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revision 1548, Mon Sep 11 22:13:07 2006 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>
879    
880            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
881    
882            * R/sparseVector.R: more *sparseVector coercions, notably for
883            non - double ones.
884    
885    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
888              notably the new ones building on the new .Call(.)s:
889    
890            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
891            all 4 of [dlin]gCMatrix_colSums().
892    
893    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
894    
895            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
896            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
897              result
898    
899    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/kronecker.R: fix typo (could lead to inf.recursion)
902            * test/simple.R: testing that
903    
904            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
905            method as well (which can have arguments, show() can't).
906    
907    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
908    
909            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
910              added dgCMatrix_colSums for [col,row][Sums,Means]
911    
912    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
913    
914            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
915              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
916              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
917            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
918              class
919            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
920              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
921              row names to store the levels - duh!  Added an example.
922    
923    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * src/Csparse.c (Csparse_validate): check for *repeated* entries
926            thanks to example from Christian Buchta; with a test here:
927            * tests/simple.R:
928    
929    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
932            of colSums(*, sparseResult = TRUE)
933    
934    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
937            'na.rm = FALSE' as "everywhere" else in R.
938    
939    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
940    
941            * [r4421] src/CSparse_install.sh: Modify for new organization of
942              CSparse package
943            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
944              SuiteSparse
945            * [r4426] src/Makefile: add ./UFconfig to the include path for
946              compilation
947            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
948            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
949              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
950    
951    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
954            * R/sparseMatrix.R (prSpMatrix): now gives a message about
955            suppressed column names.
956    
957    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
958    
959            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
960              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
961              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
962              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
963              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
964              Remove warnings after change to const char* CHAR
965    
966    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
967    
968            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
969              type of M_cholmod_ssmult
970    
971    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
972    
973            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
974              src/init.c: Yet another cholmod export - cholmod_ssmult
975    
976    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * NAMESPACE: exported drop0(), since
979            * man/drop0.Rd: I have seen several cases, I really wanted to use
980            it, so our users may want too.
981    
982    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
983    
984            * man/colSums.Rd: separately document colSums() etc, since these
985            have the extra argument 'sparseResult'.
986    
987    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
988    
989            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
990            * man/spMatrix.Rd: docu., including examples
991    
992            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
993            in order to make colMeans() etc fast *and* correct.
994            * R/sparseVector.R (replSPvec): "[<-" functionality for
995            sparseVectors; tested in
996            * tests/simple.R:
997    
998    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1001            (very) sparse Matrices; output similar to Matlab's print().
1002    
1003    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1004    
1005            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1006            0-based, indices (Jose Quesada <quesada@gmail.com>).
1007    
1008    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1009    
1010            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1011    
1012    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1015            tapply1() for large sparse matrices.
1016    
1017    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * R/Matrix.R (dim<-): reshape now via sparseVector.
1020    
1021            * R/sparseVector.R: methods and function for
1022            * R/AllClass.R: new "sparseVector" class and daughters.
1023            * NAMESPACE: export new classes
1024    
1025    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * DESCRIPTION (Version): 0.99875-1
1028            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1029    
1030    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1033            indexing
1034            * tests/indexing.R: test set for that.
1035    
1036    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1039            entries.
1040            * tests/indexing.R(out): add regression test for it
1041    
1042    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1045            name for "!" method definitions.
1046    
1047    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * R/Tsparse.R (intI): new utility, used for "[" :
1050                    Cleanup up there, and fixes for duplicated indices - more TODO!
1051    
1052            * tests/indexing.R(out): more tests
1053    
1054    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1055    
1056            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1057            code that is now part of the R Lapack library.
1058    
1059            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1060            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1061    
1062    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1063    
1064            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1065    
1066    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1067    
1068            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1069            up with extraneous names '0'...'<n-1>'
1070    
1071    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1072    
1073            * R/dgTMatrix.R (mat2dgT): care about NAs
1074    
1075    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/kronecker.R: triangularity preserving methods
1078    
1079    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1080    
1081            * R/kronecker.R: new file collecting kronecker() methods in one
1082                    place.  Goal: become much faster!
1083    
1084    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1087            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1088            can be much faster.
1089    
1090            * tests/matprod.R: add regression tests for these (upper & lower).
1091    
1092    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1093    
1094            * R/Matrix.R (diff): method for our Matrices.
1095    
1096            * R/sparseMatrix.R (isDiagonal): check dim()!
1097    
1098    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1099    
1100            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1101            proposal from Tamas Papp.
1102    
1103    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1104    
1105            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1106    
1107            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1108            rather define and export  cBind() and rBind() only.
1109            --> useRs *must* change code that used to have cbind()/rbind() !!
1110    
1111            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1112            * R/bind.Rout.save: ditto
1113    
1114    2007-02-16  Douglas Bates  <bates@r-project.org>
1115    
1116            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1117            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1118            const modifier on declaration of the array 'valid'
1119    
1120    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1121    
1122            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1123    
1124    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1125    
1126            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1127    
1128            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1129            * tests/simple.R: test the above and some of these coercions:
1130    
1131            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1132                    be careful to avoid infinite recursion, using new coercions in
1133            * R/ngCMatrix.R and nsC... and ntC...
1134            * R/lsparseMatrix.R: ditto
1135    
1136            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1137    
1138            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1139            * R/Rsparse.R: reactivate .Call()s
1140    
1141            * tests/Class+Meth.R: a bit more on actual classes
1142    
1143    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1144    
1145            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1146    
1147    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1148    
1149            * DESCRIPTION (Version): 0.9975-10 to upload
1150    
1151            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1152            specific classes less unconditionally.
1153    
1154            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1155    
1156            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1157    
1158            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1159            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1160            R_to_CMatrix segfaults on one platform.
1161            Eliminate most coercion method to *specific* classes, and replace
1162            with virtual classes coercions.
1163    
1164    
1165    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1166    
1167            * src/init.c: export the CHM...._validate() placeholders, since
1168            they *are* called.
1169    
1170            * tests/Class+Meth.R (classCanCoerce): and starting to test
1171            all as(<from>, <to>)
1172    
1173    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1174    
1175            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1176            * tests/indexing.R: tested now
1177            * tests/indexing.Rout.save: updated
1178    
1179            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1180            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1181            appropriate.
1182    
1183            * NAMESPACE: export a trivial
1184            * R/Matrix.R: drop() Matrix-method
1185    
1186            * R/AllClass.R: moved all prototypes to virtual super classes.
1187    
1188            * R/Rsparse.R: many more coercions to have less exceptions in
1189            * tests/Class+Meth.R:
1190    
1191            * R/Ops.R (Compare): tweak for case with NA
1192            * tests/simpl.R: hence another 'FIXME' eliminated
1193    
1194    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1195    
1196            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1197            objects.
1198    
1199            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1200              and more of "!", "&", "|", all, any; coercions
1201    
1202            * R/Rsparse.R: many coercions (which enable quite a few other
1203            methods), thanks to enhancements in
1204            * src/dgCMatrix.c (R_to_CMatrix): new, and
1205            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1206            symmetric & triangular and ..RMatrix objects.
1207    
1208            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1209            renamed file from src/dsTMatrix.c;
1210            now dealing with symmetric and triangular Tsparse coercions, both
1211            to dense and general.
1212    
1213    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1214    
1215            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1216    
1217            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1218            where sensible when the <numeric> is of length > 1.
1219    
1220    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1221    
1222            * R/Matrix.R ([<-): for M[] <- value: fix length
1223    
1224    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1225    
1226            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1227            * R/ndenseMatrix.R: new coercions n* -> l*
1228    
1229    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1230    
1231            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1232    
1233            * R/Ops.R ("Logic"): and other "Ops", many updates
1234    
1235    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1236    
1237            * src/Mutils.h (SET_DimNames): new utility
1238    
1239            * R/Auxiliaries.R (nnzero): improved and now exported via
1240    
1241            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1242    
1243    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1244    
1245            * R/diagMatrix.R (!): fix typo.
1246    
1247    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1248    
1249            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1250                    allow to pass class definition --> speedup
1251            * R/sparseMatrix.R: apply the above
1252    
1253            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1254    
1255            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1256            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1257            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1258    
1259            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1260    
1261            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1262            and use it for "sparse*" as well, since it's faster than the
1263            as_Csparse(.) way.
1264    
1265    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1266    
1267            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1268    
1269    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1270    
1271            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1272            as method for   M[ ij ] <- v
1273            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1274    
1275            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1276            FALSE answer
1277    
1278            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1279            * tests/indexing.R: test it, and some of the above
1280    
1281    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1282    
1283            * R/Auxiliaries.R (is_duplicatedT): new utility
1284    
1285    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1286    
1287            * src/init.c (R_init_Matrix): export cholmod_scale
1288    
1289    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1290    
1291            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1292            base::as.matrix to (x, ...)
1293    
1294    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1295    
1296            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1297            file; start using "Logic", hence
1298    
1299            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1300            * NAMESPACE: import and export "Logic"
1301    
1302    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1305            only needed previously to R version 2.5.0.
1306    
1307    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1308    
1309            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1310    
1311            * R/Tsparse.R (replTmat): fix subassignment of triangular
1312            * R/Csparse.R (replCmat): ditto
1313            * tests/indexing.R: more tests, incl the above fix
1314    
1315    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1316    
1317            * R/Auxiliaries.R (drop0): extend for non CSparse
1318            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1319    
1320            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1321                    use uplo correctly (!); other places: use uplo_P() macro
1322    
1323            * R/Csparse.R (replCmat): call diagU2N() when needed
1324            * R/Tsparse.R (replTmat): ditto
1325    
1326            * src/dtCMatrix.c (tCMatrix_validate): new
1327            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1328            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1329    
1330            * R/diagMatrix.R (replDiag): to use in [<-
1331    
1332    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1333    
1334            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1335                    also more general diagU2N().
1336    
1337    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1338    
1339            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1340            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1341    
1342    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1343    
1344            * tests/bind.R: a few more cases
1345            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1346    
1347            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1348            * R/ddenseMatrix.R (cbind2/rbind2)
1349            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1350            * tests/indexing.R
1351            * tests/indexing.Rout.save: updated
1352    
1353    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1354    
1355            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1356            * tests/indexing.R
1357    
1358    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1359    
1360            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1361            align with proper position of "0", i.e., right for integers.
1362            argument 'align' by default is "fancy".
1363    
1364    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1365    
1366            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1367            * R/Csparse.R: and fix "Compare" for more cases.
1368            * tests/Class+Meth.R: test some of these (m == m, m != m)
1369    
1370    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1371    
1372            * R/lsparseMatrix.R: all() and any() methods
1373            * R/ldenseMatrix.R:      ditto
1374            * NAMESPACE, R/Matrix.R: ditto
1375    
1376            * man/all-methods.Rd: document them minimally
1377    
1378            * tests/simple.R: add a few examples for these
1379    
1380    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1381    
1382            * R/Tsparse.R ([): fix long standing typo in symmetric case
1383            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1384    
1385    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1386    
1387            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1388            to LL before converting to a sparse matrix. (The LDL form can be
1389            converted to a sparse matrix but it is implicitly a unit
1390            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1391    
1392    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1393    
1394            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1395    
1396    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1397    
1398            * DESCRIPTION (Version): updated -> release 0.9975-7
1399            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1400    
1401    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1402    
1403            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1404    
1405    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1406    
1407            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1408            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1409            is exactly singular.
1410    
1411    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1412    
1413            * DESCRIPTION (Date): updated -> release 0.9975-6
1414    
1415    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1416    
1417            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1418            now returns symmetric.
1419    
1420            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1421    
1422            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1423            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1424    
1425            * R/Auxiliaries.R (.type.kind): added
1426    
1427    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1428    
1429            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1430            running src/CSparse_install.sh
1431    
1432            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1433    
1434    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1435    
1436            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1437            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1438    
1439            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1440    
1441            * tests/Class+Meth.R (tstMatrixClass): now assure
1442            the (important in method programming) property :
1443    
1444                    ###>>  Every "Matrix" is either
1445                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1446    
1447                    (where "*" stands for "Matrix")
1448    
1449            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1450    
1451            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1452            * tests/validObj.R: checks for "comparison"
1453    
1454            * R/sparseMatrix.R ([): improved indexing for sparse;
1455                    trying to keep <symmetric>[ n, n] symmmetric
1456    
1457            * tests/indexing.R: indexing for logical sparse now ok
1458    
1459    
1460    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1461    
1462            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1463    
1464            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1465    
1466    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1467    
1468            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1469    
1470            * tests/simple.R: validObject() checking the above.
1471    
1472            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1473            replacing both dgCMatrix_validate and lgCM*.
1474    
1475            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1476            fix dimnames setting in other places.
1477            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1478    
1479    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1480    
1481            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1482    
1483            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1484            symmetry test, via
1485            * R/Auxiliaries.R (.as.dgC.0.factors):
1486    
1487    2006-11-01  Douglas Bates  <bates@r-project.org>
1488    
1489            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1490            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1491            <CsparseMatrix>) added
1492    
1493    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1494    
1495            * tests/matprod.R: add a variation of Harri's example
1496    
1497            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1498            recursive infinitely.
1499    
1500            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1501    
1502            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1503    
1504    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1505    
1506            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1507            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1508            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1509            satisfy the above test.
1510    
1511    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1512    
1513            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1514    
1515            * R/dgCMatrix.R: solve(a, b="missing") based on
1516            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1517            RHS = NULL.
1518    
1519            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1520            add more (needed) [t]crossprod() methods.
1521    
1522            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1523    
1524            * R/Auxiliaries.R (as_CspClass): cleanup
1525            (drop0): internal utility for "Csparse_drop(*, 0)"
1526            (.bail.out.2): encourage active feedback
1527    
1528    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1529    
1530            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1531    
1532            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1533            non-valid or 'sorted' case).
1534    
1535            * R/dsparseMatrix.R: add "chol" method.
1536            * R/ddenseMatrix.R: ditto
1537    
1538            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1539            * NAMESPACE (Ops)
1540            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1541            coercion; deprecating direct lower level coercions.
1542    
1543            * R/*.R (seq): use seq_len() and seq_along() where possible.
1544    
1545    
1546    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1547    
1548            * DESCRIPTION (Version): 0.9975-5 ready for release
1549    
1550    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1551    
1552            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1553    
1554    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1555    
1556            * R/AllClass.R (corMatrix): add 'validity' check;
1557                    comment out unused "LDL" class definition
1558            * NAMESPACE: mention, but do not export "LDL" class
1559            * R/corMatrix.R: new (simple), needed for R-devel with
1560            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1561              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1562    
1563    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1564    
1565            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1566            use Rprintf and R's error handling.
1567    
1568    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1569    
1570            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1571            * tests/matprod.R: add tests for the bug fixed.
1572    
1573    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1574    
1575            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1576            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1577    
1578    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1579    
1580            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1581    
1582    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1583    
1584            * DESCRIPTION (Version): 0.9975-3
1585    
1586            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1587            (sparse) matrices.
1588            * man/bdiag.Rd: docu + examples
1589    
1590            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1591    
1592            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1593            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1594    
1595            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1596            that result is sparse or diagonal (and not dense).
1597    
1598            * man/Subassign-methods.Rd: fix examples
1599    
1600            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1601            should always return a sparse (and not sometimes a diagonal) matrix.
1602    
1603    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1604    
1605            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1606    
1607    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1608    
1609            * DESCRIPTION (Version): 0.9975-2
1610    
1611            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1612    
1613    2006-10-02  Douglas Bates  <bates@R-project.org>
1614    
1615            * tests/dg_Matrix.R: Simplify test taking into account new code.
1616    
1617    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1618    
1619            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1620    
1621            * R/lsTMatrix.R: new files w/ missing methods
1622            * R/nsTMatrix.R:  "  'for completeness'
1623    
1624            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1625    
1626            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1627    
1628    
1629    2006-09-28  Douglas Bates  <bates@R-project.org>
1630    
1631            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1632            included.
1633    
1634            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1635            Export C-callable functions used in Zt_create in lme4.
1636    
1637    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1638    
1639            * DESCRIPTION (Version): 0.9975-1
1640    
1641            * tests/simple.R: less checks fail; using NA, found that our
1642                    kronecker() is not base-compatible with NA's.
1643    
1644            * R/dMatrix.R: "Compare" method now implemented for all cases
1645    
1646            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1647    
1648            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1649    
1650            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1651            * src/dspMatrix.c (dspMatrix_validate): ditto
1652    
1653            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1654              including coercion to [nl]tTMatrix.
1655    
1656            * R/diagMatrix.R (show): print a header line as for other classes.
1657    
1658    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1659    
1660            * src/Makefile.win (SUBDIRS): fix typo
1661    
1662    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1663    
1664            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1665    
1666    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1667    
1668            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1669            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1670            accept a symmetric matrix).
1671            * tests/group-methods.R: Uncomment test of crossprod applied to
1672            lsCMatrix objects.
1673    
1674    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1675    
1676            * R/AllClass.R (symmetricMatrix): add validity method (available
1677            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1678    
1679            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1680    
1681            * tests/indexing.Rout.save:
1682            * tests/indexing.R: additions, mainly for 'lsparse'
1683    
1684            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1685            case.
1686    
1687            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1688    
1689    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1690    
1691            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1692                    as 'N' (1-letter - Ok?)
1693    
1694            * tests/group-methods.R: add test for logical + NAs
1695    
1696            * R/dMatrix.R ("Compare"): fix to work with NA's
1697    
1698            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1699    
1700            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1701                    which is implemented.
1702    
1703    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1704    
1705            * src/chm_common.c: coerce logical <-> double instead of
1706            typecasting;  needed for "l" matrix handling in cholmod.
1707    
1708            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1709    
1710            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1711            (Tsp2grNEL): other fixes needed
1712    
1713  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1714    
1715          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 1719 
1719          * tests/: adaptions          * tests/: adaptions
1720          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
1721                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1722          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
1723    
1724  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
1725    
# Line 26  Line 1738 
1738          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1739    
1740          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1741          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
1742    
1743  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1744    
# Line 69  Line 1781 
1781    
1782          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1783          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1784          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1785          * R/Csparse.R: dito          * R/Csparse.R: ditto
1786    
1787  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1788    
# Line 86  Line 1798 
1798    
1799          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1800          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1801          (.is.diagonal): dito          (.is.diagonal): ditto
1802    
1803          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1804    

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