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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1765, Mon Feb 5 16:32:04 2007 UTC
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1    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
4    
5    
6    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * DESCRIPTION (Version): 0.9975-10 to upload
9    
10            * tests/Class+Meth.R (tstMatrixClass): require coercions to
11            specific classes less unconditionally.
12    
13            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
14    
15            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
16    
17            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
18            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
19            R_to_CMatrix segfaults on one platform.
20            Eliminate most coercion method to *specific* classes, and replace
21            with virtual classes coercions.
22    
23    
24    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
25    
26            * src/init.c: export the CHM...._validate() placeholders, since
27            they *are* called.
28    
29            * tests/Class+Meth.R (classCanCoerce): and starting to test
30            all as(<from>, <to>)
31    
32    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
35            * tests/indexing.R: tested now
36            * tests/indexing.Rout.save: updated
37    
38            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
39            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
40            appropriate.
41    
42            * NAMESPACE: export a trivial
43            * R/Matrix.R: drop() Matrix-method
44    
45            * R/AllClass.R: moved all prototypes to virtual super classes.
46    
47            * R/Rsparse.R: many more coercions to have less exceptions in
48            * tests/Class+Meth.R:
49    
50            * R/Ops.R (Compare): tweak for case with NA
51            * tests/simpl.R: hence another 'FIXME' eliminated
52    
53    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
56            objects.
57    
58            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
59              and more of "!", "&", "|", all, any; coercions
60    
61            * R/Rsparse.R: many coercions (which enable quite a few other
62            methods), thanks to enhancements in
63            * src/dgCMatrix.c (R_to_CMatrix): new, and
64            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
65            symmetric & triangular and ..RMatrix objects.
66    
67            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
68            renamed file from src/dsTMatrix.c;
69            now dealing with symmetric and triangular Tsparse coercions, both
70            to dense and general.
71    
72    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
75    
76            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
77            where sensible when the <numeric> is of length > 1.
78    
79    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Matrix.R ([<-): for M[] <- value: fix length
82    
83    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
86            * R/ndenseMatrix.R: new coercions n* -> l*
87    
88    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
91    
92            * R/Ops.R ("Logic"): and other "Ops", many updates
93    
94    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * src/Mutils.h (SET_DimNames): new utility
97    
98            * R/Auxiliaries.R (nnzero): improved and now exported via
99    
100            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
101    
102    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/diagMatrix.R (!): fix typo.
105    
106    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/Auxiliaries.R (as_Csparse): and quite a few others:
109                    allow to pass class definition --> speedup
110            * R/sparseMatrix.R: apply the above
111    
112            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
113    
114            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
115            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
116            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
117    
118            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
119    
120            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
121            and use it for "sparse*" as well, since it's faster than the
122            as_Csparse(.) way.
123    
124    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
127    
128    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
131            as method for   M[ ij ] <- v
132            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
133    
134            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
135            FALSE answer
136    
137            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
138            * tests/indexing.R: test it, and some of the above
139    
140    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/Auxiliaries.R (is_duplicatedT): new utility
143    
144    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
145    
146            * src/init.c (R_init_Matrix): export cholmod_scale
147    
148    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
151            base::as.matrix to (x, ...)
152    
153    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
156            file; start using "Logic", hence
157    
158            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
159            * NAMESPACE: import and export "Logic"
160    
161    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
164            only needed previously to R version 2.5.0.
165    
166    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
169    
170            * R/Tsparse.R (replTmat): fix subassignment of triangular
171            * R/Csparse.R (replCmat): ditto
172            * tests/indexing.R: more tests, incl the above fix
173    
174    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/Auxiliaries.R (drop0): extend for non CSparse
177            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
178    
179            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
180                    use uplo correctly (!); other places: use uplo_P() macro
181    
182            * R/Csparse.R (replCmat): call diagU2N() when needed
183            * R/Tsparse.R (replTmat): ditto
184    
185            * src/dtCMatrix.c (tCMatrix_validate): new
186            * src/dtTMatrix.c (tTMatrix_validate): new, used in
187            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
188    
189            * R/diagMatrix.R (replDiag): to use in [<-
190    
191    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
194                    also more general diagU2N().
195    
196    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
199            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
200    
201    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * tests/bind.R: a few more cases
204            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
205    
206            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
207            * R/ddenseMatrix.R (cbind2/rbind2)
208            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
209            * tests/indexing.R
210            * tests/indexing.Rout.save: updated
211    
212    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
215            * tests/indexing.R
216    
217    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
220            align with proper position of "0", i.e., right for integers.
221            argument 'align' by default is "fancy".
222    
223    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
226            * R/Csparse.R: and fix "Compare" for more cases.
227            * tests/Class+Meth.R: test some of these (m == m, m != m)
228    
229    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/lsparseMatrix.R: all() and any() methods
232            * R/ldenseMatrix.R:      ditto
233            * NAMESPACE, R/Matrix.R: ditto
234    
235            * man/all-methods.Rd: document them minimally
236    
237            * tests/simple.R: add a few examples for these
238    
239    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/Tsparse.R ([): fix long standing typo in symmetric case
242            * man/dsCMatrix-class.Rd: add example exhibiting the above case
243    
244    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
245    
246            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
247            to LL before converting to a sparse matrix. (The LDL form can be
248            converted to a sparse matrix but it is implicitly a unit
249            triangular matrix and a diagonal matrix overwritten on the diagonal.)
250    
251    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
254    
255    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
256    
257            * DESCRIPTION (Version): updated -> release 0.9975-7
258            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
259    
260    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
263    
264    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
265    
266            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
267            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
268            is exactly singular.
269    
270    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * DESCRIPTION (Date): updated -> release 0.9975-6
273    
274    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
277            now returns symmetric.
278    
279            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
280    
281            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
282            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
283    
284            * R/Auxiliaries.R (.type.kind): added
285    
286    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
289            running src/CSparse_install.sh
290    
291            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
292    
293    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
296            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
297    
298            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
299    
300            * tests/Class+Meth.R (tstMatrixClass): now assure
301            the (important in method programming) property :
302    
303                    ###>>  Every "Matrix" is either
304                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
305    
306                    (where "*" stands for "Matrix")
307    
308            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
309    
310            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
311            * tests/validObj.R: checks for "comparison"
312    
313            * R/sparseMatrix.R ([): improved indexing for sparse;
314                    trying to keep <symmetric>[ n, n] symmmetric
315    
316            * tests/indexing.R: indexing for logical sparse now ok
317    
318    
319    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * src/Tsparse.c: use xTsparse_validate() , and hence remove
322    
323            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
324    
325    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
328    
329            * tests/simple.R: validObject() checking the above.
330    
331            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
332            replacing both dgCMatrix_validate and lgCM*.
333    
334            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
335            fix dimnames setting in other places.
336            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
337    
338    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
341    
342            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
343            symmetry test, via
344            * R/Auxiliaries.R (.as.dgC.0.factors):
345    
346    2006-11-01  Douglas Bates  <bates@r-project.org>
347    
348            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
349            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
350            <CsparseMatrix>) added
351    
352    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * tests/matprod.R: add a variation of Harri's example
355    
356            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
357            recursive infinitely.
358    
359            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
360    
361            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
362    
363    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
366            matrix if possible; test m+m == 2*m; now test dgRMatrix.
367            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
368            satisfy the above test.
369    
370    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
373    
374            * R/dgCMatrix.R: solve(a, b="missing") based on
375            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
376            RHS = NULL.
377    
378            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
379            add more (needed) [t]crossprod() methods.
380    
381            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
382    
383            * R/Auxiliaries.R (as_CspClass): cleanup
384            (drop0): internal utility for "Csparse_drop(*, 0)"
385            (.bail.out.2): encourage active feedback
386    
387    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dMatrix.R(Compare): new(), then slots [no validity check]
390    
391            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
392            non-valid or 'sorted' case).
393    
394            * R/dsparseMatrix.R: add "chol" method.
395            * R/ddenseMatrix.R: ditto
396    
397            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
398            * NAMESPACE (Ops)
399            * R/diagMatrix.R (diag2T): simple utility used "higher level"
400            coercion; deprecating direct lower level coercions.
401    
402            * R/*.R (seq): use seq_len() and seq_along() where possible.
403    
404    
405    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * DESCRIPTION (Version): 0.9975-5 ready for release
408    
409    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
410    
411            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
412    
413    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/AllClass.R (corMatrix): add 'validity' check;
416                    comment out unused "LDL" class definition
417            * NAMESPACE: mention, but do not export "LDL" class
418            * R/corMatrix.R: new (simple), needed for R-devel with
419            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
420              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
421    
422    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
423    
424            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
425            use Rprintf and R's error handling.
426    
427    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
430            * tests/matprod.R: add tests for the bug fixed.
431    
432    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
433    
434            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
435            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
436    
437    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
438    
439            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
440    
441    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * DESCRIPTION (Version): 0.9975-3
444    
445            * R/diagMatrix.R (bdiag): new function constructing block diagonal
446            (sparse) matrices.
447            * man/bdiag.Rd: docu + examples
448    
449            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
450    
451            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
452            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
453    
454            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
455            that result is sparse or diagonal (and not dense).
456    
457            * man/Subassign-methods.Rd: fix examples
458    
459            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
460            should always return a sparse (and not sometimes a diagonal) matrix.
461    
462    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
465    
466    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
467    
468            * DESCRIPTION (Version): 0.9975-2
469    
470            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
471    
472    2006-10-02  Douglas Bates  <bates@R-project.org>
473    
474            * tests/dg_Matrix.R: Simplify test taking into account new code.
475    
476    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
479    
480            * R/lsTMatrix.R: new files w/ missing methods
481            * R/nsTMatrix.R:  "  'for completeness'
482    
483            * tests/Class+Meth.R: a bit less 'not.ok.classes'
484    
485            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
486    
487    
488    2006-09-28  Douglas Bates  <bates@R-project.org>
489    
490            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
491            included.
492    
493            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
494            Export C-callable functions used in Zt_create in lme4.
495    
496    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * DESCRIPTION (Version): 0.9975-1
499    
500            * tests/simple.R: less checks fail; using NA, found that our
501                    kronecker() is not base-compatible with NA's.
502    
503            * R/dMatrix.R: "Compare" method now implemented for all cases
504    
505            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
506    
507            * man/dtpMatrix-class.Rd: mention length of 'x' slot
508    
509            * src/dtpMatrix.c (dtpMatrix_validate): fix check
510            * src/dspMatrix.c (dspMatrix_validate): ditto
511    
512            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
513              including coercion to [nl]tTMatrix.
514    
515            * R/diagMatrix.R (show): print a header line as for other classes.
516    
517    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * src/Makefile.win (SUBDIRS): fix typo
520    
521    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
524    
525    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
526    
527            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
528            symmetric and y missing in R code using %*% (cholmod_aat doesn't
529            accept a symmetric matrix).
530            * tests/group-methods.R: Uncomment test of crossprod applied to
531            lsCMatrix objects.
532    
533    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/AllClass.R (symmetricMatrix): add validity method (available
536            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
537    
538            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
539    
540            * tests/indexing.Rout.save:
541            * tests/indexing.R: additions, mainly for 'lsparse'
542    
543            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
544            case.
545    
546            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
547    
548    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
551                    as 'N' (1-letter - Ok?)
552    
553            * tests/group-methods.R: add test for logical + NAs
554    
555            * R/dMatrix.R ("Compare"): fix to work with NA's
556    
557            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
558    
559            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
560                    which is implemented.
561    
562    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * src/chm_common.c: coerce logical <-> double instead of
565            typecasting;  needed for "l" matrix handling in cholmod.
566    
567            * tests/other-pkgs.R (graph): small extension in "graph" checks.
568    
569            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
570            (Tsp2grNEL): other fixes needed
571    
572    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
575                    Matrices, since "lMatrix", also "lsparseM" can have NA
576            * R/ndenseMatrix.R, etc: new source files
577            * man/nsparseMatrix-classes.Rd, etc: new help files
578            * tests/: adaptions
579            * src/chm_common.c (chm_dense_to_SEXP): and others:
580                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
581            * src/Csparse.c, etc: ditto
582    
583    2006-09-11  Douglas Bates  <bates@R-project.org>
584    
585            * src/Mutils.[ch],init.c inst/include/*.h: Move the
586            alloc_d**Matrix functions to the lme4 package.
587    
588    2006-09-09  Douglas Bates  <bates@R-project.org>
589    
590            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
591            fixed
592    
593    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/lMatrix.R: new
596    
597            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
598    
599            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
600            * man/tcrossprod.Rd: ditto
601    
602    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
603    
604            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
605            for exported functions
606            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
607            Remove partitioning algorithms for sparse matrix reordering.  The
608            copyright on the Metis code was problematic and the methods were
609            rarely used.
610            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
611            operations are now done entirely in CHOLMOD code.
612    
613    2006-09-06  Douglas Bates  <bates@R-project.org>
614    
615            * src/Mutils.h: Remove functions that are no longer used.
616    
617    2006-09-04  Douglas Bates  <bates@R-project.org>
618    
619            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
620            * src/DEPS.mkf: update
621    
622    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * created branches/Matrix-for-R-2.3.x;  on trunk: do
625            * DESCRIPTION (Version): 0.9975-0
626            (Depends): R (>= 2.4.0)
627    
628    2006-09-01  Douglas Bates  <bates@R-project.org>
629    
630            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
631    
632    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
635            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
636    
637            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
638    
639    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
642            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
643            * R/dsparseMatrix.R: ditto
644            * R/Csparse.R: ditto
645    
646    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/dMatrix.R (Compare): improve availability of "<", etc
649            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
650    
651    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
654            of a 0-index which was used as 1-index (..hmm)
655    
656            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
657    
658            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
659            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
660            (.is.diagonal): ditto
661    
662            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
663    
664            * R/Matrix.R (Matrix): also work for NA data
665    
666    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
669            in all cases.
670    
671    2006-08-27  Douglas Bates  <bates@R-project.org>
672    
673            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
674            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
675    
676    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
679            subclasses of "ddenseMatrix"
680            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
681            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
682            instead of half dozen specialized ones.
683    
684    2006-08-25  Douglas Bates  <bates@R-project.org>
685    
686            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
687            <tillard@cirad.fr> - ordering standard errors to match effects.
688    
689    2006-08-24  Douglas Bates  <bates@R-project.org>
690    
691            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
692            on R_ldl.
693            * R/lCholCMatrix.R,
694            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
695            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
696            * many files in ./R and ./src: Use more general version of
697            dup_mMatrix_as_dgeMatrix to simplify method definitions.
698            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
699            dtpMatrix, dspMatrix and dppMatrix conversions.
700    
701    
702    2006-08-23  Douglas Bates  <bates@R-project.org>
703    
704            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
705            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
706            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
707            dgeMatrix_crossprod (may need to do this in other places).
708            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
709            generic and method for dsCMatrix.  Use CHOLMOD for chol().
710    
711    2006-08-22  Douglas Bates  <bates@R-project.org>
712    
713            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
714            types of classed Matrices, matrices or numeric or logical vectors.
715            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
716            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
717            to Mutils.h (as an inline) and change name to Matrix_check_class;
718            fixes in as_cholmod_factor and chm_factor_to_SEXP.
719            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
720            dsCMatrix_matrix_solve.  Comment out vestigial functions.
721            * src/Csparse.c: use diag_P and uplo_P macros.
722    
723    2006-08-21  Douglas Bates  <bates@R-project.org>
724    
725            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
726            valgrind.
727            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
728            inverses.
729            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
730            -Wall warnings.
731            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
732            Use dup_mMatrix_as_dgeMatrix.
733    
734    2006-08-20  Douglas Bates  <bates@R-project.org>
735    
736            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
737            * tests/sparseQR.R: Added
738            * man/sparseQR-class.Rd: Document methods for qr.* generics
739            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
740    
741    2006-08-19  Douglas Bates  <bates@R-project.org>
742    
743            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
744            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
745            and qr.fitted.
746            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
747            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
748    
749    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
752            the base version has no "..." argument.
753    
754            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
755    
756            * R/Matrix.R: define and
757            * NAMESPACE: export as.numeric() and as.logical() methods.
758                    Let's hope these do not badly slow down something...
759            Finally export the zapsmall() method.
760    
761    2006-08-17  Douglas Bates  <bates@R-project.org>
762    
763            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
764            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
765            * src/dtCMatrix.c :Remove code that is no longer used
766            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
767    
768    2006-08-14  Douglas Bates  <bates@R-project.org>
769    
770            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
771            Csparse_to_logical and Csparse_symmetric_to_general.
772            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
773            coercion methods between CsparseMatrix and TsparseMatrix.
774    
775    2006-08-14  Douglas Bates  <bates@R-project.org>
776    
777            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
778            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
779            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
780            possible.
781    
782  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
783    
784          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

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