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revision 1373, Mon Aug 14 21:15:38 2006 UTC revision 2011, Fri Jul 20 12:56:10 2007 UTC
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1    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
4            * tests/group-methods.R: and regression-test it
5    
6    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
7    
8            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
9              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
10              triplet_to_sparse, documentation, use typedefs
11    
12    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * man/dpoMatrix-class.Rd: added 'corMatrix' example
15    
16            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
17            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
18            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
19    
20            * R/lsparseMatrix.R: bug fix in "all" method
21            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
22    
23            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
24            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
25                    + matrix |-> nMatrix coercion
26            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
27            * man/pMatrix-class.Rd: ditto
28    
29            * R/Matrix.R (Summary): method for non-dMatrix
30    
31            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
32            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
33                    test all Summary methods.
34    
35    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
38    
39    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
42    
43            * R/pMatrix.R (t?crossprod): methods for pMatrix
44    
45    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
46    
47            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
48    
49    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
50    
51            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
52              trying to fix a subtle bug - which has been somewhere else.
53    
54    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
55    
56            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
57              solve the bug
58    
59    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * src/dgCMatrix.c (compressed_to_TMatrix):
62    
63    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * src/Csparse.c (Rsparse_validate): new, to have some validity
66            checking for RsparseMatrix
67            * src/dgCMatrix.c (xRMatrix_validate): ditto
68            * src/dtCMatrix.c (tRMatrix_validate): ditto
69    
70    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
71    
72            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
73              lgRMatrix
74            * [r4568] DESCRIPTION: Prepare for bug-fix release
75            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
76              for declaration of cholmod_symmetry
77    
78    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
81            release.
82    
83    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
84    
85            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
86              functions - no longer used
87            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
88              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
89              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
90              Alloca
91    
92    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
93    
94            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
95              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
96              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
97              src/t_gCMatrix_colSums.c: more R_CheckStack()s
98    
99    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
100    
101            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
102              the required amount of memory then call M_numeric_as_chm_dense.
103            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
104              (like Calloc but calling alloca)
105    
106    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
109            and extended with more sophisticated 'col.names' option.
110            * NAMESPACE: export  printSparseMatrix()
111            * man/printSpMatrix.Rd: document, incl. examples
112    
113    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
114    
115            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
116              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
117              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
118    
119    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * DESCRIPTION (Version): 0.99875-4
122    
123            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
124            some dimnames perservation.
125    
126            * R/dsTMatrix.R (t-method): keep dimnames
127            * R/dtTMatrix.R:  ditto
128    
129            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
130            and ncol(.) < 10
131    
132            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
133            from Mutils.h
134    
135            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
136            e.g. in as(<ngCMatrix>, "matrix")
137    
138    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
139    
140            * [r4529] .: Create a branch for the API changes from the 0.99875
141              series to the 0.999375 series
142            * [r4530] DESCRIPTION, inst/include/Matrix.h,
143              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
144              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
145              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
146              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
147              as_cholmod_x functions
148    
149    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
150    
151            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
152              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
153              to Comparisons
154    
155    >>>>>>> .merge-right.r4561
156    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * DESCRIPTION (Version): 0.99875-3 ready to be released.
159    
160            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
161    
162            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
163            that should also work in a future version of R.
164    
165    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
168    
169            * R/sparseVector.R: more *sparseVector coercions, notably for
170            non - double ones.
171    
172    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
175              notably the new ones building on the new .Call(.)s:
176    
177            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
178            all 4 of [dlin]gCMatrix_colSums().
179    
180    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
181    
182            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
183            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
184              result
185    
186    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/kronecker.R: fix typo (could lead to inf.recursion)
189            * test/simple.R: testing that
190    
191            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
192            method as well (which can have arguments, show() can't).
193    
194    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
195    
196            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
197              added dgCMatrix_colSums for [col,row][Sums,Means]
198    
199    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
200    
201            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
202              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
203              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
204            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
205              class
206            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
207              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
208              row names to store the levels - duh!  Added an example.
209    
210    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * src/Csparse.c (Csparse_validate): check for *repeated* entries
213            thanks to example from Christian Buchta; with a test here:
214            * tests/simple.R:
215    
216    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
219            of colSums(*, sparseResult = TRUE)
220    
221    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
224            'na.rm = FALSE' as "everywhere" else in R.
225    
226    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
227    
228            * [r4421] src/CSparse_install.sh: Modify for new organization of
229              CSparse package
230            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
231              SuiteSparse
232            * [r4426] src/Makefile: add ./UFconfig to the include path for
233              compilation
234            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
235            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
236              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
237    
238    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
241            * R/sparseMatrix.R (prSpMatrix): now gives a message about
242            suppressed column names.
243    
244    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
245    
246            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
247              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
248              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
249              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
250              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
251              Remove warnings after change to const char* CHAR
252    
253    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
254    
255            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
256              type of M_cholmod_ssmult
257    
258    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
259    
260            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
261              src/init.c: Yet another cholmod export - cholmod_ssmult
262    
263    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * NAMESPACE: exported drop0(), since
266            * man/drop0.Rd: I have seen several cases, I really wanted to use
267            it, so our users may want too.
268    
269    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * man/colSums.Rd: separately document colSums() etc, since these
272            have the extra argument 'sparseResult'.
273    
274    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
277            * man/spMatrix.Rd: docu., including examples
278    
279            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
280            in order to make colMeans() etc fast *and* correct.
281            * R/sparseVector.R (replSPvec): "[<-" functionality for
282            sparseVectors; tested in
283            * tests/simple.R:
284    
285    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
288            (very) sparse Matrices; output similar to Matlab's print().
289    
290    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
291    
292            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
293            0-based, indices (Jose Quesada <quesada@gmail.com>).
294    
295    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
298    
299    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/Auxiliaries.R (sparsapply): new utility, much faster than
302            tapply1() for large sparse matrices.
303    
304    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Matrix.R (dim<-): reshape now via sparseVector.
307    
308            * R/sparseVector.R: methods and function for
309            * R/AllClass.R: new "sparseVector" class and daughters.
310            * NAMESPACE: export new classes
311    
312    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * DESCRIPTION (Version): 0.99875-1
315            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
316    
317    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
320            indexing
321            * tests/indexing.R: test set for that.
322    
323    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
326            entries.
327            * tests/indexing.R(out): add regression test for it
328    
329    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
332            name for "!" method definitions.
333    
334    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Tsparse.R (intI): new utility, used for "[" :
337                    Cleanup up there, and fixes for duplicated indices - more TODO!
338    
339            * tests/indexing.R(out): more tests
340    
341    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
342    
343            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
344            code that is now part of the R Lapack library.
345    
346            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
347            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
348    
349    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
352    
353    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
356            up with extraneous names '0'...'<n-1>'
357    
358    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/dgTMatrix.R (mat2dgT): care about NAs
361    
362    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/kronecker.R: triangularity preserving methods
365    
366    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/kronecker.R: new file collecting kronecker() methods in one
369                    place.  Goal: become much faster!
370    
371    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
374            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
375            can be much faster.
376    
377            * tests/matprod.R: add regression tests for these (upper & lower).
378    
379    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Matrix.R (diff): method for our Matrices.
382    
383            * R/sparseMatrix.R (isDiagonal): check dim()!
384    
385    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Matrix.R (dim<-): new method for "reshape()" built on a
388            proposal from Tamas Papp.
389    
390    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
393    
394            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
395            rather define and export  cBind() and rBind() only.
396            --> useRs *must* change code that used to have cbind()/rbind() !!
397    
398            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
399            * R/bind.Rout.save: ditto
400    
401    2007-02-16  Douglas Bates  <bates@r-project.org>
402    
403            * DESCRIPTION (Date, Version): 0.9975-11 with new date
404            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
405            const modifier on declaration of the array 'valid'
406    
407    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
408    
409            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
410    
411    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
414    
415            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
416            * tests/simple.R: test the above and some of these coercions:
417    
418            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
419                    be careful to avoid infinite recursion, using new coercions in
420            * R/ngCMatrix.R and nsC... and ntC...
421            * R/lsparseMatrix.R: ditto
422    
423            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
424    
425            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
426            * R/Rsparse.R: reactivate .Call()s
427    
428            * tests/Class+Meth.R: a bit more on actual classes
429    
430    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
431    
432            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
433    
434    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * DESCRIPTION (Version): 0.9975-10 to upload
437    
438            * tests/Class+Meth.R (tstMatrixClass): require coercions to
439            specific classes less unconditionally.
440    
441            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
442    
443            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
444    
445            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
446            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
447            R_to_CMatrix segfaults on one platform.
448            Eliminate most coercion method to *specific* classes, and replace
449            with virtual classes coercions.
450    
451    
452    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
453    
454            * src/init.c: export the CHM...._validate() placeholders, since
455            they *are* called.
456    
457            * tests/Class+Meth.R (classCanCoerce): and starting to test
458            all as(<from>, <to>)
459    
460    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
463            * tests/indexing.R: tested now
464            * tests/indexing.Rout.save: updated
465    
466            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
467            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
468            appropriate.
469    
470            * NAMESPACE: export a trivial
471            * R/Matrix.R: drop() Matrix-method
472    
473            * R/AllClass.R: moved all prototypes to virtual super classes.
474    
475            * R/Rsparse.R: many more coercions to have less exceptions in
476            * tests/Class+Meth.R:
477    
478            * R/Ops.R (Compare): tweak for case with NA
479            * tests/simpl.R: hence another 'FIXME' eliminated
480    
481    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
484            objects.
485    
486            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
487              and more of "!", "&", "|", all, any; coercions
488    
489            * R/Rsparse.R: many coercions (which enable quite a few other
490            methods), thanks to enhancements in
491            * src/dgCMatrix.c (R_to_CMatrix): new, and
492            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
493            symmetric & triangular and ..RMatrix objects.
494    
495            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
496            renamed file from src/dsTMatrix.c;
497            now dealing with symmetric and triangular Tsparse coercions, both
498            to dense and general.
499    
500    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
503    
504            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
505            where sensible when the <numeric> is of length > 1.
506    
507    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/Matrix.R ([<-): for M[] <- value: fix length
510    
511    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
514            * R/ndenseMatrix.R: new coercions n* -> l*
515    
516    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
519    
520            * R/Ops.R ("Logic"): and other "Ops", many updates
521    
522    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * src/Mutils.h (SET_DimNames): new utility
525    
526            * R/Auxiliaries.R (nnzero): improved and now exported via
527    
528            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
529    
530    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * R/diagMatrix.R (!): fix typo.
533    
534    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/Auxiliaries.R (as_Csparse): and quite a few others:
537                    allow to pass class definition --> speedup
538            * R/sparseMatrix.R: apply the above
539    
540            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
541    
542            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
543            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
544            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
545    
546            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
547    
548            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
549            and use it for "sparse*" as well, since it's faster than the
550            as_Csparse(.) way.
551    
552    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
555    
556    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
559            as method for   M[ ij ] <- v
560            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
561    
562            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
563            FALSE answer
564    
565            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
566            * tests/indexing.R: test it, and some of the above
567    
568    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/Auxiliaries.R (is_duplicatedT): new utility
571    
572    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
573    
574            * src/init.c (R_init_Matrix): export cholmod_scale
575    
576    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
579            base::as.matrix to (x, ...)
580    
581    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
584            file; start using "Logic", hence
585    
586            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
587            * NAMESPACE: import and export "Logic"
588    
589    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
592            only needed previously to R version 2.5.0.
593    
594    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
597    
598            * R/Tsparse.R (replTmat): fix subassignment of triangular
599            * R/Csparse.R (replCmat): ditto
600            * tests/indexing.R: more tests, incl the above fix
601    
602    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/Auxiliaries.R (drop0): extend for non CSparse
605            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
606    
607            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
608                    use uplo correctly (!); other places: use uplo_P() macro
609    
610            * R/Csparse.R (replCmat): call diagU2N() when needed
611            * R/Tsparse.R (replTmat): ditto
612    
613            * src/dtCMatrix.c (tCMatrix_validate): new
614            * src/dtTMatrix.c (tTMatrix_validate): new, used in
615            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
616    
617            * R/diagMatrix.R (replDiag): to use in [<-
618    
619    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
622                    also more general diagU2N().
623    
624    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
627            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
628    
629    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * tests/bind.R: a few more cases
632            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
633    
634            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
635            * R/ddenseMatrix.R (cbind2/rbind2)
636            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
637            * tests/indexing.R
638            * tests/indexing.Rout.save: updated
639    
640    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
643            * tests/indexing.R
644    
645    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
648            align with proper position of "0", i.e., right for integers.
649            argument 'align' by default is "fancy".
650    
651    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
654            * R/Csparse.R: and fix "Compare" for more cases.
655            * tests/Class+Meth.R: test some of these (m == m, m != m)
656    
657    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/lsparseMatrix.R: all() and any() methods
660            * R/ldenseMatrix.R:      ditto
661            * NAMESPACE, R/Matrix.R: ditto
662    
663            * man/all-methods.Rd: document them minimally
664    
665            * tests/simple.R: add a few examples for these
666    
667    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/Tsparse.R ([): fix long standing typo in symmetric case
670            * man/dsCMatrix-class.Rd: add example exhibiting the above case
671    
672    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
673    
674            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
675            to LL before converting to a sparse matrix. (The LDL form can be
676            converted to a sparse matrix but it is implicitly a unit
677            triangular matrix and a diagonal matrix overwritten on the diagonal.)
678    
679    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
680    
681            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
682    
683    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
684    
685            * DESCRIPTION (Version): updated -> release 0.9975-7
686            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
687    
688    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
691    
692    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
693    
694            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
695            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
696            is exactly singular.
697    
698    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * DESCRIPTION (Date): updated -> release 0.9975-6
701    
702    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
705            now returns symmetric.
706    
707            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
708    
709            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
710            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
711    
712            * R/Auxiliaries.R (.type.kind): added
713    
714    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
717            running src/CSparse_install.sh
718    
719            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
720    
721    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
722    
723            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
724            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
725    
726            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
727    
728            * tests/Class+Meth.R (tstMatrixClass): now assure
729            the (important in method programming) property :
730    
731                    ###>>  Every "Matrix" is either
732                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
733    
734                    (where "*" stands for "Matrix")
735    
736            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
737    
738            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
739            * tests/validObj.R: checks for "comparison"
740    
741            * R/sparseMatrix.R ([): improved indexing for sparse;
742                    trying to keep <symmetric>[ n, n] symmmetric
743    
744            * tests/indexing.R: indexing for logical sparse now ok
745    
746    
747    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * src/Tsparse.c: use xTsparse_validate() , and hence remove
750    
751            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
752    
753    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
756    
757            * tests/simple.R: validObject() checking the above.
758    
759            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
760            replacing both dgCMatrix_validate and lgCM*.
761    
762            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
763            fix dimnames setting in other places.
764            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
765    
766    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
767    
768            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
769    
770            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
771            symmetry test, via
772            * R/Auxiliaries.R (.as.dgC.0.factors):
773    
774    2006-11-01  Douglas Bates  <bates@r-project.org>
775    
776            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
777            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
778            <CsparseMatrix>) added
779    
780    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * tests/matprod.R: add a variation of Harri's example
783    
784            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
785            recursive infinitely.
786    
787            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
788    
789            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
790    
791    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
794            matrix if possible; test m+m == 2*m; now test dgRMatrix.
795            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
796            satisfy the above test.
797    
798    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
801    
802            * R/dgCMatrix.R: solve(a, b="missing") based on
803            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
804            RHS = NULL.
805    
806            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
807            add more (needed) [t]crossprod() methods.
808    
809            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
810    
811            * R/Auxiliaries.R (as_CspClass): cleanup
812            (drop0): internal utility for "Csparse_drop(*, 0)"
813            (.bail.out.2): encourage active feedback
814    
815    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
816    
817            * R/dMatrix.R(Compare): new(), then slots [no validity check]
818    
819            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
820            non-valid or 'sorted' case).
821    
822            * R/dsparseMatrix.R: add "chol" method.
823            * R/ddenseMatrix.R: ditto
824    
825            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
826            * NAMESPACE (Ops)
827            * R/diagMatrix.R (diag2T): simple utility used "higher level"
828            coercion; deprecating direct lower level coercions.
829    
830            * R/*.R (seq): use seq_len() and seq_along() where possible.
831    
832    
833    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * DESCRIPTION (Version): 0.9975-5 ready for release
836    
837    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
838    
839            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
840    
841    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
842    
843            * R/AllClass.R (corMatrix): add 'validity' check;
844                    comment out unused "LDL" class definition
845            * NAMESPACE: mention, but do not export "LDL" class
846            * R/corMatrix.R: new (simple), needed for R-devel with
847            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
848              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
849    
850    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
851    
852            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
853            use Rprintf and R's error handling.
854    
855    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
858            * tests/matprod.R: add tests for the bug fixed.
859    
860    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
861    
862            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
863            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
864    
865    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
866    
867            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
868    
869    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
870    
871            * DESCRIPTION (Version): 0.9975-3
872    
873            * R/diagMatrix.R (bdiag): new function constructing block diagonal
874            (sparse) matrices.
875            * man/bdiag.Rd: docu + examples
876    
877            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
878    
879            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
880            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
881    
882            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
883            that result is sparse or diagonal (and not dense).
884    
885            * man/Subassign-methods.Rd: fix examples
886    
887            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
888            should always return a sparse (and not sometimes a diagonal) matrix.
889    
890    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
893    
894    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
895    
896            * DESCRIPTION (Version): 0.9975-2
897    
898            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
899    
900    2006-10-02  Douglas Bates  <bates@R-project.org>
901    
902            * tests/dg_Matrix.R: Simplify test taking into account new code.
903    
904    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
906            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
907    
908            * R/lsTMatrix.R: new files w/ missing methods
909            * R/nsTMatrix.R:  "  'for completeness'
910    
911            * tests/Class+Meth.R: a bit less 'not.ok.classes'
912    
913            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
914    
915    
916    2006-09-28  Douglas Bates  <bates@R-project.org>
917    
918            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
919            included.
920    
921            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
922            Export C-callable functions used in Zt_create in lme4.
923    
924    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * DESCRIPTION (Version): 0.9975-1
927    
928            * tests/simple.R: less checks fail; using NA, found that our
929                    kronecker() is not base-compatible with NA's.
930    
931            * R/dMatrix.R: "Compare" method now implemented for all cases
932    
933            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
934    
935            * man/dtpMatrix-class.Rd: mention length of 'x' slot
936    
937            * src/dtpMatrix.c (dtpMatrix_validate): fix check
938            * src/dspMatrix.c (dspMatrix_validate): ditto
939    
940            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
941              including coercion to [nl]tTMatrix.
942    
943            * R/diagMatrix.R (show): print a header line as for other classes.
944    
945    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
946    
947            * src/Makefile.win (SUBDIRS): fix typo
948    
949    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
952    
953    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
954    
955            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
956            symmetric and y missing in R code using %*% (cholmod_aat doesn't
957            accept a symmetric matrix).
958            * tests/group-methods.R: Uncomment test of crossprod applied to
959            lsCMatrix objects.
960    
961    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
962    
963            * R/AllClass.R (symmetricMatrix): add validity method (available
964            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
965    
966            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
967    
968            * tests/indexing.Rout.save:
969            * tests/indexing.R: additions, mainly for 'lsparse'
970    
971            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
972            case.
973    
974            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
975    
976    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
979                    as 'N' (1-letter - Ok?)
980    
981            * tests/group-methods.R: add test for logical + NAs
982    
983            * R/dMatrix.R ("Compare"): fix to work with NA's
984    
985            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
986    
987            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
988                    which is implemented.
989    
990    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * src/chm_common.c: coerce logical <-> double instead of
993            typecasting;  needed for "l" matrix handling in cholmod.
994    
995            * tests/other-pkgs.R (graph): small extension in "graph" checks.
996    
997            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
998            (Tsp2grNEL): other fixes needed
999    
1000    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1003                    Matrices, since "lMatrix", also "lsparseM" can have NA
1004            * R/ndenseMatrix.R, etc: new source files
1005            * man/nsparseMatrix-classes.Rd, etc: new help files
1006            * tests/: adaptions
1007            * src/chm_common.c (chm_dense_to_SEXP): and others:
1008                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1009            * src/Csparse.c, etc: ditto
1010    
1011    2006-09-11  Douglas Bates  <bates@R-project.org>
1012    
1013            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1014            alloc_d**Matrix functions to the lme4 package.
1015    
1016    2006-09-09  Douglas Bates  <bates@R-project.org>
1017    
1018            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1019            fixed
1020    
1021    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/lMatrix.R: new
1024    
1025            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1026    
1027            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1028            * man/tcrossprod.Rd: ditto
1029    
1030    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1031    
1032            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1033            for exported functions
1034            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1035            Remove partitioning algorithms for sparse matrix reordering.  The
1036            copyright on the Metis code was problematic and the methods were
1037            rarely used.
1038            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1039            operations are now done entirely in CHOLMOD code.
1040    
1041    2006-09-06  Douglas Bates  <bates@R-project.org>
1042    
1043            * src/Mutils.h: Remove functions that are no longer used.
1044    
1045    2006-09-04  Douglas Bates  <bates@R-project.org>
1046    
1047            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1048            * src/DEPS.mkf: update
1049    
1050    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1051    
1052            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1053            * DESCRIPTION (Version): 0.9975-0
1054            (Depends): R (>= 2.4.0)
1055    
1056    2006-09-01  Douglas Bates  <bates@R-project.org>
1057    
1058            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1059    
1060    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1061    
1062            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1063            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1064    
1065            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1066    
1067    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1068    
1069            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1070            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1071            * R/dsparseMatrix.R: ditto
1072            * R/Csparse.R: ditto
1073    
1074    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1075    
1076            * R/dMatrix.R (Compare): improve availability of "<", etc
1077            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1078    
1079    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1080    
1081            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1082            of a 0-index which was used as 1-index (..hmm)
1083    
1084            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1085    
1086            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1087            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1088            (.is.diagonal): ditto
1089    
1090            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1091    
1092            * R/Matrix.R (Matrix): also work for NA data
1093    
1094    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1097            in all cases.
1098    
1099    2006-08-27  Douglas Bates  <bates@R-project.org>
1100    
1101            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1102            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1103    
1104    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1105    
1106            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1107            subclasses of "ddenseMatrix"
1108            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1109            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1110            instead of half dozen specialized ones.
1111    
1112    2006-08-25  Douglas Bates  <bates@R-project.org>
1113    
1114            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1115            <tillard@cirad.fr> - ordering standard errors to match effects.
1116    
1117    2006-08-24  Douglas Bates  <bates@R-project.org>
1118    
1119            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1120            on R_ldl.
1121            * R/lCholCMatrix.R,
1122            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1123            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1124            * many files in ./R and ./src: Use more general version of
1125            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1126            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1127            dtpMatrix, dspMatrix and dppMatrix conversions.
1128    
1129    
1130    2006-08-23  Douglas Bates  <bates@R-project.org>
1131    
1132            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1133            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1134            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1135            dgeMatrix_crossprod (may need to do this in other places).
1136            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1137            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1138    
1139    2006-08-22  Douglas Bates  <bates@R-project.org>
1140    
1141            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1142            types of classed Matrices, matrices or numeric or logical vectors.
1143            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1144            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1145            to Mutils.h (as an inline) and change name to Matrix_check_class;
1146            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1147            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1148            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1149            * src/Csparse.c: use diag_P and uplo_P macros.
1150    
1151    2006-08-21  Douglas Bates  <bates@R-project.org>
1152    
1153            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1154            valgrind.
1155            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1156            inverses.
1157            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1158            -Wall warnings.
1159            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1160            Use dup_mMatrix_as_dgeMatrix.
1161    
1162    2006-08-20  Douglas Bates  <bates@R-project.org>
1163    
1164            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1165            * tests/sparseQR.R: Added
1166            * man/sparseQR-class.Rd: Document methods for qr.* generics
1167            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1168    
1169    2006-08-19  Douglas Bates  <bates@R-project.org>
1170    
1171            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1172            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1173            and qr.fitted.
1174            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1175            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1176    
1177    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1178    
1179            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1180            the base version has no "..." argument.
1181    
1182            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1183    
1184            * R/Matrix.R: define and
1185            * NAMESPACE: export as.numeric() and as.logical() methods.
1186                    Let's hope these do not badly slow down something...
1187            Finally export the zapsmall() method.
1188    
1189    2006-08-17  Douglas Bates  <bates@R-project.org>
1190    
1191            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1192            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1193            * src/dtCMatrix.c :Remove code that is no longer used
1194            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1195    
1196  2006-08-14  Douglas Bates  <bates@R-project.org>  2006-08-14  Douglas Bates  <bates@R-project.org>
1197    
1198          * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities          * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities

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