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revision 2062, Sat Sep 1 21:06:52 2007 UTC revision 2256, Fri Sep 5 16:23:39 2008 UTC
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1    2008-09-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (solve,..): use (Matrix,ANY)... instead of (Matrix,Matrix)
4            * R/Ops.R: ditto; most of these from John Chambers.
5            * man/Matrix-class.Rd
6    
7            * R/Auxiliaries.R (.diagU2N): fix for Rsparse*
8            * tests/Simple.R: test it
9    
10    2008-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * man/drop0.Rd:
13            * R/Auxiliaries.R (drop0): new argument 'tol = 0' (and
14            'is.Csparse'); entails updates in
15            * R/Csparse.R, R/lMatrix.R, R/dMatrix.R
16    
17    2008-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * DESCRIPTION (Version): 0.999375-13 released to CRAN
20    
21    2008-08-29  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/Auxiliaries.R (attrSlotNames, attrSlots, attr.all_Mat): new
24            utilities, for now to be used in all.equal() methods.
25    
26            * R/Matrix.R (all.equal_Mat): be more careful (less tolerant) in
27            all.equal() methods.
28            * R/sparseMatrix.R: ditto
29    
30    2008-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * DESCRIPTION (Version): 0.999375-12 released to CRAN
33    
34            * R/Ops.R (Compare(<Csparse>,<Csparse>): fix for nsparseMatrix
35    
36    2008-08-27  Douglas Bates <bates@stat.wisc.edu>
37    
38            * R/sparseMatrix.R: fac2sparse() for NA's
39    
40    2008-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/sparseVector.R (all.equal.sparseV): make work for nsparseVector's
43    
44    2008-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * src/dgCMatrix.c (dgCMatrix_LU): partially revert change
47            r2175 (2008-04-23) and do give an error for a singular matrix.
48            * man/lu.Rd, R/Auxiliaries.R (detSparseLU): adapt to that.
49    
50            * R/LU.R: expand( <sparseLU> )
51    
52            * NAMESPACE, man/all.equal-methods.Rd:
53            * R/Matrix.R (all.equal): methods for Matrices,
54            * R/sparseMatrix.R, R/sparseVector.R: sparseMatrices and -Vectors
55    
56    
57    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
58    
59            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
60              documentation for CHMfactor class
61            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
62              pMatrix
63    
64    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
67    
68    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
71            variable assignments {from "next version" codetools}.
72            * R/Csparse.R, R/Tsparse.R: ditto
73    
74    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/sparseVector.R (sp2vec, coerce to sparseVector):
77            make sure no integer overflows happen, and use double precision
78            (n, index) where appropriate.
79    
80            * tests/Simple.R: test "large" sparse vectors.
81    
82    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
85            just integer (allowing much longer length).
86    
87    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
90            "denseMatrix".  This renders "scarceMatrix" dispensable and
91            invalidates part of MM's presentations on "space of Matrix
92            classes", but seems cleaner overall.
93    
94            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
95            "sparseMatrix" in method signatures;
96            further, instead of coercing to "sparseMatrix", coerce to
97            "TsparseMatrix" now.
98    
99    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
102            .Call(.)
103            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
104    
105    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
108            recursion in new test in
109            * tests/matprod.R: testing the above and another solve() case, below
110    
111            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
112            e.g. triangular 'x'.
113    
114            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
115            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
116            correctly with unit-triangular x
117    
118            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
119            instead of not checking diagU.
120    
121            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
122            experiments where diagonalMatrix would extend sparse*.
123    
124    
125    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
128            "x@p[ncol(x)]" instead of length(x@i).
129            * R/Auxiliaries.R (nnzero): ditto
130    
131            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
132            since that fails for over-allocated i.
133    
134            * tests/validObj.R: more testing of over-allocated (i,x) slots
135    
136    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
139            'sort_in_place' and set it to TRUE in call from
140            * src/Csparse.c (Csparse_validate): sort in place, making sure that
141            validObject() continues sort the columns if needed.
142    
143            * tests/validObj.R: now tests that more thoroughly, and
144            * man/CsparseMatrix-class.Rd: documents it.
145    
146    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
147    
148            * [r2233] src/chm_common.c: sort columns more carefully in
149              as_cholmod_sparse
150            * [r2231] src/chm_common.c: check for sorted columns in
151              as_cholmod_sparse instead of assuming it
152            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
153              expanding diagonal
154    
155    
156    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
159            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
160            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
161            diagU2N().
162    
163            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
164            .spDiagonal() and new .trDiagonal().
165    
166            * R/dtCMatrix.R (solve): make use of .trDiagonal()
167    
168    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
171            stumbled upon by Michael H.
172    
173            * tests/validObj.R: testing the bug-fix
174    
175            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
176            versions.
177    
178            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
179            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
180    
181            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
182              AS_CHM_SP() which includes diagU2N.
183    
184            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
185            adapt to 3 arguments.
186    
187    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
190              dtCMatrix_sparse_solve
191            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
192              storage
193            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
194              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
195              new solve method
196            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
197              Csparse_diagU2N functionality into Matrix_as_cs
198    
199    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
202    
203    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
204    
205            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
206              argument with default TRUE
207            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
208              Csparse_diagU2N
209            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
210              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
211              parent array; new solve method for signature(a = "dtCMatrix", b =
212              "sparseMatrix")
213    
214    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/diagMatrix.R (.bdiag): also keep result triangular
217    
218    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
219    
220            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
221              messages
222    
223    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
226            symmetric- or nsparse-Matrix, also fixing the bug introduced with
227            the new version (.999375-10).
228    
229            * tests/Simple.R: regression test for the bugs.
230    
231    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/sparseVector.R (spV2M): fix for "isparseVector".
234            Further, fix <diag> -> <sparseVector> coercion
235            (repSpV): add rep(<sparseVector>, .) method
236    
237            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
238            use as.vector(.).
239    
240            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
241    
242            * R/AllClass.R: new (hidden) class union "scarceMatrix"
243            * R/AllClass.R: sparseVector: add prototype
244    
245            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
246            Kasper Kristensen
247    
248    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * tests/other-pkgs.R: add more interesting Matrix -> graph
251    
252    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
255            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
256    
257    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * DESCRIPTION: release 0.999375-10 to CRAN
260    
261            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
262            .bdiag().
263            * man/bdiag.Rd: update, including test.
264    
265    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * tests/Simple.R: add minimal bdiag() checks
268    
269            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
270              factor out the Tsparse - internal computation into new .bdiag()
271    
272    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/nsparseMatrix.R: specific fast all() and any() methods.
275    
276            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
277            when trying to produce too large result.
278    
279            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
280            very large matrices.
281    
282            * R/sparseMatrix.R (printSpMatrix2): new function, used by
283            show(<sparseMatrix>).
284    
285            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
286    
287    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * src/Mutils.c (m_encodeInd, m_encodeInd2):
290            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
291    
292            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
293            big matrices): -> 2nd argument 'di' instead of 'nr' !
294    
295    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/dtCMatrix.R: faster dgC* -> dtC* method
298            * tests/Simple.R: (hence removed "FIXME")
299    
300            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
301            which can be be turned off for possible speed gains.
302    
303    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
306    
307            * R/not.R: fix !<ldiMatrix>
308            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
309    
310            * R/diagMatrix.R (Ops): fix one-off thinko in
311            <diagonal> o <numeric> methods
312    
313            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
314    
315    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
318            * tests/Simple.R: testing the above
319    
320    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
323    
324    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
327            * NAMESPACE (unname): finally exported
328    
329    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Auxiliaries.R (cholMat): possibly keep packed
332    
333            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
334            for R < 2.7.0.
335    
336            * R/Tsparse.R ([): for triangularMatrix, check if result may be
337            triangular.
338            * tests/indexing.R: regression test
339    
340    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
343            * R/Ops.R: more methods, for lMatrix/nMatrix
344    
345    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/expm.R: new file for all expm() methods; notably new ones for
348            diagonal*, triangular*, symmetric* and also simple "matrix".
349    
350    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
353    
354            * inst/test-tools.R (assert.EQ.mat): better message when not equal
355    
356            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
357    
358            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
359            [dl]denseMatrix {identical slots; but more logical method dispatch}
360    
361    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
364    
365            * R/diagMatrix.R (determinant): method
366    
367    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
370    
371            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
372    
373            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
374            its diagonal
375    
376    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
379    
380            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
381    
382            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
383    
384            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
385    
386    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
389    
390            * R/Ops.R (.do.Logic.lsparse): fix NA case
391    
392            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
393    
394            * R/Auxiliaries.R (nnzero): fix special cases, using
395            * R/Auxiliaries.R (indDiag): new utility
396            * R/Auxiliaries.R (indTri): new argument 'diag'
397    
398            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
399    
400    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
403    
404            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
405            ".tCMatrix" triangular matrix.
406    
407            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
408            'clx' can be class *or* class representation.
409            (nnzSparse): new.
410            (non0ind): new 'xtendSymm' argument; used in
411            * R/Ops.R:
412    
413            * R/pMatrix.R: more efficient determinant() method
414    
415    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
418            * [disactivated] NAMESPACE: export(det)
419    
420            * R/diagMatrix.R (mkDiag): new substitute for diag()
421    
422            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
423            (as0, as1): new utility.
424    
425            * R/Csparse.R (diag, band): need diagU2N()
426    
427            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
428    
429            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
430    
431            * R/Ops.R (Compare): fix <nsp> o <nsp> case
432    
433            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
434    
435    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/Auxiliaries.R (signPerm): new utility for
438            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
439    
440            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
441            since we have our own error handler (and can use tryCatch() from R).
442    
443    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
446    
447            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
448            when not positive definite.
449    
450            * R/Auxiliaries.R (asTri): new auxiliary
451            (non0.i): make *much* faster for Tsparse with many non-zero
452            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
453    
454            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
455            test-tools.R , see below
456    
457            * R/dMatrix.R: fix "Summary" method: + diagU2N()
458    
459            * NAMESPACE, R/Matrix.R: add mean() method
460    
461    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
464            cold-hot colors; try *changed* default useAbs = FALSE
465            * man/image-methods.Rd:  nice examples
466    
467    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * inst/test-tools.R (checkMatrix): new function for modularizing part
470            of tstMatrixClass() in tests/Class+Meth.R
471    
472            * R/dsCMatrix.R: coercion from "matrix"
473            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
474    
475            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
476            add test for as(matrix(,0,0), <class>)
477    
478    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
481            work as determinant(matrix(,0,0)).
482    
483            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
484            * man/sparseLU-class.Rd: ditto
485    
486            * R/dgCMatrix.R (determinant): method building on lu()
487            * R/sparseMatrix.R, Matrix.R, ...: ditto
488    
489            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
490    
491    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
494            pattern matrices.
495    
496    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * src/dense.c (dense_to_Csparse): all declarations *before*
499            R_CheckStack(); needed e.g. for ancient gcc 2.96.
500    
501    
502    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * DESCRIPTION (Version): 0.999375-9 --- need to release
505            for R-devel (and R 2.7.0 alpha soon).
506    
507            * R/AllClass.R: drop "double" from "atomicVector" class union
508    
509            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
510            * R/dgeMatrix.R: ditto
511    
512            * R/sparseMatrix.R (summary): count NAs
513    
514            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
515    
516    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
519            order to become compatible to new R 2.7.0 base::rcond().
520    
521    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
524    
525            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
526    
527            * inst/test-tools.R (isValid): new utility, used much in
528            * tests/simple.R:
529    
530            * man/BunchKaufman-methods.Rd: added too
531    
532    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/dsyMatrix.R: add BunchKaufman() methods.
535            * R/dspMatrix.R:
536    
537            * src/init.c: add dsyMatrix_trf
538    
539    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
540    
541            * DESCRIPTION (Version): release 0.999375-7
542            * src/CHMfactor.c (CHMfactor_update): fix
543    
544    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
547            internal_chm_factor().
548    
549            * R/AllGeneric.R: do *not* define a "chol" generic
550                    (but rather use the implicit one *without* making pivot
551                    part of the signature)
552            * R/*.R: drop the 'pivot' from chol's signature and make
553                    'pivot=FALSE' a default argument of method definitions.
554    
555            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
556            version of Matrix
557    
558    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
561    
562            * R/sparseMatrix.R (is.na): new simple method
563            * R/denseMatrix.R (is.na): ditto.
564    
565            * R/diagMatrix.R (.symDiagonal): newly exported utility.
566    
567            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
568    
569            * src/UFsparse_download.sh: -->
570            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
571    
572    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
575            functionality; barely tested in
576            * tests/factorizing.R
577    
578            * src/Csparse.c (diag_tC): new functionality to enable faster
579            determinant(<dsCMatrix>, .) in
580            * R/dsCMatrix.R
581    
582    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
583    
584            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
585              src/CHMfactor.c, src/CHMfactor.h,
586              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
587              Log-determinant of the parent matrix from a CHMfactor object as
588              chm_factor_ldetL2; documentation and support
589    
590    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
593    
594    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
597            warning.
598    
599    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
602    
603            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
604              <diagonal> o <sparse_triangular>
605              setAs(., "nMatrix") added.
606    
607            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
608    
609            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
610                    new argument 'checkDense = FALSE'.
611    
612    
613    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
616            back-permutation of the matrix exponential.
617    
618            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
619    
620            * DESCRIPTION (Date,Version): ready to release 0.999375-5
621    
622            * tests/simple.R: testing diagN2U
623    
624    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Auxiliaries.R (diagN2U): interface to
627    
628            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
629    
630            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
631    
632    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * src/chm_common.c (chm_diagN2U): new utility.
635    
636            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
637            make use of chm_diagN2U() and hence now preserve triangularity and
638            unit-triangularity.
639    
640            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
641    
642    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
645    
646            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
647            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
648    
649            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
650    
651            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
652    
653            * src/chm_common.c (AS_CHM_FINISH): add note about problem
654            for triangular (diag = "U").
655    
656    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
659            * R/bind.R:  .Call(dense_to_Csparse, *)
660    
661    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/Matrix.R (Matrix): no longer use coercions to specific classes
664                    (since we are discouraging them in user code).
665    
666            * tests/*.R: also replaces coercions to specific classes by
667            coercions to super classes.
668    
669            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
670    
671    
672    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
675    
676            * src/dense.c (dense_band): generalized from ddense_band
677    
678            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
679              now for "denseMatrix" (instead of just "ddense*"); much
680              simplified setMethod()s for these.
681    
682            * src/dense.c (dense_to_symmetric): generalized from ddense_*
683    
684    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
687            version of as(*, "symmetricMatric").
688    
689            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
690            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
691    
692    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * R/Matrix.R (subset.ij): utility, as first step to faster
695               M [ <ij-matrix> ] indexing.
696    
697            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
698    
699            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
700            for more efficient symmpart() and skewpart() methods.
701    
702            * src/Mutils.c (equal_string_vectors): utility
703    
704            * src/dense.c (ddense_to_symmetric): new function used in
705    
706            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
707    
708            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
709            order to match the generic (and evade .local(..)).
710    
711            * R/dsCMatrix.R: dgC -> dsC: use C code!
712    
713            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
714            as per TODO
715    
716            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
717    
718            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
719    
720    
721    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
722    
723            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
724    
725            * R/Auxiliaries.R (non0.i): take out of non0ind
726    
727            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
728            make tril(), triu(), band() work for "matrix" and all "dense*"
729    
730            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
731            * tests/simple.R: test the fix above
732    
733            * R/sparseMatrix.R ([): simplification: no coerce to <general>
734                    before we use as(., <Tsparse>)[...] anyway
735    
736            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
737    
738            * R/triangularMatrix.R (isTriangular): methods for all subclasses
739            instead of "triangularMatrix" -- just to disambiguate
740    
741    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
744            * tests/indexing.R: example that fails above
745    
746    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
749            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
750                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
751    
752            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
753            * src/Tsparse.h, init.c: ditto
754            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
755                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
756            * R/sparseMatrix.R (isTriangular): hence simplified
757    
758    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/Ops.R (.Arith.Csparse): new utility factored out of former
761              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
762    
763    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
766    
767            * inst/test-tools.R (isOrthogonal): new function; also file restructured
768    
769    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
772            coercion to "nMatrix" and "pMatrix"
773    
774            * R/AllClass.R: "Schur" class;  "number" class union
775            * man/number-class.Rd:
776            * man/Schur-class.Rd:
777    
778            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
779            (.simpleSchur): Schur() method for diagonal matrices
780            (.triSchur):    Schur() method for triangular matrices
781            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
782    
783    
784    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
787    
788    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
791                    in order to ensure 'system = *' is not lost;
792                    formals()$system instead of cut&paste.
793            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
794    
795    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * DESCRIPTION (Date): make ready for release --> 0.999375-4
798    
799            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
800    
801    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
804                    and hence does as.vector(.).
805            * man/pMatrix-class.Rd: docs
806            * R/sparseMatrix.R: fix for printing "integer sparse"
807    
808            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
809    
810            * R/Matrix.R and others: use "exact" function argument list for
811                    both "["   : (x, i,j, ..., drop)
812                    and  "[<-" : (x, i,j, ..., value)
813    
814            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
815            * R/Tsparse.R (replTmat):    ditto
816            * R/diagMatrix.R (replDiag): ditto
817            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
818            * tests/indexing.R: testing the above
819    
820    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/sparseMatrix.R (cov2cor): method for sparse matrices
823    
824            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
825    
826            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
827    
828            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
829    
830    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * R/Matrix.R: "generic" cov2cor() method
833    
834            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
835                    speed up Q %*% D %*% t(Q)
836            * tests/dpoMatrix.R: test nearPD()
837    
838    2007-12-05  Doug Bates and Martin Maechler
839    
840            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
841            stats::xtabs() allowing to create sparse matrices.
842    
843    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
846    
847    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
850    
851    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/LU.R: solve() method for "denseLU"
854    
855    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * DESCRIPTION (Version): 0.999375-3 preparing for release
858    
859            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
860    
861            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
862    
863    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
866              thanks to Kasper Kristensen.
867            * tests/matprod.R: regression test for that.
868    
869    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
870    
871            * [r4778] R/AllGeneric.R: Check R version before defining generics for
872              primitives
873    
874    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * R/denseMatrix.R (rcond): method
877            * R/sparseQR.R (rcond): method, use x or t(x)
878    
879    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
882            matrices.
883            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
884    
885            * man/rcond.Rd: mention the more general definition, and add
886            example for non-square matrices.
887    
888            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
889    
890    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
893    
894  2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896          * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc          * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc

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