On Jun 21, 2011, at 11:44 AM, Patrick Breheny wrote:
On 06/21/2011 09:48 AM, davefrederick wrote:
Hi, I have a 500x 53380 sparse matrix and I am trying to
dichotomize it.
Under sna package I have found event2dichot yet it doesnt recognize
sparse
matrix and requires adjacency matrix or array. I tried to run a
simple loop
code
for (i in 1:500)
for (j in 1:53380)
if (matrix[i,j]>0) matrix[i,j]=1
The code you are running does not require a loop:
> A <- cbind(c(1,0),c(0,2))
> A
[,1] [,2]
[1,] 1 0
[2,] 0 2
> A[A>0] <- 1
> A
[,1] [,2]
[1,] 1 0
[2,] 0 1
However, for large sparse matrices, this and other operations will
be faster if the matrix is explicitly stored as a sparse matrix, as
implemented in the 'Matrix' package.
require(Matrix)
M <- Matrix(0, 10,10) # empty sparse matrix
M[1:10, 1] <- 1
M[1:10, 2] <- 2
M[1:10, 3] <- -3
M[M > 0] <- 1
> M
10 x 10 sparse Matrix of class "dgCMatrix"
[1,] 1 1 -3 . . . . . . .
[2,] 1 1 -3 . . . . . . .
[3,] 1 1 -3 . . . . . . .
[4,] 1 1 -3 . . . . . . .
[5,] 1 1 -3 . . . . . . .
[6,] 1 1 -3 . . . . . . .
[7,] 1 1 -3 . . . . . . .
[8,] 1 1 -3 . . . . . . .
[9,] 1 1 -3 . . . . . . .
[10,] 1 1 -3 . . . . . . .
> M2 <- as.matrix(M)
> M2
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 1 -3 0 0 0 0 0 0 0
[2,] 1 1 -3 0 0 0 0 0 0 0
[3,] 1 1 -3 0 0 0 0 0 0 0
[4,] 1 1 -3 0 0 0 0 0 0 0
[5,] 1 1 -3 0 0 0 0 0 0 0
[6,] 1 1 -3 0 0 0 0 0 0 0
[7,] 1 1 -3 0 0 0 0 0 0 0
[8,] 1 1 -3 0 0 0 0 0 0 0
[9,] 1 1 -3 0 0 0 0 0 0 0
[10,] 1 1 -3 0 0 0 0 0 0 0
There might have been a one or two second pause while the last command
was executing for this test:
> M <- Matrix(0, 500, 53380 )
> M[1:10, 1] <- 1
> M[1:10, 2] <- 2
> M[1:10, 3] <- -3
> M[M > 0] <- 1
> M2 <- as.matrix(M)
--
David.
--
Patrick Breheny
Assistant Professor
Department of Biostatistics
Department of Statistics
University of Kentucky
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David Winsemius, MD
West Hartford, CT
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
