[R] working with sparse matrix

[David Winsemius]

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