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revision 2050, Tue Aug 14 22:23:33 2007 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>
358    
359            * DESCRIPTION (Version): 0.999375-9 --- need to release
360            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
368    
369            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
370    
371    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
374            order to become compatible to new R 2.7.0 base::rcond().
375    
376    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
379    
380            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
381    
382            * inst/test-tools.R (isValid): new utility, used much in
383            * tests/simple.R:
384    
385            * man/BunchKaufman-methods.Rd: added too
386    
387    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dsyMatrix.R: add BunchKaufman() methods.
390            * R/dspMatrix.R:
391    
392            * src/init.c: add dsyMatrix_trf
393    
394    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
395    
396            * DESCRIPTION (Version): release 0.999375-7
397            * src/CHMfactor.c (CHMfactor_update): fix
398    
399    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
402            internal_chm_factor().
403    
404            * R/AllGeneric.R: do *not* define a "chol" generic
405                    (but rather use the implicit one *without* making pivot
406                    part of the signature)
407            * R/*.R: drop the 'pivot' from chol's signature and make
408                    'pivot=FALSE' a default argument of method definitions.
409    
410            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
411            version of Matrix
412    
413    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
416    
417            * R/sparseMatrix.R (is.na): new simple method
418            * R/denseMatrix.R (is.na): ditto.
419    
420            * R/diagMatrix.R (.symDiagonal): newly exported utility.
421    
422            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
423    
424            * src/UFsparse_download.sh: -->
425            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
426    
427    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
430            functionality; barely tested in
431            * tests/factorizing.R
432    
433            * src/Csparse.c (diag_tC): new functionality to enable faster
434            determinant(<dsCMatrix>, .) in
435            * R/dsCMatrix.R
436    
437    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
438    
439            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
440              src/CHMfactor.c, src/CHMfactor.h,
441              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
442              Log-determinant of the parent matrix from a CHMfactor object as
443              chm_factor_ldetL2; documentation and support
444    
445    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
448    
449    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
452            warning.
453    
454    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
457    
458            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
459              <diagonal> o <sparse_triangular>
460              setAs(., "nMatrix") added.
461    
462            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
463    
464            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
465                    new argument 'checkDense = FALSE'.
466    
467    
468    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
471            back-permutation of the matrix exponential.
472    
473            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
474    
475            * DESCRIPTION (Date,Version): ready to release 0.999375-5
476    
477            * tests/simple.R: testing diagN2U
478    
479    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/Auxiliaries.R (diagN2U): interface to
482    
483            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
484    
485            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
486    
487    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * src/chm_common.c (chm_diagN2U): new utility.
490    
491            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
492            make use of chm_diagN2U() and hence now preserve triangularity and
493            unit-triangularity.
494    
495            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
496    
497    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
500    
501            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
502            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
503    
504            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
505    
506            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
507    
508            * src/chm_common.c (AS_CHM_FINISH): add note about problem
509            for triangular (diag = "U").
510    
511    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
514            * R/bind.R:  .Call(dense_to_Csparse, *)
515    
516    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * R/Matrix.R (Matrix): no longer use coercions to specific classes
519                    (since we are discouraging them in user code).
520    
521            * tests/*.R: also replaces coercions to specific classes by
522            coercions to super classes.
523    
524            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
525    
526    
527    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
530    
531            * src/dense.c (dense_band): generalized from ddense_band
532    
533            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
534              now for "denseMatrix" (instead of just "ddense*"); much
535              simplified setMethod()s for these.
536    
537            * src/dense.c (dense_to_symmetric): generalized from ddense_*
538    
539    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
542            version of as(*, "symmetricMatric").
543    
544            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
545            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
546    
547    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/Matrix.R (subset.ij): utility, as first step to faster
550               M [ <ij-matrix> ] indexing.
551    
552            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
553    
554            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
555            for more efficient symmpart() and skewpart() methods.
556    
557            * src/Mutils.c (equal_string_vectors): utility
558    
559            * src/dense.c (ddense_to_symmetric): new function used in
560    
561            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
562    
563            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
564            order to match the generic (and evade .local(..)).
565    
566            * R/dsCMatrix.R: dgC -> dsC: use C code!
567    
568            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
569            as per TODO
570    
571            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
572    
573            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
574    
575    
576    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
579    
580            * R/Auxiliaries.R (non0.i): take out of non0ind
581    
582            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
583            make tril(), triu(), band() work for "matrix" and all "dense*"
584    
585            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
586            * tests/simple.R: test the fix above
587    
588            * R/sparseMatrix.R ([): simplification: no coerce to <general>
589                    before we use as(., <Tsparse>)[...] anyway
590    
591            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
592    
593            * R/triangularMatrix.R (isTriangular): methods for all subclasses
594            instead of "triangularMatrix" -- just to disambiguate
595    
596    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
599            * tests/indexing.R: example that fails above
600    
601    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
604            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
605                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
606    
607            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
608            * src/Tsparse.h, init.c: ditto
609            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
610                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
611            * R/sparseMatrix.R (isTriangular): hence simplified
612    
613    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/Ops.R (.Arith.Csparse): new utility factored out of former
616              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
617    
618    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
621    
622            * inst/test-tools.R (isOrthogonal): new function; also file restructured
623    
624    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
627            coercion to "nMatrix" and "pMatrix"
628    
629            * R/AllClass.R: "Schur" class;  "number" class union
630            * man/number-class.Rd:
631            * man/Schur-class.Rd:
632    
633            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
634            (.simpleSchur): Schur() method for diagonal matrices
635            (.triSchur):    Schur() method for triangular matrices
636            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
637    
638    
639    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
642    
643    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
646                    in order to ensure 'system = *' is not lost;
647                    formals()$system instead of cut&paste.
648            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
649    
650    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * DESCRIPTION (Date): make ready for release --> 0.999375-4
653    
654            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
655    
656    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
659                    and hence does as.vector(.).
660            * man/pMatrix-class.Rd: docs
661            * R/sparseMatrix.R: fix for printing "integer sparse"
662    
663            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
664    
665            * R/Matrix.R and others: use "exact" function argument list for
666                    both "["   : (x, i,j, ..., drop)
667                    and  "[<-" : (x, i,j, ..., value)
668    
669            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
670            * R/Tsparse.R (replTmat):    ditto
671            * R/diagMatrix.R (replDiag): ditto
672            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
673            * tests/indexing.R: testing the above
674    
675    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/sparseMatrix.R (cov2cor): method for sparse matrices
678    
679            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
680    
681            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
682    
683            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
684    
685    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * R/Matrix.R: "generic" cov2cor() method
688    
689            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
690                    speed up Q %*% D %*% t(Q)
691            * tests/dpoMatrix.R: test nearPD()
692    
693    2007-12-05  Doug Bates and Martin Maechler
694    
695            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
696            stats::xtabs() allowing to create sparse matrices.
697    
698    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
701    
702    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
705    
706    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * R/LU.R: solve() method for "denseLU"
709    
710    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * DESCRIPTION (Version): 0.999375-3 preparing for release
713    
714            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
715    
716            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
717    
718    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
721              thanks to Kasper Kristensen.
722            * tests/matprod.R: regression test for that.
723    
724    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
725    
726            * [r4778] R/AllGeneric.R: Check R version before defining generics for
727              primitives
728    
729    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/denseMatrix.R (rcond): method
732            * R/sparseQR.R (rcond): method, use x or t(x)
733    
734    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
737            matrices.
738            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
739    
740            * man/rcond.Rd: mention the more general definition, and add
741            example for non-square matrices.
742    
743            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
744    
745    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
748    
749    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
752            * tests/indexing.R: add new regression for the above cases.
753    
754    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * src/Mutils.h (__sun): clause for alloca.h on Solaris
757    
758    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * DESCRIPTION (Date, Version): 0.999375-2
761    
762    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/HBMM.R (readMM): make work for pattern matrices as well
765    
766  2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>  2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
767    
768          * [r4730] src/Mutils.h: declare alloca          * [r4730] src/Mutils.h: declare alloca
# Line 8  Line 773 
773            src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its            src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
774            methods; switch writeMM to use CHOLMOD code; repair readMM            methods; switch writeMM to use CHOLMOD code; repair readMM
775    
   
776  2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778          * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens          * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens

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