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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 1748, Mon Jan 29 20:48:26 2007 UTC
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1    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
4            objects.
5    
6            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
7              and more of "!", "&", "|", all, any; coercions
8    
9            * R/Rsparse.R: many coercions (which enable quite a few other
10            methods), thanks to enhancements in
11            * src/dgCMatrix.c (R_to_CMatrix): new, and
12            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
13            symmetric & triangular and ..RMatrix objects.
14    
15            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
16            renamed file from src/dsTMatrix.c;
17            now dealing with symmetric and triangular Tsparse coercions, both
18            to dense and general.
19    
20    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
23    
24            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
25            where sensible when the <numeric> is of length > 1.
26    
27    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Matrix.R ([<-): for M[] <- value: fix length
30    
31    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
34            * R/ndenseMatrix.R: new coercions n* -> l*
35    
36    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
39    
40            * R/Ops.R ("Logic"): and other "Ops", many updates
41    
42    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/Mutils.h (SET_DimNames): new utility
45    
46            * R/Auxiliaries.R (nnzero): improved and now exported via
47    
48            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
49    
50    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/diagMatrix.R (!): fix typo.
53    
54    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/Auxiliaries.R (as_Csparse): and quite a few others:
57                    allow to pass class definition --> speedup
58            * R/sparseMatrix.R: apply the above
59    
60            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
61    
62            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
63            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
64            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
65    
66            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
67    
68            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
69            and use it for "sparse*" as well, since it's faster than the
70            as_Csparse(.) way.
71    
72    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
75    
76    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
79            as method for   M[ ij ] <- v
80            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
81    
82            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
83            FALSE answer
84    
85            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
86            * tests/indexing.R: test it, and some of the above
87    
88    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/Auxiliaries.R (is_duplicatedT): new utility
91    
92    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * src/init.c (R_init_Matrix): export cholmod_scale
95    
96    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
99            base::as.matrix to (x, ...)
100    
101    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
104            file; start using "Logic", hence
105    
106            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
107            * NAMESPACE: import and export "Logic"
108    
109    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
112            only needed previously to R version 2.5.0.
113    
114    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
117    
118            * R/Tsparse.R (replTmat): fix subassignment of triangular
119            * R/Csparse.R (replCmat): ditto
120            * tests/indexing.R: more tests, incl the above fix
121    
122    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Auxiliaries.R (drop0): extend for non CSparse
125            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
126    
127            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
128                    use uplo correctly (!); other places: use uplo_P() macro
129    
130            * R/Csparse.R (replCmat): call diagU2N() when needed
131            * R/Tsparse.R (replTmat): ditto
132    
133            * src/dtCMatrix.c (tCMatrix_validate): new
134            * src/dtTMatrix.c (tTMatrix_validate): new, used in
135            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
136    
137            * R/diagMatrix.R (replDiag): to use in [<-
138    
139    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
142                    also more general diagU2N().
143    
144    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
147            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
148    
149    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * tests/bind.R: a few more cases
152            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
153    
154            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
155            * R/ddenseMatrix.R (cbind2/rbind2)
156            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
157            * tests/indexing.R
158            * tests/indexing.Rout.save: updated
159    
160    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
163            * tests/indexing.R
164    
165    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
168            align with proper position of "0", i.e., right for integers.
169            argument 'align' by default is "fancy".
170    
171    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
174            * R/Csparse.R: and fix "Compare" for more cases.
175            * tests/Class+Meth.R: test some of these (m == m, m != m)
176    
177    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/lsparseMatrix.R: all() and any() methods
180            * R/ldenseMatrix.R:      ditto
181            * NAMESPACE, R/Matrix.R: ditto
182    
183            * man/all-methods.Rd: document them minimally
184    
185            * tests/simple.R: add a few examples for these
186    
187    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Tsparse.R ([): fix long standing typo in symmetric case
190            * man/dsCMatrix-class.Rd: add example exhibiting the above case
191    
192    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
193    
194            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
195            to LL before converting to a sparse matrix. (The LDL form can be
196            converted to a sparse matrix but it is implicitly a unit
197            triangular matrix and a diagonal matrix overwritten on the diagonal.)
198    
199    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
202    
203    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * DESCRIPTION (Version): updated -> release 0.9975-7
206            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
207    
208    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
211    
212    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
213    
214            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
215            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
216            is exactly singular.
217    
218    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * DESCRIPTION (Date): updated -> release 0.9975-6
221    
222    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
225            now returns symmetric.
226    
227            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
228    
229            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
230            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
231    
232            * R/Auxiliaries.R (.type.kind): added
233    
234    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
237            running src/CSparse_install.sh
238    
239            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
240    
241    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
244            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
245    
246            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
247    
248            * tests/Class+Meth.R (tstMatrixClass): now assure
249            the (important in method programming) property :
250    
251                    ###>>  Every "Matrix" is either
252                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
253    
254                    (where "*" stands for "Matrix")
255    
256            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
257    
258            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
259            * tests/validObj.R: checks for "comparison"
260    
261            * R/sparseMatrix.R ([): improved indexing for sparse;
262                    trying to keep <symmetric>[ n, n] symmmetric
263    
264            * tests/indexing.R: indexing for logical sparse now ok
265    
266    
267    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * src/Tsparse.c: use xTsparse_validate() , and hence remove
270    
271            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
272    
273    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
276    
277            * tests/simple.R: validObject() checking the above.
278    
279            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
280            replacing both dgCMatrix_validate and lgCM*.
281    
282            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
283            fix dimnames setting in other places.
284            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
285    
286    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
289    
290            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
291            symmetry test, via
292            * R/Auxiliaries.R (.as.dgC.0.factors):
293    
294    2006-11-01  Douglas Bates  <bates@r-project.org>
295    
296            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
297            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
298            <CsparseMatrix>) added
299    
300    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * tests/matprod.R: add a variation of Harri's example
303    
304            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
305            recursive infinitely.
306    
307            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
308    
309            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
310    
311    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
314            matrix if possible; test m+m == 2*m; now test dgRMatrix.
315            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
316            satisfy the above test.
317    
318    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
321    
322            * R/dgCMatrix.R: solve(a, b="missing") based on
323            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
324            RHS = NULL.
325    
326            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
327            add more (needed) [t]crossprod() methods.
328    
329            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
330    
331            * R/Auxiliaries.R (as_CspClass): cleanup
332            (drop0): internal utility for "Csparse_drop(*, 0)"
333            (.bail.out.2): encourage active feedback
334    
335    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/dMatrix.R(Compare): new(), then slots [no validity check]
338    
339            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
340            non-valid or 'sorted' case).
341    
342            * R/dsparseMatrix.R: add "chol" method.
343            * R/ddenseMatrix.R: ditto
344    
345            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
346            * NAMESPACE (Ops)
347            * R/diagMatrix.R (diag2T): simple utility used "higher level"
348            coercion; deprecating direct lower level coercions.
349    
350            * R/*.R (seq): use seq_len() and seq_along() where possible.
351    
352    
353    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * DESCRIPTION (Version): 0.9975-5 ready for release
356    
357  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
358    
359          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.

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