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Using the .C() function in R, you can only pass vectors. Since R stores matrices columnwise as vectors anyhow, they can be passed to your C function as vectors (along with the number of rows in the matrix) and then accessed in familiar [row,col] manner using the following C functions (idea from here):
int Cmatrix(int *row, int *col, int *nrows){
/* Converts row-col notation into base-zero vector notation, based on a column-wise conversion*/
int vector_loc;
vector_loc=(*row)-1 + ((*col)-1)*(*nrows);
return(vector_loc);
}

void Rmatrix(int *vector_loc,int *row, int *col, int *nrows){
/*Converts vector notation into row-col notation*/
/*vector_loc is the vector address of the matrix (base zero)*/
/*row and col are pointers to the row and col variables that will be updated  */
*col=floor(*vector_loc / *nrows)+1;
*row=*vector_loc-((*col)-1)*(*nrows)+1;
}