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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 1855, Wed May 23 21:33:34 2007 UTC
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1    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * NAMESPACE: exported drop0(), since
4            * man/drop0.Rd: I have seen several cases, I really wanted to use
5            it, so our users may want too.
6    
7    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * man/colSums.Rd: separately document colSums() etc, since these
10            have the extra argument 'sparseResult'.
11    
12    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
15            * man/spMatrix.Rd: docu., including examples
16    
17            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
18            in order to make colMeans() etc fast *and* correct.
19            * R/sparseVector.R (replSPvec): "[<-" functionality for
20            sparseVectors; tested in
21            * tests/simple.R:
22    
23    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
26            (very) sparse Matrices; output similar to Matlab's print().
27    
28    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
31            0-based, indices (Jose Quesada <quesada@gmail.com>).
32    
33    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
36    
37    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Auxiliaries.R (sparsapply): new utility, much faster than
40            tapply1() for large sparse matrices.
41    
42    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Matrix.R (dim<-): reshape now via sparseVector.
45    
46            * R/sparseVector.R: methods and function for
47            * R/AllClass.R: new "sparseVector" class and daughters.
48            * NAMESPACE: export new classes
49    
50    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * DESCRIPTION (Version): 0.99875-1
53            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
54    
55    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
58            indexing
59            * tests/indexing.R: test set for that.
60    
61    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
64            entries.
65            * tests/indexing.R(out): add regression test for it
66    
67    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
70            name for "!" method definitions.
71    
72    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Tsparse.R (intI): new utility, used for "[" :
75                    Cleanup up there, and fixes for duplicated indices - more TODO!
76    
77            * tests/indexing.R(out): more tests
78    
79    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
80    
81            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
82            code that is now part of the R Lapack library.
83    
84            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
85            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
86    
87    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
90    
91    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
94            up with extraneous names '0'...'<n-1>'
95    
96    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dgTMatrix.R (mat2dgT): care about NAs
99    
100    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/kronecker.R: triangularity preserving methods
103    
104    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/kronecker.R: new file collecting kronecker() methods in one
107                    place.  Goal: become much faster!
108    
109    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
112            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
113            can be much faster.
114    
115            * tests/matprod.R: add regression tests for these (upper & lower).
116    
117    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/Matrix.R (diff): method for our Matrices.
120    
121            * R/sparseMatrix.R (isDiagonal): check dim()!
122    
123    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Matrix.R (dim<-): new method for "reshape()" built on a
126            proposal from Tamas Papp.
127    
128    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
131    
132            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
133            rather define and export  cBind() and rBind() only.
134            --> useRs *must* change code that used to have cbind()/rbind() !!
135    
136            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
137            * R/bind.Rout.save: ditto
138    
139    2007-02-16  Douglas Bates  <bates@r-project.org>
140    
141            * DESCRIPTION (Date, Version): 0.9975-11 with new date
142            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
143            const modifier on declaration of the array 'valid'
144    
145    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
146    
147            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
148    
149    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
152    
153            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
154            * tests/simple.R: test the above and some of these coercions:
155    
156            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
157                    be careful to avoid infinite recursion, using new coercions in
158            * R/ngCMatrix.R and nsC... and ntC...
159            * R/lsparseMatrix.R: ditto
160    
161            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
162    
163            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
164            * R/Rsparse.R: reactivate .Call()s
165    
166            * tests/Class+Meth.R: a bit more on actual classes
167    
168    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
171    
172    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * DESCRIPTION (Version): 0.9975-10 to upload
175    
176            * tests/Class+Meth.R (tstMatrixClass): require coercions to
177            specific classes less unconditionally.
178    
179            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
180    
181            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
182    
183            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
184            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
185            R_to_CMatrix segfaults on one platform.
186            Eliminate most coercion method to *specific* classes, and replace
187            with virtual classes coercions.
188    
189    
190    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
191    
192            * src/init.c: export the CHM...._validate() placeholders, since
193            they *are* called.
194    
195            * tests/Class+Meth.R (classCanCoerce): and starting to test
196            all as(<from>, <to>)
197    
198    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
201            * tests/indexing.R: tested now
202            * tests/indexing.Rout.save: updated
203    
204            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
205            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
206            appropriate.
207    
208            * NAMESPACE: export a trivial
209            * R/Matrix.R: drop() Matrix-method
210    
211            * R/AllClass.R: moved all prototypes to virtual super classes.
212    
213            * R/Rsparse.R: many more coercions to have less exceptions in
214            * tests/Class+Meth.R:
215    
216            * R/Ops.R (Compare): tweak for case with NA
217            * tests/simpl.R: hence another 'FIXME' eliminated
218    
219    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
222            objects.
223    
224            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
225              and more of "!", "&", "|", all, any; coercions
226    
227            * R/Rsparse.R: many coercions (which enable quite a few other
228            methods), thanks to enhancements in
229            * src/dgCMatrix.c (R_to_CMatrix): new, and
230            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
231            symmetric & triangular and ..RMatrix objects.
232    
233            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
234            renamed file from src/dsTMatrix.c;
235            now dealing with symmetric and triangular Tsparse coercions, both
236            to dense and general.
237    
238    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
241    
242            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
243            where sensible when the <numeric> is of length > 1.
244    
245    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Matrix.R ([<-): for M[] <- value: fix length
248    
249    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
252            * R/ndenseMatrix.R: new coercions n* -> l*
253    
254    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
257    
258            * R/Ops.R ("Logic"): and other "Ops", many updates
259    
260    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * src/Mutils.h (SET_DimNames): new utility
263    
264            * R/Auxiliaries.R (nnzero): improved and now exported via
265    
266            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
267    
268    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/diagMatrix.R (!): fix typo.
271    
272    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/Auxiliaries.R (as_Csparse): and quite a few others:
275                    allow to pass class definition --> speedup
276            * R/sparseMatrix.R: apply the above
277    
278            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
279    
280            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
281            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
282            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
283    
284            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
285    
286            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
287            and use it for "sparse*" as well, since it's faster than the
288            as_Csparse(.) way.
289    
290    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
293    
294    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
297            as method for   M[ ij ] <- v
298            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
299    
300            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
301            FALSE answer
302    
303            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
304            * tests/indexing.R: test it, and some of the above
305    
306    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/Auxiliaries.R (is_duplicatedT): new utility
309    
310    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
311    
312            * src/init.c (R_init_Matrix): export cholmod_scale
313    
314    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
317            base::as.matrix to (x, ...)
318    
319    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
322            file; start using "Logic", hence
323    
324            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
325            * NAMESPACE: import and export "Logic"
326    
327    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
330            only needed previously to R version 2.5.0.
331    
332    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
335    
336            * R/Tsparse.R (replTmat): fix subassignment of triangular
337            * R/Csparse.R (replCmat): ditto
338            * tests/indexing.R: more tests, incl the above fix
339    
340    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/Auxiliaries.R (drop0): extend for non CSparse
343            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
344    
345            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
346                    use uplo correctly (!); other places: use uplo_P() macro
347    
348            * R/Csparse.R (replCmat): call diagU2N() when needed
349            * R/Tsparse.R (replTmat): ditto
350    
351            * src/dtCMatrix.c (tCMatrix_validate): new
352            * src/dtTMatrix.c (tTMatrix_validate): new, used in
353            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
354    
355            * R/diagMatrix.R (replDiag): to use in [<-
356    
357    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
360                    also more general diagU2N().
361    
362    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
365            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
366    
367    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * tests/bind.R: a few more cases
370            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
371    
372            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
373            * R/ddenseMatrix.R (cbind2/rbind2)
374            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
375            * tests/indexing.R
376            * tests/indexing.Rout.save: updated
377    
378    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
381            * tests/indexing.R
382    
383    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
386            align with proper position of "0", i.e., right for integers.
387            argument 'align' by default is "fancy".
388    
389    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
392            * R/Csparse.R: and fix "Compare" for more cases.
393            * tests/Class+Meth.R: test some of these (m == m, m != m)
394    
395    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/lsparseMatrix.R: all() and any() methods
398            * R/ldenseMatrix.R:      ditto
399            * NAMESPACE, R/Matrix.R: ditto
400    
401            * man/all-methods.Rd: document them minimally
402    
403            * tests/simple.R: add a few examples for these
404    
405    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/Tsparse.R ([): fix long standing typo in symmetric case
408            * man/dsCMatrix-class.Rd: add example exhibiting the above case
409    
410    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
411    
412            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
413            to LL before converting to a sparse matrix. (The LDL form can be
414            converted to a sparse matrix but it is implicitly a unit
415            triangular matrix and a diagonal matrix overwritten on the diagonal.)
416    
417    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
418    
419            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
420    
421    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
422    
423            * DESCRIPTION (Version): updated -> release 0.9975-7
424            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
425    
426  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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