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revision 1922, Sat Jun 23 18:08:48 2007 UTC revision 2203, Sat Jun 14 20:09:17 2008 UTC
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1    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/nsparseMatrix.R: specific fast all() and any() methods.
4    
5            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
6            when trying to produce too large result.
7    
8            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
9            very large matrices.
10    
11            * R/sparseMatrix.R (printSpMatrix2): new function, used by
12            show(<sparseMatrix>).
13    
14            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
15    
16    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * src/Mutils.c (m_encodeInd, m_encodeInd2):
19            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
20    
21            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
22            big matrices): -> 2nd argument 'di' instead of 'nr' !
23    
24    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/dtCMatrix.R: faster dgC* -> dtC* method
27            * tests/Simple.R: (hence removed "FIXME")
28    
29            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
30            which can be be turned off for possible speed gains.
31    
32    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
35    
36            * R/not.R: fix !<ldiMatrix>
37            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
38    
39            * R/diagMatrix.R (Ops): fix one-off thinko in
40            <diagonal> o <numeric> methods
41    
42            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
43    
44    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
47            * tests/Simple.R: testing the above
48    
49    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
52    
53    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
56            * NAMESPACE (unname): finally exported
57    
58    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Auxiliaries.R (cholMat): possibly keep packed
61    
62            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
63            for R < 2.7.0.
64    
65            * R/Tsparse.R ([): for triangularMatrix, check if result may be
66            triangular.
67            * tests/indexing.R: regression test
68    
69    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
72            * R/Ops.R: more methods, for lMatrix/nMatrix
73    
74    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/expm.R: new file for all expm() methods; notably new ones for
77            diagonal*, triangular*, symmetric* and also simple "matrix".
78    
79    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
82    
83            * inst/test-tools.R (assert.EQ.mat): better message when not equal
84    
85            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
86    
87            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
88            [dl]denseMatrix {identical slots; but more logical method dispatch}
89    
90    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
93    
94            * R/diagMatrix.R (determinant): method
95    
96    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
99    
100            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
101    
102            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
103            its diagonal
104    
105    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
108    
109            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
110    
111            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
112    
113            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
114    
115    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
118    
119            * R/Ops.R (.do.Logic.lsparse): fix NA case
120    
121            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
122    
123            * R/Auxiliaries.R (nnzero): fix special cases, using
124            * R/Auxiliaries.R (indDiag): new utility
125            * R/Auxiliaries.R (indTri): new argument 'diag'
126    
127            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
128    
129    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
132    
133            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
134            ".tCMatrix" triangular matrix.
135    
136            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
137            'clx' can be class *or* class representation.
138            (nnzSparse): new.
139            (non0ind): new 'xtendSymm' argument; used in
140            * R/Ops.R:
141    
142            * R/pMatrix.R: more efficient determinant() method
143    
144    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
147            * [disactivated] NAMESPACE: export(det)
148    
149            * R/diagMatrix.R (mkDiag): new substitute for diag()
150    
151            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
152            (as0, as1): new utility.
153    
154            * R/Csparse.R (diag, band): need diagU2N()
155    
156            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
157    
158            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
159    
160            * R/Ops.R (Compare): fix <nsp> o <nsp> case
161    
162            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
163    
164    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Auxiliaries.R (signPerm): new utility for
167            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
168    
169            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
170            since we have our own error handler (and can use tryCatch() from R).
171    
172    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
175    
176            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
177            when not positive definite.
178    
179            * R/Auxiliaries.R (asTri): new auxiliary
180            (non0.i): make *much* faster for Tsparse with many non-zero
181            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
182    
183            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
184            test-tools.R , see below
185    
186            * R/dMatrix.R: fix "Summary" method: + diagU2N()
187    
188            * NAMESPACE, R/Matrix.R: add mean() method
189    
190    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
193            cold-hot colors; try *changed* default useAbs = FALSE
194            * man/image-methods.Rd:  nice examples
195    
196    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * inst/test-tools.R (checkMatrix): new function for modularizing part
199            of tstMatrixClass() in tests/Class+Meth.R
200    
201            * R/dsCMatrix.R: coercion from "matrix"
202            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
203    
204            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
205            add test for as(matrix(,0,0), <class>)
206    
207    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
210            work as determinant(matrix(,0,0)).
211    
212            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
213            * man/sparseLU-class.Rd: ditto
214    
215            * R/dgCMatrix.R (determinant): method building on lu()
216            * R/sparseMatrix.R, Matrix.R, ...: ditto
217    
218            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
219    
220    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
223            pattern matrices.
224    
225    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * src/dense.c (dense_to_Csparse): all declarations *before*
228            R_CheckStack(); needed e.g. for ancient gcc 2.96.
229    
230    
231    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * DESCRIPTION (Version): 0.999375-9 --- need to release
234            for R-devel (and R 2.7.0 alpha soon).
235    
236            * R/AllClass.R: drop "double" from "atomicVector" class union
237    
238            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
239            * R/dgeMatrix.R: ditto
240    
241            * R/sparseMatrix.R (summary): count NAs
242    
243            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
244    
245    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
248            order to become compatible to new R 2.7.0 base::rcond().
249    
250    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
253    
254            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
255    
256            * inst/test-tools.R (isValid): new utility, used much in
257            * tests/simple.R:
258    
259            * man/BunchKaufman-methods.Rd: added too
260    
261    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/dsyMatrix.R: add BunchKaufman() methods.
264            * R/dspMatrix.R:
265    
266            * src/init.c: add dsyMatrix_trf
267    
268    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
269    
270            * DESCRIPTION (Version): release 0.999375-7
271            * src/CHMfactor.c (CHMfactor_update): fix
272    
273    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
276            internal_chm_factor().
277    
278            * R/AllGeneric.R: do *not* define a "chol" generic
279                    (but rather use the implicit one *without* making pivot
280                    part of the signature)
281            * R/*.R: drop the 'pivot' from chol's signature and make
282                    'pivot=FALSE' a default argument of method definitions.
283    
284            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
285            version of Matrix
286    
287    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
290    
291            * R/sparseMatrix.R (is.na): new simple method
292            * R/denseMatrix.R (is.na): ditto.
293    
294            * R/diagMatrix.R (.symDiagonal): newly exported utility.
295    
296            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
297    
298            * src/UFsparse_download.sh: -->
299            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
300    
301    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
304            functionality; barely tested in
305            * tests/factorizing.R
306    
307            * src/Csparse.c (diag_tC): new functionality to enable faster
308            determinant(<dsCMatrix>, .) in
309            * R/dsCMatrix.R
310    
311    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
312    
313            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
314              src/CHMfactor.c, src/CHMfactor.h,
315              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
316              Log-determinant of the parent matrix from a CHMfactor object as
317              chm_factor_ldetL2; documentation and support
318    
319    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
322    
323    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
326            warning.
327    
328    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
331    
332            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
333              <diagonal> o <sparse_triangular>
334              setAs(., "nMatrix") added.
335    
336            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
337    
338            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
339                    new argument 'checkDense = FALSE'.
340    
341    
342    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
345            back-permutation of the matrix exponential.
346    
347            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
348    
349            * DESCRIPTION (Date,Version): ready to release 0.999375-5
350    
351            * tests/simple.R: testing diagN2U
352    
353    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/Auxiliaries.R (diagN2U): interface to
356    
357            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
358    
359            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
360    
361    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * src/chm_common.c (chm_diagN2U): new utility.
364    
365            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
366            make use of chm_diagN2U() and hence now preserve triangularity and
367            unit-triangularity.
368    
369            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
370    
371    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
374    
375            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
376            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
377    
378            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
379    
380            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
381    
382            * src/chm_common.c (AS_CHM_FINISH): add note about problem
383            for triangular (diag = "U").
384    
385    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
388            * R/bind.R:  .Call(dense_to_Csparse, *)
389    
390    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/Matrix.R (Matrix): no longer use coercions to specific classes
393                    (since we are discouraging them in user code).
394    
395            * tests/*.R: also replaces coercions to specific classes by
396            coercions to super classes.
397    
398            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
399    
400    
401    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
404    
405            * src/dense.c (dense_band): generalized from ddense_band
406    
407            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
408              now for "denseMatrix" (instead of just "ddense*"); much
409              simplified setMethod()s for these.
410    
411            * src/dense.c (dense_to_symmetric): generalized from ddense_*
412    
413    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
416            version of as(*, "symmetricMatric").
417    
418            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
419            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
420    
421    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/Matrix.R (subset.ij): utility, as first step to faster
424               M [ <ij-matrix> ] indexing.
425    
426            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
427    
428            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
429            for more efficient symmpart() and skewpart() methods.
430    
431            * src/Mutils.c (equal_string_vectors): utility
432    
433            * src/dense.c (ddense_to_symmetric): new function used in
434    
435            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
436    
437            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
438            order to match the generic (and evade .local(..)).
439    
440            * R/dsCMatrix.R: dgC -> dsC: use C code!
441    
442            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
443            as per TODO
444    
445            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
446    
447            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
448    
449    
450    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
453    
454            * R/Auxiliaries.R (non0.i): take out of non0ind
455    
456            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
457            make tril(), triu(), band() work for "matrix" and all "dense*"
458    
459            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
460            * tests/simple.R: test the fix above
461    
462            * R/sparseMatrix.R ([): simplification: no coerce to <general>
463                    before we use as(., <Tsparse>)[...] anyway
464    
465            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
466    
467            * R/triangularMatrix.R (isTriangular): methods for all subclasses
468            instead of "triangularMatrix" -- just to disambiguate
469    
470    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
473            * tests/indexing.R: example that fails above
474    
475    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
478            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
479                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
480    
481            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
482            * src/Tsparse.h, init.c: ditto
483            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
484                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
485            * R/sparseMatrix.R (isTriangular): hence simplified
486    
487    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/Ops.R (.Arith.Csparse): new utility factored out of former
490              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
491    
492    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
495    
496            * inst/test-tools.R (isOrthogonal): new function; also file restructured
497    
498    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
501            coercion to "nMatrix" and "pMatrix"
502    
503            * R/AllClass.R: "Schur" class;  "number" class union
504            * man/number-class.Rd:
505            * man/Schur-class.Rd:
506    
507            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
508            (.simpleSchur): Schur() method for diagonal matrices
509            (.triSchur):    Schur() method for triangular matrices
510            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
511    
512    
513    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
516    
517    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
520                    in order to ensure 'system = *' is not lost;
521                    formals()$system instead of cut&paste.
522            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
523    
524    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * DESCRIPTION (Date): make ready for release --> 0.999375-4
527    
528            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
529    
530    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
533                    and hence does as.vector(.).
534            * man/pMatrix-class.Rd: docs
535            * R/sparseMatrix.R: fix for printing "integer sparse"
536    
537            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
538    
539            * R/Matrix.R and others: use "exact" function argument list for
540                    both "["   : (x, i,j, ..., drop)
541                    and  "[<-" : (x, i,j, ..., value)
542    
543            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
544            * R/Tsparse.R (replTmat):    ditto
545            * R/diagMatrix.R (replDiag): ditto
546            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
547            * tests/indexing.R: testing the above
548    
549    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/sparseMatrix.R (cov2cor): method for sparse matrices
552    
553            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
554    
555            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
556    
557            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
558    
559    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/Matrix.R: "generic" cov2cor() method
562    
563            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
564                    speed up Q %*% D %*% t(Q)
565            * tests/dpoMatrix.R: test nearPD()
566    
567    2007-12-05  Doug Bates and Martin Maechler
568    
569            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
570            stats::xtabs() allowing to create sparse matrices.
571    
572    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
575    
576    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
579    
580    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/LU.R: solve() method for "denseLU"
583    
584    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * DESCRIPTION (Version): 0.999375-3 preparing for release
587    
588            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
589    
590            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
591    
592    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
595              thanks to Kasper Kristensen.
596            * tests/matprod.R: regression test for that.
597    
598    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
599    
600            * [r4778] R/AllGeneric.R: Check R version before defining generics for
601              primitives
602    
603    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * R/denseMatrix.R (rcond): method
606            * R/sparseQR.R (rcond): method, use x or t(x)
607    
608    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
611            matrices.
612            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
613    
614            * man/rcond.Rd: mention the more general definition, and add
615            example for non-square matrices.
616    
617            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
618    
619    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
622    
623    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
626            * tests/indexing.R: add new regression for the above cases.
627    
628    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * src/Mutils.h (__sun): clause for alloca.h on Solaris
631    
632    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * DESCRIPTION (Date, Version): 0.999375-2
635    
636    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/HBMM.R (readMM): make work for pattern matrices as well
639    
640    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
641    
642            * [r4730] src/Mutils.h: declare alloca
643            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
644              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
645              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
646              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
647              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
648              methods; switch writeMM to use CHOLMOD code; repair readMM
649    
650    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
653            Oehlschlaegel's ... result type still to be discussed!
654    
655    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * man/image-methods.Rd: new, combining all image() methods
658    
659    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
662            to work via dgC...
663    
664            * R/Matrix.R (Matrix): special treatment for "table" (S3)
665    
666    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/dgTMatrix.R (image): change defaults to
669                    aspect = "iso", colorkey = FALSE
670    
671    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
674            must copy its *expanded* x slot before LAPACK call.
675    
676            * tests/matprod.R: test the last days' changes.
677    
678    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
679    
680            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
681              as well as in sources
682            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
683              Lapack call
684    
685    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
688                    ("Matrix", "matrix") which is needed in some cases.
689            Ditto for solve().
690    
691            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
692            infinite recursion in dispatch for some cases.
693    
694    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
695    
696            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
697              so pointers match
698    
699    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * DESCRIPTION (Date): set ready for release -- 0.999375-1
702    
703    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
704    
705            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
706              src/chm_common.c, src/chm_common.h: Change API for
707              numeric_as_chm_dense and N_AS_CHM_DN
708    
709    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
712            * tests/matprod.R: regr.test for it
713    
714    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
717            * tests/group-methods.R: and regression-test it
718    
719    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
720    
721            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
722              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
723              triplet_to_sparse, documentation, use typedefs
724    
725    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * man/dpoMatrix-class.Rd: added 'corMatrix' example
728    
729            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
730            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
731            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
732    
733            * R/lsparseMatrix.R: bug fix in "all" method
734            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
735    
736            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
737            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
738                    + matrix |-> nMatrix coercion
739            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
740            * man/pMatrix-class.Rd: ditto
741    
742            * R/Matrix.R (Summary): method for non-dMatrix
743    
744            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
745            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
746                    test all Summary methods.
747    
748    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
751    
752    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
755    
756            * R/pMatrix.R (t?crossprod): methods for pMatrix
757    
758    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
759    
760            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
761    
762    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
763    
764            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
765              trying to fix a subtle bug - which has been somewhere else.
766    
767    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
768    
769            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
770              solve the bug
771    
772    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * src/dgCMatrix.c (compressed_to_TMatrix):
775    
776    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * src/Csparse.c (Rsparse_validate): new, to have some validity
779            checking for RsparseMatrix
780            * src/dgCMatrix.c (xRMatrix_validate): ditto
781            * src/dtCMatrix.c (tRMatrix_validate): ditto
782    
783    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
784    
785            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
786              lgRMatrix
787            * [r4568] DESCRIPTION: Prepare for bug-fix release
788            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
789              for declaration of cholmod_symmetry
790    
791    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
794            release.
795    
796    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
797    
798            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
799              functions - no longer used
800            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
801              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
802              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
803              Alloca
804    
805    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
806    
807            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
808              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
809              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
810              src/t_gCMatrix_colSums.c: more R_CheckStack()s
811    
812    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
813    
814            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
815              the required amount of memory then call M_numeric_as_chm_dense.
816            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
817              (like Calloc but calling alloca)
818    
819    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
822            and extended with more sophisticated 'col.names' option.
823            * NAMESPACE: export  printSparseMatrix()
824            * man/printSpMatrix.Rd: document, incl. examples
825    
826    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
827    
828            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
829              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
830              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
831    
832    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * DESCRIPTION (Version): 0.99875-4
835    
836            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
837            some dimnames perservation.
838    
839            * R/dsTMatrix.R (t-method): keep dimnames
840            * R/dtTMatrix.R:  ditto
841    
842            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
843            and ncol(.) < 10
844    
845            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
846            from Mutils.h
847    
848            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
849            e.g. in as(<ngCMatrix>, "matrix")
850    
851    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
852    
853            * [r4529] .: Create a branch for the API changes from the 0.99875
854              series to the 0.999375 series
855            * [r4530] DESCRIPTION, inst/include/Matrix.h,
856              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
857              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
858              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
859              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
860              as_cholmod_x functions
861    
862    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
863    
864            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
865              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
866              to Comparisons
867    
868    >>>>>>> .merge-right.r4561
869    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
870    
871            * DESCRIPTION (Version): 0.99875-3 ready to be released.
872    
873            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
874    
875            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
876            that should also work in a future version of R.
877    
878  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
# Line 5  Line 882 
882          * R/sparseVector.R: more *sparseVector coercions, notably for          * R/sparseVector.R: more *sparseVector coercions, notably for
883          non - double ones.          non - double ones.
884    
   
885  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,

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