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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1903, Sat Jun 16 18:31:51 2007 UTC
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1    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
4            method (which can have arguments, show() can't).
5    
6    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
7    
8            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
9              added dgCMatrix_colSums for [col,row][Sums,Means]
10    
11    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
12    
13            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
14              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
15              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
16            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
17              class
18            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
19              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
20              row names to store the levels - duh!  Added an example.
21    
22    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/Csparse.c (Csparse_validate): check for *repeated* entries
25            thanks to example from Christian Buchta; with a test here:
26            * tests/simple.R:
27    
28    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
31            of colSums(*, sparseResult = TRUE)
32    
33    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
36            'na.rm = FALSE' as "everywhere" else in R.
37    
38    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
39    
40            * [r4421] src/CSparse_install.sh: Modify for new organization of
41              CSparse package
42            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
43              SuiteSparse
44            * [r4426] src/Makefile: add ./UFconfig to the include path for
45              compilation
46            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
47            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
48              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
49    
50    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
53            * R/sparseMatrix.R (prSpMatrix): now gives a message about
54            suppressed column names.
55    
56    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
57    
58            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
59              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
60              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
61              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
62              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
63              Remove warnings after change to const char* CHAR
64    
65    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
68              type of M_cholmod_ssmult
69    
70    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
71    
72            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
73              src/init.c: Yet another cholmod export - cholmod_ssmult
74    
75    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * NAMESPACE: exported drop0(), since
78            * man/drop0.Rd: I have seen several cases, I really wanted to use
79            it, so our users may want too.
80    
81    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * man/colSums.Rd: separately document colSums() etc, since these
84            have the extra argument 'sparseResult'.
85    
86    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
89            * man/spMatrix.Rd: docu., including examples
90    
91            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
92            in order to make colMeans() etc fast *and* correct.
93            * R/sparseVector.R (replSPvec): "[<-" functionality for
94            sparseVectors; tested in
95            * tests/simple.R:
96    
97    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
100            (very) sparse Matrices; output similar to Matlab's print().
101    
102    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
105            0-based, indices (Jose Quesada <quesada@gmail.com>).
106    
107    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
110    
111    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Auxiliaries.R (sparsapply): new utility, much faster than
114            tapply1() for large sparse matrices.
115    
116    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Matrix.R (dim<-): reshape now via sparseVector.
119    
120            * R/sparseVector.R: methods and function for
121            * R/AllClass.R: new "sparseVector" class and daughters.
122            * NAMESPACE: export new classes
123    
124    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Version): 0.99875-1
127            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
128    
129    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
132            indexing
133            * tests/indexing.R: test set for that.
134    
135    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
138            entries.
139            * tests/indexing.R(out): add regression test for it
140    
141    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
144            name for "!" method definitions.
145    
146    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Tsparse.R (intI): new utility, used for "[" :
149                    Cleanup up there, and fixes for duplicated indices - more TODO!
150    
151            * tests/indexing.R(out): more tests
152    
153    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
154    
155            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
156            code that is now part of the R Lapack library.
157    
158            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
159            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
160    
161    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
164    
165    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
168            up with extraneous names '0'...'<n-1>'
169    
170    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/dgTMatrix.R (mat2dgT): care about NAs
173    
174    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/kronecker.R: triangularity preserving methods
177    
178    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/kronecker.R: new file collecting kronecker() methods in one
181                    place.  Goal: become much faster!
182    
183    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
186            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
187            can be much faster.
188    
189            * tests/matprod.R: add regression tests for these (upper & lower).
190    
191    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Matrix.R (diff): method for our Matrices.
194    
195            * R/sparseMatrix.R (isDiagonal): check dim()!
196    
197    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/Matrix.R (dim<-): new method for "reshape()" built on a
200            proposal from Tamas Papp.
201    
202    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
205    
206            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
207            rather define and export  cBind() and rBind() only.
208            --> useRs *must* change code that used to have cbind()/rbind() !!
209    
210            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
211            * R/bind.Rout.save: ditto
212    
213    2007-02-16  Douglas Bates  <bates@r-project.org>
214    
215            * DESCRIPTION (Date, Version): 0.9975-11 with new date
216            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
217            const modifier on declaration of the array 'valid'
218    
219    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
220    
221            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
222    
223    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
226    
227            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
228            * tests/simple.R: test the above and some of these coercions:
229    
230            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
231                    be careful to avoid infinite recursion, using new coercions in
232            * R/ngCMatrix.R and nsC... and ntC...
233            * R/lsparseMatrix.R: ditto
234    
235            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
236    
237            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
238            * R/Rsparse.R: reactivate .Call()s
239    
240            * tests/Class+Meth.R: a bit more on actual classes
241    
242    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
245    
246    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * DESCRIPTION (Version): 0.9975-10 to upload
249    
250            * tests/Class+Meth.R (tstMatrixClass): require coercions to
251            specific classes less unconditionally.
252    
253            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
254    
255            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
256    
257            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
258            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
259            R_to_CMatrix segfaults on one platform.
260            Eliminate most coercion method to *specific* classes, and replace
261            with virtual classes coercions.
262    
263    
264    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
265    
266            * src/init.c: export the CHM...._validate() placeholders, since
267            they *are* called.
268    
269            * tests/Class+Meth.R (classCanCoerce): and starting to test
270            all as(<from>, <to>)
271    
272    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
275            * tests/indexing.R: tested now
276            * tests/indexing.Rout.save: updated
277    
278            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
279            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
280            appropriate.
281    
282            * NAMESPACE: export a trivial
283            * R/Matrix.R: drop() Matrix-method
284    
285            * R/AllClass.R: moved all prototypes to virtual super classes.
286    
287            * R/Rsparse.R: many more coercions to have less exceptions in
288            * tests/Class+Meth.R:
289    
290            * R/Ops.R (Compare): tweak for case with NA
291            * tests/simpl.R: hence another 'FIXME' eliminated
292    
293    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
296            objects.
297    
298            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
299              and more of "!", "&", "|", all, any; coercions
300    
301            * R/Rsparse.R: many coercions (which enable quite a few other
302            methods), thanks to enhancements in
303            * src/dgCMatrix.c (R_to_CMatrix): new, and
304            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
305            symmetric & triangular and ..RMatrix objects.
306    
307            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
308            renamed file from src/dsTMatrix.c;
309            now dealing with symmetric and triangular Tsparse coercions, both
310            to dense and general.
311    
312    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
315    
316            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
317            where sensible when the <numeric> is of length > 1.
318    
319    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Matrix.R ([<-): for M[] <- value: fix length
322    
323    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
326            * R/ndenseMatrix.R: new coercions n* -> l*
327    
328    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
331    
332            * R/Ops.R ("Logic"): and other "Ops", many updates
333    
334    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * src/Mutils.h (SET_DimNames): new utility
337    
338            * R/Auxiliaries.R (nnzero): improved and now exported via
339    
340            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
341    
342    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/diagMatrix.R (!): fix typo.
345    
346    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/Auxiliaries.R (as_Csparse): and quite a few others:
349                    allow to pass class definition --> speedup
350            * R/sparseMatrix.R: apply the above
351    
352            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
353    
354            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
355            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
356            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
357    
358            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
359    
360            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
361            and use it for "sparse*" as well, since it's faster than the
362            as_Csparse(.) way.
363    
364    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
367    
368    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
371            as method for   M[ ij ] <- v
372            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
373    
374            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
375            FALSE answer
376    
377            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
378            * tests/indexing.R: test it, and some of the above
379    
380    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Auxiliaries.R (is_duplicatedT): new utility
383    
384    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
385    
386            * src/init.c (R_init_Matrix): export cholmod_scale
387    
388    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
391            base::as.matrix to (x, ...)
392    
393    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
396            file; start using "Logic", hence
397    
398            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
399            * NAMESPACE: import and export "Logic"
400    
401    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
404            only needed previously to R version 2.5.0.
405    
406    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
409    
410            * R/Tsparse.R (replTmat): fix subassignment of triangular
411            * R/Csparse.R (replCmat): ditto
412            * tests/indexing.R: more tests, incl the above fix
413    
414    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Auxiliaries.R (drop0): extend for non CSparse
417            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
418    
419            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
420                    use uplo correctly (!); other places: use uplo_P() macro
421    
422            * R/Csparse.R (replCmat): call diagU2N() when needed
423            * R/Tsparse.R (replTmat): ditto
424    
425            * src/dtCMatrix.c (tCMatrix_validate): new
426            * src/dtTMatrix.c (tTMatrix_validate): new, used in
427            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
428    
429            * R/diagMatrix.R (replDiag): to use in [<-
430    
431    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
434                    also more general diagU2N().
435    
436    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
439            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
440    
441    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * tests/bind.R: a few more cases
444            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
445    
446            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
447            * R/ddenseMatrix.R (cbind2/rbind2)
448            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
449            * tests/indexing.R
450            * tests/indexing.Rout.save: updated
451    
452    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
455            * tests/indexing.R
456    
457    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
460            align with proper position of "0", i.e., right for integers.
461            argument 'align' by default is "fancy".
462    
463    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
466            * R/Csparse.R: and fix "Compare" for more cases.
467            * tests/Class+Meth.R: test some of these (m == m, m != m)
468    
469    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * R/lsparseMatrix.R: all() and any() methods
472            * R/ldenseMatrix.R:      ditto
473            * NAMESPACE, R/Matrix.R: ditto
474    
475            * man/all-methods.Rd: document them minimally
476    
477            * tests/simple.R: add a few examples for these
478    
479    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/Tsparse.R ([): fix long standing typo in symmetric case
482            * man/dsCMatrix-class.Rd: add example exhibiting the above case
483    
484    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
485    
486            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
487            to LL before converting to a sparse matrix. (The LDL form can be
488            converted to a sparse matrix but it is implicitly a unit
489            triangular matrix and a diagonal matrix overwritten on the diagonal.)
490    
491    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
492    
493            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
494    
495    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
496    
497            * DESCRIPTION (Version): updated -> release 0.9975-7
498            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
499    
500    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
503    
504    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
505    
506            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
507            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
508            is exactly singular.
509    
510    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * DESCRIPTION (Date): updated -> release 0.9975-6
513    
514    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
517            now returns symmetric.
518    
519            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
520    
521            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
522            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
523    
524            * R/Auxiliaries.R (.type.kind): added
525    
526    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
529            running src/CSparse_install.sh
530    
531            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
532    
533    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
536            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
537    
538            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
539    
540            * tests/Class+Meth.R (tstMatrixClass): now assure
541            the (important in method programming) property :
542    
543                    ###>>  Every "Matrix" is either
544                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
545    
546                    (where "*" stands for "Matrix")
547    
548            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
549    
550            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
551            * tests/validObj.R: checks for "comparison"
552    
553            * R/sparseMatrix.R ([): improved indexing for sparse;
554                    trying to keep <symmetric>[ n, n] symmmetric
555    
556            * tests/indexing.R: indexing for logical sparse now ok
557    
558    
559    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * src/Tsparse.c: use xTsparse_validate() , and hence remove
562    
563            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
564    
565    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
568    
569            * tests/simple.R: validObject() checking the above.
570    
571            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
572            replacing both dgCMatrix_validate and lgCM*.
573    
574            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
575            fix dimnames setting in other places.
576            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
577    
578    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
581    
582            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
583            symmetry test, via
584            * R/Auxiliaries.R (.as.dgC.0.factors):
585    
586    2006-11-01  Douglas Bates  <bates@r-project.org>
587    
588            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
589            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
590            <CsparseMatrix>) added
591    
592    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * tests/matprod.R: add a variation of Harri's example
595    
596            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
597            recursive infinitely.
598    
599            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
600    
601            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
602    
603    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
606            matrix if possible; test m+m == 2*m; now test dgRMatrix.
607            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
608            satisfy the above test.
609    
610    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
613    
614            * R/dgCMatrix.R: solve(a, b="missing") based on
615            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
616            RHS = NULL.
617    
618            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
619            add more (needed) [t]crossprod() methods.
620    
621            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
622    
623            * R/Auxiliaries.R (as_CspClass): cleanup
624            (drop0): internal utility for "Csparse_drop(*, 0)"
625            (.bail.out.2): encourage active feedback
626    
627    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/dMatrix.R(Compare): new(), then slots [no validity check]
630    
631            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
632            non-valid or 'sorted' case).
633    
634            * R/dsparseMatrix.R: add "chol" method.
635            * R/ddenseMatrix.R: ditto
636    
637            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
638            * NAMESPACE (Ops)
639            * R/diagMatrix.R (diag2T): simple utility used "higher level"
640            coercion; deprecating direct lower level coercions.
641    
642            * R/*.R (seq): use seq_len() and seq_along() where possible.
643    
644    
645    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * DESCRIPTION (Version): 0.9975-5 ready for release
648    
649    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
650    
651            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
652    
653    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
654    
655            * R/AllClass.R (corMatrix): add 'validity' check;
656                    comment out unused "LDL" class definition
657            * NAMESPACE: mention, but do not export "LDL" class
658            * R/corMatrix.R: new (simple), needed for R-devel with
659            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
660              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
661    
662    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
663    
664            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
665            use Rprintf and R's error handling.
666    
667    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
670            * tests/matprod.R: add tests for the bug fixed.
671    
672    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
673    
674            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
675            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
676    
677    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
678    
679            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
680    
681    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * DESCRIPTION (Version): 0.9975-3
684    
685            * R/diagMatrix.R (bdiag): new function constructing block diagonal
686            (sparse) matrices.
687            * man/bdiag.Rd: docu + examples
688    
689            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
690    
691            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
692            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
693    
694            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
695            that result is sparse or diagonal (and not dense).
696    
697            * man/Subassign-methods.Rd: fix examples
698    
699            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
700            should always return a sparse (and not sometimes a diagonal) matrix.
701    
702    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
705    
706    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
707    
708            * DESCRIPTION (Version): 0.9975-2
709    
710            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
711    
712    2006-10-02  Douglas Bates  <bates@R-project.org>
713    
714            * tests/dg_Matrix.R: Simplify test taking into account new code.
715    
716    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
719    
720            * R/lsTMatrix.R: new files w/ missing methods
721            * R/nsTMatrix.R:  "  'for completeness'
722    
723            * tests/Class+Meth.R: a bit less 'not.ok.classes'
724    
725            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
726    
727    
728    2006-09-28  Douglas Bates  <bates@R-project.org>
729    
730            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
731            included.
732    
733            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
734            Export C-callable functions used in Zt_create in lme4.
735    
736    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * DESCRIPTION (Version): 0.9975-1
739    
740            * tests/simple.R: less checks fail; using NA, found that our
741                    kronecker() is not base-compatible with NA's.
742    
743            * R/dMatrix.R: "Compare" method now implemented for all cases
744    
745            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
746    
747            * man/dtpMatrix-class.Rd: mention length of 'x' slot
748    
749            * src/dtpMatrix.c (dtpMatrix_validate): fix check
750            * src/dspMatrix.c (dspMatrix_validate): ditto
751    
752            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
753              including coercion to [nl]tTMatrix.
754    
755            * R/diagMatrix.R (show): print a header line as for other classes.
756    
757    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * src/Makefile.win (SUBDIRS): fix typo
760    
761    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
764    
765    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
766    
767            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
768            symmetric and y missing in R code using %*% (cholmod_aat doesn't
769            accept a symmetric matrix).
770            * tests/group-methods.R: Uncomment test of crossprod applied to
771            lsCMatrix objects.
772    
773    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/AllClass.R (symmetricMatrix): add validity method (available
776            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
777    
778            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
779    
780            * tests/indexing.Rout.save:
781            * tests/indexing.R: additions, mainly for 'lsparse'
782    
783            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
784            case.
785    
786            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
787    
788    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
791                    as 'N' (1-letter - Ok?)
792    
793            * tests/group-methods.R: add test for logical + NAs
794    
795            * R/dMatrix.R ("Compare"): fix to work with NA's
796    
797            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
798    
799            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
800                    which is implemented.
801    
802    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804            * src/chm_common.c: coerce logical <-> double instead of
805            typecasting;  needed for "l" matrix handling in cholmod.
806    
807            * tests/other-pkgs.R (graph): small extension in "graph" checks.
808    
809            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
810            (Tsp2grNEL): other fixes needed
811    
812    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
815                    Matrices, since "lMatrix", also "lsparseM" can have NA
816            * R/ndenseMatrix.R, etc: new source files
817            * man/nsparseMatrix-classes.Rd, etc: new help files
818            * tests/: adaptions
819            * src/chm_common.c (chm_dense_to_SEXP): and others:
820                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
821            * src/Csparse.c, etc: ditto
822    
823    2006-09-11  Douglas Bates  <bates@R-project.org>
824    
825            * src/Mutils.[ch],init.c inst/include/*.h: Move the
826            alloc_d**Matrix functions to the lme4 package.
827    
828    2006-09-09  Douglas Bates  <bates@R-project.org>
829    
830            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
831            fixed
832    
833    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * R/lMatrix.R: new
836    
837            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
838    
839            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
840            * man/tcrossprod.Rd: ditto
841    
842    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
843    
844            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
845            for exported functions
846            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
847            Remove partitioning algorithms for sparse matrix reordering.  The
848            copyright on the Metis code was problematic and the methods were
849            rarely used.
850            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
851            operations are now done entirely in CHOLMOD code.
852    
853    2006-09-06  Douglas Bates  <bates@R-project.org>
854    
855            * src/Mutils.h: Remove functions that are no longer used.
856    
857    2006-09-04  Douglas Bates  <bates@R-project.org>
858    
859            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
860            * src/DEPS.mkf: update
861    
862    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * created branches/Matrix-for-R-2.3.x;  on trunk: do
865            * DESCRIPTION (Version): 0.9975-0
866            (Depends): R (>= 2.4.0)
867    
868    2006-09-01  Douglas Bates  <bates@R-project.org>
869    
870            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
871    
872    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
875            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
876    
877            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
878    
879    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
882            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
883            * R/dsparseMatrix.R: ditto
884            * R/Csparse.R: ditto
885    
886    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
887    
888            * R/dMatrix.R (Compare): improve availability of "<", etc
889            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
890    
891    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
894            of a 0-index which was used as 1-index (..hmm)
895    
896            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
897    
898            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
899            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
900            (.is.diagonal): ditto
901    
902            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
903    
904            * R/Matrix.R (Matrix): also work for NA data
905    
906  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
907    
908          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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