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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1909, Mon Jun 18 16:15:49 2007 UTC
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1    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
4            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
5              result
6    
7    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/kronecker.R: fix typo (could lead to inf.recursion)
10            * test/simple.R: testing that
11    
12            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
13            method (which can have arguments, show() can't).
14    
15    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
16    
17            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
18              added dgCMatrix_colSums for [col,row][Sums,Means]
19    
20    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
21    
22            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
23              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
24              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
25            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
26              class
27            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
28              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
29              row names to store the levels - duh!  Added an example.
30    
31    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * src/Csparse.c (Csparse_validate): check for *repeated* entries
34            thanks to example from Christian Buchta; with a test here:
35            * tests/simple.R:
36    
37    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
40            of colSums(*, sparseResult = TRUE)
41    
42    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
45            'na.rm = FALSE' as "everywhere" else in R.
46    
47    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
48    
49            * [r4421] src/CSparse_install.sh: Modify for new organization of
50              CSparse package
51            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
52              SuiteSparse
53            * [r4426] src/Makefile: add ./UFconfig to the include path for
54              compilation
55            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
56            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
57              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
58    
59    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
62            * R/sparseMatrix.R (prSpMatrix): now gives a message about
63            suppressed column names.
64    
65    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
68              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
69              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
70              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
71              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
72              Remove warnings after change to const char* CHAR
73    
74    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
75    
76            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
77              type of M_cholmod_ssmult
78    
79    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
80    
81            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
82              src/init.c: Yet another cholmod export - cholmod_ssmult
83    
84    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * NAMESPACE: exported drop0(), since
87            * man/drop0.Rd: I have seen several cases, I really wanted to use
88            it, so our users may want too.
89    
90    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * man/colSums.Rd: separately document colSums() etc, since these
93            have the extra argument 'sparseResult'.
94    
95    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
98            * man/spMatrix.Rd: docu., including examples
99    
100            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
101            in order to make colMeans() etc fast *and* correct.
102            * R/sparseVector.R (replSPvec): "[<-" functionality for
103            sparseVectors; tested in
104            * tests/simple.R:
105    
106    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
109            (very) sparse Matrices; output similar to Matlab's print().
110    
111    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
112    
113            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
114            0-based, indices (Jose Quesada <quesada@gmail.com>).
115    
116    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
117    
118            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
119    
120    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/Auxiliaries.R (sparsapply): new utility, much faster than
123            tapply1() for large sparse matrices.
124    
125    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Matrix.R (dim<-): reshape now via sparseVector.
128    
129            * R/sparseVector.R: methods and function for
130            * R/AllClass.R: new "sparseVector" class and daughters.
131            * NAMESPACE: export new classes
132    
133    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * DESCRIPTION (Version): 0.99875-1
136            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
137    
138    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
141            indexing
142            * tests/indexing.R: test set for that.
143    
144    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
147            entries.
148            * tests/indexing.R(out): add regression test for it
149    
150    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
153            name for "!" method definitions.
154    
155    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Tsparse.R (intI): new utility, used for "[" :
158                    Cleanup up there, and fixes for duplicated indices - more TODO!
159    
160            * tests/indexing.R(out): more tests
161    
162    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
165            code that is now part of the R Lapack library.
166    
167            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
168            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
169    
170    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
173    
174    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
177            up with extraneous names '0'...'<n-1>'
178    
179    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dgTMatrix.R (mat2dgT): care about NAs
182    
183    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/kronecker.R: triangularity preserving methods
186    
187    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/kronecker.R: new file collecting kronecker() methods in one
190                    place.  Goal: become much faster!
191    
192    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
195            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
196            can be much faster.
197    
198            * tests/matprod.R: add regression tests for these (upper & lower).
199    
200    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Matrix.R (diff): method for our Matrices.
203    
204            * R/sparseMatrix.R (isDiagonal): check dim()!
205    
206    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Matrix.R (dim<-): new method for "reshape()" built on a
209            proposal from Tamas Papp.
210    
211    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
214    
215            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
216            rather define and export  cBind() and rBind() only.
217            --> useRs *must* change code that used to have cbind()/rbind() !!
218    
219            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
220            * R/bind.Rout.save: ditto
221    
222    2007-02-16  Douglas Bates  <bates@r-project.org>
223    
224            * DESCRIPTION (Date, Version): 0.9975-11 with new date
225            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
226            const modifier on declaration of the array 'valid'
227    
228    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
229    
230            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
231    
232    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
235    
236            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
237            * tests/simple.R: test the above and some of these coercions:
238    
239            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
240                    be careful to avoid infinite recursion, using new coercions in
241            * R/ngCMatrix.R and nsC... and ntC...
242            * R/lsparseMatrix.R: ditto
243    
244            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
245    
246            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
247            * R/Rsparse.R: reactivate .Call()s
248    
249            * tests/Class+Meth.R: a bit more on actual classes
250    
251    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
254    
255    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * DESCRIPTION (Version): 0.9975-10 to upload
258    
259            * tests/Class+Meth.R (tstMatrixClass): require coercions to
260            specific classes less unconditionally.
261    
262            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
263    
264            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
265    
266            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
267            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
268            R_to_CMatrix segfaults on one platform.
269            Eliminate most coercion method to *specific* classes, and replace
270            with virtual classes coercions.
271    
272    
273    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
274    
275            * src/init.c: export the CHM...._validate() placeholders, since
276            they *are* called.
277    
278            * tests/Class+Meth.R (classCanCoerce): and starting to test
279            all as(<from>, <to>)
280    
281    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
284            * tests/indexing.R: tested now
285            * tests/indexing.Rout.save: updated
286    
287            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
288            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
289            appropriate.
290    
291            * NAMESPACE: export a trivial
292            * R/Matrix.R: drop() Matrix-method
293    
294            * R/AllClass.R: moved all prototypes to virtual super classes.
295    
296            * R/Rsparse.R: many more coercions to have less exceptions in
297            * tests/Class+Meth.R:
298    
299            * R/Ops.R (Compare): tweak for case with NA
300            * tests/simpl.R: hence another 'FIXME' eliminated
301    
302    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
305            objects.
306    
307            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
308              and more of "!", "&", "|", all, any; coercions
309    
310            * R/Rsparse.R: many coercions (which enable quite a few other
311            methods), thanks to enhancements in
312            * src/dgCMatrix.c (R_to_CMatrix): new, and
313            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
314            symmetric & triangular and ..RMatrix objects.
315    
316            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
317            renamed file from src/dsTMatrix.c;
318            now dealing with symmetric and triangular Tsparse coercions, both
319            to dense and general.
320    
321    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
324    
325            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
326            where sensible when the <numeric> is of length > 1.
327    
328    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Matrix.R ([<-): for M[] <- value: fix length
331    
332    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
335            * R/ndenseMatrix.R: new coercions n* -> l*
336    
337    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
340    
341            * R/Ops.R ("Logic"): and other "Ops", many updates
342    
343    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * src/Mutils.h (SET_DimNames): new utility
346    
347            * R/Auxiliaries.R (nnzero): improved and now exported via
348    
349            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
350    
351    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/diagMatrix.R (!): fix typo.
354    
355    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Auxiliaries.R (as_Csparse): and quite a few others:
358                    allow to pass class definition --> speedup
359            * R/sparseMatrix.R: apply the above
360    
361            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
362    
363            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
364            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
365            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
366    
367            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
368    
369            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
370            and use it for "sparse*" as well, since it's faster than the
371            as_Csparse(.) way.
372    
373    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
376    
377    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
380            as method for   M[ ij ] <- v
381            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
382    
383            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
384            FALSE answer
385    
386            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
387            * tests/indexing.R: test it, and some of the above
388    
389    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Auxiliaries.R (is_duplicatedT): new utility
392    
393    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
394    
395            * src/init.c (R_init_Matrix): export cholmod_scale
396    
397    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
400            base::as.matrix to (x, ...)
401    
402    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
405            file; start using "Logic", hence
406    
407            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
408            * NAMESPACE: import and export "Logic"
409    
410    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
413            only needed previously to R version 2.5.0.
414    
415    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
418    
419            * R/Tsparse.R (replTmat): fix subassignment of triangular
420            * R/Csparse.R (replCmat): ditto
421            * tests/indexing.R: more tests, incl the above fix
422    
423    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/Auxiliaries.R (drop0): extend for non CSparse
426            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
427    
428            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
429                    use uplo correctly (!); other places: use uplo_P() macro
430    
431            * R/Csparse.R (replCmat): call diagU2N() when needed
432            * R/Tsparse.R (replTmat): ditto
433    
434            * src/dtCMatrix.c (tCMatrix_validate): new
435            * src/dtTMatrix.c (tTMatrix_validate): new, used in
436            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
437    
438            * R/diagMatrix.R (replDiag): to use in [<-
439    
440    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
443                    also more general diagU2N().
444    
445    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
448            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
449    
450    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * tests/bind.R: a few more cases
453            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
454    
455            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
456            * R/ddenseMatrix.R (cbind2/rbind2)
457            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
458            * tests/indexing.R
459            * tests/indexing.Rout.save: updated
460    
461    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
464            * tests/indexing.R
465    
466    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
469            align with proper position of "0", i.e., right for integers.
470            argument 'align' by default is "fancy".
471    
472    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
475            * R/Csparse.R: and fix "Compare" for more cases.
476            * tests/Class+Meth.R: test some of these (m == m, m != m)
477    
478    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * R/lsparseMatrix.R: all() and any() methods
481            * R/ldenseMatrix.R:      ditto
482            * NAMESPACE, R/Matrix.R: ditto
483    
484            * man/all-methods.Rd: document them minimally
485    
486            * tests/simple.R: add a few examples for these
487    
488    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * R/Tsparse.R ([): fix long standing typo in symmetric case
491            * man/dsCMatrix-class.Rd: add example exhibiting the above case
492    
493    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
494    
495            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
496            to LL before converting to a sparse matrix. (The LDL form can be
497            converted to a sparse matrix but it is implicitly a unit
498            triangular matrix and a diagonal matrix overwritten on the diagonal.)
499    
500    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
501    
502            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
503    
504    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
505    
506            * DESCRIPTION (Version): updated -> release 0.9975-7
507            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
508    
509    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
512    
513    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
514    
515            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
516            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
517            is exactly singular.
518    
519    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * DESCRIPTION (Date): updated -> release 0.9975-6
522    
523    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
526            now returns symmetric.
527    
528            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
529    
530            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
531            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
532    
533            * R/Auxiliaries.R (.type.kind): added
534    
535    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
538            running src/CSparse_install.sh
539    
540            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
541    
542    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
545            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
546    
547            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
548    
549            * tests/Class+Meth.R (tstMatrixClass): now assure
550            the (important in method programming) property :
551    
552                    ###>>  Every "Matrix" is either
553                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
554    
555                    (where "*" stands for "Matrix")
556    
557            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
558    
559            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
560            * tests/validObj.R: checks for "comparison"
561    
562            * R/sparseMatrix.R ([): improved indexing for sparse;
563                    trying to keep <symmetric>[ n, n] symmmetric
564    
565            * tests/indexing.R: indexing for logical sparse now ok
566    
567    
568    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * src/Tsparse.c: use xTsparse_validate() , and hence remove
571    
572            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
573    
574    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
577    
578            * tests/simple.R: validObject() checking the above.
579    
580            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
581            replacing both dgCMatrix_validate and lgCM*.
582    
583            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
584            fix dimnames setting in other places.
585            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
586    
587    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
590    
591            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
592            symmetry test, via
593            * R/Auxiliaries.R (.as.dgC.0.factors):
594    
595    2006-11-01  Douglas Bates  <bates@r-project.org>
596    
597            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
598            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
599            <CsparseMatrix>) added
600    
601    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * tests/matprod.R: add a variation of Harri's example
604    
605            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
606            recursive infinitely.
607    
608            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
609    
610            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
611    
612    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
615            matrix if possible; test m+m == 2*m; now test dgRMatrix.
616            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
617            satisfy the above test.
618    
619    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
622    
623            * R/dgCMatrix.R: solve(a, b="missing") based on
624            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
625            RHS = NULL.
626    
627            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
628            add more (needed) [t]crossprod() methods.
629    
630            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
631    
632            * R/Auxiliaries.R (as_CspClass): cleanup
633            (drop0): internal utility for "Csparse_drop(*, 0)"
634            (.bail.out.2): encourage active feedback
635    
636    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/dMatrix.R(Compare): new(), then slots [no validity check]
639    
640            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
641            non-valid or 'sorted' case).
642    
643            * R/dsparseMatrix.R: add "chol" method.
644            * R/ddenseMatrix.R: ditto
645    
646            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
647            * NAMESPACE (Ops)
648            * R/diagMatrix.R (diag2T): simple utility used "higher level"
649            coercion; deprecating direct lower level coercions.
650    
651            * R/*.R (seq): use seq_len() and seq_along() where possible.
652    
653    
654    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * DESCRIPTION (Version): 0.9975-5 ready for release
657    
658    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
659    
660            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
661    
662    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/AllClass.R (corMatrix): add 'validity' check;
665                    comment out unused "LDL" class definition
666            * NAMESPACE: mention, but do not export "LDL" class
667            * R/corMatrix.R: new (simple), needed for R-devel with
668            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
669              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
670    
671    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
672    
673            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
674            use Rprintf and R's error handling.
675    
676    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
679            * tests/matprod.R: add tests for the bug fixed.
680    
681    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
682    
683            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
684            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
685    
686    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
687    
688            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
689    
690    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * DESCRIPTION (Version): 0.9975-3
693    
694            * R/diagMatrix.R (bdiag): new function constructing block diagonal
695            (sparse) matrices.
696            * man/bdiag.Rd: docu + examples
697    
698            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
699    
700            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
701            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
702    
703            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
704            that result is sparse or diagonal (and not dense).
705    
706            * man/Subassign-methods.Rd: fix examples
707    
708            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
709            should always return a sparse (and not sometimes a diagonal) matrix.
710    
711    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
714    
715    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
716    
717            * DESCRIPTION (Version): 0.9975-2
718    
719            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
720    
721    2006-10-02  Douglas Bates  <bates@R-project.org>
722    
723            * tests/dg_Matrix.R: Simplify test taking into account new code.
724    
725    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
728    
729            * R/lsTMatrix.R: new files w/ missing methods
730            * R/nsTMatrix.R:  "  'for completeness'
731    
732            * tests/Class+Meth.R: a bit less 'not.ok.classes'
733    
734            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
735    
736    
737    2006-09-28  Douglas Bates  <bates@R-project.org>
738    
739            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
740            included.
741    
742            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
743            Export C-callable functions used in Zt_create in lme4.
744    
745    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * DESCRIPTION (Version): 0.9975-1
748    
749            * tests/simple.R: less checks fail; using NA, found that our
750                    kronecker() is not base-compatible with NA's.
751    
752            * R/dMatrix.R: "Compare" method now implemented for all cases
753    
754            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
755    
756            * man/dtpMatrix-class.Rd: mention length of 'x' slot
757    
758            * src/dtpMatrix.c (dtpMatrix_validate): fix check
759            * src/dspMatrix.c (dspMatrix_validate): ditto
760    
761            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
762              including coercion to [nl]tTMatrix.
763    
764            * R/diagMatrix.R (show): print a header line as for other classes.
765    
766    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
767    
768            * src/Makefile.win (SUBDIRS): fix typo
769    
770    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
773    
774    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
775    
776            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
777            symmetric and y missing in R code using %*% (cholmod_aat doesn't
778            accept a symmetric matrix).
779            * tests/group-methods.R: Uncomment test of crossprod applied to
780            lsCMatrix objects.
781    
782    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * R/AllClass.R (symmetricMatrix): add validity method (available
785            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
786    
787            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
788    
789            * tests/indexing.Rout.save:
790            * tests/indexing.R: additions, mainly for 'lsparse'
791    
792            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
793            case.
794    
795            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
796    
797    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
800                    as 'N' (1-letter - Ok?)
801    
802            * tests/group-methods.R: add test for logical + NAs
803    
804            * R/dMatrix.R ("Compare"): fix to work with NA's
805    
806            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
807    
808            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
809                    which is implemented.
810    
811    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * src/chm_common.c: coerce logical <-> double instead of
814            typecasting;  needed for "l" matrix handling in cholmod.
815    
816            * tests/other-pkgs.R (graph): small extension in "graph" checks.
817    
818            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
819            (Tsp2grNEL): other fixes needed
820    
821    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
824                    Matrices, since "lMatrix", also "lsparseM" can have NA
825            * R/ndenseMatrix.R, etc: new source files
826            * man/nsparseMatrix-classes.Rd, etc: new help files
827            * tests/: adaptions
828            * src/chm_common.c (chm_dense_to_SEXP): and others:
829                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
830            * src/Csparse.c, etc: ditto
831    
832    2006-09-11  Douglas Bates  <bates@R-project.org>
833    
834            * src/Mutils.[ch],init.c inst/include/*.h: Move the
835            alloc_d**Matrix functions to the lme4 package.
836    
837    2006-09-09  Douglas Bates  <bates@R-project.org>
838    
839            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
840            fixed
841    
842    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * R/lMatrix.R: new
845    
846            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
847    
848            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
849            * man/tcrossprod.Rd: ditto
850    
851    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
852    
853            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
854            for exported functions
855            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
856            Remove partitioning algorithms for sparse matrix reordering.  The
857            copyright on the Metis code was problematic and the methods were
858            rarely used.
859            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
860            operations are now done entirely in CHOLMOD code.
861    
862    2006-09-06  Douglas Bates  <bates@R-project.org>
863    
864            * src/Mutils.h: Remove functions that are no longer used.
865    
866    2006-09-04  Douglas Bates  <bates@R-project.org>
867    
868            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
869            * src/DEPS.mkf: update
870    
871    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * created branches/Matrix-for-R-2.3.x;  on trunk: do
874            * DESCRIPTION (Version): 0.9975-0
875            (Depends): R (>= 2.4.0)
876    
877    2006-09-01  Douglas Bates  <bates@R-project.org>
878    
879            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
880    
881    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
882    
883            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
884            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
885    
886            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
887    
888    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
889    
890            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
891            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
892            * R/dsparseMatrix.R: ditto
893            * R/Csparse.R: ditto
894    
895    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * R/dMatrix.R (Compare): improve availability of "<", etc
898            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
899    
900    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
901    
902            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
903            of a 0-index which was used as 1-index (..hmm)
904    
905            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
906    
907            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
908            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
909            (.is.diagonal): ditto
910    
911            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
912    
913            * R/Matrix.R (Matrix): also work for NA data
914    
915  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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