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revision 2158, Fri Mar 28 17:07:54 2008 UTC revision 2226, Mon Jul 21 17:15:17 2008 UTC
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1    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
4            .spDiagonal() and new .trDiagonal().
5    
6            * R/dtCMatrix.R (solve): make use of .trDiagonal()
7    
8    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
11            stumbled upon by Michael H.
12    
13            * tests/validObj.R: testing the bug-fix
14    
15            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
16            versions.
17    
18            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
19            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
20    
21            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
22              AS_CHM_SP() which includes diagU2N.
23    
24            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
25            adapt to 3 arguments.
26    
27    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
28    
29            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
30              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
31              new solve method
32            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
33              Csparse_diagU2N functionality into Matrix_as_cs
34    
35    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
38              vignette
39            * [r2214] R/AllGeneric.R: cosmetic
40            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
41    
42    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
43    
44            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
45              argument with default TRUE
46            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
47              Csparse_diagU2N
48            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
49              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
50              parent array; new solve method for signature(a = "dtCMatrix", b =
51              "sparseMatrix")
52    
53    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/diagMatrix.R (.bdiag): also keep triangular
56            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
57              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
58              bdiag() improvements of last week
59    
60    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
61    
62            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
63              messages
64    
65    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
68            symmetric- or nsparse-Matrix, also fixing the bug introduced with
69            the new version (.999375-10).
70    
71            * tests/Simple.R: regression test for the bugs.
72    
73    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/sparseVector.R (spV2M): fix for "isparseVector".
76            Further, fix <diag> -> <sparseVector> coercion
77            (repSpV): add rep(<sparseVector>, .) method
78    
79            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
80            use as.vector(.).
81    
82            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
83    
84            * R/AllClass.R: new (hidden) class union "scarceMatrix"
85            * R/AllClass.R: sparseVector: add prototype
86    
87            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
88            Kasper Kristensen
89    
90    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * tests/other-pkgs.R: add more interesting Matrix -> graph
93    
94    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
97            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
98    
99    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * DESCRIPTION: release 0.999375-10 to CRAN
102    
103            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
104            .bdiag().
105            * man/bdiag.Rd: update, including test.
106    
107    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * tests/Simple.R: add minimal bdiag() checks
110    
111            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
112              factor out the Tsparse - internal computation into new .bdiag()
113    
114    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/nsparseMatrix.R: specific fast all() and any() methods.
117    
118            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
119            when trying to produce too large result.
120    
121            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
122            very large matrices.
123    
124            * R/sparseMatrix.R (printSpMatrix2): new function, used by
125            show(<sparseMatrix>).
126    
127            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
128    
129    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * src/Mutils.c (m_encodeInd, m_encodeInd2):
132            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
133    
134            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
135            big matrices): -> 2nd argument 'di' instead of 'nr' !
136    
137    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/dtCMatrix.R: faster dgC* -> dtC* method
140            * tests/Simple.R: (hence removed "FIXME")
141    
142            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
143            which can be be turned off for possible speed gains.
144    
145    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
148    
149            * R/not.R: fix !<ldiMatrix>
150            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
151    
152            * R/diagMatrix.R (Ops): fix one-off thinko in
153            <diagonal> o <numeric> methods
154    
155            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
156    
157    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
160            * tests/Simple.R: testing the above
161    
162    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
165    
166    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
169            * NAMESPACE (unname): finally exported
170    
171    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Auxiliaries.R (cholMat): possibly keep packed
174    
175            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
176            for R < 2.7.0.
177    
178            * R/Tsparse.R ([): for triangularMatrix, check if result may be
179            triangular.
180            * tests/indexing.R: regression test
181    
182    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
185            * R/Ops.R: more methods, for lMatrix/nMatrix
186    
187    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/expm.R: new file for all expm() methods; notably new ones for
190            diagonal*, triangular*, symmetric* and also simple "matrix".
191    
192    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
195    
196            * inst/test-tools.R (assert.EQ.mat): better message when not equal
197    
198            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
199    
200            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
201            [dl]denseMatrix {identical slots; but more logical method dispatch}
202    
203    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
206    
207            * R/diagMatrix.R (determinant): method
208    
209    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
212    
213            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
214    
215            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
216            its diagonal
217    
218    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
221    
222            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
223    
224            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
225    
226            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
227    
228    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
231    
232            * R/Ops.R (.do.Logic.lsparse): fix NA case
233    
234            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
235    
236            * R/Auxiliaries.R (nnzero): fix special cases, using
237            * R/Auxiliaries.R (indDiag): new utility
238            * R/Auxiliaries.R (indTri): new argument 'diag'
239    
240            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
241    
242    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
245    
246            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
247            ".tCMatrix" triangular matrix.
248    
249            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
250            'clx' can be class *or* class representation.
251            (nnzSparse): new.
252            (non0ind): new 'xtendSymm' argument; used in
253            * R/Ops.R:
254    
255            * R/pMatrix.R: more efficient determinant() method
256    
257    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
260            * [disactivated] NAMESPACE: export(det)
261    
262            * R/diagMatrix.R (mkDiag): new substitute for diag()
263    
264            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
265            (as0, as1): new utility.
266    
267            * R/Csparse.R (diag, band): need diagU2N()
268    
269            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
270    
271            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
272    
273            * R/Ops.R (Compare): fix <nsp> o <nsp> case
274    
275            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
276    
277    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Auxiliaries.R (signPerm): new utility for
280            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
281    
282            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
283            since we have our own error handler (and can use tryCatch() from R).
284    
285    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
288    
289            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
290            when not positive definite.
291    
292            * R/Auxiliaries.R (asTri): new auxiliary
293            (non0.i): make *much* faster for Tsparse with many non-zero
294            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
295    
296            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
297            test-tools.R , see below
298    
299            * R/dMatrix.R: fix "Summary" method: + diagU2N()
300    
301            * NAMESPACE, R/Matrix.R: add mean() method
302    
303    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
306            cold-hot colors; try *changed* default useAbs = FALSE
307            * man/image-methods.Rd:  nice examples
308    
309    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * inst/test-tools.R (checkMatrix): new function for modularizing part
312            of tstMatrixClass() in tests/Class+Meth.R
313    
314            * R/dsCMatrix.R: coercion from "matrix"
315            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
316    
317            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
318            add test for as(matrix(,0,0), <class>)
319    
320    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
323            work as determinant(matrix(,0,0)).
324    
325            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
326            * man/sparseLU-class.Rd: ditto
327    
328            * R/dgCMatrix.R (determinant): method building on lu()
329            * R/sparseMatrix.R, Matrix.R, ...: ditto
330    
331            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
332    
333    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
336            pattern matrices.
337    
338    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * src/dense.c (dense_to_Csparse): all declarations *before*
341            R_CheckStack(); needed e.g. for ancient gcc 2.96.
342    
343    
344    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * DESCRIPTION (Version): 0.999375-9 --- need to release
347            for R-devel (and R 2.7.0 alpha soon).
348    
349            * R/AllClass.R: drop "double" from "atomicVector" class union
350    
351            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
352            * R/dgeMatrix.R: ditto
353    
354            * R/sparseMatrix.R (summary): count NAs
355    
356            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
357    
358  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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