search for: csparsematrix

...column-wise using Matrix objects (Csparse). It looks like one can apply mosty any base function to these objects (i.e., apply, colSums), but there is a nasty conversion to traditional matrix objects if one does that. Is there any workaround? I can see colSum listed in the help for Class 'CsparseMatrix' , but I wonder whether I'm using the default colSums() or the one specific to CsparseMatrix... #example (z = Matrix(c(0,1,0,0), 10,10)) zr = rowSums(z) class(zr) # numeric; I'd like it to be a CSparseMatrix object Thanks a lot in advance, -Jose -- Jose Quesada, PhD. http://www.an...

...of row vectors. At a certain point I need to divide a matrix by a vector of norms. I find that the behavior of Matrix objects differs from normal matrix objects. Example the following code examples differ only in xnormed changing from normal to Matrix object: x = matrix(1:12,3,4) x = as(x, "CsparseMatrix") xnorms = sqrt(colSums(x^2)) (xnormed = t(x) * (1/xnorms)) This produces a "warning: coercing sparse to dense matrix for arithmetic in: t(x) * 1/xnorms." but gets the result (a 4 x 3 matrix) I want to stay in sparse format anyway (if it helps!) so I tried x = matrix(1:12,3,4)...

...x = x, i = i, j = j) : 'i' has no integer column number should never happen; please report In addition: Warning messages: 1: Ambiguous method selection for "%*%", target "ddiMatrix#dgCMatrix" (the first of the signatures shown will be used) diagonalMatrix#CsparseMatrix ddenseMatrix#CsparseMatrix in: .findInheritedMethods(classes, fdef, mtable) I got 4 other copies of the same warning. Will play around a bit more... This is really strange. Thanks -- Jose Quesada, PhD. http://www.andrew.cmu.edu/~jquesada

...quot; # Error in validityMethod(as(object, superClass)) : # object 'Csparse_validate' not found detach('package:Matrix', unload = TRUE); library(Matrix) sparseMatrix(1,1) # 1 x 1 sparse Matrix of class "ngCMatrix" # # [1,] | In turn, this can be traced to a copy of the CsparseMatrix class from Matrix_1.5-1 remaining in the namespace and the lazy-load database of SeuratObject: readRDS('SeuratObject/R/SeuratObject.rdx')$variables |> names() |> grep('sparseM', x = _, value = TRUE) # [1] ".__C__CsparseMatrix" ".__C__dsparseMatrix" "....

...ct, superClass)) : > # object 'Csparse_validate' not found > detach('package:Matrix', unload = TRUE); library(Matrix) > sparseMatrix(1,1) > # 1 x 1 sparse Matrix of class "ngCMatrix" > # > # [1,] | > > In turn, this can be traced to a copy of the CsparseMatrix class from > Matrix_1.5-1 remaining in the namespace and the lazy-load database of > SeuratObject: > > readRDS('SeuratObject/R/SeuratObject.rdx')$variables |> names() |> > grep('sparseM', x = _, value = TRUE) > # [1] ".__C__CsparseMatrix" ".__...

...n 'Matrix' with all the class hierarchies and the many specific classes has been to allow and foster coercing to abstract super classes, i.e, to "dMatrix" or "generalMatrix", "triangularMatrix", or then "denseMatrix", "sparseMatrix", "CsparseMatrix" or "RsparseMatrix", etc So in the above as(*, "RsparseMatrix") should work always. As a summary, in other words, for what you want, as(sparseMatrix(.....), "RsparseMatrix") should give you what you want reliably and efficiently. > Am I doing...

The bulk is on my forums - the final post for today is: Results to date: A. It looks like I am going to need a newer compiler for C - xlc/xlC V11 apparently does not understand this code: "/data/prj/cran/R-3.2.3/src/main/memory.c", line 2149.31: 1506-046 (S) Syntax error. I will have to check if R-devel has different code before asking for assistence. +2139 #ifdef

Using the Matrix package, how can I create a row-oriented sparse Matrix from scratch populated with some data? By default a column-oriented one is created and I'm aware of the note that the package is optimized for column-oriented ones, but I'm only interested in using it for holding my sparse row-oriented data and doing basic subsetting by rows (even using drop=FALSE). Here is what I

Hi, I'm finding that readMM() cannot read a file written with writeMM(). Example: library(Matrix) a = Matrix(c(1,0,3,0,0,5), 10, 10) a = as(a, "CsparseMatrix") writeMM(a, "kk.mm") b = readMM("kk.mm") Error in validObject(.Object) : invalid class "dgTMatrix" object: all row indices must be between 0 and nrow-1 Thoughts? Thanks, -Jose -- Jose Quesada, PhD. http://www.andrew.cmu.edu/~jquesada

....) is a simple utility from Matrix > which -- very efficiently for sparseMatrix objects -- gives the > number of nonzero entries of the matrix. > > All of these classes are formally defined classes and have > therefore help pages. Here ?dgCMatrix-class which then points > to ?CsparseMatrix-class (and I forget if Rstudio really helps > you find these ..; in emacs ESS they are found nicely via the usual key) > > To get started, you may further look at ?Matrix _and_ ?sparseMatrix > (and possibly the Matrix package vignettes --- though they need > work -- I'm happy...

Hi, I have sparse (tridiagonal) matrices, and I use the Matrix package for handling them. For certain computations, I need to either set the first row to zero, or double the last row. I find that neither operation preserves sparsity, eg > m <- Diagonal(5) > m 5 x 5 diagonal matrix of class "ddiMatrix" [,1] [,2] [,3] [,4] [,5] [1,] 1 . . . . [2,] . 1

...at least need to be slightly fixed before that Matrix version becomes default on CRAN, as these packages make assumptions about unspecified behavior of some Matrix functions, notably Matrix::Matrix() which in that next version of Matrix will produce "diagonalMatrix" instead of "CsparseMatrix" objects in more cases.... a good thing, but not what those packages have assumed... @Spencer: Are you actively using 'giveCsparse = ..' somewhere in your code? If not, why would you be interested in the details of the changes (which would be entirely invisible to you as user...

...n R, but after reading the docs for do.call, apply, etc, I still don't know how to write the nested loop in a vectorized way. Example data: x = matrix(rnorm(100), 10, 10) # this is actually a very large sparse matrix, but it doesn't matter for the # example library(Matrix) x = as(x,"CsparseMatrix") # cosine function cosine = function (x, y){ if (is.vector(x) && is.vector(y)) { return(crossprod(x, y)/sqrt(crossprod(x) * crossprod(y))) } else {stop("cosine: argument mismatch. Two vectors needed as input.")} } # The loop-based solution I have is: if (is(x, "...

...n R, but after reading the docs for do.call, apply, etc, I still don't know how to write the nested loop in a vectorized way. Example data: x = matrix(rnorm(100), 10, 10) # this is actually a very large sparse matrix, but it doesn't matter for the # example library(Matrix) x = as(x,"CsparseMatrix") # cosine function cosine = function (x, y){ if (is.vector(x) && is.vector(y)) { return(crossprod(x, y)/sqrt(crossprod(x) * crossprod(y))) } else {stop("cosine: argument mismatch. Two vectors needed as input.")} } # The loop-based solution I have is: if (is(x, "...

...pMatrix(nrow, ncol, i = sample(nrow, nnz, replace = TRUE), j = sample(ncol, nnz, replace = TRUE), x = rand.x(nnz)) } ## (original ir a term x doc matrix of the entire wikipedia) mm <- rSpMatrix(793251, 1027355, nnz = 205746204) # make it column based: mm <- as(mm, "CsparseMatrix") a=mm[1,,drop=F]#this takes close to 30 seconds on a 3Ghz machine Thanks, - -Jose - -- === I'm learning a new keyboard layout. I type slowly. Please excuse typos and slower-that-usual responses. Thanks for your patience=== Jose Quesada, PhD. Max Planck Institute, Center for Adaptive Beh...

Hello, I am working with a sparse matrix that is approx. 13,900 by 14,100. My goal is to select a row out of the matrix and create a new matrix with that row repeated 13,900 times without having to do any looping. Example: Starting Matrix: exampleMatrix 3 x 4 sparse Matrix of class "dgCMatrix" [1,] 1 . . . [2,] . 1 . 0.5 [3,] . . 1 .. New Matrix:.. newExampleMatrix 3 x 4 sparse

...teger overflow) and nnzero(.) is a simple utility from Matrix which -- very efficiently for sparseMatrix objects -- gives the number of nonzero entries of the matrix. All of these classes are formally defined classes and have therefore help pages. Here ?dgCMatrix-class which then points to ?CsparseMatrix-class (and I forget if Rstudio really helps you find these ..; in emacs ESS they are found nicely via the usual key) To get started, you may further look at ?Matrix _and_ ?sparseMatrix (and possibly the Matrix package vignettes --- though they need work -- I'm happy for collaborators there...

...le MRE (minimal reproducible example) for the problem seen with Matrix: S <- sparseMatrix(i=1:4, j=9:6, x=pi*1:4) n <- 410 # it succeeds for 407 -- sometimes even with 408 X <- replicate(n, S, simplify = FALSE) Xb <- do.call("rbind", X) ## -> Error in as(x, "CsparseMatrix") : node stack overflow But as I said, that's not really the Matrix package. A small reproducible example, not involving the Matrix package at all: MM <- setClass("mmatrix", contains="matrix") setMethod("rbind2", signature(x="mmatrix", y=&qu...

...htly fixed > before that Matrix version becomes default on CRAN, as these > packages make assumptions about unspecified behavior of some > Matrix functions, notably Matrix::Matrix() which in that next version > of Matrix will produce "diagonalMatrix" instead of > "CsparseMatrix" objects in more cases.... a good thing, but not > what those packages have assumed... > > @Spencer: Are you actively using 'giveCsparse = ..' somewhere > in your code? > If not, why would you be interested in the details of the changes > (which would be en...

...problems with stale caches that I described in this thread from September: https://stat.ethz.ch/pipermail/r-devel/2022-September/081971.html I've attached a script demonstrating my point. It creates and installs a package named TestPackage with importClassesFrom(Matrix, dgCMatrix, CsparseMatrix) in NAMESPACE and setClass("whatever", contains = "dgCMatrix") in R/*.R. After installing the package, I see: > ns <- asNamespace("TestPackage") > names(ns) [1] ".__C__generalMatrix" ".__C__Matrix" ".__C__sparse...