search for: ngcmatrix

Hi Martin, package arules heavily relies on ngCMatrix and uses multiplication and addition for logical operations. I think it makes sense that in a mixed operation with one dgCMatrix and one ngCMatrix the ngCMatrix should be "promoted" to a dgCMatrix. The current behavior of %*% and friends is in deed confusing: > m <- matrix(sam...

...r M >= c will also use "lMatrix" (l: logical i.e. TRUE/FALSE/NA). All the following is **not** affecting those numerical / logical computations. A few others will know that we also have "pattern" matrices (purely binary: TRUE/FALSE, no NA) notably sparse ones, those "ngCMatrix" etc, all starting with "n" (from ``patter[n]``) which do play a prominent role in the internal sparse matrix algorithms, notably of the (underlying C code) CHOLMOD library in the so-called "symbolic" cholesky decomposition and other such operations. Another reason you may...

...rom source The problem is actually slightly worse, because loading SeuratObject from step (2) breaks sparse matrices for everyone until Matrix is reloaded (and very few people can afford the $127-150 million budget for that): library(Matrix); sparseMatrix(1,1) # 1 x 1 sparse Matrix of class "ngCMatrix" # # [1,] | suppressPackageStartupMessages(library(SeuratObject)) sparseMatrix(1,1) # 1 x 1 sparse Matrix of class "ngCMatrix" # Error in validityMethod(as(object, superClass)) : # object 'Csparse_validate' not found detach('package:SeuratObject', unload = TRUE); s...

Hi The following attempt to minimize memory consumption fails. m1 <- Matrix(c(rep(1,1000), rep(0,2000)), 1500) m2 <- as(m1, "ngCMatrix") Then m1 %*% c(1,2) produces the desired matrix product, while m2 %*% c(1,2) results in the error Error in x %*% y : Cholmod error 'invalid xtype' at file:../MatrixOps/cholmod_sdmult.c, line 82 I might be making a wrong assumption that this should work, or another mistake,...

...m having difficulty working with these S4 objects. My object looks as follows. > str(rules) Formal class 'rules' [package "arules"] with 4 slots ..@ lhs :Formal class 'itemMatrix' [package "arules"] with 3 slots .. .. ..@ data :Formal class 'ngCMatrix' [package "Matrix"] with 5 slots .. .. .. .. ..@ i : int [1:2133] 3907 3519 4172 3519 4182 3519 4172 4182 4172 4182 ... .. .. .. .. ..@ p : int [1:790] 0 0 1 2 3 4 5 6 7 8 ... .. .. .. .. ..@ Dim : int [1:2] 7002 789 .. .. .. .. ..@ Dimnames:List of 2 .. .. ....

...ually slightly worse, because loading SeuratObject > from step (2) breaks sparse matrices for everyone until Matrix is > reloaded (and very few people can afford the $127-150 million budget for > that): > > library(Matrix); sparseMatrix(1,1) > # 1 x 1 sparse Matrix of class "ngCMatrix" > # > # [1,] | > suppressPackageStartupMessages(library(SeuratObject)) > sparseMatrix(1,1) > # 1 x 1 sparse Matrix of class "ngCMatrix" > # Error in validityMethod(as(object, superClass)) : > # object 'Csparse_validate' not found > detach('packa...

...atrix? now) Trevor > y=Matrix(diag(4)) > y 4 x 4 diagonal matrix of class "ddiMatrix" [,1] [,2] [,3] [,4] [1,] 1 . . . [2,] . 1 . . [3,] . . 1 . [4,] . . . 1 > z=sparseMatrix(1:4,1:4) > z 4 x 4 sparse Matrix of class "ngCMatrix" [1,] | . . . [2,] . | . . [3,] . . | . [4,] . . . | > beta=as(Matrix(1:4),"dgCMatrix") > y%*%beta 4 x 1 sparse Matrix of class "dgCMatrix" [1,] 1 [2,] 2 [3,] 3 [4,] 4 > z%*%beta 4 x 1 sparse Matrix of class "ngCMatrix" [1,] | [...

...t; e: <environment> | < __ not parse()able __: environment | --- | > dn: list(c("A", "B", "C"), c("a", "b", "c", "d", "e")) | > --> checking list(*): Ok | > --=--=--=--=-- | > e: new("ngCMatrix", i = integer(0), p = c(0L, 0L, 0L, 0L, 0L, 0L, | > 0L), Dim = c(4L, 6L), Dimnames = list(NULL, NULL), factors = list()) | > --> checking list(*): Ok | 844a1013,1015 | > i: c(1, 3, 4, 5, 6, 7, 8) | > --> checking list(*): Ok | > --=--=--=--=-- | 876a1048,1050 | &...

...lt; __ not parse()able __: environment > | --- > | > dn: list(c("A", "B", "C"), c("a", "b", "c", "d", "e")) > | > --> checking list(*): Ok > | > --=--=--=--=-- > | > e: new("ngCMatrix", i = integer(0), p = c(0L, 0L, 0L, 0L, 0L, 0L, > | > 0L), Dim = c(4L, 6L), Dimnames = list(NULL, NULL), factors = list()) > | > --> checking list(*): Ok > | 844a1013,1015 > | > i: c(1, 3, 4, 5, 6, 7, 8) > | > --> checking list(*): Ok > | >...

...item3 2 item2 2 item3 ... how do I create a transaction object of the arules package from such a table? I tried this with read.transactions(tr_dat, format="single") of the package arules but I didn'd succeed getting the following error Error: invalid class "ngCMatrix" object: slot i is not *strictly* increasing inside a column. After reading the R source of read.transactions I wrote the below function transactionsFromSingleItems, which seems to work. The problem seemed to be that the items of the list tr_basket are not atomic. That's why I used th...

Suppose this is my list of transactions: set.seed(200) tran=random.transactions(100,3) inspect(tran) items transactionID 1 {item80} trans1 2 {item8, item20} trans2 3 {item28} trans3 I want to get the 'transpose' of the data, i.e. transactionID items 1 {trans2} item8 2 {trans2} item20 3 {trans3} item28 4 {trans1} item80 I

Fine with me as long as eliminating the inconveniences associated with it can be put on the roadmap. The alias instability and the fact that the user has no way to know if s/he should do ?`foo,numeric-method` or ?`foo,numeric,ANY-method` to find the method has been a long-standing problem. H. On 3/21/19 21:29, Michael Lawrence wrote: If we started over, I'd try to avoid this sort of