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[matrix] Diff of /pkg/src/Csparse.c
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Diff of /pkg/src/Csparse.c

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revision 1366, Sat Aug 12 17:31:39 2006 UTC revision 2125, Fri Mar 7 07:58:26 2008 UTC
# Line 1  Line 1 
1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2  #include "Csparse.h"  #include "Csparse.h"
3    #include "Tsparse.h"
4  #include "chm_common.h"  #include "chm_common.h"
5    
6  SEXP Csparse_validate(SEXP x)  SEXP Csparse_validate(SEXP x)
7  {  {
8        /* NB: we do *NOT* check a potential 'x' slot here, at all */
9      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
10          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
11      int j, ncol = length(pslot) - 1,      Rboolean sorted, strictly;
12        int j, k,
13          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
14          nrow, *xp = INTEGER(pslot),          nrow = dims[0],
15            ncol = dims[1],
16            *xp = INTEGER(pslot),
17          *xi = INTEGER(islot);          *xi = INTEGER(islot);
18    
19      nrow = dims[0];      if (length(pslot) != dims[1] + 1)
20      if (length(pslot) <= 0)          return mkString(_("slot p must have length = ncol(.) + 1"));
         return mkString(_("slot p must have length > 0"));  
21      if (xp[0] != 0)      if (xp[0] != 0)
22          return mkString(_("first element of slot p must be zero"));          return mkString(_("first element of slot p must be zero"));
23      if (length(islot) != xp[ncol])      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24          return mkString(_("last element of slot p must match length of slots i and x"));          return
25                mkString(_("last element of slot p must match length of slots i and x"));
26        for (j = 0; j < length(islot); j++) {
27            if (xi[j] < 0 || xi[j] >= nrow)
28                return mkString(_("all row indices must be between 0 and nrow-1"));
29        }
30        sorted = TRUE; strictly = TRUE;
31      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
32          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
33              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
34            if(sorted)
35                for (k = xp[j] + 1; k < xp[j + 1]; k++) {
36                    if (xi[k] < xi[k - 1])
37                        sorted = FALSE;
38                    else if (xi[k] == xi[k - 1])
39                        strictly = FALSE;
40      }      }
41      for (j = 0; j < length(islot); j++) {      }
42          if (xi[j] < 0 || xi[j] >= nrow)      if (!sorted) {
43              return mkString(_("all row indices must be between 0 and nrow-1"));          CHM_SP chx = AS_CHM_SP(x);
44            R_CheckStack();
45    
46            cholmod_sort(chx, &c);
47            /* Now re-check that row indices are *strictly* increasing
48             * (and not just increasing) within each column : */
49            for (j = 0; j < ncol; j++) {
50                for (k = xp[j] + 1; k < xp[j + 1]; k++)
51                    if (xi[k] == xi[k - 1])
52                        return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));
53            }
54    
55        } else if(!strictly) {  /* sorted, but not strictly */
56            return mkString(_("slot i is not *strictly* increasing inside a column"));
57      }      }
58      return ScalarLogical(1);      return ScalarLogical(1);
59  }  }
60    
61  SEXP Csparse_to_dense(SEXP x)  SEXP Rsparse_validate(SEXP x)
62  {  {
63      cholmod_sparse *chxs = as_cholmod_sparse(x);      /* NB: we do *NOT* check a potential 'x' slot here, at all */
64      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      SEXP pslot = GET_SLOT(x, Matrix_pSym),
65            jslot = GET_SLOT(x, Matrix_jSym);
66        Rboolean sorted, strictly;
67        int i, k,
68            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
69            nrow = dims[0],
70            ncol = dims[1],
71            *xp = INTEGER(pslot),
72            *xj = INTEGER(jslot);
73    
74      Free(chxs);      if (length(pslot) != dims[0] + 1)
75      return chm_dense_to_SEXP(chxd, 1);          return mkString(_("slot p must have length = nrow(.) + 1"));
76        if (xp[0] != 0)
77            return mkString(_("first element of slot p must be zero"));
78        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
79            return
80                mkString(_("last element of slot p must match length of slots j and x"));
81        for (i = 0; i < length(jslot); i++) {
82            if (xj[i] < 0 || xj[i] >= ncol)
83                return mkString(_("all column indices must be between 0 and ncol-1"));
84        }
85        sorted = TRUE; strictly = TRUE;
86        for (i = 0; i < nrow; i++) {
87            if (xp[i] > xp[i+1])
88                return mkString(_("slot p must be non-decreasing"));
89            if(sorted)
90                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
91                    if (xj[k] < xj[k - 1])
92                        sorted = FALSE;
93                    else if (xj[k] == xj[k - 1])
94                        strictly = FALSE;
95                }
96        }
97        if (!sorted)
98            /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
99            return mkString(_("slot j is not increasing inside a column"));
100        else if(!strictly) /* sorted, but not strictly */
101            return mkString(_("slot j is not *strictly* increasing inside a column"));
102    
103        return ScalarLogical(1);
104  }  }
105    
 SEXP Csparse_to_matrix(SEXP x)  
 {  
     cholmod_sparse *chxs = as_cholmod_sparse(x);  
     cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);  
106    
107      Free(chxs);  /* Called from ../R/Csparse.R : */
108      return chm_dense_to_matrix(chxd, 1,  /* Can only return [dln]geMatrix (no symm/triang);
109     * FIXME: replace by non-CHOLMOD code ! */
110    SEXP Csparse_to_dense(SEXP x)
111    {
112        CHM_SP chxs = AS_CHM_SP(x);
113        /* This loses the symmetry property, since cholmod_dense has none,
114         * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
115         * to numeric (CHOLMOD_REAL) ones : */
116        CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
117        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
118        R_CheckStack();
119    
120        return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
121    }
122    
123    SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
124    {
125        CHM_SP chxs = AS_CHM_SP(x);
126        CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
127        int tr = asLogical(tri);
128        R_CheckStack();
129    
130        return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
131                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
132                                  0, tr ? diag_P(x) : "",
133                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
134  }  }
135    
136    SEXP Csparse_to_matrix(SEXP x)
137    {
138        return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),
139                                   1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
140    }
141    
142  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
143  {  {
144      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP(x);
145      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
146      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
147        int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
148        R_CheckStack();
149    
150        return chm_triplet_to_SEXP(chxt, 1,
151                                   tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
152                                   Rkind, tr ? diag_P(x) : "",
153                                   GET_SLOT(x, Matrix_DimNamesSym));
154    }
155    
156      Free(chxs);  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
157      if (asLogical(tri)) {       /* triangular sparse matrices */  SEXP Csparse_symmetric_to_general(SEXP x)
158          uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?  {
159              -1 : 1;      CHM_SP chx = AS_CHM_SP(x), chgx;
160          diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
161        R_CheckStack();
162    
163        if (!(chx->stype))
164            error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
165        chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
166        /* xtype: pattern, "real", complex or .. */
167        return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
168                                  GET_SLOT(x, Matrix_DimNamesSym));
169      }      }
170      return chm_triplet_to_SEXP(chxt, 1, uploT, diag,  
171                                 duplicate(GET_SLOT(x, Matrix_DimNamesSym)));  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
172    {
173        CHM_SP chx = AS_CHM_SP(x), chgx;
174        int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
175        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
176        R_CheckStack();
177    
178        chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
179        /* xtype: pattern, "real", complex or .. */
180        return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
181                                  GET_SLOT(x, Matrix_DimNamesSym));
182  }  }
183    
184  SEXP Csparse_transpose(SEXP x)  SEXP Csparse_transpose(SEXP x, SEXP tri)
185  {  {
186      cholmod_sparse *chx = as_cholmod_sparse(x);      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
187      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);       *       since cholmod (& cs) lacks sparse 'int' matrices */
188        CHM_SP chx = AS_CHM_SP(x);
189        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
190        CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
191      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
192        int tr = asLogical(tri);
193        R_CheckStack();
194    
     Free(chx);  
195      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
196      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
197      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
198      UNPROTECT(1);      UNPROTECT(1);
199      return chm_sparse_to_SEXP(chxt, 1, 0, "", dn);      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
200                                  tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
201                                  Rkind, tr ? diag_P(x) : "", dn);
202  }  }
203    
204  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
205  {  {
206      cholmod_sparse *cha = as_cholmod_sparse(a),      CHM_SP
207          *chb = as_cholmod_sparse(b);          cha = AS_CHM_SP(Csparse_diagU2N(a)),
208      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          chb = AS_CHM_SP(Csparse_diagU2N(b)),
209            chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
210                                 cha->xtype, /*out sorted:*/ 1, &c);
211        const char *cl_a = class_P(a), *cl_b = class_P(b);
212        char diag[] = {'\0', '\0'};
213        int uploT = 0;
214      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
215        R_CheckStack();
216    
217      Free(cha); Free(chb);      /* Preserve triangularity and even unit-triangularity if appropriate.
218         * Note that in that case, the multiplication itself should happen
219         * faster.  But there's no support for that in CHOLMOD */
220    
221        /* UGLY hack -- rather should have (fast!) C-level version of
222         *       is(a, "triangularMatrix") etc */
223        if (cl_a[1] == 't' && cl_b[1] == 't')
224            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
225            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
226                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
227                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
228                    /* "remove the diagonal entries": */
229                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
230                    diag[0]= 'U';
231                }
232                else diag[0]= 'N';
233            }
234      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
235                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
236      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
237                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
238      return chm_sparse_to_SEXP(chc, 1, 0, "", dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
239    }
240    
241    SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
242    {
243        int tr = asLogical(trans);
244        CHM_SP
245            cha = AS_CHM_SP(Csparse_diagU2N(a)),
246            chb = AS_CHM_SP(Csparse_diagU2N(b)),
247            chTr, chc;
248        const char *cl_a = class_P(a), *cl_b = class_P(b);
249        char diag[] = {'\0', '\0'};
250        int uploT = 0;
251        SEXP dn = allocVector(VECSXP, 2);
252        R_CheckStack();
253    
254        chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
255        chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
256                             /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
257        cholmod_free_sparse(&chTr, &c);
258    
259        /* Preserve triangularity and unit-triangularity if appropriate;
260         * see Csparse_Csparse_prod() for comments */
261        if (cl_a[1] == 't' && cl_b[1] == 't')
262            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
263                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
264                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
265                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
266                    diag[0]= 'U';
267                }
268                else diag[0]= 'N';
269            }
270    
271        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
272                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
273        SET_VECTOR_ELT(dn, 1,
274                       duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
275        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
276  }  }
277    
278  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
279  {  {
280      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));
281      cholmod_dense *chb = as_cholmod_dense(b);      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
282      cholmod_dense *chc = cholmod_allocate_dense(cha->nrow, chb->ncol,      CHM_DN chb = AS_CHM_DN(b_M);
283                                                  cha->nrow, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
284      double alpha = 1, beta = 0;                                          chb->xtype, &c);
285        SEXP dn = PROTECT(allocVector(VECSXP, 2));
286      cholmod_sdmult(cha, 0, &alpha, &beta, chb, chc, &c);      double one[] = {1,0}, zero[] = {0,0};
287      Free(cha); Free(chb);      R_CheckStack();
288      return chm_dense_to_SEXP(chc, 1);  
289        cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
290        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
291                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
292        SET_VECTOR_ELT(dn, 1,
293                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
294        UNPROTECT(2);
295        return chm_dense_to_SEXP(chc, 1, 0, dn);
296  }  }
297    
298  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
299  {  {
300      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));
301      cholmod_dense *chb = as_cholmod_dense(b);      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
302      cholmod_dense *chc = cholmod_allocate_dense(cha->ncol, chb->ncol,      CHM_DN chb = AS_CHM_DN(b_M);
303                                                  cha->ncol, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
304      double alpha = 1, beta = 0;                                          chb->xtype, &c);
305        SEXP dn = PROTECT(allocVector(VECSXP, 2));
306      cholmod_sdmult(cha, 1, &alpha, &beta, chb, chc, &c);      double one[] = {1,0}, zero[] = {0,0};
307      Free(cha); Free(chb);      R_CheckStack();
308      return chm_dense_to_SEXP(chc, 1);  
309        cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
310        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
311                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
312        SET_VECTOR_ELT(dn, 1,
313                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
314        UNPROTECT(2);
315        return chm_dense_to_SEXP(chc, 1, 0, dn);
316  }  }
317    
318    /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
319       see Csparse_Csparse_crossprod above for  x'y and x y' */
320  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
321  {  {
322      int trip = asLogical(triplet),      int trip = asLogical(triplet),
323          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
324      cholmod_triplet      CHM_TR cht = trip ? AS_CHM_TR(Tsparse_diagU2N(x)) : (CHM_TR) NULL;
325          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_SP chcp, chxt,
326      cholmod_sparse *chcp, *chxt,          chx = (trip ?
327          *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
328          : as_cholmod_sparse(x);                 AS_CHM_SP(Csparse_diagU2N(x)));
329      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
330        R_CheckStack();
331    
332      if (!tr)      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
         chxt = cholmod_transpose(chx, chx->xtype, &c);  
333      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
334      if(!chcp)      if(!chcp) {
335          error("Csparse_crossprod(): error return from cholmod_aat()");          UNPROTECT(1);
336            error(_("Csparse_crossprod(): error return from cholmod_aat()"));
337        }
338      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
339      chcp->stype = 1;      chcp->stype = 1;
340      if (trip) {      if (trip) cholmod_free_sparse(&chx, &c);
         cholmod_free_sparse(&chx, &c);  
         Free(cht);  
     } else {  
         Free(chx);  
     }  
341      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
342                                  /* create dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
     SET_VECTOR_ELT(dn, 0,  
343                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
344                                          (tr) ? 1 : 0)));                                          (tr) ? 0 : 1)));
345      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
346      UNPROTECT(1);      UNPROTECT(1);
347      return chm_sparse_to_SEXP(chcp, 1, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
348    }
349    
350    SEXP Csparse_drop(SEXP x, SEXP tol)
351    {
352        CHM_SP chx = AS_CHM_SP(x);
353        CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
354        double dtol = asReal(tol);
355        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
356        R_CheckStack();
357    
358        if(!cholmod_drop(dtol, ans, &c))
359            error(_("cholmod_drop() failed"));
360        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
361                                  GET_SLOT(x, Matrix_DimNamesSym));
362  }  }
363    
364  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
365  {  {
366      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);
367          *chy = as_cholmod_sparse(y), *ans;      int Rkind = 0; /* only for "d" - FIXME */
368        R_CheckStack();
369    
     ans = cholmod_horzcat(chx, chy, 1, &c);  
     Free(chx); Free(chy);  
370      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
371      return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
372                                  1, 0, Rkind, "", R_NilValue);
373  }  }
374    
375  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
376  {  {
377      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);
378          *chy = as_cholmod_sparse(y), *ans;      int Rkind = 0; /* only for "d" - FIXME */
379        R_CheckStack();
380    
     ans = cholmod_vertcat(chx, chy, 1, &c);  
     Free(chx); Free(chy);  
381      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
382      return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
383                                  1, 0, Rkind, "", R_NilValue);
384  }  }
385    
386  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
387  {  {
388      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      CHM_SP chx = AS_CHM_SP(x);
389        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
390        CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
391        R_CheckStack();
392    
393      ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
394      Free(chx);                                GET_SLOT(x, Matrix_DimNamesSym));
     return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);  
395  }  }
396    
397  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
398  {  {
399      cholmod_sparse *chx = as_cholmod_sparse(x);      const char *cl = class_P(x);
400      cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
401        if (cl[1] != 't' || *diag_P(x) != 'U') {
402            /* "trivially fast" when not triangular (<==> no 'diag' slot),
403               or not *unit* triangular */
404            return (x);
405        }
406        else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
407            CHM_SP chx = AS_CHM_SP(x);
408            CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
409      double one[] = {1, 0};      double one[] = {1, 0};
410      cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
411      int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
412          -1 : 1;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
413    
414      Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
415      return chm_sparse_to_SEXP(ans, 1, uploT, "N",          cholmod_free_sparse(&eye, &c);
416                                duplicate(GET_SLOT(x, Matrix_DimNamesSym)));          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
417                                      GET_SLOT(x, Matrix_DimNamesSym));
418        }
419    }
420    
421    SEXP Csparse_diagN2U(SEXP x)
422    {
423        const char *cl = class_P(x);
424        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
425        if (cl[1] != 't' || *diag_P(x) != 'N') {
426            /* "trivially fast" when not triangular (<==> no 'diag' slot),
427               or already *unit* triangular */
428            return (x);
429        }
430        else { /* triangular with diag='N'): now drop the diagonal */
431            /* duplicate, since chx will be modified: */
432            CHM_SP chx = AS_CHM_SP(duplicate(x));
433            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
434                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
435            R_CheckStack();
436    
437            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
438    
439            return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
440                                      uploT, Rkind, "U",
441                                      GET_SLOT(x, Matrix_DimNamesSym));
442        }
443  }  }
444    
445  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
446  {  {
447      cholmod_sparse *chx = as_cholmod_sparse(x);      CHM_SP chx = AS_CHM_SP(x);
448      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
449          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
450        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
451        R_CheckStack();
452    
453      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
454          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
455      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
456          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
457    
458      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
459                                                  INTEGER(j), csize,                                                  INTEGER(j), csize,
460                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
461                                1, 0, "", R_NilValue);                                1, 0, Rkind, "",
462                                  /* FIXME: drops dimnames */ R_NilValue);
463    }
464    
465    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
466    {
467        FILE *f = fopen(CHAR(asChar(fname)), "w");
468    
469        if (!f)
470            error(_("failure to open file \"%s\" for writing"),
471                  CHAR(asChar(fname)));
472        if (!cholmod_write_sparse(f, AS_CHM_SP(Csparse_diagU2N(x)),
473                                  (CHM_SP)NULL, (char*) NULL, &c))
474            error(_("cholmod_write_sparse returned error code"));
475        fclose(f);
476        return R_NilValue;
477  }  }

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