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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1911, Tue Jun 19 16:16:58 2007 UTC
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1    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
4              notably the new ones building on the new .Call(.)s:
5    
6            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
7            all 4 of [dlin]gCMatrix_colSums().
8    
9    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
10    
11            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
12            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
13              result
14    
15    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/kronecker.R: fix typo (could lead to inf.recursion)
18            * test/simple.R: testing that
19    
20            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
21            method (which can have arguments, show() can't).
22    
23    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
24    
25            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
26              added dgCMatrix_colSums for [col,row][Sums,Means]
27    
28    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
29    
30            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
31              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
32              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
33            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
34              class
35            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
36              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
37              row names to store the levels - duh!  Added an example.
38    
39    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/Csparse.c (Csparse_validate): check for *repeated* entries
42            thanks to example from Christian Buchta; with a test here:
43            * tests/simple.R:
44    
45    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
48            of colSums(*, sparseResult = TRUE)
49    
50    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
53            'na.rm = FALSE' as "everywhere" else in R.
54    
55    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r4421] src/CSparse_install.sh: Modify for new organization of
58              CSparse package
59            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
60              SuiteSparse
61            * [r4426] src/Makefile: add ./UFconfig to the include path for
62              compilation
63            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
64            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
65              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
66    
67    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
70            * R/sparseMatrix.R (prSpMatrix): now gives a message about
71            suppressed column names.
72    
73    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
74    
75            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
76              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
77              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
78              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
79              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
80              Remove warnings after change to const char* CHAR
81    
82    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
83    
84            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
85              type of M_cholmod_ssmult
86    
87    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
88    
89            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
90              src/init.c: Yet another cholmod export - cholmod_ssmult
91    
92    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * NAMESPACE: exported drop0(), since
95            * man/drop0.Rd: I have seen several cases, I really wanted to use
96            it, so our users may want too.
97    
98    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * man/colSums.Rd: separately document colSums() etc, since these
101            have the extra argument 'sparseResult'.
102    
103    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
106            * man/spMatrix.Rd: docu., including examples
107    
108            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
109            in order to make colMeans() etc fast *and* correct.
110            * R/sparseVector.R (replSPvec): "[<-" functionality for
111            sparseVectors; tested in
112            * tests/simple.R:
113    
114    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
117            (very) sparse Matrices; output similar to Matlab's print().
118    
119    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
120    
121            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
122            0-based, indices (Jose Quesada <quesada@gmail.com>).
123    
124    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
125    
126            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
127    
128    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/Auxiliaries.R (sparsapply): new utility, much faster than
131            tapply1() for large sparse matrices.
132    
133    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Matrix.R (dim<-): reshape now via sparseVector.
136    
137            * R/sparseVector.R: methods and function for
138            * R/AllClass.R: new "sparseVector" class and daughters.
139            * NAMESPACE: export new classes
140    
141    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * DESCRIPTION (Version): 0.99875-1
144            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
145    
146    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
149            indexing
150            * tests/indexing.R: test set for that.
151    
152    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
155            entries.
156            * tests/indexing.R(out): add regression test for it
157    
158    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
161            name for "!" method definitions.
162    
163    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/Tsparse.R (intI): new utility, used for "[" :
166                    Cleanup up there, and fixes for duplicated indices - more TODO!
167    
168            * tests/indexing.R(out): more tests
169    
170    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
171    
172            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
173            code that is now part of the R Lapack library.
174    
175            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
176            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
177    
178    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
181    
182    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
185            up with extraneous names '0'...'<n-1>'
186    
187    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/dgTMatrix.R (mat2dgT): care about NAs
190    
191    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/kronecker.R: triangularity preserving methods
194    
195    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/kronecker.R: new file collecting kronecker() methods in one
198                    place.  Goal: become much faster!
199    
200    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
203            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
204            can be much faster.
205    
206            * tests/matprod.R: add regression tests for these (upper & lower).
207    
208    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Matrix.R (diff): method for our Matrices.
211    
212            * R/sparseMatrix.R (isDiagonal): check dim()!
213    
214    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/Matrix.R (dim<-): new method for "reshape()" built on a
217            proposal from Tamas Papp.
218    
219    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
222    
223            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
224            rather define and export  cBind() and rBind() only.
225            --> useRs *must* change code that used to have cbind()/rbind() !!
226    
227            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
228            * R/bind.Rout.save: ditto
229    
230    2007-02-16  Douglas Bates  <bates@r-project.org>
231    
232            * DESCRIPTION (Date, Version): 0.9975-11 with new date
233            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
234            const modifier on declaration of the array 'valid'
235    
236    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
237    
238            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
239    
240    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
243    
244            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
245            * tests/simple.R: test the above and some of these coercions:
246    
247            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
248                    be careful to avoid infinite recursion, using new coercions in
249            * R/ngCMatrix.R and nsC... and ntC...
250            * R/lsparseMatrix.R: ditto
251    
252            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
253    
254            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
255            * R/Rsparse.R: reactivate .Call()s
256    
257            * tests/Class+Meth.R: a bit more on actual classes
258    
259    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
262    
263    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * DESCRIPTION (Version): 0.9975-10 to upload
266    
267            * tests/Class+Meth.R (tstMatrixClass): require coercions to
268            specific classes less unconditionally.
269    
270            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
271    
272            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
273    
274            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
275            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
276            R_to_CMatrix segfaults on one platform.
277            Eliminate most coercion method to *specific* classes, and replace
278            with virtual classes coercions.
279    
280    
281    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
282    
283            * src/init.c: export the CHM...._validate() placeholders, since
284            they *are* called.
285    
286            * tests/Class+Meth.R (classCanCoerce): and starting to test
287            all as(<from>, <to>)
288    
289    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
292            * tests/indexing.R: tested now
293            * tests/indexing.Rout.save: updated
294    
295            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
296            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
297            appropriate.
298    
299            * NAMESPACE: export a trivial
300            * R/Matrix.R: drop() Matrix-method
301    
302            * R/AllClass.R: moved all prototypes to virtual super classes.
303    
304            * R/Rsparse.R: many more coercions to have less exceptions in
305            * tests/Class+Meth.R:
306    
307            * R/Ops.R (Compare): tweak for case with NA
308            * tests/simpl.R: hence another 'FIXME' eliminated
309    
310    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
313            objects.
314    
315            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
316              and more of "!", "&", "|", all, any; coercions
317    
318            * R/Rsparse.R: many coercions (which enable quite a few other
319            methods), thanks to enhancements in
320            * src/dgCMatrix.c (R_to_CMatrix): new, and
321            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
322            symmetric & triangular and ..RMatrix objects.
323    
324            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
325            renamed file from src/dsTMatrix.c;
326            now dealing with symmetric and triangular Tsparse coercions, both
327            to dense and general.
328    
329    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
332    
333            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
334            where sensible when the <numeric> is of length > 1.
335    
336    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/Matrix.R ([<-): for M[] <- value: fix length
339    
340    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
343            * R/ndenseMatrix.R: new coercions n* -> l*
344    
345    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
348    
349            * R/Ops.R ("Logic"): and other "Ops", many updates
350    
351    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * src/Mutils.h (SET_DimNames): new utility
354    
355            * R/Auxiliaries.R (nnzero): improved and now exported via
356    
357            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
358    
359    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/diagMatrix.R (!): fix typo.
362    
363    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/Auxiliaries.R (as_Csparse): and quite a few others:
366                    allow to pass class definition --> speedup
367            * R/sparseMatrix.R: apply the above
368    
369            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
370    
371            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
372            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
373            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
374    
375            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
376    
377            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
378            and use it for "sparse*" as well, since it's faster than the
379            as_Csparse(.) way.
380    
381    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
384    
385    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
388            as method for   M[ ij ] <- v
389            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
390    
391            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
392            FALSE answer
393    
394            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
395            * tests/indexing.R: test it, and some of the above
396    
397    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/Auxiliaries.R (is_duplicatedT): new utility
400    
401    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
402    
403            * src/init.c (R_init_Matrix): export cholmod_scale
404    
405    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
408            base::as.matrix to (x, ...)
409    
410    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
413            file; start using "Logic", hence
414    
415            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
416            * NAMESPACE: import and export "Logic"
417    
418    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
421            only needed previously to R version 2.5.0.
422    
423    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
426    
427            * R/Tsparse.R (replTmat): fix subassignment of triangular
428            * R/Csparse.R (replCmat): ditto
429            * tests/indexing.R: more tests, incl the above fix
430    
431    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/Auxiliaries.R (drop0): extend for non CSparse
434            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
435    
436            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
437                    use uplo correctly (!); other places: use uplo_P() macro
438    
439            * R/Csparse.R (replCmat): call diagU2N() when needed
440            * R/Tsparse.R (replTmat): ditto
441    
442            * src/dtCMatrix.c (tCMatrix_validate): new
443            * src/dtTMatrix.c (tTMatrix_validate): new, used in
444            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
445    
446            * R/diagMatrix.R (replDiag): to use in [<-
447    
448    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
451                    also more general diagU2N().
452    
453    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
456            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
457    
458    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * tests/bind.R: a few more cases
461            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
462    
463            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
464            * R/ddenseMatrix.R (cbind2/rbind2)
465            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
466            * tests/indexing.R
467            * tests/indexing.Rout.save: updated
468    
469    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
472            * tests/indexing.R
473    
474    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
477            align with proper position of "0", i.e., right for integers.
478            argument 'align' by default is "fancy".
479    
480    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
483            * R/Csparse.R: and fix "Compare" for more cases.
484            * tests/Class+Meth.R: test some of these (m == m, m != m)
485    
486    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/lsparseMatrix.R: all() and any() methods
489            * R/ldenseMatrix.R:      ditto
490            * NAMESPACE, R/Matrix.R: ditto
491    
492            * man/all-methods.Rd: document them minimally
493    
494            * tests/simple.R: add a few examples for these
495    
496    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/Tsparse.R ([): fix long standing typo in symmetric case
499            * man/dsCMatrix-class.Rd: add example exhibiting the above case
500    
501    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
504            to LL before converting to a sparse matrix. (The LDL form can be
505            converted to a sparse matrix but it is implicitly a unit
506            triangular matrix and a diagonal matrix overwritten on the diagonal.)
507    
508    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
509    
510            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
511    
512    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
513    
514            * DESCRIPTION (Version): updated -> release 0.9975-7
515            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
516    
517    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
520    
521    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
522    
523            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
524            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
525            is exactly singular.
526    
527    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * DESCRIPTION (Date): updated -> release 0.9975-6
530    
531    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
534            now returns symmetric.
535    
536            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
537    
538            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
539            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
540    
541            * R/Auxiliaries.R (.type.kind): added
542    
543    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
546            running src/CSparse_install.sh
547    
548            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
549    
550    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
553            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
554    
555            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
556    
557            * tests/Class+Meth.R (tstMatrixClass): now assure
558            the (important in method programming) property :
559    
560                    ###>>  Every "Matrix" is either
561                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
562    
563                    (where "*" stands for "Matrix")
564    
565            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
566    
567            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
568            * tests/validObj.R: checks for "comparison"
569    
570            * R/sparseMatrix.R ([): improved indexing for sparse;
571                    trying to keep <symmetric>[ n, n] symmmetric
572    
573            * tests/indexing.R: indexing for logical sparse now ok
574    
575    
576    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * src/Tsparse.c: use xTsparse_validate() , and hence remove
579    
580            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
581    
582    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
585    
586            * tests/simple.R: validObject() checking the above.
587    
588            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
589            replacing both dgCMatrix_validate and lgCM*.
590    
591            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
592            fix dimnames setting in other places.
593            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
594    
595    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
598    
599            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
600            symmetry test, via
601            * R/Auxiliaries.R (.as.dgC.0.factors):
602    
603    2006-11-01  Douglas Bates  <bates@r-project.org>
604    
605            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
606            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
607            <CsparseMatrix>) added
608    
609    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * tests/matprod.R: add a variation of Harri's example
612    
613            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
614            recursive infinitely.
615    
616            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
617    
618            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
619    
620    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
623            matrix if possible; test m+m == 2*m; now test dgRMatrix.
624            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
625            satisfy the above test.
626    
627    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
630    
631            * R/dgCMatrix.R: solve(a, b="missing") based on
632            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
633            RHS = NULL.
634    
635            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
636            add more (needed) [t]crossprod() methods.
637    
638            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
639    
640            * R/Auxiliaries.R (as_CspClass): cleanup
641            (drop0): internal utility for "Csparse_drop(*, 0)"
642            (.bail.out.2): encourage active feedback
643    
644    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/dMatrix.R(Compare): new(), then slots [no validity check]
647    
648            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
649            non-valid or 'sorted' case).
650    
651            * R/dsparseMatrix.R: add "chol" method.
652            * R/ddenseMatrix.R: ditto
653    
654            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
655            * NAMESPACE (Ops)
656            * R/diagMatrix.R (diag2T): simple utility used "higher level"
657            coercion; deprecating direct lower level coercions.
658    
659            * R/*.R (seq): use seq_len() and seq_along() where possible.
660    
661    
662    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * DESCRIPTION (Version): 0.9975-5 ready for release
665    
666    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
667    
668            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
669    
670    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * R/AllClass.R (corMatrix): add 'validity' check;
673                    comment out unused "LDL" class definition
674            * NAMESPACE: mention, but do not export "LDL" class
675            * R/corMatrix.R: new (simple), needed for R-devel with
676            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
677              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
678    
679    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
680    
681            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
682            use Rprintf and R's error handling.
683    
684    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
687            * tests/matprod.R: add tests for the bug fixed.
688    
689    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
690    
691            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
692            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
693    
694    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
695    
696            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
697    
698    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * DESCRIPTION (Version): 0.9975-3
701    
702            * R/diagMatrix.R (bdiag): new function constructing block diagonal
703            (sparse) matrices.
704            * man/bdiag.Rd: docu + examples
705    
706            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
707    
708            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
709            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
710    
711            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
712            that result is sparse or diagonal (and not dense).
713    
714            * man/Subassign-methods.Rd: fix examples
715    
716            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
717            should always return a sparse (and not sometimes a diagonal) matrix.
718    
719    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
722    
723    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
724    
725            * DESCRIPTION (Version): 0.9975-2
726    
727            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
728    
729    2006-10-02  Douglas Bates  <bates@R-project.org>
730    
731            * tests/dg_Matrix.R: Simplify test taking into account new code.
732    
733    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
736    
737            * R/lsTMatrix.R: new files w/ missing methods
738            * R/nsTMatrix.R:  "  'for completeness'
739    
740            * tests/Class+Meth.R: a bit less 'not.ok.classes'
741    
742            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
743    
744    
745    2006-09-28  Douglas Bates  <bates@R-project.org>
746    
747            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
748            included.
749    
750            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
751            Export C-callable functions used in Zt_create in lme4.
752    
753    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * DESCRIPTION (Version): 0.9975-1
756    
757            * tests/simple.R: less checks fail; using NA, found that our
758                    kronecker() is not base-compatible with NA's.
759    
760            * R/dMatrix.R: "Compare" method now implemented for all cases
761    
762            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
763    
764            * man/dtpMatrix-class.Rd: mention length of 'x' slot
765    
766            * src/dtpMatrix.c (dtpMatrix_validate): fix check
767            * src/dspMatrix.c (dspMatrix_validate): ditto
768    
769            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
770              including coercion to [nl]tTMatrix.
771    
772            * R/diagMatrix.R (show): print a header line as for other classes.
773    
774    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * src/Makefile.win (SUBDIRS): fix typo
777    
778    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
781    
782    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
783    
784            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
785            symmetric and y missing in R code using %*% (cholmod_aat doesn't
786            accept a symmetric matrix).
787            * tests/group-methods.R: Uncomment test of crossprod applied to
788            lsCMatrix objects.
789    
790    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/AllClass.R (symmetricMatrix): add validity method (available
793            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
794    
795            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
796    
797            * tests/indexing.Rout.save:
798            * tests/indexing.R: additions, mainly for 'lsparse'
799    
800            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
801            case.
802    
803            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
804    
805    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
808                    as 'N' (1-letter - Ok?)
809    
810            * tests/group-methods.R: add test for logical + NAs
811    
812            * R/dMatrix.R ("Compare"): fix to work with NA's
813    
814            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
815    
816            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
817                    which is implemented.
818    
819    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * src/chm_common.c: coerce logical <-> double instead of
822            typecasting;  needed for "l" matrix handling in cholmod.
823    
824            * tests/other-pkgs.R (graph): small extension in "graph" checks.
825    
826            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
827            (Tsp2grNEL): other fixes needed
828    
829    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
832                    Matrices, since "lMatrix", also "lsparseM" can have NA
833            * R/ndenseMatrix.R, etc: new source files
834            * man/nsparseMatrix-classes.Rd, etc: new help files
835            * tests/: adaptions
836            * src/chm_common.c (chm_dense_to_SEXP): and others:
837                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
838            * src/Csparse.c, etc: ditto
839    
840    2006-09-11  Douglas Bates  <bates@R-project.org>
841    
842            * src/Mutils.[ch],init.c inst/include/*.h: Move the
843            alloc_d**Matrix functions to the lme4 package.
844    
845    2006-09-09  Douglas Bates  <bates@R-project.org>
846    
847            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
848            fixed
849    
850    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
851    
852            * R/lMatrix.R: new
853    
854            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
855    
856            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
857            * man/tcrossprod.Rd: ditto
858    
859    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
860    
861            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
862            for exported functions
863            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
864            Remove partitioning algorithms for sparse matrix reordering.  The
865            copyright on the Metis code was problematic and the methods were
866            rarely used.
867            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
868            operations are now done entirely in CHOLMOD code.
869    
870    2006-09-06  Douglas Bates  <bates@R-project.org>
871    
872            * src/Mutils.h: Remove functions that are no longer used.
873    
874    2006-09-04  Douglas Bates  <bates@R-project.org>
875    
876            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
877            * src/DEPS.mkf: update
878    
879    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * created branches/Matrix-for-R-2.3.x;  on trunk: do
882            * DESCRIPTION (Version): 0.9975-0
883            (Depends): R (>= 2.4.0)
884    
885    2006-09-01  Douglas Bates  <bates@R-project.org>
886    
887            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
888    
889    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
892            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
893    
894            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
895    
896    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
897    
898            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
899            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
900            * R/dsparseMatrix.R: ditto
901            * R/Csparse.R: ditto
902    
903    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/dMatrix.R (Compare): improve availability of "<", etc
906            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
907    
908    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
911            of a 0-index which was used as 1-index (..hmm)
912    
913            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
914    
915            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
916            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
917            (.is.diagonal): ditto
918    
919            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
920    
921            * R/Matrix.R (Matrix): also work for NA data
922    
923    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
926            in all cases.
927    
928    2006-08-27  Douglas Bates  <bates@R-project.org>
929    
930            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
931            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
932    
933    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
934    
935            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
936            subclasses of "ddenseMatrix"
937            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
938            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
939            instead of half dozen specialized ones.
940    
941    2006-08-25  Douglas Bates  <bates@R-project.org>
942    
943            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
944            <tillard@cirad.fr> - ordering standard errors to match effects.
945    
946    2006-08-24  Douglas Bates  <bates@R-project.org>
947    
948            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
949            on R_ldl.
950            * R/lCholCMatrix.R,
951            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
952            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
953            * many files in ./R and ./src: Use more general version of
954            dup_mMatrix_as_dgeMatrix to simplify method definitions.
955            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
956            dtpMatrix, dspMatrix and dppMatrix conversions.
957    
958    
959    2006-08-23  Douglas Bates  <bates@R-project.org>
960    
961            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
962            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
963            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
964            dgeMatrix_crossprod (may need to do this in other places).
965            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
966            generic and method for dsCMatrix.  Use CHOLMOD for chol().
967    
968    2006-08-22  Douglas Bates  <bates@R-project.org>
969    
970            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
971            types of classed Matrices, matrices or numeric or logical vectors.
972            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
973            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
974            to Mutils.h (as an inline) and change name to Matrix_check_class;
975            fixes in as_cholmod_factor and chm_factor_to_SEXP.
976            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
977            dsCMatrix_matrix_solve.  Comment out vestigial functions.
978            * src/Csparse.c: use diag_P and uplo_P macros.
979    
980  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
981    
982          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
983          valgrind.          valgrind.
984            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
985            inverses.
986            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
987            -Wall warnings.
988            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
989            Use dup_mMatrix_as_dgeMatrix.
990    
991  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
992    

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