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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2223, Fri Jul 18 23:04:48 2008 UTC
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1    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
4            versions.
5    
6            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
7            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
8    
9            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
10              AS_CHM_SP() which includes diagU2N.
11    
12    
13    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
14    
15            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
16              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
17              new solve method
18            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
19              Csparse_diagU2N functionality into Matrix_as_cs
20    
21    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
24              vignette
25            * [r2214] R/AllGeneric.R: cosmetic
26            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
27    
28    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
29    
30            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
31              argument with default TRUE
32            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
33              Csparse_diagU2N
34            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
35              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
36              parent array; new solve method for signature(a = "dtCMatrix", b =
37              "sparseMatrix")
38    
39    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/diagMatrix.R (.bdiag): also keep triangular
42            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
43              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
44              bdiag() improvements of last week
45    
46    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
47    
48            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
49              messages
50    
51    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
54            symmetric- or nsparse-Matrix, also fixing the bug introduced with
55            the new version (.999375-10).
56    
57            * tests/Simple.R: regression test for the bugs.
58    
59    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseVector.R (spV2M): fix for "isparseVector".
62            Further, fix <diag> -> <sparseVector> coercion
63            (repSpV): add rep(<sparseVector>, .) method
64    
65            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
66            use as.vector(.).
67    
68            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
69    
70            * R/AllClass.R: new (hidden) class union "scarceMatrix"
71            * R/AllClass.R: sparseVector: add prototype
72    
73            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
74            Kasper Kristensen
75    
76    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * tests/other-pkgs.R: add more interesting Matrix -> graph
79    
80    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
83            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
84    
85    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * DESCRIPTION: release 0.999375-10 to CRAN
88    
89            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
90            .bdiag().
91            * man/bdiag.Rd: update, including test.
92    
93    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * tests/Simple.R: add minimal bdiag() checks
96    
97            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
98              factor out the Tsparse - internal computation into new .bdiag()
99    
100    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/nsparseMatrix.R: specific fast all() and any() methods.
103    
104            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
105            when trying to produce too large result.
106    
107            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
108            very large matrices.
109    
110            * R/sparseMatrix.R (printSpMatrix2): new function, used by
111            show(<sparseMatrix>).
112    
113            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
114    
115    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * src/Mutils.c (m_encodeInd, m_encodeInd2):
118            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
119    
120            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
121            big matrices): -> 2nd argument 'di' instead of 'nr' !
122    
123    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/dtCMatrix.R: faster dgC* -> dtC* method
126            * tests/Simple.R: (hence removed "FIXME")
127    
128            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
129            which can be be turned off for possible speed gains.
130    
131    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
134    
135            * R/not.R: fix !<ldiMatrix>
136            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
137    
138            * R/diagMatrix.R (Ops): fix one-off thinko in
139            <diagonal> o <numeric> methods
140    
141            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
142    
143    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
146            * tests/Simple.R: testing the above
147    
148    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
151    
152    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
155            * NAMESPACE (unname): finally exported
156    
157    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/Auxiliaries.R (cholMat): possibly keep packed
160    
161            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
162            for R < 2.7.0.
163    
164            * R/Tsparse.R ([): for triangularMatrix, check if result may be
165            triangular.
166            * tests/indexing.R: regression test
167    
168    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
171            * R/Ops.R: more methods, for lMatrix/nMatrix
172    
173    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/expm.R: new file for all expm() methods; notably new ones for
176            diagonal*, triangular*, symmetric* and also simple "matrix".
177    
178    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
181    
182            * inst/test-tools.R (assert.EQ.mat): better message when not equal
183    
184            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
185    
186            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
187            [dl]denseMatrix {identical slots; but more logical method dispatch}
188    
189    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
192    
193            * R/diagMatrix.R (determinant): method
194    
195    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
198    
199            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
200    
201            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
202            its diagonal
203    
204    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
207    
208            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
209    
210            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
211    
212            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
213    
214    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
217    
218            * R/Ops.R (.do.Logic.lsparse): fix NA case
219    
220            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
221    
222            * R/Auxiliaries.R (nnzero): fix special cases, using
223            * R/Auxiliaries.R (indDiag): new utility
224            * R/Auxiliaries.R (indTri): new argument 'diag'
225    
226            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
227    
228    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
231    
232            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
233            ".tCMatrix" triangular matrix.
234    
235            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
236            'clx' can be class *or* class representation.
237            (nnzSparse): new.
238            (non0ind): new 'xtendSymm' argument; used in
239            * R/Ops.R:
240    
241            * R/pMatrix.R: more efficient determinant() method
242    
243    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
246            * [disactivated] NAMESPACE: export(det)
247    
248            * R/diagMatrix.R (mkDiag): new substitute for diag()
249    
250            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
251            (as0, as1): new utility.
252    
253            * R/Csparse.R (diag, band): need diagU2N()
254    
255            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
256    
257            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
258    
259            * R/Ops.R (Compare): fix <nsp> o <nsp> case
260    
261            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
262    
263    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Auxiliaries.R (signPerm): new utility for
266            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
267    
268            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
269            since we have our own error handler (and can use tryCatch() from R).
270    
271    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
274    
275            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
276            when not positive definite.
277    
278            * R/Auxiliaries.R (asTri): new auxiliary
279            (non0.i): make *much* faster for Tsparse with many non-zero
280            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
281    
282            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
283            test-tools.R , see below
284    
285            * R/dMatrix.R: fix "Summary" method: + diagU2N()
286    
287            * NAMESPACE, R/Matrix.R: add mean() method
288    
289    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
292            cold-hot colors; try *changed* default useAbs = FALSE
293            * man/image-methods.Rd:  nice examples
294    
295    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * inst/test-tools.R (checkMatrix): new function for modularizing part
298            of tstMatrixClass() in tests/Class+Meth.R
299    
300            * R/dsCMatrix.R: coercion from "matrix"
301            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
302    
303            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
304            add test for as(matrix(,0,0), <class>)
305    
306    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
309            work as determinant(matrix(,0,0)).
310    
311            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
312            * man/sparseLU-class.Rd: ditto
313    
314            * R/dgCMatrix.R (determinant): method building on lu()
315            * R/sparseMatrix.R, Matrix.R, ...: ditto
316    
317            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
318    
319    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
322            pattern matrices.
323    
324    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * src/dense.c (dense_to_Csparse): all declarations *before*
327            R_CheckStack(); needed e.g. for ancient gcc 2.96.
328    
329    
330  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
333          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
334    
335            * R/AllClass.R: drop "double" from "atomicVector" class union
336    
337            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
338            * R/dgeMatrix.R: ditto
339    
340          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
341    
342            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
343    
344  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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