tcrossprod() functions. > So one possibility could be to change the standard functions to behave > numerically, > and e.g., use %&% (replace the numeric "*" by a logical "&") and > crossprod(A,B, boolean=TRUE), tcrossprod(A,B, boolean=TRUE) > for the three bool...

...d graphics system # Stock Ubuntu-provided R has the same failure: andy at n88:~$ /usr/bin/R -q --vanilla > dtk.R.version() [1] "R 2.10.1, 2009-12-14, svn.rev 50720, i486-pc-linux-gnu" > x <- matrix(c(1, 0, NA, 1), 2, 2) ; y <- matrix(c(1, 0, 0, 2, 1, 0), 3, 2) > (z <- tcrossprod(x, y)) [,1] [,2] [,3] [1,] NA NA 0 [2,] 2 1 0 > identical(z, x %*% t(y)) [1] FALSE # R I just built from scratch, same failure as stock R: andy at n88:~$ /usr/local/pkg/R-2.12-branch-20110914/bin/R -q --vanilla > dtk.R.version() [1] "R 2.12.2 (Patched), 2011-03-18...

...able CPU, which isn't ideal for machines more than a couple of CPUs. Setting the environment (OMP_NUM_THREADS or OPENBLAS_NUM_THREADS) in the shell works: $ OMP_NUM_THREADS=1 R > Sys.getenv("OMP_NUM_THREADS") [1] "1" > system.time({x <- replicate(5e3, rnorm(5e3)); tcrossprod(x) }) [runs in one thread] but adding it to /etc/R/Renviron.site doesn't: $ R > Sys.getenv("OMP_NUM_THREADS") [1] "1" > system.time({x <- replicate(5e3, rnorm(5e3)); tcrossprod(x) }) [runs multi-threaded] (nor does setting the variable at runtime with `Sys.setenv...

...hm for correcting a non positive definite covariance matrix. I found this code in R: http://projects.cs.kent.ac.uk/projects/cxxr/trac/browser/trunk/src/library/Recommended/Matrix/R/nearPD.R?rev=637 I managed to understand most of it, the only line I really don't understand is this one: X <- tcrossprod(Q * rep(d[p], each=nrow(Q)), Q) This line is supposed to calculate the matrix product Q*D*Q^T, Q is an n by m matrix and R is a diagonal n by n matrix. What does this mean? I also don't understand the meaning of a cross product between matrices, I only know it between vectors. Thanks, Barisda...

...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 product. Suppose I enter this: > a = c(1, 2, 3) > b = c(2, 3, 4) > ab = crossprod(a, b) > ab [,1] [1,] 20 > ab = tcrossprod(a, b) > ab [,1] [,2] [,3] [1,] 2 3 4 [2,] 4 6 8 [3,] 6 9 12 Does any k...

...ones. Further, it may still seem surprising that matrix multiplication does not behave numerically for a pair of such matrices, and by the principle of "least surprise" we should provide the boolean arithmetic matrix products in another way than by the standard %*%, crossprod() and tcrossprod() functions. So one possibility could be to change the standard functions to behave numerically, and e.g., use %&% (replace the numeric "*" by a logical "&") and crossprod(A,B, boolean=TRUE), tcrossprod(A,B, boolean=TRUE) for the three boolean arithmetic version o...

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,"+") - 2*mtm)} It takes less than 50 seconds for my (dense) matrix of 5,054 rows and 12,803 co...

...-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 tcrossprod 41.147 1.286 11.9 transposition and reuse 40.407 3.525 43.606 elementwise after reshape 21.474 1.828 23.124 columnwise sapply 34.695 32.35 66.592 for loop over columns 37.237 29.471 67.2 On the same day upgrading to 2.12.1 on the same dual core...

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...cation of first column of first matrix with first column of second matrix of second matrix [2,] ? 2*5+5*2 ? ? cant figure out how these were derived, definitely this is NOT identical to e.g. http://en.wikipedia.org/wiki/Cross_product I can work it out for the tcrossprod > c <- tcrossprod(g, h) > c [,1] [,2] [1,] 32 14 [2,] 77 32 because [,1] [,2] [1,] 1*4+2*5+3*6 1*1+2*2+3*3 #sum of elementwise multiplication of first line of first matrix with first line of second matrix sum of elementwise multi...

...th, cbind2, rbind2, Arith, Math, Math2, Summary, Compare, !, +, %*%, Schur, as.array, as.matrix, as.vector, band, chol, colMeans, colSums, coerce, crossprod, determinant, diag, dim, dimnames, dimnames<-, expand, expm, kronecker, image, isSymmetric, norm, rcond, rowMeans, rowSums, show, solve, t, tcrossprod, tril, triu Error: package/namespace load failed for 'Matrix' > sessionInfo() R version 2.4.0 alpha (2006-09-05 r39134) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Chile.1252;LC_CTYPE=Spanish_Chile.1252;LC_MONETARY=Spanish_Chile.1252;LC_NUMERIC=C;LC_TIME=Spanish_Chile.1252 attached base...

Dear All, I'm preparing a simple algorithm for matrix multiplication for a specific purpose, but I'm getting some unexpected results. If anyone could give a clue, I would really appreciate. Basically what I want to do is a simple matrix multiplication: (WB) %*% t(WB). The WB is in the disk so I compared to approaches: - Load 'WB' using 'read.table' (put it in WB.tmp) and

...case where transposition does not occur simultaneously with complex conjugation. And I'm not 100% sure that that wasn't a mistake. Matlab and Octave sort of recognize this, as "A'" means the Hermitian transpose of "A". In R, this issue makes t(), crossprod(), and tcrossprod() pretty much useless to me. OK, so what to do? I have several options: 1. define functions myt(), and mycrossprod() to get round the problem: myt <- function(x){t(Conj(x))} 2. Try to redefine t.default(): t.default <- function(x){if(is.complex(x)){return(base::t(Conj(x)))} else {r...

...machines more than a couple of CPUs. > > Setting the environment (OMP_NUM_THREADS or OPENBLAS_NUM_THREADS) in the > shell works: > > $ OMP_NUM_THREADS=1 R >> Sys.getenv("OMP_NUM_THREADS") > [1] "1" >> system.time({x <- replicate(5e3, rnorm(5e3)); tcrossprod(x) }) > [runs in one thread] > > but adding it to /etc/R/Renviron.site doesn't: > > $ R >> Sys.getenv("OMP_NUM_THREADS") > [1] "1" >> system.time({x <- replicate(5e3, rnorm(5e3)); tcrossprod(x) }) > [runs multi-threaded] > > (nor doe...

> By the way, since the tcrossprod function in the Matrix package is so fast, the Euclidean distance can be computed very fast: Indeed. > euc_dist <- function(m) {mtm <- Matrix::tcrossprod(m); sq <- rowSums(m*m); sqrt(outer(sq,sq,"+") - 2*mtm)} There are two reasons why I didn't use this optimization in...

...(1,2,3),3),ncol=3) ## > x ## [,1] [,2] [,3] ## [1,] 1 1 1 ## [2,] 2 2 2 ## [3,] 3 3 3 ## and a storage matrix like this cross <- matrix(rep(0,9),ncol=3) ## then use a loop to sum up the cross products of the rows for (i in 1:nrow(x)){ cross <- cross+tcrossprod(x[i,]) } ## The result ## ## > cross ## [,1] [,2] [,3] ## [1,] 14 14 14 ## [2,] 14 14 14 ## [3,] 14 14 14 -- ----------------------- Stephan Lindner University of Michigan

...e) : in 'Matrix' methods specified for export, but none defined: Arith, Math, Math2, +, %*%, Schur, as.matrix, chol, colMeans, colSums, coerce, crossprod, determinant, diag, dim, dimnames, dimnames<-, expand, expm, kronecker, image, norm, rcond, rowMeans, rowSums, show, solve, t, tcrossprod Error: package/namespace load failed for 'Matrix' Here is my system: > sessionInfo() R version 2.4.0 (2006-10-03) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8...

Dear all, how can I convert an m x n incidence matrix into an m x m adjacency matrix or an n x n adjacency matrix? The current matrix contains binary data, hence the new matrix would contain counts of common occurrences. Thank you for your help. Phil