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revision 2050, Tue Aug 14 22:23:33 2007 UTC revision 2237, Fri Jul 25 06:55:42 2008 UTC
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1    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
4            recursion in new test in
5            * tests/matprod.R: testing the above and another solve() case, below
6    
7            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
8            e.g. triangular 'x'.
9    
10            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
11            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
12            correctly with unit-triangular x
13    
14            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
15            instead of not checking diagU.
16    
17            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
18            experiments where diagonalMatrix would extend sparse*.
19    
20    
21    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
24            "x@p[ncol(x)]" instead of length(x@i).
25            * R/Auxiliaries.R (nnzero): ditto
26    
27            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
28            since that fails for over-allocated i.
29    
30            * tests/validObj.R: more testing of over-allocated (i,x) slots
31    
32    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
35            'sort_in_place' and set it to TRUE in call from
36            * src/Csparse.c (Csparse_validate): sort in place, making sure that
37            validObject() continues sort the columns if needed.
38    
39            * tests/validObj.R: now tests that more thoroughly, and
40            * man/CsparseMatrix-class.Rd: documents it.
41    
42    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
45            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
46            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
47            diagU2N().
48    
49            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
50            .spDiagonal() and new .trDiagonal().
51    
52            * R/dtCMatrix.R (solve): make use of .trDiagonal()
53    
54    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
57            stumbled upon by Michael H.
58    
59            * tests/validObj.R: testing the bug-fix
60    
61            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
62            versions.
63    
64            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
65            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
66    
67            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
68              AS_CHM_SP() which includes diagU2N.
69    
70            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
71            adapt to 3 arguments.
72    
73    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
74    
75            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
76              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
77              new solve method
78            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
79              Csparse_diagU2N functionality into Matrix_as_cs
80    
81    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
84    
85    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
86    
87            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
88              argument with default TRUE
89            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
90              Csparse_diagU2N
91            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
92              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
93              parent array; new solve method for signature(a = "dtCMatrix", b =
94              "sparseMatrix")
95    
96    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/diagMatrix.R (.bdiag): also keep result triangular
99    
100    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
101    
102            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
103              messages
104    
105    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
108            symmetric- or nsparse-Matrix, also fixing the bug introduced with
109            the new version (.999375-10).
110    
111            * tests/Simple.R: regression test for the bugs.
112    
113    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/sparseVector.R (spV2M): fix for "isparseVector".
116            Further, fix <diag> -> <sparseVector> coercion
117            (repSpV): add rep(<sparseVector>, .) method
118    
119            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
120            use as.vector(.).
121    
122            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
123    
124            * R/AllClass.R: new (hidden) class union "scarceMatrix"
125            * R/AllClass.R: sparseVector: add prototype
126    
127            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
128            Kasper Kristensen
129    
130    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * tests/other-pkgs.R: add more interesting Matrix -> graph
133    
134    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
137            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
138    
139    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * DESCRIPTION: release 0.999375-10 to CRAN
142    
143            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
144            .bdiag().
145            * man/bdiag.Rd: update, including test.
146    
147    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * tests/Simple.R: add minimal bdiag() checks
150    
151            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
152              factor out the Tsparse - internal computation into new .bdiag()
153    
154    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/nsparseMatrix.R: specific fast all() and any() methods.
157    
158            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
159            when trying to produce too large result.
160    
161            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
162            very large matrices.
163    
164            * R/sparseMatrix.R (printSpMatrix2): new function, used by
165            show(<sparseMatrix>).
166    
167            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
168    
169    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * src/Mutils.c (m_encodeInd, m_encodeInd2):
172            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
173    
174            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
175            big matrices): -> 2nd argument 'di' instead of 'nr' !
176    
177    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/dtCMatrix.R: faster dgC* -> dtC* method
180            * tests/Simple.R: (hence removed "FIXME")
181    
182            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
183            which can be be turned off for possible speed gains.
184    
185    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
188    
189            * R/not.R: fix !<ldiMatrix>
190            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
191    
192            * R/diagMatrix.R (Ops): fix one-off thinko in
193            <diagonal> o <numeric> methods
194    
195            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
196    
197    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
200            * tests/Simple.R: testing the above
201    
202    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
205    
206    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
209            * NAMESPACE (unname): finally exported
210    
211    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Auxiliaries.R (cholMat): possibly keep packed
214    
215            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
216            for R < 2.7.0.
217    
218            * R/Tsparse.R ([): for triangularMatrix, check if result may be
219            triangular.
220            * tests/indexing.R: regression test
221    
222    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
225            * R/Ops.R: more methods, for lMatrix/nMatrix
226    
227    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/expm.R: new file for all expm() methods; notably new ones for
230            diagonal*, triangular*, symmetric* and also simple "matrix".
231    
232    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
235    
236            * inst/test-tools.R (assert.EQ.mat): better message when not equal
237    
238            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
239    
240            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
241            [dl]denseMatrix {identical slots; but more logical method dispatch}
242    
243    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
246    
247            * R/diagMatrix.R (determinant): method
248    
249    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
252    
253            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
254    
255            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
256            its diagonal
257    
258    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
261    
262            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
263    
264            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
265    
266            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
267    
268    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
271    
272            * R/Ops.R (.do.Logic.lsparse): fix NA case
273    
274            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
275    
276            * R/Auxiliaries.R (nnzero): fix special cases, using
277            * R/Auxiliaries.R (indDiag): new utility
278            * R/Auxiliaries.R (indTri): new argument 'diag'
279    
280            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
281    
282    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
285    
286            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
287            ".tCMatrix" triangular matrix.
288    
289            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
290            'clx' can be class *or* class representation.
291            (nnzSparse): new.
292            (non0ind): new 'xtendSymm' argument; used in
293            * R/Ops.R:
294    
295            * R/pMatrix.R: more efficient determinant() method
296    
297    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
300            * [disactivated] NAMESPACE: export(det)
301    
302            * R/diagMatrix.R (mkDiag): new substitute for diag()
303    
304            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
305            (as0, as1): new utility.
306    
307            * R/Csparse.R (diag, band): need diagU2N()
308    
309            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
310    
311            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
312    
313            * R/Ops.R (Compare): fix <nsp> o <nsp> case
314    
315            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
316    
317    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/Auxiliaries.R (signPerm): new utility for
320            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
321    
322            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
323            since we have our own error handler (and can use tryCatch() from R).
324    
325    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
328    
329            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
330            when not positive definite.
331    
332            * R/Auxiliaries.R (asTri): new auxiliary
333            (non0.i): make *much* faster for Tsparse with many non-zero
334            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
335    
336            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
337            test-tools.R , see below
338    
339            * R/dMatrix.R: fix "Summary" method: + diagU2N()
340    
341            * NAMESPACE, R/Matrix.R: add mean() method
342    
343    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
346            cold-hot colors; try *changed* default useAbs = FALSE
347            * man/image-methods.Rd:  nice examples
348    
349    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * inst/test-tools.R (checkMatrix): new function for modularizing part
352            of tstMatrixClass() in tests/Class+Meth.R
353    
354            * R/dsCMatrix.R: coercion from "matrix"
355            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
356    
357            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
358            add test for as(matrix(,0,0), <class>)
359    
360    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
363            work as determinant(matrix(,0,0)).
364    
365            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
366            * man/sparseLU-class.Rd: ditto
367    
368            * R/dgCMatrix.R (determinant): method building on lu()
369            * R/sparseMatrix.R, Matrix.R, ...: ditto
370    
371            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
372    
373    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
376            pattern matrices.
377    
378    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * src/dense.c (dense_to_Csparse): all declarations *before*
381            R_CheckStack(); needed e.g. for ancient gcc 2.96.
382    
383    
384    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * DESCRIPTION (Version): 0.999375-9 --- need to release
387            for R-devel (and R 2.7.0 alpha soon).
388    
389            * R/AllClass.R: drop "double" from "atomicVector" class union
390    
391            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
392            * R/dgeMatrix.R: ditto
393    
394            * R/sparseMatrix.R (summary): count NAs
395    
396            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
397    
398    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
401            order to become compatible to new R 2.7.0 base::rcond().
402    
403    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
406    
407            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
408    
409            * inst/test-tools.R (isValid): new utility, used much in
410            * tests/simple.R:
411    
412            * man/BunchKaufman-methods.Rd: added too
413    
414    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/dsyMatrix.R: add BunchKaufman() methods.
417            * R/dspMatrix.R:
418    
419            * src/init.c: add dsyMatrix_trf
420    
421    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
422    
423            * DESCRIPTION (Version): release 0.999375-7
424            * src/CHMfactor.c (CHMfactor_update): fix
425    
426    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
429            internal_chm_factor().
430    
431            * R/AllGeneric.R: do *not* define a "chol" generic
432                    (but rather use the implicit one *without* making pivot
433                    part of the signature)
434            * R/*.R: drop the 'pivot' from chol's signature and make
435                    'pivot=FALSE' a default argument of method definitions.
436    
437            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
438            version of Matrix
439    
440    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
443    
444            * R/sparseMatrix.R (is.na): new simple method
445            * R/denseMatrix.R (is.na): ditto.
446    
447            * R/diagMatrix.R (.symDiagonal): newly exported utility.
448    
449            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
450    
451            * src/UFsparse_download.sh: -->
452            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
453    
454    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
457            functionality; barely tested in
458            * tests/factorizing.R
459    
460            * src/Csparse.c (diag_tC): new functionality to enable faster
461            determinant(<dsCMatrix>, .) in
462            * R/dsCMatrix.R
463    
464    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
465    
466            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
467              src/CHMfactor.c, src/CHMfactor.h,
468              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
469              Log-determinant of the parent matrix from a CHMfactor object as
470              chm_factor_ldetL2; documentation and support
471    
472    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
475    
476    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
479            warning.
480    
481    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
484    
485            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
486              <diagonal> o <sparse_triangular>
487              setAs(., "nMatrix") added.
488    
489            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
490    
491            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
492                    new argument 'checkDense = FALSE'.
493    
494    
495    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
498            back-permutation of the matrix exponential.
499    
500            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
501    
502            * DESCRIPTION (Date,Version): ready to release 0.999375-5
503    
504            * tests/simple.R: testing diagN2U
505    
506    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/Auxiliaries.R (diagN2U): interface to
509    
510            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
511    
512            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
513    
514    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * src/chm_common.c (chm_diagN2U): new utility.
517    
518            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
519            make use of chm_diagN2U() and hence now preserve triangularity and
520            unit-triangularity.
521    
522            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
523    
524    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
527    
528            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
529            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
530    
531            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
532    
533            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
534    
535            * src/chm_common.c (AS_CHM_FINISH): add note about problem
536            for triangular (diag = "U").
537    
538    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
541            * R/bind.R:  .Call(dense_to_Csparse, *)
542    
543    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/Matrix.R (Matrix): no longer use coercions to specific classes
546                    (since we are discouraging them in user code).
547    
548            * tests/*.R: also replaces coercions to specific classes by
549            coercions to super classes.
550    
551            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
552    
553    
554    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
557    
558            * src/dense.c (dense_band): generalized from ddense_band
559    
560            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
561              now for "denseMatrix" (instead of just "ddense*"); much
562              simplified setMethod()s for these.
563    
564            * src/dense.c (dense_to_symmetric): generalized from ddense_*
565    
566    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
569            version of as(*, "symmetricMatric").
570    
571            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
572            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
573    
574    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/Matrix.R (subset.ij): utility, as first step to faster
577               M [ <ij-matrix> ] indexing.
578    
579            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
580    
581            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
582            for more efficient symmpart() and skewpart() methods.
583    
584            * src/Mutils.c (equal_string_vectors): utility
585    
586            * src/dense.c (ddense_to_symmetric): new function used in
587    
588            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
589    
590            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
591            order to match the generic (and evade .local(..)).
592    
593            * R/dsCMatrix.R: dgC -> dsC: use C code!
594    
595            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
596            as per TODO
597    
598            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
599    
600            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
601    
602    
603    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
606    
607            * R/Auxiliaries.R (non0.i): take out of non0ind
608    
609            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
610            make tril(), triu(), band() work for "matrix" and all "dense*"
611    
612            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
613            * tests/simple.R: test the fix above
614    
615            * R/sparseMatrix.R ([): simplification: no coerce to <general>
616                    before we use as(., <Tsparse>)[...] anyway
617    
618            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
619    
620            * R/triangularMatrix.R (isTriangular): methods for all subclasses
621            instead of "triangularMatrix" -- just to disambiguate
622    
623    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
626            * tests/indexing.R: example that fails above
627    
628    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
631            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
632                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
633    
634            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
635            * src/Tsparse.h, init.c: ditto
636            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
637                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
638            * R/sparseMatrix.R (isTriangular): hence simplified
639    
640    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/Ops.R (.Arith.Csparse): new utility factored out of former
643              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
644    
645    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
648    
649            * inst/test-tools.R (isOrthogonal): new function; also file restructured
650    
651    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
654            coercion to "nMatrix" and "pMatrix"
655    
656            * R/AllClass.R: "Schur" class;  "number" class union
657            * man/number-class.Rd:
658            * man/Schur-class.Rd:
659    
660            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
661            (.simpleSchur): Schur() method for diagonal matrices
662            (.triSchur):    Schur() method for triangular matrices
663            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
664    
665    
666    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
669    
670    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
673                    in order to ensure 'system = *' is not lost;
674                    formals()$system instead of cut&paste.
675            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
676    
677    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * DESCRIPTION (Date): make ready for release --> 0.999375-4
680    
681            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
682    
683    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
686                    and hence does as.vector(.).
687            * man/pMatrix-class.Rd: docs
688            * R/sparseMatrix.R: fix for printing "integer sparse"
689    
690            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
691    
692            * R/Matrix.R and others: use "exact" function argument list for
693                    both "["   : (x, i,j, ..., drop)
694                    and  "[<-" : (x, i,j, ..., value)
695    
696            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
697            * R/Tsparse.R (replTmat):    ditto
698            * R/diagMatrix.R (replDiag): ditto
699            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
700            * tests/indexing.R: testing the above
701    
702    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/sparseMatrix.R (cov2cor): method for sparse matrices
705    
706            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
707    
708            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
709    
710            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
711    
712    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * R/Matrix.R: "generic" cov2cor() method
715    
716            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
717                    speed up Q %*% D %*% t(Q)
718            * tests/dpoMatrix.R: test nearPD()
719    
720    2007-12-05  Doug Bates and Martin Maechler
721    
722            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
723            stats::xtabs() allowing to create sparse matrices.
724    
725    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
728    
729    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
732    
733    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/LU.R: solve() method for "denseLU"
736    
737    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * DESCRIPTION (Version): 0.999375-3 preparing for release
740    
741            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
742    
743            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
744    
745    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
748              thanks to Kasper Kristensen.
749            * tests/matprod.R: regression test for that.
750    
751    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
752    
753            * [r4778] R/AllGeneric.R: Check R version before defining generics for
754              primitives
755    
756    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/denseMatrix.R (rcond): method
759            * R/sparseQR.R (rcond): method, use x or t(x)
760    
761    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
764            matrices.
765            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
766    
767            * man/rcond.Rd: mention the more general definition, and add
768            example for non-square matrices.
769    
770            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
771    
772    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
775    
776    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
779            * tests/indexing.R: add new regression for the above cases.
780    
781    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * src/Mutils.h (__sun): clause for alloca.h on Solaris
784    
785    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * DESCRIPTION (Date, Version): 0.999375-2
788    
789    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/HBMM.R (readMM): make work for pattern matrices as well
792    
793  2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>  2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
794    
795          * [r4730] src/Mutils.h: declare alloca          * [r4730] src/Mutils.h: declare alloca
# Line 8  Line 800 
800            src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its            src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
801            methods; switch writeMM to use CHOLMOD code; repair readMM            methods; switch writeMM to use CHOLMOD code; repair readMM
802    
   
803  2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805          * 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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