I am using bigmemory package to handle large matrix of size 8000 x 8000.
What is the equivalent of row() and col() for big matrix?
When I tried using the above two functions to access the big.matrix object, I am receiving the following error.
"Error in row(phi) : a matrix-like object is required as argument to 'row'"
Below is my code snippet.
k <- big.matrix(nrow = 8000, ncol = 8000, type = 'double', init = 0)
k <- ifelse(row(k) < col(k), 0, (row(k)-col(k))^5 + 2)
So, with Rcpp, you can do:
// [[Rcpp::depends(BH, bigmemory)]]
#include <bigmemory/MatrixAccessor.hpp>
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
void fillBM(SEXP pBigMat) {
XPtr<BigMatrix> xpMat(pBigMat);
MatrixAccessor<double> macc(*xpMat);
int n = macc.nrow();
int m = macc.ncol();
for (int j = 0; j < m; j++) {
for (int i = j; i < n; i++) {
macc[j][i] = pow(i - j, 5) + 2;
}
}
}
/*** R
library(bigmemory)
k <- big.matrix(nrow = 8000, ncol = 8000, type = 'double', init = 0)
k.mat <- k[]
system.time(
fillBM(k@address)
)
k[1:5, 1:5]
system.time(
k.mat <- ifelse(row(k.mat) < col(k.mat), 0, (row(k.mat)-col(k.mat))^5 + 2)
)
k.mat[1:5, 1:5]
all.equal(k.mat, k[])
*/
The Rcpp function takes 2 sec while the R version (on a standard R matrix) takes 10 seconds (and much more memory).