Revision f584db857045d794fb5a587b18f1ca3ed40b8679 authored by Douglas Bates on 15 January 2006, 00:00:00 UTC, committed by Gabor Csardi on 15 January 2006, 00:00:00 UTC
1 parent a2d2fd0
dgeMatrix.c
#include "dgeMatrix.h"
SEXP dMatrix_validate(SEXP obj)
{
SEXP x = GET_SLOT(obj, Matrix_xSym),
Dim = GET_SLOT(obj, Matrix_DimSym);
int m, n;
if (length(Dim) != 2)
return mkString(_("Dim slot must have length 2"));
m = INTEGER(Dim)[0]; n = INTEGER(Dim)[1];
if (m < 0 || n < 0)
return mkString(_("Negative value(s) in Dim"));
if (!isReal(x))
return mkString(_("x slot must be numeric \"double\""));
return ScalarLogical(1);
}
SEXP dgeMatrix_validate(SEXP obj)
{
SEXP val,
fact = GET_SLOT(obj, Matrix_factorSym);
if (isString(val = dense_nonpacked_validate(obj)))
return(val);
if (length(fact) > 0 && getAttrib(fact, R_NamesSymbol) == R_NilValue)
return mkString(_("factors slot must be named list"));
return ScalarLogical(1);
}
static
double get_norm(SEXP obj, char *typstr)
{
char typnm[] = {'\0', '\0'};
int *dims = INTEGER(GET_SLOT(obj, Matrix_DimSym));
double *work = (double *) NULL;
typnm[0] = norm_type(typstr);
if (*typnm == 'I') {
work = (double *) R_alloc(dims[0], sizeof(double));
}
return F77_CALL(dlange)(typstr, dims, dims+1,
REAL(GET_SLOT(obj, Matrix_xSym)),
dims, work);
}
SEXP dgeMatrix_norm(SEXP obj, SEXP type)
{
return ScalarReal(get_norm(obj, CHAR(asChar(type))));
}
SEXP dgeMatrix_rcond(SEXP obj, SEXP type)
{
SEXP LU = dgeMatrix_LU(obj);
char typnm[] = {'\0', '\0'};
int *dims = INTEGER(GET_SLOT(LU, Matrix_DimSym)), info;
double anorm, rcond;
if (dims[0] != dims[1] || dims[0] < 1)
error(_("rcond requires a square, non-empty matrix"));
typnm[0] = rcond_type(CHAR(asChar(type)));
anorm = get_norm(obj, typnm);
F77_CALL(dgecon)(typnm,
dims, REAL(GET_SLOT(LU, Matrix_xSym)),
dims, &anorm, &rcond,
(double *) R_alloc(4*dims[0], sizeof(double)),
(int *) R_alloc(dims[0], sizeof(int)), &info);
return ScalarReal(rcond);
}
SEXP dgeMatrix_crossprod(SEXP x, SEXP trans)
{
int tr = asLogical(trans);/* trans=TRUE: tcrossprod(x) */
SEXP val = PROTECT(NEW_OBJECT(MAKE_CLASS("dpoMatrix")));
int *Dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
*vDims = INTEGER(ALLOC_SLOT(val, Matrix_DimSym, INTSXP, 2));
int k = tr ? Dims[1] : Dims[0], n = tr ? Dims[0] : Dims[1];
double one = 1.0, zero = 0.0;
SET_SLOT(val, Matrix_uploSym, mkString("U"));
vDims[0] = vDims[1] = n;
F77_CALL(dsyrk)("U", tr ? "N" : "T", &n, &k,
&one, REAL(GET_SLOT(x, Matrix_xSym)), Dims, &zero,
REAL(ALLOC_SLOT(val, Matrix_xSym, REALSXP, n * n)), &n);
UNPROTECT(1);
return val;
}
SEXP dgeMatrix_dgeMatrix_crossprod(SEXP x, SEXP y, SEXP trans)
{
int tr = asLogical(trans);/* trans=TRUE: tcrossprod(x,y) */
SEXP val = PROTECT(NEW_OBJECT(MAKE_CLASS("dgeMatrix")));
int *xDims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
*yDims = INTEGER(GET_SLOT(y, Matrix_DimSym)),
*vDims;
int m = xDims[!tr], n = yDims[!tr];/* -> result dim */
int xd = xDims[ tr], yd = yDims[ tr];/* the conformable dims */
double one = 1.0, zero = 0.0;
SET_SLOT(val, Matrix_factorSym, allocVector(VECSXP, 0));
SET_SLOT(val, Matrix_DimSym, allocVector(INTSXP, 2));
vDims = INTEGER(GET_SLOT(val, Matrix_DimSym));
if (xd > 0 && yd > 0 && n > 0 && m > 0) {
if (xd != yd)
error(_("Dimensions of x and y are not compatible for %s"),
tr ? "tcrossprod" : "crossprod");
vDims[0] = m; vDims[1] = n;
SET_SLOT(val, Matrix_xSym, allocVector(REALSXP, m * n));
F77_CALL(dgemm)(tr ? "N" : "T", tr ? "T" : "N", &m, &n, &xd, &one,
REAL(GET_SLOT(x, Matrix_xSym)), xDims,
REAL(GET_SLOT(y, Matrix_xSym)), yDims,
&zero, REAL(GET_SLOT(val, Matrix_xSym)), &m);
}
UNPROTECT(1);
return val;
}
SEXP dgeMatrix_matrix_crossprod(SEXP x, SEXP y, SEXP trans)
{
int tr = asLogical(trans);/* trans=TRUE: tcrossprod(x,y) */
SEXP val = PROTECT(NEW_OBJECT(MAKE_CLASS("dgeMatrix")));
int *xDims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
*yDims = INTEGER(getAttrib(y, R_DimSymbol)),
*vDims;
int m = xDims[!tr], n = yDims[!tr];/* -> result dim */
int xd = xDims[ tr], yd = yDims[ tr];/* the conformable dims */
double one = 1.0, zero = 0.0;
if (!(isMatrix(y) && isReal(y)))
error(_("Argument y must be a numeric (real) matrix"));
SET_SLOT(val, Matrix_factorSym, allocVector(VECSXP, 0));
SET_SLOT(val, Matrix_DimSym, allocVector(INTSXP, 2));
vDims = INTEGER(GET_SLOT(val, Matrix_DimSym));
if (xd > 0 && yd > 0 && n > 0 && m > 0) {
if (xd != yd)
error(_("Dimensions of x and y are not compatible for %s"),
tr ? "tcrossprod" : "crossprod");
vDims[0] = m; vDims[1] = n;
SET_SLOT(val, Matrix_xSym, allocVector(REALSXP, m * n));
F77_CALL(dgemm)(tr ? "N" : "T", tr ? "T" : "N", &m, &n, &xd, &one,
REAL(GET_SLOT(x, Matrix_xSym)), xDims,
REAL(y), yDims,
&zero, REAL(GET_SLOT(val, Matrix_xSym)), &m);
}
UNPROTECT(1);
return val;
}
SEXP dgeMatrix_getDiag(SEXP x)
{
int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym));
int i, m = dims[0], nret = (m < dims[1]) ? m : dims[1];
SEXP ret = PROTECT(allocVector(REALSXP, nret)),
xv = GET_SLOT(x, Matrix_xSym);
for (i = 0; i < nret; i++) {
REAL(ret)[i] = REAL(xv)[i * (m + 1)];
}
UNPROTECT(1);
return ret;
}
SEXP dgeMatrix_LU(SEXP x)
{
SEXP val = get_factors(x, "LU");
int *dims, npiv, info;
if (val != R_NilValue) return val;
dims = INTEGER(GET_SLOT(x, Matrix_DimSym));
if (dims[0] < 1 || dims[1] < 1)
error(_("Cannot factor a matrix with zero extents"));
npiv = (dims[0] <dims[1]) ? dims[0] : dims[1];
val = PROTECT(NEW_OBJECT(MAKE_CLASS("LU")));
SET_SLOT(val, Matrix_xSym, duplicate(GET_SLOT(x, Matrix_xSym)));
SET_SLOT(val, Matrix_DimSym, duplicate(GET_SLOT(x, Matrix_DimSym)));
F77_CALL(dgetrf)(dims, dims + 1, REAL(GET_SLOT(val, Matrix_xSym)),
dims,
INTEGER(ALLOC_SLOT(val, Matrix_permSym, INTSXP, npiv)),
&info);
if (info < 0)
error(_("Lapack routine %s returned error code %d"), "dgetrf", info);
else if (info > 0)
warning(_("Exact singularity detected during LU decomposition."));
UNPROTECT(1);
return set_factors(x, val, "LU");
}
SEXP dgeMatrix_determinant(SEXP x, SEXP logarithm)
{
int lg = asLogical(logarithm);
SEXP lu = dgeMatrix_LU(x);
int *dims = INTEGER(GET_SLOT(lu, Matrix_DimSym)),
*jpvt = INTEGER(GET_SLOT(lu, Matrix_permSym)),
i, n = dims[0], sign = 1;
double *luvals = REAL(GET_SLOT(lu, Matrix_xSym)), modulus;
if (n != dims[1])
error(_("Determinant requires a square matrix"));
for (i = 0; i < n; i++) if (jpvt[i] != (i + 1)) sign = -sign;
if (lg) {
modulus = 0.0;
for (i = 0; i < n; i++) {
double dii = luvals[i*(n + 1)]; /* ith diagonal element */
modulus += log(dii < 0 ? -dii : dii);
if (dii < 0) sign = -sign;
}
} else {
modulus = 1.0;
for (i = 0; i < n; i++)
modulus *= luvals[i*(n + 1)];
if (modulus < 0) {
modulus = -modulus;
sign = -sign;
}
}
return as_det_obj(modulus, lg, sign);
}
SEXP dgeMatrix_solve(SEXP a)
{
SEXP val = PROTECT(NEW_OBJECT(MAKE_CLASS("dgeMatrix"))),
lu = dgeMatrix_LU(a);
int *dims = INTEGER(GET_SLOT(lu, Matrix_DimSym)),
*pivot = INTEGER(GET_SLOT(lu, Matrix_permSym));
double *x, tmp;
int info, lwork = -1;
if (dims[0] != dims[1]) error(_("Solve requires a square matrix"));
SET_SLOT(val, Matrix_xSym, duplicate(GET_SLOT(lu, Matrix_xSym)));
x = REAL(GET_SLOT(val, Matrix_xSym));
SET_SLOT(val, Matrix_DimSym, duplicate(GET_SLOT(lu, Matrix_DimSym)));
F77_CALL(dgetri)(dims, x, dims, pivot, &tmp, &lwork, &info);
lwork = (int) tmp;
F77_CALL(dgetri)(dims, x, dims, pivot,
(double *) R_alloc((size_t) lwork, sizeof(double)),
&lwork, &info);
UNPROTECT(1);
return val;
}
SEXP dgeMatrix_matrix_solve(SEXP a, SEXP b, SEXP classed)
{
int cl = asLogical(classed);
SEXP val = PROTECT(NEW_OBJECT(MAKE_CLASS("dgeMatrix"))),
lu = dgeMatrix_LU(a);
int *adims = INTEGER(GET_SLOT(lu, Matrix_DimSym)),
*bdims = INTEGER(cl ? GET_SLOT(b, Matrix_DimSym) :
getAttrib(b, R_DimSymbol));
int info, n = bdims[0], nrhs = bdims[1];
int sz = n * nrhs;
if (*adims != *bdims || bdims[1] < 1 || *adims < 1 || *adims != adims[1])
error(_("Dimensions of system to be solved are inconsistent"));
Memcpy(INTEGER(ALLOC_SLOT(val, Matrix_DimSym, INTSXP, 2)), bdims, 2);
F77_CALL(dgetrs)("N", &n, &nrhs, REAL(GET_SLOT(lu, Matrix_xSym)), &n,
INTEGER(GET_SLOT(lu, Matrix_permSym)),
Memcpy(REAL(ALLOC_SLOT(val, Matrix_xSym, REALSXP, sz)),
REAL(cl ? GET_SLOT(b, Matrix_xSym):b), sz),
&n, &info);
UNPROTECT(1);
return val;
}
SEXP dgeMatrix_matrix_mm(SEXP a, SEXP b, SEXP classed, SEXP right)
{
int cl = asLogical(classed);
SEXP val = PROTECT(NEW_OBJECT(MAKE_CLASS("dgeMatrix")));
int *adims = INTEGER(GET_SLOT(a, Matrix_DimSym)),
*bdims = INTEGER(cl ? GET_SLOT(b, Matrix_DimSym) :
getAttrib(b, R_DimSymbol)),
*cdims = INTEGER(ALLOC_SLOT(val, Matrix_DimSym, INTSXP, 2));
double one = 1., zero = 0.;
if (asLogical(right)) {
int m = bdims[0], n = adims[1], k = bdims[1];
if (adims[0] != k)
error(_("Matrices are not conformable for multiplication"));
if (m < 1 || n < 1 || k < 1)
error(_("Matrices with zero extents cannot be multiplied"));
cdims[0] = m; cdims[1] = n;
F77_CALL(dgemm) ("N", "N", &m, &n, &k, &one,
REAL(cl ? GET_SLOT(b, Matrix_xSym) : b), &m,
REAL(GET_SLOT(a, Matrix_xSym)), &k, &zero,
REAL(ALLOC_SLOT(val, Matrix_xSym, REALSXP, m * n)),
&m);
} else {
int m = adims[0], n = bdims[1], k = adims[1];
if (bdims[0] != k)
error(_("Matrices are not conformable for multiplication"));
if (m < 1 || n < 1 || k < 1)
error(_("Matrices with zero extents cannot be multiplied"));
cdims[0] = m; cdims[1] = n;
F77_CALL(dgemm)
("N", "N", &m, &n, &k, &one, REAL(GET_SLOT(a, Matrix_xSym)),
&m, REAL(cl ? GET_SLOT(b, Matrix_xSym) : b), &k, &zero,
REAL(ALLOC_SLOT(val, Matrix_xSym, REALSXP, m * n)), &m);
}
UNPROTECT(1);
return val;
}
SEXP dgeMatrix_svd(SEXP x, SEXP nnu, SEXP nnv)
{
int /* nu = asInteger(nnu),
nv = asInteger(nnv), */
*dims = INTEGER(GET_SLOT(x, Matrix_DimSym));
double *xx = REAL(GET_SLOT(x, Matrix_xSym));
SEXP val = PROTECT(allocVector(VECSXP, 3));
if (dims[0] && dims[1]) {
int m = dims[0], n = dims[1], mm = (m < n)?m:n,
lwork = -1, info;
int *iwork = Calloc(8 * mm, int);
double tmp, *work;
/* int bdspac = 3*m*m + 4*m, */
/* wrkbl, maxwrk, minwrk, itmp, */
/* ione = 1, iminus1 = -1; */
/* int i1, i2, i3; */
SET_VECTOR_ELT(val, 0, allocVector(REALSXP, mm));
SET_VECTOR_ELT(val, 1, allocMatrix(REALSXP, m, mm));
SET_VECTOR_ELT(val, 2, allocMatrix(REALSXP, mm, n));
F77_CALL(dgesdd)("S", &m, &n, xx, &m,
REAL(VECTOR_ELT(val, 0)),
REAL(VECTOR_ELT(val, 1)), &m,
REAL(VECTOR_ELT(val, 2)), &mm,
&tmp, &lwork, iwork, &info);
lwork = (int) tmp;
/* F77_CALL(foo)(&i1, &i2, &i3); */
/* wrkbl = 3*m+(m+n)*i1; */
/* if (wrkbl < (itmp = 3*m + m*i2)) wrkbl = itmp; */
/* if (wrkbl < (itmp = 3*m + m*i3)) wrkbl = itmp; */
/* itmp = bdspac+3*m; */
/* maxwrk = (wrkbl > itmp) ? wrkbl : itmp; */
/* minwrk = 3*m + ((bdspac > n) ? bdspac : n); */
work = Calloc(lwork, double);
F77_CALL(dgesdd)("S", &m, &n, xx, &m,
REAL(VECTOR_ELT(val, 0)),
REAL(VECTOR_ELT(val, 1)), &m,
REAL(VECTOR_ELT(val, 2)), &mm,
work, &lwork, iwork, &info);
Free(iwork); Free(work);
}
UNPROTECT(1);
return val;
}
static double padec [] = /* Constants for matrix exponential calculation. */
{
5.0000000000000000e-1,
1.1666666666666667e-1,
1.6666666666666667e-2,
1.6025641025641026e-3,
1.0683760683760684e-4,
4.8562548562548563e-6,
1.3875013875013875e-7,
1.9270852604185938e-9,
};
/**
* Matrix exponential - based on the code for Octave's expm function.
*
* @param x real square matrix to exponentiate
*
* @return matrix exponential of x
*/
SEXP dgeMatrix_exp(SEXP x)
{
SEXP val = PROTECT(duplicate(x));
int *Dims = INTEGER(GET_SLOT(x, Matrix_DimSym));
int i, ilo, ilos, ihi, ihis, j, nc = Dims[1], sqpow;
int ncp1 = Dims[1] + 1, ncsqr = nc * nc;
int *pivot = Calloc(nc, int);
int *iperm = Calloc(nc, int);
double *dpp = Calloc(ncsqr, double), /* denominator power Pade' */
*npp = Calloc(ncsqr, double), /* numerator power Pade' */
*perm = Calloc(nc, double),
*scale = Calloc(nc, double),
*v = REAL(GET_SLOT(val, Matrix_xSym)),
*work = Calloc(ncsqr, double), inf_norm, m1_j, /* (-1)^j */
one = 1., trshift, zero = 0.;
if (nc < 1 || Dims[0] != nc)
error(_("Matrix exponential requires square, non-null matrix"));
/* FIXME: Add special treatment for nc == 1 */
/* Preconditioning 1. Shift diagonal by average diagonal if positive. */
trshift = 0; /* determine average diagonal element */
for (i = 0; i < nc; i++) trshift += v[i * ncp1];
trshift /= nc;
if (trshift > 0.) { /* shift diagonal by -trshift */
for (i = 0; i < nc; i++) v[i * ncp1] -= trshift;
}
/* Preconditioning 2. Balancing with dgebal. */
F77_CALL(dgebal)("P", &nc, v, &nc, &ilo, &ihi, perm, &j);
if (j) error(_("dgeMatrix_exp: LAPACK routine dgebal returned %d"), j);
F77_CALL(dgebal)("S", &nc, v, &nc, &ilos, &ihis, scale, &j);
if (j) error(_("dgeMatrix_exp: LAPACK routine dgebal returned %d"), j);
/* Preconditioning 3. Scaling according to infinity norm */
inf_norm = F77_CALL(dlange)("I", &nc, &nc, v, &nc, work);
sqpow = (inf_norm > 0) ? (int) (1 + log(inf_norm)/log(2.)) : 0;
if (sqpow < 0) sqpow = 0;
if (sqpow > 0) {
double scale_factor = 1.0;
for (i = 0; i < sqpow; i++) scale_factor *= 2.;
for (i = 0; i < ncsqr; i++) v[i] /= scale_factor;
}
/* Pade' approximation. Powers v^8, v^7, ..., v^1 */
AZERO(npp, ncsqr);
AZERO(dpp, ncsqr);
m1_j = -1;
for (j = 7; j >=0; j--) {
double mult = padec[j];
/* npp = m * npp + padec[j] *m */
F77_CALL(dgemm)("N", "N", &nc, &nc, &nc, &one, v, &nc, npp, &nc,
&zero, work, &nc);
for (i = 0; i < ncsqr; i++) npp[i] = work[i] + mult * v[i];
/* dpp = m * dpp * (m1_j * padec[j]) * m */
mult *= m1_j;
F77_CALL(dgemm)("N", "N", &nc, &nc, &nc, &one, v, &nc, dpp, &nc,
&zero, work, &nc);
for (i = 0; i < ncsqr; i++) dpp[i] = work[i] + mult * v[i];
m1_j *= -1;
}
/* Zero power */
for (i = 0; i < ncsqr; i++) dpp[i] *= -1.;
for (j = 0; j < nc; j++) {
npp[j * ncp1] += 1.;
dpp[j * ncp1] += 1.;
}
/* Pade' approximation is solve(dpp, npp) */
F77_CALL(dgetrf)(&nc, &nc, dpp, &nc, pivot, &j);
if (j) error(_("dgeMatrix_exp: dgetrf returned error code %d"), j);
F77_CALL(dgetrs)("N", &nc, &nc, dpp, &nc, pivot, npp, &nc, &j);
if (j) error(_("dgeMatrix_exp: dgetrs returned error code %d"), j);
Memcpy(v, npp, ncsqr);
/* Now undo all of the preconditioning */
/* Preconditioning 3: square the result for every power of 2 */
while (sqpow--) {
F77_CALL(dgemm)("N", "N", &nc, &nc, &nc, &one, v, &nc, v, &nc,
&zero, work, &nc);
Memcpy(v, work, ncsqr);
}
/* Preconditioning 2: apply inverse scaling */
for (j = 0; j < nc; j++)
for (i = 0; i < nc; i++)
v[i + j * nc] *= scale[i]/scale[j];
/* Construct balancing permutation vector */
for (i = 0; i < nc; i++) iperm[i] = i; /* identity permutation */
/* Leading permutations applied in forward order */
for (i = 0; i < (ilo - 1); i++) {
int swapidx = (int) (perm[i]) - 1;
int tmp = iperm[i];
iperm[i] = iperm[swapidx];
iperm[swapidx] = tmp;
}
/* Trailing permutations applied in reverse order */
for (i = nc - 1; i >= ihi; i--) {
int swapidx = (int) (perm[i]) - 1;
int tmp = iperm[i];
iperm[i] = iperm[swapidx];
iperm[swapidx] = tmp;
}
/* Construct inverse balancing permutation vector */
Memcpy(pivot, iperm, nc);
for (i = 0; i < nc; i++) iperm[pivot[i]] = i;
/* Apply inverse permutation */
Memcpy(work, v, ncsqr);
for (j = 0; j < nc; j++)
for (i = 0; i < nc; i++)
v[i + j * nc] = work[iperm[i] + iperm[j] * nc];
/* Preconditioning 1: Trace normalization */
if (trshift > 0.) {
double mult = exp(trshift);
for (i = 0; i < ncsqr; i++) v[i] *= mult;
}
/* Clean up */
Free(dpp); Free(npp); Free(perm); Free(iperm); Free(pivot); Free(scale); Free(work);
UNPROTECT(1);
return val;
}
SEXP dgeMatrix_Schur(SEXP x, SEXP vectors)
{
int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym));
int vecs = asLogical(vectors), info, izero = 0, lwork = -1, n = dims[0];
double *work, tmp;
char *nms[] = {"WR", "WI", "T", "Z", ""};
SEXP val = PROTECT(Matrix_make_named(VECSXP, nms));
if (n != dims[1] || n < 1)
error(_("dgeMatrix_Schur: argument x must be a non-null square matrix"));
SET_VECTOR_ELT(val, 0, allocVector(REALSXP, n));
SET_VECTOR_ELT(val, 1, allocVector(REALSXP, n));
SET_VECTOR_ELT(val, 2, allocMatrix(REALSXP, n, n));
Memcpy(REAL(VECTOR_ELT(val, 2)), REAL(GET_SLOT(x, Matrix_xSym)), n * n);
SET_VECTOR_ELT(val, 3, allocMatrix(REALSXP, vecs ? n : 0, vecs ? n : 0));
F77_CALL(dgees)(vecs ? "V" : "N", "N", NULL, dims, (double *) NULL, dims, &izero,
(double *) NULL, (double *) NULL, (double *) NULL, dims,
&tmp, &lwork, (int *) NULL, &info);
if (info) error(_("dgeMatrix_Schur: first call to dgees failed"));
lwork = (int) tmp;
work = Calloc(lwork, double);
F77_CALL(dgees)(vecs ? "V" : "N", "N", NULL, dims, REAL(VECTOR_ELT(val, 2)), dims,
&izero, REAL(VECTOR_ELT(val, 0)), REAL(VECTOR_ELT(val, 1)),
REAL(VECTOR_ELT(val, 3)), dims, work, &lwork,
(int *) NULL, &info);
if (info) error(_("dgeMatrix_Schur: dgees returned code %d"), info);
Free(work);
UNPROTECT(1);
return val;
}
SEXP dgeMatrix_colsums(SEXP x, SEXP naRmP, SEXP cols, SEXP mean)
{
int keepNA = !asLogical(naRmP);
int doMean = asLogical(mean);
int useCols = asLogical(cols);
int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym));
int cnt = 0, i, j, n = dims[0], p = dims[1];
SEXP ans = PROTECT(allocVector(REALSXP, (useCols) ? p : n));
double *xx = REAL(GET_SLOT(x, Matrix_xSym)), *rx, sum;
if (useCols) {
cnt = n;
for (j = 0; j < p; j++) {
rx = xx + n*j;
if (keepNA)
for (sum = 0., i = 0; i < n; i++) sum += *rx++;
else {
for (cnt = 0, sum = 0., i = 0; i < n; i++, rx++)
if (!ISNAN(*rx)) {cnt++; sum += *rx;}
}
if (doMean) {
if (cnt > 0) sum /= cnt; else sum = NA_REAL;
}
REAL(ans)[j] = sum;
}
} else {
double *rans = REAL(ans), *ra = rans, *rx = xx, *Cnt = NULL, *c;
cnt = p;
if (!keepNA && doMean) Cnt = Calloc(n, double);
for (ra = rans, i = 0; i < n; i++) *ra++ = 0.0;
for (j = 0; j < p; j++) {
ra = rans;
if (keepNA)
for (i = 0; i < n; i++) *ra++ += *rx++;
else
for (c = Cnt, i = 0; i < n; i++, ra++, rx++, c++)
if (!ISNAN(*rx)) {
*ra += *rx;
if (doMean) (*c)++;
}
}
if (doMean) {
if (keepNA)
for (ra = rans, i = 0; i < n; i++)
*ra++ /= p;
else {
for (ra = rans, c = Cnt, i = 0; i < n; i++, c++)
if (*c > 0) *ra++ /= *c; else *ra++ = NA_REAL;
Free(Cnt);
}
}
}
UNPROTECT(1);
return ans;
}
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