The R Project SVN R-packages

			/* Sparse matrices in compressed column-oriented form */

#include "Csparse.h"

#include "chm_common.h"

SEXP Csparse_validate(SEXP x)

{

    /* NB: we do *NOT* check a potential 'x' slot here, at all */

    SEXP pslot = GET_SLOT(x, Matrix_pSym),

	islot = GET_SLOT(x, Matrix_iSym);

    Rboolean sorted, strictly;

    int j, k,

	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),

	nrow = dims[0],

	ncol = dims[1],

	*xp = INTEGER(pslot),

	*xi = INTEGER(islot);

    if (length(pslot) != dims[1] + 1)

	return mkString(_("slot p must have length = ncol(.) + 1"));

    if (xp[0] != 0)

	return mkString(_("first element of slot p must be zero"));

    if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/

	return

	    mkString(_("last element of slot p must match length of slots i and x"));

    for (j = 0; j < length(islot); j++) {

	if (xi[j] < 0 || xi[j] >= nrow)

	    return mkString(_("all row indices must be between 0 and nrow-1"));

    }

    sorted = TRUE; strictly = TRUE;

    for (j = 0; j < ncol; j++) {

	if (xp[j] > xp[j+1])

	    return mkString(_("slot p must be non-decreasing"));

	if(sorted)

	    for (k = xp[j] + 1; k < xp[j + 1]; k++) {

		if (xi[k] < xi[k - 1])

		    sorted = FALSE;

		else if (xi[k] == xi[k - 1])

		    strictly = FALSE;

	    }

    }

    if (!sorted) {

	CHM_SP chx = AS_CHM_SP(x);

	R_CheckStack();

	cholmod_sort(chx, &c);

	/* Now re-check that row indices are *strictly* increasing

	 * (and not just increasing) within each column : */

	for (j = 0; j < ncol; j++) {

	    for (k = xp[j] + 1; k < xp[j + 1]; k++)

		if (xi[k] == xi[k - 1])

		    return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));

	}

    } else if(!strictly) {  /* sorted, but not strictly */

	return mkString(_("slot i is not *strictly* increasing inside a column"));

    }

    return ScalarLogical(1);

}

/* Called from ../R/Csparse.R : */

/* Can only return [dln]geMatrix (no symm/triang);

 * FIXME: replace by non-CHOLMOD code ! */

SEXP Csparse_to_dense(SEXP x)

{

    CHM_SP chxs = AS_CHM_SP(x);

    /* This loses the symmetry property, since cholmod_dense has none,

     * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices

     * to numeric (CHOLMOD_REAL) ones : */

    CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);

    int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);

    R_CheckStack();

    return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)

{

    CHM_SP chxs = AS_CHM_SP(x);

    CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);

    int tr = asLogical(tri);

    R_CheckStack();

    return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,

			      tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,

			      0, tr ? diag_P(x) : "",

			      GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_to_matrix(SEXP x)

{

    return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),

			       1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)

{

    CHM_SP chxs = AS_CHM_SP(x);

    CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);

    int tr = asLogical(tri);

    int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;

    R_CheckStack();

    return chm_triplet_to_SEXP(chxt, 1,

			       tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,

			       Rkind, tr ? diag_P(x) : "",

			       GET_SLOT(x, Matrix_DimNamesSym));

}

/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */

SEXP Csparse_symmetric_to_general(SEXP x)

{

    CHM_SP chx = AS_CHM_SP(x), chgx;

    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;

    R_CheckStack();

    if (!(chx->stype))

	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));

    chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);

    /* xtype: pattern, "real", complex or .. */

    return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",

			      GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)

{

    CHM_SP chx = AS_CHM_SP(x), chgx;

    int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;

    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;

    R_CheckStack();

    chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);

    /* xtype: pattern, "real", complex or .. */

    return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",

			      GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_transpose(SEXP x, SEXP tri)

{

    /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -

     *       since cholmod (& cs) lacks sparse 'int' matrices */

    CHM_SP chx = AS_CHM_SP(x);

    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;

    CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);

    SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;

    int tr = asLogical(tri);

    R_CheckStack();

    tmp = VECTOR_ELT(dn, 0);	/* swap the dimnames */

    SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));

    SET_VECTOR_ELT(dn, 1, tmp);

    UNPROTECT(1);

    return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */

			      tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,

			      Rkind, tr ? diag_P(x) : "", dn);

}

SEXP Csparse_Csparse_prod(SEXP a, SEXP b)

{

    CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);

    CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);

    SEXP dn = allocVector(VECSXP, 2);

    R_CheckStack();

    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */

		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));

    SET_VECTOR_ELT(dn, 1,

		   duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));

    return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);

}

SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)

{

    int tr = asLogical(trans);

    CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;

    SEXP dn = allocVector(VECSXP, 2);

    R_CheckStack();

    chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);

    chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,

			 0, cha->xtype, 1, &c);

    cholmod_free_sparse(&chTr, &c);

    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */

		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));

    SET_VECTOR_ELT(dn, 1,

		   duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));

    return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);

}

SEXP Csparse_dense_prod(SEXP a, SEXP b)

{

    CHM_SP cha = AS_CHM_SP(a);

    SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));

    CHM_DN chb = AS_CHM_DN(b_M);

    CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,

					chb->xtype, &c);

    SEXP dn = PROTECT(allocVector(VECSXP, 2));

    double one[] = {1,0}, zero[] = {0,0};

    R_CheckStack();

    cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);

    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */

		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));

    SET_VECTOR_ELT(dn, 1,

		   duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));

    UNPROTECT(2);

    return chm_dense_to_SEXP(chc, 1, 0, dn);

}

SEXP Csparse_dense_crossprod(SEXP a, SEXP b)

{

    CHM_SP cha = AS_CHM_SP(a);

    SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));

    CHM_DN chb = AS_CHM_DN(b_M);

    CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,

					chb->xtype, &c);

    SEXP dn = PROTECT(allocVector(VECSXP, 2));

    double one[] = {1,0}, zero[] = {0,0};

    R_CheckStack();

    cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);

    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */

		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));

    SET_VECTOR_ELT(dn, 1,

		   duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));

    UNPROTECT(2);

    return chm_dense_to_SEXP(chc, 1, 0, dn);

}

/* Computes   x'x  or  x x'  -- see Csparse_Csparse_crossprod above for  x'y and x y' */

SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)

{

    int trip = asLogical(triplet),

	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */

    CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;

    CHM_SP chcp, chxt,

	chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);

    SEXP dn = PROTECT(allocVector(VECSXP, 2));

    R_CheckStack();

    if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);

    chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);

    if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));

    cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);

    chcp->stype = 1;

    if (trip) cholmod_free_sparse(&chx, &c);

    if (!tr) cholmod_free_sparse(&chxt, &c);

    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */

		   duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),

					(tr) ? 0 : 1)));

    SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));

    UNPROTECT(1);

    return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);

}

SEXP Csparse_drop(SEXP x, SEXP tol)

{

    CHM_SP chx = AS_CHM_SP(x);

    CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);

    double dtol = asReal(tol);

    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;

    R_CheckStack();

    if(!cholmod_drop(dtol, ans, &c))

	error(_("cholmod_drop() failed"));

    return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",

			      GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_horzcat(SEXP x, SEXP y)

{

    CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);

    int Rkind = 0; /* only for "d" - FIXME */

    R_CheckStack();

    /* FIXME: currently drops dimnames */

    return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),

			      1, 0, Rkind, "", R_NilValue);

}

SEXP Csparse_vertcat(SEXP x, SEXP y)

{

    CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);

    int Rkind = 0; /* only for "d" - FIXME */

    R_CheckStack();

    /* FIXME: currently drops dimnames */

    return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),

			      1, 0, Rkind, "", R_NilValue);

}

SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)

{

    CHM_SP chx = AS_CHM_SP(x);

    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;

    CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);

    R_CheckStack();

    return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",

			      GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_diagU2N(SEXP x)

{

    if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */

	return (x);

    }

    else {

	CHM_SP chx = AS_CHM_SP(x);

	CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);

	double one[] = {1, 0};

	CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);

	int uploT = (*uplo_P(x) == 'U') ? 1 : -1;

	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;

	R_CheckStack();

	cholmod_free_sparse(&eye, &c);

	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",

				  GET_SLOT(x, Matrix_DimNamesSym));

    }

}

SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)

{

    CHM_SP chx = AS_CHM_SP(x);

    int rsize = (isNull(i)) ? -1 : LENGTH(i),

	csize = (isNull(j)) ? -1 : LENGTH(j);

    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;

    R_CheckStack();

    if (rsize >= 0 && !isInteger(i))

	error(_("Index i must be NULL or integer"));

    if (csize >= 0 && !isInteger(j))

	error(_("Index j must be NULL or integer"));

    return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,

						INTEGER(j), csize,

						TRUE, TRUE, &c),

			      1, 0, Rkind, "",

			      /* FIXME: drops dimnames */ R_NilValue);

}