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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1904, Sat Jun 16 18:34:05 2007 UTC
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1    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/kronecker.R: fix typo (could lead to inf.recursion)
4            * test/simple.R: testing that
5    
6            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
7            method (which can have arguments, show() can't).
8    
9    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
10    
11            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
12              added dgCMatrix_colSums for [col,row][Sums,Means]
13    
14    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
15    
16            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
17              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
18              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
19            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
20              class
21            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
22              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
23              row names to store the levels - duh!  Added an example.
24    
25    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * src/Csparse.c (Csparse_validate): check for *repeated* entries
28            thanks to example from Christian Buchta; with a test here:
29            * tests/simple.R:
30    
31    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
34            of colSums(*, sparseResult = TRUE)
35    
36    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
39            'na.rm = FALSE' as "everywhere" else in R.
40    
41    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
42    
43            * [r4421] src/CSparse_install.sh: Modify for new organization of
44              CSparse package
45            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
46              SuiteSparse
47            * [r4426] src/Makefile: add ./UFconfig to the include path for
48              compilation
49            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
50            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
51              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
52    
53    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
56            * R/sparseMatrix.R (prSpMatrix): now gives a message about
57            suppressed column names.
58    
59    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
60    
61            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
62              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
63              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
64              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
65              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
66              Remove warnings after change to const char* CHAR
67    
68    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
69    
70            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
71              type of M_cholmod_ssmult
72    
73    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
74    
75            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
76              src/init.c: Yet another cholmod export - cholmod_ssmult
77    
78    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * NAMESPACE: exported drop0(), since
81            * man/drop0.Rd: I have seen several cases, I really wanted to use
82            it, so our users may want too.
83    
84    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * man/colSums.Rd: separately document colSums() etc, since these
87            have the extra argument 'sparseResult'.
88    
89    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
92            * man/spMatrix.Rd: docu., including examples
93    
94            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
95            in order to make colMeans() etc fast *and* correct.
96            * R/sparseVector.R (replSPvec): "[<-" functionality for
97            sparseVectors; tested in
98            * tests/simple.R:
99    
100    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
103            (very) sparse Matrices; output similar to Matlab's print().
104    
105    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
106    
107            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
108            0-based, indices (Jose Quesada <quesada@gmail.com>).
109    
110    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
111    
112            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
113    
114    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/Auxiliaries.R (sparsapply): new utility, much faster than
117            tapply1() for large sparse matrices.
118    
119    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Matrix.R (dim<-): reshape now via sparseVector.
122    
123            * R/sparseVector.R: methods and function for
124            * R/AllClass.R: new "sparseVector" class and daughters.
125            * NAMESPACE: export new classes
126    
127    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * DESCRIPTION (Version): 0.99875-1
130            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
131    
132    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
135            indexing
136            * tests/indexing.R: test set for that.
137    
138    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
141            entries.
142            * tests/indexing.R(out): add regression test for it
143    
144    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
147            name for "!" method definitions.
148    
149    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/Tsparse.R (intI): new utility, used for "[" :
152                    Cleanup up there, and fixes for duplicated indices - more TODO!
153    
154            * tests/indexing.R(out): more tests
155    
156    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
157    
158            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
159            code that is now part of the R Lapack library.
160    
161            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
162            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
163    
164    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
167    
168    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
171            up with extraneous names '0'...'<n-1>'
172    
173    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgTMatrix.R (mat2dgT): care about NAs
176    
177    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/kronecker.R: triangularity preserving methods
180    
181    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/kronecker.R: new file collecting kronecker() methods in one
184                    place.  Goal: become much faster!
185    
186    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
189            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
190            can be much faster.
191    
192            * tests/matprod.R: add regression tests for these (upper & lower).
193    
194    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/Matrix.R (diff): method for our Matrices.
197    
198            * R/sparseMatrix.R (isDiagonal): check dim()!
199    
200    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Matrix.R (dim<-): new method for "reshape()" built on a
203            proposal from Tamas Papp.
204    
205    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
208    
209            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
210            rather define and export  cBind() and rBind() only.
211            --> useRs *must* change code that used to have cbind()/rbind() !!
212    
213            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
214            * R/bind.Rout.save: ditto
215    
216    2007-02-16  Douglas Bates  <bates@r-project.org>
217    
218            * DESCRIPTION (Date, Version): 0.9975-11 with new date
219            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
220            const modifier on declaration of the array 'valid'
221    
222    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
223    
224            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
225    
226    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
229    
230            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
231            * tests/simple.R: test the above and some of these coercions:
232    
233            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
234                    be careful to avoid infinite recursion, using new coercions in
235            * R/ngCMatrix.R and nsC... and ntC...
236            * R/lsparseMatrix.R: ditto
237    
238            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
239    
240            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
241            * R/Rsparse.R: reactivate .Call()s
242    
243            * tests/Class+Meth.R: a bit more on actual classes
244    
245    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
246    
247            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
248    
249    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * DESCRIPTION (Version): 0.9975-10 to upload
252    
253            * tests/Class+Meth.R (tstMatrixClass): require coercions to
254            specific classes less unconditionally.
255    
256            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
257    
258            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
259    
260            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
261            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
262            R_to_CMatrix segfaults on one platform.
263            Eliminate most coercion method to *specific* classes, and replace
264            with virtual classes coercions.
265    
266    
267    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
268    
269            * src/init.c: export the CHM...._validate() placeholders, since
270            they *are* called.
271    
272            * tests/Class+Meth.R (classCanCoerce): and starting to test
273            all as(<from>, <to>)
274    
275    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
278            * tests/indexing.R: tested now
279            * tests/indexing.Rout.save: updated
280    
281            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
282            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
283            appropriate.
284    
285            * NAMESPACE: export a trivial
286            * R/Matrix.R: drop() Matrix-method
287    
288            * R/AllClass.R: moved all prototypes to virtual super classes.
289    
290            * R/Rsparse.R: many more coercions to have less exceptions in
291            * tests/Class+Meth.R:
292    
293            * R/Ops.R (Compare): tweak for case with NA
294            * tests/simpl.R: hence another 'FIXME' eliminated
295    
296    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
299            objects.
300    
301            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
302              and more of "!", "&", "|", all, any; coercions
303    
304            * R/Rsparse.R: many coercions (which enable quite a few other
305            methods), thanks to enhancements in
306            * src/dgCMatrix.c (R_to_CMatrix): new, and
307            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
308            symmetric & triangular and ..RMatrix objects.
309    
310            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
311            renamed file from src/dsTMatrix.c;
312            now dealing with symmetric and triangular Tsparse coercions, both
313            to dense and general.
314    
315    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
318    
319            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
320            where sensible when the <numeric> is of length > 1.
321    
322    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Matrix.R ([<-): for M[] <- value: fix length
325    
326    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
329            * R/ndenseMatrix.R: new coercions n* -> l*
330    
331    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
334    
335            * R/Ops.R ("Logic"): and other "Ops", many updates
336    
337    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * src/Mutils.h (SET_DimNames): new utility
340    
341            * R/Auxiliaries.R (nnzero): improved and now exported via
342    
343            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
344    
345    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/diagMatrix.R (!): fix typo.
348    
349    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Auxiliaries.R (as_Csparse): and quite a few others:
352                    allow to pass class definition --> speedup
353            * R/sparseMatrix.R: apply the above
354    
355            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
356    
357            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
358            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
359            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
360    
361            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
362    
363            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
364            and use it for "sparse*" as well, since it's faster than the
365            as_Csparse(.) way.
366    
367    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
370    
371    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
374            as method for   M[ ij ] <- v
375            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
376    
377            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
378            FALSE answer
379    
380            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
381            * tests/indexing.R: test it, and some of the above
382    
383    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/Auxiliaries.R (is_duplicatedT): new utility
386    
387    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
388    
389            * src/init.c (R_init_Matrix): export cholmod_scale
390    
391    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
394            base::as.matrix to (x, ...)
395    
396    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
399            file; start using "Logic", hence
400    
401            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
402            * NAMESPACE: import and export "Logic"
403    
404    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
407            only needed previously to R version 2.5.0.
408    
409    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
412    
413            * R/Tsparse.R (replTmat): fix subassignment of triangular
414            * R/Csparse.R (replCmat): ditto
415            * tests/indexing.R: more tests, incl the above fix
416    
417    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/Auxiliaries.R (drop0): extend for non CSparse
420            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
421    
422            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
423                    use uplo correctly (!); other places: use uplo_P() macro
424    
425            * R/Csparse.R (replCmat): call diagU2N() when needed
426            * R/Tsparse.R (replTmat): ditto
427    
428            * src/dtCMatrix.c (tCMatrix_validate): new
429            * src/dtTMatrix.c (tTMatrix_validate): new, used in
430            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
431    
432            * R/diagMatrix.R (replDiag): to use in [<-
433    
434    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
437                    also more general diagU2N().
438    
439    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
442            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
443    
444    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * tests/bind.R: a few more cases
447            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
448    
449            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
450            * R/ddenseMatrix.R (cbind2/rbind2)
451            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
452            * tests/indexing.R
453            * tests/indexing.Rout.save: updated
454    
455    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
458            * tests/indexing.R
459    
460    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
463            align with proper position of "0", i.e., right for integers.
464            argument 'align' by default is "fancy".
465    
466    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
469            * R/Csparse.R: and fix "Compare" for more cases.
470            * tests/Class+Meth.R: test some of these (m == m, m != m)
471    
472    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/lsparseMatrix.R: all() and any() methods
475            * R/ldenseMatrix.R:      ditto
476            * NAMESPACE, R/Matrix.R: ditto
477    
478            * man/all-methods.Rd: document them minimally
479    
480            * tests/simple.R: add a few examples for these
481    
482    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/Tsparse.R ([): fix long standing typo in symmetric case
485            * man/dsCMatrix-class.Rd: add example exhibiting the above case
486    
487    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
488    
489            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
490            to LL before converting to a sparse matrix. (The LDL form can be
491            converted to a sparse matrix but it is implicitly a unit
492            triangular matrix and a diagonal matrix overwritten on the diagonal.)
493    
494    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
495    
496            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
497    
498    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
499    
500            * DESCRIPTION (Version): updated -> release 0.9975-7
501            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
502    
503    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
506    
507    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
508    
509            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
510            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
511            is exactly singular.
512    
513    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * DESCRIPTION (Date): updated -> release 0.9975-6
516    
517    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
520            now returns symmetric.
521    
522            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
523    
524            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
525            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
526    
527            * R/Auxiliaries.R (.type.kind): added
528    
529    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
532            running src/CSparse_install.sh
533    
534            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
535    
536    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
539            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
540    
541            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
542    
543            * tests/Class+Meth.R (tstMatrixClass): now assure
544            the (important in method programming) property :
545    
546                    ###>>  Every "Matrix" is either
547                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
548    
549                    (where "*" stands for "Matrix")
550    
551            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
552    
553            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
554            * tests/validObj.R: checks for "comparison"
555    
556            * R/sparseMatrix.R ([): improved indexing for sparse;
557                    trying to keep <symmetric>[ n, n] symmmetric
558    
559            * tests/indexing.R: indexing for logical sparse now ok
560    
561    
562    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * src/Tsparse.c: use xTsparse_validate() , and hence remove
565    
566            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
567    
568    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
571    
572            * tests/simple.R: validObject() checking the above.
573    
574            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
575            replacing both dgCMatrix_validate and lgCM*.
576    
577            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
578            fix dimnames setting in other places.
579            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
580    
581    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
584    
585            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
586            symmetry test, via
587            * R/Auxiliaries.R (.as.dgC.0.factors):
588    
589    2006-11-01  Douglas Bates  <bates@r-project.org>
590    
591            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
592            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
593            <CsparseMatrix>) added
594    
595    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * tests/matprod.R: add a variation of Harri's example
598    
599            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
600            recursive infinitely.
601    
602            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
603    
604            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
605    
606    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
609            matrix if possible; test m+m == 2*m; now test dgRMatrix.
610            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
611            satisfy the above test.
612    
613    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
616    
617            * R/dgCMatrix.R: solve(a, b="missing") based on
618            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
619            RHS = NULL.
620    
621            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
622            add more (needed) [t]crossprod() methods.
623    
624            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
625    
626            * R/Auxiliaries.R (as_CspClass): cleanup
627            (drop0): internal utility for "Csparse_drop(*, 0)"
628            (.bail.out.2): encourage active feedback
629    
630    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/dMatrix.R(Compare): new(), then slots [no validity check]
633    
634            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
635            non-valid or 'sorted' case).
636    
637            * R/dsparseMatrix.R: add "chol" method.
638            * R/ddenseMatrix.R: ditto
639    
640            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
641            * NAMESPACE (Ops)
642            * R/diagMatrix.R (diag2T): simple utility used "higher level"
643            coercion; deprecating direct lower level coercions.
644    
645            * R/*.R (seq): use seq_len() and seq_along() where possible.
646    
647    
648    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * DESCRIPTION (Version): 0.9975-5 ready for release
651    
652    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
653    
654            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
655    
656    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/AllClass.R (corMatrix): add 'validity' check;
659                    comment out unused "LDL" class definition
660            * NAMESPACE: mention, but do not export "LDL" class
661            * R/corMatrix.R: new (simple), needed for R-devel with
662            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
663              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
664    
665    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
666    
667            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
668            use Rprintf and R's error handling.
669    
670    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
673            * tests/matprod.R: add tests for the bug fixed.
674    
675    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
676    
677            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
678            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
679    
680    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
681    
682            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
683    
684    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * DESCRIPTION (Version): 0.9975-3
687    
688            * R/diagMatrix.R (bdiag): new function constructing block diagonal
689            (sparse) matrices.
690            * man/bdiag.Rd: docu + examples
691    
692            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
693    
694            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
695            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
696    
697            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
698            that result is sparse or diagonal (and not dense).
699    
700            * man/Subassign-methods.Rd: fix examples
701    
702            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
703            should always return a sparse (and not sometimes a diagonal) matrix.
704    
705    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
708    
709    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
710    
711            * DESCRIPTION (Version): 0.9975-2
712    
713            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
714    
715    2006-10-02  Douglas Bates  <bates@R-project.org>
716    
717            * tests/dg_Matrix.R: Simplify test taking into account new code.
718    
719    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
722    
723            * R/lsTMatrix.R: new files w/ missing methods
724            * R/nsTMatrix.R:  "  'for completeness'
725    
726            * tests/Class+Meth.R: a bit less 'not.ok.classes'
727    
728            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
729    
730    
731    2006-09-28  Douglas Bates  <bates@R-project.org>
732    
733            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
734            included.
735    
736            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
737            Export C-callable functions used in Zt_create in lme4.
738    
739    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * DESCRIPTION (Version): 0.9975-1
742    
743            * tests/simple.R: less checks fail; using NA, found that our
744                    kronecker() is not base-compatible with NA's.
745    
746            * R/dMatrix.R: "Compare" method now implemented for all cases
747    
748            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
749    
750            * man/dtpMatrix-class.Rd: mention length of 'x' slot
751    
752            * src/dtpMatrix.c (dtpMatrix_validate): fix check
753            * src/dspMatrix.c (dspMatrix_validate): ditto
754    
755            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
756              including coercion to [nl]tTMatrix.
757    
758            * R/diagMatrix.R (show): print a header line as for other classes.
759    
760    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * src/Makefile.win (SUBDIRS): fix typo
763    
764    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
767    
768    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
769    
770            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
771            symmetric and y missing in R code using %*% (cholmod_aat doesn't
772            accept a symmetric matrix).
773            * tests/group-methods.R: Uncomment test of crossprod applied to
774            lsCMatrix objects.
775    
776    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/AllClass.R (symmetricMatrix): add validity method (available
779            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
780    
781            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
782    
783            * tests/indexing.Rout.save:
784            * tests/indexing.R: additions, mainly for 'lsparse'
785    
786            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
787            case.
788    
789            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
790    
791    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
794                    as 'N' (1-letter - Ok?)
795    
796            * tests/group-methods.R: add test for logical + NAs
797    
798            * R/dMatrix.R ("Compare"): fix to work with NA's
799    
800            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
801    
802            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
803                    which is implemented.
804    
805    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * src/chm_common.c: coerce logical <-> double instead of
808            typecasting;  needed for "l" matrix handling in cholmod.
809    
810            * tests/other-pkgs.R (graph): small extension in "graph" checks.
811    
812            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
813            (Tsp2grNEL): other fixes needed
814    
815    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
816    
817            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
818                    Matrices, since "lMatrix", also "lsparseM" can have NA
819            * R/ndenseMatrix.R, etc: new source files
820            * man/nsparseMatrix-classes.Rd, etc: new help files
821            * tests/: adaptions
822            * src/chm_common.c (chm_dense_to_SEXP): and others:
823                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
824            * src/Csparse.c, etc: ditto
825    
826    2006-09-11  Douglas Bates  <bates@R-project.org>
827    
828            * src/Mutils.[ch],init.c inst/include/*.h: Move the
829            alloc_d**Matrix functions to the lme4 package.
830    
831    2006-09-09  Douglas Bates  <bates@R-project.org>
832    
833            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
834            fixed
835    
836    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/lMatrix.R: new
839    
840            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
841    
842            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
843            * man/tcrossprod.Rd: ditto
844    
845    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
846    
847            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
848            for exported functions
849            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
850            Remove partitioning algorithms for sparse matrix reordering.  The
851            copyright on the Metis code was problematic and the methods were
852            rarely used.
853            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
854            operations are now done entirely in CHOLMOD code.
855    
856    2006-09-06  Douglas Bates  <bates@R-project.org>
857    
858            * src/Mutils.h: Remove functions that are no longer used.
859    
860    2006-09-04  Douglas Bates  <bates@R-project.org>
861    
862            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
863            * src/DEPS.mkf: update
864    
865    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
866    
867            * created branches/Matrix-for-R-2.3.x;  on trunk: do
868            * DESCRIPTION (Version): 0.9975-0
869            (Depends): R (>= 2.4.0)
870    
871    2006-09-01  Douglas Bates  <bates@R-project.org>
872    
873            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
874    
875    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
876    
877            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
878            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
879    
880            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
881    
882    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
885            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
886            * R/dsparseMatrix.R: ditto
887            * R/Csparse.R: ditto
888    
889    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * R/dMatrix.R (Compare): improve availability of "<", etc
892            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
893    
894    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
897            of a 0-index which was used as 1-index (..hmm)
898    
899            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
900    
901            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
902            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
903            (.is.diagonal): ditto
904    
905            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
906    
907            * R/Matrix.R (Matrix): also work for NA data
908    
909    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
912            in all cases.
913    
914    2006-08-27  Douglas Bates  <bates@R-project.org>
915    
916            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
917            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
918    
919    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
922            subclasses of "ddenseMatrix"
923            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
924            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
925            instead of half dozen specialized ones.
926    
927    2006-08-25  Douglas Bates  <bates@R-project.org>
928    
929            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
930            <tillard@cirad.fr> - ordering standard errors to match effects.
931    
932    2006-08-24  Douglas Bates  <bates@R-project.org>
933    
934            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
935            on R_ldl.
936            * R/lCholCMatrix.R,
937            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
938            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
939            * many files in ./R and ./src: Use more general version of
940            dup_mMatrix_as_dgeMatrix to simplify method definitions.
941            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
942            dtpMatrix, dspMatrix and dppMatrix conversions.
943    
944    
945    2006-08-23  Douglas Bates  <bates@R-project.org>
946    
947            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
948            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
949            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
950            dgeMatrix_crossprod (may need to do this in other places).
951            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
952            generic and method for dsCMatrix.  Use CHOLMOD for chol().
953    
954    2006-08-22  Douglas Bates  <bates@R-project.org>
955    
956            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
957            types of classed Matrices, matrices or numeric or logical vectors.
958            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
959            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
960            to Mutils.h (as an inline) and change name to Matrix_check_class;
961            fixes in as_cholmod_factor and chm_factor_to_SEXP.
962            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
963            dsCMatrix_matrix_solve.  Comment out vestigial functions.
964            * src/Csparse.c: use diag_P and uplo_P macros.
965    
966    2006-08-21  Douglas Bates  <bates@R-project.org>
967    
968            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
969            valgrind.
970            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
971            inverses.
972            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
973            -Wall warnings.
974            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
975            Use dup_mMatrix_as_dgeMatrix.
976    
977    2006-08-20  Douglas Bates  <bates@R-project.org>
978    
979            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
980            * tests/sparseQR.R: Added
981            * man/sparseQR-class.Rd: Document methods for qr.* generics
982            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
983    
984    2006-08-19  Douglas Bates  <bates@R-project.org>
985    
986            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
987            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
988            and qr.fitted.
989            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
990            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
991    
992    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
995            the base version has no "..." argument.
996    
997            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
998    
999            * R/Matrix.R: define and
1000            * NAMESPACE: export as.numeric() and as.logical() methods.
1001                    Let's hope these do not badly slow down something...
1002            Finally export the zapsmall() method.
1003    
1004    2006-08-17  Douglas Bates  <bates@R-project.org>
1005    
1006            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1007            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1008            * src/dtCMatrix.c :Remove code that is no longer used
1009            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1010    
1011    2006-08-14  Douglas Bates  <bates@R-project.org>
1012    
1013            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1014            Csparse_to_logical and Csparse_symmetric_to_general.
1015            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1016            coercion methods between CsparseMatrix and TsparseMatrix.
1017    
1018    2006-08-14  Douglas Bates  <bates@R-project.org>
1019    
1020            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1021            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1022            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1023            possible.
1024    
1025  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
1026    
1027          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

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