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[matrix] Diff of /pkg/src/Mutils.h
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Diff of /pkg/src/Mutils.h

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revision 255, Fri Aug 20 16:27:15 2004 UTC revision 1507, Mon Sep 4 18:41:34 2006 UTC
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1  #ifndef MATRIX_MUTILS_H  #ifndef MATRIX_MUTILS_H
2  #define MATRIX_MUTILS_H  #define MATRIX_MUTILS_H
3    
4  #include <Rdefines.h>  #ifdef __cplusplus
5    extern "C" {
6    #endif
7    
8    #include <Rdefines.h> /* Rinternals.h + GET_SLOT etc */
9    #include <R.h>  /* includes Rconfig.h */
10    
11    #ifdef ENABLE_NLS
12    #include <libintl.h>
13    #define _(String) dgettext ("Matrix", String)
14    #else
15    #define _(String) (String)
16    #endif
17    
18    SEXP triangularMatrix_validate(SEXP obj);
19    SEXP symmetricMatrix_validate(SEXP obj);
20    SEXP dense_nonpacked_validate(SEXP obj);
21    
22    /* enum constants from cblas.h and some short forms */
23    enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};
24    enum CBLAS_TRANSPOSE {CblasNoTrans=111, CblasTrans=112, CblasConjTrans=113};
25    enum CBLAS_UPLO {CblasUpper=121, CblasLower=122};
26    enum CBLAS_DIAG {CblasNonUnit=131, CblasUnit=132};
27    enum CBLAS_SIDE {CblasLeft=141, CblasRight=142};
28    #define RMJ CblasRowMajor
29    #define CMJ CblasColMajor
30    #define NTR CblasNoTrans
31    #define TRN CblasTrans
32    #define CTR CblasConjTrans
33    #define UPP CblasUpper
34    #define LOW CblasLower
35    #define NUN CblasNonUnit
36    #define UNT CblasUnit
37    #define LFT CblasLeft
38    #define RGT CblasRight
39    
40  char norm_type(char *typstr);  char norm_type(char *typstr);
41  char rcond_type(char *typstr);  char rcond_type(char *typstr);
42  double get_double_by_name(SEXP obj, char *nm);  double get_double_by_name(SEXP obj, char *nm);
43  SEXP set_double_by_name(SEXP obj, double val, char *nm);  SEXP set_double_by_name(SEXP obj, double val, char *nm);
44  SEXP as_det_obj(double val, int log, int sign);  SEXP as_det_obj(double val, int log, int sign);
45  SEXP get_factorization(SEXP obj, char *nm);  SEXP get_factors(SEXP obj, char *nm);
46  SEXP set_factorization(SEXP obj, SEXP val, char *nm);  SEXP set_factors(SEXP obj, SEXP val, char *nm);
47  SEXP cscMatrix_set_Dim(SEXP x, int nrow);  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);
48    char uplo_value(SEXP x);
49    char diag_value(SEXP x);
50    
51  int csc_unsorted_columns(int ncol, const int p[], const int i[]);  int csc_unsorted_columns(int ncol, const int p[], const int i[]);
52  void csc_sort_columns(int ncol, const int p[], int i[], double x[]);  void csc_sort_columns(int ncol, const int p[], int i[], double x[]);
 SEXP triple_as_SEXP(int nrow, int ncol, int nz,  
                     const int Ti [], const int Tj [], const double Tx [],  
                     char *Rclass);  
53  SEXP csc_check_column_sorting(SEXP A);  SEXP csc_check_column_sorting(SEXP A);
54  void csc_components_transpose(int m, int n, int nnz,  SEXP Matrix_make_named(int TYP, char **names);
55                                const int xp[], const int xi[],  SEXP check_scalar_string(SEXP sP, char *vals, char *nm);
56                                const double xx[],  double *packed_getDiag(double *dest, SEXP x);
57                                int ap[], int ai[], double ax[]);  SEXP Matrix_getElement(SEXP list, char *nm);
58  void triplet_to_col(int nrow, int ncol, int nz,  
59                      const int Ti [], const int Tj [], const double Tx [],  #define PACKED_TO_FULL(TYPE)                                            \
60                      int Ap [], int Ai [], double Ax []);  TYPE *packed_to_full_ ## TYPE(TYPE *dest, const TYPE *src,              \
61  void ssc_symbolic_permute(int n, int upper, const int perm[],                               int n, enum CBLAS_UPLO uplo)
62                            int Ap[], int Ai[]);  PACKED_TO_FULL(double);
63  double *nlme_symmetrize(double *a, const int nc);  PACKED_TO_FULL(int);
64  void nlme_check_Lapack_error(int info, const char *laName);  #undef PACKED_TO_FULL
65  SEXP nlme_replaceSlot(SEXP obj, SEXP names, SEXP value);  
66  SEXP nlme_weight_matrix_list(SEXP MLin, SEXP wts, SEXP adjst, SEXP MLout);  #define FULL_TO_PACKED(TYPE)                                            \
67    TYPE *full_to_packed_ ## TYPE(TYPE *dest, const TYPE *src, int n,       \
68                                  /* stored pointers to symbols */                                enum CBLAS_UPLO uplo, enum CBLAS_DIAG diag)
69                                  /* initialized in Matrix_init */  FULL_TO_PACKED(double);
70  extern SEXP  FULL_TO_PACKED(int);
71      Matrix_DSym,  #undef FULL_TO_PACKED
72      Matrix_DIsqrtSym,  
73      Matrix_DimSym,  
74      Matrix_GpSym,  extern   /* stored pointers to symbols initialized in R_init_Matrix */
75      Matrix_LiSym,  #include "Syms.h"
76      Matrix_LpSym,  
77      Matrix_LxSym,  /* zero an array */
78      Matrix_OmegaSym,  #define AZERO(x, n) {int _I_, _SZ_ = (n); for(_I_ = 0; _I_ < _SZ_; _I_++) (x)[_I_] = 0;}
79      Matrix_ParentSym,  
80      Matrix_RXXSym,  /* number of elements in one triangle of a square matrix of order n */
81      Matrix_RZXSym,  #define PACKED_LENGTH(n)   ((n) * ((n) + 1))/2
82      Matrix_XtXSym,  
83      Matrix_ZtXSym,  /* duplicate the slot with name given by sym from src to dest */
84      Matrix_ZZxSym,  #define slot_dup(dest, src, sym)  SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
85      Matrix_bVarSym,  
86      Matrix_cnamesSym,  #define uplo_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_uploSym), 0))
87      Matrix_devianceSym,  #define diag_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_diagSym), 0))
88      Matrix_devCompSym,  #define class_P(_x_) CHAR(asChar(getAttrib(_x_, R_ClassSymbol)))
89      Matrix_diagSym,  
90      Matrix_iSym,  /**
91      Matrix_ipermSym,   * Check for valid length of a packed triangular array and return the
92      Matrix_jSym,   * corresponding number of columns
93      Matrix_matSym,   *
94      Matrix_ncSym,   * @param len length of a packed triangular array
95      Matrix_pSym,   *
96      Matrix_permSym,   * @return number of columns
97      Matrix_statusSym,   */
98      Matrix_uploSym,  static R_INLINE
99      Matrix_xSym,  int packed_ncol(int len)
100      Matrix_zSym;  {
101        int disc = 8 * len + 1;     /* discriminant */
102        int sqrtd = (int) sqrt((double) disc);
103    
104        if (len < 0 || disc != sqrtd * sqrtd)
105            error(_("invalid 'len' = %d in packed_ncol"));
106        return (sqrtd - 1)/2;
107    }
108    
109    /**
110     * Allocate an SEXP of given type and length, assign it as slot nm in
111     * the object, and return the SEXP.  The validity of this function
112     * depends on SET_SLOT not duplicating val when NAMED(val) == 0.  If
113     * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by
114     * GET_SLOT to ensure that the value returned is indeed the SEXP in
115     * the slot.
116     *
117     * @param obj object in which to assign the slot
118     * @param nm name of the slot, as an R name object
119     * @param type type of SEXP to allocate
120     * @param length length of SEXP to allocate
121     *
122     * @return SEXP of given type and length assigned as slot nm in obj
123     */
124    static R_INLINE
125    SEXP ALLOC_SLOT(SEXP obj, SEXP nm, SEXPTYPE type, int length)
126    {
127        SEXP val = allocVector(type, length);
128    
129        SET_SLOT(obj, nm, val);
130        return val;
131    }
132    
133    /**
134     * Expand compressed pointers in the array mp into a full set of indices
135     * in the array mj.
136     *
137     * @param ncol number of columns (or rows)
138     * @param mp column pointer vector of length ncol + 1
139     * @param mj vector of length mp[ncol] to hold the result
140     *
141     * @return mj
142     */
143    static R_INLINE
144    int* expand_cmprPt(int ncol, const int mp[], int mj[])
145    {
146        int j;
147        for (j = 0; j < ncol; j++) {
148            int j2 = mp[j+1], jj;
149            for (jj = mp[j]; jj < j2; jj++) mj[jj] = j;
150        }
151        return mj;
152    }
153    
154    
155    /**
156     * Return the linear index of the (row, col) entry in a csc structure.
157     * If the entry is not found and missing is 0 an error is signaled;
158     * otherwise the missing value is returned.
159     *
160     * @param p vector of column pointers
161     * @param i vector of row indices
162     * @param row row index
163     * @param col column index
164     * @param missing the value to return is the row, col entry does not
165     * exist.  If this is zero and the row, col entry does not exist an
166     * error is signaled.
167     *
168     * @return index of element at (row, col) if it exists, otherwise missing
169     */
170    static R_INLINE int
171    check_csc_index(const int p[], const int i[], int row, int col, int missing)
172    {
173        int k, k2 = p[col + 1];
174                                    /* linear search - perhaps replace by bsearch */
175        for (k = p[col]; k < k2; k++) if (i[k] == row) return k;
176        if (!missing)
177            error("row %d and column %d not defined in rowind and colptr",
178                  row, col);
179        return missing;
180    }
181    
182    /**
183     * Calculate the zero-based index in a row-wise packed lower triangular matrix.
184     * This is used for the arrays of blocked sparse matrices.
185     *
186     * @param i column number (zero-based)
187     * @param k row number (zero-based)
188     *
189     * @return The index of the (k,i) element of a packed lower triangular matrix
190     */
191    static R_INLINE
192    int Lind(int k, int i)
193    {
194        if (k < i) error("Lind(k = %d, i = %d) must have k >= i", k, i);
195        return (k * (k + 1))/2 + i;
196    }
197    
198    double *expand_csc_column(double *dest, int m, int j,
199                              const int Ap[], const int Ai[], const double Ax[]);
200    
201    /**
202     * Apply a permutation to an integer vector
203     *
204     * @param i vector of 0-based indices
205     * @param n length of vector i
206     * @param perm 0-based permutation vector of length max(i) + 1
207     */
208    static R_INLINE void
209    int_permute(int i[], int n, const int perm[])
210    {
211        int j;
212        for (j = 0; j < n; j++) i[j] = perm[i[j]];
213    }
214    
215    /**
216     * Force index pairs to be in the upper triangle of a matrix
217     *
218     * @param i vector of 0-based row indices
219     * @param j vector of 0-based column indices
220     * @param nnz length of index vectors
221     */
222    static R_INLINE void
223    make_upper_triangular(int i[], int j[], int nnz)
224    {
225        int k;
226        for (k = 0; k < nnz; k++) {
227            if (i[k] > j[k]) {
228                int tmp = i[k];
229                i[k] = j[k];
230                j[k] = tmp;
231            }
232        }
233    }
234    
235    void make_d_matrix_triangular(double *x, SEXP from);
236    void make_i_matrix_triangular(   int *x, SEXP from);
237    
238    void make_d_matrix_symmetric(double *to, SEXP from);
239    void make_i_matrix_symmetric(   int *to, SEXP from);
240    
241    SEXP Matrix_expand_pointers(SEXP pP);
242    
243    
244    /**
245     * Elementwise increment dest by src
246     *
247     * @param dest vector to be incremented
248     * @param src vector to be added to dest
249     * @param n length of vectors
250     *
251     * @return dest
252     */
253    static R_INLINE double*
254    vecIncrement(double dest[], const double src[], int n) {
255        int i;
256        for (i = 0; i < n; i++) dest[i] += src[i];
257        return dest;
258    }
259    
260    /**
261     * Elementwise sum of src1 and src2 into dest
262     *
263     * @param dest vector to be incremented
264     * @param src1 vector to be added
265     * @param src1 second vector to be added
266     * @param n length of vectors
267     *
268     * @return dest
269     */
270    static R_INLINE double*
271    vecSum(double dest[], const double src1[], const double src2[],
272           int n) {
273        int i;
274        for (i = 0; i < n; i++) dest[i] = src1[i] + src2[i];
275        return dest;
276    }
277    
278    SEXP alloc_dgeMatrix(int m, int n, SEXP rownms, SEXP colnms);
279    SEXP alloc_dpoMatrix(int n, char *uplo, SEXP rownms, SEXP colnms);
280    SEXP alloc_dtrMatrix(int n, char *uplo, char *diag, SEXP rownms, SEXP colnms);
281    SEXP alloc_dsCMatrix(int n, int nz, char *uplo, SEXP rownms, SEXP colnms);
282    
283    SEXP dup_mMatrix_as_dgeMatrix(SEXP A);
284    
285    static R_INLINE SEXP
286    mMatrix_as_dgeMatrix(SEXP A)
287    {
288        return strcmp(class_P(A), "dgeMatrix") ? dup_mMatrix_as_dgeMatrix(A) : A;
289    }
290    
291    /**
292     * Return the 0-based index of a string match in a vector of strings
293     * terminated by an empty string.  Returns -1 for no match.
294     *
295     * @param dest class string to match
296     * @param valid vector of possible matches terminated by an empty string
297     *
298     * @return index of match or -1 for no match
299     */
300    static R_INLINE int
301    Matrix_check_class(char *class, char **valid)
302    {
303        int ans;
304        for (ans = 0; ; ans++) {
305            if (!strlen(valid[ans])) return -1;
306            if (!strcmp(class, valid[ans])) return ans;
307        }
308    }
309    
310    #ifdef __cplusplus
311    }
312  #endif  #endif
313    
314    #endif /* MATRIX_MUTILS_H_ */

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