Re: [R] column permutation of sparse matrix
Sorry. I erred somewhere in making the original M1 matrix using sampling call
in the spMatrix function. I still don't really understand why the matrix
values do not match exactly with M1@x. If I regenerate M1 this way...
i=c(1:5,5:1)
j=c(1:5,2:6)
x=rnorm(10,2)
M1 - spMatrix(nrow=5,ncol=6,i=i,j=j,x=x)
M1
5 x 6 sparse Matrix of class dgTMatrix
[1,] 1.876193 ....2.040574
[2,] .1.032214 ..1.786480 .
[3,] ..1.716743 3.711979 ..
[4,] ..2.534000 3.302921 ..
[5,] .1.084763 ..1.511992 .
Then the str(M1) makes sense and all the methods described so far appears to
work as expected.
M1@x
[1] 1.876193 1.032214 1.716743 3.302921 1.511992 1.084763 2.534000 3.711979
[9] 1.786480 2.040574
The solution is still not apparent to me though without doing a lapply.
spVecs - lapply(1:nrow(M1), function(a)
{
nnz - nnzero(M1[a,])
tmp - as(M1[a,],'sparseVector')
tmp@x - tmp@x[sample(nnz,nnz)]
return(tmp)
})
To get back a sparse matrix...I can do this.
x - do.call(c,lapply(spVecs,function(v) v@x))
j= do.call(c,lapply(spVecs,function(v) v@i))
i = do.call(c,lapply(1:length(spVecs), function(n)
rep(n,length(spVecs[[n]]@i
permM1 - sparseMatrix(i=i,j=j,x=x)
permM1
5 x 6 sparse Matrix of class dgCMatrix
[1,] 2.040574 ....1.876193
[2,] .1.786480 ..1.032214 .
[3,] ..1.716743 3.711979 ..
[4,] ..2.534000 3.302921 ..
[5,] .1.511992 ..1.084763 .
In this case, rows 3 and 4 remained unchanged. But now this takes a really
long time for a large sparse matrix.
Thanks for any advice.
--
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Re: [R] column permutation of sparse matrix
Douglas Bates ba...@stat.wisc.edu writes: On Tue, Dec 20, 2011 at 8:20 AM, Jean V Adams jvad...@usgs.gov wrote: Hi Jean, khai wrote on 12/19/2011 11:26:55 PM: Hi, I'm very new to working with sparse matrices and would like to know how I can column permute a sparse matrix. Here is a small example: M1 - spMatrix(nrow=5,ncol=6,i=sample(5,15,replace=TRUE),j=sample(6, 15,replace=TRUE),x=round_any(rnorm(15,2),0.001)) M1 5 x 6 sparse Matrix of class dgTMatrix [1,] 2.983 . 1.656 5.003 . . [2,] . . 2.990 . . . [3,] . 0.592 5.349 1.115 . . [4,] 1.836 . 2.804 . . . [5,] . 6.961 . . . 1.077 I know I can permute entire columns this way M1[,sample(6,6)] 5 x 6 sparse Matrix of class dgTMatrix [1,] 5.003 . . . 1.656 2.983 [2,] . . . . 2.990 . [3,] 1.115 0.592 . . 5.349 . [4,] . . . . 2.804 1.836 [5,] . 6.961 1.077 . . . But I would like the new sparse matrix to look like this...where only the nonzero elements are permuted. [1,] 1.656 . 5.003 2.983 . . [2,] . . 2.990 . . . [3,] . 5.349 1.115 0.592 . . [4,] 2.804 . 1.836 . . . [5,] . 1.077 . . . 6.961 Thanks in advance for any advice! A peculiar request but you can do that by permuting the 'x' slot in your original matrix. set.seed(1) (M1 - spMatrix(nrow=5,ncol=6,i=sample(5,15,replace=TRUE),j=sample(6, 15,replace=TRUE),x=round(rnorm(15,2),3))) 5 x 6 sparse Matrix of class dgTMatrix [1,] . . 2.738 . 3.595 . [2,] . . . . . . [3,] 3.879 . 4.289 -0.215 1.374 . [4,] . 4.966 1.180 1.379 . 2.487 [5,] 3.512 . . . 2.330 . (nnz - nnzero(M1)) [1] 15 M2 - M1 M2@x - M2@x[sample(nnz, nnz)] M2 5 x 6 sparse Matrix of class dgTMatrix [1,] . . 2.487 . 3.595 . [2,] . . . . . . [3,] 3.709 . 2.875 3.512 -0.215 . [4,] . 3.764 1.164 2.576 . 3.125 [5,] 2.184 . . . 2.738 . I do not think this is what was wanted. M1 and M2 are matrices with 12 non-zero elements, not 15 as nnzero() reports. The dgTMatrix representation effectively treats the slots of M1 like this: res - tapply(M1@x, list(M1@i,M1@j), sum) res[is.na(res)] - 0 res So permuting 'x' will return a different dgTMatrix with the same number of non-zero elements in place of the existing non-zero elements, but not necessarily having the same values when the (i,j) pairs are not unique. (e.g. 3.709 is seen in M2, but not M1) I think the OP was asking for permutations of the non-zero values in 'res', rather than permutations of M1@x. HTH, Chuck I don't have experience with sparse matrices, but I was able to get this to work by converting the sparse matrix to a base matrix and back again. library(Matrix) nonzero.cols - !apply(M1==0, 2, all) M2 - as.matrix(M1) reord - sample(seq(dim(M1)[2])[nonzero.cols]) M2[, nonzero.cols] - as.matrix(M1[, reord]) Matrix(M2, sparse=TRUE) This solution has the disadvantage of converting the sparse matrix to a dense matrix, which may end up producing a much larger object. -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] column permutation of sparse matrix
khai wrote on 12/19/2011 11:26:55 PM: Hi, I'm very new to working with sparse matrices and would like to know how I can column permute a sparse matrix. Here is a small example: M1 - spMatrix(nrow=5,ncol=6,i=sample(5,15,replace=TRUE),j=sample(6, 15,replace=TRUE),x=round_any(rnorm(15,2),0.001)) M1 5 x 6 sparse Matrix of class dgTMatrix [1,] 2.983 . 1.6565.003.. [2,].. 2.990. .. [3,]. 0.592 5.3491.115.. [4,] 1.836 . 2.804. .. [5,]. 6.961 . . . 1.077 I know I can permute entire columns this way M1[,sample(6,6)] 5 x 6 sparse Matrix of class dgTMatrix [1,] 5.003. . . 1.6562.983 [2,] . . . . 2.990 . [3,] 1.1150.592 . . 5.349 . [4,] . . . . 2.804 1.836 [5,] . 6.961 1.077 . .. But I would like the new sparse matrix to look like this...where only the nonzero elements are permuted. [1,] 1.656 . 5.0032.983.. [2,].. 2.990. .. [3,].5.3491.1150.592.. [4,] 2.804 . 1.836. .. [5,]. 1.077 . . . 6.961 Thanks in advance for any advice! I don't have experience with sparse matrices, but I was able to get this to work by converting the sparse matrix to a base matrix and back again. library(Matrix) nonzero.cols - !apply(M1==0, 2, all) M2 - as.matrix(M1) reord - sample(seq(dim(M1)[2])[nonzero.cols]) M2[, nonzero.cols] - as.matrix(M1[, reord]) Matrix(M2, sparse=TRUE) Jean [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] column permutation of sparse matrix
On Tue, Dec 20, 2011 at 8:20 AM, Jean V Adams jvad...@usgs.gov wrote: Hi Jean, khai wrote on 12/19/2011 11:26:55 PM: Hi, I'm very new to working with sparse matrices and would like to know how I can column permute a sparse matrix. Here is a small example: M1 - spMatrix(nrow=5,ncol=6,i=sample(5,15,replace=TRUE),j=sample(6, 15,replace=TRUE),x=round_any(rnorm(15,2),0.001)) M1 5 x 6 sparse Matrix of class dgTMatrix [1,] 2.983 . 1.656 5.003 . . [2,] . . 2.990 . . . [3,] . 0.592 5.349 1.115 . . [4,] 1.836 . 2.804 . . . [5,] . 6.961 . . . 1.077 I know I can permute entire columns this way M1[,sample(6,6)] 5 x 6 sparse Matrix of class dgTMatrix [1,] 5.003 . . . 1.656 2.983 [2,] . . . . 2.990 . [3,] 1.115 0.592 . . 5.349 . [4,] . . . . 2.804 1.836 [5,] . 6.961 1.077 . . . But I would like the new sparse matrix to look like this...where only the nonzero elements are permuted. [1,] 1.656 . 5.003 2.983 . . [2,] . . 2.990 . . . [3,] . 5.349 1.115 0.592 . . [4,] 2.804 . 1.836 . . . [5,] . 1.077 . . . 6.961 Thanks in advance for any advice! A peculiar request but you can do that by permuting the 'x' slot in your original matrix. set.seed(1) (M1 - spMatrix(nrow=5,ncol=6,i=sample(5,15,replace=TRUE),j=sample(6, 15,replace=TRUE),x=round(rnorm(15,2),3))) 5 x 6 sparse Matrix of class dgTMatrix [1,] . . 2.738 . 3.595 . [2,] . . . . . . [3,] 3.879 . 4.289 -0.215 1.374 . [4,] . 4.966 1.180 1.379 . 2.487 [5,] 3.512 . . . 2.330 . (nnz - nnzero(M1)) [1] 15 M2 - M1 M2@x - M2@x[sample(nnz, nnz)] M2 5 x 6 sparse Matrix of class dgTMatrix [1,] . . 2.487 . 3.595 . [2,] . . . . . . [3,] 3.709 . 2.875 3.512 -0.215 . [4,] . 3.764 1.164 2.576 . 3.125 [5,] 2.184 . . . 2.738 . I don't have experience with sparse matrices, but I was able to get this to work by converting the sparse matrix to a base matrix and back again. library(Matrix) nonzero.cols - !apply(M1==0, 2, all) M2 - as.matrix(M1) reord - sample(seq(dim(M1)[2])[nonzero.cols]) M2[, nonzero.cols] - as.matrix(M1[, reord]) Matrix(M2, sparse=TRUE) This solution has the disadvantage of converting the sparse matrix to a dense matrix, which may end up producing a much larger object. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] column permutation of sparse matrix
Thanks very much for responses. The 2 suggestions each do a part of what I want. Jean's proposal permutes nonzero elements within each row but shifts the location of the nonzero element around in the j slot of each i row. And Douglas's idea keeps the second part but permutes the entire x slot values. I'll try to see how I can combine these 2 ideas but it's not immediately obvious to me. =} -khai -- View this message in context: http://r.789695.n4.nabble.com/column-permutation-of-sparse-matrix-tp4216726p4219031.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] column permutation of sparse matrix
khai wrote on 12/20/2011 01:24:10 PM: Thanks very much for responses. The 2 suggestions each do a part of what I want. Jean's proposal permutes nonzero elements within each row but shifts the location of the nonzero element around in the j slot of each i row. And Douglas's idea keeps the second part but permutes the entire x slot values. I'll try to see how I can combine these 2 ideas but it's not immediately obvious to me. =} -khai I'm not sure what you mean by shifting the location of the nonzero element around in the j slot of each i row. My code shifts the nonzero columns around at random, but keeps the zero column in its original location. I thought that this is what you wanted to do. In the example below, the zero column starts as column 5 and ends as column 5, and the nonzero columns are reordered. Columns 1, 2, 3, 4, 5, 6 end up as 2, 1, 6, 3, 5, 4. Jean M1 5 x 6 sparse Matrix of class dgTMatrix [1,] . 6.569 5.592 .. . [2,] 1.163 2.688 . 1.85 . 3.217 [3,] 2.527 3.375 . .. 6.481 [4,] . . . .. 1.483 [5,] 1.004 . . .. . nonzero.cols - !apply(M1==0, 2, all) M2 - as.matrix(M1) reord - sample(seq(dim(M1)[2])[nonzero.cols]) M2[, nonzero.cols] - as.matrix(M1[, reord]) Matrix(M2, sparse=TRUE) 5 x 6 sparse Matrix of class dgCMatrix [1,] 6.569 . . 5.592 . . [2,] 2.688 1.163 3.217 . . 1.85 [3,] 3.375 2.527 6.481 . . . [4,] . . 1.483 . . . [5,] . 1.004 . . . . [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] column permutation of sparse matrix
Hi, I'm very new to working with sparse matrices and would like to know how I can column permute a sparse matrix. Here is a small example: M1 - spMatrix(nrow=5,ncol=6,i=sample(5,15,replace=TRUE),j=sample(6,15,replace=TRUE),x=round_any(rnorm(15,2),0.001)) M1 5 x 6 sparse Matrix of class dgTMatrix [1,] 2.983 . 1.6565.003.. [2,].. 2.990. .. [3,]. 0.592 5.3491.115.. [4,] 1.836 . 2.804. .. [5,]. 6.961 . . . 1.077 I know I can permute entire columns this way M1[,sample(6,6)] 5 x 6 sparse Matrix of class dgTMatrix [1,] 5.003. . . 1.6562.983 [2,] . . . . 2.990 . [3,] 1.1150.592 . . 5.349 . [4,] . . . . 2.804 1.836 [5,] . 6.961 1.077 . .. But I would like the new sparse matrix to look like this...where only the nonzero elements are permuted. [1,] 1.656 . 5.0032.983.. [2,].. 2.990. .. [3,].5.3491.1150.592.. [4,] 2.804 . 1.836. .. [5,]. 1.077 . . . 6.961 Thanks in advance for any advice! -- View this message in context: http://r.789695.n4.nabble.com/column-permutation-of-sparse-matrix-tp4216726p4216726.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
