cholmod-api.c File Reference

#include "Mdefines.h"
#include "cholmod-api.h"

Go to the source code of this file.

Macros
#define	errorFree(...)
#define	MAYBE_FREE
#define	MAYBE_FREE
#define	MAYBE_FREE
#define	MAYBE_FREE

Functions
cholmod_factor *	sexp_as_cholmod_factor (cholmod_factor *L, SEXP from)
	Coerce from sparseCholesky to (cholmod_factor *)
cholmod_sparse *	sexp_as_cholmod_sparse (cholmod_sparse *A, SEXP from, Rboolean allocUnit, Rboolean sortInPlace)
	Coerce from [CR]sparseMatrix to (cholmod_sparse *)
cholmod_triplet *	sexp_as_cholmod_triplet (cholmod_triplet *A, SEXP from, Rboolean allocUnit)
	Coerce from TsparseMatrix to (cholmod_triplet *)
cholmod_dense *	sexp_as_cholmod_dense (cholmod_dense *A, SEXP from)
	Coerce from .geMatrix or vector to (cholmod_dense *)
cholmod_dense *	numeric_as_cholmod_dense (cholmod_dense *A, double *data, int nrow, int ncol)
	Coerce from (double *) to (cholmod_dense *) with given dimensions.
SEXP	cholmod_factor_as_sexp (cholmod_factor *L, int doFree)
	Coerce from (cholmod_factor *) to sparseCholesky.
SEXP	cholmod_sparse_as_sexp (cholmod_sparse *A, int doFree, int ttype, int doLogic, const char *diagString, SEXP dimnames)
	Coerce from (cholmod_sparse *) to CsparseMatrix.
SEXP	cholmod_triplet_as_sexp (cholmod_triplet *A, int doFree, int ttype, int doLogic, const char *diagString, SEXP dimnames)
	Coerce from (cholmod_triplet *) to TsparseMatrix.
SEXP	cholmod_dense_as_sexp (cholmod_dense *A, int doFree)
	Coerce from (cholmod_dense *) to [dz]geMatrix.
double	cholmod_factor_ldetA (cholmod_factor *L)
	Log determinant from Cholesky factorization.
cholmod_factor *	cholmod_factor_update (cholmod_factor *L, cholmod_sparse *A, double beta)
	Update a Cholesky factorization.

Macro Definition Documentation

errorFree

#define errorFree

(

...

)

Value:

    do { \
        MAYBE_FREE; \
        Rf_error(__VA_ARGS__); \
    } while (0)

Referenced by cholmod_dense_as_sexp(), cholmod_factor_as_sexp(), cholmod_sparse_as_sexp(), and cholmod_triplet_as_sexp().

MAYBE_FREE [1/4]

#define MAYBE_FREE

Value:

    do { \
        if (doFree != 0) { \
            if (doFree < 0) \
                R_Free(L); \
            else if (L->itype == CHOLMOD_INT) \
                cholmod_free_factor(&L, &c); \
            else \
                cholmod_l_free_factor(&L, &cl); \
        } \
    } while (0)

Referenced by cholmod_dense_as_sexp(), cholmod_factor_as_sexp(), cholmod_sparse_as_sexp(), and cholmod_triplet_as_sexp().

MAYBE_FREE [2/4]

#define MAYBE_FREE

Value:

    do { \
        if (doFree != 0) { \
        if (doFree < 0) \
            R_Free(A_); \
        else if (A_->itype == CHOLMOD_INT) \
            cholmod_free_sparse(&A_, &c); \
        else \
            cholmod_l_free_sparse(&A_, &cl); \
        } \
    } while (0)

MAYBE_FREE [3/4]

#define MAYBE_FREE

Value:

    do { \
        if (doFree != 0) { \
        if (doFree < 0) \
            R_Free(A); \
        else if (A->itype == CHOLMOD_INT) \
            cholmod_free_triplet(&A, &c); \
        else \
            cholmod_l_free_triplet(&A, &cl); \
        } \
    } while (0)

MAYBE_FREE [4/4]

#define MAYBE_FREE

Value:

    do { \
        if (doFree != 0) { \
        if (doFree < 0) \
            R_Free(A); \
        else \
            cholmod_free_dense(&A, &c); \
        } \
    } while (0)

Function Documentation

cholmod_dense_as_sexp()

SEXP cholmod_dense_as_sexp	(	cholmod_dense *	A,
		int	doFree )

Coerce from (cholmod_dense *) to [dz]geMatrix.

Allocates an S4 object of class [dz]geMatrix and copies into the slots from members of a pointed-to cholmod_dense struct. The specific class of the result is determined by struct member xtype.

Parameters

A	a pointer to a cholmod_dense struct.
doFree	a flag indicating if and how to free A before returning. (0) don't free, (>0) free with cholmod_free_dense, (<0) free with R_Free.

Returns

A [dz]geMatrix.

Definition at line 851 of file cholmod-api.c.

References _, errorFree, GET_SLOT, Matrix_DimSym, Matrix_xSym, MAYBE_FREE, newObject(), and SET_SLOT.

Referenced by R_init_Matrix().

cholmod_factor_as_sexp()

SEXP cholmod_factor_as_sexp	(	cholmod_factor *	L,
		int	doFree )

Coerce from (cholmod_factor *) to sparseCholesky.

Allocates an S4 object inheriting from virtual class sparseCholesky and copies into the slots from members of a pointed-to cholmod_factor struct. The specific class of the result is determined by struct members xtype and is_super.

Parameters

L	a pointer to a cholmod_factor struct.
doFree	a flag indicating if and how to free L before returning. (0) don't free, (>0) free with cholmod_free_factor, (<0) free with R_Free.

Returns

A sparseCholesky.

Definition at line 466 of file cholmod-api.c.

References _, errorFree, GET_SLOT, Matrix_colcountSym, Matrix_DimSym, Matrix_isllSym, Matrix_ismtSym, Matrix_iSym, Matrix_maxcsizeSym, Matrix_maxesizeSym, Matrix_minorSym, Matrix_nextSym, Matrix_nzSym, Matrix_orderingSym, Matrix_permSym, Matrix_piSym, Matrix_prevSym, Matrix_pSym, Matrix_pxSym, Matrix_sSym, Matrix_superSym, Matrix_xSym, MAYBE_FREE, newObject(), and SET_SLOT.

Referenced by R_init_Matrix().

cholmod_factor_ldetA()

double cholmod_factor_ldetA

(

cholmod_factor *

L

)

Log determinant from Cholesky factorization.

Computes log(det(A)) given the Cholesky factorization of A as P1 * A * P1' = L1 * D * L1' = L * L', L = L1 * sqrt(D). The result is computed as sum(log(diag(D))) or 2*sum(log(diag(L))), depending on members is_super and is_ll of the supplied struct. Note that CHOLMOD does not require diag(D) to be positive and that this routine does not check (FIXME).

Parameters

L	a pointer to a cholmod_factor struct.

Definition at line 911 of file cholmod-api.c.

References _.

Referenced by R_init_Matrix().

cholmod_factor_update()

cholmod_factor * cholmod_factor_update	(	cholmod_factor *	L,
		cholmod_sparse *	A,
		double	beta )

Update a Cholesky factorization.

Updates in-place the Cholesky factorization of a symmetric matrix X+alpha*I with the Cholesky factorization of (1) A+beta*I, where A is a symmetric matrix sharing the nonzero pattern of X, or (2) A*A'+beta*I, where A is a general matrix sharing the nonzero pattern of Y, assuming that X = Y*Y'.

Parameters

L	a pointer to a cholmod_factor struct, to be modified in-place.
A	a pointer to a cholmod_sparse struct.
beta	a multiplier, typically positive, to guarantee strict diagonal dominance.

Returns

L.

Definition at line 958 of file cholmod-api.c.

References _, and c.

Referenced by R_init_Matrix().

cholmod_sparse_as_sexp()

SEXP cholmod_sparse_as_sexp	(	cholmod_sparse *	A,
		int	doFree,
		int	ttype,
		int	doLogic,
		const char *	diagString,
		SEXP	dimnames )

Coerce from (cholmod_sparse *) to CsparseMatrix.

Allocates an S4 object inheriting from virtual class CsparseMatrix and copies into the slots from members of a pointed-to cholmod_sparse struct. The specific class of the result is determined by struct members xtype and stype and by arguments ttype and doLogic.

Parameters

A	a pointer to a cholmod_sparse struct.
doFree	a flag indicating if and how to free A before returning. (0) don't free, (>0) free with cholmod_free_sparse, (<0) free with R_Free.
ttype	a flag indicating if the result should be a .tCMatrix. (0) not .tCMatrix, (>0) .tCMatrix with uplo="U", (<0) .tCMatrix with uplo="L". If ttype=0, then the result is a .gCMatrix or .sCMatrix depending on stype. (0) .gCMatrix, (>0) .sCMatrix with uplo="U", (<0) .sCMatrix with uplo="L".
doLogic	a flag indicating if the result should be a l.CMatrix if xtype=CHOLMOD_REAL.
diagString	a null-terminated string or NULL. The diag slot of a .tCMatrix result is "N" if and only if diagString is NULL or diagString[0] is 'N'.
dimnames	an R object specifying the Dimnames slot of the result, unused if not a list of length 2.

Returns

A CsparseMatrix.

Definition at line 625 of file cholmod-api.c.

References _, c, errorFree, GET_SLOT, Matrix_diagSym, Matrix_DimNamesSym, Matrix_DimSym, Matrix_iSym, Matrix_pSym, Matrix_uploSym, Matrix_xSym, MAYBE_FREE, newObject(), SET_SLOT, and TYPEOF.

Referenced by R_init_Matrix().

cholmod_triplet_as_sexp()

SEXP cholmod_triplet_as_sexp	(	cholmod_triplet *	A,
		int	doFree,
		int	ttype,
		int	doLogic,
		const char *	diagString,
		SEXP	dimnames )

Coerce from (cholmod_triplet *) to TsparseMatrix.

Allocates an S4 object inheriting from virtual class TsparseMatrix and copies into the slots from members of a pointed-to cholmod_triplet struct. The specific class of the result is determined by struct members xtype and stype and by arguments ttype and doLogic.

Parameters

A	a pointer to a cholmod_triplet struct.
doFree	a flag indicating if and how to free A before returning. (0) don't free, (>0) free with cholmod_free_triplet, (<0) free with R_Free.
ttype	a flag indicating if the result should be a .tTMatrix. (0) not .tTMatrix, (>0) .tTMatrix with uplo="U", (<0) .tTMatrix with uplo="L". If ttype=0, then the result is a .gTMatrix or .sTMatrix depending on stype. (0) .gTMatrix, (>0) .sTMatrix with uplo="U", (<0) .sTMatrix with uplo="L".
doLogic	a flag indicating if the result should be an l.TMatrix if xtype=CHOLMOD_REAL.
diagString	a null-terminated string or NULL. The diag slot of a .tTMatrix result is "N" if and only if diagString is NULL or diagString[0] is 'N'.
dimnames	an R object specifying the Dimnames slot of the result, unused if not a list of length 2.

Returns

A TsparseMatrix.

Definition at line 740 of file cholmod-api.c.

References _, errorFree, GET_SLOT, Matrix_diagSym, Matrix_DimNamesSym, Matrix_DimSym, Matrix_iSym, Matrix_jSym, Matrix_uploSym, Matrix_xSym, MAYBE_FREE, newObject(), SET_SLOT, and TYPEOF.

Referenced by R_init_Matrix().

numeric_as_cholmod_dense()

cholmod_dense * numeric_as_cholmod_dense	(	cholmod_dense *	A,
		double *	data,
		int	nrow,
		int	ncol )

Coerce from (double *) to (cholmod_dense *) with given dimensions.

An analogue of base::matrix(data, nrow, ncol), where typeof(data)=="double" and length(data)==nrow*ncol.

Parameters

A	a pointer to a cholmod_dense struct, to be modified in-place.
data	a pointer to an nrow*ncol*sizeof(double) block of memory.
nrow	the desired number of rows.
ncol	the desired number of columns.

Returns

A.

Definition at line 436 of file cholmod-api.c.

Referenced by R_init_Matrix().

sexp_as_cholmod_dense()

cholmod_dense * sexp_as_cholmod_dense	(	cholmod_dense *	A,
		SEXP	from )

Coerce from .geMatrix or vector to (cholmod_dense *)

Sets the members of a pointed-to cholmod_dense struct, using "data" obtained from slots of a .geMatrix. The result should not be freed using cholmod_free_dense, as the resulting members point to memory controlled by R, not by CHOLMOD.

Parameters

A	a pointer to a cholmod_dense struct, to be modified in-place.
from	an S4 object inheriting from class .geMatrix or a traditional vector of type "logical", "integer", "double", or "complex" (to be handled as a 1-column matrix if not a matrix).

Returns

A.

Definition at line 356 of file cholmod-api.c.

References ERROR_INVALID_TYPE, GET_SLOT, Matrix_class(), Matrix_DimSym, Matrix_xSym, and TYPEOF.

Referenced by R_init_Matrix().

sexp_as_cholmod_factor()

cholmod_factor * sexp_as_cholmod_factor	(	cholmod_factor *	L,
		SEXP	from )

Coerce from sparseCholesky to (cholmod_factor *)

Sets the members of a pointed-to cholmod_factor struct, using "data" obtained from slots of a sparseCholesky. The result should not be freed using cholmod_free_factor, as the resulting members point to memory controlled by R, not by CHOLMOD.

Parameters

L	a pointer to a cholmod_factor struct, to be modified in-place.
from	an S4 object inheriting from virtual class sparseCholesky.

Returns

L.

Definition at line 18 of file cholmod-api.c.

References GET_SLOT, Matrix_class(), Matrix_colcountSym, Matrix_DimSym, Matrix_isllSym, Matrix_ismtSym, Matrix_iSym, Matrix_maxcsizeSym, Matrix_maxesizeSym, Matrix_minorSym, Matrix_nextSym, Matrix_nzSym, Matrix_orderingSym, Matrix_permSym, Matrix_piSym, Matrix_prevSym, Matrix_pSym, Matrix_pxSym, Matrix_sSym, Matrix_superSym, and Matrix_xSym.

Referenced by R_init_Matrix().

sexp_as_cholmod_sparse()

cholmod_sparse * sexp_as_cholmod_sparse	(	cholmod_sparse *	A,
		SEXP	from,
		Rboolean	allocUnit,
		Rboolean	sortInPlace )

Coerce from [CR]sparseMatrix to (cholmod_sparse *)

Sets the members of a pointed-to cholmod_sparse struct, using "data" obtained from slots of a [CR]sparseMatrix. The result should not be freed using cholmod_free_sparse, as the resulting members point to memory controlled by R, not by CHOLMOD.

Parameters

A	a pointer to a cholmod_sparse struct, to be modified in-place.
from	an S4 object inheriting from virtual class [CR]sparseMatrix.
allocUnit	a boolean indicating if the unit diagonal of formally unit triangular [CR]sparseMatrix should be allocated.
sortInPlace	a boolean indicating if unsorted [CR]sparseMatrix should be sorted in place to avoid an allocation.

Returns

A.

Definition at line 127 of file cholmod-api.c.

References _, allocUnit(), c, checkpi(), GET_SLOT, Matrix_class(), Matrix_diagSym, Matrix_DimSym, Matrix_iSym, Matrix_jSym, Matrix_pSym, Matrix_uploSym, Matrix_xSym, TYPEOF, and valid_sparse_compressed.

Referenced by R_init_Matrix().

sexp_as_cholmod_triplet()

cholmod_triplet * sexp_as_cholmod_triplet	(	cholmod_triplet *	A,
		SEXP	from,
		Rboolean	allocUnit )

Coerce from TsparseMatrix to (cholmod_triplet *)

Sets the members of a pointed-to cholmod_triplet struct, using "data" obtained from slots of a TsparseMatrix. The result should not be freed using cholmod_free_sparse, as the resulting members point to memory controlled by R, not by CHOLMOD.

Parameters

A	a pointer to a cholmod_triplet struct, to be modified in-place.
from	an S4 object inheriting from virtual class TsparseMatrix.
allocUnit	a boolean indicating if the unit diagonal of formally unit triangular TsparseMatrix should be allocated.

Returns

A.

Definition at line 247 of file cholmod-api.c.

References allocUnit(), GET_SLOT, Matrix_class(), Matrix_diagSym, Matrix_DimSym, Matrix_iSym, Matrix_pSym, Matrix_uploSym, Matrix_xSym, Matrix_zunit, TYPEOF, and valid_sparse_triplet.

Referenced by R_init_Matrix().