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)

{

    SEXP pslot = GET_SLOT(x, Matrix_pSym),

	islot = GET_SLOT(x, Matrix_iSym);

    int j, ncol = length(pslot) - 1,

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

	nrow, *xp = INTEGER(pslot),

	*xi = INTEGER(islot);

    nrow = dims[0];

    if (length(pslot) <= 0)

	return mkString(_("slot p must have length > 0"));

    if (xp[0] != 0)

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

    if (length(islot) != xp[ncol])

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

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

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

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

    }

    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"));

    }

    return ScalarLogical(1);

}

SEXP Csparse_to_dense(SEXP x)

{

    cholmod_sparse *chxs = as_cholmod_sparse(x);

    cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);

    Free(chxs);

    return chm_dense_to_SEXP(chxd, 1);

}

SEXP Csparse_to_logical(SEXP x, SEXP tri)

{

    cholmod_sparse *chxs = as_cholmod_sparse(x);

    cholmod_sparse

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

    int uploT = 0; char *diag = "";

    Free(chxs);

    if (asLogical(tri)) {	/* triangular sparse matrices */

	uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?

	    -1 : 1;

	diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));

    }

    return chm_sparse_to_SEXP(chxcp, 1, uploT, diag,

				GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_to_matrix(SEXP x)

{

    cholmod_sparse *chxs = as_cholmod_sparse(x);

    cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);

    Free(chxs);

    return chm_dense_to_matrix(chxd, 1,

			       GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)

{

    cholmod_sparse *chxs = as_cholmod_sparse(x);

    cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);

    int uploT = 0; char *diag = "";

    Free(chxs);

    if (asLogical(tri)) {	/* triangular sparse matrices */

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

	diag = diag_P(x);

    }

    return chm_triplet_to_SEXP(chxt, 1, uploT, diag,

			       GET_SLOT(x, Matrix_DimNamesSym));

}

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

SEXP Csparse_symmetric_to_general(SEXP x)

{

    cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;

    if (!(chx->stype))

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

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

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

    Free(chx);

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

			      GET_SLOT(x, Matrix_DimNamesSym));

}

SEXP Csparse_transpose(SEXP x, SEXP tri)

{

    cholmod_sparse *chx = as_cholmod_sparse(x);

    cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);

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

    int uploT = 0; char *diag = "";

    Free(chx);

    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);

    if (asLogical(tri)) {	/* triangular sparse matrices */

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

	diag = diag_P(x);

    }

    return chm_sparse_to_SEXP(chxt, 1, uploT, diag, dn);

}

SEXP Csparse_Csparse_prod(SEXP a, SEXP b)

{

    cholmod_sparse *cha = as_cholmod_sparse(a),

	*chb = as_cholmod_sparse(b);

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

    SEXP dn = allocVector(VECSXP, 2);

    Free(cha); Free(chb);

    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, "", dn);

}

SEXP Csparse_dense_prod(SEXP a, SEXP b)

{

    cholmod_sparse *cha = as_cholmod_sparse(a);

    cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));

    cholmod_dense *chc = 

	cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);

    double alpha[] = {1,0}, beta[] = {0,0};

    cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);

    Free(cha); Free(chb);

    UNPROTECT(1);

    return chm_dense_to_SEXP(chc, 1);

}

SEXP Csparse_dense_crossprod(SEXP a, SEXP b)

{

    cholmod_sparse *cha = as_cholmod_sparse(a);

    cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));

    cholmod_dense *chc =

	cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);

    double alpha[] = {1,0}, beta[] = {0,0};

    cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);

    Free(cha); Free(chb);

    UNPROTECT(1);

    return chm_dense_to_SEXP(chc, 1);

}

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

{

    int trip = asLogical(triplet),

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

    cholmod_triplet

	*cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;

    cholmod_sparse *chcp, *chxt,

	*chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)

	: as_cholmod_sparse(x);

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

    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);

	Free(cht);

    } else {

	Free(chx);

    }

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

				/* create dimnames */

    SET_VECTOR_ELT(dn, 0,

		   duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),

					(tr) ? 1 : 0)));

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

    UNPROTECT(1);

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

}

SEXP Csparse_horzcat(SEXP x, SEXP y)

{

    cholmod_sparse *chx = as_cholmod_sparse(x),

	*chy = as_cholmod_sparse(y), *ans;

    ans = cholmod_horzcat(chx, chy, 1, &c);

    Free(chx); Free(chy);

    /* FIXME: currently drops dimnames */

    return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);

}

SEXP Csparse_vertcat(SEXP x, SEXP y)

{

    cholmod_sparse *chx = as_cholmod_sparse(x),

	*chy = as_cholmod_sparse(y), *ans;

    ans = cholmod_vertcat(chx, chy, 1, &c);

    Free(chx); Free(chy);

    /* FIXME: currently drops dimnames */

    return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);

}

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

{

    cholmod_sparse *chx = as_cholmod_sparse(x), *ans;

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

    Free(chx);

    return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);

}

SEXP Csparse_diagU2N(SEXP x)

{

    cholmod_sparse *chx = as_cholmod_sparse(x);

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

    double one[] = {1, 0};

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

    int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?

	-1 : 1;

    Free(chx); cholmod_free_sparse(&eye, &c);

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

			      duplicate(GET_SLOT(x, Matrix_DimNamesSym)));

}

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

{

    cholmod_sparse *chx = as_cholmod_sparse(x);

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

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

    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, "", R_NilValue);

}