int main(void)
{
int n=400, noisy=0, i,j;
int nr=10, ir, TimeSquare=10, algorithm; /* TimeSquare should be larger for large t */
double t=5, *Q, *pi, *space, s;
char timestr[96], *AlgStr[2]={"repeated squaring", "eigensolution"};
if((Q=(double*)malloc(n*n*5*sizeof(double))) ==NULL) error2("oom");
pi=Q+n*n; space=pi+n;
for(algorithm=0; algorithm<2; algorithm++) {
starttime();
SetSeed(1234567);
for (i=0; i<n; i++) pi[i]=rndu();
s=sum(pi,n);
for (i=0; i<n; i++) pi[i]/=s;
for(ir=0; ir<nr; ir++) {
printf("Replicate %d/%d ", ir+1,nr);
for (i=0; i<n; i++)
for (j=0,Q[i*n+i]=0; j<i; j++)
Q[i*n+j]=Q[j*n+i] = square(rndu());
for (i=0; i<n; i++)
for (j=0; j<n; j++)
Q[i*n+j] *= pi[j];
for(i=0,s=0; i<n; i++) { /* rescaling Q so that average rate is 1 */
Q[i*n+i]=0; Q[i*n+i]=-sum(Q+i*n, n);
s-=pi[i]*Q[i*n+i];
}
if(noisy) {
matout(stdout, pi, 1, n);
matout(stdout, Q, n, n);
}
if(algorithm==0)
matexp(Q, 1, n, TimeSquare, space);
else
PMatQRev(Q, pi, 1, n, space);
printf("%s, time: %s\n", AlgStr[algorithm], printtime(timestr));
if(noisy)
matout(stdout, Q, n, n);
}
}
return (0);
}
SEXP R_matexp(SEXP A, SEXP p)
{
R_INIT;
const int n = nrows(A);
int i;
double *A_cp;
SEXP R;
newRmat(R, n, n, "dbl");
A_cp = (double *) R_alloc(n*n, sizeof(A_cp));
for (i=0; i<n*n; i++)
A_cp[i] = REAL(A)[i];
matexp(n, INT(p), A_cp, REAL(R));
R_END;
return R;
}
