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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1834, Fri May 11 10:07:17 2007 UTC
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1    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
4            indexing
5            * tests/indexing.R: test set for that.
6    
7    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
10            entries.
11            * tests/indexing.R(out): add regression test for it
12    
13    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
16            name for "!" method definitions.
17    
18    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/Tsparse.R (intI): new utility, used for "[" :
21                    Cleanup up there, and fixes for duplicated indices - more TODO!
22    
23            * tests/indexing.R(out): more tests
24    
25    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
26    
27            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
28            code that is now part of the R Lapack library.
29    
30            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
31            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
32    
33    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
36    
37    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
40            up with extraneous names '0'...'<n-1>'
41    
42    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dgTMatrix.R (mat2dgT): care about NAs
45    
46    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/kronecker.R: triangularity preserving methods
49    
50    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/kronecker.R: new file collecting kronecker() methods in one
53                    place.  Goal: become much faster!
54    
55    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
58            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
59            can be much faster.
60    
61            * tests/matprod.R: add regression tests for these (upper & lower).
62    
63    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Matrix.R (diff): method for our Matrices.
66    
67            * R/sparseMatrix.R (isDiagonal): check dim()!
68    
69    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Matrix.R (dim<-): new method for "reshape()" built on a
72            proposal from Tamas Papp.
73    
74    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
77    
78            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
79            rather define and export  cBind() and rBind() only.
80            --> useRs *must* change code that used to have cbind()/rbind() !!
81    
82            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
83            * R/bind.Rout.save: ditto
84    
85    2007-02-16  Douglas Bates  <bates@r-project.org>
86    
87            * DESCRIPTION (Date, Version): 0.9975-11 with new date
88            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
89            const modifier on declaration of the array 'valid'
90    
91    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
92    
93            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
94    
95    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
98    
99            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
100            * tests/simple.R: test the above and some of these coercions:
101    
102            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
103                    be careful to avoid infinite recursion, using new coercions in
104            * R/ngCMatrix.R and nsC... and ntC...
105            * R/lsparseMatrix.R: ditto
106    
107            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
108    
109            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
110            * R/Rsparse.R: reactivate .Call()s
111    
112            * tests/Class+Meth.R: a bit more on actual classes
113    
114    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
115    
116            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
117    
118    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * DESCRIPTION (Version): 0.9975-10 to upload
121    
122            * tests/Class+Meth.R (tstMatrixClass): require coercions to
123            specific classes less unconditionally.
124    
125            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
126    
127            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
128    
129            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
130            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
131            R_to_CMatrix segfaults on one platform.
132            Eliminate most coercion method to *specific* classes, and replace
133            with virtual classes coercions.
134    
135    
136    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
137    
138            * src/init.c: export the CHM...._validate() placeholders, since
139            they *are* called.
140    
141            * tests/Class+Meth.R (classCanCoerce): and starting to test
142            all as(<from>, <to>)
143    
144    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
147            * tests/indexing.R: tested now
148            * tests/indexing.Rout.save: updated
149    
150            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
151            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
152            appropriate.
153    
154            * NAMESPACE: export a trivial
155            * R/Matrix.R: drop() Matrix-method
156    
157            * R/AllClass.R: moved all prototypes to virtual super classes.
158    
159            * R/Rsparse.R: many more coercions to have less exceptions in
160            * tests/Class+Meth.R:
161    
162            * R/Ops.R (Compare): tweak for case with NA
163            * tests/simpl.R: hence another 'FIXME' eliminated
164    
165    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
168            objects.
169    
170            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
171              and more of "!", "&", "|", all, any; coercions
172    
173            * R/Rsparse.R: many coercions (which enable quite a few other
174            methods), thanks to enhancements in
175            * src/dgCMatrix.c (R_to_CMatrix): new, and
176            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
177            symmetric & triangular and ..RMatrix objects.
178    
179            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
180            renamed file from src/dsTMatrix.c;
181            now dealing with symmetric and triangular Tsparse coercions, both
182            to dense and general.
183    
184    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
187    
188            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
189            where sensible when the <numeric> is of length > 1.
190    
191    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Matrix.R ([<-): for M[] <- value: fix length
194    
195    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
198            * R/ndenseMatrix.R: new coercions n* -> l*
199    
200    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
203    
204            * R/Ops.R ("Logic"): and other "Ops", many updates
205    
206    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * src/Mutils.h (SET_DimNames): new utility
209    
210            * R/Auxiliaries.R (nnzero): improved and now exported via
211    
212            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
213    
214    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/diagMatrix.R (!): fix typo.
217    
218    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Auxiliaries.R (as_Csparse): and quite a few others:
221                    allow to pass class definition --> speedup
222            * R/sparseMatrix.R: apply the above
223    
224            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
225    
226            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
227            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
228            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
229    
230            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
231    
232            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
233            and use it for "sparse*" as well, since it's faster than the
234            as_Csparse(.) way.
235    
236    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
239    
240    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
243            as method for   M[ ij ] <- v
244            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
245    
246            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
247            FALSE answer
248    
249            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
250            * tests/indexing.R: test it, and some of the above
251    
252    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Auxiliaries.R (is_duplicatedT): new utility
255    
256    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
257    
258            * src/init.c (R_init_Matrix): export cholmod_scale
259    
260    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
263            base::as.matrix to (x, ...)
264    
265    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
268            file; start using "Logic", hence
269    
270            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
271            * NAMESPACE: import and export "Logic"
272    
273    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
276            only needed previously to R version 2.5.0.
277    
278    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
281    
282            * R/Tsparse.R (replTmat): fix subassignment of triangular
283            * R/Csparse.R (replCmat): ditto
284            * tests/indexing.R: more tests, incl the above fix
285    
286    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Auxiliaries.R (drop0): extend for non CSparse
289            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
290    
291            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
292                    use uplo correctly (!); other places: use uplo_P() macro
293    
294            * R/Csparse.R (replCmat): call diagU2N() when needed
295            * R/Tsparse.R (replTmat): ditto
296    
297            * src/dtCMatrix.c (tCMatrix_validate): new
298            * src/dtTMatrix.c (tTMatrix_validate): new, used in
299            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
300    
301            * R/diagMatrix.R (replDiag): to use in [<-
302    
303    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
306                    also more general diagU2N().
307    
308    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
311            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
312    
313    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * tests/bind.R: a few more cases
316            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
317    
318            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
319            * R/ddenseMatrix.R (cbind2/rbind2)
320            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
321            * tests/indexing.R
322            * tests/indexing.Rout.save: updated
323    
324    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
327            * tests/indexing.R
328    
329    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
332            align with proper position of "0", i.e., right for integers.
333            argument 'align' by default is "fancy".
334    
335    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
338            * R/Csparse.R: and fix "Compare" for more cases.
339            * tests/Class+Meth.R: test some of these (m == m, m != m)
340    
341    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/lsparseMatrix.R: all() and any() methods
344            * R/ldenseMatrix.R:      ditto
345            * NAMESPACE, R/Matrix.R: ditto
346    
347            * man/all-methods.Rd: document them minimally
348    
349            * tests/simple.R: add a few examples for these
350    
351    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Tsparse.R ([): fix long standing typo in symmetric case
354            * man/dsCMatrix-class.Rd: add example exhibiting the above case
355    
356    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
357    
358            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
359            to LL before converting to a sparse matrix. (The LDL form can be
360            converted to a sparse matrix but it is implicitly a unit
361            triangular matrix and a diagonal matrix overwritten on the diagonal.)
362    
363    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
364    
365            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
366    
367    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
368    
369            * DESCRIPTION (Version): updated -> release 0.9975-7
370            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
371    
372    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
375    
376    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
377    
378            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
379            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
380            is exactly singular.
381    
382    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * DESCRIPTION (Date): updated -> release 0.9975-6
385    
386    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
389            now returns symmetric.
390    
391            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
392    
393            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
394            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
395    
396            * R/Auxiliaries.R (.type.kind): added
397    
398    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
401            running src/CSparse_install.sh
402    
403            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
404    
405    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
408            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
409    
410            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
411    
412            * tests/Class+Meth.R (tstMatrixClass): now assure
413            the (important in method programming) property :
414    
415                    ###>>  Every "Matrix" is either
416                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
417    
418                    (where "*" stands for "Matrix")
419    
420            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
421    
422            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
423            * tests/validObj.R: checks for "comparison"
424    
425            * R/sparseMatrix.R ([): improved indexing for sparse;
426                    trying to keep <symmetric>[ n, n] symmmetric
427    
428            * tests/indexing.R: indexing for logical sparse now ok
429    
430    
431    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * src/Tsparse.c: use xTsparse_validate() , and hence remove
434    
435            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
436    
437    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
440    
441            * tests/simple.R: validObject() checking the above.
442    
443            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
444            replacing both dgCMatrix_validate and lgCM*.
445    
446            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
447            fix dimnames setting in other places.
448            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
449    
450    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
453    
454            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
455            symmetry test, via
456            * R/Auxiliaries.R (.as.dgC.0.factors):
457    
458    2006-11-01  Douglas Bates  <bates@r-project.org>
459    
460            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
461            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
462            <CsparseMatrix>) added
463    
464    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * tests/matprod.R: add a variation of Harri's example
467    
468            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
469            recursive infinitely.
470    
471            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
472    
473            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
474    
475    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
478            matrix if possible; test m+m == 2*m; now test dgRMatrix.
479            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
480            satisfy the above test.
481    
482    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
485    
486            * R/dgCMatrix.R: solve(a, b="missing") based on
487            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
488            RHS = NULL.
489    
490            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
491            add more (needed) [t]crossprod() methods.
492    
493            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
494    
495            * R/Auxiliaries.R (as_CspClass): cleanup
496            (drop0): internal utility for "Csparse_drop(*, 0)"
497            (.bail.out.2): encourage active feedback
498    
499    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/dMatrix.R(Compare): new(), then slots [no validity check]
502    
503            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
504            non-valid or 'sorted' case).
505    
506            * R/dsparseMatrix.R: add "chol" method.
507            * R/ddenseMatrix.R: ditto
508    
509            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
510            * NAMESPACE (Ops)
511            * R/diagMatrix.R (diag2T): simple utility used "higher level"
512            coercion; deprecating direct lower level coercions.
513    
514            * R/*.R (seq): use seq_len() and seq_along() where possible.
515    
516    
517    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * DESCRIPTION (Version): 0.9975-5 ready for release
520    
521    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
522    
523            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
524    
525    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/AllClass.R (corMatrix): add 'validity' check;
528                    comment out unused "LDL" class definition
529            * NAMESPACE: mention, but do not export "LDL" class
530            * R/corMatrix.R: new (simple), needed for R-devel with
531            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
532              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
533    
534    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
535    
536            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
537            use Rprintf and R's error handling.
538    
539    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
542            * tests/matprod.R: add tests for the bug fixed.
543    
544    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
545    
546            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
547            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
548    
549    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
550    
551            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
552    
553    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * DESCRIPTION (Version): 0.9975-3
556    
557            * R/diagMatrix.R (bdiag): new function constructing block diagonal
558            (sparse) matrices.
559            * man/bdiag.Rd: docu + examples
560    
561            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
562    
563            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
564            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
565    
566            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
567            that result is sparse or diagonal (and not dense).
568    
569            * man/Subassign-methods.Rd: fix examples
570    
571            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
572            should always return a sparse (and not sometimes a diagonal) matrix.
573    
574    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
577    
578    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
579    
580            * DESCRIPTION (Version): 0.9975-2
581    
582            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
583    
584    2006-10-02  Douglas Bates  <bates@R-project.org>
585    
586            * tests/dg_Matrix.R: Simplify test taking into account new code.
587    
588    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
591    
592            * R/lsTMatrix.R: new files w/ missing methods
593            * R/nsTMatrix.R:  "  'for completeness'
594    
595            * tests/Class+Meth.R: a bit less 'not.ok.classes'
596    
597            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
598    
599    
600    2006-09-28  Douglas Bates  <bates@R-project.org>
601    
602            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
603            included.
604    
605            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
606            Export C-callable functions used in Zt_create in lme4.
607    
608    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * DESCRIPTION (Version): 0.9975-1
611    
612            * tests/simple.R: less checks fail; using NA, found that our
613                    kronecker() is not base-compatible with NA's.
614    
615            * R/dMatrix.R: "Compare" method now implemented for all cases
616    
617            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
618    
619            * man/dtpMatrix-class.Rd: mention length of 'x' slot
620    
621            * src/dtpMatrix.c (dtpMatrix_validate): fix check
622            * src/dspMatrix.c (dspMatrix_validate): ditto
623    
624            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
625              including coercion to [nl]tTMatrix.
626    
627            * R/diagMatrix.R (show): print a header line as for other classes.
628    
629    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * src/Makefile.win (SUBDIRS): fix typo
632    
633    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
636    
637    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
638    
639            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
640            symmetric and y missing in R code using %*% (cholmod_aat doesn't
641            accept a symmetric matrix).
642            * tests/group-methods.R: Uncomment test of crossprod applied to
643            lsCMatrix objects.
644    
645    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * R/AllClass.R (symmetricMatrix): add validity method (available
648            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
649    
650            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
651    
652            * tests/indexing.Rout.save:
653            * tests/indexing.R: additions, mainly for 'lsparse'
654    
655            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
656            case.
657    
658            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
659    
660    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
663                    as 'N' (1-letter - Ok?)
664    
665            * tests/group-methods.R: add test for logical + NAs
666    
667            * R/dMatrix.R ("Compare"): fix to work with NA's
668    
669            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
670    
671            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
672                    which is implemented.
673    
674    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * src/chm_common.c: coerce logical <-> double instead of
677            typecasting;  needed for "l" matrix handling in cholmod.
678    
679            * tests/other-pkgs.R (graph): small extension in "graph" checks.
680    
681            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
682            (Tsp2grNEL): other fixes needed
683    
684    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
687                    Matrices, since "lMatrix", also "lsparseM" can have NA
688            * R/ndenseMatrix.R, etc: new source files
689            * man/nsparseMatrix-classes.Rd, etc: new help files
690            * tests/: adaptions
691            * src/chm_common.c (chm_dense_to_SEXP): and others:
692                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
693            * src/Csparse.c, etc: ditto
694    
695    2006-09-11  Douglas Bates  <bates@R-project.org>
696    
697            * src/Mutils.[ch],init.c inst/include/*.h: Move the
698            alloc_d**Matrix functions to the lme4 package.
699    
700    2006-09-09  Douglas Bates  <bates@R-project.org>
701    
702            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
703            fixed
704    
705    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/lMatrix.R: new
708    
709            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
710    
711            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
712            * man/tcrossprod.Rd: ditto
713    
714    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
715    
716            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
717            for exported functions
718            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
719            Remove partitioning algorithms for sparse matrix reordering.  The
720            copyright on the Metis code was problematic and the methods were
721            rarely used.
722            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
723            operations are now done entirely in CHOLMOD code.
724    
725    2006-09-06  Douglas Bates  <bates@R-project.org>
726    
727            * src/Mutils.h: Remove functions that are no longer used.
728    
729    2006-09-04  Douglas Bates  <bates@R-project.org>
730    
731            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
732            * src/DEPS.mkf: update
733    
734    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * created branches/Matrix-for-R-2.3.x;  on trunk: do
737            * DESCRIPTION (Version): 0.9975-0
738            (Depends): R (>= 2.4.0)
739    
740    2006-09-01  Douglas Bates  <bates@R-project.org>
741    
742            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
743    
744    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
747            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
748    
749            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
750    
751    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
754            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
755            * R/dsparseMatrix.R: ditto
756            * R/Csparse.R: ditto
757    
758    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/dMatrix.R (Compare): improve availability of "<", etc
761            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
762    
763    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
766            of a 0-index which was used as 1-index (..hmm)
767    
768            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
769    
770            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
771            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
772            (.is.diagonal): ditto
773    
774            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
775    
776            * R/Matrix.R (Matrix): also work for NA data
777    
778    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
781            in all cases.
782    
783    2006-08-27  Douglas Bates  <bates@R-project.org>
784    
785            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
786            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
787    
788    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
791            subclasses of "ddenseMatrix"
792            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
793            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
794            instead of half dozen specialized ones.
795    
796    2006-08-25  Douglas Bates  <bates@R-project.org>
797    
798            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
799            <tillard@cirad.fr> - ordering standard errors to match effects.
800    
801    2006-08-24  Douglas Bates  <bates@R-project.org>
802    
803            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
804            on R_ldl.
805            * R/lCholCMatrix.R,
806            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
807            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
808            * many files in ./R and ./src: Use more general version of
809            dup_mMatrix_as_dgeMatrix to simplify method definitions.
810            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
811            dtpMatrix, dspMatrix and dppMatrix conversions.
812    
813    
814    2006-08-23  Douglas Bates  <bates@R-project.org>
815    
816            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
817            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
818            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
819            dgeMatrix_crossprod (may need to do this in other places).
820            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
821            generic and method for dsCMatrix.  Use CHOLMOD for chol().
822    
823    2006-08-22  Douglas Bates  <bates@R-project.org>
824    
825            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
826            types of classed Matrices, matrices or numeric or logical vectors.
827            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
828            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
829            to Mutils.h (as an inline) and change name to Matrix_check_class;
830            fixes in as_cholmod_factor and chm_factor_to_SEXP.
831            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
832            dsCMatrix_matrix_solve.  Comment out vestigial functions.
833            * src/Csparse.c: use diag_P and uplo_P macros.
834    
835  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
836    
837          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
838          valgrind.          valgrind.
839            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
840            inverses.
841            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
842            -Wall warnings.
843            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
844            Use dup_mMatrix_as_dgeMatrix.
845    
846  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
847    

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