rsparse-matrixexponential

Element by element exponential of a sparse matrix in R

I have a large sparse matrix (dgCMatrix) in R, and I would like to have the exponential of each element of this matrix. More precisely, I would like to do 1-exp(-x) to each element of the matrix. Unfortunately, when I do this in R, there is a sparse->dense coercion which takes a lot of time and memory (see example below).

library(Matrix)
i <- sample(20000, 20000); j <- sample(20000, 20000); x <- 7 * (1:20000)
A <- sparseMatrix(i, j, x = x)
1 - exp(-A)

Is there a way to avoid this coercion in R? As 1-exp(0) is 0, maybe sparsity can be preserved.

Solution

  • Probably you can try

    A@x <- 1 - exp(-A@x)

    such that you update the non-sparse entries only.

    For very small A@x, we can use

    A@x <- -expm1(-A@x) # thanks for the comment from jblood94

    or just simply

    A <- -expm1(-A) # thanks for the comment from Ben Bolker