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[matrix] Diff of /pkg/ChangeLog
 [matrix] / pkg / ChangeLog

Diff of /pkg/ChangeLog

revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 2098, Sun Dec 9 00:35:14 2007 UTC
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3    >>>>>> FIXME  rcond(matrix(1:6, 2,3))   gives infinite recursion !!! <<<<<<<<<<
4
5
6    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
7
8            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
9                    and hence does as.vector(.).
10            * man/pMatrix-class.Rd: docs
11            * R/sparseMatrix.R: fix for printing "integer sparse"
12
13            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
14
15            * R/Matrix.R and others: use "exact" function argument list for
16                    both "["   : (x, i,j, ..., drop)
17                    and  "[<-" : (x, i,j, ..., value)
18
19            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
20            * R/Tsparse.R (replTmat):    ditto
21            * R/diagMatrix.R (replDiag): ditto
22            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
23            * tests/indexing.R: testing the above
24
25    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
26
27            * R/sparseMatrix.R (cov2cor): method for sparse matrices
28
29            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
30
31            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
32
33            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
34
35    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
36
37            * R/Matrix.R: "generic" cov2cor() method
38
39            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
40                    speed up Q %*% D %*% t(Q)
41            * tests/dpoMatrix.R: test nearPD()
42
43    2007-12-05  Doug Bates and Martin Maechler
44
45            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
46            stats::xtabs() allowing to create sparse matrices.
47
48    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
49
50            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
51
52    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
53
54            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
55
56    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
57
58            * R/LU.R: solve() method for "denseLU"
59
60    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
61
62            * DESCRIPTION (Version): 0.999375-3 preparing for release
63
64            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
65
66            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
67
68    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
69
70            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
71              thanks to Kasper Kristensen.
72            * tests/matprod.R: regression test for that.
73
74    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
75
76            * [r4778] R/AllGeneric.R: Check R version before defining generics for
77              primitives
78
79    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
80
81            * R/denseMatrix.R (rcond): method
82            * R/sparseQR.R (rcond): method, use x or t(x)
83
84    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
85
86            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
87            matrices.
88            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
89
90            * man/rcond.Rd: mention the more general definition, and add
91            example for non-square matrices.
92
93            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
94
95    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
96
97            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
98
99    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
100
101            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
102            * tests/indexing.R: add new regression for the above cases.
103
104    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
105
106            * src/Mutils.h (__sun): clause for alloca.h on Solaris
107
108    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
109
110            * DESCRIPTION (Date, Version): 0.999375-2
111
112    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
113
114            * R/HBMM.R (readMM): make work for pattern matrices as well
115
116    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
117
118            * [r4730] src/Mutils.h: declare alloca
119            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
120              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
121              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
122              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
123              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
124              methods; switch writeMM to use CHOLMOD code; repair readMM
125
126    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
127
128            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
129            Oehlschlaegel's ... result type still to be discussed!
130
131    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
132
133            * man/image-methods.Rd: new, combining all image() methods
134
135    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
136
137            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
138            to work via dgC...
139
140            * R/Matrix.R (Matrix): special treatment for "table" (S3)
141
142    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
143
144            * R/dgTMatrix.R (image): change defaults to
145                    aspect = "iso", colorkey = FALSE
146
147    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
148
149            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
150            must copy its *expanded* x slot before LAPACK call.
151
152            * tests/matprod.R: test the last days' changes.
153
154    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
155
156            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
157              as well as in sources
158            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
159              Lapack call
160
161    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
162
163            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
164                    ("Matrix", "matrix") which is needed in some cases.
165            Ditto for solve().
166
167            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
168            infinite recursion in dispatch for some cases.
169
170    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
171
172            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
173              so pointers match
174
175    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
176
177            * DESCRIPTION (Date): set ready for release -- 0.999375-1
178
179    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
180
181            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
182              src/chm_common.c, src/chm_common.h: Change API for
183              numeric_as_chm_dense and N_AS_CHM_DN
184
185    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
186
187            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
188            * tests/matprod.R: regr.test for it
189
190    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
191
192            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
193            * tests/group-methods.R: and regression-test it
194
195    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
196
197            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
198              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
199              triplet_to_sparse, documentation, use typedefs
200
201    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
202
203            * man/dpoMatrix-class.Rd: added 'corMatrix' example
204
205            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
206            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
207            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
208
209            * R/lsparseMatrix.R: bug fix in "all" method
210            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
211
212            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
213            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
214                    + matrix |-> nMatrix coercion
215            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
216            * man/pMatrix-class.Rd: ditto
217
218            * R/Matrix.R (Summary): method for non-dMatrix
219
220            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
221            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
222                    test all Summary methods.
223
224    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
225
226            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
227
228    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
229
230            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
231
232            * R/pMatrix.R (t?crossprod): methods for pMatrix
233
234    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
235
236            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
237
238    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
239
240            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
241              trying to fix a subtle bug - which has been somewhere else.
242
243    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
244
245            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
246              solve the bug
247
248    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
249
250            * src/dgCMatrix.c (compressed_to_TMatrix):
251
252    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
253
254            * src/Csparse.c (Rsparse_validate): new, to have some validity
255            checking for RsparseMatrix
256            * src/dgCMatrix.c (xRMatrix_validate): ditto
257            * src/dtCMatrix.c (tRMatrix_validate): ditto
258
259    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
260
261            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
262              lgRMatrix
263            * [r4568] DESCRIPTION: Prepare for bug-fix release
264            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
265              for declaration of cholmod_symmetry
266
267    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
268
269            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
270            release.
271
272    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
273
274            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
275              functions - no longer used
276            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
277              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
278              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
279              Alloca
280
281    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
282
283            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
284              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
285              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
286              src/t_gCMatrix_colSums.c: more R_CheckStack()s
287
288    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
289
290            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
291              the required amount of memory then call M_numeric_as_chm_dense.
292            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
293              (like Calloc but calling alloca)
294
295    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
296
297            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
298            and extended with more sophisticated 'col.names' option.
299            * NAMESPACE: export  printSparseMatrix()
300            * man/printSpMatrix.Rd: document, incl. examples
301
302    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
303
304            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
305              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
306              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
307
308    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
309
310            * DESCRIPTION (Version): 0.99875-4
311
312            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
313            some dimnames perservation.
314
315            * R/dsTMatrix.R (t-method): keep dimnames
316            * R/dtTMatrix.R:  ditto
317
318            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
319            and ncol(.) < 10
320
321            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
322            from Mutils.h
323
324            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
325            e.g. in as(<ngCMatrix>, "matrix")
326
327    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
328
329            * [r4529] .: Create a branch for the API changes from the 0.99875
330              series to the 0.999375 series
331            * [r4530] DESCRIPTION, inst/include/Matrix.h,
332              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
333              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
334              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
335              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
336              as_cholmod_x functions
337
338    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
339
340            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
341              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
342              to Comparisons
343
344    >>>>>>> .merge-right.r4561
345    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
346
347            * DESCRIPTION (Version): 0.99875-3 ready to be released.
348
349            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
350
351            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
352            that should also work in a future version of R.
353
354    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
355
356            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
357
358            * R/sparseVector.R: more *sparseVector coercions, notably for
359            non - double ones.
360
361    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
362
363            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
364              notably the new ones building on the new .Call(.)s:
365
366            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
367            all 4 of [dlin]gCMatrix_colSums().
368
369    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
370
371            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
372            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
373              result
374
375    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
376
377            * R/kronecker.R: fix typo (could lead to inf.recursion)
378            * test/simple.R: testing that
379
380            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
381            method as well (which can have arguments, show() can't).
382
383    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
384
385            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
386              added dgCMatrix_colSums for [col,row][Sums,Means]
387
388    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
389
390            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
391              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
392              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
393            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
394              class
395            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
396              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
397              row names to store the levels - duh!  Added an example.
398
399    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
400
401            * src/Csparse.c (Csparse_validate): check for *repeated* entries
402            thanks to example from Christian Buchta; with a test here:
403            * tests/simple.R:
404
405    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
406
407            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
408            of colSums(*, sparseResult = TRUE)
409
410    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
411
412            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
413            'na.rm = FALSE' as "everywhere" else in R.
414
415    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
416
417            * [r4421] src/CSparse_install.sh: Modify for new organization of
418              CSparse package
419            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
420              SuiteSparse
421            * [r4426] src/Makefile: add ./UFconfig to the include path for
422              compilation
423            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
424            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
425              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
426
427    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
428
429            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
430            * R/sparseMatrix.R (prSpMatrix): now gives a message about
431            suppressed column names.
432
433    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
434
435            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
436              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
437              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
438              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
439              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
440              Remove warnings after change to const char* CHAR
441
442    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
443
444            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
445              type of M_cholmod_ssmult
446
447    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
448
449            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
450              src/init.c: Yet another cholmod export - cholmod_ssmult
451
452    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
453
454            * NAMESPACE: exported drop0(), since
455            * man/drop0.Rd: I have seen several cases, I really wanted to use
456            it, so our users may want too.
457
458    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
459
460            * man/colSums.Rd: separately document colSums() etc, since these
461            have the extra argument 'sparseResult'.
462
463    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
464
465            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
466            * man/spMatrix.Rd: docu., including examples
467
468            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
469            in order to make colMeans() etc fast *and* correct.
470            * R/sparseVector.R (replSPvec): "[<-" functionality for
471            sparseVectors; tested in
472            * tests/simple.R:
473
474    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
475
476            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
477            (very) sparse Matrices; output similar to Matlab's print().
478
479    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
480
481            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
482            0-based, indices (Jose Quesada <quesada@gmail.com>).
483
484    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
485
486            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
487
488    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
489
490            * R/Auxiliaries.R (sparsapply): new utility, much faster than
491            tapply1() for large sparse matrices.
492
493    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
494
495            * R/Matrix.R (dim<-): reshape now via sparseVector.
496
497            * R/sparseVector.R: methods and function for
498            * R/AllClass.R: new "sparseVector" class and daughters.
499            * NAMESPACE: export new classes
500
501    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
502
503            * DESCRIPTION (Version): 0.99875-1
504            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
505
506    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
507
508            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
509            indexing
510            * tests/indexing.R: test set for that.
511
512    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
513
514            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
515            entries.
516            * tests/indexing.R(out): add regression test for it
517
518    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
519
520            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
521            name for "!" method definitions.
522
523    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
524
525            * R/Tsparse.R (intI): new utility, used for "[" :
526                    Cleanup up there, and fixes for duplicated indices - more TODO!
527
528            * tests/indexing.R(out): more tests
529
530    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
531
532            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
533            code that is now part of the R Lapack library.
534
535            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
536            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
537
538    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
539
540            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
541
542    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
543
544            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
545            up with extraneous names '0'...'<n-1>'
546
547    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
548
549            * R/dgTMatrix.R (mat2dgT): care about NAs
550
551    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
552
553            * R/kronecker.R: triangularity preserving methods
554
555    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
556
557            * R/kronecker.R: new file collecting kronecker() methods in one
558                    place.  Goal: become much faster!
559
560    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
561
562            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
563            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
564            can be much faster.
565
566            * tests/matprod.R: add regression tests for these (upper & lower).
567
568    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
569
570            * R/Matrix.R (diff): method for our Matrices.
571
572            * R/sparseMatrix.R (isDiagonal): check dim()!
573
574    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
575
576            * R/Matrix.R (dim<-): new method for "reshape()" built on a
577            proposal from Tamas Papp.
578
579    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
580
581            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
582
583            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
584            rather define and export  cBind() and rBind() only.
585            --> useRs *must* change code that used to have cbind()/rbind() !!
586
587            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
588            * R/bind.Rout.save: ditto
589
590    2007-02-16  Douglas Bates  <bates@r-project.org>
591
592            * DESCRIPTION (Date, Version): 0.9975-11 with new date
593            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
594            const modifier on declaration of the array 'valid'
595
596    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
597
598            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
599
600    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
601
602            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
603
604            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
605            * tests/simple.R: test the above and some of these coercions:
606
607            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
608                    be careful to avoid infinite recursion, using new coercions in
609            * R/ngCMatrix.R and nsC... and ntC...
610            * R/lsparseMatrix.R: ditto
611
612            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
613
614            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
615            * R/Rsparse.R: reactivate .Call()s
616
617            * tests/Class+Meth.R: a bit more on actual classes
618
619    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
620
621            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
622
623    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
624
625            * DESCRIPTION (Version): 0.9975-10 to upload
626
627            * tests/Class+Meth.R (tstMatrixClass): require coercions to
628            specific classes less unconditionally.
629
630            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
631
632            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
633
634            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
635            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
636            R_to_CMatrix segfaults on one platform.
637            Eliminate most coercion method to *specific* classes, and replace
638            with virtual classes coercions.
639
640
641    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
642
643            * src/init.c: export the CHM...._validate() placeholders, since
644            they *are* called.
645
646            * tests/Class+Meth.R (classCanCoerce): and starting to test
647            all as(<from>, <to>)
648
649    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
650
651            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
652            * tests/indexing.R: tested now
653            * tests/indexing.Rout.save: updated
654
655            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
656            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
657            appropriate.
658
659            * NAMESPACE: export a trivial
660            * R/Matrix.R: drop() Matrix-method
661
662            * R/AllClass.R: moved all prototypes to virtual super classes.
663
664            * R/Rsparse.R: many more coercions to have less exceptions in
665            * tests/Class+Meth.R:
666
667            * R/Ops.R (Compare): tweak for case with NA
668            * tests/simpl.R: hence another 'FIXME' eliminated
669
670    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
671
672            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
673            objects.
674
675            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
676              and more of "!", "&", "|", all, any; coercions
677
678            * R/Rsparse.R: many coercions (which enable quite a few other
679            methods), thanks to enhancements in
680            * src/dgCMatrix.c (R_to_CMatrix): new, and
681            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
682            symmetric & triangular and ..RMatrix objects.
683
684            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
685            renamed file from src/dsTMatrix.c;
686            now dealing with symmetric and triangular Tsparse coercions, both
687            to dense and general.
688
689    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
690
691            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
692
693            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
694            where sensible when the <numeric> is of length > 1.
695
696    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
697
698            * R/Matrix.R ([<-): for M[] <- value: fix length
699
700    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
701
702            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
703            * R/ndenseMatrix.R: new coercions n* -> l*
704
705    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
706
707            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
708
709            * R/Ops.R ("Logic"): and other "Ops", many updates
710
711    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
712
713            * src/Mutils.h (SET_DimNames): new utility
714
715            * R/Auxiliaries.R (nnzero): improved and now exported via
716
717            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
718
719    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
720
721            * R/diagMatrix.R (!): fix typo.
722
723    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
724
725            * R/Auxiliaries.R (as_Csparse): and quite a few others:
726                    allow to pass class definition --> speedup
727            * R/sparseMatrix.R: apply the above
728
729            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
730
731            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
732            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
733            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
734
735            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
736
737            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
738            and use it for "sparse*" as well, since it's faster than the
739            as_Csparse(.) way.
740
741    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
742
743            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
744
745    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
746
747            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
748            as method for   M[ ij ] <- v
749            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
750
751            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
752            FALSE answer
753
754            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
755            * tests/indexing.R: test it, and some of the above
756
757    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
758
759            * R/Auxiliaries.R (is_duplicatedT): new utility
760
761    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
762
763            * src/init.c (R_init_Matrix): export cholmod_scale
764
765    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
766
767            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
768            base::as.matrix to (x, ...)
769
770    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
771
772            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
773            file; start using "Logic", hence
774
775            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
776            * NAMESPACE: import and export "Logic"
777
778    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
779
780            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
781            only needed previously to R version 2.5.0.
782
783    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
784
785            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
786
787            * R/Tsparse.R (replTmat): fix subassignment of triangular
788            * R/Csparse.R (replCmat): ditto
789            * tests/indexing.R: more tests, incl the above fix
790
791    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
792
793            * R/Auxiliaries.R (drop0): extend for non CSparse
794            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
795
796            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
797                    use uplo correctly (!); other places: use uplo_P() macro
798
799            * R/Csparse.R (replCmat): call diagU2N() when needed
800            * R/Tsparse.R (replTmat): ditto
801
802            * src/dtCMatrix.c (tCMatrix_validate): new
803            * src/dtTMatrix.c (tTMatrix_validate): new, used in
804            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
805
806            * R/diagMatrix.R (replDiag): to use in [<-
807
808    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
809
810            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
811                    also more general diagU2N().
812
813    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
814
815            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
816            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
817
818    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
819
820            * tests/bind.R: a few more cases
821            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
822
823            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
824            * R/ddenseMatrix.R (cbind2/rbind2)
825            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
826            * tests/indexing.R
827            * tests/indexing.Rout.save: updated
828
829    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
830
831            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
832            * tests/indexing.R
833
834    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
835
836            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
837            align with proper position of "0", i.e., right for integers.
838            argument 'align' by default is "fancy".
839
840    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
841
842            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
843            * R/Csparse.R: and fix "Compare" for more cases.
844            * tests/Class+Meth.R: test some of these (m == m, m != m)
845
846    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
847
848            * R/lsparseMatrix.R: all() and any() methods
849            * R/ldenseMatrix.R:      ditto
850            * NAMESPACE, R/Matrix.R: ditto
851
852            * man/all-methods.Rd: document them minimally
853
854            * tests/simple.R: add a few examples for these
855
856    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
857
858            * R/Tsparse.R ([): fix long standing typo in symmetric case
859            * man/dsCMatrix-class.Rd: add example exhibiting the above case
860
861    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
862
863            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
864            to LL before converting to a sparse matrix. (The LDL form can be
865            converted to a sparse matrix but it is implicitly a unit
866            triangular matrix and a diagonal matrix overwritten on the diagonal.)
867
868    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
869
870            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
871
872    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
873
874            * DESCRIPTION (Version): updated -> release 0.9975-7
875            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
876
877    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
878
879            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
880
881    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
882
883            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
884            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
885            is exactly singular.
886
887    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
888
889            * DESCRIPTION (Date): updated -> release 0.9975-6
890
891    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
892
893            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
894            now returns symmetric.
895
896            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
897
898            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
899            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
900
901            * R/Auxiliaries.R (.type.kind): added
902
903    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
904
905            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
906            running src/CSparse_install.sh
907
908            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
909
910    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
911
912            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
913            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
914
915            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
916
917            * tests/Class+Meth.R (tstMatrixClass): now assure
918            the (important in method programming) property :
919
920                    ###>>  Every "Matrix" is either
921                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
922
923                    (where "*" stands for "Matrix")
924
925            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
926
927            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
928            * tests/validObj.R: checks for "comparison"
929
930            * R/sparseMatrix.R ([): improved indexing for sparse;
931                    trying to keep <symmetric>[ n, n] symmmetric
932
933            * tests/indexing.R: indexing for logical sparse now ok
934
935
936    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
937
938            * src/Tsparse.c: use xTsparse_validate() , and hence remove
939
940            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
941
942    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
943
944            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
945
946            * tests/simple.R: validObject() checking the above.
947
948            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
949            replacing both dgCMatrix_validate and lgCM*.
950
951            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
952            fix dimnames setting in other places.
953            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
954
955    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
956
957            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
958
959            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
960            symmetry test, via
961            * R/Auxiliaries.R (.as.dgC.0.factors):
962
963    2006-11-01  Douglas Bates  <bates@r-project.org>
964
965            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
966            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
967            <CsparseMatrix>) added
968
969    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
970
971            * tests/matprod.R: add a variation of Harri's example
972
973            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
974            recursive infinitely.
975
976            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
977
978            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
979
980    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
981
982            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
983            matrix if possible; test m+m == 2*m; now test dgRMatrix.
984            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
985            satisfy the above test.
986
987    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
988
989            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
990
991            * R/dgCMatrix.R: solve(a, b="missing") based on
992            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
993            RHS = NULL.
994
995            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
996            add more (needed) [t]crossprod() methods.
997
998            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
999
1000            * R/Auxiliaries.R (as_CspClass): cleanup
1001            (drop0): internal utility for "Csparse_drop(*, 0)"
1002            (.bail.out.2): encourage active feedback
1003
1004    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1005
1006            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1007
1008            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1009            non-valid or 'sorted' case).
1010
1011            * R/dsparseMatrix.R: add "chol" method.
1012            * R/ddenseMatrix.R: ditto
1013
1014            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1015            * NAMESPACE (Ops)
1016            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1017            coercion; deprecating direct lower level coercions.
1018
1019            * R/*.R (seq): use seq_len() and seq_along() where possible.
1020
1021
1022    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1023
1024            * DESCRIPTION (Version): 0.9975-5 ready for release
1025
1026    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1027
1028            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1029
1030    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1031
1032            * R/AllClass.R (corMatrix): add 'validity' check;
1033                    comment out unused "LDL" class definition
1034            * NAMESPACE: mention, but do not export "LDL" class
1035            * R/corMatrix.R: new (simple), needed for R-devel with
1036            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1037              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1038
1039    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1040
1041            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1042            use Rprintf and R's error handling.
1043
1044    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1045
1046            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1047            * tests/matprod.R: add tests for the bug fixed.
1048
1049    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1050
1051            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1052            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1053
1054    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1055
1056            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1057
1058    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1059
1060            * DESCRIPTION (Version): 0.9975-3
1061
1062            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1063            (sparse) matrices.
1064            * man/bdiag.Rd: docu + examples
1065
1066            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1067
1068            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1069            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1070
1071            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1072            that result is sparse or diagonal (and not dense).
1073
1074            * man/Subassign-methods.Rd: fix examples
1075
1076            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1077            should always return a sparse (and not sometimes a diagonal) matrix.
1078
1079    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1080
1081            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1082
1083    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1084
1085            * DESCRIPTION (Version): 0.9975-2
1086
1087            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1088
1089    2006-10-02  Douglas Bates  <bates@R-project.org>
1090
1091            * tests/dg_Matrix.R: Simplify test taking into account new code.
1092
1093    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1094
1095            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1096
1097            * R/lsTMatrix.R: new files w/ missing methods
1098            * R/nsTMatrix.R:  "  'for completeness'
1099
1100            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1101
1102            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1103
1104
1105    2006-09-28  Douglas Bates  <bates@R-project.org>
1106
1107            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1108            included.
1109
1110            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1111            Export C-callable functions used in Zt_create in lme4.
1112
1113    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1114
1115            * DESCRIPTION (Version): 0.9975-1
1116
1117            * tests/simple.R: less checks fail; using NA, found that our
1118                    kronecker() is not base-compatible with NA's.
1119
1120            * R/dMatrix.R: "Compare" method now implemented for all cases
1121
1122            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1123
1124            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1125
1126            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1127            * src/dspMatrix.c (dspMatrix_validate): ditto
1128
1129            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1130              including coercion to [nl]tTMatrix.
1131
1132            * R/diagMatrix.R (show): print a header line as for other classes.
1133
1134    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1135
1136            * src/Makefile.win (SUBDIRS): fix typo
1137
1138    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1139
1140            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1141
1142    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1143
1144            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1145            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1146            accept a symmetric matrix).
1147            * tests/group-methods.R: Uncomment test of crossprod applied to
1148            lsCMatrix objects.
1149
1150    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1151
1152            * R/AllClass.R (symmetricMatrix): add validity method (available
1153            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1154
1155            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1156
1157            * tests/indexing.Rout.save:
1158            * tests/indexing.R: additions, mainly for 'lsparse'
1159
1160            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1161            case.
1162
1163            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1164
1165    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1166
1167            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1168                    as 'N' (1-letter - Ok?)
1169
1170            * tests/group-methods.R: add test for logical + NAs
1171
1172            * R/dMatrix.R ("Compare"): fix to work with NA's
1173
1174            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1175
1176            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1177                    which is implemented.
1178
1179    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1180
1181            * src/chm_common.c: coerce logical <-> double instead of
1182            typecasting;  needed for "l" matrix handling in cholmod.
1183
1184            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1185
1186            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1187            (Tsp2grNEL): other fixes needed
1188
1189    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1190
1191            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1192                    Matrices, since "lMatrix", also "lsparseM" can have NA
1193            * R/ndenseMatrix.R, etc: new source files
1194            * man/nsparseMatrix-classes.Rd, etc: new help files
1195            * tests/: adaptions
1196            * src/chm_common.c (chm_dense_to_SEXP): and others:
1197                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1198            * src/Csparse.c, etc: ditto
1199
1200    2006-09-11  Douglas Bates  <bates@R-project.org>
1201
1202            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1203            alloc_d**Matrix functions to the lme4 package.
1204
1205    2006-09-09  Douglas Bates  <bates@R-project.org>
1206
1207            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1208            fixed
1209
1210    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1211
1212            * R/lMatrix.R: new
1213
1214            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1215
1216            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1217            * man/tcrossprod.Rd: ditto
1218
1219    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1220
1221            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1222            for exported functions
1223            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1224            Remove partitioning algorithms for sparse matrix reordering.  The
1225            copyright on the Metis code was problematic and the methods were
1226            rarely used.
1227            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1228            operations are now done entirely in CHOLMOD code.
1229
1230    2006-09-06  Douglas Bates  <bates@R-project.org>
1231
1232            * src/Mutils.h: Remove functions that are no longer used.
1233
1234    2006-09-04  Douglas Bates  <bates@R-project.org>
1235
1236            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1237            * src/DEPS.mkf: update
1238
1239    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1240
1241            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1242            * DESCRIPTION (Version): 0.9975-0
1243            (Depends): R (>= 2.4.0)
1244
1245    2006-09-01  Douglas Bates  <bates@R-project.org>
1246
1247            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1248
1249    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1250
1251            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1252            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1253
1254            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1255
1256    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1257
1258            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1259            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1260            * R/dsparseMatrix.R: ditto
1261            * R/Csparse.R: ditto
1262
1263    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1264
1265            * R/dMatrix.R (Compare): improve availability of "<", etc
1266            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1267
1268    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1269
1270            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1271            of a 0-index which was used as 1-index (..hmm)
1272
1273            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1274
1275            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1276            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1277            (.is.diagonal): ditto
1278
1279            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1280
1281            * R/Matrix.R (Matrix): also work for NA data
1282
1283    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1284
1285            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1286            in all cases.
1287
1288    2006-08-27  Douglas Bates  <bates@R-project.org>
1289
1290            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1291            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1292
1293    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1294
1295            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1296            subclasses of "ddenseMatrix"
1297            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1298            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1299            instead of half dozen specialized ones.
1300
1301    2006-08-25  Douglas Bates  <bates@R-project.org>
1302
1303            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1304            <tillard@cirad.fr> - ordering standard errors to match effects.
1305
1306    2006-08-24  Douglas Bates  <bates@R-project.org>
1307
1308            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1309            on R_ldl.
1310            * R/lCholCMatrix.R,
1311            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1312            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1313            * many files in ./R and ./src: Use more general version of
1314            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1315            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1316            dtpMatrix, dspMatrix and dppMatrix conversions.
1317
1318
1319    2006-08-23  Douglas Bates  <bates@R-project.org>
1320
1321            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1322            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1323            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1324            dgeMatrix_crossprod (may need to do this in other places).
1325            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1326            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1327
1328    2006-08-22  Douglas Bates  <bates@R-project.org>
1329
1330            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1331            types of classed Matrices, matrices or numeric or logical vectors.
1332            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1333            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1334            to Mutils.h (as an inline) and change name to Matrix_check_class;
1335            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1336            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1337            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1338            * src/Csparse.c: use diag_P and uplo_P macros.
1339
1340  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
1341
1342          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1343          valgrind.          valgrind.
1344            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1345            inverses.
1346            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1347            -Wall warnings.
1348            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1349            Use dup_mMatrix_as_dgeMatrix.
1350
1351  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
1352

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