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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 2236, Wed Jul 23 16:48:14 2008 UTC
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1    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
4            "x@p[ncol(x)]" instead of length(x@i).
5            * R/Auxiliaries.R (nnzero): ditto
6    
7            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
8            since that fails for over-allocated i.
9    
10            * tests/validObj.R: more testing of over-allocated (i,x) slots
11    
12    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
15            'sort_in_place' and set it to TRUE in call from
16            * src/Csparse.c (Csparse_validate): sort in place, making sure that
17            validObject() continues sort the columns if needed.
18    
19            * tests/validObj.R: now tests that more thoroughly, and
20            * man/CsparseMatrix-class.Rd: documents it.
21    
22    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
25            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
26            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
27            diagU2N().
28    
29            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
30            .spDiagonal() and new .trDiagonal().
31    
32            * R/dtCMatrix.R (solve): make use of .trDiagonal()
33    
34    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
37            stumbled upon by Michael H.
38    
39            * tests/validObj.R: testing the bug-fix
40    
41            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
42            versions.
43    
44            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
45            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
46    
47            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
48              AS_CHM_SP() which includes diagU2N.
49    
50            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
51            adapt to 3 arguments.
52    
53    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
54    
55            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
56              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
57              new solve method
58            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
59              Csparse_diagU2N functionality into Matrix_as_cs
60    
61    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
64    
65    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
68              argument with default TRUE
69            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
70              Csparse_diagU2N
71            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
72              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
73              parent array; new solve method for signature(a = "dtCMatrix", b =
74              "sparseMatrix")
75    
76    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/diagMatrix.R (.bdiag): also keep result triangular
79    
80    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
81    
82            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
83              messages
84    
85    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
88            symmetric- or nsparse-Matrix, also fixing the bug introduced with
89            the new version (.999375-10).
90    
91            * tests/Simple.R: regression test for the bugs.
92    
93    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/sparseVector.R (spV2M): fix for "isparseVector".
96            Further, fix <diag> -> <sparseVector> coercion
97            (repSpV): add rep(<sparseVector>, .) method
98    
99            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
100            use as.vector(.).
101    
102            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
103    
104            * R/AllClass.R: new (hidden) class union "scarceMatrix"
105            * R/AllClass.R: sparseVector: add prototype
106    
107            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
108            Kasper Kristensen
109    
110    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * tests/other-pkgs.R: add more interesting Matrix -> graph
113    
114    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
117            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
118    
119    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * DESCRIPTION: release 0.999375-10 to CRAN
122    
123            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
124            .bdiag().
125            * man/bdiag.Rd: update, including test.
126    
127    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * tests/Simple.R: add minimal bdiag() checks
130    
131            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
132              factor out the Tsparse - internal computation into new .bdiag()
133    
134    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/nsparseMatrix.R: specific fast all() and any() methods.
137    
138            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
139            when trying to produce too large result.
140    
141            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
142            very large matrices.
143    
144            * R/sparseMatrix.R (printSpMatrix2): new function, used by
145            show(<sparseMatrix>).
146    
147            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
148    
149    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * src/Mutils.c (m_encodeInd, m_encodeInd2):
152            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
153    
154            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
155            big matrices): -> 2nd argument 'di' instead of 'nr' !
156    
157    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/dtCMatrix.R: faster dgC* -> dtC* method
160            * tests/Simple.R: (hence removed "FIXME")
161    
162            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
163            which can be be turned off for possible speed gains.
164    
165    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
168    
169            * R/not.R: fix !<ldiMatrix>
170            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
171    
172            * R/diagMatrix.R (Ops): fix one-off thinko in
173            <diagonal> o <numeric> methods
174    
175            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
176    
177    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
180            * tests/Simple.R: testing the above
181    
182    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
185    
186    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
189            * NAMESPACE (unname): finally exported
190    
191    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Auxiliaries.R (cholMat): possibly keep packed
194    
195            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
196            for R < 2.7.0.
197    
198            * R/Tsparse.R ([): for triangularMatrix, check if result may be
199            triangular.
200            * tests/indexing.R: regression test
201    
202    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
205            * R/Ops.R: more methods, for lMatrix/nMatrix
206    
207    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/expm.R: new file for all expm() methods; notably new ones for
210            diagonal*, triangular*, symmetric* and also simple "matrix".
211    
212    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
215    
216            * inst/test-tools.R (assert.EQ.mat): better message when not equal
217    
218            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
219    
220            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
221            [dl]denseMatrix {identical slots; but more logical method dispatch}
222    
223    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
226    
227            * R/diagMatrix.R (determinant): method
228    
229    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
232    
233            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
234    
235            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
236            its diagonal
237    
238    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
241    
242            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
243    
244            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
245    
246            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
247    
248    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
251    
252            * R/Ops.R (.do.Logic.lsparse): fix NA case
253    
254            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
255    
256            * R/Auxiliaries.R (nnzero): fix special cases, using
257            * R/Auxiliaries.R (indDiag): new utility
258            * R/Auxiliaries.R (indTri): new argument 'diag'
259    
260            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
261    
262    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
265    
266            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
267            ".tCMatrix" triangular matrix.
268    
269            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
270            'clx' can be class *or* class representation.
271            (nnzSparse): new.
272            (non0ind): new 'xtendSymm' argument; used in
273            * R/Ops.R:
274    
275            * R/pMatrix.R: more efficient determinant() method
276    
277    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
280            * [disactivated] NAMESPACE: export(det)
281    
282            * R/diagMatrix.R (mkDiag): new substitute for diag()
283    
284            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
285            (as0, as1): new utility.
286    
287            * R/Csparse.R (diag, band): need diagU2N()
288    
289            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
290    
291            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
292    
293            * R/Ops.R (Compare): fix <nsp> o <nsp> case
294    
295            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
296    
297    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Auxiliaries.R (signPerm): new utility for
300            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
301    
302            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
303            since we have our own error handler (and can use tryCatch() from R).
304    
305    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
308    
309            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
310            when not positive definite.
311    
312            * R/Auxiliaries.R (asTri): new auxiliary
313            (non0.i): make *much* faster for Tsparse with many non-zero
314            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
315    
316            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
317            test-tools.R , see below
318    
319            * R/dMatrix.R: fix "Summary" method: + diagU2N()
320    
321            * NAMESPACE, R/Matrix.R: add mean() method
322    
323    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
326            cold-hot colors; try *changed* default useAbs = FALSE
327            * man/image-methods.Rd:  nice examples
328    
329    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * inst/test-tools.R (checkMatrix): new function for modularizing part
332            of tstMatrixClass() in tests/Class+Meth.R
333    
334            * R/dsCMatrix.R: coercion from "matrix"
335            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
336    
337            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
338            add test for as(matrix(,0,0), <class>)
339    
340    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
343            work as determinant(matrix(,0,0)).
344    
345            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
346            * man/sparseLU-class.Rd: ditto
347    
348            * R/dgCMatrix.R (determinant): method building on lu()
349            * R/sparseMatrix.R, Matrix.R, ...: ditto
350    
351            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
352    
353    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
356            pattern matrices.
357    
358    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * src/dense.c (dense_to_Csparse): all declarations *before*
361            R_CheckStack(); needed e.g. for ancient gcc 2.96.
362    
363    
364    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * DESCRIPTION (Version): 0.999375-9 --- need to release
367            for R-devel (and R 2.7.0 alpha soon).
368    
369            * R/AllClass.R: drop "double" from "atomicVector" class union
370    
371            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
372            * R/dgeMatrix.R: ditto
373    
374            * R/sparseMatrix.R (summary): count NAs
375    
376            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
377    
378    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
381            order to become compatible to new R 2.7.0 base::rcond().
382    
383    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
386    
387            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
388    
389            * inst/test-tools.R (isValid): new utility, used much in
390            * tests/simple.R:
391    
392            * man/BunchKaufman-methods.Rd: added too
393    
394    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/dsyMatrix.R: add BunchKaufman() methods.
397            * R/dspMatrix.R:
398    
399            * src/init.c: add dsyMatrix_trf
400    
401    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
402    
403            * DESCRIPTION (Version): release 0.999375-7
404            * src/CHMfactor.c (CHMfactor_update): fix
405    
406    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
409            internal_chm_factor().
410    
411            * R/AllGeneric.R: do *not* define a "chol" generic
412                    (but rather use the implicit one *without* making pivot
413                    part of the signature)
414            * R/*.R: drop the 'pivot' from chol's signature and make
415                    'pivot=FALSE' a default argument of method definitions.
416    
417            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
418            version of Matrix
419    
420    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
423    
424            * R/sparseMatrix.R (is.na): new simple method
425            * R/denseMatrix.R (is.na): ditto.
426    
427            * R/diagMatrix.R (.symDiagonal): newly exported utility.
428    
429            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
430    
431            * src/UFsparse_download.sh: -->
432            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
433    
434    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
437            functionality; barely tested in
438            * tests/factorizing.R
439    
440            * src/Csparse.c (diag_tC): new functionality to enable faster
441            determinant(<dsCMatrix>, .) in
442            * R/dsCMatrix.R
443    
444    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
445    
446            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
447              src/CHMfactor.c, src/CHMfactor.h,
448              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
449              Log-determinant of the parent matrix from a CHMfactor object as
450              chm_factor_ldetL2; documentation and support
451    
452    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
455    
456    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
459            warning.
460    
461    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
464    
465            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
466              <diagonal> o <sparse_triangular>
467              setAs(., "nMatrix") added.
468    
469            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
470    
471            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
472                    new argument 'checkDense = FALSE'.
473    
474    
475    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
478            back-permutation of the matrix exponential.
479    
480            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
481    
482            * DESCRIPTION (Date,Version): ready to release 0.999375-5
483    
484            * tests/simple.R: testing diagN2U
485    
486    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/Auxiliaries.R (diagN2U): interface to
489    
490            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
491    
492            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
493    
494    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * src/chm_common.c (chm_diagN2U): new utility.
497    
498            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
499            make use of chm_diagN2U() and hence now preserve triangularity and
500            unit-triangularity.
501    
502            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
503    
504    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
507    
508            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
509            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
510    
511            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
512    
513            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
514    
515            * src/chm_common.c (AS_CHM_FINISH): add note about problem
516            for triangular (diag = "U").
517    
518    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
521            * R/bind.R:  .Call(dense_to_Csparse, *)
522    
523    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/Matrix.R (Matrix): no longer use coercions to specific classes
526                    (since we are discouraging them in user code).
527    
528            * tests/*.R: also replaces coercions to specific classes by
529            coercions to super classes.
530    
531            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
532    
533    
534    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
537    
538            * src/dense.c (dense_band): generalized from ddense_band
539    
540            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
541              now for "denseMatrix" (instead of just "ddense*"); much
542              simplified setMethod()s for these.
543    
544            * src/dense.c (dense_to_symmetric): generalized from ddense_*
545    
546    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
549            version of as(*, "symmetricMatric").
550    
551            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
552            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
553    
554    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * R/Matrix.R (subset.ij): utility, as first step to faster
557               M [ <ij-matrix> ] indexing.
558    
559            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
560    
561            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
562            for more efficient symmpart() and skewpart() methods.
563    
564            * src/Mutils.c (equal_string_vectors): utility
565    
566            * src/dense.c (ddense_to_symmetric): new function used in
567    
568            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
569    
570            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
571            order to match the generic (and evade .local(..)).
572    
573            * R/dsCMatrix.R: dgC -> dsC: use C code!
574    
575            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
576            as per TODO
577    
578            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
579    
580            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
581    
582    
583    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
586    
587            * R/Auxiliaries.R (non0.i): take out of non0ind
588    
589            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
590            make tril(), triu(), band() work for "matrix" and all "dense*"
591    
592            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
593            * tests/simple.R: test the fix above
594    
595            * R/sparseMatrix.R ([): simplification: no coerce to <general>
596                    before we use as(., <Tsparse>)[...] anyway
597    
598            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
599    
600            * R/triangularMatrix.R (isTriangular): methods for all subclasses
601            instead of "triangularMatrix" -- just to disambiguate
602    
603    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
606            * tests/indexing.R: example that fails above
607    
608    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
611            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
612                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
613    
614            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
615            * src/Tsparse.h, init.c: ditto
616            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
617                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
618            * R/sparseMatrix.R (isTriangular): hence simplified
619    
620    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/Ops.R (.Arith.Csparse): new utility factored out of former
623              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
624    
625    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
628    
629            * inst/test-tools.R (isOrthogonal): new function; also file restructured
630    
631    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
634            coercion to "nMatrix" and "pMatrix"
635    
636            * R/AllClass.R: "Schur" class;  "number" class union
637            * man/number-class.Rd:
638            * man/Schur-class.Rd:
639    
640            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
641            (.simpleSchur): Schur() method for diagonal matrices
642            (.triSchur):    Schur() method for triangular matrices
643            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
644    
645    
646    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
649    
650    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
653                    in order to ensure 'system = *' is not lost;
654                    formals()$system instead of cut&paste.
655            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
656    
657    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * DESCRIPTION (Date): make ready for release --> 0.999375-4
660    
661            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
662    
663    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
666                    and hence does as.vector(.).
667            * man/pMatrix-class.Rd: docs
668            * R/sparseMatrix.R: fix for printing "integer sparse"
669    
670            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
671    
672            * R/Matrix.R and others: use "exact" function argument list for
673                    both "["   : (x, i,j, ..., drop)
674                    and  "[<-" : (x, i,j, ..., value)
675    
676            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
677            * R/Tsparse.R (replTmat):    ditto
678            * R/diagMatrix.R (replDiag): ditto
679            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
680            * tests/indexing.R: testing the above
681    
682    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/sparseMatrix.R (cov2cor): method for sparse matrices
685    
686            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
687    
688            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
689    
690            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
691    
692    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * R/Matrix.R: "generic" cov2cor() method
695    
696            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
697                    speed up Q %*% D %*% t(Q)
698            * tests/dpoMatrix.R: test nearPD()
699    
700    2007-12-05  Doug Bates and Martin Maechler
701    
702            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
703            stats::xtabs() allowing to create sparse matrices.
704    
705    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
708    
709    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
712    
713    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/LU.R: solve() method for "denseLU"
716    
717    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * DESCRIPTION (Version): 0.999375-3 preparing for release
720    
721            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
722    
723            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
724    
725    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
728              thanks to Kasper Kristensen.
729            * tests/matprod.R: regression test for that.
730    
731    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
732    
733            * [r4778] R/AllGeneric.R: Check R version before defining generics for
734              primitives
735    
736    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * R/denseMatrix.R (rcond): method
739            * R/sparseQR.R (rcond): method, use x or t(x)
740    
741    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
744            matrices.
745            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
746    
747            * man/rcond.Rd: mention the more general definition, and add
748            example for non-square matrices.
749    
750            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
751    
752    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
755    
756    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
759            * tests/indexing.R: add new regression for the above cases.
760    
761    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * src/Mutils.h (__sun): clause for alloca.h on Solaris
764    
765    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * DESCRIPTION (Date, Version): 0.999375-2
768    
769    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * R/HBMM.R (readMM): make work for pattern matrices as well
772    
773    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
774    
775            * [r4730] src/Mutils.h: declare alloca
776            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
777              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
778              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
779              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
780              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
781              methods; switch writeMM to use CHOLMOD code; repair readMM
782    
783    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
786            Oehlschlaegel's ... result type still to be discussed!
787    
788    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * man/image-methods.Rd: new, combining all image() methods
791    
792    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
793    
794            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
795            to work via dgC...
796    
797            * R/Matrix.R (Matrix): special treatment for "table" (S3)
798    
799    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/dgTMatrix.R (image): change defaults to
802                    aspect = "iso", colorkey = FALSE
803    
804    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
807            must copy its *expanded* x slot before LAPACK call.
808    
809            * tests/matprod.R: test the last days' changes.
810    
811    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
812    
813            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
814              as well as in sources
815            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
816              Lapack call
817    
818    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
821                    ("Matrix", "matrix") which is needed in some cases.
822            Ditto for solve().
823    
824            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
825            infinite recursion in dispatch for some cases.
826    
827    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
828    
829            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
830              so pointers match
831    
832    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * DESCRIPTION (Date): set ready for release -- 0.999375-1
835    
836    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
837    
838            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
839              src/chm_common.c, src/chm_common.h: Change API for
840              numeric_as_chm_dense and N_AS_CHM_DN
841    
842    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
845            * tests/matprod.R: regr.test for it
846    
847    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
850            * tests/group-methods.R: and regression-test it
851    
852    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
853    
854            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
855              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
856              triplet_to_sparse, documentation, use typedefs
857    
858    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * man/dpoMatrix-class.Rd: added 'corMatrix' example
861    
862            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
863            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
864            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
865    
866            * R/lsparseMatrix.R: bug fix in "all" method
867            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
868    
869            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
870            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
871                    + matrix |-> nMatrix coercion
872            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
873            * man/pMatrix-class.Rd: ditto
874    
875            * R/Matrix.R (Summary): method for non-dMatrix
876    
877            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
878            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
879                    test all Summary methods.
880    
881    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
882    
883            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
884    
885    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
888    
889            * R/pMatrix.R (t?crossprod): methods for pMatrix
890    
891    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
892    
893            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
894    
895    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
896    
897            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
898              trying to fix a subtle bug - which has been somewhere else.
899    
900    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
901    
902            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
903              solve the bug
904    
905    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * src/dgCMatrix.c (compressed_to_TMatrix):
908    
909    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * src/Csparse.c (Rsparse_validate): new, to have some validity
912            checking for RsparseMatrix
913            * src/dgCMatrix.c (xRMatrix_validate): ditto
914            * src/dtCMatrix.c (tRMatrix_validate): ditto
915    
916    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
917    
918            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
919              lgRMatrix
920            * [r4568] DESCRIPTION: Prepare for bug-fix release
921            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
922              for declaration of cholmod_symmetry
923    
924    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
927            release.
928    
929    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
930    
931            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
932              functions - no longer used
933            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
934              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
935              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
936              Alloca
937    
938    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
939    
940            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
941              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
942              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
943              src/t_gCMatrix_colSums.c: more R_CheckStack()s
944    
945    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
946    
947            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
948              the required amount of memory then call M_numeric_as_chm_dense.
949            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
950              (like Calloc but calling alloca)
951    
952    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
953    
954            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
955            and extended with more sophisticated 'col.names' option.
956            * NAMESPACE: export  printSparseMatrix()
957            * man/printSpMatrix.Rd: document, incl. examples
958    
959    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
960    
961            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
962              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
963              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
964    
965    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
966    
967            * DESCRIPTION (Version): 0.99875-4
968    
969            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
970            some dimnames perservation.
971    
972            * R/dsTMatrix.R (t-method): keep dimnames
973            * R/dtTMatrix.R:  ditto
974    
975            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
976            and ncol(.) < 10
977    
978            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
979            from Mutils.h
980    
981            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
982            e.g. in as(<ngCMatrix>, "matrix")
983    
984    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
985    
986            * [r4529] .: Create a branch for the API changes from the 0.99875
987              series to the 0.999375 series
988            * [r4530] DESCRIPTION, inst/include/Matrix.h,
989              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
990              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
991              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
992              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
993              as_cholmod_x functions
994    
995    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
996    
997            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
998              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
999              to Comparisons
1000    
1001    >>>>>>> .merge-right.r4561
1002    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1003    
1004            * DESCRIPTION (Version): 0.99875-3 ready to be released.
1005    
1006            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
1007    
1008            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
1009            that should also work in a future version of R.
1010    
1011    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1012    
1013            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
1014    
1015            * R/sparseVector.R: more *sparseVector coercions, notably for
1016            non - double ones.
1017    
1018    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1019    
1020            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
1021              notably the new ones building on the new .Call(.)s:
1022    
1023            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
1024            all 4 of [dlin]gCMatrix_colSums().
1025    
1026    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1027    
1028            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1029            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1030              result
1031    
1032    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1033    
1034            * R/kronecker.R: fix typo (could lead to inf.recursion)
1035            * test/simple.R: testing that
1036    
1037            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1038            method as well (which can have arguments, show() can't).
1039    
1040    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1041    
1042            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1043              added dgCMatrix_colSums for [col,row][Sums,Means]
1044    
1045    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1046    
1047            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1048              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1049              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1050            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1051              class
1052            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1053              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1054              row names to store the levels - duh!  Added an example.
1055    
1056    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1057    
1058            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1059            thanks to example from Christian Buchta; with a test here:
1060            * tests/simple.R:
1061    
1062    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1063    
1064            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1065            of colSums(*, sparseResult = TRUE)
1066    
1067    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1068    
1069            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1070            'na.rm = FALSE' as "everywhere" else in R.
1071    
1072    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1073    
1074            * [r4421] src/CSparse_install.sh: Modify for new organization of
1075              CSparse package
1076            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1077              SuiteSparse
1078            * [r4426] src/Makefile: add ./UFconfig to the include path for
1079              compilation
1080            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1081            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1082              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1083    
1084    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1087            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1088            suppressed column names.
1089    
1090    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1091    
1092            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1093              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1094              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1095              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1096              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1097              Remove warnings after change to const char* CHAR
1098    
1099    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1100    
1101            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1102              type of M_cholmod_ssmult
1103    
1104    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1105    
1106            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1107              src/init.c: Yet another cholmod export - cholmod_ssmult
1108    
1109    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1110    
1111            * NAMESPACE: exported drop0(), since
1112            * man/drop0.Rd: I have seen several cases, I really wanted to use
1113            it, so our users may want too.
1114    
1115    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1116    
1117            * man/colSums.Rd: separately document colSums() etc, since these
1118            have the extra argument 'sparseResult'.
1119    
1120    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1123            * man/spMatrix.Rd: docu., including examples
1124    
1125            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1126            in order to make colMeans() etc fast *and* correct.
1127            * R/sparseVector.R (replSPvec): "[<-" functionality for
1128            sparseVectors; tested in
1129            * tests/simple.R:
1130    
1131    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1132    
1133            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1134            (very) sparse Matrices; output similar to Matlab's print().
1135    
1136    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1137    
1138            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1139            0-based, indices (Jose Quesada <quesada@gmail.com>).
1140    
1141    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1142    
1143            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1144    
1145    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1146    
1147            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1148            tapply1() for large sparse matrices.
1149    
1150    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1151    
1152            * R/Matrix.R (dim<-): reshape now via sparseVector.
1153    
1154            * R/sparseVector.R: methods and function for
1155            * R/AllClass.R: new "sparseVector" class and daughters.
1156            * NAMESPACE: export new classes
1157    
1158    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * DESCRIPTION (Version): 0.99875-1
1161            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1162    
1163    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1164    
1165            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1166            indexing
1167            * tests/indexing.R: test set for that.
1168    
1169    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1170    
1171            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1172            entries.
1173            * tests/indexing.R(out): add regression test for it
1174    
1175    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1176    
1177            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1178            name for "!" method definitions.
1179    
1180    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1181    
1182            * R/Tsparse.R (intI): new utility, used for "[" :
1183                    Cleanup up there, and fixes for duplicated indices - more TODO!
1184    
1185            * tests/indexing.R(out): more tests
1186    
1187    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1188    
1189            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1190            code that is now part of the R Lapack library.
1191    
1192            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1193            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1194    
1195    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1196    
1197            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1198    
1199    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1200    
1201            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1202            up with extraneous names '0'...'<n-1>'
1203    
1204    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1205    
1206            * R/dgTMatrix.R (mat2dgT): care about NAs
1207    
1208    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1209    
1210            * R/kronecker.R: triangularity preserving methods
1211    
1212    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1213    
1214            * R/kronecker.R: new file collecting kronecker() methods in one
1215                    place.  Goal: become much faster!
1216    
1217    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1218    
1219            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1220            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1221            can be much faster.
1222    
1223            * tests/matprod.R: add regression tests for these (upper & lower).
1224    
1225    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1226    
1227            * R/Matrix.R (diff): method for our Matrices.
1228    
1229            * R/sparseMatrix.R (isDiagonal): check dim()!
1230    
1231    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1232    
1233            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1234            proposal from Tamas Papp.
1235    
1236    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1237    
1238            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1239    
1240            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1241            rather define and export  cBind() and rBind() only.
1242            --> useRs *must* change code that used to have cbind()/rbind() !!
1243    
1244            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1245            * R/bind.Rout.save: ditto
1246    
1247    2007-02-16  Douglas Bates  <bates@r-project.org>
1248    
1249            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1250            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1251            const modifier on declaration of the array 'valid'
1252    
1253    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1254    
1255            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1256    
1257    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1258    
1259            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1260    
1261            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1262            * tests/simple.R: test the above and some of these coercions:
1263    
1264            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1265                    be careful to avoid infinite recursion, using new coercions in
1266            * R/ngCMatrix.R and nsC... and ntC...
1267            * R/lsparseMatrix.R: ditto
1268    
1269            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1270    
1271            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1272            * R/Rsparse.R: reactivate .Call()s
1273    
1274            * tests/Class+Meth.R: a bit more on actual classes
1275    
1276    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1277    
1278            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1279    
1280    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1281    
1282            * DESCRIPTION (Version): 0.9975-10 to upload
1283    
1284            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1285            specific classes less unconditionally.
1286    
1287            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1288    
1289            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1290    
1291            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1292            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1293            R_to_CMatrix segfaults on one platform.
1294            Eliminate most coercion method to *specific* classes, and replace
1295            with virtual classes coercions.
1296    
1297    
1298    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1299    
1300            * src/init.c: export the CHM...._validate() placeholders, since
1301            they *are* called.
1302    
1303            * tests/Class+Meth.R (classCanCoerce): and starting to test
1304            all as(<from>, <to>)
1305    
1306    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1307    
1308            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1309            * tests/indexing.R: tested now
1310            * tests/indexing.Rout.save: updated
1311    
1312            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1313            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1314            appropriate.
1315    
1316            * NAMESPACE: export a trivial
1317            * R/Matrix.R: drop() Matrix-method
1318    
1319            * R/AllClass.R: moved all prototypes to virtual super classes.
1320    
1321            * R/Rsparse.R: many more coercions to have less exceptions in
1322            * tests/Class+Meth.R:
1323    
1324            * R/Ops.R (Compare): tweak for case with NA
1325            * tests/simpl.R: hence another 'FIXME' eliminated
1326    
1327    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1328    
1329            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1330            objects.
1331    
1332            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1333              and more of "!", "&", "|", all, any; coercions
1334    
1335            * R/Rsparse.R: many coercions (which enable quite a few other
1336            methods), thanks to enhancements in
1337            * src/dgCMatrix.c (R_to_CMatrix): new, and
1338            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1339            symmetric & triangular and ..RMatrix objects.
1340    
1341            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1342            renamed file from src/dsTMatrix.c;
1343            now dealing with symmetric and triangular Tsparse coercions, both
1344            to dense and general.
1345    
1346    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1347    
1348            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1349    
1350            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1351            where sensible when the <numeric> is of length > 1.
1352    
1353    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1354    
1355            * R/Matrix.R ([<-): for M[] <- value: fix length
1356    
1357    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1358    
1359            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1360            * R/ndenseMatrix.R: new coercions n* -> l*
1361    
1362    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1363    
1364            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1365    
1366            * R/Ops.R ("Logic"): and other "Ops", many updates
1367    
1368    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1369    
1370            * src/Mutils.h (SET_DimNames): new utility
1371    
1372            * R/Auxiliaries.R (nnzero): improved and now exported via
1373    
1374            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1375    
1376    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1377    
1378            * R/diagMatrix.R (!): fix typo.
1379    
1380    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1381    
1382            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1383                    allow to pass class definition --> speedup
1384            * R/sparseMatrix.R: apply the above
1385    
1386            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1387    
1388            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1389            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1390            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1391    
1392            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1393    
1394            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1395            and use it for "sparse*" as well, since it's faster than the
1396            as_Csparse(.) way.
1397    
1398    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1399    
1400            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1401    
1402    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1403    
1404            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1405            as method for   M[ ij ] <- v
1406            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1407    
1408            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1409            FALSE answer
1410    
1411            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1412            * tests/indexing.R: test it, and some of the above
1413    
1414    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1415    
1416            * R/Auxiliaries.R (is_duplicatedT): new utility
1417    
1418    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1419    
1420            * src/init.c (R_init_Matrix): export cholmod_scale
1421    
1422    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1423    
1424            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1425            base::as.matrix to (x, ...)
1426    
1427    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1428    
1429            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1430            file; start using "Logic", hence
1431    
1432            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1433            * NAMESPACE: import and export "Logic"
1434    
1435    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1436    
1437            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1438            only needed previously to R version 2.5.0.
1439    
1440    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1441    
1442            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1443    
1444            * R/Tsparse.R (replTmat): fix subassignment of triangular
1445            * R/Csparse.R (replCmat): ditto
1446            * tests/indexing.R: more tests, incl the above fix
1447    
1448    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1449    
1450            * R/Auxiliaries.R (drop0): extend for non CSparse
1451            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1452    
1453            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1454                    use uplo correctly (!); other places: use uplo_P() macro
1455    
1456            * R/Csparse.R (replCmat): call diagU2N() when needed
1457            * R/Tsparse.R (replTmat): ditto
1458    
1459            * src/dtCMatrix.c (tCMatrix_validate): new
1460            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1461            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1462    
1463            * R/diagMatrix.R (replDiag): to use in [<-
1464    
1465    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1466    
1467            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1468                    also more general diagU2N().
1469    
1470    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1471    
1472            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1473            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1474    
1475    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1476    
1477            * tests/bind.R: a few more cases
1478            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1479    
1480            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1481            * R/ddenseMatrix.R (cbind2/rbind2)
1482            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1483            * tests/indexing.R
1484            * tests/indexing.Rout.save: updated
1485    
1486    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1487    
1488            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1489            * tests/indexing.R
1490    
1491    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1492    
1493            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1494            align with proper position of "0", i.e., right for integers.
1495            argument 'align' by default is "fancy".
1496    
1497    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1498    
1499            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1500            * R/Csparse.R: and fix "Compare" for more cases.
1501            * tests/Class+Meth.R: test some of these (m == m, m != m)
1502    
1503    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1504    
1505            * R/lsparseMatrix.R: all() and any() methods
1506            * R/ldenseMatrix.R:      ditto
1507            * NAMESPACE, R/Matrix.R: ditto
1508    
1509            * man/all-methods.Rd: document them minimally
1510    
1511            * tests/simple.R: add a few examples for these
1512    
1513    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1514    
1515            * R/Tsparse.R ([): fix long standing typo in symmetric case
1516            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1517    
1518    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1519    
1520            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1521            to LL before converting to a sparse matrix. (The LDL form can be
1522            converted to a sparse matrix but it is implicitly a unit
1523            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1524    
1525    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1526    
1527            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1528    
1529    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1530    
1531            * DESCRIPTION (Version): updated -> release 0.9975-7
1532            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1533    
1534  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1535    
1536          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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