cholmod-common.h File Reference

#include "cholmod-etc.h"

Go to the source code of this file.

Functions
cholmod_factor *	sexp_as_cholmod_factor (cholmod_factor *, SEXP)
	Coerce from CHMfactor to (cholmod_factor *)
cholmod_sparse *	sexp_as_cholmod_sparse (cholmod_sparse *, SEXP, Rboolean, Rboolean)
	Coerce from CsparseMatrix to (cholmod_sparse *)
cholmod_triplet *	sexp_as_cholmod_triplet (cholmod_triplet *, SEXP, Rboolean)
	Coerce from TsparseMatrix to (cholmod_triplet *)
cholmod_dense *	sexp_as_cholmod_dense (cholmod_dense *, SEXP)
	Coerce from [nlidz]geMatrix or vector to (cholmod_dense *)
cholmod_dense *	numeric_as_cholmod_dense (cholmod_dense *, double *, int, int)
	Coerce from (double *) to (cholmod_dense *) with given dimensions.
SEXP	cholmod_factor_as_sexp (cholmod_factor *, int)
	Coerce from (cholmod_factor *) to CHMfactor.
SEXP	cholmod_sparse_as_sexp (cholmod_sparse *, int, int, int, const char *, SEXP)
	Coerce from (cholmod_sparse *) to CsparseMatrix.
SEXP	cholmod_triplet_as_sexp (cholmod_triplet *, int, int, int, const char *, SEXP)
	Coerce from (cholmod_triplet *) to TsparseMatrix.
SEXP	cholmod_dense_as_sexp (cholmod_dense *, int)
	Coerce from (cholmod_dense *) to [dz]geMatrix.
double	cholmod_factor_ldetA (cholmod_factor *)
	Log determinant from Cholesky factorization.
cholmod_factor *	cholmod_factor_update (cholmod_factor *, cholmod_sparse *, double)
	Update a Cholesky factorization.
int	R_cholmod_start (cholmod_common *)
int	R_cholmod_finish (cholmod_common *)
SEXP	R_cholmod_common_envini (SEXP)
void	R_cholmod_common_envset (void)
void	R_cholmod_common_envget (void)

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 954 of file cholmod-common.c.

References _, FREE_THEN, GET_SLOT, Matrix_DimSym, Matrix_xSym, 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 CHMfactor.

Allocates an S4 object inheriting from virtual class CHMfactor 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 CHMfactor.

Definition at line 584 of file cholmod-common.c.

References _, FREE_THEN, GET_SLOT, Matrix_DimSym, Matrix_iSym, Matrix_permSym, Matrix_pSym, Matrix_xSym, 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. It is assumed that L->xtype=CHOLMOD_REAL.

Definition at line 1017 of file cholmod-common.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 1064 of file cholmod-common.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 732 of file cholmod-common.c.

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

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 848 of file cholmod-common.c.

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

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 554 of file cholmod-common.c.

Referenced by R_init_Matrix().

R_cholmod_common_envget()

void R_cholmod_common_envget

(

void

)

Definition at line 1217 of file cholmod-common.c.

References c, cholmod_common_env, GET_MEMBER_FROM_FRAME, and m0_ordSym.

Referenced by dpCMatrix_trf_(), and R_cholmod_error_handler().

R_cholmod_common_envini()

SEXP R_cholmod_common_envini

(

SEXP

rho

)

Definition at line 1154 of file cholmod-common.c.

References cholmod_common_env, dboundSym, ERROR_INVALID_TYPE, final_asisSym, final_llSym, final_monotonicSym, final_packSym, final_resymbolSym, final_superSym, grow0Sym, grow1Sym, grow2Sym, m0_ordSym, maxrankSym, nmethodsSym, postorderSym, prefer_upperSym, prefer_zomplexSym, quick_return_if_not_posdefSym, R_cholmod_common_envset(), supernodal_switchSym, and supernodalSym.

R_cholmod_common_envset()

void R_cholmod_common_envset

(

void

)

Definition at line 1181 of file cholmod-common.c.

References c, cholmod_common_env, m0_ordSym, and SET_FRAME_FROM_MEMBER.

Referenced by dpCMatrix_trf_(), and R_cholmod_common_envini().

R_cholmod_finish()

int R_cholmod_finish

(

cholmod_common *

Common

)

Definition at line 1122 of file cholmod-common.c.

References _.

Referenced by R_unload_Matrix().

R_cholmod_start()

int R_cholmod_start

(

cholmod_common *

Common

)

Definition at line 1104 of file cholmod-common.c.

References _, and R_cholmod_error_handler().

Referenced by R_init_Matrix().

sexp_as_cholmod_dense()

cholmod_dense * sexp_as_cholmod_dense	(	cholmod_dense *	A,
		SEXP	from
	)

Coerce from [nlidz]geMatrix or vector to (cholmod_dense *)

Sets the members of a pointed-to cholmod_dense struct, using "data" obtained from slots of a [nlidz]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 [nlidz]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 470 of file cholmod-common.c.

References ERROR_INVALID_TYPE, GET_SLOT, Matrix_DimSym, Matrix_xSym, and valid.

Referenced by R_init_Matrix().

sexp_as_cholmod_factor()

cholmod_factor * sexp_as_cholmod_factor	(	cholmod_factor *	L,
		SEXP	from
	)

Coerce from CHMfactor to (cholmod_factor *)

Sets the members of a pointed-to cholmod_factor struct, using "data" obtained from slots of a CHMfactor. 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 CHMfactor.

Returns

L.

Definition at line 80 of file cholmod-common.c.

References _, c, ERROR_INVALID_CLASS, ERROR_INVALID_TYPE, GET_SLOT, Matrix_DimSym, Matrix_iSym, Matrix_permSym, Matrix_pSym, Matrix_xSym, and valid.

Referenced by R_init_Matrix().

sexp_as_cholmod_sparse()

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

Coerce from CsparseMatrix to (cholmod_sparse *)

Sets the members of a pointed-to cholmod_sparse struct, using "data" obtained from slots of a CsparseMatrix. 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 CsparseMatrix.
checkUnit	a boolean indicating if the unit diagonal of formally unit triangular CsparseMatrix should be allocated.
sortInPlace	a boolean indicating if unsorted CsparseMatrix should be sorted in place to avoid an allocation.

Returns

A.

Definition at line 188 of file cholmod-common.c.

References _, c, checkpi(), ERROR_INVALID_CLASS, GET_SLOT, Matrix_diagSym, Matrix_DimSym, Matrix_iSym, Matrix_pSym, Matrix_uploSym, Matrix_xSym, and valid.

Referenced by R_init_Matrix().

sexp_as_cholmod_triplet()

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

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.
checkUnit	a boolean indicating if the unit diagonal of formally unit triangular TsparseMatrix should be allocated.

Returns

A.

Definition at line 340 of file cholmod-common.c.

References ERROR_INVALID_CLASS, GET_SLOT, Matrix_diagSym, Matrix_DimSym, Matrix_iSym, Matrix_pSym, Matrix_uploSym, Matrix_xSym, Matrix_zone, and valid.

Referenced by R_init_Matrix().