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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 1863, Sun Jun 3 14:57:55 2007 UTC
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1    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
4              src/init.c: Yet another cholmod export - cholmod_ssmult
5    
6    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * NAMESPACE: exported drop0(), since
9            * man/drop0.Rd: I have seen several cases, I really wanted to use
10            it, so our users may want too.
11    
12    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * man/colSums.Rd: separately document colSums() etc, since these
15            have the extra argument 'sparseResult'.
16    
17    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
20            * man/spMatrix.Rd: docu., including examples
21    
22            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
23            in order to make colMeans() etc fast *and* correct.
24            * R/sparseVector.R (replSPvec): "[<-" functionality for
25            sparseVectors; tested in
26            * tests/simple.R:
27    
28    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
31            (very) sparse Matrices; output similar to Matlab's print().
32    
33    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
36            0-based, indices (Jose Quesada <quesada@gmail.com>).
37    
38    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
41    
42    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Auxiliaries.R (sparsapply): new utility, much faster than
45            tapply1() for large sparse matrices.
46    
47    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Matrix.R (dim<-): reshape now via sparseVector.
50    
51            * R/sparseVector.R: methods and function for
52            * R/AllClass.R: new "sparseVector" class and daughters.
53            * NAMESPACE: export new classes
54    
55    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * DESCRIPTION (Version): 0.99875-1
58            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
59    
60    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
63            indexing
64            * tests/indexing.R: test set for that.
65    
66    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
69            entries.
70            * tests/indexing.R(out): add regression test for it
71    
72    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
75            name for "!" method definitions.
76    
77    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/Tsparse.R (intI): new utility, used for "[" :
80                    Cleanup up there, and fixes for duplicated indices - more TODO!
81    
82            * tests/indexing.R(out): more tests
83    
84    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
85    
86            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
87            code that is now part of the R Lapack library.
88    
89            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
90            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
91    
92    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
95    
96    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
99            up with extraneous names '0'...'<n-1>'
100    
101    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/dgTMatrix.R (mat2dgT): care about NAs
104    
105    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/kronecker.R: triangularity preserving methods
108    
109    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/kronecker.R: new file collecting kronecker() methods in one
112                    place.  Goal: become much faster!
113    
114    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
117            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
118            can be much faster.
119    
120            * tests/matprod.R: add regression tests for these (upper & lower).
121    
122    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Matrix.R (diff): method for our Matrices.
125    
126            * R/sparseMatrix.R (isDiagonal): check dim()!
127    
128    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/Matrix.R (dim<-): new method for "reshape()" built on a
131            proposal from Tamas Papp.
132    
133    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
136    
137            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
138            rather define and export  cBind() and rBind() only.
139            --> useRs *must* change code that used to have cbind()/rbind() !!
140    
141            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
142            * R/bind.Rout.save: ditto
143    
144    2007-02-16  Douglas Bates  <bates@r-project.org>
145    
146            * DESCRIPTION (Date, Version): 0.9975-11 with new date
147            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
148            const modifier on declaration of the array 'valid'
149    
150    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
153    
154    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
157    
158            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
159            * tests/simple.R: test the above and some of these coercions:
160    
161            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
162                    be careful to avoid infinite recursion, using new coercions in
163            * R/ngCMatrix.R and nsC... and ntC...
164            * R/lsparseMatrix.R: ditto
165    
166            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
167    
168            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
169            * R/Rsparse.R: reactivate .Call()s
170    
171            * tests/Class+Meth.R: a bit more on actual classes
172    
173    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
174    
175            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
176    
177    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * DESCRIPTION (Version): 0.9975-10 to upload
180    
181            * tests/Class+Meth.R (tstMatrixClass): require coercions to
182            specific classes less unconditionally.
183    
184            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
185    
186            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
187    
188            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
189            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
190            R_to_CMatrix segfaults on one platform.
191            Eliminate most coercion method to *specific* classes, and replace
192            with virtual classes coercions.
193    
194    
195    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
196    
197            * src/init.c: export the CHM...._validate() placeholders, since
198            they *are* called.
199    
200            * tests/Class+Meth.R (classCanCoerce): and starting to test
201            all as(<from>, <to>)
202    
203    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
206            * tests/indexing.R: tested now
207            * tests/indexing.Rout.save: updated
208    
209            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
210            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
211            appropriate.
212    
213            * NAMESPACE: export a trivial
214            * R/Matrix.R: drop() Matrix-method
215    
216            * R/AllClass.R: moved all prototypes to virtual super classes.
217    
218            * R/Rsparse.R: many more coercions to have less exceptions in
219            * tests/Class+Meth.R:
220    
221            * R/Ops.R (Compare): tweak for case with NA
222            * tests/simpl.R: hence another 'FIXME' eliminated
223    
224    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
227            objects.
228    
229            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
230              and more of "!", "&", "|", all, any; coercions
231    
232            * R/Rsparse.R: many coercions (which enable quite a few other
233            methods), thanks to enhancements in
234            * src/dgCMatrix.c (R_to_CMatrix): new, and
235            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
236            symmetric & triangular and ..RMatrix objects.
237    
238            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
239            renamed file from src/dsTMatrix.c;
240            now dealing with symmetric and triangular Tsparse coercions, both
241            to dense and general.
242    
243    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
246    
247            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
248            where sensible when the <numeric> is of length > 1.
249    
250    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/Matrix.R ([<-): for M[] <- value: fix length
253    
254    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
257            * R/ndenseMatrix.R: new coercions n* -> l*
258    
259    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
262    
263            * R/Ops.R ("Logic"): and other "Ops", many updates
264    
265    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * src/Mutils.h (SET_DimNames): new utility
268    
269            * R/Auxiliaries.R (nnzero): improved and now exported via
270    
271            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
272    
273    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/diagMatrix.R (!): fix typo.
276    
277    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Auxiliaries.R (as_Csparse): and quite a few others:
280                    allow to pass class definition --> speedup
281            * R/sparseMatrix.R: apply the above
282    
283            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
284    
285            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
286            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
287            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
288    
289            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
290    
291            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
292            and use it for "sparse*" as well, since it's faster than the
293            as_Csparse(.) way.
294    
295    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
298    
299    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
302            as method for   M[ ij ] <- v
303            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
304    
305            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
306            FALSE answer
307    
308            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
309            * tests/indexing.R: test it, and some of the above
310    
311    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Auxiliaries.R (is_duplicatedT): new utility
314    
315  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
316    
317          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
318    
319    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
322            base::as.matrix to (x, ...)
323    
324  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R

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