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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2235, Wed Jul 23 10:24:17 2008 UTC
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1    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/chm_common.c (as_cholmod_sparse): add 4th argument
4            'sort_in_place' and set it to TRUE in call from
5            * src/Csparse.c (Csparse_validate): sort in place, making sure that
6            validObject() continues sort the columns if needed.
7            * tests/validObj.R: now tests that.
8    
9    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
12            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
13            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
14            diagU2N().
15    
16            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
17            .spDiagonal() and new .trDiagonal().
18    
19            * R/dtCMatrix.R (solve): make use of .trDiagonal()
20    
21    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
24            stumbled upon by Michael H.
25    
26            * tests/validObj.R: testing the bug-fix
27    
28            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
29            versions.
30    
31            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
32            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
33    
34            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
35              AS_CHM_SP() which includes diagU2N.
36    
37            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
38            adapt to 3 arguments.
39    
40    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
41    
42            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
43              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
44              new solve method
45            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
46              Csparse_diagU2N functionality into Matrix_as_cs
47    
48    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
51              vignette
52            * [r2214] R/AllGeneric.R: cosmetic
53            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
54    
55    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
58              argument with default TRUE
59            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
60              Csparse_diagU2N
61            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
62              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
63              parent array; new solve method for signature(a = "dtCMatrix", b =
64              "sparseMatrix")
65    
66    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/diagMatrix.R (.bdiag): also keep triangular
69            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
70              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
71              bdiag() improvements of last week
72    
73    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
74    
75            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
76              messages
77    
78    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
81            symmetric- or nsparse-Matrix, also fixing the bug introduced with
82            the new version (.999375-10).
83    
84            * tests/Simple.R: regression test for the bugs.
85    
86    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/sparseVector.R (spV2M): fix for "isparseVector".
89            Further, fix <diag> -> <sparseVector> coercion
90            (repSpV): add rep(<sparseVector>, .) method
91    
92            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
93            use as.vector(.).
94    
95            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
96    
97            * R/AllClass.R: new (hidden) class union "scarceMatrix"
98            * R/AllClass.R: sparseVector: add prototype
99    
100            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
101            Kasper Kristensen
102    
103    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * tests/other-pkgs.R: add more interesting Matrix -> graph
106    
107    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
110            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
111    
112    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * DESCRIPTION: release 0.999375-10 to CRAN
115    
116            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
117            .bdiag().
118            * man/bdiag.Rd: update, including test.
119    
120    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * tests/Simple.R: add minimal bdiag() checks
123    
124            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
125              factor out the Tsparse - internal computation into new .bdiag()
126    
127    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/nsparseMatrix.R: specific fast all() and any() methods.
130    
131            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
132            when trying to produce too large result.
133    
134            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
135            very large matrices.
136    
137            * R/sparseMatrix.R (printSpMatrix2): new function, used by
138            show(<sparseMatrix>).
139    
140            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
141    
142    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * src/Mutils.c (m_encodeInd, m_encodeInd2):
145            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
146    
147            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
148            big matrices): -> 2nd argument 'di' instead of 'nr' !
149    
150    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/dtCMatrix.R: faster dgC* -> dtC* method
153            * tests/Simple.R: (hence removed "FIXME")
154    
155            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
156            which can be be turned off for possible speed gains.
157    
158    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
161    
162            * R/not.R: fix !<ldiMatrix>
163            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
164    
165            * R/diagMatrix.R (Ops): fix one-off thinko in
166            <diagonal> o <numeric> methods
167    
168            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
169    
170    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
173            * tests/Simple.R: testing the above
174    
175    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
178    
179    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
182            * NAMESPACE (unname): finally exported
183    
184    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/Auxiliaries.R (cholMat): possibly keep packed
187    
188            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
189            for R < 2.7.0.
190    
191            * R/Tsparse.R ([): for triangularMatrix, check if result may be
192            triangular.
193            * tests/indexing.R: regression test
194    
195    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
198            * R/Ops.R: more methods, for lMatrix/nMatrix
199    
200    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/expm.R: new file for all expm() methods; notably new ones for
203            diagonal*, triangular*, symmetric* and also simple "matrix".
204    
205    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
208    
209            * inst/test-tools.R (assert.EQ.mat): better message when not equal
210    
211            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
212    
213            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
214            [dl]denseMatrix {identical slots; but more logical method dispatch}
215    
216    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
219    
220            * R/diagMatrix.R (determinant): method
221    
222    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
225    
226            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
227    
228            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
229            its diagonal
230    
231    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
234    
235            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
236    
237            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
238    
239            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
240    
241    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
244    
245            * R/Ops.R (.do.Logic.lsparse): fix NA case
246    
247            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
248    
249            * R/Auxiliaries.R (nnzero): fix special cases, using
250            * R/Auxiliaries.R (indDiag): new utility
251            * R/Auxiliaries.R (indTri): new argument 'diag'
252    
253            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
254    
255    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
258    
259            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
260            ".tCMatrix" triangular matrix.
261    
262            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
263            'clx' can be class *or* class representation.
264            (nnzSparse): new.
265            (non0ind): new 'xtendSymm' argument; used in
266            * R/Ops.R:
267    
268            * R/pMatrix.R: more efficient determinant() method
269    
270    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
273            * [disactivated] NAMESPACE: export(det)
274    
275            * R/diagMatrix.R (mkDiag): new substitute for diag()
276    
277            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
278            (as0, as1): new utility.
279    
280            * R/Csparse.R (diag, band): need diagU2N()
281    
282            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
283    
284            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
285    
286            * R/Ops.R (Compare): fix <nsp> o <nsp> case
287    
288            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
289    
290    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Auxiliaries.R (signPerm): new utility for
293            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
294    
295            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
296            since we have our own error handler (and can use tryCatch() from R).
297    
298    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
301    
302            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
303            when not positive definite.
304    
305            * R/Auxiliaries.R (asTri): new auxiliary
306            (non0.i): make *much* faster for Tsparse with many non-zero
307            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
308    
309            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
310            test-tools.R , see below
311    
312            * R/dMatrix.R: fix "Summary" method: + diagU2N()
313    
314            * NAMESPACE, R/Matrix.R: add mean() method
315    
316    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
319            cold-hot colors; try *changed* default useAbs = FALSE
320            * man/image-methods.Rd:  nice examples
321    
322    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * inst/test-tools.R (checkMatrix): new function for modularizing part
325            of tstMatrixClass() in tests/Class+Meth.R
326    
327            * R/dsCMatrix.R: coercion from "matrix"
328            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
329    
330            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
331            add test for as(matrix(,0,0), <class>)
332    
333    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
336            work as determinant(matrix(,0,0)).
337    
338            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
339            * man/sparseLU-class.Rd: ditto
340    
341            * R/dgCMatrix.R (determinant): method building on lu()
342            * R/sparseMatrix.R, Matrix.R, ...: ditto
343    
344            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
345    
346    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
349            pattern matrices.
350    
351    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * src/dense.c (dense_to_Csparse): all declarations *before*
354            R_CheckStack(); needed e.g. for ancient gcc 2.96.
355    
356    
357  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
360          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
361    
362            * R/AllClass.R: drop "double" from "atomicVector" class union
363    
364            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
365            * R/dgeMatrix.R: ditto
366    
367          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
368    
369            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
370    
371  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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