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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 478, Wed Feb 2 14:33:51 2005 UTC revision 2298, Fri Oct 17 13:45:12 2008 UTC
# Line 1  Line 1 
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  #include <Rconfig.h>  extern "C" {
6  #include "cblas.h"  #endif
7    
8    #include <ctype.h>
9    #include <R.h>  /* includes Rconfig.h */
10    #include <Rversion.h>
11    #include <Rdefines.h> /* Rinternals.h + GET_SLOT etc */
12    
13    #ifdef ENABLE_NLS
14    #include <libintl.h>
15    #define _(String) dgettext ("Matrix", String)
16    #else
17    #define _(String) (String)
18    #endif
19    
20    #ifdef __GNUC__
21    # undef alloca
22    # define alloca(x) __builtin_alloca((x))
23    #elif defined(__sun) || defined(_AIX)
24    /* this is necessary (and sufficient) for Solaris 10 and AIX 6: */
25    # include <alloca.h>
26    #endif
27    
28  /* short forms of some enum constants from cblas.h */  #define Alloca(n, t)   (t *) alloca( (size_t) ( (n) * sizeof(t) ) )
29    
30    SEXP triangularMatrix_validate(SEXP obj);
31    SEXP symmetricMatrix_validate(SEXP obj);
32    SEXP dense_nonpacked_validate(SEXP obj);
33    
34    /* enum constants from cblas.h and some short forms */
35    enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};
36    enum CBLAS_TRANSPOSE {CblasNoTrans=111, CblasTrans=112, CblasConjTrans=113};
37    enum CBLAS_UPLO {CblasUpper=121, CblasLower=122};
38    enum CBLAS_DIAG {CblasNonUnit=131, CblasUnit=132};
39    enum CBLAS_SIDE {CblasLeft=141, CblasRight=142};
40  #define RMJ CblasRowMajor  #define RMJ CblasRowMajor
41  #define CMJ CblasColMajor  #define CMJ CblasColMajor
42  #define NTR CblasNoTrans  #define NTR CblasNoTrans
# Line 18  Line 49 
49  #define LFT CblasLeft  #define LFT CblasLeft
50  #define RGT CblasRight  #define RGT CblasRight
51    
52  char norm_type(char *typstr);  #if !defined(R_VERSION) || R_VERSION < R_Version(2, 7, 0)
53  char rcond_type(char *typstr);  char La_norm_type(const char *typstr);
54    char La_rcond_type(const char *typstr);
55    #endif
56    
57  double get_double_by_name(SEXP obj, char *nm);  double get_double_by_name(SEXP obj, char *nm);
58  SEXP set_double_by_name(SEXP obj, double val, char *nm);  SEXP set_double_by_name(SEXP obj, double val, char *nm);
59  SEXP as_det_obj(double val, int log, int sign);  SEXP as_det_obj(double val, int log, int sign);
60  SEXP get_factors(SEXP obj, char *nm);  SEXP get_factors(SEXP obj, char *nm);
61  SEXP set_factors(SEXP obj, SEXP val, char *nm);  SEXP set_factors(SEXP obj, SEXP val, char *nm);
62    
63    #if 0
64  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);
65  int csc_unsorted_columns(int ncol, const int p[], const int i[]);  #endif  /* unused */
66  void csc_sort_columns(int ncol, const int p[], int i[], double x[]);  
67  SEXP triple_as_SEXP(int nrow, int ncol, int nz,  /* int csc_unsorted_columns(int ncol, const int p[], const int i[]); */
68                      const int Ti [], const int Tj [], const double Tx [],  /* void csc_sort_columns(int ncol, const int p[], int i[], double x[]); */
69                      char *Rclass);  /* SEXP csc_check_column_sorting(SEXP A); */
70  SEXP csc_check_column_sorting(SEXP A);  SEXP Matrix_make_named(int TYP, char **names);
71  void csc_components_transpose(int m, int n, int nnz,  SEXP check_scalar_string(SEXP sP, char *vals, char *nm);
72                                const int xp[], const int xi[],  Rboolean equal_string_vectors(SEXP s1, SEXP s2);
73                                const double xx[],  
74                                int ap[], int ai[], double ax[]);  void d_packed_getDiag(double *dest, SEXP x, int n);
75  void ssc_symbolic_permute(int n, int upper, const int perm[],  void l_packed_getDiag(   int *dest, SEXP x, int n);
76                            int Ap[], int Ai[]);  void tr_d_packed_getDiag(double *dest, SEXP x);
77  double *nlme_symmetrize(double *a, const int nc);  void tr_l_packed_getDiag(   int *dest, SEXP x);
78  void nlme_check_Lapack_error(int info, const char *laName);  
79  SEXP nlme_replaceSlot(SEXP obj, SEXP names, SEXP value);  SEXP Matrix_getElement(SEXP list, char *nm);
80  SEXP nlme_weight_matrix_list(SEXP MLin, SEXP wts, SEXP adjst, SEXP MLout);  
81    #define PACKED_TO_FULL(TYPE)                                            \
82                                  /* stored pointers to symbols */  TYPE *packed_to_full_ ## TYPE(TYPE *dest, const TYPE *src,              \
83                                  /* initialized in R_init_Matrix */                               int n, enum CBLAS_UPLO uplo)
84  extern  PACKED_TO_FULL(double);
85    PACKED_TO_FULL(int);
86    #undef PACKED_TO_FULL
87    
88    #define FULL_TO_PACKED(TYPE)                                            \
89    TYPE *full_to_packed_ ## TYPE(TYPE *dest, const TYPE *src, int n,       \
90                                  enum CBLAS_UPLO uplo, enum CBLAS_DIAG diag)
91    FULL_TO_PACKED(double);
92    FULL_TO_PACKED(int);
93    #undef FULL_TO_PACKED
94    
95    
96    extern   /* stored pointers to symbols initialized in R_init_Matrix */
97  #include "Syms.h"  #include "Syms.h"
98    
99  /* zero an array */  /* zero an array */
100  #define AZERO(x, n) {int _I_, _SZ_ = (n); for(_I_ = 0; _I_ < _SZ_; _I_++) (x)[_I_] = 0;}  #define AZERO(x, n) {int _I_, _SZ_ = (n); for(_I_ = 0; _I_ < _SZ_; _I_++) (x)[_I_] = 0;}
101    
102    /* number of elements in one triangle of a square matrix of order n */
103    #define PACKED_LENGTH(n)   ((n) * ((n) + 1))/2
104    
105    /* duplicate the slot with name given by sym from src to dest */
106    
107    #define slot_dup(dest, src, sym)  SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
108    
109    /* is not yet used: */
110    #define slot_nonNull_dup(dest, src, sym)                        \
111        if(GET_SLOT(src, sym) != R_NilValue)                        \
112            SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
113    
114    /* TODO: Make this faster for the case where dimnames = list(NULL,NULL)
115     *       and hence don't have to be set ! */
116    #define SET_DimNames(dest, src) slot_dup(dest, src, Matrix_DimNamesSym)
117    
118    
119    #define uplo_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_uploSym), 0))
120    #define diag_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_diagSym), 0))
121    #define class_P(_x_) CHAR(asChar(getAttrib(_x_, R_ClassSymbol)))
122    
123    /* should also work for "matrix" matrices: */
124    #define Real_KIND(_x_)  (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
125                             (isReal(_x_) ? 0 : (isLogical(_x_) ? 1 : -1)))
126    /* This one gives '0' also for integer "matrix" :*/
127    #define Real_KIND2(_x_) (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
128                             (isLogical(_x_) ? 1 : 0))
129    
130    /* requires 'x' slot: */
131    #define Real_kind(_x_)  (isReal(GET_SLOT(_x_, Matrix_xSym)) ? 0 :       \
132                             (isLogical(GET_SLOT(_x_, Matrix_xSym)) ? 1 : -1))
133    
134    #define DECLARE_AND_GET_X_SLOT(__C_TYPE, __SEXP)        \
135        __C_TYPE *xx = __SEXP(GET_SLOT(x, Matrix_xSym))
136    
137    
138    /**
139     * Check for valid length of a packed triangular array and return the
140     * corresponding number of columns
141     *
142     * @param len length of a packed triangular array
143     *
144     * @return number of columns
145     */
146    static R_INLINE
147    int packed_ncol(int len)
148    {
149        int disc = 8 * len + 1;     /* discriminant */
150        int sqrtd = (int) sqrt((double) disc);
151    
152        if (len < 0 || disc != sqrtd * sqrtd)
153            error(_("invalid 'len' = %d in packed_ncol"));
154        return (sqrtd - 1)/2;
155    }
156    
157    /**
158     * Allocate an SEXP of given type and length, assign it as slot nm in
159     * the object, and return the SEXP.  The validity of this function
160     * depends on SET_SLOT not duplicating val when NAMED(val) == 0.  If
161     * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by
162     * GET_SLOT to ensure that the value returned is indeed the SEXP in
163     * the slot.
164     * NOTE:  GET_SLOT(x, what)        :== R_do_slot       (x, what)
165     * ----   SET_SLOT(x, what, value) :== R_do_slot_assign(x, what, value)
166     * and the R_do_slot* are in src/main/attrib.c
167     *
168     * @param obj object in which to assign the slot
169     * @param nm name of the slot, as an R name object
170     * @param type type of SEXP to allocate
171     * @param length length of SEXP to allocate
172     *
173     * @return SEXP of given type and length assigned as slot nm in obj
174     */
175    static R_INLINE
176    SEXP ALLOC_SLOT(SEXP obj, SEXP nm, SEXPTYPE type, int length)
177    {
178        SEXP val = allocVector(type, length);
179    
180        SET_SLOT(obj, nm, val);
181        return val;
182    }
183    
184    /**
185     * Expand compressed pointers in the array mp into a full set of indices
186     * in the array mj.
187     *
188     * @param ncol number of columns (or rows)
189     * @param mp column pointer vector of length ncol + 1
190     * @param mj vector of length mp[ncol] to hold the result
191     *
192     * @return mj
193     */
194    static R_INLINE
195    int* expand_cmprPt(int ncol, const int mp[], int mj[])
196    {
197        int j;
198        for (j = 0; j < ncol; j++) {
199            int j2 = mp[j+1], jj;
200            for (jj = mp[j]; jj < j2; jj++) mj[jj] = j;
201        }
202        return mj;
203    }
204    
205    /**
206     * Check if slot(obj, "x") contains any NA (or NaN).
207     *
208     * @param obj   a 'Matrix' object with an 'x' slot.
209     *
210     * @return Rboolean :== any(is.na(slot(obj, "x") )
211     */
212    static R_INLINE
213    Rboolean any_NA(SEXP obj)
214    {
215        double *x = REAL(GET_SLOT(obj, Matrix_xSym));
216        int i, n = LENGTH(GET_SLOT(obj, Matrix_xSym));
217        for(i=0; i < n; i++)
218            if(ISNAN(x[i])) return TRUE;
219        /* else */
220        return FALSE;
221    }
222    
223    
224    void make_d_matrix_triangular(double *x, SEXP from);
225    void make_i_matrix_triangular(   int *x, SEXP from);
226    
227    void make_d_matrix_symmetric(double *to, SEXP from);
228    void make_i_matrix_symmetric(   int *to, SEXP from);
229    
230    SEXP Matrix_expand_pointers(SEXP pP);
231    
232    SEXP dup_mMatrix_as_dgeMatrix(SEXP A);
233    SEXP dup_mMatrix_as_geMatrix (SEXP A);
234    
235    SEXP new_dgeMatrix(int nrow, int ncol);
236    SEXP m_encodeInd (SEXP ij, SEXP di);
237    SEXP m_encodeInd2(SEXP i, SEXP j, SEXP di);
238    
239    
240    static R_INLINE SEXP
241    mMatrix_as_dgeMatrix(SEXP A)
242    {
243        return strcmp(class_P(A), "dgeMatrix") ? dup_mMatrix_as_dgeMatrix(A) : A;
244    }
245    
246    static R_INLINE SEXP
247    mMatrix_as_geMatrix(SEXP A)
248    {
249        return strcmp(class_P(A) + 1, "geMatrix") ? dup_mMatrix_as_geMatrix(A) : A;
250    }
251    
252    /**
253     * Return the 0-based index of a string match in a vector of strings
254     * terminated by an empty string.  Returns -1 for no match.
255     *
256     * @param class string to match
257     * @param valid vector of possible matches terminated by an empty string
258     *
259     * @return index of match or -1 for no match
260     */
261    static R_INLINE int
262    Matrix_check_class(const char *class, char **valid)
263    {
264        int ans;
265        for (ans = 0; ; ans++) {
266            if (!strlen(valid[ans])) return -1;
267            if (!strcmp(class, valid[ans])) return ans;
268        }
269    }
270    
271    
272    #ifdef __cplusplus
273    }
274  #endif  #endif
275    
276    #endif /* MATRIX_MUTILS_H_ */

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