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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1845, Wed May 16 21:24:41 2007 UTC
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1    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
4    
5    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Auxiliaries.R (sparsapply): new utility, much faster than
8            tapply1() for large sparse matrices.
9    
10    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Matrix.R (dim<-): reshape now via sparseVector.
13    
14            * R/sparseVector.R: methods and function for
15            * R/AllClass.R: new "sparseVector" class and daughters.
16            * NAMESPACE: export new classes
17    
18    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * DESCRIPTION (Version): 0.99875-1
21            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
22    
23    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
26            indexing
27            * tests/indexing.R: test set for that.
28    
29    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
32            entries.
33            * tests/indexing.R(out): add regression test for it
34    
35    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
38            name for "!" method definitions.
39    
40    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/Tsparse.R (intI): new utility, used for "[" :
43                    Cleanup up there, and fixes for duplicated indices - more TODO!
44    
45            * tests/indexing.R(out): more tests
46    
47    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
50            code that is now part of the R Lapack library.
51    
52            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
53            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
54    
55    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
58    
59    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
62            up with extraneous names '0'...'<n-1>'
63    
64    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/dgTMatrix.R (mat2dgT): care about NAs
67    
68    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/kronecker.R: triangularity preserving methods
71    
72    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/kronecker.R: new file collecting kronecker() methods in one
75                    place.  Goal: become much faster!
76    
77    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
80            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
81            can be much faster.
82    
83            * tests/matprod.R: add regression tests for these (upper & lower).
84    
85    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Matrix.R (diff): method for our Matrices.
88    
89            * R/sparseMatrix.R (isDiagonal): check dim()!
90    
91    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R (dim<-): new method for "reshape()" built on a
94            proposal from Tamas Papp.
95    
96    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
99    
100            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
101            rather define and export  cBind() and rBind() only.
102            --> useRs *must* change code that used to have cbind()/rbind() !!
103    
104            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
105            * R/bind.Rout.save: ditto
106    
107    2007-02-16  Douglas Bates  <bates@r-project.org>
108    
109            * DESCRIPTION (Date, Version): 0.9975-11 with new date
110            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
111            const modifier on declaration of the array 'valid'
112    
113    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
116    
117    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
120    
121            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
122            * tests/simple.R: test the above and some of these coercions:
123    
124            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
125                    be careful to avoid infinite recursion, using new coercions in
126            * R/ngCMatrix.R and nsC... and ntC...
127            * R/lsparseMatrix.R: ditto
128    
129            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
130    
131            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
132            * R/Rsparse.R: reactivate .Call()s
133    
134            * tests/Class+Meth.R: a bit more on actual classes
135    
136    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
139    
140    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Version): 0.9975-10 to upload
143    
144            * tests/Class+Meth.R (tstMatrixClass): require coercions to
145            specific classes less unconditionally.
146    
147            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
148    
149            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
150    
151            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
152            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
153            R_to_CMatrix segfaults on one platform.
154            Eliminate most coercion method to *specific* classes, and replace
155            with virtual classes coercions.
156    
157    
158    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
159    
160            * src/init.c: export the CHM...._validate() placeholders, since
161            they *are* called.
162    
163            * tests/Class+Meth.R (classCanCoerce): and starting to test
164            all as(<from>, <to>)
165    
166    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
169            * tests/indexing.R: tested now
170            * tests/indexing.Rout.save: updated
171    
172            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
173            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
174            appropriate.
175    
176            * NAMESPACE: export a trivial
177            * R/Matrix.R: drop() Matrix-method
178    
179            * R/AllClass.R: moved all prototypes to virtual super classes.
180    
181            * R/Rsparse.R: many more coercions to have less exceptions in
182            * tests/Class+Meth.R:
183    
184            * R/Ops.R (Compare): tweak for case with NA
185            * tests/simpl.R: hence another 'FIXME' eliminated
186    
187    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
190            objects.
191    
192            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
193              and more of "!", "&", "|", all, any; coercions
194    
195            * R/Rsparse.R: many coercions (which enable quite a few other
196            methods), thanks to enhancements in
197            * src/dgCMatrix.c (R_to_CMatrix): new, and
198            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
199            symmetric & triangular and ..RMatrix objects.
200    
201            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
202            renamed file from src/dsTMatrix.c;
203            now dealing with symmetric and triangular Tsparse coercions, both
204            to dense and general.
205    
206    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
209    
210            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
211            where sensible when the <numeric> is of length > 1.
212    
213    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Matrix.R ([<-): for M[] <- value: fix length
216    
217    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
220            * R/ndenseMatrix.R: new coercions n* -> l*
221    
222    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
225    
226            * R/Ops.R ("Logic"): and other "Ops", many updates
227    
228    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * src/Mutils.h (SET_DimNames): new utility
231    
232            * R/Auxiliaries.R (nnzero): improved and now exported via
233    
234            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
235    
236    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/diagMatrix.R (!): fix typo.
239    
240    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Auxiliaries.R (as_Csparse): and quite a few others:
243                    allow to pass class definition --> speedup
244            * R/sparseMatrix.R: apply the above
245    
246            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
247    
248            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
249            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
250            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
251    
252            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
253    
254            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
255            and use it for "sparse*" as well, since it's faster than the
256            as_Csparse(.) way.
257    
258    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
261    
262    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
265            as method for   M[ ij ] <- v
266            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
267    
268            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
269            FALSE answer
270    
271            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
272            * tests/indexing.R: test it, and some of the above
273    
274    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/Auxiliaries.R (is_duplicatedT): new utility
277    
278    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
279    
280            * src/init.c (R_init_Matrix): export cholmod_scale
281    
282    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
285            base::as.matrix to (x, ...)
286    
287    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
290            file; start using "Logic", hence
291    
292            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
293            * NAMESPACE: import and export "Logic"
294    
295    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
298            only needed previously to R version 2.5.0.
299    
300    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
303    
304            * R/Tsparse.R (replTmat): fix subassignment of triangular
305            * R/Csparse.R (replCmat): ditto
306            * tests/indexing.R: more tests, incl the above fix
307    
308    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Auxiliaries.R (drop0): extend for non CSparse
311            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
312    
313            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
314                    use uplo correctly (!); other places: use uplo_P() macro
315    
316            * R/Csparse.R (replCmat): call diagU2N() when needed
317            * R/Tsparse.R (replTmat): ditto
318    
319            * src/dtCMatrix.c (tCMatrix_validate): new
320            * src/dtTMatrix.c (tTMatrix_validate): new, used in
321            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
322    
323            * R/diagMatrix.R (replDiag): to use in [<-
324    
325    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
328                    also more general diagU2N().
329    
330    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
333            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
334    
335    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * tests/bind.R: a few more cases
338            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
339    
340            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
341            * R/ddenseMatrix.R (cbind2/rbind2)
342            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
343            * tests/indexing.R
344            * tests/indexing.Rout.save: updated
345    
346    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
349            * tests/indexing.R
350    
351    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
354            align with proper position of "0", i.e., right for integers.
355            argument 'align' by default is "fancy".
356    
357    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
360            * R/Csparse.R: and fix "Compare" for more cases.
361            * tests/Class+Meth.R: test some of these (m == m, m != m)
362    
363    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/lsparseMatrix.R: all() and any() methods
366            * R/ldenseMatrix.R:      ditto
367            * NAMESPACE, R/Matrix.R: ditto
368    
369            * man/all-methods.Rd: document them minimally
370    
371            * tests/simple.R: add a few examples for these
372    
373    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/Tsparse.R ([): fix long standing typo in symmetric case
376            * man/dsCMatrix-class.Rd: add example exhibiting the above case
377    
378    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
379    
380            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
381            to LL before converting to a sparse matrix. (The LDL form can be
382            converted to a sparse matrix but it is implicitly a unit
383            triangular matrix and a diagonal matrix overwritten on the diagonal.)
384    
385    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
388    
389    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
390    
391            * DESCRIPTION (Version): updated -> release 0.9975-7
392            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
393    
394    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
397    
398    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
399    
400            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
401            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
402            is exactly singular.
403    
404    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * DESCRIPTION (Date): updated -> release 0.9975-6
407    
408    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
411            now returns symmetric.
412    
413            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
414    
415            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
416            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
417    
418            * R/Auxiliaries.R (.type.kind): added
419    
420    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
423            running src/CSparse_install.sh
424    
425            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
426    
427    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
430            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
431    
432            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
433    
434            * tests/Class+Meth.R (tstMatrixClass): now assure
435            the (important in method programming) property :
436    
437                    ###>>  Every "Matrix" is either
438                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
439    
440                    (where "*" stands for "Matrix")
441    
442            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
443    
444            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
445            * tests/validObj.R: checks for "comparison"
446    
447            * R/sparseMatrix.R ([): improved indexing for sparse;
448                    trying to keep <symmetric>[ n, n] symmmetric
449    
450            * tests/indexing.R: indexing for logical sparse now ok
451    
452    
453    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * src/Tsparse.c: use xTsparse_validate() , and hence remove
456    
457            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
458    
459    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
462    
463            * tests/simple.R: validObject() checking the above.
464    
465            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
466            replacing both dgCMatrix_validate and lgCM*.
467    
468            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
469            fix dimnames setting in other places.
470            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
471    
472    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
475    
476            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
477            symmetry test, via
478            * R/Auxiliaries.R (.as.dgC.0.factors):
479    
480    2006-11-01  Douglas Bates  <bates@r-project.org>
481    
482            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
483            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
484            <CsparseMatrix>) added
485    
486    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * tests/matprod.R: add a variation of Harri's example
489    
490            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
491            recursive infinitely.
492    
493            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
494    
495            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
496    
497    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
500            matrix if possible; test m+m == 2*m; now test dgRMatrix.
501            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
502            satisfy the above test.
503    
504    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
507    
508            * R/dgCMatrix.R: solve(a, b="missing") based on
509            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
510            RHS = NULL.
511    
512            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
513            add more (needed) [t]crossprod() methods.
514    
515            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
516    
517            * R/Auxiliaries.R (as_CspClass): cleanup
518            (drop0): internal utility for "Csparse_drop(*, 0)"
519            (.bail.out.2): encourage active feedback
520    
521    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * R/dMatrix.R(Compare): new(), then slots [no validity check]
524    
525            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
526            non-valid or 'sorted' case).
527    
528            * R/dsparseMatrix.R: add "chol" method.
529            * R/ddenseMatrix.R: ditto
530    
531            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
532            * NAMESPACE (Ops)
533            * R/diagMatrix.R (diag2T): simple utility used "higher level"
534            coercion; deprecating direct lower level coercions.
535    
536            * R/*.R (seq): use seq_len() and seq_along() where possible.
537    
538    
539    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * DESCRIPTION (Version): 0.9975-5 ready for release
542    
543    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
544    
545            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
546    
547    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/AllClass.R (corMatrix): add 'validity' check;
550                    comment out unused "LDL" class definition
551            * NAMESPACE: mention, but do not export "LDL" class
552            * R/corMatrix.R: new (simple), needed for R-devel with
553            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
554              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
555    
556    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
557    
558            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
559            use Rprintf and R's error handling.
560    
561    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
564            * tests/matprod.R: add tests for the bug fixed.
565    
566    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
567    
568            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
569            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
570    
571    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
572    
573            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
574    
575    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * DESCRIPTION (Version): 0.9975-3
578    
579            * R/diagMatrix.R (bdiag): new function constructing block diagonal
580            (sparse) matrices.
581            * man/bdiag.Rd: docu + examples
582    
583            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
584    
585            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
586            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
587    
588            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
589            that result is sparse or diagonal (and not dense).
590    
591            * man/Subassign-methods.Rd: fix examples
592    
593            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
594            should always return a sparse (and not sometimes a diagonal) matrix.
595    
596    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
599    
600    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
601    
602            * DESCRIPTION (Version): 0.9975-2
603    
604            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
605    
606    2006-10-02  Douglas Bates  <bates@R-project.org>
607    
608            * tests/dg_Matrix.R: Simplify test taking into account new code.
609    
610    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
613    
614            * R/lsTMatrix.R: new files w/ missing methods
615            * R/nsTMatrix.R:  "  'for completeness'
616    
617            * tests/Class+Meth.R: a bit less 'not.ok.classes'
618    
619            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
620    
621    
622    2006-09-28  Douglas Bates  <bates@R-project.org>
623    
624            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
625            included.
626    
627            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
628            Export C-callable functions used in Zt_create in lme4.
629    
630    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * DESCRIPTION (Version): 0.9975-1
633    
634            * tests/simple.R: less checks fail; using NA, found that our
635                    kronecker() is not base-compatible with NA's.
636    
637            * R/dMatrix.R: "Compare" method now implemented for all cases
638    
639            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
640    
641            * man/dtpMatrix-class.Rd: mention length of 'x' slot
642    
643            * src/dtpMatrix.c (dtpMatrix_validate): fix check
644            * src/dspMatrix.c (dspMatrix_validate): ditto
645    
646            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
647              including coercion to [nl]tTMatrix.
648    
649            * R/diagMatrix.R (show): print a header line as for other classes.
650    
651    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * src/Makefile.win (SUBDIRS): fix typo
654    
655    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
658    
659    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
660    
661            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
662            symmetric and y missing in R code using %*% (cholmod_aat doesn't
663            accept a symmetric matrix).
664            * tests/group-methods.R: Uncomment test of crossprod applied to
665            lsCMatrix objects.
666    
667    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/AllClass.R (symmetricMatrix): add validity method (available
670            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
671    
672            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
673    
674            * tests/indexing.Rout.save:
675            * tests/indexing.R: additions, mainly for 'lsparse'
676    
677            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
678            case.
679    
680            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
681    
682    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
685                    as 'N' (1-letter - Ok?)
686    
687            * tests/group-methods.R: add test for logical + NAs
688    
689            * R/dMatrix.R ("Compare"): fix to work with NA's
690    
691            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
692    
693            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
694                    which is implemented.
695    
696    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * src/chm_common.c: coerce logical <-> double instead of
699            typecasting;  needed for "l" matrix handling in cholmod.
700    
701            * tests/other-pkgs.R (graph): small extension in "graph" checks.
702    
703            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
704            (Tsp2grNEL): other fixes needed
705    
706    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
709                    Matrices, since "lMatrix", also "lsparseM" can have NA
710            * R/ndenseMatrix.R, etc: new source files
711            * man/nsparseMatrix-classes.Rd, etc: new help files
712            * tests/: adaptions
713            * src/chm_common.c (chm_dense_to_SEXP): and others:
714                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
715            * src/Csparse.c, etc: ditto
716    
717    2006-09-11  Douglas Bates  <bates@R-project.org>
718    
719            * src/Mutils.[ch],init.c inst/include/*.h: Move the
720            alloc_d**Matrix functions to the lme4 package.
721    
722    2006-09-09  Douglas Bates  <bates@R-project.org>
723    
724            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
725            fixed
726    
727    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/lMatrix.R: new
730    
731            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
732    
733            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
734            * man/tcrossprod.Rd: ditto
735    
736    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
737    
738            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
739            for exported functions
740            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
741            Remove partitioning algorithms for sparse matrix reordering.  The
742            copyright on the Metis code was problematic and the methods were
743            rarely used.
744            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
745            operations are now done entirely in CHOLMOD code.
746    
747    2006-09-06  Douglas Bates  <bates@R-project.org>
748    
749            * src/Mutils.h: Remove functions that are no longer used.
750    
751    2006-09-04  Douglas Bates  <bates@R-project.org>
752    
753            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
754            * src/DEPS.mkf: update
755    
756    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * created branches/Matrix-for-R-2.3.x;  on trunk: do
759            * DESCRIPTION (Version): 0.9975-0
760            (Depends): R (>= 2.4.0)
761    
762    2006-09-01  Douglas Bates  <bates@R-project.org>
763    
764            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
765    
766    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
767    
768            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
769            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
770    
771            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
772    
773    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
776            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
777            * R/dsparseMatrix.R: ditto
778            * R/Csparse.R: ditto
779    
780    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * R/dMatrix.R (Compare): improve availability of "<", etc
783            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
784    
785    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
788            of a 0-index which was used as 1-index (..hmm)
789    
790            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
791    
792            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
793            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
794            (.is.diagonal): ditto
795    
796            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
797    
798            * R/Matrix.R (Matrix): also work for NA data
799    
800  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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