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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 2218, Thu Jul 17 20:26:19 2008 UTC
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1    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
4              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
5              new solve method
6            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
7              Csparse_diagU2N functionality into Matrix_as_cs
8    
9    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
12              vignette
13            * [r2214] R/AllGeneric.R: cosmetic
14            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
15    
16    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
17    
18            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
19              argument with default TRUE
20            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
21              Csparse_diagU2N
22            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
23              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
24              parent array; new solve method for signature(a = "dtCMatrix", b =
25              "sparseMatrix")
26    
27    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/diagMatrix.R (.bdiag): also keep triangular
30            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
31              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
32              bdiag() improvements of last week
33    
34    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
35    
36            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
37              messages
38    
39    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
42            symmetric- or nsparse-Matrix, also fixing the bug introduced with
43            the new version (.999375-10).
44    
45            * tests/Simple.R: regression test for the bugs.
46    
47    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/sparseVector.R (spV2M): fix for "isparseVector".
50            Further, fix <diag> -> <sparseVector> coercion
51            (repSpV): add rep(<sparseVector>, .) method
52    
53            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
54            use as.vector(.).
55    
56            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
57    
58            * R/AllClass.R: new (hidden) class union "scarceMatrix"
59            * R/AllClass.R: sparseVector: add prototype
60    
61            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
62            Kasper Kristensen
63    
64    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * tests/other-pkgs.R: add more interesting Matrix -> graph
67    
68    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
71            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
72    
73    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * DESCRIPTION: release 0.999375-10 to CRAN
76    
77            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
78            .bdiag().
79            * man/bdiag.Rd: update, including test.
80    
81    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * tests/Simple.R: add minimal bdiag() checks
84    
85            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
86              factor out the Tsparse - internal computation into new .bdiag()
87    
88    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/nsparseMatrix.R: specific fast all() and any() methods.
91    
92            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
93            when trying to produce too large result.
94    
95            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
96            very large matrices.
97    
98            * R/sparseMatrix.R (printSpMatrix2): new function, used by
99            show(<sparseMatrix>).
100    
101            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
102    
103    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * src/Mutils.c (m_encodeInd, m_encodeInd2):
106            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
107    
108            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
109            big matrices): -> 2nd argument 'di' instead of 'nr' !
110    
111    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/dtCMatrix.R: faster dgC* -> dtC* method
114            * tests/Simple.R: (hence removed "FIXME")
115    
116            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
117            which can be be turned off for possible speed gains.
118    
119    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
122    
123            * R/not.R: fix !<ldiMatrix>
124            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
125    
126            * R/diagMatrix.R (Ops): fix one-off thinko in
127            <diagonal> o <numeric> methods
128    
129            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
130    
131    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
134            * tests/Simple.R: testing the above
135    
136    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
139    
140    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
143            * NAMESPACE (unname): finally exported
144    
145    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/Auxiliaries.R (cholMat): possibly keep packed
148    
149            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
150            for R < 2.7.0.
151    
152            * R/Tsparse.R ([): for triangularMatrix, check if result may be
153            triangular.
154            * tests/indexing.R: regression test
155    
156    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
159            * R/Ops.R: more methods, for lMatrix/nMatrix
160    
161    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/expm.R: new file for all expm() methods; notably new ones for
164            diagonal*, triangular*, symmetric* and also simple "matrix".
165    
166    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
169    
170            * inst/test-tools.R (assert.EQ.mat): better message when not equal
171    
172            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
173    
174            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
175            [dl]denseMatrix {identical slots; but more logical method dispatch}
176    
177    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
180    
181            * R/diagMatrix.R (determinant): method
182    
183    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
186    
187            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
188    
189            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
190            its diagonal
191    
192    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
195    
196            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
197    
198            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
199    
200            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
201    
202    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
205    
206            * R/Ops.R (.do.Logic.lsparse): fix NA case
207    
208            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
209    
210            * R/Auxiliaries.R (nnzero): fix special cases, using
211            * R/Auxiliaries.R (indDiag): new utility
212            * R/Auxiliaries.R (indTri): new argument 'diag'
213    
214            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
215    
216    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
219    
220            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
221            ".tCMatrix" triangular matrix.
222    
223            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
224            'clx' can be class *or* class representation.
225            (nnzSparse): new.
226            (non0ind): new 'xtendSymm' argument; used in
227            * R/Ops.R:
228    
229            * R/pMatrix.R: more efficient determinant() method
230    
231    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
234            * [disactivated] NAMESPACE: export(det)
235    
236            * R/diagMatrix.R (mkDiag): new substitute for diag()
237    
238            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
239            (as0, as1): new utility.
240    
241            * R/Csparse.R (diag, band): need diagU2N()
242    
243            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
244    
245            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
246    
247            * R/Ops.R (Compare): fix <nsp> o <nsp> case
248    
249            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
250    
251    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Auxiliaries.R (signPerm): new utility for
254            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
255    
256            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
257            since we have our own error handler (and can use tryCatch() from R).
258    
259    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
262    
263            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
264            when not positive definite.
265    
266            * R/Auxiliaries.R (asTri): new auxiliary
267            (non0.i): make *much* faster for Tsparse with many non-zero
268            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
269    
270            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
271            test-tools.R , see below
272    
273            * R/dMatrix.R: fix "Summary" method: + diagU2N()
274    
275            * NAMESPACE, R/Matrix.R: add mean() method
276    
277    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
280            cold-hot colors; try *changed* default useAbs = FALSE
281            * man/image-methods.Rd:  nice examples
282    
283    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * inst/test-tools.R (checkMatrix): new function for modularizing part
286            of tstMatrixClass() in tests/Class+Meth.R
287    
288            * R/dsCMatrix.R: coercion from "matrix"
289            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
290    
291            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
292            add test for as(matrix(,0,0), <class>)
293    
294    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
297            work as determinant(matrix(,0,0)).
298    
299            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
300            * man/sparseLU-class.Rd: ditto
301    
302            * R/dgCMatrix.R (determinant): method building on lu()
303            * R/sparseMatrix.R, Matrix.R, ...: ditto
304    
305            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
306    
307    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
310            pattern matrices.
311    
312    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * src/dense.c (dense_to_Csparse): all declarations *before*
315            R_CheckStack(); needed e.g. for ancient gcc 2.96.
316    
317    
318    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * DESCRIPTION (Version): 0.999375-9 --- need to release
321            for R-devel (and R 2.7.0 alpha soon).
322    
323            * R/AllClass.R: drop "double" from "atomicVector" class union
324    
325            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
326            * R/dgeMatrix.R: ditto
327    
328            * R/sparseMatrix.R (summary): count NAs
329    
330            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
331    
332    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
335            order to become compatible to new R 2.7.0 base::rcond().
336    
337    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
340    
341            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
342    
343            * inst/test-tools.R (isValid): new utility, used much in
344            * tests/simple.R:
345    
346            * man/BunchKaufman-methods.Rd: added too
347    
348    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/dsyMatrix.R: add BunchKaufman() methods.
351            * R/dspMatrix.R:
352    
353            * src/init.c: add dsyMatrix_trf
354    
355    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
356    
357            * DESCRIPTION (Version): release 0.999375-7
358            * src/CHMfactor.c (CHMfactor_update): fix
359    
360    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
363            internal_chm_factor().
364    
365            * R/AllGeneric.R: do *not* define a "chol" generic
366                    (but rather use the implicit one *without* making pivot
367                    part of the signature)
368            * R/*.R: drop the 'pivot' from chol's signature and make
369                    'pivot=FALSE' a default argument of method definitions.
370    
371            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
372            version of Matrix
373    
374    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
377    
378            * R/sparseMatrix.R (is.na): new simple method
379            * R/denseMatrix.R (is.na): ditto.
380    
381            * R/diagMatrix.R (.symDiagonal): newly exported utility.
382    
383            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
384    
385            * src/UFsparse_download.sh: -->
386            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
387    
388    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
391            functionality; barely tested in
392            * tests/factorizing.R
393    
394            * src/Csparse.c (diag_tC): new functionality to enable faster
395            determinant(<dsCMatrix>, .) in
396            * R/dsCMatrix.R
397    
398    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
399    
400            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
401              src/CHMfactor.c, src/CHMfactor.h,
402              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
403              Log-determinant of the parent matrix from a CHMfactor object as
404              chm_factor_ldetL2; documentation and support
405    
406    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
409    
410    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
413            warning.
414    
415    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
418    
419            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
420              <diagonal> o <sparse_triangular>
421              setAs(., "nMatrix") added.
422    
423            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
424    
425            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
426                    new argument 'checkDense = FALSE'.
427    
428    
429    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
432            back-permutation of the matrix exponential.
433    
434            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
435    
436            * DESCRIPTION (Date,Version): ready to release 0.999375-5
437    
438            * tests/simple.R: testing diagN2U
439    
440    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/Auxiliaries.R (diagN2U): interface to
443    
444            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
445    
446            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
447    
448    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * src/chm_common.c (chm_diagN2U): new utility.
451    
452            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
453            make use of chm_diagN2U() and hence now preserve triangularity and
454            unit-triangularity.
455    
456            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
457    
458    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
461    
462            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
463            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
464    
465            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
466    
467            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
468    
469            * src/chm_common.c (AS_CHM_FINISH): add note about problem
470            for triangular (diag = "U").
471    
472    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
475            * R/bind.R:  .Call(dense_to_Csparse, *)
476    
477    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
478    
479            * R/Matrix.R (Matrix): no longer use coercions to specific classes
480                    (since we are discouraging them in user code).
481    
482            * tests/*.R: also replaces coercions to specific classes by
483            coercions to super classes.
484    
485            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
486    
487    
488    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
491    
492            * src/dense.c (dense_band): generalized from ddense_band
493    
494            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
495              now for "denseMatrix" (instead of just "ddense*"); much
496              simplified setMethod()s for these.
497    
498            * src/dense.c (dense_to_symmetric): generalized from ddense_*
499    
500    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
503            version of as(*, "symmetricMatric").
504    
505            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
506            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
507    
508    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/Matrix.R (subset.ij): utility, as first step to faster
511               M [ <ij-matrix> ] indexing.
512    
513            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
514    
515            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
516            for more efficient symmpart() and skewpart() methods.
517    
518            * src/Mutils.c (equal_string_vectors): utility
519    
520            * src/dense.c (ddense_to_symmetric): new function used in
521    
522            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
523    
524            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
525            order to match the generic (and evade .local(..)).
526    
527            * R/dsCMatrix.R: dgC -> dsC: use C code!
528    
529            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
530            as per TODO
531    
532            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
533    
534            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
535    
536    
537    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
540    
541            * R/Auxiliaries.R (non0.i): take out of non0ind
542    
543            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
544            make tril(), triu(), band() work for "matrix" and all "dense*"
545    
546            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
547            * tests/simple.R: test the fix above
548    
549            * R/sparseMatrix.R ([): simplification: no coerce to <general>
550                    before we use as(., <Tsparse>)[...] anyway
551    
552            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
553    
554            * R/triangularMatrix.R (isTriangular): methods for all subclasses
555            instead of "triangularMatrix" -- just to disambiguate
556    
557    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
560            * tests/indexing.R: example that fails above
561    
562    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
565            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
566                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
567    
568            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
569            * src/Tsparse.h, init.c: ditto
570            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
571                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
572            * R/sparseMatrix.R (isTriangular): hence simplified
573    
574    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/Ops.R (.Arith.Csparse): new utility factored out of former
577              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
578    
579    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
582    
583            * inst/test-tools.R (isOrthogonal): new function; also file restructured
584    
585    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
588            coercion to "nMatrix" and "pMatrix"
589    
590            * R/AllClass.R: "Schur" class;  "number" class union
591            * man/number-class.Rd:
592            * man/Schur-class.Rd:
593    
594            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
595            (.simpleSchur): Schur() method for diagonal matrices
596            (.triSchur):    Schur() method for triangular matrices
597            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
598    
599    
600    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
603    
604    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
607                    in order to ensure 'system = *' is not lost;
608                    formals()$system instead of cut&paste.
609            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
610    
611    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * DESCRIPTION (Date): make ready for release --> 0.999375-4
614    
615            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
616    
617    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
620                    and hence does as.vector(.).
621            * man/pMatrix-class.Rd: docs
622            * R/sparseMatrix.R: fix for printing "integer sparse"
623    
624            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
625    
626            * R/Matrix.R and others: use "exact" function argument list for
627                    both "["   : (x, i,j, ..., drop)
628                    and  "[<-" : (x, i,j, ..., value)
629    
630            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
631            * R/Tsparse.R (replTmat):    ditto
632            * R/diagMatrix.R (replDiag): ditto
633            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
634            * tests/indexing.R: testing the above
635    
636    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/sparseMatrix.R (cov2cor): method for sparse matrices
639    
640            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
641    
642            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
643    
644            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
645    
646    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/Matrix.R: "generic" cov2cor() method
649    
650            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
651                    speed up Q %*% D %*% t(Q)
652            * tests/dpoMatrix.R: test nearPD()
653    
654    2007-12-05  Doug Bates and Martin Maechler
655    
656            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
657            stats::xtabs() allowing to create sparse matrices.
658    
659    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
662    
663    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
666    
667    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/LU.R: solve() method for "denseLU"
670    
671    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * DESCRIPTION (Version): 0.999375-3 preparing for release
674    
675            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
676    
677            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
678    
679    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
682              thanks to Kasper Kristensen.
683            * tests/matprod.R: regression test for that.
684    
685    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
686    
687            * [r4778] R/AllGeneric.R: Check R version before defining generics for
688              primitives
689    
690    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/denseMatrix.R (rcond): method
693            * R/sparseQR.R (rcond): method, use x or t(x)
694    
695    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
698            matrices.
699            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
700    
701            * man/rcond.Rd: mention the more general definition, and add
702            example for non-square matrices.
703    
704            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
705    
706    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
709    
710    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
713            * tests/indexing.R: add new regression for the above cases.
714    
715    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * src/Mutils.h (__sun): clause for alloca.h on Solaris
718    
719    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * DESCRIPTION (Date, Version): 0.999375-2
722    
723    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * R/HBMM.R (readMM): make work for pattern matrices as well
726    
727    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
728    
729            * [r4730] src/Mutils.h: declare alloca
730            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
731              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
732              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
733              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
734              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
735              methods; switch writeMM to use CHOLMOD code; repair readMM
736    
737    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
740            Oehlschlaegel's ... result type still to be discussed!
741    
742    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * man/image-methods.Rd: new, combining all image() methods
745    
746    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
749            to work via dgC...
750    
751            * R/Matrix.R (Matrix): special treatment for "table" (S3)
752    
753    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/dgTMatrix.R (image): change defaults to
756                    aspect = "iso", colorkey = FALSE
757    
758    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
761            must copy its *expanded* x slot before LAPACK call.
762    
763            * tests/matprod.R: test the last days' changes.
764    
765    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
766    
767            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
768              as well as in sources
769            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
770              Lapack call
771    
772    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
775                    ("Matrix", "matrix") which is needed in some cases.
776            Ditto for solve().
777    
778            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
779            infinite recursion in dispatch for some cases.
780    
781    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
782    
783            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
784              so pointers match
785    
786    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * DESCRIPTION (Date): set ready for release -- 0.999375-1
789    
790    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
791    
792            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
793              src/chm_common.c, src/chm_common.h: Change API for
794              numeric_as_chm_dense and N_AS_CHM_DN
795    
796    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
799            * tests/matprod.R: regr.test for it
800    
801    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
804            * tests/group-methods.R: and regression-test it
805    
806    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
807    
808            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
809              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
810              triplet_to_sparse, documentation, use typedefs
811    
812    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * man/dpoMatrix-class.Rd: added 'corMatrix' example
815    
816            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
817            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
818            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
819    
820            * R/lsparseMatrix.R: bug fix in "all" method
821            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
822    
823            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
824            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
825                    + matrix |-> nMatrix coercion
826            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
827            * man/pMatrix-class.Rd: ditto
828    
829            * R/Matrix.R (Summary): method for non-dMatrix
830    
831            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
832            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
833                    test all Summary methods.
834    
835    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
838    
839    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
840    
841            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
842    
843            * R/pMatrix.R (t?crossprod): methods for pMatrix
844    
845    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
846    
847            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
848    
849    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
850    
851            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
852              trying to fix a subtle bug - which has been somewhere else.
853    
854    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
855    
856            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
857              solve the bug
858    
859    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * src/dgCMatrix.c (compressed_to_TMatrix):
862    
863    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * src/Csparse.c (Rsparse_validate): new, to have some validity
866            checking for RsparseMatrix
867            * src/dgCMatrix.c (xRMatrix_validate): ditto
868            * src/dtCMatrix.c (tRMatrix_validate): ditto
869    
870    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
871    
872            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
873              lgRMatrix
874            * [r4568] DESCRIPTION: Prepare for bug-fix release
875            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
876              for declaration of cholmod_symmetry
877    
878    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
881            release.
882    
883    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
884    
885            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
886              functions - no longer used
887            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
888              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
889              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
890              Alloca
891    
892    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
893    
894            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
895              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
896              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
897              src/t_gCMatrix_colSums.c: more R_CheckStack()s
898    
899    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
900    
901            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
902              the required amount of memory then call M_numeric_as_chm_dense.
903            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
904              (like Calloc but calling alloca)
905    
906    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
907    
908            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
909            and extended with more sophisticated 'col.names' option.
910            * NAMESPACE: export  printSparseMatrix()
911            * man/printSpMatrix.Rd: document, incl. examples
912    
913    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
914    
915            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
916              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
917              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
918    
919    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * DESCRIPTION (Version): 0.99875-4
922    
923            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
924            some dimnames perservation.
925    
926            * R/dsTMatrix.R (t-method): keep dimnames
927            * R/dtTMatrix.R:  ditto
928    
929            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
930            and ncol(.) < 10
931    
932            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
933            from Mutils.h
934    
935            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
936            e.g. in as(<ngCMatrix>, "matrix")
937    
938    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
939    
940            * [r4529] .: Create a branch for the API changes from the 0.99875
941              series to the 0.999375 series
942            * [r4530] DESCRIPTION, inst/include/Matrix.h,
943              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
944              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
945              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
946              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
947              as_cholmod_x functions
948    
949    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
950    
951            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
952              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
953              to Comparisons
954    
955    >>>>>>> .merge-right.r4561
956    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
957    
958            * DESCRIPTION (Version): 0.99875-3 ready to be released.
959    
960            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
961    
962            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
963            that should also work in a future version of R.
964    
965    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
966    
967            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
968    
969            * R/sparseVector.R: more *sparseVector coercions, notably for
970            non - double ones.
971    
972    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
973    
974            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
975              notably the new ones building on the new .Call(.)s:
976    
977            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
978            all 4 of [dlin]gCMatrix_colSums().
979    
980    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
981    
982            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
983            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
984              result
985    
986    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * R/kronecker.R: fix typo (could lead to inf.recursion)
989            * test/simple.R: testing that
990    
991            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
992            method as well (which can have arguments, show() can't).
993    
994    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
995    
996            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
997              added dgCMatrix_colSums for [col,row][Sums,Means]
998    
999    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1000    
1001            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1002              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1003              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1004            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1005              class
1006            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1007              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1008              row names to store the levels - duh!  Added an example.
1009    
1010    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1011    
1012            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1013            thanks to example from Christian Buchta; with a test here:
1014            * tests/simple.R:
1015    
1016    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1019            of colSums(*, sparseResult = TRUE)
1020    
1021    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1024            'na.rm = FALSE' as "everywhere" else in R.
1025    
1026    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1027    
1028            * [r4421] src/CSparse_install.sh: Modify for new organization of
1029              CSparse package
1030            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1031              SuiteSparse
1032            * [r4426] src/Makefile: add ./UFconfig to the include path for
1033              compilation
1034            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1035            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1036              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1037    
1038    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1039    
1040            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1041            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1042            suppressed column names.
1043    
1044    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1045    
1046            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1047              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1048              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1049              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1050              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1051              Remove warnings after change to const char* CHAR
1052    
1053    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1054    
1055            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1056              type of M_cholmod_ssmult
1057    
1058    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1059    
1060            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1061              src/init.c: Yet another cholmod export - cholmod_ssmult
1062    
1063    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * NAMESPACE: exported drop0(), since
1066            * man/drop0.Rd: I have seen several cases, I really wanted to use
1067            it, so our users may want too.
1068    
1069    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1070    
1071            * man/colSums.Rd: separately document colSums() etc, since these
1072            have the extra argument 'sparseResult'.
1073    
1074    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1075    
1076            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1077            * man/spMatrix.Rd: docu., including examples
1078    
1079            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1080            in order to make colMeans() etc fast *and* correct.
1081            * R/sparseVector.R (replSPvec): "[<-" functionality for
1082            sparseVectors; tested in
1083            * tests/simple.R:
1084    
1085    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1086    
1087            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1088            (very) sparse Matrices; output similar to Matlab's print().
1089    
1090    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1091    
1092            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1093            0-based, indices (Jose Quesada <quesada@gmail.com>).
1094    
1095    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1096    
1097            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1098    
1099    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1100    
1101            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1102            tapply1() for large sparse matrices.
1103    
1104    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1105    
1106            * R/Matrix.R (dim<-): reshape now via sparseVector.
1107    
1108            * R/sparseVector.R: methods and function for
1109            * R/AllClass.R: new "sparseVector" class and daughters.
1110            * NAMESPACE: export new classes
1111    
1112    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1113    
1114            * DESCRIPTION (Version): 0.99875-1
1115            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1116    
1117    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1118    
1119            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1120            indexing
1121            * tests/indexing.R: test set for that.
1122    
1123    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1124    
1125            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1126            entries.
1127            * tests/indexing.R(out): add regression test for it
1128    
1129    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1132            name for "!" method definitions.
1133    
1134    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1135    
1136            * R/Tsparse.R (intI): new utility, used for "[" :
1137                    Cleanup up there, and fixes for duplicated indices - more TODO!
1138    
1139            * tests/indexing.R(out): more tests
1140    
1141    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1142    
1143            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1144            code that is now part of the R Lapack library.
1145    
1146            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1147            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1148    
1149    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1152    
1153    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1154    
1155            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1156            up with extraneous names '0'...'<n-1>'
1157    
1158    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * R/dgTMatrix.R (mat2dgT): care about NAs
1161    
1162    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * R/kronecker.R: triangularity preserving methods
1165    
1166    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * R/kronecker.R: new file collecting kronecker() methods in one
1169                    place.  Goal: become much faster!
1170    
1171    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1172    
1173            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1174            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1175            can be much faster.
1176    
1177            * tests/matprod.R: add regression tests for these (upper & lower).
1178    
1179    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1180    
1181            * R/Matrix.R (diff): method for our Matrices.
1182    
1183            * R/sparseMatrix.R (isDiagonal): check dim()!
1184    
1185    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1188            proposal from Tamas Papp.
1189    
1190    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1191    
1192            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1193    
1194            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1195            rather define and export  cBind() and rBind() only.
1196            --> useRs *must* change code that used to have cbind()/rbind() !!
1197    
1198            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1199            * R/bind.Rout.save: ditto
1200    
1201    2007-02-16  Douglas Bates  <bates@r-project.org>
1202    
1203            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1204            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1205            const modifier on declaration of the array 'valid'
1206    
1207    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1208    
1209            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1210    
1211    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1212    
1213            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1214    
1215            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1216            * tests/simple.R: test the above and some of these coercions:
1217    
1218            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1219                    be careful to avoid infinite recursion, using new coercions in
1220            * R/ngCMatrix.R and nsC... and ntC...
1221            * R/lsparseMatrix.R: ditto
1222    
1223            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1224    
1225            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1226            * R/Rsparse.R: reactivate .Call()s
1227    
1228            * tests/Class+Meth.R: a bit more on actual classes
1229    
1230    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1231    
1232            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1233    
1234    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1235    
1236            * DESCRIPTION (Version): 0.9975-10 to upload
1237    
1238            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1239            specific classes less unconditionally.
1240    
1241            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1242    
1243            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1244    
1245            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1246            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1247            R_to_CMatrix segfaults on one platform.
1248            Eliminate most coercion method to *specific* classes, and replace
1249            with virtual classes coercions.
1250    
1251    
1252    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1253    
1254            * src/init.c: export the CHM...._validate() placeholders, since
1255            they *are* called.
1256    
1257            * tests/Class+Meth.R (classCanCoerce): and starting to test
1258            all as(<from>, <to>)
1259    
1260    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1261    
1262            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1263            * tests/indexing.R: tested now
1264            * tests/indexing.Rout.save: updated
1265    
1266            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1267            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1268            appropriate.
1269    
1270            * NAMESPACE: export a trivial
1271            * R/Matrix.R: drop() Matrix-method
1272    
1273            * R/AllClass.R: moved all prototypes to virtual super classes.
1274    
1275            * R/Rsparse.R: many more coercions to have less exceptions in
1276            * tests/Class+Meth.R:
1277    
1278            * R/Ops.R (Compare): tweak for case with NA
1279            * tests/simpl.R: hence another 'FIXME' eliminated
1280    
1281    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1282    
1283            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1284            objects.
1285    
1286            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1287              and more of "!", "&", "|", all, any; coercions
1288    
1289            * R/Rsparse.R: many coercions (which enable quite a few other
1290            methods), thanks to enhancements in
1291            * src/dgCMatrix.c (R_to_CMatrix): new, and
1292            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1293            symmetric & triangular and ..RMatrix objects.
1294    
1295            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1296            renamed file from src/dsTMatrix.c;
1297            now dealing with symmetric and triangular Tsparse coercions, both
1298            to dense and general.
1299    
1300    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1303    
1304            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1305            where sensible when the <numeric> is of length > 1.
1306    
1307    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1308    
1309            * R/Matrix.R ([<-): for M[] <- value: fix length
1310    
1311    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1312    
1313            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1314            * R/ndenseMatrix.R: new coercions n* -> l*
1315    
1316    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1317    
1318            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1319    
1320            * R/Ops.R ("Logic"): and other "Ops", many updates
1321    
1322    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1323    
1324            * src/Mutils.h (SET_DimNames): new utility
1325    
1326            * R/Auxiliaries.R (nnzero): improved and now exported via
1327    
1328            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1329    
1330    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1331    
1332            * R/diagMatrix.R (!): fix typo.
1333    
1334    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1335    
1336            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1337                    allow to pass class definition --> speedup
1338            * R/sparseMatrix.R: apply the above
1339    
1340            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1341    
1342            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1343            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1344            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1345    
1346            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1347    
1348            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1349            and use it for "sparse*" as well, since it's faster than the
1350            as_Csparse(.) way.
1351    
1352    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1353    
1354            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1355    
1356    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1357    
1358            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1359            as method for   M[ ij ] <- v
1360            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1361    
1362            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1363            FALSE answer
1364    
1365            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1366            * tests/indexing.R: test it, and some of the above
1367    
1368    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1369    
1370            * R/Auxiliaries.R (is_duplicatedT): new utility
1371    
1372    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1373    
1374            * src/init.c (R_init_Matrix): export cholmod_scale
1375    
1376    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1377    
1378            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1379            base::as.matrix to (x, ...)
1380    
1381    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1382    
1383            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1384            file; start using "Logic", hence
1385    
1386            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1387            * NAMESPACE: import and export "Logic"
1388    
1389    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1390    
1391            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1392            only needed previously to R version 2.5.0.
1393    
1394    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1395    
1396            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1397    
1398            * R/Tsparse.R (replTmat): fix subassignment of triangular
1399            * R/Csparse.R (replCmat): ditto
1400            * tests/indexing.R: more tests, incl the above fix
1401    
1402    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1403    
1404            * R/Auxiliaries.R (drop0): extend for non CSparse
1405            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1406    
1407            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1408                    use uplo correctly (!); other places: use uplo_P() macro
1409    
1410            * R/Csparse.R (replCmat): call diagU2N() when needed
1411            * R/Tsparse.R (replTmat): ditto
1412    
1413            * src/dtCMatrix.c (tCMatrix_validate): new
1414            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1415            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1416    
1417            * R/diagMatrix.R (replDiag): to use in [<-
1418    
1419    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1420    
1421            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1422                    also more general diagU2N().
1423    
1424    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1425    
1426            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1427            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1428    
1429    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1430    
1431            * tests/bind.R: a few more cases
1432            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1433    
1434            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1435            * R/ddenseMatrix.R (cbind2/rbind2)
1436            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1437            * tests/indexing.R
1438            * tests/indexing.Rout.save: updated
1439    
1440    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1441    
1442            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1443            * tests/indexing.R
1444    
1445    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1446    
1447            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1448            align with proper position of "0", i.e., right for integers.
1449            argument 'align' by default is "fancy".
1450    
1451    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1452    
1453            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1454            * R/Csparse.R: and fix "Compare" for more cases.
1455            * tests/Class+Meth.R: test some of these (m == m, m != m)
1456    
1457    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1458    
1459            * R/lsparseMatrix.R: all() and any() methods
1460            * R/ldenseMatrix.R:      ditto
1461            * NAMESPACE, R/Matrix.R: ditto
1462    
1463            * man/all-methods.Rd: document them minimally
1464    
1465            * tests/simple.R: add a few examples for these
1466    
1467    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1468    
1469            * R/Tsparse.R ([): fix long standing typo in symmetric case
1470            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1471    
1472    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1473    
1474            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1475            to LL before converting to a sparse matrix. (The LDL form can be
1476            converted to a sparse matrix but it is implicitly a unit
1477            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1478    
1479    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1480    
1481            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1482    
1483    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1484    
1485            * DESCRIPTION (Version): updated -> release 0.9975-7
1486            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1487    
1488    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1489    
1490            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1491    
1492    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1493    
1494            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1495            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1496            is exactly singular.
1497    
1498    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1499    
1500            * DESCRIPTION (Date): updated -> release 0.9975-6
1501    
1502    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1503    
1504            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1505            now returns symmetric.
1506    
1507            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1508    
1509            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1510            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1511    
1512            * R/Auxiliaries.R (.type.kind): added
1513    
1514    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1515    
1516            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1517            running src/CSparse_install.sh
1518    
1519            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1520    
1521    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1522    
1523            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1524            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1525    
1526            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1527    
1528            * tests/Class+Meth.R (tstMatrixClass): now assure
1529            the (important in method programming) property :
1530    
1531                    ###>>  Every "Matrix" is either
1532                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1533    
1534                    (where "*" stands for "Matrix")
1535    
1536            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1537    
1538            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1539            * tests/validObj.R: checks for "comparison"
1540    
1541            * R/sparseMatrix.R ([): improved indexing for sparse;
1542                    trying to keep <symmetric>[ n, n] symmmetric
1543    
1544            * tests/indexing.R: indexing for logical sparse now ok
1545    
1546    
1547    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1548    
1549            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1550    
1551            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1552    
1553    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1554    
1555            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1556    
1557            * tests/simple.R: validObject() checking the above.
1558    
1559            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1560            replacing both dgCMatrix_validate and lgCM*.
1561    
1562            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1563            fix dimnames setting in other places.
1564            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1565    
1566    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1567    
1568            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1569    
1570            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1571            symmetry test, via
1572            * R/Auxiliaries.R (.as.dgC.0.factors):
1573    
1574    2006-11-01  Douglas Bates  <bates@r-project.org>
1575    
1576            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1577            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1578            <CsparseMatrix>) added
1579    
1580    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1581    
1582            * tests/matprod.R: add a variation of Harri's example
1583    
1584            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1585            recursive infinitely.
1586    
1587            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1588    
1589            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1590    
1591    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1592    
1593            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1594            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1595            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1596            satisfy the above test.
1597    
1598    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1599    
1600            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1601    
1602            * R/dgCMatrix.R: solve(a, b="missing") based on
1603            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1604            RHS = NULL.
1605    
1606            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1607            add more (needed) [t]crossprod() methods.
1608    
1609            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1610    
1611            * R/Auxiliaries.R (as_CspClass): cleanup
1612            (drop0): internal utility for "Csparse_drop(*, 0)"
1613            (.bail.out.2): encourage active feedback
1614    
1615    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1616    
1617            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1618    
1619            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1620            non-valid or 'sorted' case).
1621    
1622            * R/dsparseMatrix.R: add "chol" method.
1623            * R/ddenseMatrix.R: ditto
1624    
1625            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1626            * NAMESPACE (Ops)
1627            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1628            coercion; deprecating direct lower level coercions.
1629    
1630            * R/*.R (seq): use seq_len() and seq_along() where possible.
1631    
1632    
1633    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1634    
1635            * DESCRIPTION (Version): 0.9975-5 ready for release
1636    
1637    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1638    
1639            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1640    
1641    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1642    
1643            * R/AllClass.R (corMatrix): add 'validity' check;
1644                    comment out unused "LDL" class definition
1645            * NAMESPACE: mention, but do not export "LDL" class
1646            * R/corMatrix.R: new (simple), needed for R-devel with
1647            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1648              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1649    
1650    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1651    
1652            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1653            use Rprintf and R's error handling.
1654    
1655    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1656    
1657            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1658            * tests/matprod.R: add tests for the bug fixed.
1659    
1660    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1661    
1662            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1663            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1664    
1665    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1666    
1667            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1668    
1669    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1670    
1671            * DESCRIPTION (Version): 0.9975-3
1672    
1673            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1674            (sparse) matrices.
1675            * man/bdiag.Rd: docu + examples
1676    
1677            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1678    
1679            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1680            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1681    
1682            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1683            that result is sparse or diagonal (and not dense).
1684    
1685            * man/Subassign-methods.Rd: fix examples
1686    
1687            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1688            should always return a sparse (and not sometimes a diagonal) matrix.
1689    
1690    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1691    
1692            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1693    
1694    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1695    
1696            * DESCRIPTION (Version): 0.9975-2
1697    
1698            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1699    
1700    2006-10-02  Douglas Bates  <bates@R-project.org>
1701    
1702            * tests/dg_Matrix.R: Simplify test taking into account new code.
1703    
1704    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1705    
1706            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1707    
1708            * R/lsTMatrix.R: new files w/ missing methods
1709            * R/nsTMatrix.R:  "  'for completeness'
1710    
1711            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1712    
1713            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1714    
1715    
1716    2006-09-28  Douglas Bates  <bates@R-project.org>
1717    
1718            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1719            included.
1720    
1721            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1722            Export C-callable functions used in Zt_create in lme4.
1723    
1724    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1725    
1726            * DESCRIPTION (Version): 0.9975-1
1727    
1728            * tests/simple.R: less checks fail; using NA, found that our
1729                    kronecker() is not base-compatible with NA's.
1730    
1731            * R/dMatrix.R: "Compare" method now implemented for all cases
1732    
1733            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1734    
1735            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1736    
1737            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1738            * src/dspMatrix.c (dspMatrix_validate): ditto
1739    
1740            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1741              including coercion to [nl]tTMatrix.
1742    
1743            * R/diagMatrix.R (show): print a header line as for other classes.
1744    
1745    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1746    
1747            * src/Makefile.win (SUBDIRS): fix typo
1748    
1749    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1750    
1751            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1752    
1753    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1754    
1755            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1756            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1757            accept a symmetric matrix).
1758            * tests/group-methods.R: Uncomment test of crossprod applied to
1759            lsCMatrix objects.
1760    
1761    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1762    
1763            * R/AllClass.R (symmetricMatrix): add validity method (available
1764            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1765    
1766            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1767    
1768            * tests/indexing.Rout.save:
1769            * tests/indexing.R: additions, mainly for 'lsparse'
1770    
1771            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1772            case.
1773    
1774            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1775    
1776    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1777    
1778            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1779                    as 'N' (1-letter - Ok?)
1780    
1781            * tests/group-methods.R: add test for logical + NAs
1782    
1783            * R/dMatrix.R ("Compare"): fix to work with NA's
1784    
1785            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1786    
1787            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1788                    which is implemented.
1789    
1790    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1791    
1792            * src/chm_common.c: coerce logical <-> double instead of
1793            typecasting;  needed for "l" matrix handling in cholmod.
1794    
1795            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1796    
1797            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1798            (Tsp2grNEL): other fixes needed
1799    
1800    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1801    
1802            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1803                    Matrices, since "lMatrix", also "lsparseM" can have NA
1804            * R/ndenseMatrix.R, etc: new source files
1805            * man/nsparseMatrix-classes.Rd, etc: new help files
1806            * tests/: adaptions
1807            * src/chm_common.c (chm_dense_to_SEXP): and others:
1808                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1809            * src/Csparse.c, etc: ditto
1810    
1811    2006-09-11  Douglas Bates  <bates@R-project.org>
1812    
1813            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1814            alloc_d**Matrix functions to the lme4 package.
1815    
1816    2006-09-09  Douglas Bates  <bates@R-project.org>
1817    
1818            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1819            fixed
1820    
1821    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1822    
1823            * R/lMatrix.R: new
1824    
1825            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1826    
1827            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1828            * man/tcrossprod.Rd: ditto
1829    
1830    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1831    
1832            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1833            for exported functions
1834            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1835            Remove partitioning algorithms for sparse matrix reordering.  The
1836            copyright on the Metis code was problematic and the methods were
1837            rarely used.
1838            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1839            operations are now done entirely in CHOLMOD code.
1840    
1841    2006-09-06  Douglas Bates  <bates@R-project.org>
1842    
1843            * src/Mutils.h: Remove functions that are no longer used.
1844    
1845    2006-09-04  Douglas Bates  <bates@R-project.org>
1846    
1847            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1848            * src/DEPS.mkf: update
1849    
1850    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1851    
1852            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1853            * DESCRIPTION (Version): 0.9975-0
1854            (Depends): R (>= 2.4.0)
1855    
1856    2006-09-01  Douglas Bates  <bates@R-project.org>
1857    
1858            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1859    
1860    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1861    
1862            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1863            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1864    
1865            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1866    
1867    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1868    
1869            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1870            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1871            * R/dsparseMatrix.R: ditto
1872            * R/Csparse.R: ditto
1873    
1874    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1875    
1876            * R/dMatrix.R (Compare): improve availability of "<", etc
1877            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1878    
1879    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1880    
1881            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1882            of a 0-index which was used as 1-index (..hmm)
1883    
1884            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1885    
1886            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1887            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1888            (.is.diagonal): ditto
1889    
1890            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1891    
1892            * R/Matrix.R (Matrix): also work for NA data
1893    
1894  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1895    
1896          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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