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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 1507, Mon Sep 4 18:41:34 2006 UTC revision 2175, Wed Apr 23 11:23:50 2008 UTC
# Line 5  Line 5 
5  extern "C" {  extern "C" {
6  #endif  #endif
7    
8  #include <Rdefines.h> /* Rinternals.h + GET_SLOT etc */  #include <ctype.h>
9  #include <R.h>  /* includes Rconfig.h */  #include <R.h>  /* includes Rconfig.h */
10    #include <Rversion.h>
11    #include <Rdefines.h> /* Rinternals.h + GET_SLOT etc */
12    
13  #ifdef ENABLE_NLS  #ifdef ENABLE_NLS
14  #include <libintl.h>  #include <libintl.h>
# Line 15  Line 17 
17  #define _(String) (String)  #define _(String) (String)
18  #endif  #endif
19    
20    #ifdef __GNUC__
21    # undef alloca
22    # define alloca(x) __builtin_alloca((x))
23    #else
24    /* this is necessary (and sufficient) for Solaris 10: */
25    #ifdef __sun
26    # include <alloca.h>
27    #endif
28    #endif
29    
30    #define Alloca(n, t)   (t *) alloca( (size_t) ( (n) * sizeof(t) ) )
31    
32  SEXP triangularMatrix_validate(SEXP obj);  SEXP triangularMatrix_validate(SEXP obj);
33  SEXP symmetricMatrix_validate(SEXP obj);  SEXP symmetricMatrix_validate(SEXP obj);
34  SEXP dense_nonpacked_validate(SEXP obj);  SEXP dense_nonpacked_validate(SEXP obj);
# Line 37  Line 51 
51  #define LFT CblasLeft  #define LFT CblasLeft
52  #define RGT CblasRight  #define RGT CblasRight
53    
54  char norm_type(char *typstr);  #if !defined(R_VERSION) || R_VERSION < R_Version(2, 7, 0)
55  char rcond_type(char *typstr);  char La_norm_type(const char *typstr);
56    char La_rcond_type(const char *typstr);
57    #endif
58    
59  double get_double_by_name(SEXP obj, char *nm);  double get_double_by_name(SEXP obj, char *nm);
60  SEXP set_double_by_name(SEXP obj, double val, char *nm);  SEXP set_double_by_name(SEXP obj, double val, char *nm);
61  SEXP as_det_obj(double val, int log, int sign);  SEXP as_det_obj(double val, int log, int sign);
62  SEXP get_factors(SEXP obj, char *nm);  SEXP get_factors(SEXP obj, char *nm);
63  SEXP set_factors(SEXP obj, SEXP val, char *nm);  SEXP set_factors(SEXP obj, SEXP val, char *nm);
64    
65    #if 0
66  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);
67  char uplo_value(SEXP x);  #endif  /* unused */
 char diag_value(SEXP x);  
68    
69  int csc_unsorted_columns(int ncol, const int p[], const int i[]);  /* int csc_unsorted_columns(int ncol, const int p[], const int i[]); */
70  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[]); */
71  SEXP csc_check_column_sorting(SEXP A);  /* SEXP csc_check_column_sorting(SEXP A); */
72  SEXP Matrix_make_named(int TYP, char **names);  SEXP Matrix_make_named(int TYP, char **names);
73  SEXP check_scalar_string(SEXP sP, char *vals, char *nm);  SEXP check_scalar_string(SEXP sP, char *vals, char *nm);
74  double *packed_getDiag(double *dest, SEXP x);  Rboolean equal_string_vectors(SEXP s1, SEXP s2);
75    
76    void d_packed_getDiag(double *dest, SEXP x, int n);
77    void l_packed_getDiag(   int *dest, SEXP x, int n);
78    void tr_d_packed_getDiag(double *dest, SEXP x);
79    void tr_l_packed_getDiag(   int *dest, SEXP x);
80    
81  SEXP Matrix_getElement(SEXP list, char *nm);  SEXP Matrix_getElement(SEXP list, char *nm);
82    
83  #define PACKED_TO_FULL(TYPE)                                            \  #define PACKED_TO_FULL(TYPE)                                            \
# Line 81  Line 105 
105  #define PACKED_LENGTH(n)   ((n) * ((n) + 1))/2  #define PACKED_LENGTH(n)   ((n) * ((n) + 1))/2
106    
107  /* duplicate the slot with name given by sym from src to dest */  /* duplicate the slot with name given by sym from src to dest */
108    
109  #define slot_dup(dest, src, sym)  SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))  #define slot_dup(dest, src, sym)  SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
110    
111    /* is not yet used: */
112    #define slot_nonNull_dup(dest, src, sym)                        \
113        if(GET_SLOT(src, sym) != R_NilValue)                        \
114            SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
115    
116    /* TODO: Make this faster for the case where dimnames = list(NULL,NULL)
117     *       and hence don't have to be set ! */
118    #define SET_DimNames(dest, src) slot_dup(dest, src, Matrix_DimNamesSym)
119    
120    
121  #define uplo_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_uploSym), 0))  #define uplo_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_uploSym), 0))
122  #define diag_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_diagSym), 0))  #define diag_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_diagSym), 0))
123  #define class_P(_x_) CHAR(asChar(getAttrib(_x_, R_ClassSymbol)))  #define class_P(_x_) CHAR(asChar(getAttrib(_x_, R_ClassSymbol)))
124    
125    /* should also work for "matrix" matrices: */
126    #define Real_KIND(_x_)  (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
127                             (isReal(_x_) ? 0 : (isLogical(_x_) ? 1 : -1)))
128    /* This one gives '0' also for integer "matrix" :*/
129    #define Real_KIND2(_x_) (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
130                             (isLogical(_x_) ? 1 : 0))
131    
132    /* requires 'x' slot: */
133    #define Real_kind(_x_)  (isReal(GET_SLOT(_x_, Matrix_xSym)) ? 0 :       \
134                             (isLogical(GET_SLOT(_x_, Matrix_xSym)) ? 1 : -1))
135    
136    #define DECLARE_AND_GET_X_SLOT(__C_TYPE, __SEXP)        \
137        __C_TYPE *xx = __SEXP(GET_SLOT(x, Matrix_xSym))
138    
139    
140  /**  /**
141   * Check for valid length of a packed triangular array and return the   * Check for valid length of a packed triangular array and return the
142   * corresponding number of columns   * corresponding number of columns
# Line 113  Line 163 
163   * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by   * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by
164   * GET_SLOT to ensure that the value returned is indeed the SEXP in   * GET_SLOT to ensure that the value returned is indeed the SEXP in
165   * the slot.   * the slot.
166     * NOTE:  GET_SLOT(x, what)        :== R_do_slot       (x, what)
167     * ----   SET_SLOT(x, what, value) :== R_do_slot_assign(x, what, value)
168     * and the R_do_slot* are in src/main/attrib.c
169   *   *
170   * @param obj object in which to assign the slot   * @param obj object in which to assign the slot
171   * @param nm name of the slot, as an R name object   * @param nm name of the slot, as an R name object
# Line 151  Line 204 
204      return mj;      return mj;
205  }  }
206    
   
207  /**  /**
208   * Return the linear index of the (row, col) entry in a csc structure.   * Check if  obj@x  contains any NA (or NaN).
  * If the entry is not found and missing is 0 an error is signaled;  
  * otherwise the missing value is returned.  
209   *   *
210   * @param p vector of column pointers   * @param obj   a 'Matrix' object with an 'x' slot.
  * @param i vector of row indices  
  * @param row row index  
  * @param col column index  
  * @param missing the value to return is the row, col entry does not  
  * exist.  If this is zero and the row, col entry does not exist an  
  * error is signaled.  
211   *   *
212   * @return index of element at (row, col) if it exists, otherwise missing   * @return Rboolean :== any(is.na( obj @ x) )
  */  
 static R_INLINE int  
 check_csc_index(const int p[], const int i[], int row, int col, int missing)  
 {  
     int k, k2 = p[col + 1];  
                                 /* linear search - perhaps replace by bsearch */  
     for (k = p[col]; k < k2; k++) if (i[k] == row) return k;  
     if (!missing)  
         error("row %d and column %d not defined in rowind and colptr",  
               row, col);  
     return missing;  
 }  
   
 /**  
  * Calculate the zero-based index in a row-wise packed lower triangular matrix.  
  * This is used for the arrays of blocked sparse matrices.  
  *  
  * @param i column number (zero-based)  
  * @param k row number (zero-based)  
  *  
  * @return The index of the (k,i) element of a packed lower triangular matrix  
213   */   */
214  static R_INLINE  static R_INLINE
215  int Lind(int k, int i)  Rboolean any_NA(SEXP obj)
216  {  {
217      if (k < i) error("Lind(k = %d, i = %d) must have k >= i", k, i);      double *x = REAL(GET_SLOT(obj, Matrix_xSym));
218      return (k * (k + 1))/2 + i;      int i, n = LENGTH(GET_SLOT(obj, Matrix_xSym));
219        for(i=0; i < n; i++)
220            if(ISNAN(x[i])) return TRUE;
221        /* else */
222        return FALSE;
223  }  }
224    
 double *expand_csc_column(double *dest, int m, int j,  
                           const int Ap[], const int Ai[], const double Ax[]);  
   
 /**  
  * Apply a permutation to an integer vector  
  *  
  * @param i vector of 0-based indices  
  * @param n length of vector i  
  * @param perm 0-based permutation vector of length max(i) + 1  
  */  
 static R_INLINE void  
 int_permute(int i[], int n, const int perm[])  
 {  
     int j;  
     for (j = 0; j < n; j++) i[j] = perm[i[j]];  
 }  
   
 /**  
  * Force index pairs to be in the upper triangle of a matrix  
  *  
  * @param i vector of 0-based row indices  
  * @param j vector of 0-based column indices  
  * @param nnz length of index vectors  
  */  
 static R_INLINE void  
 make_upper_triangular(int i[], int j[], int nnz)  
 {  
     int k;  
     for (k = 0; k < nnz; k++) {  
         if (i[k] > j[k]) {  
             int tmp = i[k];  
             i[k] = j[k];  
             j[k] = tmp;  
         }  
     }  
 }  
225    
226  void make_d_matrix_triangular(double *x, SEXP from);  void make_d_matrix_triangular(double *x, SEXP from);
227  void make_i_matrix_triangular(   int *x, SEXP from);  void make_i_matrix_triangular(   int *x, SEXP from);
# Line 240  Line 231 
231    
232  SEXP Matrix_expand_pointers(SEXP pP);  SEXP Matrix_expand_pointers(SEXP pP);
233    
   
 /**  
  * Elementwise increment dest by src  
  *  
  * @param dest vector to be incremented  
  * @param src vector to be added to dest  
  * @param n length of vectors  
  *  
  * @return dest  
  */  
 static R_INLINE double*  
 vecIncrement(double dest[], const double src[], int n) {  
     int i;  
     for (i = 0; i < n; i++) dest[i] += src[i];  
     return dest;  
 }  
   
 /**  
  * Elementwise sum of src1 and src2 into dest  
  *  
  * @param dest vector to be incremented  
  * @param src1 vector to be added  
  * @param src1 second vector to be added  
  * @param n length of vectors  
  *  
  * @return dest  
  */  
 static R_INLINE double*  
 vecSum(double dest[], const double src1[], const double src2[],  
        int n) {  
     int i;  
     for (i = 0; i < n; i++) dest[i] = src1[i] + src2[i];  
     return dest;  
 }  
   
 SEXP alloc_dgeMatrix(int m, int n, SEXP rownms, SEXP colnms);  
 SEXP alloc_dpoMatrix(int n, char *uplo, SEXP rownms, SEXP colnms);  
 SEXP alloc_dtrMatrix(int n, char *uplo, char *diag, SEXP rownms, SEXP colnms);  
 SEXP alloc_dsCMatrix(int n, int nz, char *uplo, SEXP rownms, SEXP colnms);  
   
234  SEXP dup_mMatrix_as_dgeMatrix(SEXP A);  SEXP dup_mMatrix_as_dgeMatrix(SEXP A);
235    SEXP dup_mMatrix_as_geMatrix (SEXP A);
236    
237    SEXP new_dgeMatrix(int nrow, int ncol);
238    
239  static R_INLINE SEXP  static R_INLINE SEXP
240  mMatrix_as_dgeMatrix(SEXP A)  mMatrix_as_dgeMatrix(SEXP A)
# Line 288  Line 242 
242      return strcmp(class_P(A), "dgeMatrix") ? dup_mMatrix_as_dgeMatrix(A) : A;      return strcmp(class_P(A), "dgeMatrix") ? dup_mMatrix_as_dgeMatrix(A) : A;
243  }  }
244    
245    static R_INLINE SEXP
246    mMatrix_as_geMatrix(SEXP A)
247    {
248        return strcmp(class_P(A) + 1, "geMatrix") ? dup_mMatrix_as_geMatrix(A) : A;
249    }
250    
251  /**  /**
252   * Return the 0-based index of a string match in a vector of strings   * Return the 0-based index of a string match in a vector of strings
253   * terminated by an empty string.  Returns -1 for no match.   * terminated by an empty string.  Returns -1 for no match.
254   *   *
255   * @param dest class string to match   * @param class string to match
256   * @param valid vector of possible matches terminated by an empty string   * @param valid vector of possible matches terminated by an empty string
257   *   *
258   * @return index of match or -1 for no match   * @return index of match or -1 for no match
259   */   */
260  static R_INLINE int  static R_INLINE int
261  Matrix_check_class(char *class, char **valid)  Matrix_check_class(const char *class, char **valid)
262  {  {
263      int ans;      int ans;
264      for (ans = 0; ; ans++) {      for (ans = 0; ; ans++) {

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