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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 2048, Tue Aug 14 15:09:10 2007 UTC
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1    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
4            Oehlschlaegel's ... result type still to be discussed!
5    
6    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * man/image-methods.Rd: new, combining all image() methods
9    
10    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
13            to work via dgC...
14    
15            * R/Matrix.R (Matrix): special treatment for "table" (S3)
16    
17    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/dgTMatrix.R (image): change defaults to
20                    aspect = "iso", colorkey = FALSE
21    
22    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
25            must copy its *expanded* x slot before LAPACK call.
26    
27            * tests/matprod.R: test the last days' changes.
28    
29    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
30    
31            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
32              as well as in sources
33    
34    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
37                    ("Matrix", "matrix") which is needed in some cases.
38            Ditto for solve().
39    
40            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
41            infinite recursion in dispatch for some cases.
42    
43    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
44    
45            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
46              so pointers match
47    
48    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * DESCRIPTION (Date): set ready for release -- 0.999375-1
51    
52    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
53    
54            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
55              src/chm_common.c, src/chm_common.h: Change API for
56              numeric_as_chm_dense and N_AS_CHM_DN
57    
58    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
61            * tests/matprod.R: regr.test for it
62    
63    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
66            * tests/group-methods.R: and regression-test it
67    
68    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
69    
70            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
71              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
72              triplet_to_sparse, documentation, use typedefs
73    
74    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * man/dpoMatrix-class.Rd: added 'corMatrix' example
77    
78            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
79            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
80            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
81    
82            * R/lsparseMatrix.R: bug fix in "all" method
83            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
84    
85            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
86            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
87                    + matrix |-> nMatrix coercion
88            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
89            * man/pMatrix-class.Rd: ditto
90    
91            * R/Matrix.R (Summary): method for non-dMatrix
92    
93            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
94            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
95                    test all Summary methods.
96    
97    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
100    
101    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
104    
105            * R/pMatrix.R (t?crossprod): methods for pMatrix
106    
107    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
110    
111    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
112    
113            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
114              trying to fix a subtle bug - which has been somewhere else.
115    
116    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
117    
118            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
119              solve the bug
120    
121    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * src/dgCMatrix.c (compressed_to_TMatrix):
124    
125    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * src/Csparse.c (Rsparse_validate): new, to have some validity
128            checking for RsparseMatrix
129            * src/dgCMatrix.c (xRMatrix_validate): ditto
130            * src/dtCMatrix.c (tRMatrix_validate): ditto
131    
132    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
133    
134            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
135              lgRMatrix
136            * [r4568] DESCRIPTION: Prepare for bug-fix release
137            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
138              for declaration of cholmod_symmetry
139    
140    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
143            release.
144    
145    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
146    
147            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
148              functions - no longer used
149            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
150              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
151              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
152              Alloca
153    
154    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
155    
156            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
157              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
158              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
159              src/t_gCMatrix_colSums.c: more R_CheckStack()s
160    
161    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
162    
163            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
164              the required amount of memory then call M_numeric_as_chm_dense.
165            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
166              (like Calloc but calling alloca)
167    
168    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
171            and extended with more sophisticated 'col.names' option.
172            * NAMESPACE: export  printSparseMatrix()
173            * man/printSpMatrix.Rd: document, incl. examples
174    
175    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
176    
177            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
178              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
179              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
180    
181    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * DESCRIPTION (Version): 0.99875-4
184    
185            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
186            some dimnames perservation.
187    
188            * R/dsTMatrix.R (t-method): keep dimnames
189            * R/dtTMatrix.R:  ditto
190    
191            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
192            and ncol(.) < 10
193    
194            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
195            from Mutils.h
196    
197            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
198            e.g. in as(<ngCMatrix>, "matrix")
199    
200    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
201    
202            * [r4529] .: Create a branch for the API changes from the 0.99875
203              series to the 0.999375 series
204            * [r4530] DESCRIPTION, inst/include/Matrix.h,
205              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
206              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
207              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
208              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
209              as_cholmod_x functions
210    
211    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
212    
213            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
214              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
215              to Comparisons
216    
217    >>>>>>> .merge-right.r4561
218    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * DESCRIPTION (Version): 0.99875-3 ready to be released.
221    
222            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
223    
224            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
225            that should also work in a future version of R.
226    
227    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
230    
231            * R/sparseVector.R: more *sparseVector coercions, notably for
232            non - double ones.
233    
234    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
237              notably the new ones building on the new .Call(.)s:
238    
239            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
240            all 4 of [dlin]gCMatrix_colSums().
241    
242    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
243    
244            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
245            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
246              result
247    
248    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/kronecker.R: fix typo (could lead to inf.recursion)
251            * test/simple.R: testing that
252    
253            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
254            method as well (which can have arguments, show() can't).
255    
256    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
257    
258            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
259              added dgCMatrix_colSums for [col,row][Sums,Means]
260    
261    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
262    
263            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
264              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
265              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
266            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
267              class
268            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
269              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
270              row names to store the levels - duh!  Added an example.
271    
272    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * src/Csparse.c (Csparse_validate): check for *repeated* entries
275            thanks to example from Christian Buchta; with a test here:
276            * tests/simple.R:
277    
278    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
281            of colSums(*, sparseResult = TRUE)
282    
283    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
286            'na.rm = FALSE' as "everywhere" else in R.
287    
288    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
289    
290            * [r4421] src/CSparse_install.sh: Modify for new organization of
291              CSparse package
292            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
293              SuiteSparse
294            * [r4426] src/Makefile: add ./UFconfig to the include path for
295              compilation
296            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
297            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
298              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
299    
300    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
303            * R/sparseMatrix.R (prSpMatrix): now gives a message about
304            suppressed column names.
305    
306    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
307    
308            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
309              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
310              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
311              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
312              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
313              Remove warnings after change to const char* CHAR
314    
315    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
316    
317            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
318              type of M_cholmod_ssmult
319    
320    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
321    
322            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
323              src/init.c: Yet another cholmod export - cholmod_ssmult
324    
325    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * NAMESPACE: exported drop0(), since
328            * man/drop0.Rd: I have seen several cases, I really wanted to use
329            it, so our users may want too.
330    
331    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * man/colSums.Rd: separately document colSums() etc, since these
334            have the extra argument 'sparseResult'.
335    
336    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
339            * man/spMatrix.Rd: docu., including examples
340    
341            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
342            in order to make colMeans() etc fast *and* correct.
343            * R/sparseVector.R (replSPvec): "[<-" functionality for
344            sparseVectors; tested in
345            * tests/simple.R:
346    
347    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
350            (very) sparse Matrices; output similar to Matlab's print().
351    
352    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
353    
354            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
355            0-based, indices (Jose Quesada <quesada@gmail.com>).
356    
357    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
358    
359            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
360    
361    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Auxiliaries.R (sparsapply): new utility, much faster than
364            tapply1() for large sparse matrices.
365    
366    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Matrix.R (dim<-): reshape now via sparseVector.
369    
370            * R/sparseVector.R: methods and function for
371            * R/AllClass.R: new "sparseVector" class and daughters.
372            * NAMESPACE: export new classes
373    
374    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * DESCRIPTION (Version): 0.99875-1
377            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
378    
379    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
382            indexing
383            * tests/indexing.R: test set for that.
384    
385    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
388            entries.
389            * tests/indexing.R(out): add regression test for it
390    
391    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
394            name for "!" method definitions.
395    
396    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/Tsparse.R (intI): new utility, used for "[" :
399                    Cleanup up there, and fixes for duplicated indices - more TODO!
400    
401            * tests/indexing.R(out): more tests
402    
403    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
404    
405            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
406            code that is now part of the R Lapack library.
407    
408            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
409            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
410    
411    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
414    
415    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
418            up with extraneous names '0'...'<n-1>'
419    
420    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/dgTMatrix.R (mat2dgT): care about NAs
423    
424    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/kronecker.R: triangularity preserving methods
427    
428    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/kronecker.R: new file collecting kronecker() methods in one
431                    place.  Goal: become much faster!
432    
433    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
436            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
437            can be much faster.
438    
439            * tests/matprod.R: add regression tests for these (upper & lower).
440    
441    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/Matrix.R (diff): method for our Matrices.
444    
445            * R/sparseMatrix.R (isDiagonal): check dim()!
446    
447    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * R/Matrix.R (dim<-): new method for "reshape()" built on a
450            proposal from Tamas Papp.
451    
452    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
455    
456            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
457            rather define and export  cBind() and rBind() only.
458            --> useRs *must* change code that used to have cbind()/rbind() !!
459    
460            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
461            * R/bind.Rout.save: ditto
462    
463    2007-02-16  Douglas Bates  <bates@r-project.org>
464    
465            * DESCRIPTION (Date, Version): 0.9975-11 with new date
466            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
467            const modifier on declaration of the array 'valid'
468    
469    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
470    
471            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
472    
473    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
476    
477            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
478            * tests/simple.R: test the above and some of these coercions:
479    
480            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
481                    be careful to avoid infinite recursion, using new coercions in
482            * R/ngCMatrix.R and nsC... and ntC...
483            * R/lsparseMatrix.R: ditto
484    
485            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
486    
487            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
488            * R/Rsparse.R: reactivate .Call()s
489    
490            * tests/Class+Meth.R: a bit more on actual classes
491    
492    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
493    
494            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
495    
496    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * DESCRIPTION (Version): 0.9975-10 to upload
499    
500            * tests/Class+Meth.R (tstMatrixClass): require coercions to
501            specific classes less unconditionally.
502    
503            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
504    
505            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
506    
507            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
508            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
509            R_to_CMatrix segfaults on one platform.
510            Eliminate most coercion method to *specific* classes, and replace
511            with virtual classes coercions.
512    
513    
514    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
515    
516            * src/init.c: export the CHM...._validate() placeholders, since
517            they *are* called.
518    
519            * tests/Class+Meth.R (classCanCoerce): and starting to test
520            all as(<from>, <to>)
521    
522    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
525            * tests/indexing.R: tested now
526            * tests/indexing.Rout.save: updated
527    
528            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
529            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
530            appropriate.
531    
532            * NAMESPACE: export a trivial
533            * R/Matrix.R: drop() Matrix-method
534    
535            * R/AllClass.R: moved all prototypes to virtual super classes.
536    
537            * R/Rsparse.R: many more coercions to have less exceptions in
538            * tests/Class+Meth.R:
539    
540            * R/Ops.R (Compare): tweak for case with NA
541            * tests/simpl.R: hence another 'FIXME' eliminated
542    
543    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
546            objects.
547    
548            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
549              and more of "!", "&", "|", all, any; coercions
550    
551            * R/Rsparse.R: many coercions (which enable quite a few other
552            methods), thanks to enhancements in
553            * src/dgCMatrix.c (R_to_CMatrix): new, and
554            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
555            symmetric & triangular and ..RMatrix objects.
556    
557            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
558            renamed file from src/dsTMatrix.c;
559            now dealing with symmetric and triangular Tsparse coercions, both
560            to dense and general.
561    
562    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
565    
566            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
567            where sensible when the <numeric> is of length > 1.
568    
569    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/Matrix.R ([<-): for M[] <- value: fix length
572    
573    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
576            * R/ndenseMatrix.R: new coercions n* -> l*
577    
578    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
581    
582            * R/Ops.R ("Logic"): and other "Ops", many updates
583    
584    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * src/Mutils.h (SET_DimNames): new utility
587    
588            * R/Auxiliaries.R (nnzero): improved and now exported via
589    
590            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
591    
592    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/diagMatrix.R (!): fix typo.
595    
596    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Auxiliaries.R (as_Csparse): and quite a few others:
599                    allow to pass class definition --> speedup
600            * R/sparseMatrix.R: apply the above
601    
602            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
603    
604            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
605            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
606            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
607    
608            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
609    
610            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
611            and use it for "sparse*" as well, since it's faster than the
612            as_Csparse(.) way.
613    
614    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
617    
618    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
621            as method for   M[ ij ] <- v
622            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
623    
624            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
625            FALSE answer
626    
627            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
628            * tests/indexing.R: test it, and some of the above
629    
630    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/Auxiliaries.R (is_duplicatedT): new utility
633    
634    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
635    
636            * src/init.c (R_init_Matrix): export cholmod_scale
637    
638    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
641            base::as.matrix to (x, ...)
642    
643    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
646            file; start using "Logic", hence
647    
648            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
649            * NAMESPACE: import and export "Logic"
650    
651    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
654            only needed previously to R version 2.5.0.
655    
656    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
659    
660            * R/Tsparse.R (replTmat): fix subassignment of triangular
661            * R/Csparse.R (replCmat): ditto
662            * tests/indexing.R: more tests, incl the above fix
663    
664    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/Auxiliaries.R (drop0): extend for non CSparse
667            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
668    
669            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
670                    use uplo correctly (!); other places: use uplo_P() macro
671    
672            * R/Csparse.R (replCmat): call diagU2N() when needed
673            * R/Tsparse.R (replTmat): ditto
674    
675            * src/dtCMatrix.c (tCMatrix_validate): new
676            * src/dtTMatrix.c (tTMatrix_validate): new, used in
677            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
678    
679            * R/diagMatrix.R (replDiag): to use in [<-
680    
681    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
684                    also more general diagU2N().
685    
686    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
689            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
690    
691    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * tests/bind.R: a few more cases
694            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
695    
696            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
697            * R/ddenseMatrix.R (cbind2/rbind2)
698            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
699            * tests/indexing.R
700            * tests/indexing.Rout.save: updated
701    
702    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
705            * tests/indexing.R
706    
707    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
710            align with proper position of "0", i.e., right for integers.
711            argument 'align' by default is "fancy".
712    
713    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
716            * R/Csparse.R: and fix "Compare" for more cases.
717            * tests/Class+Meth.R: test some of these (m == m, m != m)
718    
719    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/lsparseMatrix.R: all() and any() methods
722            * R/ldenseMatrix.R:      ditto
723            * NAMESPACE, R/Matrix.R: ditto
724    
725            * man/all-methods.Rd: document them minimally
726    
727            * tests/simple.R: add a few examples for these
728    
729    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/Tsparse.R ([): fix long standing typo in symmetric case
732            * man/dsCMatrix-class.Rd: add example exhibiting the above case
733    
734    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
735    
736            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
737            to LL before converting to a sparse matrix. (The LDL form can be
738            converted to a sparse matrix but it is implicitly a unit
739            triangular matrix and a diagonal matrix overwritten on the diagonal.)
740    
741    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
742    
743            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
744    
745    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
746    
747            * DESCRIPTION (Version): updated -> release 0.9975-7
748            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
749    
750    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
753    
754    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
757            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
758            is exactly singular.
759    
760    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * DESCRIPTION (Date): updated -> release 0.9975-6
763    
764    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
767            now returns symmetric.
768    
769            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
770    
771            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
772            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
773    
774            * R/Auxiliaries.R (.type.kind): added
775    
776    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
779            running src/CSparse_install.sh
780    
781            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
782    
783    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
786            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
787    
788            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
789    
790            * tests/Class+Meth.R (tstMatrixClass): now assure
791            the (important in method programming) property :
792    
793                    ###>>  Every "Matrix" is either
794                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
795    
796                    (where "*" stands for "Matrix")
797    
798            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
799    
800            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
801            * tests/validObj.R: checks for "comparison"
802    
803            * R/sparseMatrix.R ([): improved indexing for sparse;
804                    trying to keep <symmetric>[ n, n] symmmetric
805    
806            * tests/indexing.R: indexing for logical sparse now ok
807    
808    
809    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
810    
811            * src/Tsparse.c: use xTsparse_validate() , and hence remove
812    
813            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
814    
815    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
816    
817            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
818    
819            * tests/simple.R: validObject() checking the above.
820    
821            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
822            replacing both dgCMatrix_validate and lgCM*.
823    
824            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
825            fix dimnames setting in other places.
826            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
827    
828    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
831    
832            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
833            symmetry test, via
834            * R/Auxiliaries.R (.as.dgC.0.factors):
835    
836    2006-11-01  Douglas Bates  <bates@r-project.org>
837    
838            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
839            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
840            <CsparseMatrix>) added
841    
842    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * tests/matprod.R: add a variation of Harri's example
845    
846            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
847            recursive infinitely.
848    
849            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
850    
851            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
852    
853    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
854    
855            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
856            matrix if possible; test m+m == 2*m; now test dgRMatrix.
857            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
858            satisfy the above test.
859    
860    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
861    
862            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
863    
864            * R/dgCMatrix.R: solve(a, b="missing") based on
865            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
866            RHS = NULL.
867    
868            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
869            add more (needed) [t]crossprod() methods.
870    
871            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
872    
873            * R/Auxiliaries.R (as_CspClass): cleanup
874            (drop0): internal utility for "Csparse_drop(*, 0)"
875            (.bail.out.2): encourage active feedback
876    
877    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
878    
879            * R/dMatrix.R(Compare): new(), then slots [no validity check]
880    
881            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
882            non-valid or 'sorted' case).
883    
884            * R/dsparseMatrix.R: add "chol" method.
885            * R/ddenseMatrix.R: ditto
886    
887            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
888            * NAMESPACE (Ops)
889            * R/diagMatrix.R (diag2T): simple utility used "higher level"
890            coercion; deprecating direct lower level coercions.
891    
892            * R/*.R (seq): use seq_len() and seq_along() where possible.
893    
894    
895    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * DESCRIPTION (Version): 0.9975-5 ready for release
898    
899    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
900    
901            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
902    
903    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/AllClass.R (corMatrix): add 'validity' check;
906                    comment out unused "LDL" class definition
907            * NAMESPACE: mention, but do not export "LDL" class
908            * R/corMatrix.R: new (simple), needed for R-devel with
909            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
910              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
911    
912    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
913    
914            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
915            use Rprintf and R's error handling.
916    
917    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
918    
919            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
920            * tests/matprod.R: add tests for the bug fixed.
921    
922    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
923    
924            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
925            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
926    
927    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
928    
929            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
930    
931    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * DESCRIPTION (Version): 0.9975-3
934    
935            * R/diagMatrix.R (bdiag): new function constructing block diagonal
936            (sparse) matrices.
937            * man/bdiag.Rd: docu + examples
938    
939            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
940    
941            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
942            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
943    
944            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
945            that result is sparse or diagonal (and not dense).
946    
947            * man/Subassign-methods.Rd: fix examples
948    
949            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
950            should always return a sparse (and not sometimes a diagonal) matrix.
951    
952    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
953    
954            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
955    
956    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
957    
958            * DESCRIPTION (Version): 0.9975-2
959    
960            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
961    
962    2006-10-02  Douglas Bates  <bates@R-project.org>
963    
964            * tests/dg_Matrix.R: Simplify test taking into account new code.
965    
966    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
967    
968            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
969    
970            * R/lsTMatrix.R: new files w/ missing methods
971            * R/nsTMatrix.R:  "  'for completeness'
972    
973            * tests/Class+Meth.R: a bit less 'not.ok.classes'
974    
975            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
976    
977    
978    2006-09-28  Douglas Bates  <bates@R-project.org>
979    
980            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
981            included.
982    
983            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
984            Export C-callable functions used in Zt_create in lme4.
985    
986    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * DESCRIPTION (Version): 0.9975-1
989    
990            * tests/simple.R: less checks fail; using NA, found that our
991                    kronecker() is not base-compatible with NA's.
992    
993            * R/dMatrix.R: "Compare" method now implemented for all cases
994    
995            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
996    
997            * man/dtpMatrix-class.Rd: mention length of 'x' slot
998    
999            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1000            * src/dspMatrix.c (dspMatrix_validate): ditto
1001    
1002            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1003              including coercion to [nl]tTMatrix.
1004    
1005            * R/diagMatrix.R (show): print a header line as for other classes.
1006    
1007    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * src/Makefile.win (SUBDIRS): fix typo
1010    
1011    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1012    
1013            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1014    
1015    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1016    
1017            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1018            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1019            accept a symmetric matrix).
1020            * tests/group-methods.R: Uncomment test of crossprod applied to
1021            lsCMatrix objects.
1022    
1023    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1024    
1025            * R/AllClass.R (symmetricMatrix): add validity method (available
1026            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1027    
1028            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1029    
1030            * tests/indexing.Rout.save:
1031            * tests/indexing.R: additions, mainly for 'lsparse'
1032    
1033            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1034            case.
1035    
1036            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1037    
1038    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1039    
1040            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1041                    as 'N' (1-letter - Ok?)
1042    
1043            * tests/group-methods.R: add test for logical + NAs
1044    
1045            * R/dMatrix.R ("Compare"): fix to work with NA's
1046    
1047            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1048    
1049            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1050                    which is implemented.
1051    
1052    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1053    
1054            * src/chm_common.c: coerce logical <-> double instead of
1055            typecasting;  needed for "l" matrix handling in cholmod.
1056    
1057            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1058    
1059            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1060            (Tsp2grNEL): other fixes needed
1061    
1062    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1063    
1064            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1065                    Matrices, since "lMatrix", also "lsparseM" can have NA
1066            * R/ndenseMatrix.R, etc: new source files
1067            * man/nsparseMatrix-classes.Rd, etc: new help files
1068            * tests/: adaptions
1069            * src/chm_common.c (chm_dense_to_SEXP): and others:
1070                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1071            * src/Csparse.c, etc: ditto
1072    
1073    2006-09-11  Douglas Bates  <bates@R-project.org>
1074    
1075            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1076            alloc_d**Matrix functions to the lme4 package.
1077    
1078    2006-09-09  Douglas Bates  <bates@R-project.org>
1079    
1080            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1081            fixed
1082    
1083    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1084    
1085            * R/lMatrix.R: new
1086    
1087            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1088    
1089            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1090            * man/tcrossprod.Rd: ditto
1091    
1092    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1093    
1094            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1095            for exported functions
1096            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1097            Remove partitioning algorithms for sparse matrix reordering.  The
1098            copyright on the Metis code was problematic and the methods were
1099            rarely used.
1100            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1101            operations are now done entirely in CHOLMOD code.
1102    
1103    2006-09-06  Douglas Bates  <bates@R-project.org>
1104    
1105            * src/Mutils.h: Remove functions that are no longer used.
1106    
1107    2006-09-04  Douglas Bates  <bates@R-project.org>
1108    
1109            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1110            * src/DEPS.mkf: update
1111    
1112    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1113    
1114            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1115            * DESCRIPTION (Version): 0.9975-0
1116            (Depends): R (>= 2.4.0)
1117    
1118    2006-09-01  Douglas Bates  <bates@R-project.org>
1119    
1120            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1121    
1122    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1123    
1124            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1125            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1126    
1127            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1128    
1129    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1132            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1133            * R/dsparseMatrix.R: ditto
1134            * R/Csparse.R: ditto
1135    
1136    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1137    
1138            * R/dMatrix.R (Compare): improve availability of "<", etc
1139            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1140    
1141    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1142    
1143            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1144            of a 0-index which was used as 1-index (..hmm)
1145    
1146            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1147    
1148            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1149            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1150            (.is.diagonal): ditto
1151    
1152            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1153    
1154            * R/Matrix.R (Matrix): also work for NA data
1155    
1156    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1157    
1158            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1159            in all cases.
1160    
1161    2006-08-27  Douglas Bates  <bates@R-project.org>
1162    
1163            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1164            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1165    
1166    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1169            subclasses of "ddenseMatrix"
1170            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1171            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1172            instead of half dozen specialized ones.
1173    
1174    2006-08-25  Douglas Bates  <bates@R-project.org>
1175    
1176            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1177            <tillard@cirad.fr> - ordering standard errors to match effects.
1178    
1179    2006-08-24  Douglas Bates  <bates@R-project.org>
1180    
1181            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1182            on R_ldl.
1183            * R/lCholCMatrix.R,
1184            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1185            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1186            * many files in ./R and ./src: Use more general version of
1187            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1188            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1189            dtpMatrix, dspMatrix and dppMatrix conversions.
1190    
1191    
1192    2006-08-23  Douglas Bates  <bates@R-project.org>
1193    
1194            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1195            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1196            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1197            dgeMatrix_crossprod (may need to do this in other places).
1198            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1199            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1200    
1201    2006-08-22  Douglas Bates  <bates@R-project.org>
1202    
1203            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1204            types of classed Matrices, matrices or numeric or logical vectors.
1205            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1206            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1207            to Mutils.h (as an inline) and change name to Matrix_check_class;
1208            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1209            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1210            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1211            * src/Csparse.c: use diag_P and uplo_P macros.
1212    
1213  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
1214    
1215          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1216          valgrind.          valgrind.
1217            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1218            inverses.
1219            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1220            -Wall warnings.
1221            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1222            Use dup_mMatrix_as_dgeMatrix.
1223    
1224  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
1225    

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